1
|
Zhang Y, Ke Z, Xu L, Yang Y, Chang L, Zhang J. A faster killing effect of plastid-mediated RNA interference on a leaf beetle through induced dysbiosis of the gut bacteria. PLANT COMMUNICATIONS 2024:100974. [PMID: 38751119 DOI: 10.1016/j.xplc.2024.100974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/10/2024] [Accepted: 05/10/2024] [Indexed: 06/16/2024]
Abstract
The expression of double-stranded RNAs (dsRNAs) from the plastid genome has been proven to be an effective method for controlling herbivorous pests by targeting essential insect genes. However, there are limitations to the efficiency of plastid-mediated RNA interference (PM-RNAi) due to the initial damage caused by the insects and their slow response to RNA interference. In this study, we developed transplastomic poplar plants that express dsRNAs targeting the β-Actin (dsACT) and Srp54k (dsSRP54K) genes of Plagiodera versicolora. Feeding experiments showed that transplastomic poplar plants can cause significantly higher mortality in P. versicolora larvae compared with nuclear transgenic or wild-type poplar plants. The efficient killing effect of PM-RNAi on P. versicolora larvae was found to be dependent on the presence of gut bacteria. Importantly, foliar application of a gut bacterial strain, Pseudomonas putida, will induce dysbiosis in the gut bacteria of P. versicolora larvae, leading to a significant acceleration in the speed of killing by PM-RNAi. Overall, our findings suggest that interfering with gut bacteria could be a promising strategy to enhance the effectiveness of PM-RNAi for insect pest control, offering a novel and effective approach for crop protection based on RNAi technology.
Collapse
Affiliation(s)
- Yiqiu Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zebin Ke
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Letian Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Ling Chang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Jiang Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan 430062, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
| |
Collapse
|
2
|
Lee FFY, Harris C, Alper S. RNA Binding Proteins that Mediate LPS-induced Alternative Splicing of the MyD88 Innate Immune Regulator. J Mol Biol 2024; 436:168497. [PMID: 38369277 PMCID: PMC11001520 DOI: 10.1016/j.jmb.2024.168497] [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: 12/10/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
Inflammation driven by Toll-like receptor (TLR) signaling pathways is required to combat infection. However, inflammation can damage host tissues; thus it is essential that TLR signaling ultimately is terminated to prevent chronic inflammatory disorders. One mechanism that terminates persistent TLR signaling is alternative splicing of the MyD88 signaling adaptor, which functions in multiple TLR signaling pathways. While the canonical long isoform of MyD88 (MyD88-L) mediates TLR signaling and promotes inflammation, an alternatively-spliced shorter isoform of MyD88 (MyD88-S) produces a dominant negative inhibitor of TLR signaling. MyD88-S production is induced by inflammatory agonists including lipopolysaccharide (LPS), and thus MyD88-S induction is thought to act as a negative feedback loop that prevents chronic inflammation. Despite the potential role that MyD88-S production plays in inflammatory disorders, the mechanisms controlling MyD88 alternative splicing remain unclear. Here, we identify two RNA binding proteins, SRSF1 and HNRNPU, that regulate LPS-induced alternative splicing of MyD88.
Collapse
Affiliation(s)
- Frank Fang Yao Lee
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA; Center for Genes, Environment and Health, National Jewish Health, Denver, CO 80206, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Anschutz, CO 80045, USA
| | - Chelsea Harris
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA; Center for Genes, Environment and Health, National Jewish Health, Denver, CO 80206, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Anschutz, CO 80045, USA
| | - Scott Alper
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA; Center for Genes, Environment and Health, National Jewish Health, Denver, CO 80206, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Anschutz, CO 80045, USA.
| |
Collapse
|
3
|
Xiang M, Li H, Zhan Y, Ma D, Gao Q, Fang Y. Functional CRISPR screens in T cells reveal new opportunities for cancer immunotherapies. Mol Cancer 2024; 23:73. [PMID: 38581063 PMCID: PMC10996278 DOI: 10.1186/s12943-024-01987-z] [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: 12/19/2023] [Accepted: 03/25/2024] [Indexed: 04/07/2024] Open
Abstract
T cells are fundamental components in tumour immunity and cancer immunotherapies, which have made immense strides and revolutionized cancer treatment paradigm. However, recent studies delineate the predicament of T cell dysregulation in tumour microenvironment and the compromised efficacy of cancer immunotherapies. CRISPR screens enable unbiased interrogation of gene function in T cells and have revealed functional determinators, genetic regulatory networks, and intercellular interactions in T cell life cycle, thereby providing opportunities to revamp cancer immunotherapies. In this review, we briefly described the central roles of T cells in successful cancer immunotherapies, comprehensively summarised the studies of CRISPR screens in T cells, elaborated resultant master genes that control T cell activation, proliferation, fate determination, effector function, and exhaustion, and highlighted genes (BATF, PRDM1, and TOX) and signalling cascades (JAK-STAT and NF-κB pathways) that extensively engage in multiple branches of T cell responses. In conclusion, this review bridged the gap between discovering element genes to a specific process of T cell activities and apprehending these genes in the global T cell life cycle, deepened the understanding of T cell biology in tumour immunity, and outlined CRISPR screens resources that might facilitate the development and implementation of cancer immunotherapies in the clinic.
Collapse
Affiliation(s)
- Minghua Xiang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huayi Li
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuanyuan Zhan
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ding Ma
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qinglei Gao
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yong Fang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| |
Collapse
|
4
|
Lin K, Chang YC, Billmann M, Ward HN, Le K, Hassan AZ, Bhojoo U, Chan K, Costanzo M, Moffat J, Boone C, Bielinsky AK, Myers CL. A scalable platform for efficient CRISPR-Cas9 chemical-genetic screens of DNA damage-inducing compounds. Sci Rep 2024; 14:2508. [PMID: 38291084 PMCID: PMC10828508 DOI: 10.1038/s41598-024-51735-y] [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: 09/20/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024] Open
Abstract
Current approaches to define chemical-genetic interactions (CGIs) in human cell lines are resource-intensive. We designed a scalable chemical-genetic screening platform by generating a DNA damage response (DDR)-focused custom sgRNA library targeting 1011 genes with 3033 sgRNAs. We performed five proof-of-principle compound screens and found that the compounds' known modes-of-action (MoA) were enriched among the compounds' CGIs. These scalable screens recapitulated expected CGIs at a comparable signal-to-noise ratio (SNR) relative to genome-wide screens. Furthermore, time-resolved CGIs, captured by sequencing screens at various time points, suggested an unexpected, late interstrand-crosslinking (ICL) repair pathway response to camptothecin-induced DNA damage. Our approach can facilitate screening compounds at scale with 20-fold fewer resources than commonly used genome-wide libraries and produce biologically informative CGI profiles.
Collapse
Affiliation(s)
- Kevin Lin
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Ya-Chu Chang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Henry N Ward
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Khoi Le
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Arshia Z Hassan
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Urvi Bhojoo
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Katherine Chan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael Costanzo
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Institute for Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Charles Boone
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
| |
Collapse
|
5
|
Meyers S, Demeyer S, Cools J. CRISPR screening in hematology research: from bulk to single-cell level. J Hematol Oncol 2023; 16:107. [PMID: 37875911 PMCID: PMC10594891 DOI: 10.1186/s13045-023-01495-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/21/2023] [Indexed: 10/26/2023] Open
Abstract
The CRISPR genome editing technology has revolutionized the way gene function is studied. Genome editing can be achieved in single genes or for thousands of genes simultaneously in sensitive genetic screens. While conventional genetic screens are limited to bulk measurements of cell behavior, recent developments in single-cell technologies make it possible to combine CRISPR screening with single-cell profiling. In this way, cell behavior and gene expression can be monitored simultaneously, with the additional possibility of including data on chromatin accessibility and protein levels. Moreover, the availability of various Cas proteins leading to inactivation, activation, or other effects on gene function further broadens the scope of such screens. The integration of single-cell multi-omics approaches with CRISPR screening open the path to high-content information on the impact of genetic perturbations at single-cell resolution. Current limitations in cell throughput and data density need to be taken into consideration, but new technologies are rapidly evolving and are likely to easily overcome these limitations. In this review, we discuss the use of bulk CRISPR screening in hematology research, as well as the emergence of single-cell CRISPR screening and its added value to the field.
