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Qi J, Li Y, Yao X, Li G, Xu W, Chen L, Xie Z, Gu J, Wu H, Li Z. Rational design of ROS scavenging and fluorescent gold nanoparticles to deliver siRNA to improve plant resistance to Pseudomonas syringae. J Nanobiotechnology 2024; 22:446. [PMID: 39075467 PMCID: PMC11285324 DOI: 10.1186/s12951-024-02733-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 07/22/2024] [Indexed: 07/31/2024] Open
Abstract
Bacterial diseases are one of the most common issues that result in crop loss worldwide, and the increasing usage of chemical pesticides has caused the occurrence of resistance in pathogenic bacteria and environmental pollution problems. Nanomaterial mediated gene silencing is starting to display powerful efficiency and environmental friendliness for improving plant disease resistance. However, the internalization of nanomaterials and the physiological mechanisms behind nano-improved plant disease resistance are still rarely understood. We engineered the polyethyleneimine (PEI) functionalized gold nanoparticles (PEI-AuNPs) with fluorescent properties and ROS scavenging activity to act as siRNA delivery platforms. Besides the loading, protection, and delivery of nucleic acid molecules in plant mature leaf cells by PEI-AuNPs, its fluorescent property further enables the traceability of the distribution of the loaded nucleic acid molecules in cells. Additionally, the PEI-AuNPs-based RNAi delivery system successfully mediated the silencing of defense-regulated gene AtWRKY1. Compared to control plants, the silenced plants performed better resistance to Pseudomonas syringae, showing a reduced bacterial number, decreased ROS content, increased antioxidant enzyme activities, and improved chlorophyll fluorescence performance. Our results showed the advantages of AuNP-based RNAi technology in improving plant disease resistance, as well as the potential of plant nanobiotechnology to protect agricultural production.
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Affiliation(s)
- Jie Qi
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, The Center of Crop Nanobiotechnology, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yanhui Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, The Center of Crop Nanobiotechnology, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xue Yao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, The Center of Crop Nanobiotechnology, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Guangjing Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, The Center of Crop Nanobiotechnology, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Wenying Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, The Center of Crop Nanobiotechnology, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Lingling Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, The Center of Crop Nanobiotechnology, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Zhouli Xie
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, The Center of Crop Nanobiotechnology, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Jiangjiang Gu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, The Center of Crop Nanobiotechnology, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- College of Chemistry, Huazhong Agricultural University, Wuhan, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 511464, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 511464, China
| | - Honghong Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, The Center of Crop Nanobiotechnology, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 511464, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 511464, China.
| | - Zhaohu Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, The Center of Crop Nanobiotechnology, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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2
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Cheng H, Xu L, Jia C. Characterization of double-stranded RNA and its silencing efficiency for insects using hybrid deep-learning framework. Brief Funct Genomics 2024:elae027. [PMID: 38912767 DOI: 10.1093/bfgp/elae027] [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: 03/25/2024] [Revised: 05/24/2024] [Accepted: 06/06/2024] [Indexed: 06/25/2024] Open
Abstract
RNA interference (RNAi) technology is widely used in the biological prevention and control of terrestrial insects. One of the main factors with the application of RNAi in insects is the difference in RNAi efficiency, which may vary not only in different insects, but also in different genes of the same insect, and even in different double-stranded RNAs (dsRNAs) of the same gene. This work focuses on the last question and establishes a bioinformatics software that can help researchers screen for the most efficient dsRNA targeting target genes. Among insects, the red flour beetle (Tribolium castaneum) is known to be one of the most sensitive to RNAi. From iBeetle-Base, we extracted 12 027 efficient dsRNA sequences with a lethality rate of ≥20% or with experimentation-induced phenotypic changes and processed these data to correspond to specific silence efficiency. Based on the first complied novel benchmark dataset, we specifically designed a deep neural network to identify and characterize efficient dsRNA for RNAi in insects. The dna2vec word embedding model was trained to extract distributed feature representations, and three powerful modules, namely convolutional neural network, bidirectional long short-term memory network, and self-attention mechanism, were integrated to form our predictor model to characterize the extracted dsRNAs and their silencing efficiencies for T. castaneum. Our model dsRNAPredictor showed reliable performance in multiple independent tests based on different species, including both T. castaneum and Aedes aegypti. This indicates that dsRNAPredictor can facilitate prescreening for designing high-efficiency dsRNA targeting target genes of insects in advance.
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Affiliation(s)
- Han Cheng
- Mathematics Department of the School of Science, Dalian Maritime University, Dalian 116026, China
| | - Liping Xu
- Mathematics Department of the School of Science, Dalian Maritime University, Dalian 116026, China
| | - Cangzhi Jia
- Mathematics Department of the School of Science, Dalian Maritime University, Dalian 116026, China
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3
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Reisbitzer A, Krauß S. The dynamic world of RNA: beyond translation to subcellular localization and function. Front Genet 2024; 15:1373899. [PMID: 38533205 PMCID: PMC10963542 DOI: 10.3389/fgene.2024.1373899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 03/04/2024] [Indexed: 03/28/2024] Open
Affiliation(s)
| | - Sybille Krauß
- University of Siegen, Institute of Biology, Human Biology / Neurobiology, Siegen, Germany
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4
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Grunert M, Dorn C, Dopazo A, Sánchez-Cabo F, Vázquez J, Rickert-Sperling S, Lara-Pezzi E. Technologies to Study Genetics and Molecular Pathways. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:435-458. [PMID: 38884724 DOI: 10.1007/978-3-031-44087-8_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Over the last few decades, the study of congenital heart disease (CHD) has benefited from various model systems and the development of molecular biological techniques enabling the analysis of single gene as well as global effects. In this chapter, we first describe different models including CHD patients and their families, animal models ranging from invertebrates to mammals, and various cell culture systems. Moreover, techniques to experimentally manipulate these models are discussed. Second, we introduce cardiac phenotyping technologies comprising the analysis of mouse and cell culture models, live imaging of cardiogenesis, and histological methods for fixed hearts. Finally, the most important and latest molecular biotechniques are described. These include genotyping technologies, different applications of next-generation sequencing, and the analysis of transcriptome, epigenome, proteome, and metabolome. In summary, the models and technologies presented in this chapter are essential to study the function and development of the heart and to understand the molecular pathways underlying CHD.
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Affiliation(s)
- Marcel Grunert
- Cardiovascular Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- DiNAQOR AG, Schlieren, Switzerland
| | - Cornelia Dorn
- Cardiovascular Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ana Dopazo
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Fátima Sánchez-Cabo
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Jésus Vázquez
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | | | - Enrique Lara-Pezzi
- Myocardial Homeostasis and Cardiac Injury Programme, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain.
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5
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Wu MY, Li ZW, Lu JH. Molecular Modulators and Receptors of Selective Autophagy: Disease Implication and Identification Strategies. Int J Biol Sci 2024; 20:751-764. [PMID: 38169614 PMCID: PMC10758101 DOI: 10.7150/ijbs.83205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 08/31/2023] [Indexed: 01/05/2024] Open
Abstract
Autophagy is a highly conserved physiological process that maintains cellular homeostasis by recycling cellular contents. Selective autophagy is based on the specificity of cargo recognition and has been implicated in various human diseases, including neurodegenerative diseases and cancer. Selective autophagy receptors and modulators play key roles in this process. Identifying these receptors and modulators and their roles is critical for understanding the machinery and physiological function of selective autophagy and providing therapeutic value for diseases. Using modern researching tools and novel screening technologies, an increasing number of selective autophagy receptors and modulators have been identified. A variety of Strategies and approaches, including protein-protein interactions (PPIs)-based identification and genome-wide screening, have been used to identify selective autophagy receptors and modulators. Understanding the strengths and challenges of these approaches not only promotes the discovery of even more such receptors and modulators but also provides a useful reference for the identification of regulatory proteins or genes involved in other cellular mechanisms. In this review, we summarize the functions, disease association, and identification strategies of selective autophagy receptors and modulators.
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Affiliation(s)
| | | | - Jia-Hong Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
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6
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Ahmad M, Weiswald LB, Poulain L, Denoyelle C, Meryet-Figuiere M. Involvement of lncRNAs in cancer cells migration, invasion and metastasis: cytoskeleton and ECM crosstalk. J Exp Clin Cancer Res 2023; 42:173. [PMID: 37464436 PMCID: PMC10353155 DOI: 10.1186/s13046-023-02741-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/26/2023] [Indexed: 07/20/2023] Open
Abstract
Cancer is the main cause of death worldwide and metastasis is a major cause of poor prognosis and cancer-associated mortality. Metastatic conversion of cancer cells is a multiplex process, including EMT through cytoskeleton remodeling and interaction with TME. Tens of thousands of putative lncRNAs have been identified, but the biological functions of most are still to be identified. However, lncRNAs have already emerged as key regulators of gene expression at transcriptional and post-transcriptional level to control gene expression in a spatio-temporal fashion. LncRNA-dependent mechanisms can control cell fates during development and their perturbed expression is associated with the onset and progression of many diseases including cancer. LncRNAs have been involved in each step of cancer cells metastasis through different modes of action. The investigation of lncRNAs different roles in cancer metastasis could possibly lead to the identification of new biomarkers and innovative cancer therapeutic options.
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Affiliation(s)
- Mohammad Ahmad
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
- Biochemistry Division, Chemistry Department, Faculty of Science, Damanhour University, Damanhour, 14000, Egypt
| | - Louis-Bastien Weiswald
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
| | - Laurent Poulain
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
| | - Christophe Denoyelle
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
| | - Matthieu Meryet-Figuiere
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France.
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France.
