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Li Z, Li X, Lin J, Wang Y, Cao H, Zhou J. Reevaluation by the CRISPR/Cas9 knockout approach revealed that multiple pluripotency-associated lncRNAs are dispensable for pluripotency maintenance while Snora73a/b is essential for pluripotency exit. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2594-3. [PMID: 38995489 DOI: 10.1007/s11427-023-2594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 03/15/2024] [Indexed: 07/13/2024]
Abstract
Many long noncoding RNAs (lncRNAs) have been identified through siRNA-based screening as essential regulators of embryonic stem cell (ESC) pluripotency. However, the biological and molecular functions of most lncRNAs remain unclear. Here, we employed CRISPR/Cas9-mediated knockout technology to explore the functions of 8 lncRNAs previously reported to promote pluripotency in mouse ESCs. Unexpectedly, all of these lncRNAs were dispensable for pluripotency maintenance and proliferation in mouse ESCs when disrupted individually or in combination. Single-cell transcriptomic analysis also showed that the knockout of these lncRNAs has a minimal impact on pluripotency gene expression and cell identity. We further showed that several small hairpin RNAs (shRNAs) previously used to knock down lncRNAs caused the downregulation of pluripotency genes in the corresponding lncRNA-knockout ESCs, indicating that off-target effects likely responsible for the pluripotency defects caused by these shRNAs. Interestingly, linc1343-knockout and linc1343-knockdown ESCs failed to form cystic structures and exhibited high expression of pluripotency genes during embryoid body (EB) differentiation. By reintroducing RNA products generated from the linc1343 locus, we found that two snoRNAs, Snora73a and Snora73b, but not lncRNAs, could rescue pluripotency silencing defects during EB differentiation of linc1343 knockout ESCs. Our results suggest that the 8 previously annotated pluripotency-regulating lncRNAs have no overt functions in conventional ESC culture; however, we identified snoRNA products derived from an annotated lncRNA locus as essential regulators for silencing pluripotency genes.
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Affiliation(s)
- Zhen Li
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China
| | - Xuefei Li
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Jingxia Lin
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Yangming Wang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China
- Beijing Advanced Center of RNA Biology (BEACON), Peking University, Beijing, 100871, China
| | - Huiqing Cao
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China.
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China.
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2
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Zhao RJ, Zhang WY, Fan XX. Circular RNAs: Potential biomarkers and therapeutic targets for autoimmune diseases. Heliyon 2024; 10:e23694. [PMID: 38205329 PMCID: PMC10776946 DOI: 10.1016/j.heliyon.2023.e23694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/06/2023] [Accepted: 12/09/2023] [Indexed: 01/12/2024] Open
Abstract
The outcomes and prognosis of autoimmune diseases depend on early diagnosis and effective treatments. However, symptoms of early autoimmune diseases are often remarkably similar to many inflammatory diseases, leading to difficulty in precise diagnosis. Circular RNAs (circRNAs) belong to a novel class of endogenous RNAs, functioning as microRNA (miRNA) sponges or participating in protein coding. It has been shown in many studies that patients with autoimmune diseases have aberrant circRNA expression in liquid biopsy samples (such as plasma, saliva, and urine). Thus, circRNAs are potential biomarkers for the diagnosis and prognosis of autoimmune diseases. Moreover, overexpression and depletion of target circRNAs can be utilized as possible therapeutic approaches for treating autoimmune diseases. In this review, we summarized recent progress in the roles of circRNAs in the pathogenesis of autoimmune diseases, including rheumatoid arthritis, systemic lupus erythematosus, multiple sclerosis, and type 1 diabetes. We also discussed their potential as biomarkers and therapeutic targets.
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Affiliation(s)
| | | | - Xing-Xing Fan
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau(SAR), China
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3
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Huang C, Esfani Sarafraz P, Enayati P, Mortazavi Mamaghani E, Babakhanzadeh E, Nazari M. Circular RNAs in renal cell carcinoma: from mechanistic to clinical perspective. Cancer Cell Int 2023; 23:288. [PMID: 37993909 PMCID: PMC10664289 DOI: 10.1186/s12935-023-03128-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 11/07/2023] [Indexed: 11/24/2023] Open
Abstract
CircRNAs, a special type of noncoding RNAs characterized by their stable structure and unique abilities to form backsplicing loops, have recently attracted the interest of scientists. These RNAs are abundant throughout the body and play important roles such as microRNA sponges, templates for transcription, and regulation of protein translation and RNA-binding proteins. Renal cancer development is highly correlated with abnormal circRNA expression in vivo. CircRNAs are currently considered promising targets for novel therapeutic approaches as well as possible biomarkers for prognosis and diagnosis of various malignancies. Despite our growing understanding of circRNA, numerous questions remain unanswered. Here, we address the characteristics of circRNAs and their function, focusing in particular on their impact on drug resistance, metabolic processes, metastasis, cell growth, and programmed cell death in renal cancer. In addition, the application of circRNAs as prognostic and diagnostic biomarkers will be discussed.
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Affiliation(s)
- Chunjie Huang
- School of Medicine, Nantong University, Nantong, China
| | | | - Parisa Enayati
- Biological Sciences Department, Northern Illinois University, DeKalb, Illinois, USA
| | | | - Emad Babakhanzadeh
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Majid Nazari
- Department of Medical Genetics, Shahid Sadoughi University of Medical Sciences, 64155-65117, Yazd, Iran.
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4
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Liu Z, Yang F, Xiao Z, Liu Y. Review of novel functions and implications of circular RNAs in hepatocellular carcinoma. Front Oncol 2023; 13:1093063. [PMID: 36890830 PMCID: PMC9986438 DOI: 10.3389/fonc.2023.1093063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/27/2023] [Indexed: 02/22/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most frequent malignancies, with high incidence and mortality. As the majority of HCC patients are diagnosed at an advanced stage and die of recurrence and metastasis, its pathology and new biomarkers are needed. Circular RNAs (circRNAs) are a large subclass of long non-coding RNAs (lncRNAs) with covalently closed loop structures and abundant, conserved, stable, tissue-specific expression in mammalian cells. CircRNAs exert multiple functions in HCC initiation, growth and progression, serving as promising biomarkers for diagnosis, prognosis and therapeutic targets for this disease. This review briefly describes the biogenesis and biological functions of circRNAs and elucidates the roles of circRNAs in the development and progression of HCC, especially regarding epithelial-mesenchymal transition (EMT), drug resistance and interactions with epigenetic modifications. In addition, this review highlights the implications of circRNAs as potential biomarkers and therapeutic targets for HCC. We hope to provide novel insight into the roles of circRNAs in HCC.
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Affiliation(s)
- Zheng Liu
- Department of Combination of Traditional Chinese Medicine and Western Medicine, School of Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - Fangming Yang
- Department of Digestive Diseases, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Zhun Xiao
- Department of Digestive Diseases, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Yuexuan Liu
- Department of Combination of Traditional Chinese Medicine and Western Medicine, School of Medicine, Henan University of Chinese Medicine, Zhengzhou, China
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5
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Nishita-Hiresha V, Varsha R, Jayasuriya R, Ramkumar KM. The role of circRNA-miRNA-mRNA interaction network in endothelial dysfunction. Gene 2023; 851:146950. [DOI: 10.1016/j.gene.2022.146950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/24/2022] [Accepted: 10/03/2022] [Indexed: 11/27/2022]
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Small RNA Targets: Advances in Prediction Tools and High-Throughput Profiling. BIOLOGY 2022; 11:biology11121798. [PMID: 36552307 PMCID: PMC9775672 DOI: 10.3390/biology11121798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/27/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are an abundant class of small non-coding RNAs that regulate gene expression at the post-transcriptional level. They are suggested to be involved in most biological processes of the cell primarily by targeting messenger RNAs (mRNAs) for cleavage or translational repression. Their binding to their target sites is mediated by the Argonaute (AGO) family of proteins. Thus, miRNA target prediction is pivotal for research and clinical applications. Moreover, transfer-RNA-derived fragments (tRFs) and other types of small RNAs have been found to be potent regulators of Ago-mediated gene expression. Their role in mRNA regulation is still to be fully elucidated, and advancements in the computational prediction of their targets are in their infancy. To shed light on these complex RNA-RNA interactions, the availability of good quality high-throughput data and reliable computational methods is of utmost importance. Even though the arsenal of computational approaches in the field has been enriched in the last decade, there is still a degree of discrepancy between the results they yield. This review offers an overview of the relevant advancements in the field of bioinformatics and machine learning and summarizes the key strategies utilized for small RNA target prediction. Furthermore, we report the recent development of high-throughput sequencing technologies, and explore the role of non-miRNA AGO driver sequences.
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7
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Nedorezova DD, Dubovichenko MV, Belyaeva EP, Grigorieva ED, Peresadina AV, Kolpashchikov DM. Specificity of oligonucleotide gene therapy (OGT) agents. Theranostics 2022; 12:7132-7157. [PMID: 36276652 PMCID: PMC9576606 DOI: 10.7150/thno.77830] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/11/2022] [Indexed: 11/24/2022] Open
Abstract
Oligonucleotide gene therapy (OGT) agents (e. g. antisense, deoxyribozymes, siRNA and CRISPR/Cas) are promising therapeutic tools. Despite extensive efforts, only few OGT drugs have been approved for clinical use. Besides the problem of efficient delivery to targeted cells, hybridization specificity is a potential limitation of OGT agents. To ensure tight binding, a typical OGT agent hybridizes to the stretch of 15-25 nucleotides of a unique targeted sequence. However, hybrids of such lengths tolerate one or more mismatches under physiological conditions, the problem known as the affinity/specificity dilemma. Here, we assess the scale of this problem by analyzing OGT hybridization-dependent off-target effects (HD OTE) in vitro, in animal models and clinical studies. All OGT agents except deoxyribozymes exhibit HD OTE in vitro, with most thorough evidence of poor specificity reported for siRNA and CRISPR/Cas9. Notably, siRNA suppress non-targeted genes due to (1) the partial complementarity to mRNA 3'-untranslated regions (3'-UTR), and (2) the antisense activity of the sense strand. CRISPR/Cas9 system can cause hundreds of non-intended dsDNA breaks due to low specificity of the guide RNA, which can limit therapeutic applications of CRISPR/Cas9 by ex-vivo formats. Contribution of this effects to the observed in vivo toxicity of OGT agents is unclear and requires further investigation. Locked or peptide nucleic acids improve OGT nuclease resistance but not specificity. Approaches that use RNA marker dependent (conditional) activation of OGT agents may improve specificity but require additional validation in cell culture and in vivo.
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Affiliation(s)
- Daria D. Nedorezova
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Mikhail V. Dubovichenko
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Ekaterina P. Belyaeva
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Ekaterina D. Grigorieva
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Arina V. Peresadina
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Dmitry M. Kolpashchikov
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
- Chemistry Department, University of Central Florida, Orlando, FL 32816-2366, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
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8
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Yadav P, Kundu P, Pandey VK, Amin PJ, Nair J, Shankar BS. Effects of prolonged treatment of TGF-βR inhibitor SB431542 on radiation-induced signaling in breast cancer cells. Int J Radiat Biol 2022; 98:1-15. [PMID: 35446183 DOI: 10.1080/09553002.2022.2069299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 01/04/2022] [Accepted: 03/31/2022] [Indexed: 10/18/2022]
Abstract
PURPOSE We have earlier characterized increased TGF-β signaling in radioresistant breast cancer cells. In this study, we wanted to determine the effect of prolonged treatment of TGF-βR inhibitor SB431542 on radiation-induced signaling, viz., genes regulating apoptosis, EMT, anti and pro-inflammatory cytokines. MATERIALS AND METHODS Breast cancer cells were pretreated with TGF-βR inhibitor (SB 431542) followed by exposure to 6 Gy and recovery period of 7 days (D7-6G). We assessed cell survival by MTT assay, cytokines by ELISA and expression analysis by RT-PCR, flow cytometry, and western blot. We carried out migration assays using trans well inserts. We performed bioinformatics analyses of human cancer database through cBioportal. RESULTS There was an upregulation of TGF-β1 and 3 and downregulation of TGF-β2, TGF-βR1, and TGF-βR2 in invasive breast carcinoma samples compared to normal tissue. TGF-β1 and TNF-α was higher in radioresistant D7-6G cells with upregulation of pSMAD3, pNF-kB, and ERK signaling. Pretreatment of D7-6G cells with TGF-βR inhibitor SB431542 abrogated pSMAD3, increased proliferation, and migration along with an increase in apoptosis and pro-apoptotic genes. This was associated with hybrid E/M phenotype and downregulation of TGF-β downstream genes, HMGA2 and Snail. There was complete agreement in the expression of mRNA and protein data in genes like vimentin, Snail and HMGA2 in different treatment groups. However, there was disagreement in expression of mRNA and protein in genes like Bax, Bcl-2, E-cadherin, Zeb-1 among the different treatment groups indicating post-transcriptional and post-translational processing of these proteins. Treatment of cells with only SB431542 also increased expression of some E/M genes indicating TGF-β independent effects. Increased IL-6 and IL-10 secretion by SB431542 along with increase in pSTAT3 and pCREB1 could probably explain these TGF-β/Smad3 independent effects. CONCLUSION These results highlight that TGF-β-pSMAD3 and TNF-α-pNF-kB are the predominant signaling pathways in radioresistant cells and possibility of some TGF-β/Smad3 independent effects on prolonged treatment with the drug SB431542.