Collapse
Affiliation(s)
- Sarah Meyers
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Sofie Demeyer
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Jan Cools
- Center for Human Genetics, KU Leuven, Leuven, Belgium.
- Center for Cancer Biology, VIB, Leuven, Belgium.
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium.
| |
Collapse
|
6
|
Fang X, Weng Y, Zheng X. Involvement of CCL2 and CH25H Genes and TNF signaling pathways in mast cell activation and pathogenesis of chronic spontaneous urticaria. Front Immunol 2023; 14:1247432. [PMID: 37646031 PMCID: PMC10461452 DOI: 10.3389/fimmu.2023.1247432] [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: 06/26/2023] [Accepted: 07/28/2023] [Indexed: 09/01/2023] Open
Abstract
Chronic spontaneous urticaria (CSU), a mast cell-driven disease, substantially affects the quality of life. While genetics affect CSU susceptibility and severity, the specific genetic factors associated with mast cell activation in CSU remain elusive. We aimed to identify key genetic factors and investigate their roles in CSU pathogenesis. Two gene expression datasets from the Gene Expression Omnibus were merged and validated using principal component analysis and boxplots. The merged dataset was subjected to limma and weighted gene co-expression network analyses. Genes whose expression correlated highly with CSU were identified and analyzed using Gene Set Enrichment Analysis (GSEA), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. As GSEA, GO, and KEGG analyses highlighted the importance of chemokine (C-C motif) ligand 2 (CCL2) and cholesterol 25-hydroxylase (CH25H) gene and tumor necrosis factor (TNF) signaling pathways in CSU; the three corresponding genes were knocked down in human mast cell line-1 (HMC-1), followed by incubation with thrombin to mimic CSU pathogenesis. CCL2, CH25H, and TNF knockdown reduced excitability and cytokine production in HMC-1. Our findings suggest that genes involved in the CCL2, CH25H, and TNF pathways play crucial roles in CSU pathogenesis, providing insights into potential therapeutic targets for CSU treatment.
Collapse
Affiliation(s)
- Xiaobin Fang
- Department of Anesthesiology/Critical Care Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Key Laboratory of Critical Care Medicine, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Yueyi Weng
- Department of Anesthesiology/Critical Care Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Key Laboratory of Critical Care Medicine, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Xiaochun Zheng
- Department of Anesthesiology, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University & Fujian Emergency Medical Center, Fujian Provincial Key Laboratory of Emergency Medicine, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Critical Medicine, Fuzhou, Fujian, China
- Fujian Provincial Co-constructed Laboratory of “Belt and Road”, Fuzhou, Fujian, China
| |
Collapse
|
7
|
Tang HW, Spirohn K, Hu Y, Hao T, Kovács IA, Gao Y, Binari R, Yang-Zhou D, Wan KH, Bader JS, Balcha D, Bian W, Booth BW, Coté AG, de Rouck S, Desbuleux A, Goh KY, Kim DK, Knapp JJ, Lee WX, Lemmens I, Li C, Li M, Li R, Lim HJ, Liu Y, Luck K, Markey D, Pollis C, Rangarajan S, Rodiger J, Schlabach S, Shen Y, Sheykhkarimli D, TeeKing B, Roth FP, Tavernier J, Calderwood MA, Hill DE, Celniker SE, Vidal M, Perrimon N, Mohr SE. Next-generation large-scale binary protein interaction network for Drosophila melanogaster. Nat Commun 2023; 14:2162. [PMID: 37061542 PMCID: PMC10105736 DOI: 10.1038/s41467-023-37876-0] [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: 08/17/2022] [Accepted: 04/04/2023] [Indexed: 04/17/2023] Open
Abstract
Generating reference maps of interactome networks illuminates genetic studies by providing a protein-centric approach to finding new components of existing pathways, complexes, and processes. We apply state-of-the-art methods to identify binary protein-protein interactions (PPIs) for Drosophila melanogaster. Four all-by-all yeast two-hybrid (Y2H) screens of > 10,000 Drosophila proteins result in the 'FlyBi' dataset of 8723 PPIs among 2939 proteins. Testing subsets of data from FlyBi and previous PPI studies using an orthogonal assay allows for normalization of data quality; subsequent integration of FlyBi and previous data results in an expanded binary Drosophila reference interaction network, DroRI, comprising 17,232 interactions among 6511 proteins. We use FlyBi data to generate an autophagy network, then validate in vivo using autophagy-related assays. The deformed wings (dwg) gene encodes a protein that is both a regulator and a target of autophagy. Altogether, these resources provide a foundation for building new hypotheses regarding protein networks and function.
Collapse
Affiliation(s)
- Hong-Wen Tang
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Division of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, 169610, Singapore
| | - Kerstin Spirohn
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Tong Hao
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - István A Kovács
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Department of Physics and Astronomy, Northwestern University, 633 Clark Street, Evanston, IL, 60208, USA
- Northwestern Institute on Complex Systems, Chambers Hall, Northwestern University, 600 Foster St, Evanston, IL, 60208, USA
| | - Yue Gao
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Richard Binari
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Donghui Yang-Zhou
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Kenneth H Wan
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
- High-Throughput Biology Center, Institute of Basic Biological Sciences, Johns Hopkins School of Medicine, 733 North Broadway, Baltimore, MD, 21205, USA
| | - Dawit Balcha
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Wenting Bian
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Benjamin W Booth
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Atina G Coté
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health, 600 University Ave, Toronto, ON, M5G 1×5, Canada
| | - Steffi de Rouck
- Cytokine Receptor Lab, VIB Center for Medical Biotechnology, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Alice Desbuleux
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Kah Yong Goh
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Dae-Kyum Kim
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, 665 Elm St., Buffalo, NY, 14203, USA
| | - Jennifer J Knapp
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health, 600 University Ave, Toronto, ON, M5G 1×5, Canada
| | - Wen Xing Lee
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Irma Lemmens
- Cytokine Receptor Lab, VIB Center for Medical Biotechnology, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Cathleen Li
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Mian Li
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Roujia Li
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health, 600 University Ave, Toronto, ON, M5G 1×5, Canada
| | - Hyobin Julianne Lim
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, 665 Elm St., Buffalo, NY, 14203, USA
| | - Yifang Liu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Katja Luck
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Dylan Markey
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Carl Pollis
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Sudharshan Rangarajan
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Jonathan Rodiger
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Sadie Schlabach
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Yun Shen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Dayag Sheykhkarimli
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health, 600 University Ave, Toronto, ON, M5G 1×5, Canada
| | - Bridget TeeKing
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Frederick P Roth
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health, 600 University Ave, Toronto, ON, M5G 1×5, Canada
- Department of Computer Science, University of Toronto, 40 St George St, Toronto, ON, M5S 2E4, Canada
| | - Jan Tavernier
- Cytokine Receptor Lab, VIB Center for Medical Biotechnology, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Michael A Calderwood
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - David E Hill
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Susan E Celniker
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA.
| | - Marc Vidal
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
- Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
| | - Stephanie E Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
| |
Collapse
|
8
|
Jeong BR, Jang J, Jin E. Genome engineering via gene editing technologies in microalgae. BIORESOURCE TECHNOLOGY 2023; 373:128701. [PMID: 36746216 DOI: 10.1016/j.biortech.2023.128701] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
CRISPR-Cas has revolutionized genetic modification with its comparative simplicity and accuracy, and it can be used even at the genomic level. Microalgae are excellent feedstocks for biofuels and nutraceuticals because they contain high levels of fatty acids, carotenoids, and other metabolites; however, genome engineering for microalgae is not yet as developed as for other model organisms. Microalgal engineering at the genetic and metabolic levels is relatively well established, and a few genomic resources are available. Their genomic information was used for a "safe harbor" site for stable transgene expression in microalgae. This review proposes further genome engineering schemes including the construction of sgRNA libraries, pan-genomic and epigenomic resources, and mini-genomes, which can together be developed into synthetic biology for carbon-based engineering in microalgae. Acetyl-CoA is at the center of carbon metabolic pathways and is further reviewed for the production of molecules including terpenoids in microalgae.