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7
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Neagu AN, Whitham D, Bruno P, Morrissiey H, Darie CA, Darie CC. Omics-Based Investigations of Breast Cancer. Molecules 2023; 28:4768. [PMID: 37375323 DOI: 10.3390/molecules28124768] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Breast cancer (BC) is characterized by an extensive genotypic and phenotypic heterogeneity. In-depth investigations into the molecular bases of BC phenotypes, carcinogenesis, progression, and metastasis are necessary for accurate diagnoses, prognoses, and therapy assessments in predictive, precision, and personalized oncology. This review discusses both classic as well as several novel omics fields that are involved or should be used in modern BC investigations, which may be integrated as a holistic term, onco-breastomics. Rapid and recent advances in molecular profiling strategies and analytical techniques based on high-throughput sequencing and mass spectrometry (MS) development have generated large-scale multi-omics datasets, mainly emerging from the three "big omics", based on the central dogma of molecular biology: genomics, transcriptomics, and proteomics. Metabolomics-based approaches also reflect the dynamic response of BC cells to genetic modifications. Interactomics promotes a holistic view in BC research by constructing and characterizing protein-protein interaction (PPI) networks that provide a novel hypothesis for the pathophysiological processes involved in BC progression and subtyping. The emergence of new omics- and epiomics-based multidimensional approaches provide opportunities to gain insights into BC heterogeneity and its underlying mechanisms. The three main epiomics fields (epigenomics, epitranscriptomics, and epiproteomics) are focused on the epigenetic DNA changes, RNAs modifications, and posttranslational modifications (PTMs) affecting protein functions for an in-depth understanding of cancer cell proliferation, migration, and invasion. Novel omics fields, such as epichaperomics or epimetabolomics, could investigate the modifications in the interactome induced by stressors and provide PPI changes, as well as in metabolites, as drivers of BC-causing phenotypes. Over the last years, several proteomics-derived omics, such as matrisomics, exosomics, secretomics, kinomics, phosphoproteomics, or immunomics, provided valuable data for a deep understanding of dysregulated pathways in BC cells and their tumor microenvironment (TME) or tumor immune microenvironment (TIMW). Most of these omics datasets are still assessed individually using distinct approches and do not generate the desired and expected global-integrative knowledge with applications in clinical diagnostics. However, several hyphenated omics approaches, such as proteo-genomics, proteo-transcriptomics, and phosphoproteomics-exosomics are useful for the identification of putative BC biomarkers and therapeutic targets. To develop non-invasive diagnostic tests and to discover new biomarkers for BC, classic and novel omics-based strategies allow for significant advances in blood/plasma-based omics. Salivaomics, urinomics, and milkomics appear as integrative omics that may develop a high potential for early and non-invasive diagnoses in BC. Thus, the analysis of the tumor circulome is considered a novel frontier in liquid biopsy. Omics-based investigations have applications in BC modeling, as well as accurate BC classification and subtype characterization. The future in omics-based investigations of BC may be also focused on multi-omics single-cell analyses.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Carol I Bvd, No. 20A, 700505 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Pathea Bruno
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Hailey Morrissiey
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Celeste A Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Costel C Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
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8
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Nikonova E, Mukherjee A, Kamble K, Barz C, Nongthomba U, Spletter ML. Rbfox1 is required for myofibril development and maintaining fiber type-specific isoform expression in Drosophila muscles. Life Sci Alliance 2022; 5:5/4/e202101342. [PMID: 34996845 PMCID: PMC8742874 DOI: 10.26508/lsa.202101342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/24/2022] Open
Abstract
Protein isoform transitions confer muscle fibers with distinct properties and are regulated by differential transcription and alternative splicing. RNA-binding Fox protein 1 (Rbfox1) can affect both transcript levels and splicing, and is known to contribute to normal muscle development and physiology in vertebrates, although the detailed mechanisms remain obscure. In this study, we report that Rbfox1 contributes to the generation of adult muscle diversity in Drosophila Rbfox1 is differentially expressed among muscle fiber types, and RNAi knockdown causes a hypercontraction phenotype that leads to behavioral and eclosion defects. Misregulation of fiber type-specific gene and splice isoform expression, notably loss of an indirect flight muscle-specific isoform of Troponin-I that is critical for regulating myosin activity, leads to structural defects. We further show that Rbfox1 directly binds the 3'-UTR of target transcripts, regulates the expression level of myogenic transcription factors myocyte enhancer factor 2 and Salm, and both modulates expression of and genetically interacts with the CELF family RNA-binding protein Bruno1 (Bru1). Rbfox1 and Bru1 co-regulate fiber type-specific alternative splicing of structural genes, indicating that regulatory interactions between FOX and CELF family RNA-binding proteins are conserved in fly muscle. Rbfox1 thus affects muscle development by regulating fiber type-specific splicing and expression dynamics of identity genes and structural proteins.
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Affiliation(s)
- Elena Nikonova
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Martinsried-Planegg, Germany
| | - Amartya Mukherjee
- Department of Molecular Reproduction, Development and Genetics (MRDG), Indian Institute of Science, Bangalore, India
| | - Ketaki Kamble
- Department of Molecular Reproduction, Development and Genetics (MRDG), Indian Institute of Science, Bangalore, India
| | - Christiane Barz
- Muscle Dynamics Group, Max Planck Institute of Biochemistry, Martinsried-Planegg, Germany
| | - Upendra Nongthomba
- Department of Molecular Reproduction, Development and Genetics (MRDG), Indian Institute of Science, Bangalore, India
| | - Maria L Spletter
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Martinsried-Planegg, Germany
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9
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Piyawajanusorn C, Nguyen LC, Ghislat G, Ballester PJ. A gentle introduction to understanding preclinical data for cancer pharmaco-omic modeling. Brief Bioinform 2021; 22:6343527. [PMID: 34368843 DOI: 10.1093/bib/bbab312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/25/2021] [Accepted: 07/20/2021] [Indexed: 12/16/2022] Open
Abstract
A central goal of precision oncology is to administer an optimal drug treatment to each cancer patient. A common preclinical approach to tackle this problem has been to characterize the tumors of patients at the molecular and drug response levels, and employ the resulting datasets for predictive in silico modeling (mostly using machine learning). Understanding how and why the different variants of these datasets are generated is an important component of this process. This review focuses on providing such introduction aimed at scientists with little previous exposure to this research area.
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Affiliation(s)
- Chayanit Piyawajanusorn
- Cancer Research Center of Marseille, INSERM U1068, F-13009 Marseille, France.,Institut Paoli-Calmettes, F-13009 Marseille, France.,Aix-Marseille Université, F-13284 Marseille, France.,CNRS UMR7258, F-13009 Marseille, France.,Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Linh C Nguyen
- Cancer Research Center of Marseille, INSERM U1068, F-13009 Marseille, France.,Institut Paoli-Calmettes, F-13009 Marseille, France.,Aix-Marseille Université, F-13284 Marseille, France.,CNRS UMR7258, F-13009 Marseille, France.,Department of Life Sciences, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ghita Ghislat
- U1104, CNRS UMR7280, Centre d'Immunologie de Marseille-Luminy, Inserm, Marseille, France
| | - Pedro J Ballester
- Cancer Research Center of Marseille, INSERM U1068, F-13009 Marseille, France.,Institut Paoli-Calmettes, F-13009 Marseille, France.,Aix-Marseille Université, F-13284 Marseille, France.,CNRS UMR7258, F-13009 Marseille, France
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10
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Daack CW, Yeh D, Busch M, Kliethermes CL. GABAergic regulation of locomotion before and during an ethanol exposure in Drosophila melanogaster. Behav Brain Res 2021; 410:113369. [PMID: 34015397 DOI: 10.1016/j.bbr.2021.113369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/30/2021] [Accepted: 05/14/2021] [Indexed: 11/17/2022]
Abstract
Ethanol at low doses induces a locomotor stimulant response across a range of phylogenetically diverse species. In rodents, this response is commonly used as an index of ethanol's disinhibitory, anxiolytic, or reinforcing effects, and its expression is regulated by signaling through a number of conserved neurotransmitter systems. In the current experiments, we asked whether ethanol-induced locomotor stimulation in the fruit fly Drosophila melanogaster might be mediated by ionotropic GABA receptors. We measured basal and ethanol-stimulated locomotion in flies expressing RNAi directed against three known subunits of ionotropic GABA receptors, and also examined the effects of picrotoxin feeding on these behaviors. We found that RNAi-mediated knockdown of a subunit of fly ionotropic GABA receptors, RDL, in all neurons resulted in an increased ethanol-induced locomotor stimulant response, while knockdown of two other subunits, LCCH3 and GRD, did not affect the responses. The effect of pan neuronal RDL knockdown was recapitulated with selective RDL knockdown in cholinergic neurons, and increased ethanol-induced locomotor stimulation was also seen by feeding the GABAA antagonist picrotoxin to flies prior to behavioral testing. However, the increase in ethanol-stimulated locomotion in each of these experiments was largely accounted for by decreased baseline activity. Our results indicate that ionotropic GABA receptors might be a conserved mediator of the locomotor stimulant effects of ethanol, but that alternative experimental approaches will be necessary to disentangle effects of GABAergic manipulations on baseline and ethanol-stimulated locomotion in flies.
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Affiliation(s)
- Calvin W Daack
- Drake University, 318 Olin Hall, 1344 27thStreet, Des Moines, IA, 50311, United States
| | - Derek Yeh
- Drake University, 318 Olin Hall, 1344 27thStreet, Des Moines, IA, 50311, United States
| | - Marc Busch
- Drake University, 318 Olin Hall, 1344 27thStreet, Des Moines, IA, 50311, United States
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11
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Watters KE, Kirkpatrick J, Palmer MJ, Koblentz GD. The CRISPR revolution and its potential impact on global health security. Pathog Glob Health 2021; 115:80-92. [PMID: 33590814 PMCID: PMC8550201 DOI: 10.1080/20477724.2021.1880202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Global health security is constantly under threat from infectious diseases. Despite advances in biotechnology that have improved diagnosis and treatment of such diseases, delays in detecting outbreaks and the lack of countermeasures for some biological agents continue to pose severe challenges to global health security. In this review, we describe some of the challenges facing global health security and how genome editing technologies can help overcome them. We provide specific examples of how the genome-editing tool CRISPR is being used to develop new tools to characterize pathogenic agents, diagnose infectious disease, and develop vaccines and therapeutics to mitigate the effects of an outbreak. The article also discusses some of the challenges associated with genome-editing technologies and the efforts that scientists are undertaking to mitigate them. Overall, CRISPR and genome-editing technologies are poised to have a significant positive influence on global health security over the years to come.
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Affiliation(s)
- Kyle E Watters
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jesse Kirkpatrick
- Institute for Philosophy and Public Policy, George Mason University, Fairfax, VA, USA
| | - Megan J Palmer
- Department of Bioengineering, Stanford University, Stanford, CA, USAs
| | - Gregory D Koblentz
- Schar School of Policy and Government, George Mason University, Fairfax, VA, USA
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12
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Fernandes F, Kotharkar P, Chakravorty A, Kowshik M, Talukdar I. Nanocarrier Mediated siRNA Delivery Targeting Stem Cell Differentiation. Curr Stem Cell Res Ther 2020; 15:155-172. [PMID: 31789134 DOI: 10.2174/1574888x14666191202095041] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/16/2019] [Accepted: 11/12/2019] [Indexed: 12/17/2022]
Abstract
Stem cell-based regenerative medicine holds exceptional therapeutic potential and hence the development of efficient techniques to enhance control over the rate of differentiation has been the focus of active research. One of the strategies to achieve this involves delivering siRNA into stem cells and exploiting the RNA interference (RNAi) mechanism. Transport of siRNA across the cell membrane is a challenge due to its anionic property, especially in primary human cells and stem cells. Moreover, naked siRNA incites immune responses, may cause off-target effects, exhibits low stability and is easily degraded by endonucleases in the bloodstream. Although siRNA delivery using viral vectors and electroporation has been used in stem cells, these methods demonstrate low transfection efficiency, cytotoxicity, immunogenicity, events of integration and may involve laborious customization. With the advent of nanotechnology, nanocarriers which act as novel gene delivery vehicles designed to overcome the problems associated with safety and practicality are being developed. The various nanomaterials that are currently being explored and discussed in this review include liposomes, carbon nanotubes, quantum dots, protein and peptide nanocarriers, magnetic nanoparticles, polymeric nanoparticles, etc. These nanodelivery agents exhibit advantages such as low immunogenic response, biocompatibility, design flexibility allowing for surface modification and functionalization, and control over the surface topography for achieving the desired rate of siRNA delivery and improved gene knockdown efficiency. This review also includes discussion on siRNA co-delivery with imaging agents, plasmid DNA, drugs etc. to achieve combined diagnostic and enhanced therapeutic functionality, both for in vitro and in vivo applications.