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Affiliation(s)
- Poonam Yadav
- Radiation Biology and Health Sciences Division, Bio-Science Group, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Priya Kundu
- Radiation Biology and Health Sciences Division, Bio-Science Group, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Vipul K Pandey
- Radiation Biology and Health Sciences Division, Bio-Science Group, Bhabha Atomic Research Centre, Mumbai, India
| | - Prayag J Amin
- Radiation Biology and Health Sciences Division, Bio-Science Group, Bhabha Atomic Research Centre, Mumbai, India
| | - Jisha Nair
- Radiation Biology and Health Sciences Division, Bio-Science Group, Bhabha Atomic Research Centre, Mumbai, India
| | - Bhavani S Shankar
- Radiation Biology and Health Sciences Division, Bio-Science Group, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
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9
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Elmes K, Schmich F, Szczurek E, Jenkins J, Beerenwinkel N, Gavryushkin A. Learning epistatic gene interactions from perturbation screens. PLoS One 2021; 16:e0254491. [PMID: 34255784 PMCID: PMC8277066 DOI: 10.1371/journal.pone.0254491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/28/2021] [Indexed: 11/21/2022] Open
Abstract
The treatment of complex diseases often relies on combinatorial therapy, a strategy where drugs are used to target multiple genes simultaneously. Promising candidate genes for combinatorial perturbation often constitute epistatic genes, i.e., genes which contribute to a phenotype in a non-linear fashion. Experimental identification of the full landscape of genetic interactions by perturbing all gene combinations is prohibitive due to the exponential growth of testable hypotheses. Here we present a model for the inference of pairwise epistatic, including synthetic lethal, gene interactions from siRNA-based perturbation screens. The model exploits the combinatorial nature of siRNA-based screens resulting from the high numbers of sequence-dependent off-target effects, where each siRNA apart from its intended target knocks down hundreds of additional genes. We show that conditional and marginal epistasis can be estimated as interaction coefficients of regression models on perturbation data. We compare two methods, namely glinternet and xyz, for selecting non-zero effects in high dimensions as components of the model, and make recommendations for the appropriate use of each. For data simulated from real RNAi screening libraries, we show that glinternet successfully identifies epistatic gene pairs with high accuracy across a wide range of relevant parameters for the signal-to-noise ratio of observed phenotypes, the effect size of epistasis and the number of observations per double knockdown. xyz is also able to identify interactions from lower dimensional data sets (fewer genes), but is less accurate for many dimensions. Higher accuracy of glinternet, however, comes at the cost of longer running time compared to xyz. The general model is widely applicable and allows mining the wealth of publicly available RNAi screening data for the estimation of epistatic interactions between genes. As a proof of concept, we apply the model to search for interactions, and potential targets for treatment, among previously published sets of siRNA perturbation screens on various pathogens. The identified interactions include both known epistatic interactions as well as novel findings.
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Affiliation(s)
- Kieran Elmes
- Department of Computer Science, University of Otago, Dunedin, New Zealand
| | - Fabian Schmich
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Ewa Szczurek
- Institute of Informatics, University of Warsaw, Warsaw, Poland
| | - Jeremy Jenkins
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
- * E-mail: (NB); (AG)
| | - Alex Gavryushkin
- Department of Computer Science, University of Otago, Dunedin, New Zealand
- School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
- * E-mail: (NB); (AG)
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10
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He AT, Liu J, Li F, Yang BB. Targeting circular RNAs as a therapeutic approach: current strategies and challenges. Signal Transduct Target Ther 2021; 6:185. [PMID: 34016945 PMCID: PMC8137869 DOI: 10.1038/s41392-021-00569-5] [Citation(s) in RCA: 235] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/28/2021] [Accepted: 03/16/2021] [Indexed: 02/04/2023] Open
Abstract
Significant progress has been made in circular RNA (circRNA) research in recent years. Increasing evidence suggests that circRNAs play important roles in many cellular processes, and their dysregulation is implicated in the pathogenesis of various diseases. CircRNAs are highly stable and usually expressed in a tissue- or cell type-specific manner. Therefore, they are currently being explored as potential therapeutic targets. Gain-of-function and loss-of-function approaches are typically performed using circRNA expression plasmids and RNA interference-based strategies, respectively. These strategies have limitations that can be mitigated using nanoparticle and exosome delivery systems. Furthermore, recent developments show that the cre-lox system can be used to knockdown circRNAs in a cell-specific manner. While still in the early stages of development, the CRISPR/Cas13 system has shown promise in knocking down circRNAs with high specificity and efficiency. In this review, we describe circRNA properties and functions and highlight their significance in disease. We summarize strategies that can be used to overexpress or knockdown circRNAs as a therapeutic approach. Lastly, we discuss major challenges and propose future directions for the development of circRNA-based therapeutics.
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Affiliation(s)
- Alina T. He
- grid.17063.330000 0001 2157 2938Sunnybrook Research Institute, Toronto, ON Canada
| | - Jinglei Liu
- Department of Bioinformatics, ATCGene Inc, Guangzhou, China
| | - Feiya Li
- grid.17063.330000 0001 2157 2938Sunnybrook Research Institute, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
| | - Burton B. Yang
- grid.17063.330000 0001 2157 2938Sunnybrook Research Institute, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
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11
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Rautela I, Sharma A, Dheer P, Thapliyal P, Sahni S, Sinha VB, Sharma MD. Extension in the approaches to treat cancer through siRNA system: a beacon of hope in cancer therapy. Drug Deliv Transl Res 2021; 12:1002-1016. [PMID: 33970462 DOI: 10.1007/s13346-021-00995-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2021] [Indexed: 12/14/2022]
Abstract
Along with the evolutionary breakthrough of RNA interference and the applicability for gene knockdown, a subsequent development in siRNA-based therapeutics has been attained. The gene therapy based on RNAi is in transition progress from the research aspects to clinical base. Being a potent tool, siRNA is used as therapeutic against several disorders. Cancer which is one of the deadliest diseases is now treated with an advanced mechanism of siRNA delivery inside the genome, leading to gene silencing; thereby, blocking translation of gene to form protein. siRNA tool delivers remedial effects with the advantages of safe delivery and efficiency. Despite its merits, barriers including instability at physiological conditions, lack of ability to cross biological membranes, off-targets, and safety are also associated with siRNA delivery system. The gene silencing efficiency values both in vitro and in vivo reported in the past years have been reviewed by material type (lipid, polymer, silica, porous silicon, and metal). This review presents a deep insight in the development of targeted delivery of siRNA. Since several clinical trials have also been performed regarding the siRNA delivery against cancer, it can also be stated that the delivery system should be good enough to achieve effective siRNA drug development.
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Affiliation(s)
- Indra Rautela
- Department of Biotechnology, School of Applied and Life Sciences (SALS), Uttaranchal University, Dehradun, 248001, Uttarakhand, India
| | - Aditi Sharma
- Department of Biotechnology and Department of Life Sciences, Graphic Era Deemed to be University, Dehradun, 248002, Uttarakhand, India
| | - Pallavi Dheer
- Department of Biotechnology, School of Basic and Applied Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun, 248001, Uttarakhand, India
| | - Priya Thapliyal
- Department of Biochemistry, H.N.B. Garhwal (A Central) University, Srinagar, 246174, Uttarakhand, India
| | - Shweta Sahni
- Department of Microbiology, School of Basic and Applied Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun, 248001, Uttarakhand, India
| | | | - Manish Dev Sharma
- Department of Biotechnology, School of Basic and Applied Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun, 248001, Uttarakhand, India.
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12
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Li J, Levin DS, Kim AJ, Pappas SS, Dauer WT. TorsinA restoration in a mouse model identifies a critical therapeutic window for DYT1 dystonia. J Clin Invest 2021; 131:139606. [PMID: 33529159 DOI: 10.1172/jci139606] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/27/2021] [Indexed: 12/18/2022] Open
Abstract
In inherited neurodevelopmental diseases, pathogenic processes unique to critical periods during early brain development may preclude the effectiveness of gene modification therapies applied later in life. We explored this question in a mouse model of DYT1 dystonia, a neurodevelopmental disease caused by a loss-of-function mutation in the TOR1A gene encoding torsinA. To define the temporal requirements for torsinA in normal motor function and gene replacement therapy, we developed a mouse line enabling spatiotemporal control of the endogenous torsinA allele. Suppressing torsinA during embryogenesis caused dystonia-mimicking behavioral and neuropathological phenotypes. Suppressing torsinA during adulthood, however, elicited no discernible abnormalities, establishing an essential requirement for torsinA during a developmental critical period. The developing CNS exhibited a parallel "therapeutic critical period" for torsinA repletion. Although restoring torsinA in juvenile DYT1 mice rescued motor phenotypes, there was no benefit from adult torsinA repletion. These data establish a unique requirement for torsinA in the developing nervous system and demonstrate that the critical period genetic insult provokes permanent pathophysiology mechanistically delinked from torsinA function. These findings imply that to be effective, torsinA-based therapeutic strategies must be employed early in the course of DYT1 dystonia.
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Affiliation(s)
- Jay Li
- Medical Scientist Training Program.,Cellular and Molecular Biology Graduate Program
| | - Daniel S Levin
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Samuel S Pappas
- Peter O'Donnell Jr. Brain Institute.,Department of Neurology
| | - William T Dauer
- Peter O'Donnell Jr. Brain Institute.,Department of Neurology.,Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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13
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Kleefeldt JM, Pozarska A, Nardiello C, Pfeffer T, Vadász I, Herold S, Seeger W, Morty RE. Commercially available transfection reagents and negative control siRNA are not inert. Anal Biochem 2020; 606:113828. [PMID: 32745542 DOI: 10.1016/j.ab.2020.113828] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 01/17/2023]
Abstract
The transfection of synthetic small interfering (si)RNA into cultured cells forms the basis of studies that use RNA interference (commonly referred to as "gene knockdown") to study the impact of loss of gene or protein expression on a biological pathway or process. In these studies, mock transfections (with transfection reagents alone), and the use of synthetic negative control (apparently inert) siRNA are both essential negative controls. This report reveals that three widely-used transfection reagents (X-tremeGENE™, HiPerFect, and Lipofectamine® 2000) and five commercially-available control siRNA (from Ambion, Sigma, Santa Cruz, Cell Signaling Technology, and Qiagen) are not inert in cell-culture studies. Both transfection reagents and control siRNA perturbed steady-state mRNA and protein levels in primary mouse lung fibroblasts and in NIH/3T3 cells (a widely-used mouse embryonic fibroblast cell-line), using components of the canonical transforming growth factor-β signaling machinery as a model system. Furthermore, transfection reagents and control siRNA reduced the viability and proliferation of both lung fibroblasts and NIH/3T3 cells. These data collectively provide a cautionary note to investigators to carefully consider the impact of control interventions, such as mock transfections and control siRNA, in RNA interference studies with synthetic siRNA.