Collapse
Affiliation(s)
- Byeong-Ryool Jeong
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Junhwan Jang
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - EonSeon Jin
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea; Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul 04763, Korea.
| |
Collapse
|
9
|
Potential of siRNA-Bearing Subtilosomes in the Treatment of Diethylnitrosamine-Induced Hepatocellular Carcinoma. Molecules 2023; 28:molecules28052191. [PMID: 36903437 PMCID: PMC10004640 DOI: 10.3390/molecules28052191] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/02/2023] Open
Abstract
Therapeutics, based on small interfering RNA (siRNA), have demonstrated tremendous potential for treating cancer. However, issues such as non-specific targeting, premature degradation, and the intrinsic toxicity of the siRNA, have to be solved before they are ready for use in translational medicines. To address these challenges, nanotechnology-based tools might help to shield siRNA and ensure its specific delivery to the target site. Besides playing a crucial role in prostaglandin synthesis, the cyclo-oxygenase-2 (COX-2) enzyme has been reported to mediate carcinogenesis in various types of cancer, including hepatocellular carcinoma (HCC). We encapsulated COX-2-specific siRNA in Bacillus subtilis membrane lipid-based liposomes (subtilosomes) and evaluated their potential in the treatment of diethylnitrosamine (DEN)-induced hepatocellular carcinoma. Our findings suggested that the subtilosome-based formulation was stable, releasing COX-2 siRNA in a sustained manner, and has the potential to abruptly release encapsulated material at acidic pH. The fusogenic property of subtilosomes was revealed by FRET, fluorescence dequenching, content-mixing assay, etc. The subtilosome-based siRNA formulation was successful in inhibiting TNF-α expression in the experimental animals. The apoptosis study indicated that the subtilosomized siRNA inhibits DEN-induced carcinogenesis more effectively than free siRNA. The as-developed formulation also suppressed COX-2 expression, which in turn up-regulated the expression of wild-type p53 and Bax on one hand and down-regulated Bcl-2 expression on the other. The survival data established the increased efficacy of subtilosome-encapsulated COX-2 siRNA against hepatocellular carcinoma.
Collapse
|
10
|
Avar M, Heinzer D, Thackray AM, Liu Y, Hruska‐Plochan M, Sellitto S, Schaper E, Pease DP, Yin J, Lakkaraju AKK, Emmenegger M, Losa M, Chincisan A, Hornemann S, Polymenidou M, Bujdoso R, Aguzzi A. An arrayed genome-wide perturbation screen identifies the ribonucleoprotein Hnrnpk as rate-limiting for prion propagation. EMBO J 2022; 41:e112338. [PMID: 36254605 PMCID: PMC9713719 DOI: 10.15252/embj.2022112338] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/17/2022] [Accepted: 09/22/2022] [Indexed: 01/15/2023] Open
Abstract
A defining characteristic of mammalian prions is their capacity for self-sustained propagation. Theoretical considerations and experimental evidence suggest that prion propagation is modulated by cell-autonomous and non-autonomous modifiers. Using a novel quantitative phospholipase protection assay (QUIPPER) for high-throughput prion measurements, we performed an arrayed genome-wide RNA interference (RNAi) screen aimed at detecting cellular host-factors that can modify prion propagation. We exposed prion-infected cells in high-density microplates to 35,364 ternary pools of 52,746 siRNAs targeting 17,582 genes representing the majority of the mouse protein-coding transcriptome. We identified 1,191 modulators of prion propagation. While 1,151 modified the expression of both the pathological prion protein, PrPSc , and its cellular counterpart, PrPC , 40 genes selectively affected PrPSc . Of the latter 40 genes, 20 augmented prion production when suppressed. A prominent limiter of prion propagation was the heterogeneous nuclear ribonucleoprotein Hnrnpk. Psammaplysene A (PSA), which binds Hnrnpk, reduced prion levels in cultured cells and protected them from cytotoxicity. PSA also reduced prion levels in infected cerebellar organotypic slices and alleviated locomotor deficits in prion-infected Drosophila melanogaster expressing ovine PrPC . Hence, genome-wide QUIPPER-based perturbations can discover actionable cellular pathways involved in prion propagation. Further, the unexpected identification of a prion-controlling ribonucleoprotein suggests a role for RNA in the generation of infectious prions.
Collapse
Affiliation(s)
- Merve Avar
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | - Daniel Heinzer
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | - Alana M Thackray
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Yingjun Liu
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | | | - Stefano Sellitto
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | - Elke Schaper
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | - Daniel P Pease
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | - Jiang‐An Yin
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | | | - Marc Emmenegger
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | - Marco Losa
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | - Andra Chincisan
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | - Simone Hornemann
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| | | | - Raymond Bujdoso
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Adriano Aguzzi
- Institute of NeuropathologyUniversity of ZurichZurichSwitzerland
| |
Collapse
|
11
|
Lyu F, An S, Kobayashi Y, Nomura K, Baba R, Abe N, Hiraoka H, Hashiya F, Shu Z, Ui-Tei K, Kimura Y, Abe H. A 2'-modified uridine analog, 2'-O-(methylthiomethoxy)methyl uridine, for siRNA applications. Bioorg Med Chem Lett 2022; 74:128939. [PMID: 35964844 DOI: 10.1016/j.bmcl.2022.128939] [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: 05/15/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 11/18/2022]
Abstract
The medicinal applications of siRNAs have been intensively examined but are still hindered by their low molecular stability under biological conditions and off-target effects, etc. The introduction of chemical modifications to the nucleoside is a promising strategy for solving these limitations. Herein, we describe the development of a new uridine analog, U*, that has a (methylthiomethoxy)methoxy group at the 2' position. The phosphoramidite reagent corresponding to U* was easily synthesized and the RNA oligonucleotides containing U* were stably prepared using a standard protocol for oligonucleotide synthesis. The introduction of U* into the siRNA resulted in positive or negative effects on the targeted gene silencing in a position-dependent manner, and the positive effects were attributed to the improved stability under biological conditions. The thermodynamic analysis of the U*-modified RNAs revealed a slight destabilization of the dsRNA, based depending on which U was strategically utilized to restrain the off-target effects of the siRNA. This study describes a rare example of nucleoside analogs with a large substitution at the 2'-position in the context of an siRNA application and is informative for the development of other analogs to further improve the molecular properties of siRNAs for medicinal applications.