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Affiliation(s)
- Fiona Fernandes
- Department of Biological Sciences, BITS Pilani, K. K. Birla Goa campus, Zuarinagar, Goa-403726, India
| | - Pooja Kotharkar
- Department of Biological Sciences, BITS Pilani, K. K. Birla Goa campus, Zuarinagar, Goa-403726, India
| | - Adrija Chakravorty
- Department of Biological Sciences, BITS Pilani, K. K. Birla Goa campus, Zuarinagar, Goa-403726, India
| | - Meenal Kowshik
- Department of Biological Sciences, BITS Pilani, K. K. Birla Goa campus, Zuarinagar, Goa-403726, India
| | - Indrani Talukdar
- Department of Biological Sciences, BITS Pilani, K. K. Birla Goa campus, Zuarinagar, Goa-403726, India
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13
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Anthony EJ, Bolitho EM, Bridgewater HE, Carter OWL, Donnelly JM, Imberti C, Lant EC, Lermyte F, Needham RJ, Palau M, Sadler PJ, Shi H, Wang FX, Zhang WY, Zhang Z. Metallodrugs are unique: opportunities and challenges of discovery and development. Chem Sci 2020; 11:12888-12917. [PMID: 34123239 PMCID: PMC8163330 DOI: 10.1039/d0sc04082g] [Citation(s) in RCA: 319] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022] Open
Abstract
Metals play vital roles in nutrients and medicines and provide chemical functionalities that are not accessible to purely organic compounds. At least 10 metals are essential for human life and about 46 other non-essential metals (including radionuclides) are also used in drug therapies and diagnostic agents. These include platinum drugs (in 50% of cancer chemotherapies), lithium (bipolar disorders), silver (antimicrobials), and bismuth (broad-spectrum antibiotics). While the quest for novel and better drugs is now as urgent as ever, drug discovery and development pipelines established for organic drugs and based on target identification and high-throughput screening of compound libraries are less effective when applied to metallodrugs. Metallodrugs are often prodrugs which undergo activation by ligand substitution or redox reactions, and are multi-targeting, all of which need to be considered when establishing structure-activity relationships. We focus on early-stage in vitro drug discovery, highlighting the challenges of evaluating anticancer, antimicrobial and antiviral metallo-pharmacophores in cultured cells, and identifying their targets. We highlight advances in the application of metal-specific techniques that can assist the preclinical development, including synchrotron X-ray spectro(micro)scopy, luminescence, and mass spectrometry-based methods, combined with proteomic and genomic (metallomic) approaches. A deeper understanding of the behavior of metals and metallodrugs in biological systems is not only key to the design of novel agents with unique mechanisms of action, but also to new understanding of clinically-established drugs.
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Affiliation(s)
- Elizabeth J Anthony
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Elizabeth M Bolitho
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Hannah E Bridgewater
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Oliver W L Carter
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Jane M Donnelly
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Cinzia Imberti
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Edward C Lant
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Frederik Lermyte
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Russell J Needham
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Marta Palau
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Peter J Sadler
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Huayun Shi
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Fang-Xin Wang
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Wen-Ying Zhang
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Zijin Zhang
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
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14
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Banerjee S, Benji S, Liberow S, Steinhauer J. Using Drosophila melanogaster To Discover Human Disease Genes: An Educational Primer for Use with "Amyotrophic Lateral Sclerosis Modifiers in Drosophila Reveal the Phospholipase D Pathway as a Potential Therapeutic Target". Genetics 2020; 216:633-641. [PMID: 33158986 PMCID: PMC7648582 DOI: 10.1534/genetics.120.303495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 08/28/2020] [Indexed: 01/11/2023] Open
Abstract
Since the dawn of the 20th century, the fruit fly Drosophila melanogaster has been used as a model organism to understand the nature of genes and how they control development, behavior, and physiology. One of the most powerful experimental approaches employed in Drosophila is the forward genetic screen. In the 21st century, genome-wide screens have become popular tools for identifying evolutionarily conserved genes involved in complex human diseases. In the accompanying article "Amyotrophic Lateral Sclerosis Modifiers in Drosophila Reveal thePhospholipase DPathway as a Potential Therapeutic Target," Kankel and colleagues describe a forward genetic modifier screen to discover factors that contribute to the severe neurodegenerative disease amyotrophic lateral sclerosis (ALS). This primer briefly traces the history of genetic screens in Drosophila and introduces students to ALS. We then provide a set of guided reading questions to help students work through the data presented in the research article. Finally, several ideas for literature-based research projects are offered as opportunities for students to expand their appreciation of the potential scope of genetic screens. The primer is intended to help students and instructors thoroughly examine a current study that uses forward genetics in Drosophila to identify human disease genes.
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Affiliation(s)
| | | | - Sarah Liberow
- Biology Department, Yeshiva University, New York 10033
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15
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Mohammadi E, Benfeitas R, Turkez H, Boren J, Nielsen J, Uhlen M, Mardinoglu A. Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning. Cancers (Basel) 2020; 12:E2694. [PMID: 32967266 PMCID: PMC7563533 DOI: 10.3390/cancers12092694] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/24/2022] Open
Abstract
Modern drug discovery through de novo drug discovery entails high financial costs, low success rates, and lengthy trial periods. Drug repositioning presents a suitable approach for overcoming these issues by re-evaluating biological targets and modes of action of approved drugs. Coupling high-throughput technologies with genome-wide essentiality screens, network analysis, genome-scale metabolic modeling, and machine learning techniques enables the proposal of new drug-target signatures and uncovers unanticipated modes of action for available drugs. Here, we discuss the current issues associated with drug repositioning in light of curated high-throughput multi-omic databases, genome-wide screening technologies, and their application in systems biology/medicine approaches.
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Affiliation(s)
- Elyas Mohammadi
- Science for Life Laboratory, KTH–Royal Institute of Technology, SE-17121 Stockholm, Sweden; (E.M.); (M.U.)
- Department of Animal Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden;
| | - Hasan Turkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, 25240 Erzurum, Turkey;
| | - Jan Boren
- Department of Molecular and Clinical Medicine, University of Gothenburg, The Wallenberg Laboratory, Sahlgrenska University Hospital, SE-41345 Gothenburg, Sweden;
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden;
- BioInnovation Institute, DK-2200 Copenhagen N, Denmark
| | - Mathias Uhlen
- Science for Life Laboratory, KTH–Royal Institute of Technology, SE-17121 Stockholm, Sweden; (E.M.); (M.U.)
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH–Royal Institute of Technology, SE-17121 Stockholm, Sweden; (E.M.); (M.U.)
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London SE1 9RT, UK
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16
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Lundstrom K. Viral Vectors Applied for RNAi-Based Antiviral Therapy. Viruses 2020; 12:v12090924. [PMID: 32842491 PMCID: PMC7552024 DOI: 10.3390/v12090924] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/19/2020] [Accepted: 08/21/2020] [Indexed: 12/12/2022] Open
Abstract
RNA interference (RNAi) provides the means for alternative antiviral therapy. Delivery of RNAi in the form of short interfering RNA (siRNA), short hairpin RNA (shRNA) and micro-RNA (miRNA) have demonstrated efficacy in gene silencing for therapeutic applications against viral diseases. Bioinformatics has played an important role in the design of efficient RNAi sequences targeting various pathogenic viruses. However, stability and delivery of RNAi molecules have presented serious obstacles for reaching therapeutic efficacy. For this reason, RNA modifications and formulation of nanoparticles have proven useful for non-viral delivery of RNAi molecules. On the other hand, utilization of viral vectors and particularly self-replicating RNA virus vectors can be considered as an attractive alternative. In this review, examples of antiviral therapy applying RNAi-based approaches in various animal models will be described. Due to the current coronavirus pandemic, a special emphasis will be dedicated to targeting Coronavirus Disease-19 (COVID-19).
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17
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Li Q, Zheng L, Yang F, Li H, Li J, Cheng D. Effects of regular exercise on sleep and activity status in aging and Clk RNAi Drosophila melanogaster. BIOL RHYTHM RES 2020. [DOI: 10.1080/09291016.2019.1566990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Qiufang Li
- Key Laboratory of Physical Fitness and Exercise Rehabilitation of Hunan Province, Hunan Normal University, Changsha City, China
| | - Lan Zheng
- Key Laboratory of Physical Fitness and Exercise Rehabilitation of Hunan Province, Hunan Normal University, Changsha City, China
| | - Fan Yang
- Key Laboratory of Physical Fitness and Exercise Rehabilitation of Hunan Province, Hunan Normal University, Changsha City, China
| | - Hanzhe Li
- Key Laboratory of Physical Fitness and Exercise Rehabilitation of Hunan Province, Hunan Normal University, Changsha City, China
| | - Jinxiu Li
- Key Laboratory of Physical Fitness and Exercise Rehabilitation of Hunan Province, Hunan Normal University, Changsha City, China
| | - Dan Cheng
- Key Laboratory of Physical Fitness and Exercise Rehabilitation of Hunan Province, Hunan Normal University, Changsha City, China
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18
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Gopal S, Rodrigues AL, Dordick JS. Exploiting CRISPR Cas9 in Three-Dimensional Stem Cell Cultures to Model Disease. Front Bioeng Biotechnol 2020; 8:692. [PMID: 32671050 PMCID: PMC7326781 DOI: 10.3389/fbioe.2020.00692] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/03/2020] [Indexed: 12/14/2022] Open
Abstract
Three-dimensional (3D) cell culture methods have been widely used on a range of cell types, including stem cells to modulate precisely the cellular biophysical and biochemical microenvironment and control various cell signaling cues. As a result, more in vivo-like microenvironments are recapitulated, particularly through the formation of multicellular spheroids and organoids, which may yield more valid mechanisms of disease. Recently, genome-engineering tools such as CRISPR Cas9 have expanded the repertoire of techniques to control gene expression, which complements external signaling cues with intracellular control elements. As a result, the combination of CRISPR Cas9 and 3D cell culture methods enhance our understanding of the molecular mechanisms underpinning several disease phenotypes and may lead to developing new therapeutics that may advance more quickly and effectively into clinical candidates. In addition, using CRISPR Cas9 tools to rescue genes brings us one step closer to its use as a gene therapy tool for various degenerative diseases. Herein, we provide an overview of bridging of CRISPR Cas9 genome editing with 3D spheroid and organoid cell culture to better understand disease progression in both patient and non-patient derived cells, and we address potential remaining gaps that must be overcome to gain widespread use.