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Affiliation(s)
- Jan M Kleefeldt
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Member of the German Center for Lung Research (DZL), Parkstrasse 1, 60231, Bad Nauheim, Germany; Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany
| | - Agnieszka Pozarska
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Member of the German Center for Lung Research (DZL), Parkstrasse 1, 60231, Bad Nauheim, Germany; Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany
| | - Claudio Nardiello
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Member of the German Center for Lung Research (DZL), Parkstrasse 1, 60231, Bad Nauheim, Germany; Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany
| | - Tilman Pfeffer
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Member of the German Center for Lung Research (DZL), Parkstrasse 1, 60231, Bad Nauheim, Germany
| | - István Vadász
- Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany
| | - Susanne Herold
- Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany
| | - Werner Seeger
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Member of the German Center for Lung Research (DZL), Parkstrasse 1, 60231, Bad Nauheim, Germany; Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany
| | - Rory E Morty
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Member of the German Center for Lung Research (DZL), Parkstrasse 1, 60231, Bad Nauheim, Germany; Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany.
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14
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Coutinho MF, Santos JI, S. Mendonça L, Matos L, Prata MJ, S. Jurado A, Pedroso de Lima MC, Alves S. Lysosomal Storage Disease-Associated Neuropathy: Targeting Stable Nucleic Acid Lipid Particle (SNALP)-Formulated siRNAs to the Brain as a Therapeutic Approach. Int J Mol Sci 2020; 21:ijms21165732. [PMID: 32785133 PMCID: PMC7461213 DOI: 10.3390/ijms21165732] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 12/22/2022] Open
Abstract
More than two thirds of Lysosomal Storage Diseases (LSDs) present central nervous system involvement. Nevertheless, only one of the currently approved therapies has an impact on neuropathology. Therefore, alternative approaches are under development, either addressing the underlying enzymatic defect or its downstream consequences. Also under study is the possibility to block substrate accumulation upstream, by promoting a decrease of its synthesis. This concept is known as substrate reduction therapy and may be triggered by several molecules, such as small interfering RNAs (siRNAs). siRNAs promote RNA interference, a naturally occurring sequence-specific post-transcriptional gene-silencing mechanism, and may target virtually any gene of interest, inhibiting its expression. Still, naked siRNAs have limited cellular uptake, low biological stability, and unfavorable pharmacokinetics. Thus, their translation into clinics requires proper delivery methods. One promising platform is a special class of liposomes called stable nucleic acid lipid particles (SNALPs), which are characterized by high cargo encapsulation efficiency and may be engineered to promote targeted delivery to specific receptors. Here, we review the concept of SNALPs, presenting a series of examples on their efficacy as siRNA nanodelivery systems. By doing so, we hope to unveil the therapeutic potential of these nanosystems for targeted brain delivery of siRNAs in LSDs.
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Affiliation(s)
- Maria Francisca Coutinho
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA I.P), Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (J.I.S.); (L.M.); (S.A.)
- Center for the Study of Animal Science, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Correspondence: ; Tel.: +351-(223)-401-113
| | - Juliana Inês Santos
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA I.P), Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (J.I.S.); (L.M.); (S.A.)
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal;
| | - Liliana S. Mendonça
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (L.S.M.); (M.C.P.d.L.)
- CIBB—Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Liliana Matos
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA I.P), Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (J.I.S.); (L.M.); (S.A.)
- Center for the Study of Animal Science, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
| | - Maria João Prata
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal;
- i3S—Institute of Research and Innovation in Health/IPATIMUP—Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen, 208 4200-135 Porto, Portugal
| | - Amália S. Jurado
- University of Coimbra, CNC—Center for Neuroscience and Cell Biology, Department of Life Sciences, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal;
| | - Maria C. Pedroso de Lima
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (L.S.M.); (M.C.P.d.L.)
| | - Sandra Alves
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA I.P), Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (J.I.S.); (L.M.); (S.A.)
- Center for the Study of Animal Science, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
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15
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Efficient nanocarriers of siRNA therapeutics for cancer treatment. Transl Res 2019; 214:62-91. [PMID: 31369717 DOI: 10.1016/j.trsl.2019.07.006] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/01/2019] [Accepted: 07/15/2019] [Indexed: 02/02/2023]
Abstract
Nanocarriers as drug delivery systems are promising and becoming popular, especially for cancer treatment. In addition to improving the pharmacokinetics of poorly soluble hydrophobic drugs by solubilizing them in a hydrophobic core, nanocarriers allow cancer-specific combination drug deliveries by inherent passive targeting phenomena and adoption of active targeting strategies. Nanoparticle-drug formulations can enhance the safety, pharmacokinetic profiles, and bioavailability of locally or systemically administered drugs, leading to improved therapeutic efficacy. Gene silencing by RNA interference (RNAi) is rapidly developing as a personalized field of cancer treatment. Small interfering RNAs (siRNAs) can be used to switch off specific cancer genes, in effect, "silence the gene, silence the cancer." siRNA can be used to silence specific genes that produce harmful or abnormal proteins. The activity of siRNA can be used to harness cellular machinery to destroy a corresponding sequence of mRNA that encodes a disease-causing protein. At present, the main barrier to implementing siRNA therapies in clinical practice is the lack of an effective delivery system that protects the siRNA from nuclease degradation, delivers to it to cancer cells, and releases it into the cytoplasm of targeted cancer cells, without creating adverse effects. This review provides an overview of various nanocarrier formulations in both research and clinical applications with a focus on combinations of siRNA and chemotherapeutic drug delivery systems for the treatment of multidrug resistant cancer. The use of various nanoparticles for siRNA-drug delivery, including liposomes, polymeric nanoparticles, dendrimers, inorganic nanoparticles, exosomes, and red blood cells for targeted drug delivery in cancer is discussed.
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16
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Abstract
ABSTRACT
The rapid development of genomics and other “-omics” approaches has significantly impacted how we have investigated host-pathogen interactions since the turn of the millennium. Technologies such as next-generation sequencing, stem cell biology, and high-throughput proteomics have transformed the scale and sensitivity with which we interrogate biological samples. These approaches are impacting experimental design in the laboratory and transforming clinical management in health care systems. Here, we review this area from the perspective of research on bacterial pathogens.
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17
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Okamura Y, Makita N, Hizukuri Y, Hayashi Y. Genome-wide siRNA screening in mouse bone marrow-derived macrophages revealed that knockdown of ribosomal proteins suppresses IL-10 and enhances TNF-α production. J Clin Exp Hematop 2018; 58:87-94. [PMID: 29657255 PMCID: PMC6413152 DOI: 10.3960/jslrt.17036] [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] [Received: 12/04/2017] [Revised: 02/15/2018] [Accepted: 02/26/2018] [Indexed: 11/01/2022] Open
Abstract
Macrophages play a central role in the immune response, and their diverse functions are attributed to the spectrum of their functional states. To elucidate molecules involved in modulating the balance between the anti-inflammatory cytokine IL-10 and the pro-inflammatory cytokine TNF-α, we conducted genome-wide siRNA screening. First, we established an siRNA screening system using mouse bone marrow-derived macrophages, which are a suitable model for studying functional states of macrophages in vitro. In the primary screen and the subsequent reproducibility assay, 112 siRNA pools demonstrated enhancement of IL-10 production and 497 siRNA pools suppressed IL-10 production. After a deconvolution assay for IL-10-up-regulating siRNA pools, 8 genes were identified as IL-10 repressors, including Cnot1 and Rc3h1, components of the CCR4-NOT complex known to degrade cytokine mRNAs. On the other hand, siRNA pools targeting ribosomal proteins were frequently found among those that down-regulated IL-10 production and up-regulated TNF-α production. Four pools were assayed using deconvoluted siRNAs and identified as high-confidence hits. Thus, we found that the genome-wide knockdown of 19 ribosomal proteins resulted in decreased IL-10 and increased TNF-α production.
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Affiliation(s)
| | | | | | - Yasuhiro Hayashi
- Asubio Pharma Co., Ltd.,
Kobe, Japan
- Present Address: Oncology Laboratories, Daiichi Sankyo Co.,
Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710,
Japan. E-mail:
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18
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Hochheiser K, Kueh AJ, Gebhardt T, Herold MJ. CRISPR/Cas9: A tool for immunological research. Eur J Immunol 2018; 48:576-583. [PMID: 29415333 DOI: 10.1002/eji.201747131] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 12/01/2017] [Accepted: 02/02/2018] [Indexed: 12/27/2022]
Abstract
The CRISPR/Cas9-system was originally identified as part of the adaptive immune system in bacteria and has since been adapted for the genetic manipulation of eukaryotic cells. The technique is of particular value for biomedical sciences, as it enables the genetic manipulation of cell lines and primary cells as well as whole organisms with unprecedented ease and efficiency. Furthermore, the CRISPR/Cas9-technology has the potential for future therapeutic applications in the clinic. Here, we discuss the use of CRISPR/Cas9 for the genetic modification of haematopoietic cells and the generation of mouse models for immunological research. Additionally, we explain how the technique can be applied as a screening-tool to identify genes involved in different immunological processes. Moreover, we will talk about recent extensions of using the CRISPR/Cas9 technology, such as a transcriptional activator or repressor. Finally, we discuss the first clinical trials that use CRISPR/Cas9 and discuss potential future applications.
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Affiliation(s)
- Katharina Hochheiser
- Department of Microbiology & Immunology, The University of Melbourne, the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Andrew J Kueh
- The Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Thomas Gebhardt
- Department of Microbiology & Immunology, The University of Melbourne, the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Marco J Herold
- The Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
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19
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Suter SR, Ball-Jones A, Mumbleau MM, Valenzuela R, Ibarra-Soza J, Owens H, Fisher AJ, Beal PA. Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications. Org Biomol Chem 2018; 15:10029-10036. [PMID: 29164215 DOI: 10.1039/c7ob02654d] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
SiRNAs can cause unintended gene silencing due to miRNA-like effects because of the similarity in function of an siRNA guide strand and a miRNA. Here we evaluate the effect on miRNA-like off targeting of introducing the adenosine derivative 7-EAA and triazoles prepared from 7-EAA at different positions in an siRNA guide strand. We find that a sterically demanding triazole placed in the RNA duplex major groove at position six of the guide strand dramatically reduces miRNA-like off targeting potency. A high-resolution structure of an RNA duplex bearing a novel, major-groove localized triazole is reported, which suggests that modified triazoles could be disrupting the hAgo2-guide-target RNA ternary complex. Five different triazole modifications were tested at the guide strand 6-position for effects on on-target and miRNA-like off target knockdown potency. A 7-EAA triazole bearing a benzylamine substituent displayed on-target knockdown activity as potent as the native siRNA, while having an IC50 against a miRNA-like off target >100-fold higher. Melting temperature studies revealed no obvious correlation between potency in knockdown assays and a modification's effect on duplex stability. These results, along with known structures of hAgo2-guide-target ternary complexes, are used to rationalize the effect of 7-EAA triazoles on miRNA-like off target effects.
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Affiliation(s)
- Scott R Suter
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, California, 95616 USA.
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20
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Seok H, Lee H, Jang ES, Chi SW. Evaluation and control of miRNA-like off-target repression for RNA interference. Cell Mol Life Sci 2018; 75:797-814. [PMID: 28905147 PMCID: PMC11105550 DOI: 10.1007/s00018-017-2656-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 01/08/2023]
Abstract
RNA interference (RNAi) has been widely adopted to repress specific gene expression and is easily achieved by designing small interfering RNAs (siRNAs) with perfect sequence complementarity to the intended target mRNAs. Although siRNAs direct Argonaute (Ago), a core component of the RNA-induced silencing complex (RISC), to recognize and silence target mRNAs, they also inevitably function as microRNAs (miRNAs) and suppress hundreds of off-targets. Such miRNA-like off-target repression is potentially detrimental, resulting in unwanted toxicity and phenotypes. Despite early recognition of the severity of miRNA-like off-target repression, this effect has often been overlooked because of difficulties in recognizing and avoiding off-targets. However, recent advances in genome-wide methods and knowledge of Ago-miRNA target interactions have set the stage for properly evaluating and controlling miRNA-like off-target repression. Here, we describe the intrinsic problems of miRNA-like off-target effects caused by canonical and noncanonical interactions. We particularly focus on various genome-wide approaches and chemical modifications for the evaluation and prevention of off-target repression to facilitate the use of RNAi with secured specificity.