Collapse
Affiliation(s)
- Fangjie Lyu
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Seongjin An
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
| | - Yoshiaki Kobayashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Kohei Nomura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Rintaro Baba
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Naoko Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Haruka Hiraoka
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Zhaoma Shu
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Kumiko Ui-Tei
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yasuaki Kimura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan; Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan; CREST, Japan Science and Technology Agency, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan; Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| |
Collapse
|
12
|
Time-Resolved Fluorescence Microscopy Screens on Host Protein Subversion During Bacterial Cell Invasion. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2523:113-131. [PMID: 35759194 DOI: 10.1007/978-1-0716-2449-4_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Intracellular bacterial pathogens have evolved a plethora of strategies to invade eukaryotic cells. By manipulating host signaling pathways, in particular vesicular trafficking, these microbes subvert host functions to promote their internalization and to establish an intracellular niche. During these events, host endomembrane compartments are dynamically reorganized. Shigella flexneri, the causative agent of bacillary dysentery, recruits components of the host recycling pathway and the exocyst of non-phagocytic enterocytes in the vicinity of its entry site to facilitate its access to the host cytosol. These factors are either dynamically tethered to in situ formed macropinosomes or to the bacteria-containing vacuole itself. The underlying interactions cannot readily be monitored as individual bacterial infection events take place without synchronicity using cellular infection models. Therefore, time-resolved screens by fluorescence microscopy represent a powerful tool for the study of host subversion. Such screens can be performed with libraries of fluorescently tagged host factors. Using the cytosolic pathogenic agent Shigella flexneri as a model, we provide detailed protocols for such medium-to-high throughput multidimensional imaging screening of the dynamic host-pathogen cross talk. Our workflow is designed to be easily adapted for the study of different host factor libraries and different pathogen models.
Collapse
|
13
|
Yue X, Liang Y, Wei Z, Lv J, Cai Y, Fan X, Zhang W, Chen J. Genome-wide in vitro and in vivo RNAi screens reveal Fer3 to be an important regulator of kkv transcription in Drosophila. INSECT SCIENCE 2022; 29:614-630. [PMID: 34351065 DOI: 10.1111/1744-7917.12954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/24/2021] [Accepted: 07/11/2021] [Indexed: 06/13/2023]
Abstract
Krotzkopf verkehrt (kkv) is a key enzyme that catalyzes the synthesis of chitin, an important component of the Drosophila epidermis, trachea, and other tissues. Here, we report the use of comprehensive RNA interference (RNAi) analyses to search for kkv transcriptional regulators. A cell-based RNAi screen identified 537 candidate kkv regulators on a genome-wide scale. Subsequent use of transgenic Drosophila lines expressing RNAi constructs enabled in vivo validation, and we identified six genes as potential kkv transcriptional regulators. Weakening of the kkvDsRed signal, an in vivo reporter indicating kkv promoter activity, was observed when the expression of Akirin, NFAT, 48 related 3 (Fer3), or Autophagy-related 101(Atg101) was knocked down in Drosophila at the 3rd-instar larval stage; whereas we observed disoriented taenidial folds on larval tracheae when Lines (lin) or Autophagy-related 3 (Atg3) was knocked down in the tracheae. Fer3, in particular, has been shown to be an important factor in the activation of kkv transcription via specific binding with the kkv promoter. The genes involved in the chitin synthesis pathway were widely affected by the downregulation of Fer3. Furthermore, Atg101, Atg3, Akirin, Lin, NFAT, Pnr, and Abd-A showed that the potential complex mechanism of kkv transcription is regulated by an interaction network with bithorax complex components. Our study revealed the hitherto unappreciated diversity of modulators impinging on kkv transcription and opens new avenues in the study of kkv regulation and chitin biosynthesis.
Collapse
Affiliation(s)
- Xiangzhao Yue
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- College of Life Sciences, Shangrao Normal University, Shangrao, Jiangxi Province, China
| | - Yongkang Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhishuang Wei
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jun Lv
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yongjin Cai
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaobin Fan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jie Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
14
|
Fischer F, Benner C, Goyala A, Grigolon G, Vitiello D, Wu J, Zarse K, Ewald CY, Ristow M. Ingestion of single guide RNAs induces gene overexpression and extends lifespan in Caenorhabditis elegans via CRISPR activation. J Biol Chem 2022; 298:102085. [PMID: 35636511 PMCID: PMC9243178 DOI: 10.1016/j.jbc.2022.102085] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/21/2022] Open
Abstract
Inhibition of gene expression in Caenorhabditis elegans, a versatile model organism for studying the genetics of development and aging, is achievable by feeding nematodes with bacteria expressing specific dsRNAs. Overexpression of hypoxia-inducible factor 1 (hif-1) or heat-shock factor 1 (hsf-1) by conventional transgenesis has previously been shown to promote nematodal longevity. However, it is unclear whether other methods of gene overexpression are feasible, particularly with the advent of CRISPR-based techniques. Here, we show that feeding C. elegans engineered to stably express a Cas9-derived synthetic transcription factor with bacteria expressing promoter-specific single guide RNAs (sgRNAs) also allows activation of gene expression. We demonstrate that CRISPR activation via ingested sgRNAs specific for the respective promoter regions of hif-1 or hsf-1 increases gene expression and extends lifespan of C. elegans. Furthermore, and as an in silico resource for future studies aiming to use CRISPR activation in C. elegans, we provide predicted promoter-specific sgRNA target sequences for >13,000 C. elegans genes with experimentally defined transcription start sites. We anticipate that the approach and components described herein will help to facilitate genome-wide gene overexpression studies, for example, to identify modulators of aging or other phenotypes of interest, by enabling induction of transcription by feeding of sgRNA-expressing bacteria to nematodes.
Collapse
Affiliation(s)
- Fabian Fischer
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland.
| | - Christoph Benner
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland; Science and Policy Program, Life Science Zurich Graduate School, Zurich, Switzerland
| | - Anita Goyala
- Extracellular Matrix Regeneration Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Giovanna Grigolon
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Davide Vitiello
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - JiaYee Wu
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Kim Zarse
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland; Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Experimental Endocrinology and Diabetology, Berlin, Germany
| | - Collin Y Ewald
- Extracellular Matrix Regeneration Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Michael Ristow
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland; Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Experimental Endocrinology and Diabetology, Berlin, Germany.
| |
Collapse
|
15
|
Brooks IR, Garrone CM, Kerins C, Kiar CS, Syntaka S, Xu JZ, Spagnoli FM, Watt FM. Functional genomics and the future of iPSCs in disease modeling. Stem Cell Reports 2022; 17:1033-1047. [PMID: 35487213 PMCID: PMC9133703 DOI: 10.1016/j.stemcr.2022.03.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 10/28/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) are valuable in disease modeling because of their potential to expand and differentiate into virtually any cell type and recapitulate key aspects of human biology. Functional genomics are genome-wide studies that aim to discover genotype-phenotype relationships, thereby revealing the impact of human genetic diversity on normal and pathophysiology. In this review, we make the case that human iPSCs (hiPSCs) are a powerful tool for functional genomics, since they provide an in vitro platform for the study of population genetics. We describe cutting-edge tools and strategies now available to researchers, including multi-omics technologies, advances in hiPSC culture techniques, and innovations in drug development. Functional genomics approaches based on hiPSCs hold great promise for advancing drug discovery, disease etiology, and the impact of genetic variation on human biology.
Collapse
Affiliation(s)
- Imogen R Brooks
- St John's Institute of Dermatology, King's College London, London, SE1 9RT, UK
| | - Cristina M Garrone
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK
| | - Caoimhe Kerins
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, UK
| | - Cher Shen Kiar
- Peter Gorer Department of Immunobiology, King's College London, London, SE1 9RT, UK
| | - Sofia Syntaka
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK
| | - Jessie Z Xu
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK
| | - Francesca M Spagnoli
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK.
| | - Fiona M Watt
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK; Directors' Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| |
Collapse
|
16
|
Murray J, Bergeron HC, Jones LP, Reener ZB, Martin DE, Sancilio FD, Tripp RA. Probenecid Inhibits Respiratory Syncytial Virus (RSV) Replication. Viruses 2022; 14:v14050912. [PMID: 35632652 PMCID: PMC9147281 DOI: 10.3390/v14050912] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 01/27/2023] Open
Abstract
RNA viruses like SARS-CoV-2, influenza virus, and respiratory syncytial virus (RSV) are dependent on host genes for replication. We investigated if probenecid, an FDA-approved and safe urate-lowering drug that inhibits organic anion transporters (OATs) has prophylactic or therapeutic efficacy to inhibit RSV replication in three epithelial cell lines used in RSV studies, i.e., Vero E6 cells, HEp-2 cells, and in primary normal human bronchoepithelial (NHBE) cells, and in BALB/c mice. The studies showed that nanomolar concentrations of all probenecid regimens prevent RSV strain A and B replication in vitro and RSV strain A in vivo, representing a potential prophylactic and chemotherapeutic for RSV.