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Affiliation(s)
- Sneha Gopal
- Department of Chemical and Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - André Lopes Rodrigues
- Department of Chemical and Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
- Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Jonathan S. Dordick
- Department of Chemical and Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, United States
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
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19
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Tiuryn J, Szczurek E. Learning signaling networks from combinatorial perturbations by exploiting siRNA off-target effects. Bioinformatics 2020; 35:i605-i614. [PMID: 31510678 PMCID: PMC6612802 DOI: 10.1093/bioinformatics/btz334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Motivation Perturbation experiments constitute the central means to study cellular networks. Several confounding factors complicate computational modeling of signaling networks from this data. First, the technique of RNA interference (RNAi), designed and commonly used to knock-down specific genes, suffers from off-target effects. As a result, each experiment is a combinatorial perturbation of multiple genes. Second, the perturbations propagate along unknown connections in the signaling network. Once the signal is blocked by perturbation, proteins downstream of the targeted proteins also become inactivated. Finally, all perturbed network members, either directly targeted by the experiment, or by propagation in the network, contribute to the observed effect, either in a positive or negative manner. One of the key questions of computational inference of signaling networks from such data are, how many and what combinations of perturbations are required to uniquely and accurately infer the model? Results Here, we introduce an enhanced version of linear effects models (LEMs), which extends the original by accounting for both negative and positive contributions of the perturbed network proteins to the observed phenotype. We prove that the enhanced LEMs are identified from data measured under perturbations of all single, pairs and triplets of network proteins. For small networks of up to five nodes, only perturbations of single and pairs of proteins are required for identifiability. Extensive simulations demonstrate that enhanced LEMs achieve excellent accuracy of parameter estimation and network structure learning, outperforming the previous version on realistic data. LEMs applied to Bartonella henselae infection RNAi screening data identified known interactions between eight nodes of the infection network, confirming high specificity of our model and suggested one new interaction. Availability and implementation https://github.com/EwaSzczurek/LEM Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jerzy Tiuryn
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Ewa Szczurek
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
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20
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Campos TL, Korhonen PK, Sternberg PW, Gasser RB, Young ND. Predicting gene essentiality in Caenorhabditis elegans by feature engineering and machine-learning. Comput Struct Biotechnol J 2020; 18:1093-1102. [PMID: 32489524 PMCID: PMC7251299 DOI: 10.1016/j.csbj.2020.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 02/08/2023] Open
Abstract
Defining genes that are essential for life has major implications for understanding critical biological processes and mechanisms. Although essential genes have been identified and characterised experimentally using functional genomic tools, it is challenging to predict with confidence such genes from molecular and phenomic data sets using computational methods. Using extensive data sets available for the model organism Caenorhabditis elegans, we constructed here a machine-learning (ML)-based workflow for the prediction of essential genes on a genome-wide scale. We identified strong predictors for such genes and showed that trained ML models consistently achieve highly-accurate classifications. Complementary analyses revealed an association between essential genes and chromosomal location. Our findings reveal that essential genes in C. elegans tend to be located in or near the centre of autosomal chromosomes; are positively correlated with low single nucleotide polymorphim (SNP) densities and epigenetic markers in promoter regions; are involved in protein and nucleotide processing; are transcribed in most cells; are enriched in reproductive tissues or are targets for small RNAs bound to the argonaut CSR-1. Based on these results, we hypothesise an interplay between epigenetic markers and small RNA pathways in the germline, with transcription-based memory; this hypothesis warrants testing. From a technical perspective, further work is needed to evaluate whether the present ML-based approach will be applicable to other metazoans (including Drosophila melanogaster) for which comprehensive data sets (i.e. genomic, transcriptomic, proteomic, variomic, epigenetic and phenomic) are available.
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Key Words
- CDS, coding sequence
- CRISPR, Clustered Regularly Interspaced Short Palindromic Repeats
- Caenorhabditis elegans
- ES, Essentiality Score
- EST, expressed sequence tag
- Essential genes
- Essentiality predictions
- GBM, Gradient Boosting Method
- GFF, general feature format
- GLM, Generalised Linear Model
- GO, gene ontology
- ML, machine-learning
- Machine-learning
- NN, Artificial Neural Network
- PPI, protein-protein interaction
- PR-AUC, Area Under the Precision-Recall Curve
- RF, Random Forest
- RNAi, RNA interference
- ROC-AUC, Area Under the Receiver Operating Characteristic Curve
- SNP, single nucleotide polymorphism
- SPLS, Sparse Partial Least Squares
- SVM, Support-Vector Machine
- TEA, Tissue Enrichment Analysis tool (WormBase)
- TSS, transcription start site
- VCF, variant call file
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Affiliation(s)
- Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.,Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (IAM-Fiocruz), Recife, Pernambuco, Brazil
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
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21
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Shifat-E-Rabbi M, Yin X, Fitzgerald CE, Rohde GK. Cell Image Classification: A Comparative Overview. Cytometry A 2020; 97:347-362. [PMID: 32040260 DOI: 10.1002/cyto.a.23984] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/18/2019] [Accepted: 01/18/2020] [Indexed: 12/13/2022]
Abstract
Cell image classification methods are currently being used in numerous applications in cell biology and medicine. Applications include understanding the effects of genes and drugs in screening experiments, understanding the role and subcellular localization of different proteins, as well as diagnosis and prognosis of cancer from images acquired using cytological and histological techniques. The article also reviews three main approaches for cell image classification most often used: numerical feature extraction, end-to-end classification with neural networks (NNs), and transport-based morphometry (TBM). In addition, we provide comparisons on four different cell imaging datasets to highlight the relative strength of each method. The results computed using four publicly available datasets show that numerical features tend to carry the best discriminative information for most of the classification tasks. Results also show that NN-based methods produce state-of-the-art results in the dataset that contains a relatively large number of training samples. Data augmentation or the choice of a more recently reported architecture does not necessarily improve the classification performance of NNs in the datasets with limited number of training samples. If understanding and visualization are desired aspects, TBM methods can offer the ability to invert classification functions, and thus can aid in the interpretation of results. These and other comparison outcomes are discussed with the aim of clarifying the advantages and disadvantages of each method. © 2020 International Society for Advancement of Cytometry.
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Affiliation(s)
- Mohammad Shifat-E-Rabbi
- Imaging and Data Science Lab, Charlottesville, Virginia, 22903
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, 22903
| | - Xuwang Yin
- Imaging and Data Science Lab, Charlottesville, Virginia, 22903
- Department of Electrical & Computer Engineering, University of Virginia, Charlottesville, Virginia, 22903
| | - Cailey E Fitzgerald
- Imaging and Data Science Lab, Charlottesville, Virginia, 22903
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, 22903
| | - Gustavo K Rohde
- Imaging and Data Science Lab, Charlottesville, Virginia, 22903
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, 22903
- Department of Electrical & Computer Engineering, University of Virginia, Charlottesville, Virginia, 22903
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22
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Zins K, Abraham D. Cancer Immunotherapy: Targeting Tumor-Associated Macrophages by Gene Silencing. Methods Mol Biol 2020; 2115:289-325. [PMID: 32006408 DOI: 10.1007/978-1-0716-0290-4_17] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tumor-associated macrophages (TAMs) are representing a major leukocyte population in solid tumors. Macrophages are very heterogeneous and plastic cells and can acquire distinct functional phenotypes ranging from antitumorigenic to immunosuppressive tumor-promoting M2-like TAMs, depending on the local tissue microenvironment (TME). TAMs express cytokines, chemokines, growth factors, and extracellular matrix (ECM) modifying factors, and the cross talk with the TME regulates pathways involved in the recruitment, polarization, and metabolism of TAMs during tumor progression. Due to their crucial role in tumor growth and metastasis, selective targeting of TAM for the treatment of cancer with therapeutic agents that promote phagocytosis or suppress survival, proliferation, trafficking, or polarization of TAMs may prove to be beneficial in cancer therapy. In this chapter, we will discuss TAM biology and current strategies for the targeting of TAMs using small interfering RNA (siRNA)-based drugs. In the past few years, advances in the field of nanomedicine pave the way for the development of siRNA-based drugs as an additional class of personalized cancer immuno-nanomedicines. Fundamental challenges associated with this group of therapeutics include the development process, delivery system, and clinical translation for siRNA-based drugs.
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Affiliation(s)
- Karin Zins
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Dietmar Abraham
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria.
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23
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Unpredictable Effects of the Genetic Background of Transgenic Lines in Physiological Quantitative Traits. G3-GENES GENOMES GENETICS 2019; 9:3877-3890. [PMID: 31540975 PMCID: PMC6829147 DOI: 10.1534/g3.119.400715] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Physiology, fitness and disease phenotypes are complex traits exhibiting continuous variation in natural populations. To understand complex trait gene functions transgenic lines of undefined genetic background are often combined to assess quantitative phenotypes ignoring the impact of genetic polymorphisms. Here, we used inbred wild-type strains of the Drosophila Genetics Reference Panel to assess the phenotypic variation of six physiological and fitness traits, namely, female fecundity, survival and intestinal mitosis upon oral infection, defecation rate and fecal pH upon oral infection, and terminal tracheal cell branching in hypoxia. We found continuous variation in the approximately 150 strains tested for each trait, with extreme values differing by more than four standard deviations for all traits. In addition, we assessed the effects of commonly used Drosophila UAS-RNAi transgenic strains and their backcrossed isogenized counterparts, in the same traits plus baseline intestinal mitosis and tracheal branching in normoxia, in heterozygous conditions, when only half of the genetic background was different among strains. We tested 20 non-isogenic strains (10 KK and 10 GD) from the Vienna Drosophila Resource Center and their isogenized counterparts without Gal4 induction. Survival upon infection and female fecundity exhibited differences in 50% and 40% of the tested isogenic vs. non-isogenic pairs, respectively, whereas all other traits were affected in only 10–25% of the cases. When 11 isogenic and their corresponding non-isogenic UAS-RNAi lines were expressed ubiquitously with Gal4, 4 isogenic vs. non-isogenic pairs exhibited differences in survival to infection. Furthermore, when a single UAS-RNAi line was crossed with the same Gal4 transgene inserted in different genetic backgrounds, the quantitative variations observed were unpredictable on the basis of pure line performance. Thus, irrespective of the trait of interest, the genetic background of commonly used transgenic strains needs to be considered carefully during experimentation.
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24
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Krzysztoń R, Woschée D, Reiser A, Schwake G, Strey HH, Rädler JO. Single-cell kinetics of siRNA-mediated mRNA degradation. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2019; 21:102077. [PMID: 31400572 DOI: 10.1016/j.nano.2019.102077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/26/2022]
Abstract
RNA interference (RNAi) enables the therapeutic use of small interfering RNAs (siRNAs) to silence disease-related genes. The efficiency of silencing is commonly assessed by measuring expression levels of the target protein at a given time point post-transfection. Here, we determine the siRNA-induced fold change in mRNA degradation kinetics from single-cell fluorescence time-courses obtained using live-cell imaging on single-cell arrays (LISCA). After simultaneous transfection of mRNAs encoding eGFP (target) and CayRFP (reference), the eGFP expression is silenced by siRNA. The single-cell time-courses are fitted using a mathematical model of gene expression. Analysis yields best estimates of related kinetic rate constants, including mRNA degradation constants. We determine the siRNA-induced changes in kinetic rates and their correlations between target and reference protein expression. Assessment of mRNA degradation constants using single-cell time-lapse imaging is fast (<30 h) and returns an accurate, time-independent measure of siRNA-induced silencing, thus allowing the exact evaluation of siRNA therapeutics.