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Affiliation(s)
- Heeyoung Seok
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Haejeong Lee
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Eun-Sook Jang
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
- EncodeGEN Co. Ltd, Seoul, 06329, Korea
| | - Sung Wook Chi
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea.
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21
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Zhang L, Zhang Y, Wong SH, Law PTY, Zhao S, Yu J, Chan MTV, Wu WKK. Common Deregulation of Seven Biological Processes by MicroRNAs in Gastrointestinal Cancers. Sci Rep 2018; 8:3287. [PMID: 29459716 PMCID: PMC5818544 DOI: 10.1038/s41598-018-21573-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/07/2018] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs are frequently dysregulated in human neoplasms, including gastrointestinal cancers. Nevertheless, the global influence of microRNA dysregulation on cellular signaling is still unknown. Here we sought to elucidate cellular signaling dysregulation by microRNAs in gastrointestinal cancers at the systems biology level followed by experimental validation. Signature dysregulated microRNAs in gastric, colorectal and liver cancers were defined based on our previous studies. Targets of signature dysregulated miRNAs were predicted using multiple computer algorithms followed by gene enrichment analysis to identify biological processes perturbed by dysregulated microRNAs. Effects of microRNAs on endocytosis were measured by epidermal growth factor (EGF) internalization assay. Our analysis revealed that, aside from well-established cancer-related signaling pathways, several novel pathways, including axon guidance, neurotrophin/nerve growth factor signaling, and endocytosis, were found to be involved in the pathogenesis of gastrointestinal cancers. The regulation of EGF receptor (EGFR) endocytosis by two predicted miRNAs, namely miR-17 and miR-145, was confirmed experimentally. Functionally, miR-145, which blocked EGFR endocytosis, prolonged EGFR membrane signaling and altered responsiveness of colon cancer cells to EGFR-targeting drugs. In conclusion, our analysis depicts a comprehensive picture of cellular signaling dysregulation, including endocytosis, by microRNAs in gastrointestinal cancers.
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Affiliation(s)
- Lin Zhang
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuchen Zhang
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Sunny H Wong
- Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences and Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Priscilla T Y Law
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Shan Zhao
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences and Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Jun Yu
- Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences and Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Matthew T V Chan
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China.
| | - William K K Wu
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China. .,Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences and Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.
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22
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Aguiar S, van der Gaag B, Cortese FAB. RNAi mechanisms in Huntington's disease therapy: siRNA versus shRNA. Transl Neurodegener 2017; 6:30. [PMID: 29209494 PMCID: PMC5702971 DOI: 10.1186/s40035-017-0101-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/30/2017] [Indexed: 12/19/2022] Open
Abstract
Huntington's Disease (HD) is a genetically dominant trinucleotide repeat disorder resulting from CAG repeats within the Huntingtin (HTT) gene exceeding a normal range (> 36 CAGs). Symptoms of the disease manifest in middle age and include chorea, dystonia, and cognitive decline. Typical latency from diagnosis to death is 20 years. There are currently no disease-modifying therapies available to HD patients. RNAi is a potentially curative therapy for HD. A popular line of research employs siRNA or antisense oligonucleotides (ASO) to knock down mutant Huntingtin mRNA (mHTT). Unfortunately, this modality requires repeated dosing, commonly exhibit off target effects (OTEs), and exert renal and hepatic toxicity. In contrast, a single AAV-mediated short-hairpin RNA (shRNA) dose can last years with low toxicity. In addition, we highlight research indicating that shRNA elicits fewer OTEs than siRNA when tested head-to-head. Despite this promise, shRNA therapy has been held back by difficulties controlling expression (oversaturating cells with toxic levels of RNA construct). In this review, we compare RNAi modalities for HD and propose novel methods of optimizing shRNA expression and on-target fidelity.
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Affiliation(s)
- Sebastian Aguiar
- Molecular Neuroscience Laboratory, Swammerdam Institute for Life Sciences (SILS-CNS), University of Amsterdam, Amsterdam, Netherlands
- Fulbright Program, US Department of State (IIE), New York City, NY USA
| | - Bram van der Gaag
- Molecular Neuroscience Laboratory, Swammerdam Institute for Life Sciences (SILS-CNS), University of Amsterdam, Amsterdam, Netherlands
- Department of Neurobiology, Care Sciences and Society, Karolinska Institute, Stockholm, Sweden
| | - Francesco Albert Bosco Cortese
- Biogerontology Research Foundation (BGRF), Oxford, UK
- Department of Biomedical and Molecular Sciences, Queen’s University School of Medicine, Queen’s University, Kingston, Canada
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23
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Li G, Wu F, Yang H, Deng X, Yuan Y. MiR-9-5p promotes cell growth and metastasis in non-small cell lung cancer through the repression of TGFBR2. Biomed Pharmacother 2017; 96:1170-1178. [PMID: 29239816 DOI: 10.1016/j.biopha.2017.11.105] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 11/11/2017] [Accepted: 11/20/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Increasing evidence indicates that the dysregulation of microRNAs (miRNAs) play critical roles tumor progression and metastasis, but very few papers had reported the function of miR-9-5p in lung cancer, especially in NSCLCs. METHODS In this study, we investigated the role of miR-9-5p in non-small cell lung cancers (NSCLCs). MiR-9-5p level were analyzed in 62 clinical NSCLC lung tissue samples and adjacent normal lung tissues by RT-PCR. The target of miR-9-5p was predicted by TargetScan and luciferase reporter assay was used to verify the binding site of miR-9-5p on TGFBR2 mRNA. MTT assay, wound healing assay and invasion assay were performed in both miR-5p inhibitor transfected A549 and miR-5p mimic transfected SK-MES-1 cells. To further investigate whether TGFBR2 is the major target of miR-9-5p, we used TGFBR2 siRNA to transfect A549 and SK-MES-1 cells with miR-9-5p inhibitor or miR-9-5p mimic transfection. Western blot were then used to analyze TGFBR2, p-smad2 and p-smad3 protein expressions after transfection. RESULTS Results indicated that NSCLC patients' tissues had a significantly higher expression of miR-9-5p compared to adjacent normal lung tissues. MiR-9-5p mimic transfection promoted proliferation, metastasis and invasion abilities in both A549 and SK-MES-1 cells. Conversely, miR-9-5p inhibitor transfection showed the decreased abilities of these cells. Luciferase reporter assay indicated that TGFBR2 is a direct target of miR-9-5p and the up-regulation of TGFBR2 suppressed cell proliferation, metastasis and invasion. The knock down of TGFBR2 abrogated the effect of miR-9-5p in down-regulating p-smad2 and p-smad3 expressions, which indicated that TGFBR2 is the major target of miR-9-5p in NSCLC cells. CONCLUSIONS Our finding indicated that miR-9-5p promotes the proliferation, metastasis and invasion of NSCLC cells by down-regulating TGFBR2 expression.
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Affiliation(s)
- Gang Li
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, PR China; Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Fang Wu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Han Yang
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Xia Deng
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Yawei Yuan
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, PR China; Department of Radiation Oncology, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, PR China.
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24
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Welsbie DS, Mitchell KL, Jaskula-Ranga V, Sluch VM, Yang Z, Kim J, Buehler E, Patel A, Martin SE, Zhang PW, Ge Y, Duan Y, Fuller J, Kim BJ, Hamed E, Chamling X, Lei L, Fraser IDC, Ronai ZA, Berlinicke CA, Zack DJ. Enhanced Functional Genomic Screening Identifies Novel Mediators of Dual Leucine Zipper Kinase-Dependent Injury Signaling in Neurons. Neuron 2017. [PMID: 28641113 DOI: 10.1016/j.neuron.2017.06.008] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Dual leucine zipper kinase (DLK) has been implicated in cell death signaling secondary to axonal damage in retinal ganglion cells (RGCs) and other neurons. To better understand the pathway through which DLK acts, we developed enhanced functional genomic screens in primary RGCs, including use of arrayed, whole-genome, small interfering RNA libraries. Explaining why DLK inhibition is only partially protective, we identify leucine zipper kinase (LZK) as cooperating with DLK to activate downstream signaling and cell death in RGCs, including in a mouse model of optic nerve injury, and show that the same pathway is active in human stem cell-derived RGCs. Moreover, we identify four transcription factors, JUN, activating transcription factor 2 (ATF2), myocyte-specific enhancer factor 2A (MEF2A), and SRY-Box 11 (SOX11), as being the major downstream mediators through which DLK/LZK activation leads to RGC cell death. Increased understanding of the DLK pathway has implications for understanding and treating neurodegenerative diseases.
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Affiliation(s)
- Derek S Welsbie
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Shiley Eye Institute, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Katherine L Mitchell
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Vinod Jaskula-Ranga
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Valentin M Sluch
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Zhiyong Yang
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Shiley Eye Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jessica Kim
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Eugen Buehler
- National Center for Advancing Translational Sciences, NIH, Bethesda, MD 20892, USA
| | - Amit Patel
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Shiley Eye Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - Scott E Martin
- National Center for Advancing Translational Sciences, NIH, Bethesda, MD 20892, USA
| | - Ping-Wu Zhang
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yan Ge
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yukan Duan
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - John Fuller
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Byung-Jin Kim
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Eman Hamed
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Xitiz Chamling
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Lei Lei
- Department of Biology, University of New England, Biddeford, ME 04005, USA
| | - Iain D C Fraser
- Signaling Systems Unit, Laboratory of Systems Biology, National Institute for Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Ze'ev A Ronai
- Signal Transduction Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Cynthia A Berlinicke
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Donald J Zack
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Solomon H. Snyder Department of Neuroscience, Department of Molecular Biology and Genetics, Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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25
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Riba A, Emmenlauer M, Chen A, Sigoillot F, Cong F, Dehio C, Jenkins J, Zavolan M. Explicit Modeling of siRNA-Dependent On- and Off-Target Repression Improves the Interpretation of Screening Results. Cell Syst 2017; 4:182-193.e4. [PMID: 28215525 DOI: 10.1016/j.cels.2017.01.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/09/2016] [Accepted: 01/13/2017] [Indexed: 12/31/2022]
Abstract
RNAi is broadly used to map gene regulatory networks, but the identification of genes that are responsible for the observed phenotypes is challenging, as small interfering RNAs (siRNAs) simultaneously downregulate the intended on targets and many partially complementary off targets. Additionally, the scarcity of publicly available control datasets hinders the development and comparative evaluation of computational methods for analyzing the data. Here, we introduce PheLiM (https://github.com/andreariba/PheLiM), a method that uses predictions of siRNA on- and off-target downregulation to infer gene-specific contributions to phenotypes. To assess the performance of PheLiM, we carried out siRNA- and CRISPR/Cas9-based genome-wide screening of two well-characterized pathways, bone morphogenetic protein (BMP) and nuclear factor κB (NF-κB), and we reanalyzed publicly available siRNA screens. We demonstrate that PheLiM has the overall highest accuracy and most reproducible results compared to other available methods. PheLiM can accommodate various methods for predicting siRNA off targets and is broadly applicable to the identification of genes underlying complex phenotypes.
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Affiliation(s)
- Andrea Riba
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Mario Emmenlauer
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Amy Chen
- Developmental & Molecular Pathways, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Frederic Sigoillot
- Developmental & Molecular Pathways, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Feng Cong
- Developmental & Molecular Pathways, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Christoph Dehio
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Jeremy Jenkins
- Developmental & Molecular Pathways, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Mihaela Zavolan
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland.