Collapse
Affiliation(s)
- Jackelyn Murray
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA; (J.M.); (H.C.B.); (L.P.J.); (Z.B.R.)
| | - Harrison C. Bergeron
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA; (J.M.); (H.C.B.); (L.P.J.); (Z.B.R.)
| | - Les P. Jones
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA; (J.M.); (H.C.B.); (L.P.J.); (Z.B.R.)
| | - Zachary Beau Reener
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA; (J.M.); (H.C.B.); (L.P.J.); (Z.B.R.)
| | | | - Fred D. Sancilio
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, FL 33431, USA;
| | - Ralph A. Tripp
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA; (J.M.); (H.C.B.); (L.P.J.); (Z.B.R.)
- TrippBio, Inc., Jacksonville, FL 32256, USA;
- Correspondence: ; Tel.: +1-706-542-1557
| |
Collapse
|
17
|
An E3 Ubiquitin Ligase Scaffolding Protein Is Proviral during Chikungunya Virus Infection in Aedes aegypti. Microbiol Spectr 2022; 10:e0059522. [PMID: 35435754 PMCID: PMC9241663 DOI: 10.1128/spectrum.00595-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Chikungunya virus (CHIKV) is a reemerging alphavirus causing chikungunya disease (CHIKD) and is transmitted to humans by Aedes mosquitoes. The virus establishes an intricate balance of cellular interactions that ultimately helps in its replication and dodges cellular immune response. In an attempt to identify cellular host factors required during CHIKV replication in Aag2 cells, we performed global transcriptomics of CHIKV-infected Aag2 cells, and further, we compared this library with the Drosophila RNAi Screening Center (DRSC) database and identified transcripts that were regulated in Aedes aegypti during CHIKV infection. These analyses revealed specific pathways, such as ubiquitin-related pathways, proteolysis pathways, protein catabolic processes, protein modification, and cellular protein metabolic processes, involved during replication of the virus. Loss-of-function assays of selected candidates revealed their proviral or antiviral characteristics upon CHIKV infection in A. aegypti-derived Aag2 cells. Further validations identified that the ubiquitin proteasomal pathway is required for CHIKV infection in A. aegypti and that an important member of this family of proteins, namely, AeCullin-3 (Aedes ortholog of human cullin-3), is a proviral host factor of CHIKV replication in Aag2 cells. IMPORTANCE Arboviruses cause several diseases in humans and livestock. Vector control is the main strategy for controlling diseases transmitted by mosquitoes. In this context, it becomes paramount to understand how the viruses replicate in the vector for designing better transmission blocking strategies. We obtained the global transcriptome signature of A. aegypti cells during CHIKV infection, and in order to obtain the maximum information from these data sets, we further utilized the well-characterized Drosophila system and arrived upon a set of transcripts and their pathways that affect A. aegypti cells during CHIKV infection. These analyses and further validations reveal that important pathways related to protein degradation are actively involved during CHIKV infection in A. aegypti and are mainly proviral. Targeting these molecules may provide novel approaches for blocking CHIKV replication in A. aegypti.
Collapse
|
18
|
OUP accepted manuscript. Brief Funct Genomics 2022; 21:243-269. [DOI: 10.1093/bfgp/elac007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 11/14/2022] Open
|
19
|
Wimmer E, Zink IA, Schleper C. Reprogramming CRISPR-Mediated RNA Interference for Silencing of Essential Genes in Sulfolobales. Methods Mol Biol 2022; 2522:177-201. [PMID: 36125750 DOI: 10.1007/978-1-0716-2445-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The manipulation of gene expression levels in vivo is often key to elucidating gene function and regulatory network interactions, especially when it comes to the investigation of essential genes that cannot be deleted from the model organism's genome. Several techniques have been developed for prokaryotes that allow to interfere with transcription initiation of specific genes by blocking or modifying promoter regions. However, a tool functionally similar to RNAi used in eukaryotes to efficiently degrade mRNA posttranscriptionally did not exist until recently. Type III CRISPR-Cas systems use small RNAs (crRNAs) that guide effector complexes (encoded by cas genes) which act as site-specific RNA endonuclease and can thus be harnessed for targeted posttranscriptional gene silencing. Guide RNAs complementary to the desired target mRNA that, in addition, exhibit complementarity to repeat sequences found in the CRISPR arrays, effectively suppress unspecific DNA and RNA activities of the CRISPR-Cas complexes. Here we describe the use of endogenous type III CRISPR-Cas systems in two model organisms of Crenarchaeota, Saccharolobus solfataricus and Sulfolobus acidocaldarius.
Collapse
Affiliation(s)
- Erika Wimmer
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria
| | - Isabelle Anna Zink
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria.
| |
Collapse
|
20
|
Saito K. Drosophila Genetic Resources for Elucidating piRNA Pathway. Methods Mol Biol 2022; 2509:135-141. [PMID: 35796961 DOI: 10.1007/978-1-0716-2380-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Emerging evidence indicates that PIWI proteins, in collaboration with PIWI-interacting RNAs (piRNAs), play a critical role in gonadal development and retrotransposon silencing in metazoans. Numerous studies have characterized the mechanism of retrotransposon silencing and identified dozens of factors involved in the piRNA pathways. Drosophila is an attractive model organism for piRNA studies due to its great availability of genetic tools and the low cost of maintenance. Here, I introduce Drosophila genetic resources and techniques valuable for studying piRNA pathway genes via their impact on retrotransposon silencing.
Collapse
Affiliation(s)
- Kuniaki Saito
- Invertebrate Genetics Laboratory, Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka, Japan.
- Division of Invertebrate Genetics, Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan.
| |
Collapse
|
21
|
Exploring liver cancer biology through functional genetic screens. Nat Rev Gastroenterol Hepatol 2021; 18:690-704. [PMID: 34163045 DOI: 10.1038/s41575-021-00465-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/06/2021] [Indexed: 02/06/2023]
Abstract
As the fourth leading cause of cancer-related death in the world, liver cancer poses a major threat to human health. Although a growing number of therapies have been approved for the treatment of hepatocellular carcinoma in the past few years, most of them only provide a limited survival benefit. Therefore, an urgent need exists to identify novel targetable vulnerabilities and powerful drug combinations for the treatment of liver cancer. The advent of functional genetic screening has contributed to the advancement of liver cancer biology, uncovering many novel genes involved in tumorigenesis and cancer progression in a high-throughput manner. In addition, this unbiased screening platform also provides an efficient tool for the exploration of the mechanisms involved in therapy resistance as well as identifying potential targets for therapy. In this Review, we describe how functional screens can help to deepen our understanding of liver cancer and guide the development of new therapeutic strategies.