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Affiliation(s)
- Rafał Krzysztoń
- Faculty of Physics, Ludwig-Maximilians-Universität Munich (LMU), Munich, Germany; Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität Munich (LMU), Munich, Germany; Nano systems Initiative Munich (NIM) and Center for NanoScience (CeNS), Munich, Germany.
| | - Daniel Woschée
- Faculty of Physics, Ludwig-Maximilians-Universität Munich (LMU), Munich, Germany; Nano systems Initiative Munich (NIM) and Center for NanoScience (CeNS), Munich, Germany
| | - Anita Reiser
- Faculty of Physics, Ludwig-Maximilians-Universität Munich (LMU), Munich, Germany; Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität Munich (LMU), Munich, Germany; Nano systems Initiative Munich (NIM) and Center for NanoScience (CeNS), Munich, Germany
| | - Gerlinde Schwake
- Faculty of Physics, Ludwig-Maximilians-Universität Munich (LMU), Munich, Germany
| | - Helmut H Strey
- Department of Biomedical Engineering and Laufer Center for Quantitative Biology, Stony Brook University, Stony Brook, NY
| | - Joachim O Rädler
- Faculty of Physics, Ludwig-Maximilians-Universität Munich (LMU), Munich, Germany; Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität Munich (LMU), Munich, Germany; Nano systems Initiative Munich (NIM) and Center for NanoScience (CeNS), Munich, Germany.
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25
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Vorontsova YE, Zavoloka EL, Cherezov RO, Simonova OB. Drosophila as a Model System Used for Searching the Genes, Signaling Pathways, and Mechanisms Controlling Cytoskeleton Formation. Russ J Dev Biol 2019. [DOI: 10.1134/s1062360419010065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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26
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Chen X, Mangala LS, Rodriguez-Aguayo C, Kong X, Lopez-Berestein G, Sood AK. RNA interference-based therapy and its delivery systems. Cancer Metastasis Rev 2019; 37:107-124. [PMID: 29243000 DOI: 10.1007/s10555-017-9717-6] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNA interference (RNAi) is considered a highly specific approach for gene silencing and holds tremendous potential for treatment of various pathologic conditions such as cardiovascular diseases, viral infections, and cancer. Although gene silencing approaches such as RNAi are widely used in preclinical models, the clinical application of RNAi is challenging primarily because of the difficulty in achieving successful systemic delivery. Effective delivery systems are essential to enable the full therapeutic potential of RNAi. An ideal nanocarrier not only addresses the challenges of delivering naked siRNA/miRNA, including its chemically unstable features, extracellular and intracellular barriers, and innate immune stimulation, but also offers "smart" targeted delivery. Over the past decade, great efforts have been undertaken to develop RNAi delivery systems that overcome these obstacles. This review presents an update on current progress in the therapeutic application of RNAi with a focus on cancer therapy and strategies for optimizing delivery systems, such as lipid-based nanoparticles.
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Affiliation(s)
- Xiuhui Chen
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lingegowda S Mangala
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cristian Rodriguez-Aguayo
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xianchao Kong
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Gabriel Lopez-Berestein
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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27
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Kaya-Çopur A, Schnorrer F. RNA Interference Screening for Genes Regulating Drosophila Muscle Morphogenesis. Methods Mol Biol 2019; 1889:331-348. [PMID: 30367424 DOI: 10.1007/978-1-4939-8897-6_20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
RNA interference (RNAi) is the method of choice to systematically test for gene function in an intact organism. The model organism Drosophila has the advantage that RNAi is cell autonomous, meaning it does not spread from one cell to the next. Hence, RNAi can be performed in a tissue-specific manner by expressing short or long inverted repeat constructs (hairpins) designed to target mRNAs from one specific target gene. This achieves tissue-specific knock-down of a target gene of choice. Here, we detail the methodology to test gene function in Drosophila muscle tissue by expressing hairpins in a muscle-specific manner using the GAL4-UAS system. We further discuss the systematic RNAi resource collections available which also permit large scale screens in a muscle-specific manner. The full power of such screens is revealed by combination of high-throughput assays followed by detailed morphological assays. Together, this chapter should be a practical guide to enable the reader to either test a few candidate genes, or large gene sets for particular functions in Drosophila muscle tissue and provide first insights into the biological process the gene might be important for in muscle.
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28
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Gu KX, Song XS, Xiao XM, Duan XX, Wang JX, Duan YB, Hou YP, Zhou MG. A β 2-tubulin dsRNA derived from Fusarium asiaticum confers plant resistance to multiple phytopathogens and reduces fungicide resistance. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 153:36-46. [PMID: 30744895 DOI: 10.1016/j.pestbp.2018.10.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/28/2018] [Accepted: 10/29/2018] [Indexed: 05/20/2023]
Abstract
Crops are attacked by a large number of pathogens which are responsible for an approximately 30% loss in global crop production at pre- and post-harvest levels. In light of the continuing emergence of fungicide resistance, the needs for new agricultural drugs turn out to be much more critical. Here we demonstrated a Faβ2Tub-3 dsRNA derived from Fusarium asiaticum had broad-spectrum antifungal activity against Fusarium spp., Botrytis cinerea, Magnaporthe oryzae and Colletotrichum truncatum, with an additional function of reducing the dosage of carbendazim (MBC) fungicide. RNAi molecules derived from different regions of β2-tubulin gene had different effects on mycelial growth, asexual reproduction and virulence. Faβ2Tub-3 (one of β2-tubulin segments) exhibited a strong silencing efficacy both on β1-tubulin and β2-tubulin genes in F. asiaticum. Faβ2Tub-3 sequence was found to be highly conserved among Fusarium spp., Botrytis cinerea, Magnaporthe oryzae and Colletotrichum truncatum. The Faβ2Tub-3 dsRNA demonstrated a broad-spectrum antifungal activity against these fungi in vitro and on living plant. More importantly, Faβ2Tub-3 dsRNA increased the fungal sensitivity to MBC, while MBC increased the duration of Faβ2Tub-3 dsRNA. Our findings suggest a new anti-fungal agent (Faβ2Tub-3 dsRNA) for plant protection against diverse pathogens and for fungicide reduction.
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Affiliation(s)
- Kai-Xin Gu
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Jiangsu Province, Nanjing 210095, China
| | - Xiu-Shi Song
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Jiangsu Province, Nanjing 210095, China
| | - Xue-Mei Xiao
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Jiangsu Province, Nanjing 210095, China
| | - Xiao-Xin Duan
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Jiangsu Province, Nanjing 210095, China
| | - Jian-Xin Wang
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Jiangsu Province, Nanjing 210095, China
| | - Ya-Bing Duan
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Jiangsu Province, Nanjing 210095, China
| | - Yi-Ping Hou
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Jiangsu Province, Nanjing 210095, China
| | - Ming-Guo Zhou
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Jiangsu Province, Nanjing 210095, China.
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Abstract
RNA interference (RNAi) is the biological process of mRNA degradation induced by complementary sequences double-stranded (ds) small interfering RNAs (siRNA) and suppression of target gene expression. Exogenous siRNAs (perfectly paired dsRNAs of ∼21–25 nt in length) play an important role in host defense against RNA viruses and in transcriptional and post-transcriptional gene regulation in plants and other eukaryotes. Using RNAi technology by transfecting synthetic siRNAs into eukaryotic cells to silence genes has become an indispensable tool to investigate gene functions, and siRNA-based therapy is being developed to knockdown genes implicated in diseases. Other examples of RNAi technology include method of producing highly potent and purified siRNAs directly from Escherichiacoli cells, based on an unexpected discovery that ectopic expression of p19, a plant viral siRNA-binding protein, stabilizes a cryptic siRNA-like RNA species in bacteria. Those siRNAs, named as pro-siRNA for “prokaryotic siRNA”, are bacterial RNase III products that have chemical and functional properties that like eukaryotic siRNAs.
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30
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Luhur A, Klueg KM, Zelhof AC. Generating and working with Drosophila cell cultures: Current challenges and opportunities. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2018; 8:e339. [PMID: 30561900 DOI: 10.1002/wdev.339] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/30/2018] [Accepted: 11/21/2018] [Indexed: 12/26/2022]
Abstract
The use of Drosophila cell cultures has positively impacted both fundamental and biomedical research. The most widely used cell lines: Schneider, Kc, the CNS and imaginal disc lines continue to be the choice for many applications. Drosophila cell lines provide a homogenous source of cells suitable for biochemical experimentations, transcriptomics, functional genomics, and biomedical applications. They are amenable to RNA interference and serve as a platform for high-throughput screens to identify relevant candidate genes or drugs for any biological process. Currently, CRISPR-based functional genomics are also being developed for Drosophila cell lines. Even though many uniquely derived cell lines exist, cell genetic techniques such the transgenic UAS-GAL4-based RasV12 oncogene expression, CRISPR-Cas9 editing and recombination mediated cassette exchange are likely to drive the establishment of many more lines from specific tissues, cells, or genotypes. However, the pace of creating new lines is hindered by several factors inherent to working with Drosophila cell cultures: single cell cloning, optimal media formulations and culture conditions capable of supporting lines from novel tissue sources or genotypes. Moreover, even though many Drosophila cell lines are morphologically and transcriptionally distinct it may be necessary to implement a standard for Drosophila cell line authentication, ensuring the identity and purity of each cell line. Altogether, recent advances and a standardized authentication effort should improve the utility of Drosophila cell cultures as a relevant model for fundamental and biomedical research. This article is categorized under: Technologies > Analysis of Cell, Tissue, and Animal Phenotypes.
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Affiliation(s)
- Arthur Luhur
- Department of Biology, Drosophila Genomics Resource Center, Indiana University Bloomington, Bloomington, Indiana
| | - Kristin M Klueg
- Department of Biology, Drosophila Genomics Resource Center, Indiana University Bloomington, Bloomington, Indiana
| | - Andrew C Zelhof
- Department of Biology, Drosophila Genomics Resource Center, Indiana University Bloomington, Bloomington, Indiana
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31
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Davidson BA, Hassan S, Garcia EJ, Tayebi N, Sidransky E. Exploring genetic modifiers of Gaucher disease: The next horizon. Hum Mutat 2018; 39:1739-1751. [PMID: 30098107 PMCID: PMC6240360 DOI: 10.1002/humu.23611] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/01/2018] [Accepted: 08/03/2018] [Indexed: 12/26/2022]
Abstract
Gaucher disease is an autosomal recessive lysosomal storage disorder resulting from mutations in the gene GBA1 that lead to a deficiency in the enzyme glucocerebrosidase. Accumulation of the enzyme's substrates, glucosylceramide and glucosylsphingosine, results in symptoms ranging from skeletal and visceral involvement to neurological manifestations. Nonetheless, there is significant variability in clinical presentations amongst patients, with limited correlation between genotype and phenotype. Contributing to this clinical variation are genetic modifiers that influence the phenotypic outcome of the disorder. In this review, we explore the role of genetic modifiers in Mendelian disorders and describe methods to facilitate their discovery. In addition, we provide examples of candidate modifiers of Gaucher disease, explore their relevance in the development of potential therapeutics, and discuss the impact of GBA1 and modifying mutations on other more common diseases like Parkinson disease. Identifying these important modulators of Gaucher phenotype may ultimately unravel the complex relationship between genotype and phenotype and lead to improved counseling and treatments.