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26
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Flores-Pérez A, Marchat LA, Rodríguez-Cuevas S, Bautista-Piña V, Hidalgo-Miranda A, Ocampo EA, Martínez MS, Palma-Flores C, Fonseca-Sánchez MA, Astudillo-de la Vega H, Ruíz-García E, González-Barrios JA, Pérez-Plasencia C, Streber ML, López-Camarillo C. Dual targeting of ANGPT1 and TGFBR2 genes by miR-204 controls angiogenesis in breast cancer. Sci Rep 2016; 6:34504. [PMID: 27703260 PMCID: PMC5050489 DOI: 10.1038/srep34504] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 09/15/2016] [Indexed: 12/22/2022] Open
Abstract
Deregulated expression of microRNAs has been associated with angiogenesis. Studying the miRNome of locally advanced breast tumors we unsuspectedly found a dramatically repression of miR-204, a small non-coding RNA with no previous involvement in tumor angiogenesis. Downregulation of miR-204 was confirmed in an independent cohort of patients and breast cancer cell lines. Gain-of-function analysis indicates that ectopic expression of miR-204 impairs cell proliferation, anchorage-independent growth, migration, invasion, and the formation of 3D capillary networks in vitro. Likewise, in vivo vascularization and angiogenesis were suppressed by miR-204 in a nu/nu mice model. Genome-wide profiling of MDA-MB-231 cells expressing miR-204 revealed changes in the expression of hundred cancer-related genes. Of these, we focused on the study of pro-angiogenic ANGPT1 and TGFβR2. Functional analysis using luciferase reporter and rescue assays confirmed that ANGPT1 and TGFβR2 are novel effectors downstream of miR-204. Accordingly, an inverse correlation between miR-204 and ANGPT1/TGFβR2 expression was found in breast tumors. Knockdown of TGFβR2, but not ANGPT1, impairs cell proliferation and migration whereas inhibition of both genes inhibits angiogenesis. Taken altogether, our findings reveal a novel role for miR-204/ANGPT1/TGFβR2 axis in tumor angiogenesis. We propose that therapeutic manipulation of miR-204 levels may represent a promising approach in breast cancer.
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Affiliation(s)
- Ali Flores-Pérez
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
| | - Laurence A Marchat
- Programa en Biomedicina Molecular y Red de Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, México
| | | | | | | | - Elena Aréchaga Ocampo
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Ciudad de México, México
| | - Mónica Sierra Martínez
- Laboratorio de Genética y Diagnóstico Molecular, Hospital Juárez, Ciudad de México, México
| | - Carlos Palma-Flores
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
| | - Miguel A Fonseca-Sánchez
- Departamento de Genética Humana, Hospital General de Mexico "Dr Eduardo Liceaga", Ciudad de México, México
| | - Horacio Astudillo-de la Vega
- Laboratorio de Investigación en Cáncer Translacional y Terapia Celular, Centro Médico Siglo XXI, Ciudad de México, México
| | - Erika Ruíz-García
- Laboratorio de Medicina Translacional, Instituto Nacional de Cancerología, Ciudad de México, México
| | | | - Carlos Pérez-Plasencia
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Ciudad de México, México; Universidad Nacional Autónoma de México UNAM, FES-Iztacala, UBIMED, Tlalnepantla, Estado de México, México
| | - María L Streber
- Laboratorio de Investigación Experimental y Animal. Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
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27
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Kamola PJ, Nakano Y, Takahashi T, Wilson PA, Ui-Tei K. The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects. PLoS Comput Biol 2015; 11:e1004656. [PMID: 26657993 PMCID: PMC4676691 DOI: 10.1371/journal.pcbi.1004656] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/16/2015] [Indexed: 01/06/2023] Open
Abstract
RNA interference (RNAi) is a powerful tool for post-transcriptional gene silencing. However, the siRNA guide strand may bind unintended off-target transcripts via partial sequence complementarity by a mechanism closely mirroring micro RNA (miRNA) silencing. To better understand these off-target effects, we investigated the correlation between sequence features within various subsections of siRNA guide strands, and its corresponding target sequences, with off-target activities. Our results confirm previous reports that strength of base-pairing in the siRNA seed region is the primary factor determining the efficiency of off-target silencing. However, the degree of downregulation of off-target transcripts with shared seed sequence is not necessarily similar, suggesting that there are additional auxiliary factors that influence the silencing potential. Here, we demonstrate that both the melting temperature (Tm) in a subsection of siRNA non-seed region, and the GC contents of its corresponding target sequences, are negatively correlated with the efficiency of off-target effect. Analysis of experimentally validated miRNA targets demonstrated a similar trend, indicating a putative conserved mechanistic feature of seed region-dependent targeting mechanism. These observations may prove useful as parameters for off-target prediction algorithms and improve siRNA ‘specificity’ design rules. Small interfering RNAs (siRNAs) are double stranded RNA molecules designed to perfectly match the sequence of a target gene and silence its expression. The function is exerted through the RNA interference (RNAi) pathway and has revolutionised biological research due to its ease-of-use and high potency. While siRNAs were initially believed to be highly specific, they have subsequently been observed to interact with other, unintended messenger RNAs. However, the mechanistic details of this process remain poorly understood, and there is a paucity of strategies and guidelines directed toward mitigating this issue. To address this potential safety liability, we performed a comprehensive analysis of sequence characteristics of siRNA duplexes and their target regions. Results from luciferase-reporter assays and global expression data confirmed previous observations that the siRNA seed region is the primary determinant for off-target gene recognition and binding. Furthermore, our analysis revealed the important contribution of siRNA non-seed region, and its corresponding target sequences, to the potency of off-target knockdown. Similar results were observed in an equivalent evaluation of the miRNA-targeting mechanism, suggesting that the correlating features arise through an evolutionary conserved mechanistic factor.
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Affiliation(s)
- Piotr J. Kamola
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Safety Assessment, GlaxoSmithKline R&D, Ware, Hertfordshire, United Kingdom
- Computational Biology, GlaxoSmithKline R&D, Stevenage, Hertfordshire, United Kingdom
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Harwell Science and Innovation Campus, United Kingdom
| | - Yuko Nakano
- Department of Biological Sciences, University of Tokyo, Bunkyo, Tokyo, Japan
| | - Tomoko Takahashi
- Department of Biological Sciences, University of Tokyo, Bunkyo, Tokyo, Japan
| | - Paul A. Wilson
- Computational Biology, GlaxoSmithKline R&D, Stevenage, Hertfordshire, United Kingdom
| | - Kumiko Ui-Tei
- Department of Biological Sciences, University of Tokyo, Bunkyo, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, University of Tokyo, Kashiwa, Chiba, Japan
- * E-mail:
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28
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Schmich F, Szczurek E, Kreibich S, Dilling S, Andritschke D, Casanova A, Low SH, Eicher S, Muntwiler S, Emmenlauer M, Rämö P, Conde-Alvarez R, von Mering C, Hardt WD, Dehio C, Beerenwinkel N. gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens. Genome Biol 2015; 16:220. [PMID: 26445817 PMCID: PMC4597449 DOI: 10.1186/s13059-015-0783-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/16/2015] [Indexed: 12/31/2022] Open
Abstract
Small interfering RNAs (siRNAs) exhibit strong off-target effects, which confound the gene-level interpretation of RNA interference screens and thus limit their utility for functional genomics studies. Here, we present gespeR, a statistical model for reconstructing individual, gene-specific phenotypes. Using 115,878 siRNAs, single and pooled, from three companies in three pathogen infection screens, we demonstrate that deconvolution of image-based phenotypes substantially improves the reproducibility between independent siRNA sets targeting the same genes. Genes selected and prioritized by gespeR are validated and shown to constitute biologically relevant components of pathogen entry mechanisms and TGF-β signaling. gespeR is available as a Bioconductor R-package.
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Affiliation(s)
- Fabian Schmich
- Department of Biosystems Science and Engineering, ETH, Zurich, Switzerland. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Ewa Szczurek
- Department of Biosystems Science and Engineering, ETH, Zurich, Switzerland. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | | | | | | | | | | | - Simone Eicher
- Biozentrum, University of Basel, Basel, Switzerland.
| | | | | | - Pauli Rämö
- Biozentrum, University of Basel, Basel, Switzerland.
| | - Raquel Conde-Alvarez
- Institute for Tropical Health and Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain.
| | - Christian von Mering
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
| | | | | | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH, Zurich, Switzerland. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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29
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Zhang Y, Zhao FJ, Chen LL, Wang LQ, Nephew KP, Wu YL, Zhang S. MiR-373 targeting of the Rab22a oncogene suppresses tumor invasion and metastasis in ovarian cancer. Oncotarget 2015; 5:12291-303. [PMID: 25460499 PMCID: PMC4323008 DOI: 10.18632/oncotarget.2577] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 10/06/2014] [Indexed: 12/19/2022] Open
Abstract
Metastasis is major cause of mortality in patients with ovarian cancer. MiR-373 has been shown to play pivotal roles in tumorigenesis and metastasis; however, a role for miR-373 in ovarian cancer has not been investigated. In this study, we show that the miR-373 expression is down-regulated in human epithelial ovarian cancer (EOC) and inversely correlated with clinical stage and histological grade. Ectopic overexpression of miR-373 in human EOC cells suppressed cell invasion in vitro and metastasis in vivo, and the epithelial–mesenchymal transition process. Silencing the expression of miR-373 resulted in an increased migration and invasion of EOC cells. Using integrated bioinformatics analysis, gene expression arrays, and luciferase assay, we identified Rab22a as a direct and functional target of miR-373 in EOC cells. Expression levels of miR-373 were inversely correlated with Rab22a protein levels in human EOC tissues. Rab22a knockdown inhibited invasion and migration of EOC cells, increased E-cadherin expression, and suppressed the expression of N-cadherin. Moreover, overexpression of Rab22a abrogated miR-373-induced invasion and migration of EOC cells. Taken together, these results demonstrate that miR-373 suppresses EOC invasion and metastasis by directly targeting Rab22a gene, a new potential therapeutic target in EOC.
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Affiliation(s)
- Yue Zhang
- Department of Obstetrics and Gynecology, RenJi Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, 200127, China
| | - Fu-Jun Zhao
- Department of Urology, Shanghai First People's Hospital, Shanghai Jiao-Tong University, Shanghai, 200080, China
| | - Li-Lan Chen
- Department of Obstetrics and Gynecology, RenJi Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, 200127, China
| | - Luo-Qiao Wang
- Department of Obstetrics and Gynecology, RenJi Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, 200127, China
| | - Kenneth P Nephew
- Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Ying-Li Wu
- Department of Pathophysiology, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Shanghai Jiao-Tong University School of Medicine, Shanghai, 200025, China
| | - Shu Zhang
- Department of Obstetrics and Gynecology, RenJi Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, 200127, China
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30
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Deciphering Seed Sequence Based Off-Target Effects in a Large-Scale RNAi Reporter Screen for E-Cadherin Expression. PLoS One 2015; 10:e0137640. [PMID: 26361354 PMCID: PMC4567318 DOI: 10.1371/journal.pone.0137640] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 08/19/2015] [Indexed: 12/28/2022] Open
Abstract
Functional RNAi based screening is affected by large numbers of false positive and negative hits due to prevalent sequence based off-target effects. We performed a druggable genome targeting siRNA screen intended to identify novel regulators of E-cadherin (CDH1) expression, a known key player in epithelial mesenchymal transition (EMT). Analysis of primary screening results indicated a large number of false-positive hits. To address these crucial difficulties we developed an analysis method, SENSORS, which, similar to published methods, is a seed enrichment strategy for analyzing siRNA off-targets in RNAi screens. Using our approach, we were able to demonstrate that accounting for seed based off-target effects stratifies primary screening results and enables the discovery of additional screening hits. While traditional hit detection methods are prone to false positive results which are undetected, we were able to identify false positive hits robustly. Transcription factor MYBL1 was identified as a putative novel target required for CDH1 expression and verified experimentally. No siRNA pool targeting MYBL1 was present in the used siRNA library. Instead, MYBL1 was identified as a putative CDH1 regulating target solely based on the SENSORS off-target score, i.e. as a gene that is a cause for off-target effects down regulating E-cadherin expression.