Collapse
|
22
|
Orthogonal genome-wide screens of bat cells identify MTHFD1 as a target of broad antiviral therapy. Proc Natl Acad Sci U S A 2021; 118:2104759118. [PMID: 34544865 DOI: 10.1073/pnas.2104759118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2021] [Indexed: 11/18/2022] Open
Abstract
Bats are responsible for the zoonotic transmission of several major viral diseases, including those leading to the 2003 SARS outbreak and likely the ongoing COVID-19 pandemic. While comparative genomics studies have revealed characteristic adaptations of the bat innate immune system, functional genomic studies are urgently needed to provide a foundation for the molecular dissection of the viral tolerance in bats. Here we report the establishment of genome-wide RNA interference (RNAi) and CRISPR libraries for the screening of the model megabat, Pteropus alecto. We used the complementary RNAi and CRISPR libraries to interrogate P. alecto cells for infection with two different viruses: mumps virus and influenza A virus, respectively. Independent screening results converged on the endocytosis pathway and the protein secretory pathway as required for both viral infections. Additionally, we revealed a general dependence of the C1-tetrahydrofolate synthase gene, MTHFD1, for viral replication in bat cells and human cells. The MTHFD1 inhibitor, carolacton, potently blocked replication of several RNA viruses, including SARS-CoV-2. We also discovered that bats have lower expression levels of MTHFD1 than humans. Our studies provide a resource for systematic inquiry into the genetic underpinnings of bat biology and a potential target for developing broad-spectrum antiviral therapy.
Collapse
|
23
|
Abstract
The past 25 years of genomics research first revealed which genes are encoded by the human genome and then a detailed catalogue of human genome variation associated with many diseases. Despite this, the function of many genes and gene regulatory elements remains poorly characterized, which limits our ability to apply these insights to human disease. The advent of new CRISPR functional genomics tools allows for scalable and multiplexable characterization of genes and gene regulatory elements encoded by the human genome. These approaches promise to reveal mechanisms of gene function and regulation, and to enable exploration of how genes work together to modulate complex phenotypes.
Collapse
|
24
|
Inal MA, Bui KC, Marar A, Li S, Kner P, Kamiyama D. Imaging of In Vitro and In Vivo Neurons in Drosophila Using Stochastic Optical Reconstruction Microscopy. Curr Protoc 2021; 1:e203. [PMID: 34289261 DOI: 10.1002/cpz1.203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Drosophila melanogaster brain comprises different neuronal cell types that interconnect with precise patterns of synaptic connections. These patterns are essential for the normal function of the brain. To understand the connectivity patterns requires characterizing them at single-cell resolution, for which a fluorescence microscope becomes an indispensable tool. Additionally, because the neurons connect at the nanoscale, the investigation often demands super-resolution microscopy. Here, we adopt one super-resolution microscopy technique, called stochastic optical reconstruction microscopy (STORM), improving the lateral and axial resolution to ∼20 nm. This article extensively describes our methods along with considerations for sample preparation of neurons in vitro and in vivo, conjugation of dyes to antibodies, immunofluorescence labeling, and acquisition and processing of STORM data. With these tools and techniques, we open up the potential to investigate cell-cell interactions using STORM in the Drosophila nervous system. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Preparation of Drosophila primary neuronal culture and embryonic fillets Basic Protocol 2: Immunofluorescence labeling of samples Basic Protocol 3: Single-molecule fluorescence imaging Basic Protocol 4: Localization and visualization of single-molecule data Supporting Protocol: Conjugation of antibodies with STORM-compatible dyes.
Collapse
Affiliation(s)
- Melissa Ana Inal
- Department of Cellular Biology, University of Georgia, Athens, Georgia
| | - Kathy Clara Bui
- Department of Cellular Biology, University of Georgia, Athens, Georgia
| | - Abhijit Marar
- School of Electrical and Computer Engineering, University of Georgia, Athens, Georgia
| | - Shaoheng Li
- School of Electrical and Computer Engineering, University of Georgia, Athens, Georgia
| | - Peter Kner
- School of Electrical and Computer Engineering, University of Georgia, Athens, Georgia
| | - Daichi Kamiyama
- Department of Cellular Biology, University of Georgia, Athens, Georgia
| |
Collapse
|
25
|
Mattiazzi Usaj M, Yeung CHL, Friesen H, Boone C, Andrews BJ. Single-cell image analysis to explore cell-to-cell heterogeneity in isogenic populations. Cell Syst 2021; 12:608-621. [PMID: 34139168 DOI: 10.1016/j.cels.2021.05.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/26/2021] [Accepted: 05/12/2021] [Indexed: 12/26/2022]
Abstract
Single-cell image analysis provides a powerful approach for studying cell-to-cell heterogeneity, which is an important attribute of isogenic cell populations, from microbial cultures to individual cells in multicellular organisms. This phenotypic variability must be explained at a mechanistic level if biologists are to fully understand cellular function and address the genotype-to-phenotype relationship. Variability in single-cell phenotypes is obscured by bulk readouts or averaging of phenotypes from individual cells in a sample; thus, single-cell image analysis enables a higher resolution view of cellular function. Here, we consider examples of both small- and large-scale studies carried out with isogenic cell populations assessed by fluorescence microscopy, and we illustrate the advantages, challenges, and the promise of quantitative single-cell image analysis.
Collapse
Affiliation(s)
- Mojca Mattiazzi Usaj
- Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Clarence Hue Lok Yeung
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Helena Friesen
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Charles Boone
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; RIKEN Centre for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Brenda J Andrews
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada.
| |
Collapse
|
26
|
Zink IA, Fouqueau T, Tarrason Risa G, Werner F, Baum B, Bläsi U, Schleper C. Comparative CRISPR type III-based knockdown of essential genes in hyperthermophilic Sulfolobales and the evasion of lethal gene silencing. RNA Biol 2021; 18:421-434. [PMID: 32957821 PMCID: PMC7951960 DOI: 10.1080/15476286.2020.1813411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/22/2020] [Accepted: 08/16/2020] [Indexed: 02/07/2023] Open
Abstract
CRISPR type III systems, which are abundantly found in archaea, recognize and degrade RNA in their specific response to invading nucleic acids. Therefore, these systems can be harnessed for gene knockdown technologies even in hyperthermophilic archaea to study essential genes. We show here the broader usability of this posttranscriptional silencing technology by expanding the application to further essential genes and systematically analysing and comparing silencing thresholds and escape mutants. Synthetic guide RNAs expressed from miniCRISPR cassettes were used to silence genes involved in cell division (cdvA), transcription (rpo8), and RNA metabolism (smAP2) of the two crenarchaeal model organisms Saccharolobus solfataricus and Sulfolobus acidocaldarius. Results were systematically analysed together with those obtained from earlier experiments of cell wall biogenesis (slaB) and translation (aif5A). Comparison of over 100 individual transformants revealed gene-specific silencing maxima ranging between 40 and 75%, which induced specific knockdown phenotypes leading to growth retardation. Exceedance of this threshold by strong miniCRISPR constructs was not tolerated and led to specific mutation of the silencing miniCRISPR array and phenotypical reversion of cultures. In two thirds of sequenced reverted cultures, the targeting spacers were found to be precisely excised from the miniCRISPR array, indicating a still hypothetical, but highly active recombination system acting on the dynamics of CRISPR spacer arrays. Our results indicate that CRISPR type III - based silencing is a broadly applicable tool to study in vivo functions of essential genes in Sulfolobales which underlies a specific mechanism to avoid malignant silencing overdose.
Collapse
Affiliation(s)
- Isabelle Anna Zink
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Thomas Fouqueau
- RNAP Lab, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Gabriel Tarrason Risa
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Finn Werner
- RNAP Lab, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Buzz Baum
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Udo Bläsi
- Max Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| |
Collapse
|
27
|
Duan L, Hu M, Tamm JA, Grinberg YY, Shen F, Chai Y, Xi H, Gibilisco L, Ravikumar B, Gautam V, Karran E, Townsend M, Talanian RV. Arrayed CRISPR reveals genetic regulators of tau aggregation, autophagy and mitochondria in Alzheimer's disease model. Sci Rep 2021; 11:2879. [PMID: 33536571 PMCID: PMC7859211 DOI: 10.1038/s41598-021-82658-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/22/2021] [Indexed: 01/30/2023] Open
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disease with poor prognosis. New options for drug discovery targets are needed. We developed an imaging based arrayed CRISPR method to interrogate the human genome for modulation of in vitro correlates of AD features, and used this to assess 1525 human genes related to tau aggregation, autophagy and mitochondria. This work revealed (I) a network of tau aggregation modulators including the NF-κB pathway and inflammatory signaling, (II) a correlation between mitochondrial morphology, respiratory function and transcriptomics, (III) machine learning predicted novel roles of genes and pathways in autophagic processes and (IV) individual gene function inferences and interactions among biological processes via multi-feature clustering. These studies provide a platform to interrogate underexplored aspects of AD biology and offer several specific hypotheses for future drug discovery efforts.