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Affiliation(s)
- Brad A. Davidson
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Shahzeb Hassan
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Eric Joshua Garcia
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Nahid Tayebi
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Ellen Sidransky
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
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32
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Song X, Gu K, Duan X, Xiao X, Hou Y, Duan Y, Wang J, Yu N, Zhou M. Secondary amplification of siRNA machinery limits the application of spray-induced gene silencing. MOLECULAR PLANT PATHOLOGY 2018; 19:2543-2560. [PMID: 30027625 PMCID: PMC6638038 DOI: 10.1111/mpp.12728] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Spray-induced gene silencing (SIGS) is an innovative strategy for crop protection. However, the mechanism of SIGS is not known. Here, we first demonstrate that secondary small interfering RNA (siRNA) amplification limits the application of SIGS. A myosin5 gene (Myo5) was chosen as the target of SIGS in an agronomically important pathogen-Fusarium asiaticum. Five segments corresponding to the different regions of the Myo5 gene were found to efficiently silence Myo5, resulting in cell wall defects, life cycle disruption and virulence reduction. Myo5-8 (one of the Myo5 segments) induced sequence-specific RNA interference (RNAi) activity in F. asiaticum, F. graminearum, F. tricinctum and F. oxysporum, but not in other fungi, in vitro. Remarkably, the silencing of Myo5 lasted for only 9 h unless the double-stranded RNA (dsRNA) was continuously supplied, because F. asiaticum is unable to maintain siRNA amplification. After spraying on plants, dsRNAs were more efficiently taken up via the wounded surface. The antifungal activity of dsRNAs taken up by plant cells was higher and longer lasting than that dried onto the plant surface. In contrast with dsRNAs in fungi, dsRNAs in plant cells could efficiently turn into substantial siRNAs via secondary amplification machinery. Our findings provide new implications to develop SIGS as a mainstream disease control strategy against Fusarium and other fungi.
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Affiliation(s)
- Xiu‐Shi Song
- Key Laboratory of Pesticide, College of Plant ProtectionNanjing Agricultural UniversityNanjingJiangsu Province210095China
| | - Kai‐Xin Gu
- Key Laboratory of Pesticide, College of Plant ProtectionNanjing Agricultural UniversityNanjingJiangsu Province210095China
| | - Xiao‐Xin Duan
- Key Laboratory of Pesticide, College of Plant ProtectionNanjing Agricultural UniversityNanjingJiangsu Province210095China
| | - Xue‐Mei Xiao
- Key Laboratory of Pesticide, College of Plant ProtectionNanjing Agricultural UniversityNanjingJiangsu Province210095China
| | - Yi‐Ping Hou
- Key Laboratory of Pesticide, College of Plant ProtectionNanjing Agricultural UniversityNanjingJiangsu Province210095China
| | - Ya‐Bing Duan
- Key Laboratory of Pesticide, College of Plant ProtectionNanjing Agricultural UniversityNanjingJiangsu Province210095China
| | - Jian‐Xin Wang
- Key Laboratory of Pesticide, College of Plant ProtectionNanjing Agricultural UniversityNanjingJiangsu Province210095China
| | - Na Yu
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant ProtectionNanjing Agricultural UniversityNanjingJiangsu Province210095China
| | - Ming‐Guo Zhou
- Key Laboratory of Pesticide, College of Plant ProtectionNanjing Agricultural UniversityNanjingJiangsu Province210095China
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33
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Naganathan SR, Fürthauer S, Rodriguez J, Fievet BT, Jülicher F, Ahringer J, Cannistraci CV, Grill SW. Morphogenetic degeneracies in the actomyosin cortex. eLife 2018; 7:37677. [PMID: 30346273 PMCID: PMC6226289 DOI: 10.7554/elife.37677] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/16/2018] [Indexed: 01/07/2023] Open
Abstract
One of the great challenges in biology is to understand the mechanisms by which morphogenetic processes arise from molecular activities. We investigated this problem in the context of actomyosin-based cortical flow in C. elegans zygotes, where large-scale flows emerge from the collective action of actomyosin filaments and actin binding proteins (ABPs). Large-scale flow dynamics can be captured by active gel theory by considering force balances and conservation laws in the actomyosin cortex. However, which molecular activities contribute to flow dynamics and large-scale physical properties such as viscosity and active torque is largely unknown. By performing a candidate RNAi screen of ABPs and actomyosin regulators we demonstrate that perturbing distinct molecular processes can lead to similar flow phenotypes. This is indicative for a ‘morphogenetic degeneracy’ where multiple molecular processes contribute to the same large-scale physical property. We speculate that morphogenetic degeneracies contribute to the robustness of bulk biological matter in development.
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Affiliation(s)
| | - Sebastian Fürthauer
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Computational Biology, Flatiron Institute, New York, United States
| | - Josana Rodriguez
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, United Kingdom.,Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, United Kingdom
| | - Bruno Thomas Fievet
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, United Kingdom
| | - Frank Jülicher
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Julie Ahringer
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, United Kingdom
| | - Carlo Vittorio Cannistraci
- BIOTEC, Technische Universität Dresden, Dresden, Germany.,Brain Bio-Inspired Computing (BBC) Lab, IRCCS Centro Neurolesi "Bonino Pulejo", Messina, Italy
| | - Stephan W Grill
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,BIOTEC, Technische Universität Dresden, Dresden, Germany
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34
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Park SH, Lee CW, Lee JH, Park JY, Roshandell M, Brennan CA, Choe KM. Requirement for and polarized localization of integrin proteins during Drosophila wound closure. Mol Biol Cell 2018; 29:2137-2147. [PMID: 29995573 PMCID: PMC6249799 DOI: 10.1091/mbc.e17-11-0635] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 06/19/2018] [Accepted: 07/05/2018] [Indexed: 01/06/2023] Open
Abstract
Wound reepithelialization is an evolutionarily conserved process in which skin cells migrate as sheets to heal the breach and is critical to prevent infection but impaired in chronic wounds. Integrin heterodimers mediate attachment between epithelia and underlying extracellular matrix and also act in large signaling complexes. The complexity of the mammalian wound environment and evident redundancy among integrins has impeded determination of their specific contributions to reepithelialization. Taking advantage of the genetic tools and smaller number of integrins in Drosophila, we undertook a systematic in vivo analysis of integrin requirements in the reepithelialization of skin wounds in the larva. We identify αPS2-βPS and αPS3-βPS as the crucial integrin dimers and talin as the only integrin adhesion component required for reepithelialization. The integrins rapidly accumulate in a JNK-dependent manner in a few rows of cells surrounding a wound. Intriguingly, the integrins localize to the distal margin in these cells, instead of the frontal or lamellipodial distribution expected for proteins providing traction and recruit nonmuscle myosin II to the same location. These findings indicate that signaling roles of integrins may be important for epithelial polarization around wounds and lay the groundwork for using Drosophila to better understand integrin contributions to reepithelialization.
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Affiliation(s)
- Si-Hyoung Park
- Department of Systems Biology, Yonsei University, Seodaemun-gu, Seoul 03722, South Korea
| | - Chan-wool Lee
- Department of Systems Biology, Yonsei University, Seodaemun-gu, Seoul 03722, South Korea
| | - Ji-Hyun Lee
- Department of Systems Biology, Yonsei University, Seodaemun-gu, Seoul 03722, South Korea
| | - Jin Young Park
- Department of Systems Biology, Yonsei University, Seodaemun-gu, Seoul 03722, South Korea
| | - Mobina Roshandell
- Department of Biological Science, California State University, Fullerton, Fullerton, CA 92831
| | - Catherine A. Brennan
- Department of Biological Science, California State University, Fullerton, Fullerton, CA 92831
| | - Kwang-Min Choe
- Department of Systems Biology, Yonsei University, Seodaemun-gu, Seoul 03722, South Korea
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35
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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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36
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KIFC1 is essential for acrosome formation and nuclear shaping during spermiogenesis in the lobster Procambarus clarkii. Oncotarget 2018; 8:36082-36098. [PMID: 28415605 PMCID: PMC5482640 DOI: 10.18632/oncotarget.16429] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/14/2017] [Indexed: 01/13/2023] Open
Abstract
In order to study the function of kinesin-14 motor protein KIFC1 during spermatogenesis of Procambarus clarkii, the full length of kifc1 was cloned from testes cDNA using Rapid-Amplification of cDNA Ends (RACE). The deduced KIFC1 protein sequence showed the highest similarity between Procambarus clarkii and Eriocheir senensis (similarity rate as 64%). According to the results of in situ hybridization (ISH), the kifc1 mRNA was gathered in the acrosome location above nucleus in the mid- and late-stage spermatids. Immunofluorescence results were partly consistent with the ISH in middle spermatids, while in the late spermatids the KIFC1 was distributed around the nucleus which had large deformation and formed four to six nuclear arms. In the mature sperm, KIFC1 and microtubules were distributed around the sperm, playing a role in maintaining the sperm morphology and normal function. Overexpression of P. clarkii kifc1 in GC1 cells for 24 hours resulted in disorganization of microtubules which changed the cell morphology from circular and spherical into fusiform. In addition, the overexpression also resulted in triple centrosomes during mitosis which eventually led to cell apoptosis. RNAi experiments showed that decreased KIFC1 protein levels resulted in total inhibition of spermatogenesis, with only mature sperm found in the RNAi-testis, implying an indispensable role of KIFC1 during P. clarkii spermiogenesis.
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37
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Heigwer F, Port F, Boutros M. RNA Interference (RNAi) Screening in Drosophila. Genetics 2018; 208:853-874. [PMID: 29487145 PMCID: PMC5844339 DOI: 10.1534/genetics.117.300077] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/28/2017] [Indexed: 12/22/2022] Open
Abstract
In the last decade, RNA interference (RNAi), a cellular mechanism that uses RNA-guided degradation of messenger RNA transcripts, has had an important impact on identifying and characterizing gene function. First discovered in Caenorhabditis elegans, RNAi can be used to silence the expression of genes through introduction of exogenous double-stranded RNA into cells. In Drosophila, RNAi has been applied in cultured cells or in vivo to perturb the function of single genes or to systematically probe gene function on a genome-wide scale. In this review, we will describe the use of RNAi to study gene function in Drosophila with a particular focus on high-throughput screening methods applied in cultured cells. We will discuss available reagent libraries and cell lines, methodological approaches for cell-based assays, and computational methods for the analysis of high-throughput screens. Furthermore, we will review the generation and use of genome-scale RNAi libraries for tissue-specific knockdown analysis in vivo and discuss the differences and similarities with the use of genome-engineering methods such as CRISPR/Cas9 for functional analysis.
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Affiliation(s)
- Florian Heigwer
- Division of Signaling and Functional Genomics, German Cancer Research Center, and Department of Cell and Molecular Biology, Heidelberg University, Medical Faculty Mannheim, D-69120, Germany
| | - Fillip Port
- Division of Signaling and Functional Genomics, German Cancer Research Center, and Department of Cell and Molecular Biology, Heidelberg University, Medical Faculty Mannheim, D-69120, Germany
| | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center, and Department of Cell and Molecular Biology, Heidelberg University, Medical Faculty Mannheim, D-69120, Germany
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Adams FF, Hoffmann T, Zuber J, Heckl D, Schambach A, Schwarzer A. Pooled Generation of Lentiviral Tetracycline-Regulated microRNA Embedded Short Hairpin RNA Libraries. Hum Gene Ther Methods 2018; 29:16-29. [PMID: 29325442 DOI: 10.1089/hgtb.2017.182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Short hairpin RNA (shRNA) screens are powerful tools to probe genetic dependencies in loss-of-function studies, such as the identification of therapeutic targets in cancer research. Lentivirally delivered shRNAs embedded in endogenous microRNA contexts (shRNAmiRs) mediate efficient long-term suppression of target genes suitable for numerous experimental contexts and clinical applications. Here, an easy-to-use laboratory protocol is described, covering the design and pooled assembly of focused shRNAmiR libraries into an optimized, Tet-inducible all-in-one lentiviral vector, packaging of viral particles, followed by retrieval and quantification of hairpin sequences after cellular DNA-recovery. Starting from a gene list to the identification of hits, the protocol enables shRNA screens within 6 weeks.