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31
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Rodriguez-Barrueco R, Yu J, Saucedo-Cuevas LP, Olivan M, Llobet-Navas D, Putcha P, Castro V, Murga-Penas EM, Collazo-Lorduy A, Castillo-Martin M, Alvarez M, Cordon-Cardo C, Kalinsky K, Maurer M, Califano A, Silva JM. Inhibition of the autocrine IL-6-JAK2-STAT3-calprotectin axis as targeted therapy for HR-/HER2+ breast cancers. Genes Dev 2015; 29:1631-48. [PMID: 26227964 PMCID: PMC4536311 DOI: 10.1101/gad.262642.115] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/14/2015] [Indexed: 12/22/2022]
Abstract
Rodriguez-Barrueco et al. found that HR−/HER2+ cells secrete high levels of IL-6, inducing the activation of STAT3, which in turn promotes a second autocrine stimulus to increase S100A8/9 complex (calprotectin) production and secretion. Inhibition of the IL-6–JAK2–STAT3–calprotectin axis with FDA-approved drugs, alone and in combination with HER2 inhibitors, reduced the tumorigenicity of HR−/HER2+ breast cancers. HER2-positive (HER2+) breast adenocarcinomas are a heterogeneous group in which hormone receptor (HR) status influences therapeutic decisions and patient outcome. By combining genome-wide RNAi screens with regulatory network analysis, we identified STAT3 as a critically activated master regulator of HR−/HER2+ tumors, eliciting tumor dependency in these cells. Mechanistically, HR−/HER2+ cells secrete high levels of the interleukin-6 (IL-6) cytokine, inducing the activation of STAT3, which in turn promotes a second autocrine stimulus to increase S100A8/9 complex (calprotectin) production and secretion. Increased calprotectin levels activate signaling pathways involved in proliferation and resistance. Importantly, we demonstrated that inhibition of the IL-6–Janus kinase 2 (JAK2)–STAT3–calprotectin axis with FDA-approved drugs, alone and in combination with HER2 inhibitors, reduced the tumorigenicity of HR−/HER2+ breast cancers, opening novel targeted therapeutic opportunities.
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Affiliation(s)
- Ruth Rodriguez-Barrueco
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Jiyang Yu
- Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York 10032, USA
| | - Laura P Saucedo-Cuevas
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Mireia Olivan
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - David Llobet-Navas
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Preeti Putcha
- Institute for Cancer Genetics, Department of Pathology, Irving Cancer Research Center, Columbia University, New York, New York 10032, USA
| | - Veronica Castro
- Institute for Cancer Genetics, Department of Pathology, Irving Cancer Research Center, Columbia University, New York, New York 10032, USA
| | - Eva M Murga-Penas
- Institute for Cancer Genetics, Department of Pathology, Irving Cancer Research Center, Columbia University, New York, New York 10032, USA
| | - Ana Collazo-Lorduy
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Mireia Castillo-Martin
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Mariano Alvarez
- Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York 10032, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Kevin Kalinsky
- Department of Medicine, Columbia University Medical Center, New York, New York 10032, USA
| | - Matthew Maurer
- Institute for Cancer Genetics, Department of Pathology, Irving Cancer Research Center, Columbia University, New York, New York 10032, USA; Department of Medicine, Columbia University Medical Center, New York, New York 10032, USA
| | - Andrea Califano
- Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York 10032, USA; Department of Biomedical Informatics, Institute for Cancer Genetics, Columbia University, New York, New York 10032; Department of Biochemistry and Molecular Biophysics, Institute for Cancer Genetics, Columbia University, New York, New York 10032
| | - Jose M Silva
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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32
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Liang C, Li X, Zhang L, Cui D, Quan X, Yang W. The anti-fibrotic effects of microRNA-153 by targeting TGFBR-2 in pulmonary fibrosis. Exp Mol Pathol 2015. [PMID: 26216407 DOI: 10.1016/j.yexmp.2015.07.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive interstitial fibrotic lung disease with an undefined etiology and no effective treatments. By binding to cell surface receptors, transforming growth factor-β (TGF-β) plays a pivotal role in lung fibrosis. Therefore, the screening of microRNAs (miRNAs), especially those interrupting the effects of TGF-β, may provide information not only on the pathomechanism, but also on the treatment of this disease. In the present study, we found that miR-153 expression was dysregulated in the lungs of mice with experimental pulmonary fibrosis and TGF-β1 decreased miR-153 expression in pulmonary fibroblasts. Moreover, increased miR-153 levels attenuated, whereas the knock down of miR-153 promoted the pro-fibrogenic activity of TGF-β1, and miR-153 reduced the contractile and migratory activities of fibroblasts. In addition, TGFBR2, a transmembrane serine/threonine kinase receptor for TGF-β, was identified as a direct target of miR-153. Furthermore, by post-transcriptional regulation of the expression of TGFBR2, phosphorylation of SMAD2/3 was also influenced by miR-153. These data suggest that miR-153 disturbs TGF-β1 signal transduction and its effects on fibroblast activation, acting as an anti-fibrotic element in the development of pulmonary fibrosis.
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Affiliation(s)
- Chunlian Liang
- Department of Geriatrics, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, PR China
| | - Xiuli Li
- Department of Geriatrics, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, PR China
| | - Lin Zhang
- Department of Geriatrics, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, PR China
| | - Dajiang Cui
- Department of Geriatrics, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, PR China
| | - Xiaojuan Quan
- Department of Geriatrics, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, PR China.
| | - Weilin Yang
- Department of Geriatrics, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, PR China
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33
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Singh S, Wu X, Ljosa V, Bray MA, Piccioni F, Root DE, Doench JG, Boehm JS, Carpenter AE. Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects. PLoS One 2015. [PMID: 26197079 PMCID: PMC4511418 DOI: 10.1371/journal.pone.0131370] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
RNA interference and morphological profiling-the measurement of thousands of phenotypes from individual cells by microscopy and image analysis-are a potentially powerful combination. We show that morphological profiles of RNAi-induced knockdown using the Cell Painting assay are in fact highly sensitive and reproducible. However, we find that the magnitude and prevalence of off-target effects via the RNAi seed-based mechanism make morphological profiles of RNAi reagents targeting the same gene look no more similar than reagents targeting different genes. Pairs of RNAi reagents that share the same seed sequence produce image-based profiles that are much more similar to each other than profiles from pairs designed to target the same gene, a phenomenon previously observed in small-scale gene-expression profiling experiments. Various strategies have been used to enrich on-target versus off-target effects in the context of RNAi screening where a narrow set of phenotypes are measured, mostly based on comparing multiple sequences targeting the same gene; however, new approaches will be needed to make RNAi morphological profiling (that is, comparing multi-dimensional phenotypes) viable. We have shared our raw data and computational pipelines to facilitate research.
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Affiliation(s)
- Shantanu Singh
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Xiaoyun Wu
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Vebjorn Ljosa
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Mark-Anthony Bray
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Federica Piccioni
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - David E. Root
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - John G. Doench
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Jesse S. Boehm
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Anne E. Carpenter
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- * E-mail:
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Alleviation of off-target effects from vector-encoded shRNAs via codelivered RNA decoys. Proc Natl Acad Sci U S A 2015; 112:E4007-16. [PMID: 26170322 DOI: 10.1073/pnas.1510476112] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Exogenous RNAi triggers such as shRNAs ideally exert their activities exclusively via the antisense strand that binds and silences designated target mRNAs. However, in principle, the sense strand also possesses silencing capacity that may contribute to adverse RNAi side effects including off-target gene regulation. Here, we address this concern with a novel strategy that reduces sense strand activity of vector-encoded shRNAs via codelivery of inhibitory tough decoy (TuD) RNAs. Using various shRNAs for proof of concept, we validate that coexpression of TuDs can sequester and inactivate shRNA sense strands in human cells selectively without affecting desired antisense activities from the same shRNAs. Moreover, we show how coexpressed TuDs can alleviate shRNA-mediated perturbation of global gene expression by specifically de-repressing off-target transcripts carrying seed matches to the shRNA sense strand. Our combination of shRNA and TuD in a single bicistronic gene transfer vector derived from Adeno-associated virus (AAV) enables a wide range of applications, including gene therapies. To this end, we engineered our constructs in a modular fashion and identified simple hairpin design rules permitting adaptation to preexisting or new shRNAs. Finally, we demonstrate the power of our vectors for combinatorial RNAi strategies by showing robust suppression of hepatitis C virus (HCV) with an AAV expressing a bifunctional TuD against an anti-HCV shRNA sense strand and an HCV-related cellular miRNA. The data and tools reported here represent an important step toward the next generation of RNAi triggers with increased specificity and thus ultimately safety in humans.
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Affiliation(s)
- Kenneth M Yamada
- Academic Editor and Editor-in-Chief, The Journal of Cell Biology Laboratory of Cell and Developmental Biology, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892
| | - Alan Hall
- Academic Editor and Editor-in-Chief, The Journal of Cell Biology Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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Valizadeh M, Mirzaei B, Tavallaei M, Noorani MR, Amiri M, Soroush MR, Mowla SJ. Down-regulation of TGF-b1, TGF-b receptor 2, and TGF-b-associated microRNAs, miR-20a and miR-21, in skin lesions of sulfur mustard-exposed Iranian war veterans. J Recept Signal Transduct Res 2015; 35:634-9. [PMID: 26498464 DOI: 10.3109/10799893.2015.1041646] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Sulfur mustard (SM) affects divergent cellular pathways including cell cycle, apoptosis, necrosis, and inflammatory responses. SM-induced lesions in skin include late-onset hyper-pigmentation, xerosis, and atrophy. It seems that TGF-b signaling pathway is a major player for SM pathogenesis. Here, we have employed a real-time polymerase chain reaction (PCR) approach to evaluate the expression alterations of all TGF-b variants and their receptors in skin biopsies obtained from 10 Iran-Iraq war veterans. Using specific LNA primers, the expression alteration of a TGF-bR2 regulator, miR-20a, and TGF-b downstream target, miR-21, was also assessed in the same samples Our real-time PCR data revealed a significant down-regulation of TGF-b1 and TGF-bR2, the major mediators of TGF-b signaling pathway, in skin biopsies of SM-exposed patients (p = 0.0015 and p = 0.0115, respectively). Down-regulation of TGF-b signaling pathway seems to contribute in severe inflammation observed in SM-exposed patients' tissues. MiR-20a and miR-21, as two important TGF-b associated microRNAs (miRNAs), were also down-regulated in SM-exposed skin lesions, compared to those of control group (p = 0.0003). Based on our findings, these miRNAs could be directly or indirectly involve in the pathogenesis of SM. Altogether, our data suggest the suitability of TGF-b1, TGF-bR2, as well as miR-20a and miR-21 as potential biomarkers for diagnosis and treatment of SM-exposed patients.
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Affiliation(s)
- Mohadeseh Valizadeh
- a Department of Genetics , Science and Research Branch Islamic Azad University , Tehran , Iran .,b ParsGenome Company , Tehran , Iran
| | - Behnaz Mirzaei
- a Department of Genetics , Science and Research Branch Islamic Azad University , Tehran , Iran .,b ParsGenome Company , Tehran , Iran
| | - Mahmood Tavallaei
- c Genetics Research Center, Baqyiatallah Medical Sciences University , Tehran , Iran
| | - Mohammad Reza Noorani
- d Chemical Injuries Research Center, Baqiatallah University of Medical Sciences , Tehran , Iran
| | - Mojtaba Amiri
- d Chemical Injuries Research Center, Baqiatallah University of Medical Sciences , Tehran , Iran
| | | | - Seyed Javad Mowla
- f Faculty of Biological Sciences, Molecular Genetics Department , Tarbiat Modares University , Tehran , Iran
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Siebourg-Polster J, Mudrak D, Emmenlauer M, Rämö P, Dehio C, Greber U, Fröhlich H, Beerenwinkel N. NEMix: single-cell nested effects models for probabilistic pathway stimulation. PLoS Comput Biol 2015; 11:e1004078. [PMID: 25879530 PMCID: PMC4400057 DOI: 10.1371/journal.pcbi.1004078] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 12/08/2014] [Indexed: 11/18/2022] Open
Abstract
Nested effects models have been used successfully for learning subcellular networks from high-dimensional perturbation effects that result from RNA interference (RNAi) experiments. Here, we further develop the basic nested effects model using high-content single-cell imaging data from RNAi screens of cultured cells infected with human rhinovirus. RNAi screens with single-cell readouts are becoming increasingly common, and they often reveal high cell-to-cell variation. As a consequence of this cellular heterogeneity, knock-downs result in variable effects among cells and lead to weak average phenotypes on the cell population level. To address this confounding factor in network inference, we explicitly model the stimulation status of a signaling pathway in individual cells. We extend the framework of nested effects models to probabilistic combinatorial knock-downs and propose NEMix, a nested effects mixture model that accounts for unobserved pathway activation. We analyzed the identifiability of NEMix and developed a parameter inference scheme based on the Expectation Maximization algorithm. In an extensive simulation study, we show that NEMix improves learning of pathway structures over classical NEMs significantly in the presence of hidden pathway stimulation. We applied our model to single-cell imaging data from RNAi screens monitoring human rhinovirus infection, where limited infection efficiency of the assay results in uncertain pathway stimulation. Using a subset of genes with known interactions, we show that the inferred NEMix network has high accuracy and outperforms the classical nested effects model without hidden pathway activity. NEMix is implemented as part of the R/Bioconductor package ‘nem’ and available at www.cbg.ethz.ch/software/NEMix. Experiments monitoring individual cells show that cells can behave differently even under same experimental conditions. Summarizing measurements over a population of cells can lead to weak and widely deviating signals, and subsequently applied modeling approaches, like network inference, will suffer from this information loss. Nested effects models, a method tailored to reconstruct signaling networks from high-dimensional read-outs of gene silencing experiments, have so far been only applied on the cell population level. These models assume the pathway under consideration to be activated in all cells. The signal flow is only disrupted, when genes are silenced. However, if this assumption is not met, inference results can be incorrect, because observed effects are interpreted wrongly. We extended nested effects models, to use the power of single-cell resolution data sets. We introduce a new unobserved factor, which describes the pathway activity of single cells. The pathway activity is learned for each cell during network inference. We apply our model to gene silencing screens, investigating human rhino virus infection of single cells from microscopy imaging features. Comparing the learned network to the known KEGG pathway of the genes shows that our method recovers networks significantly better than classical nested effects models without capturing of hidden signaling.