Collapse
Affiliation(s)
- Lishu Duan
- Cambridge Research Center, AbbVie, 200 Sidney Street, Cambridge, MA, 02139, USA.
| | - Mufeng Hu
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | - Joseph A Tamm
- Cambridge Research Center, AbbVie, 200 Sidney Street, Cambridge, MA, 02139, USA
| | - Yelena Y Grinberg
- Cambridge Research Center, AbbVie, 200 Sidney Street, Cambridge, MA, 02139, USA
| | - Fang Shen
- Cambridge Research Center, AbbVie, 200 Sidney Street, Cambridge, MA, 02139, USA
| | - Yating Chai
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | - Hualin Xi
- Cambridge Research Center, AbbVie, 200 Sidney Street, Cambridge, MA, 02139, USA
| | - Lauren Gibilisco
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | - Brinda Ravikumar
- Cambridge Research Center, AbbVie, 200 Sidney Street, Cambridge, MA, 02139, USA
| | - Vivek Gautam
- Cambridge Research Center, AbbVie, 200 Sidney Street, Cambridge, MA, 02139, USA
| | - Eric Karran
- Cambridge Research Center, AbbVie, 200 Sidney Street, Cambridge, MA, 02139, USA
| | - Matthew Townsend
- Cambridge Research Center, AbbVie, 200 Sidney Street, Cambridge, MA, 02139, USA
| | - Robert V Talanian
- Cambridge Research Center, AbbVie, 200 Sidney Street, Cambridge, MA, 02139, USA
| |
Collapse
|
28
|
DGK and DZHK position paper on genome editing: basic science applications and future perspective. Basic Res Cardiol 2021; 116:2. [PMID: 33449167 PMCID: PMC7810637 DOI: 10.1007/s00395-020-00839-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022]
Abstract
For a long time, gene editing had been a scientific concept, which was limited to a few applications. With recent developments, following the discovery of TALEN zinc-finger endonucleases and in particular the CRISPR/Cas system, gene editing has become a technique applicable in most laboratories. The current gain- and loss-of function models in basic science are revolutionary as they allow unbiased screens of unprecedented depth and complexity and rapid development of transgenic animals. Modifications of CRISPR/Cas have been developed to precisely interrogate epigenetic regulation or to visualize DNA complexes. Moreover, gene editing as a clinical treatment option is rapidly developing with first trials on the way. This article reviews the most recent progress in the field, covering expert opinions gathered during joint conferences on genome editing of the German Cardiac Society (DGK) and the German Center for Cardiovascular Research (DZHK). Particularly focusing on the translational aspect and the combination of cellular and animal applications, the authors aim to provide direction for the development of the field and the most frequent applications with their problems.
Collapse
|
29
|
De Cesco S, Davis JB, Brennan PE. TargetDB: A target information aggregation tool and tractability predictor. PLoS One 2020; 15:e0232644. [PMID: 32877430 PMCID: PMC7467329 DOI: 10.1371/journal.pone.0232644] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022] Open
Abstract
When trying to identify new potential therapeutic protein targets, access to data and knowledge is increasingly important. In a field where new resources and data sources become available every day, it is crucial to be able to take a step back and look at the wider picture in order to identify potential drug targets. While this task is routinely performed by bespoke literature searches, it is often time-consuming and lacks uniformity when comparing multiple targets at one time. To address this challenge, we developed TargetDB, a tool that aggregates public information available on given target(s) (links to disease, safety, 3D structures, ligandability, novelty, etc.) and assembles it in an easy to read output ready for the researcher to analyze. In addition, we developed a target scoring system based on the desirable attributes of good therapeutic targets and machine learning classification system to categorize novel targets as having promising or challenging tractrability. In this manuscript, we present the methodology used to develop TargetDB as well as test cases.
Collapse
Affiliation(s)
- Stephane De Cesco
- Nuffield Department of Medicine, ARUK Oxford Drug Discovery Institute, Target Discovery Institute, University of Oxford, Oxford, United-Kingdom
- * E-mail: (PEB); (SDC)
| | - John B. Davis
- Nuffield Department of Medicine, ARUK Oxford Drug Discovery Institute, Target Discovery Institute, University of Oxford, Oxford, United-Kingdom
| | - Paul E. Brennan
- Nuffield Department of Medicine, ARUK Oxford Drug Discovery Institute, Target Discovery Institute, University of Oxford, Oxford, United-Kingdom
- * E-mail: (PEB); (SDC)
| |
Collapse
|
30
|
Mast FD, Navare AT, van der Sloot AM, Coulombe-Huntington J, Rout MP, Baliga NS, Kaushansky A, Chait BT, Aderem A, Rice CM, Sali A, Tyers M, Aitchison JD. Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality. J Cell Biol 2020; 219:152015. [PMID: 32785687 PMCID: PMC7659715 DOI: 10.1083/jcb.202006159] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023] Open
Abstract
With the rapid global spread of SARS-CoV-2, we have become acutely aware of the inadequacies of our ability to respond to viral epidemics. Although disrupting the viral life cycle is critical for limiting viral spread and disease, it has proven challenging to develop targeted and selective therapeutics. Synthetic lethality offers a promising but largely unexploited strategy against infectious viral disease; as viruses infect cells, they abnormally alter the cell state, unwittingly exposing new vulnerabilities in the infected cell. Therefore, we propose that effective therapies can be developed to selectively target the virally reconfigured host cell networks that accompany altered cellular states to cripple the host cell that has been converted into a virus factory, thus disrupting the viral life cycle.
Collapse
Affiliation(s)
- Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - Arti T Navare
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - Almer M van der Sloot
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Canada
| | | | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY
| | | | - Alexis Kaushansky
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA.,Department of Pediatrics, University of Washington, Seattle, WA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Alan Aderem
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA.,Department of Pediatrics, University of Washington, Seattle, WA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Canada
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA.,Department of Pediatrics, University of Washington, Seattle, WA.,Department of Biochemistry, University of Washington, Seattle, WA
| |
Collapse
|
31
|
Haley B, Roudnicky F. Functional Genomics for Cancer Drug Target Discovery. Cancer Cell 2020; 38:31-43. [PMID: 32442401 DOI: 10.1016/j.ccell.2020.04.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 02/06/2020] [Accepted: 04/08/2020] [Indexed: 12/15/2022]
Abstract
Functional genomics describes a field of biology that uses a range of approaches for assessing gene function with high-throughput molecular, genetic, and cellular technologies. The near limitless potential for applying these concepts to study the activities of all genetic loci has completely upended how today's cancer biologists tackle drug target discovery. We provide an overview of contemporary functional genomics platforms, highlighting areas of distinction and complementarity across technologies, so as to aid in the development or interpretation of cancer-focused screening efforts.
Collapse
Affiliation(s)
- Benjamin Haley
- Molecular Biology Department, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Filip Roudnicky
- Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel 4070, Switzerland.