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Affiliation(s)
- Felix F Adams
- 1 Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Thomas Hoffmann
- 2 Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Johannes Zuber
- 2 Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Dirk Heckl
- 3 Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Axel Schambach
- 1 Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany .,4 Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Adrian Schwarzer
- 1 Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany .,5 Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
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Ma L, Zhao Y, Chen Y, Cheng B, Peng A, Huang K. Caenorhabditis elegans as a model system for target identification and drug screening against neurodegenerative diseases. Eur J Pharmacol 2017; 819:169-180. [PMID: 29208474 DOI: 10.1016/j.ejphar.2017.11.051] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 11/30/2017] [Indexed: 12/12/2022]
Abstract
Over the past decades, Caenorhabditis elegans (C. elegans) has been widely used as a model system because of its small size, transparent body, short generation time and lifespan (~3 days and 3 weeks, respectively), completely sequenced genome and tractability to genetic manipulation. Protein misfolding and aggregation are key pathological features in neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease and Amyotrophic lateral sclerosis. Animal models, including C. elegans, have been extensively used to discover and validate new drugs against neurodegenerative diseases. The well-defined and genetically tractable nervous system of C. elegans offers an effective model to explore basic mechanistic pathways of neurodegenerative diseases. Recent progress in high-throughput drug screening also provides a powerful approach for identifying chemical modulators of biological processes. Here, we summarize the latest progress of using C. elegans as a model system for target identification and drug screening in neurodegenerative diseases.
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Affiliation(s)
- Liang Ma
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yudan Zhao
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuchen Chen
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Biao Cheng
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Anlin Peng
- Department of Pharmacy, The Third Hospital of Wuhan, Wuhan 430060, China
| | - Kun Huang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China; Center for Biomedicine Research, Wuhan Institute of Biotechnology, Wuhan 430075, China.
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40
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Kumar D, Gong C. Insect RNAi: Integrating a New Tool in the Crop Protection Toolkit. TRENDS IN INSECT MOLECULAR BIOLOGY AND BIOTECHNOLOGY 2017. [PMCID: PMC7121382 DOI: 10.1007/978-3-319-61343-7_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protecting crops against insect pests is a major focus area in crop protection. Over the past two decades, biotechnological interventions, especially Bt proteins, have been successfully implemented across the world and have had major impacts on reducing chemical pesticide applications. As insects continue to adapt to insecticides, both chemical and protein-based, new methods, molecules, and modes of action are necessary to provide sustainable solutions. RNA interference (RNAi) has emerged as a significant tool to knock down or alter gene expression profiles in a species-specific manner. In the past decade, there has been intense research on RNAi applications in crop protection. This chapter looks at the current state of knowledge in the field and outlines the methodology, delivery methods, and precautions required in designing targets. Assessing the targeting of specific gene expression is also an important part of a successful RNAi strategy. The current literature on the use of RNAi in major orders of insect pests is reviewed, along with a perspective on the regulatory aspects of the approach. Risk assessment of RNAi would focus on molecular characterization, food/feed risk assessment, and environmental risk assessment. As more RNAi-based products come through regulatory systems, either via direct application or plant expression based, the impact of this approach on crop protection will become clearer.
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Affiliation(s)
- Dhiraj Kumar
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Chengliang Gong
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
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Kondo S, Vedanayagam J, Mohammed J, Eizadshenass S, Kan L, Pang N, Aradhya R, Siepel A, Steinhauer J, Lai EC. New genes often acquire male-specific functions but rarely become essential in Drosophila. Genes Dev 2017; 31:1841-1846. [PMID: 29051389 PMCID: PMC5695085 DOI: 10.1101/gad.303131.117] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 09/12/2017] [Indexed: 12/30/2022]
Abstract
In this study, Kondo et al. performed large-scale CRISPR/Cas9 mutagenesis of “conserved, essential” and “young, RNAi-lethal” genes and confirmed the lethality of conserved genes but not young genes. Additionally, two young gene mutants resulted in spermatogenesis and/or male sterility, indicating that young genes have a preferential impact on male reproductive system function. Relatively little is known about the in vivo functions of newly emerging genes, especially in metazoans. Although prior RNAi studies reported prevalent lethality among young gene knockdowns, our phylogenomic analyses reveal that young Drosophila genes are frequently restricted to the nonessential male reproductive system. We performed large-scale CRISPR/Cas9 mutagenesis of “conserved, essential” and “young, RNAi-lethal” genes and broadly confirmed the lethality of the former but the viability of the latter. Nevertheless, certain young gene mutants exhibit defective spermatogenesis and/or male sterility. Moreover, we detected widespread signatures of positive selection on young male-biased genes. Thus, young genes have a preferential impact on male reproductive system function.
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Affiliation(s)
- Shu Kondo
- Invertebrate Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jeffrey Vedanayagam
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Jaaved Mohammed
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA.,Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA.,Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10021, USA
| | - Sogol Eizadshenass
- Department of Biology, Yeshiva University, New York, New York 10033, USA
| | - Lijuan Kan
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Nan Pang
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Rajaguru Aradhya
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Josefa Steinhauer
- Department of Biology, Yeshiva University, New York, New York 10033, USA
| | - Eric C Lai
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA
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Wang YL, Shao X, Wang F, Zeng L, Hu L, Cui SQ, Hou G, Huang DN. Intron-specific shRNA-mediated downregulation of survivin and promotion of apoptosis in HeLa cells. Oncol Lett 2017; 14:5927-5933. [PMID: 29113228 PMCID: PMC5661408 DOI: 10.3892/ol.2017.6996] [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: 01/20/2016] [Accepted: 06/02/2017] [Indexed: 11/26/2022] Open
Abstract
Overexpression of the survivin gene contributes to tumorigenesis; it has been recognized as an important target for cancer therapy. In the present study, survivin expression was suppressed using recombinant plasmid mediated short hairpin RNAs (shRNAs) that were constructed to target exonic or intronic sequences of the survivin gene. In addition, a negative control shRNA was constructed. HeLa cells were transfected with specific shRNA constructs and the blocking efficiency of each shRNA was assessed at the mRNA and protein levels; and the five shRNA constructs with higher blocking efficiency were selected. Cell apoptosis was assessed by flow cytometry (FCM) following Annexin V-fluorescein isothiocyanate/propidium iodide double staining. Hoechst staining was used to detect the morphological diversity of the nuclei in apoptotic cells. The results demonstrated that survivin expression was effectively reduced by the transfection of shRNAs in HeLa cells. In addition, the apoptotic rates of the shRNA-treated groups were significantly increased compared with the negative control group according to the FCM results. The nuclei of HeLa cells exhibited apoptotic characteristics in the shRNA-treated groups as identified by Hoechst staining. Survivin-targeting shRNAs effectively downregulated the expression of the gene and markedly increased the apoptotic rate of HeLa cells. Data from the present study also indicated that the intron-specific shRNA demonstrate a high efficiency of inhibition of survivin expression and were able to induce cell apoptosis of HeLa cells through RNAi, potentially providing novel target sites for tumor therapy. In conclusion, the present study suggests that intron-specific blocking of survivin by RNAi may provide a tool for anticancer therapy.
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Affiliation(s)
- Yue-Li Wang
- Department of Basic Medicine, Guangdong Medical University, Zhanjiang, Guangdong 524023, P.R. China
| | - Xin Shao
- People's Hospital of Shiyan, Shiyan, Hubei 442000, P.R. China
| | - Fa Wang
- Department of Basic Medicine, Guangdong Medical University, Zhanjiang, Guangdong 524023, P.R. China
| | - Liang Zeng
- Department of Basic Medicine, Guangdong Medical University, Zhanjiang, Guangdong 524023, P.R. China
| | - Liang Hu
- Department of Basic Medicine, Guangdong Medical University, Zhanjiang, Guangdong 524023, P.R. China
| | - Shi-Quan Cui
- Department of Basic Medicine, Guangdong Medical University, Zhanjiang, Guangdong 524023, P.R. China
| | - Gan Hou
- Department of Clinical Biochemistry, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Di-Nan Huang
- Department of Clinical Biochemistry, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
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Rioualen C, Da Costa Q, Chetrit B, Charafe-Jauffret E, Ginestier C, Bidaut G. HTS-Net: An integrated regulome-interactome approach for establishing network regulation models in high-throughput screenings. PLoS One 2017; 12:e0185400. [PMID: 28949986 PMCID: PMC5614607 DOI: 10.1371/journal.pone.0185400] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/12/2017] [Indexed: 12/28/2022] Open
Abstract
High-throughput RNAi screenings (HTS) allow quantifying the impact of the deletion of each gene in any particular function, from virus-host interactions to cell differentiation. However, there has been less development for functional analysis tools dedicated to RNAi analyses. HTS-Net, a network-based analysis program, was developed to identify gene regulatory modules impacted in high-throughput screenings, by integrating transcription factors-target genes interaction data (regulome) and protein-protein interaction networks (interactome) on top of screening z-scores. HTS-Net produces exhaustive HTML reports for results navigation and exploration. HTS-Net is a new pipeline for RNA interference screening analyses that proves better performance than simple gene rankings by z-scores, by re-prioritizing genes and replacing them in their biological context, as shown by the three studies that we reanalyzed. Formatted input data for the three studied datasets, source code and web site for testing the system are available from the companion web site at http://htsnet.marseille.inserm.fr/. We also compared our program with existing algorithms (CARD and hotnet2).
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Affiliation(s)
- Claire Rioualen
- Aix-Marseille Univ, Marseille, France
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Quentin Da Costa
- Aix-Marseille Univ, Marseille, France
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Bernard Chetrit
- Aix-Marseille Univ, Marseille, France
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Emmanuelle Charafe-Jauffret
- Aix-Marseille Univ, Marseille, France
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Christophe Ginestier
- Aix-Marseille Univ, Marseille, France
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Ghislain Bidaut
- Aix-Marseille Univ, Marseille, France
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- * E-mail:
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44
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Adams FF, Heckl D, Hoffmann T, Talbot SR, Kloos A, Thol F, Heuser M, Zuber J, Schambach A, Schwarzer A. An optimized lentiviral vector system for conditional RNAi and efficient cloning of microRNA embedded short hairpin RNA libraries. Biomaterials 2017; 139:102-115. [PMID: 28599149 DOI: 10.1016/j.biomaterials.2017.05.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/17/2017] [Accepted: 05/19/2017] [Indexed: 02/06/2023]
Abstract
RNA interference (RNAi) and CRISPR-Cas9-based screening systems have emerged as powerful and complementary tools to unravel genetic dependencies through systematic gain- and loss-of-function studies. In recent years, a series of technical advances helped to enhance the performance of virally delivered RNAi. For instance, the incorporation of short hairpin RNAs (shRNAs) into endogenous microRNA contexts (shRNAmiRs) allows the use of Tet-regulated promoters for synchronous onset of gene knockdown and precise interrogation of gene dosage effects. However, remaining challenges include lack of efficient cloning strategies, inconsistent knockdown potencies and leaky expression. Here, we present a simple, one-step cloning approach for rapid and efficient cloning of miR-30 shRNAmiR libraries. We combined a human miR-30 backbone retaining native flanking sequences with an optimized all-in-one lentiviral vector system for conditional RNAi to generate a versatile toolbox characterized by higher doxycycline sensitivity, reduced leakiness and enhanced titer. Furthermore, refinement of existing shRNA design rules resulted in substantially improved prediction of powerful shRNAs. Our approach was validated by accurate quantification of the knockdown potency of over 250 single shRNAmiRs. To facilitate access and use by the scientific community, an online tool was developed for the automated design of refined shRNA-coding oligonucleotides ready for cloning into our system.