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Affiliation(s)
- Juliane Siebourg-Polster
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Daria Mudrak
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | - Pauli Rämö
- Biozentrum, University of Basel, Basel, Switzerland
| | | | - Urs Greber
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Holger Fröhlich
- Algorithmic Bioinformatics, Bonn-Aachen International Center for IT, University of Bonn, Bonn, Germany
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
- * E-mail:
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Gumienny R, Zavolan M. Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G. Nucleic Acids Res 2015; 43:1380-91. [PMID: 25628353 PMCID: PMC4330396 DOI: 10.1093/nar/gkv050] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Small interfering RNA (siRNA)-mediated knock-down is a widely used experimental approach to characterizing gene function. Although siRNAs are designed to guide the cleavage of perfectly complementary mRNA targets, acting similarly to microRNAs (miRNAs), siRNAs down-regulate the expression of hundreds of genes to which they have only partial complementarity. Prediction of these siRNA ‘off-targets’ remains difficult, due to the incomplete understanding of siRNA/miRNA–target interactions. Combining a biophysical model of miRNA–target interaction with structure and sequence features of putative target sites we developed a suite of algorithms, MIRZA-G, for the prediction of miRNA targets and siRNA off-targets on a genome-wide scale. The MIRZA-G variant that uses evolutionary conservation performs better than currently available methods in predicting canonical miRNA target sites and in addition, it predicts non-canonical miRNA target sites with similarly high accuracy. Furthermore, MIRZA-G variants predict siRNA off-target sites with an accuracy unmatched by currently available programs. Thus, MIRZA-G may prove instrumental in the analysis of data resulting from large-scale siRNA screens.
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Affiliation(s)
- Rafal Gumienny
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
| | - Mihaela Zavolan
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
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Nyati S, Schinske-Sebolt K, Pitchiaya S, Chekhovskiy K, Chator A, Chaudhry N, Dosch J, Van Dort ME, Varambally S, Kumar-Sinha C, Nyati MK, Ray D, Walter NG, Yu H, Ross BD, Rehemtulla A. The kinase activity of the Ser/Thr kinase BUB1 promotes TGF-β signaling. Sci Signal 2015; 8:ra1. [PMID: 25564677 DOI: 10.1126/scisignal.2005379] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Transforming growth factor-β (TGF-β) signaling regulates cell proliferation and differentiation, which contributes to development and disease. Upon binding TGF-β, the type I receptor (TGFBRI) binds TGFBRII, leading to the activation of the transcription factors SMAD2 and SMAD3. Using an RNA interference screen of the human kinome and a live-cell reporter for TGFBR activity, we identified the kinase BUB1 (budding uninhibited by benzimidazoles-1) as a key mediator of TGF-β signaling. BUB1 interacted with TGFBRI in the presence of TGF-β and promoted the heterodimerization of TGFBRI and TGFBRII. Additionally, BUB1 interacted with TGFBRII, suggesting the formation of a ternary complex. Knocking down BUB1 prevented the recruitment of SMAD3 to the receptor complex, the phosphorylation of SMAD2 and SMAD3 and their interaction with SMAD4, SMAD-dependent transcription, and TGF-β-mediated changes in cellular phenotype including epithelial-mesenchymal transition (EMT), migration, and invasion. Knockdown of BUB1 also impaired noncanonical TGF-β signaling mediated by the kinases AKT and p38 MAPK (mitogen-activated protein kinase). The ability of BUB1 to promote TGF-β signaling depended on the kinase activity of BUB1. A small-molecule inhibitor of the kinase activity of BUB1 (2OH-BNPP1) and a kinase-deficient mutant of BUB1 suppressed TGF-β signaling and formation of the ternary complex in various normal and cancer cell lines. 2OH-BNPP1 administration to mice bearing lung carcinoma xenografts reduced the amount of phosphorylated SMAD2 in tumor tissue. These findings indicated that BUB1 functions as a kinase in the TGF-β pathway in a role beyond its established function in cell cycle regulation and chromosome cohesion.
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Affiliation(s)
- Shyam Nyati
- Center for Molecular Imaging, University of Michigan, Ann Arbor, MI 48109, USA. Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Sethuramasundaram Pitchiaya
- Single Molecule Analysis in Real-Time (SMART) Center, University of Michigan, Ann Arbor, MI 48109, USA. Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Katerina Chekhovskiy
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Areeb Chator
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nauman Chaudhry
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joseph Dosch
- Department of Radiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcian E Van Dort
- Department of Radiology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Chandan Kumar-Sinha
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA. Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mukesh Kumar Nyati
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dipankar Ray
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nils G Walter
- Single Molecule Analysis in Real-Time (SMART) Center, University of Michigan, Ann Arbor, MI 48109, USA. Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hongtao Yu
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brian Dale Ross
- Center for Molecular Imaging, University of Michigan, Ann Arbor, MI 48109, USA. Department of Radiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alnawaz Rehemtulla
- Center for Molecular Imaging, University of Michigan, Ann Arbor, MI 48109, USA. Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA.
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Ma ZL, Hou PP, Li YL, Wang DT, Yuan TW, Wei JL, Zhao BT, Lou JT, Zhao XT, Jin Y, Jin YX. MicroRNA-34a inhibits the proliferation and promotes the apoptosis of non-small cell lung cancer H1299 cell line by targeting TGFβR2. Tumour Biol 2014; 36:2481-90. [PMID: 25501507 DOI: 10.1007/s13277-014-2861-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 11/14/2014] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (MiRNAs) are small non-coding RNA molecules which act as important regulators of post-transcriptional gene expression by binding 3'-untranslated region (3'-UTR) of target messenger RNA (mRNA). In this study, we analyzed miRNA-34a (miR-34a) as a tumor suppressor in non-small cell lung cancer (NSCLC) H1299 cell line. The expression level of miR-34a in four different NSCLC cell lines, H1299, A549, SPCA-1, and HCC827, was significantly lower than that in the non-tumorigenic bronchial epithelium cell line BEAS-2B. In human NSCLC tissues, miR-34a expression level was also significantly decreased in pT2-4 compared with the pT1 group. Moreover, miR-34a mimic could inhibit the proliferation and triggered apoptosis in H1299 cells. Luciferase assays revealed that miR-34a inhibited TGFβR2 expression by targeting one binding site in the 3'-UTR of TGFβR2 mRNA. Quantitative real-time PCR (qRT-PCR) and Western blot assays verified that miR-34a reduced TGFβR2 expression at both mRNA and protein levels. Furthermore, downregulation of TGFβR2 by siRNA showed the same effects on the proliferation and apoptosis as miR-34a mimic in H1299 cells. Our results demonstrated that miR-34a could inhibit the proliferation and promote the apoptosis of H1299 cells partially through the downregulation of its target gene TGFβR2.
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Affiliation(s)
- Zhong-Liang Ma
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
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Gu S, Zhang Y, Jin L, Huang Y, Zhang F, Bassik MC, Kampmann M, Kay MA. Weak base pairing in both seed and 3' regions reduces RNAi off-targets and enhances si/shRNA designs. Nucleic Acids Res 2014; 42:12169-76. [PMID: 25270879 PMCID: PMC4231738 DOI: 10.1093/nar/gku854] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The use of RNA interference is becoming routine in scientific discovery and treatment of human disease. However, its applications are hampered by unwanted effects, particularly off-targeting through miRNA-like pathways. Recent studies suggest that the efficacy of such off-targeting might be dependent on binding stability. Here, by testing shRNAs and siRNAs of various GC content in different guide strand segments with reporter assays, we establish that weak base pairing in both seed and 3' regions is required to achieve minimal off-targeting while maintaining the intended on-target activity. The reduced off-targeting was confirmed by RNA-Seq analyses from mouse liver RNAs expressing various anti-HCV shRNAs. Finally, our protocol was validated on a large scale by analyzing results of a genome-wide shRNA screen. Compared with previously established work, the new algorithm was more effective in reducing off-targeting without jeopardizing on-target potency. These studies provide new rules that should significantly improve on siRNA/shRNA design.
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Affiliation(s)
- Shuo Gu
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Yue Zhang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Lan Jin
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Yong Huang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Feijie Zhang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Martin Kampmann
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Mark A Kay
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
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Bhinder B, Djaballah H. A simple method for analyzing actives in random RNAi screens: introducing the "H Score" for hit nomination & gene prioritization. Comb Chem High Throughput Screen 2014; 15:686-704. [PMID: 22934950 DOI: 10.2174/138620712803519671] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Revised: 08/06/2012] [Accepted: 08/07/2012] [Indexed: 12/21/2022]
Abstract
Due to the numerous challenges in hit identification from random RNAi screening, we have examined current practices with a discovery of a variety of methodologies employed and published in many reports; majority of them, unfortunately, do not address the minimum associated criteria for hit nomination, as this could potentially have been the cause or may well be the explanation as to the lack of confirmation and follow up studies, currently facing the RNAi field. Overall, we find that these criteria or parameters are not well defined, in most cases arbitrary in nature, and hence rendering it extremely difficult to judge the quality of and confidence in nominated hits across published studies. For this purpose, we have developed a simple method to score actives independent of assay readout; and provide, for the first time, a homogenous platform enabling cross-comparison of active gene lists resulting from different RNAi screening technologies. Here, we report on our recently developed method dedicated to RNAi data output analysis referred to as the BDA method applicable to both arrayed and pooled RNAi technologies; wherein the concerns pertaining to inconsistent hit nomination and off-target silencing in conjugation with minimal activity criteria to identify a high value target are addressed. In this report, a combined hit rate per gene, called "H score", is introduced and defined. The H score provides a very useful tool for stringent active gene nomination, gene list comparison across multiple studies, prioritization of hits, and evaluation of the quality of the nominated gene hits.
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Affiliation(s)
- Bhavneet Bhinder
- HTS Core Facility, Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, USA
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Bhinder B, Shum D, Li M, Ibáñez G, Vlassov AV, Magdaleno S, Djaballah H. Discovery of a dicer-independent, cell-type dependent alternate targeting sequence generator: implications in gene silencing & pooled RNAi screens. PLoS One 2014; 9:e100676. [PMID: 24987961 PMCID: PMC4079264 DOI: 10.1371/journal.pone.0100676] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 05/02/2014] [Indexed: 12/20/2022] Open
Abstract
There is an acceptance that plasmid-based delivery of interfering RNA always generates the intended targeting sequences in cells, making it as specific as its synthetic counterpart. However, recent studies have reported on cellular inefficiencies of the former, especially in light of emerging gene discordance at inter-screen level and across formats. Focusing primarily on the TRC plasmid-based shRNA hairpins, we reasoned that alleged specificities were perhaps compromised due to altered processing; resulting in a multitude of random interfering sequences. For this purpose, we opted to study the processing of hairpin TRCN#40273 targeting CTTN; which showed activity in a miRNA-21 gain-of-function shRNA screen, but inactive when used as an siRNA duplex. Using a previously described walk-through method, we identified 36 theoretical cleavage variants resulting in 78 potential siRNA duplexes targeting 53 genes. We synthesized and tested all of them. Surprisingly, six duplexes targeting ASH1L, DROSHA, GNG7, PRKCH, THEM4, and WDR92 scored as active. QRT-PCR analysis on hairpin transduced reporter cells confirmed knockdown of all six genes, besides CTTN; revealing a surprising 7 gene-signature perturbation by this one single hairpin. We expanded our qRT-PCR studies to 26 additional cell lines and observed unique knockdown profiles associated with each cell line tested; even for those lacking functional DICER1 gene suggesting no obvious dependence on dicer for shRNA hairpin processing; contrary to published models. Taken together, we report on a novel dicer independent, cell-type dependent mechanism for non-specific RNAi gene silencing we coin Alternate Targeting Sequence Generator (ATSG). In summary, ATSG adds another dimension to the already complex interpretation of RNAi screening data, and provides for the first time strong evidence in support of arrayed screening, and questions the scientific merits of performing pooled RNAi screens, where deconvolution of up to genome-scale pools is indispensable for target identification.
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Affiliation(s)
- Bhavneet Bhinder
- HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - David Shum
- HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Mu Li
- Thermo Fisher Scientific, Austin, Texas, United States of America
| | - Glorymar Ibáñez
- HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | | | - Susan Magdaleno
- Thermo Fisher Scientific, Austin, Texas, United States of America
| | - Hakim Djaballah
- HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- * E-mail:
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Ramirez H, Patel SB, Pastar I. The Role of TGFβ Signaling in Wound Epithelialization. Adv Wound Care (New Rochelle) 2014; 3:482-491. [PMID: 25032068 DOI: 10.1089/wound.2013.0466] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Indexed: 01/06/2023] Open
Abstract
Significance: Transforming growth factor β (TGFβ) has a crucial role in maintaining skin homeostasis. TGFβ signaling is important for re-epithelialization, inflammation, angiogenesis, and granulation tissue formation during wound healing. This review will discuss the most important findings regarding the role of TGFβ in epidermal maintenance and its restoration after injury. Recent Advances: Latest findings on the role of TGFβ signaling in normal and impaired wound healing, including the role of TGFβ pathway in tissue regeneration observed in super-healer animal models, will be reviewed. Critical Issues: The TGFβ pathway is attenuated in nonhealing wounds. Observed suppression of TGFβ signaling in chronic ulcers may contribute to the loss of tissue homeostasis and the inability of keratinocytes to migrate and close a wound. Future Directions: A better understanding of TGFβ signaling may provide new insights not only in the normal epithelialization process, but also in tissue regeneration. Future studies focused on TGFβ-mediated crosstalk between multiple cell types involved in wound healing may lead to development of novel therapeutic advances for chronic wounds.
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Affiliation(s)
- Horacio Ramirez
- Wound Healing and Regenerative Medicine Research Program, Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida
- PIBS Human Genetics and Genomics Program, University of Miami Miller School of Medicine, Miami, Florida
| | - Shailee B. Patel
- Wound Healing and Regenerative Medicine Research Program, Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida
| | - Irena Pastar
- Wound Healing and Regenerative Medicine Research Program, Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida
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Yilmazel B, Hu Y, Sigoillot F, Smith JA, Shamu CE, Perrimon N, Mohr SE. Online GESS: prediction of miRNA-like off-target effects in large-scale RNAi screen data by seed region analysis. BMC Bioinformatics 2014; 15:192. [PMID: 24934636 PMCID: PMC4073188 DOI: 10.1186/1471-2105-15-192] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 06/10/2014] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND RNA interference (RNAi) is an effective and important tool used to study gene function. For large-scale screens, RNAi is used to systematically down-regulate genes of interest and analyze their roles in a biological process. However, RNAi is associated with off-target effects (OTEs), including microRNA (miRNA)-like OTEs. The contribution of reagent-specific OTEs to RNAi screen data sets can be significant. In addition, the post-screen validation process is time and labor intensive. Thus, the availability of robust approaches to identify candidate off-targeted transcripts would be beneficial. RESULTS Significant efforts have been made to eliminate false positive results attributable to sequence-specific OTEs associated with RNAi. These approaches have included improved algorithms for RNAi reagent design, incorporation of chemical modifications into siRNAs, and the use of various bioinformatics strategies to identify possible OTEs in screen results. Genome-wide Enrichment of Seed Sequence matches (GESS) was developed to identify potential off-targeted transcripts in large-scale screen data by seed-region analysis. Here, we introduce a user-friendly web application that provides researchers a relatively quick and easy way to perform GESS analysis on data from human or mouse cell-based screens using short interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs), as well as for Drosophila screens using shRNAs. Online GESS relies on up-to-date transcript sequence annotations for human and mouse genes extracted from NCBI Reference Sequence (RefSeq) and Drosophila genes from FlyBase. The tool also accommodates analysis with user-provided reference sequence files. CONCLUSION Online GESS provides a straightforward user interface for genome-wide seed region analysis for human, mouse and Drosophila RNAi screen data. With the tool, users can either use a built-in database or provide a database of transcripts for analysis. This makes it possible to analyze RNAi data from any organism for which the user can provide transcript sequences.
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Affiliation(s)
| | | | | | | | | | | | - Stephanie E Mohr
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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Bergström SE, Bergdahl E, Sundqvist KG. A cytokine-controlled mechanism for integrated regulation of T-lymphocyte motility, adhesion and activation. Immunology 2014; 140:441-55. [PMID: 23866045 DOI: 10.1111/imm.12154] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 07/04/2013] [Accepted: 07/14/2013] [Indexed: 12/15/2022] Open
Abstract
The co-ordination of T-cell motility, adhesion and activation remains poorly understood. It is also unclear how these functions are co-ordinated with external stimuli. Here we unveil a series of molecular interactions in cis at the surface of T lymphocytes with potent effects on motility and adhesion in these cells, and communicating with proliferative responses. These interactions were controlled by the signature cytokines of T helper subsets interleukin-2 (IL-2) and IL-4. Low-density lipoprotein receptor-related protein 1 (LRP1) was found to play a key role for T-cell motility by promoting development of polarized cell shape and cell movement. Endogenous thrombospondin-1 (TSP-1) enhanced cell surface expression of LRP1 through CD47. Cell surface expressed LRP1 induced motility and processing of TSP-1 while inhibiting adhesion to intercellular adhesion molecule 1 and fibronectin. Interleukin-2, but not IL-4, stimulated synthesis of TSP-1 and motility through TSP-1 and LRP1. Stimulation of the T-cell receptor (TCR)/CD3 complex inhibited TSP-1 expression. Inhibitor studies indicated that LRP1 regulated TSP-1 expression and promoted motility through JAK signalling. This LRP1-mediated motogenic signalling was connected to CD47/Gi protein signalling and IL-2-induced signalling through TSP-1. The motogenic TSP-1/LRP1 mechanism antagonized TCR/CD3-induced T-cell proliferation. These results indicate that LRP1 in collaboration with TSP-1 directs a counter-adhesive and counter-proliferative motogenic cascade. T cells seem programmed to prioritize movement before adhesion through this cascade. In conclusion, vital decision-making in T lymphocytes regulating motility, adhesive interactions and proliferation, are integrated through a molecular mechanism connecting different cell surface receptors and their signalling pathways.
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Affiliation(s)
- Sten-Erik Bergström
- Department of Medicine, Karolinska Institute, Huddinge, Sweden; Division of Clinical Immunology, Division of Therapeutic Immunology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden; Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
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Zouk H, D'Hennezel E, Du X, Ounissi-Benkalha H, Piccirillo CA, Polychronakos C. Functional evaluation of the role of C-type lectin domain family 16A at the chromosome 16p13 locus. Clin Exp Immunol 2014; 175:485-97. [PMID: 24237155 DOI: 10.1111/cei.12240] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2013] [Indexed: 01/17/2023] Open
Abstract
The type 1 diabetes-associated 16p13 locus contains the CLEC16A gene. Its preferential immune cell expression suggests involvement in autoimmunity. Given its elevated expression in dendritic and B cells - known professional antigen-presenting cells (APCs) - we hypothesize that C-type lectin domain family 16 member A (CLEC16A) may be involved in T cell co-stimulation and consequent activation and proliferation. We also sought to identify CLEC16A's subcellular localization. The effect of the CLEC16A knock-down (KD) on B cell co-stimulation and activation of T cells was tested in human lymphoblastoid cell lines (LCLs) by co-culture with CD4(+) T cells. T cell activation and proliferation were determined by flow-cytometric analysis of CD69 and CD25 expression and carboxyfluorescein succinimidyl ester (CFSE) dilution, respectively. CLEC16A subcellular localization in K562 cells was examined by immunofluorescence. We show that the CLEC16A KD did not affect the tested indices of lymphoblastoid cell line (LCL) APC capacity. Additionally, the percentage of activated T cells following LCL co-culture was not affected significantly by the CLEC16A KD. T cells co-cultured with KD or control LCLs also exhibited similar cell division profiles. CLEC16A co-localized with an endoplasmic reticulum (ER) marker, suggesting that it may be an ER protein. In conclusion, CLEC16A may not be involved in T cell co-stimulation. Additional studies on CLEC16A, accounting for its ER localization, are needed to uncover its biological role.
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Affiliation(s)
- H Zouk
- Endocrine Genetics Laboratory, McGill University Health Center, Montreal Children's Hospital Research Institute, McGill University, QC, Montreal, Canada; Department of Human Genetics, McGill University, QC, Montreal, Canada
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Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens. Proc Natl Acad Sci U S A 2014; 111:4548-53. [PMID: 24616511 DOI: 10.1073/pnas.1402353111] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Systematic genetic perturbation screening in human cells remains technically challenging. Typically, large libraries of chemically synthesized siRNA oligonucleotides are used, each designed to degrade a specific cellular mRNA via the RNA interference (RNAi) mechanism. Here, we report on data from three genome-wide siRNA screens, conducted to uncover host factors required for infection of human cells by two bacterial and one viral pathogen. We find that the majority of phenotypic effects of siRNAs are unrelated to the intended "on-target" mechanism, defined by full complementarity of the 21-nt siRNA sequence to a target mRNA. Instead, phenotypes are largely dictated by "off-target" effects resulting from partial complementarity of siRNAs to multiple mRNAs via the "seed" region (i.e., nucleotides 2-8), reminiscent of the way specificity is determined for endogenous microRNAs. Quantitative analysis enabled the prediction of seeds that strongly and specifically block infection, independent of the intended on-target effect. This prediction was confirmed experimentally by designing oligos that do not have any on-target sequence match at all, yet can strongly reproduce the predicted phenotypes. Our results suggest that published RNAi screens have primarily, and unintentionally, screened the sequence space of microRNA seeds instead of the intended on-target space of protein-coding genes. This helps to explain why previously published RNAi screens have exhibited relatively little overlap. Our analysis suggests a possible way of identifying "seed reagents" for controlling phenotypes of interest and establishes a general strategy for extracting valuable untapped information from past and future RNAi screens.
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Ng ACH, Baird SD, Screaton RA. High-content functional genomic screening to identify novel regulators of the PINK1-Parkin pathway. Methods Enzymol 2014; 547:1-20. [PMID: 25416349 DOI: 10.1016/b978-0-12-801415-8.00001-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PINK1/PARK6 and Parkin/PARK2 are amongst the most commonly mutated genes associated with recessive forms of familial Parkinson's disease. Recent evidence indicates that the proteins they encode, PINK1 and Parkin, function in the same pathway to mediate the selective autophagic clearance of dysfunctional mitochondria. Upon mitochondrial damage, PINK1 is stabilized on the outer mitochondrial membrane where it phosphorylates ubiquitin, generating a signal for the recruitment and activation of Parkin. However, key mechanistic questions still exist regarding Parkin recruitment, including whether or not other factors are required for the PINK1 and Parkin pathway. We describe a method below using high-throughput RNA interference technology to interrogate the genome for novel components of the PINK1 and Parkin pathway.
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Affiliation(s)
- Andy Cheuk-Him Ng
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Stephen D Baird
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Robert A Screaton
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada; Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada.
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