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Affiliation(s)
- Felix F Adams
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Dirk Heckl
- Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Thomas Hoffmann
- Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
| | - Steven R Talbot
- Institute of Physiological Chemistry, Hannover Medical School, 30625 Hannover, Germany
| | - Arnold Kloos
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, USA
| | - Adrian Schwarzer
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany.
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45
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Lee JH, Lee CW, Park SH, Choe KM. Spatiotemporal regulation of cell fusion by JNK and JAK/STAT signaling during Drosophila wound healing. J Cell Sci 2017; 130:1917-1928. [PMID: 28424232 DOI: 10.1242/jcs.187658] [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: 02/10/2016] [Accepted: 04/18/2017] [Indexed: 12/23/2022] Open
Abstract
Cell-cell fusion is widely observed during development and disease, and imposes a dramatic change on participating cells. Cell fusion should be tightly controlled, but the underlying mechanism is poorly understood. Here, we found that the JAK/STAT pathway suppressed cell fusion during wound healing in the Drosophila larval epidermis, restricting cell fusion to the vicinity of the wound. In the absence of JAK/STAT signaling, a large syncytium containing a 3-fold higher number of nuclei than observed in wild-type tissue formed in wounded epidermis. The JAK/STAT ligand-encoding genes upd2 and upd3 were transcriptionally induced by wounding, and were required for suppressing excess cell fusion. JNK (also known as Basket in flies) was activated in the wound vicinity and activity peaked at ∼8 h after injury, whereas JAK/STAT signaling was activated in an adjoining concentric ring and activity peaked at a later stage. Cell fusion occurred primarily in the wound vicinity, where JAK/STAT activation was suppressed by fusion-inducing JNK signaling. JAK/STAT signaling was both necessary and sufficient for the induction of βPS integrin (also known as Myospheroid) expression, suggesting that the suppression of cell fusion was mediated at least in part by integrin protein.
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Affiliation(s)
- Ji-Hyun Lee
- Department of Systems Biology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Chan-Wool Lee
- Department of Systems Biology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Si-Hyoung Park
- Department of Systems Biology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Kwang-Min Choe
- Department of Systems Biology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
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46
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Ortega-Arellano HF, Jimenez-Del-Rio M, Velez-Pardo C. Minocycline protects, rescues and prevents knockdown transgenic parkin Drosophila against paraquat/iron toxicity: Implications for autosomic recessive juvenile parkinsonism. Neurotoxicology 2017; 60:42-53. [PMID: 28284907 DOI: 10.1016/j.neuro.2017.03.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/03/2017] [Accepted: 03/06/2017] [Indexed: 01/03/2023]
Abstract
Autosomal recessive Juvenile Parkinsonism (AR-JP) is a chronic, progressive neurodegenerative disorder caused by mutation in the PARKIN gene, and invariably associated with dopaminergic (DAergic) neuronal loss and brain iron accumulation. Since current medical therapy is symptomatic and lacks significant disease-modifying effects, other treatment approaches are urgently needed it. In the present work, we investigate the role of minocycline (MC) in paraquat (PQ)/iron-induced neurotoxicity in the Drosophila TH>parkin-RNAi/+ (w[*]; UAS-parkin-RNAi; TH-GAL4) fly and have shown the following: (i) MC increased life span and restored the locomotor activity of knockdown (KD) transgenic parkin flies in comparison with the control (vehicle) group; (ii) MC at low (0.1 and 0.3mM) and middle (0.5mM) concentrations protected, rescued and prevented KD parkin Drosophila against PQ toxicity. However, MC at high (1mM) concentration aggravated the toxic effect of PQ; (iii) MC protected and rescued DAergic neurons against the PQ toxic effect according to tyrosine hydroxylase (TH)>green-fluorescent protein (GFP) reporter protein microscopy and anti-TH Western blotting analysis; (iv) MC protected DAergic neurons against PQ/iron toxicity; (v) MC significantly abridged lipid peroxidation (LPO) in the protection, rescue and prevention treatment in TH>parkin-RNAi/+ flies against PQ or iron alone or combined (PQ/iron)-induced neuronal oxidative stress (OS). Our results suggest that MC exerts neuroprotection against PQ/iron-induced OS in DAergic neurons most probably by the scavenging activity of reactive oxygen species (ROS), and by chelating iron. Therefore, MC might be a potential therapeutic drug to delay, revert, or prevent AR-JP.
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Affiliation(s)
- Hector Flavio Ortega-Arellano
- Neuroscience Research Group, Medical Research Institute, Faculty of Medicine, University of Antioquia (UdeA), Calle 70 No. 52-21, and Calle 62 # 52-59, Building 1, Room 412, SIU, Medellin, Colombia
| | - Marlene Jimenez-Del-Rio
- Neuroscience Research Group, Medical Research Institute, Faculty of Medicine, University of Antioquia (UdeA), Calle 70 No. 52-21, and Calle 62 # 52-59, Building 1, Room 412, SIU, Medellin, Colombia.
| | - Carlos Velez-Pardo
- Neuroscience Research Group, Medical Research Institute, Faculty of Medicine, University of Antioquia (UdeA), Calle 70 No. 52-21, and Calle 62 # 52-59, Building 1, Room 412, SIU, Medellin, Colombia.
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47
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Misra A, Green MR. Fluorescence Reporter-Based Genome-Wide RNA Interference Screening to Identify Alternative Splicing Regulators. Methods Mol Biol 2017; 1507:1-12. [PMID: 27832528 PMCID: PMC5508546 DOI: 10.1007/978-1-4939-6518-2_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Alternative splicing is a regulated process that leads to inclusion or exclusion of particular exons in a pre-mRNA transcript, resulting in multiple protein isoforms being encoded by a single gene. With more than 90 % of human genes known to undergo alternative splicing, it represents a major source for biological diversity inside cells. Although in vitro splicing assays have revealed insights into the mechanisms regulating individual alternative splicing events, our global understanding of alternative splicing regulation is still evolving. In recent years, genome-wide RNA interference (RNAi) screening has transformed biological research by enabling genome-scale loss-of-function screens in cultured cells and model organisms. In addition to resulting in the identification of new cellular pathways and potential drug targets, these screens have also uncovered many previously unknown mechanisms regulating alternative splicing. Here, we describe a method for the identification of alternative splicing regulators using genome-wide RNAi screening, as well as assays for further validation of the identified candidates. With modifications, this method can also be adapted to study the splicing regulation of pre-mRNAs that contain two or more splice isoforms.
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Affiliation(s)
- Ashish Misra
- Howard Hughes Medical Institute and Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Michael R Green
- Howard Hughes Medical Institute and Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.
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48
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Nierode G, Kwon PS, Dordick JS, Kwon SJ. Cell-Based Assay Design for High-Content Screening of Drug Candidates. J Microbiol Biotechnol 2016; 26:213-25. [PMID: 26428732 DOI: 10.4014/jmb.1508.08007] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To reduce attrition in drug development, it is crucial to consider the development and implementation of translational phenotypic assays as well as decipher diverse molecular mechanisms of action for new molecular entities. High-throughput fluorescence and confocal microscopes with advanced analysis software have simplified the simultaneous identification and quantification of various cellular processes through what is now referred to as highcontent screening (HCS). HCS permits automated identification of modifiers of accessible and biologically relevant targets and can thus be used to detect gene interactions or identify toxic pathways of drug candidates to improve drug discovery and development processes. In this review, we summarize several HCS-compatible, biochemical, and molecular biology-driven assays, including immunohistochemistry, RNAi, reporter gene assay, CRISPR-Cas9 system, and protein-protein interactions to assess a variety of cellular processes, including proliferation, morphological changes, protein expression, localization, post-translational modifications, and protein-protein interactions. These cell-based assay methods can be applied to not only 2D cell culture but also 3D cell culture systems in a high-throughput manner.
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Affiliation(s)
- Gregory Nierode
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Paul S Kwon
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Jonathan S Dordick
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Seok-Joon Kwon
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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Functional Genomic Strategies for Elucidating Human-Virus Interactions: Will CRISPR Knockout RNAi and Haploid Cells? Adv Virus Res 2016; 94:1-51. [PMID: 26997589 PMCID: PMC7112329 DOI: 10.1016/bs.aivir.2015.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Over the last several years a wealth of transformative human–virus interaction discoveries have been produced using loss-of-function functional genomics. These insights have greatly expanded our understanding of how human pathogenic viruses exploit our cells to replicate. Two technologies have been at the forefront of this genetic revolution, RNA interference (RNAi) and random retroviral insertional mutagenesis using haploid cell lines (haploid cell screening), with the former technology largely predominating. Now the cutting edge gene editing of the CRISPR/Cas9 system has also been harnessed for large-scale functional genomics and is poised to possibly displace these earlier methods. Here we compare and contrast these three screening approaches for elucidating host–virus interactions, outline their key strengths and weaknesses including a comparison of an arrayed multiple orthologous RNAi reagent screen to a pooled CRISPR/Cas9 human rhinovirus 14–human cell interaction screen, and recount some notable insights made possible by each. We conclude with a brief perspective on what might lie ahead for the fast evolving field of human–virus functional genomics.
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50
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Design, simplified cloning, and in-silico analysis of multisite small interfering RNA-targeting cassettes. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2016; 5:31-43. [PMID: 27844018 PMCID: PMC5019331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Multiple gene silencing is being required to target and tangle metabolic pathways in eukaryotes and researchers have to develop a subtle method for construction of RNA interference (RNAi) cassettes. Although, several vectors have been developed due to different screening and cloning strategies but still some potential limitations remain to be dissolved. Here, we worked out a simple cloning strategy to develop multisite small interfering RNA (siRNA) cassette from different genes by two cloning steps. In this method, effective siRNA sites in the target messenger RNAs (mRNAs) were determined using in silico analysis and consecutively arranged to reduce length of inverted repeats. Here, we used one-step (polymerase chain reaction) PCR by designed long primer sets covering the selected siRNA sites. Rapid screening, cost-effective and shorten procedure are advantages of this method compare to PCR classic cloning. Validity of constructs was confirmed by optimal centroid secondary structures with high stability in plants.
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