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Kumar A, Baruah A, Tomioka M, Iino Y, Kalita MC, Khan M. Caenorhabditis elegans: a model to understand host-microbe interactions. Cell Mol Life Sci 2020; 77:1229-1249. [PMID: 31584128 PMCID: PMC11104810 DOI: 10.1007/s00018-019-03319-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/18/2019] [Accepted: 09/23/2019] [Indexed: 12/11/2022]
Abstract
Host-microbe interactions within the gut are fundamental to all higher organisms. Caenorhabditis elegans has been in use as a surrogate model to understand the conserved mechanisms in host-microbe interactions. Morphological and functional similarities of C. elegans gut with the human have allowed the mechanistic investigation of gut microbes and their effects on metabolism, development, reproduction, behavior, pathogenesis, immune responses and lifespan. Recent reports suggest their suitability for functional investigations of human gut bacteria, such as gut microbiota of healthy and diseased individuals. Our knowledge on the gut microbial diversity of C. elegans in their natural environment and the effect of host genetics on their core gut microbiota is important. Caenorhabditis elegans, as a model, is continuously bridging the gap in our understanding the role of genetics, environment, and dietary factors on physiology of the host.
Collapse
Affiliation(s)
- Arun Kumar
- Molecular Biology and Microbial Biotechnology Laboratory, Division of Life Sciences, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, 781035, India
| | - Aiswarya Baruah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Masahiro Tomioka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yuichi Iino
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
- JST, CREST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Mohan C Kalita
- Department of Biotechnology, Gauhati University, Guwahati, Assam, 781014, India
| | - Mojibur Khan
- Molecular Biology and Microbial Biotechnology Laboratory, Division of Life Sciences, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, 781035, India.
| |
Collapse
|
34
|
Ding M, Tyrchan C, Bäck E, Östling J, Schubert S, McCrae C. Combined siRNA and Small-Molecule Phenotypic Screening Identifies Targets Regulating Rhinovirus Replication in Primary Human Bronchial Epithelial Cells. SLAS DISCOVERY 2020; 25:634-645. [PMID: 32189556 DOI: 10.1177/2472555220909726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Human rhinovirus (RV) is the most common cause of acute upper respiratory tract infections and has recently been shown to play a significant role in exacerbations of asthma and chronic obstructive pulmonary disease (COPD). There is a significant unmet medical need for agents for the prevention and/or treatment of exacerbations triggered by human RV infection. Phenotypic drug discovery programs using different perturbation modalities, for example, siRNA, small-molecule compounds, and CRISPR, hold significant value for identifying novel drug targets. We have previously reported the identification of lanosterol synthase as a novel regulator of RV2 replication through a phenotypic screen of a library of siRNAs against druggable genes in normal human bronchial epithelial (NHBE) cells. Here, we describe a follow-up phenotypic screen of small-molecule compounds that are annotated to be pharmacological regulators of target genes that were identified to significantly affect RV2 replication in the siRNA primary screen of 10,500 druggable genes. Two hundred seventy small-molecule compounds selected for interacting with 122 target gene hits were screened in the primary RV2 assay in NHBE cells by quantifying viral replication via in situ hybridization followed by secondary quantitative PCR-based assays for RV2, RV14, and RV16. The described follow-up phenotypic screening allowed us to identify Fms-related tyrosine kinase 4 (FLT4) as a novel target regulating RV replication. We demonstrate that a combination of siRNA and small-molecule compound screening models is a useful phenotypic drug discovery approach for the identification of novel drug targets.
Collapse
Affiliation(s)
- Mei Ding
- Discovery Sciences, Research and Early Development, R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | - Christian Tyrchan
- Medicinal Chemistry, Research and Early Development, Respiratory, Inflammation and Autoimmune (RIA), R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | - Elisabeth Bäck
- Discovery Sciences, Research and Early Development, R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | - Jörgen Östling
- Bioscience, Research and Early Development, Respiratory, Inflammation and Autoimmune (RIA), R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | | | - Christopher McCrae
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory, Inflammation and Autoimmune (RIA), R&D BioPharmaceuticals, AstraZeneca, Gaithersburg, MD, USA
| |
Collapse
|
35
|
Barrass SV, Butcher SJ. Advances in high-throughput methods for the identification of virus receptors. Med Microbiol Immunol 2019; 209:309-323. [PMID: 31865406 PMCID: PMC7248041 DOI: 10.1007/s00430-019-00653-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/02/2019] [Indexed: 12/26/2022]
Abstract
Viruses have evolved many mechanisms to invade host cells and establish successful infections. The interaction between viral attachment proteins and host cell receptors is the first and decisive step in establishing such infections, initiating virus entry into the host cells. Therefore, the identification of host receptors is fundamental in understanding pathogenesis and tissue tropism. Furthermore, receptor identification can inform the development of antivirals, vaccines, and diagnostic technologies, which have a substantial impact on human health. Nevertheless, due to the complex nature of virus entry, the redundancy in receptor usage, and the limitations in current identification methods, many host receptors remain elusive. Recent advances in targeted gene perturbation, high-throughput screening, and mass spectrometry have facilitated the discovery of virus receptors in recent years. In this review, we compare the current methods used within the field to identify virus receptors, focussing on genomic- and interactome-based approaches.
Collapse
Affiliation(s)
- Sarah V Barrass
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme and Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland.
| | - Sarah J Butcher
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme and Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland.
| |
Collapse
|
36
|
Jabre I, Reddy ASN, Kalyna M, Chaudhary S, Khokhar W, Byrne LJ, Wilson CM, Syed NH. Does co-transcriptional regulation of alternative splicing mediate plant stress responses? Nucleic Acids Res 2019; 47:2716-2726. [PMID: 30793202 PMCID: PMC6451118 DOI: 10.1093/nar/gkz121] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 12/15/2022] Open
Abstract
Plants display exquisite control over gene expression to elicit appropriate responses under normal and stress conditions. Alternative splicing (AS) of pre-mRNAs, a process that generates two or more transcripts from multi-exon genes, adds another layer of regulation to fine-tune condition-specific gene expression in animals and plants. However, exactly how plants control splice isoform ratios and the timing of this regulation in response to environmental signals remains elusive. In mammals, recent evidence indicate that epigenetic and epitranscriptome changes, such as DNA methylation, chromatin modifications and RNA methylation, regulate RNA polymerase II processivity, co-transcriptional splicing, and stability and translation efficiency of splice isoforms. In plants, the role of epigenetic modifications in regulating transcription rate and mRNA abundance under stress is beginning to emerge. However, the mechanisms by which epigenetic and epitranscriptomic modifications regulate AS and translation efficiency require further research. Dynamic changes in the chromatin landscape in response to stress may provide a scaffold around which gene expression, AS and translation are orchestrated. Finally, we discuss CRISPR/Cas-based strategies for engineering chromatin architecture to manipulate AS patterns (or splice isoforms levels) to obtain insight into the epigenetic regulation of AS.
Collapse
Affiliation(s)
- Ibtissam Jabre
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, CT1 1QU, UK
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Maria Kalyna
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences - BOKU, Muthgasse 18, 1190 Vienna, Austria
| | - Saurabh Chaudhary
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, CT1 1QU, UK
| | - Waqas Khokhar
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, CT1 1QU, UK
| | - Lee J Byrne
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, CT1 1QU, UK
| | - Cornelia M Wilson
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, CT1 1QU, UK
| | - Naeem H Syed
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, CT1 1QU, UK
| |
Collapse
|
37
|
Challenges of gene delivery to the central nervous system and the growing use of biomaterial vectors. Brain Res Bull 2019; 150:216-230. [PMID: 31173859 DOI: 10.1016/j.brainresbull.2019.05.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 05/08/2019] [Accepted: 05/29/2019] [Indexed: 12/18/2022]
Abstract
Gene therapy is a promising form of treatment for those suffering from neurological disorders or central nervous system (CNS) injury, however, obstacles remain that limit its translational potential. The CNS is protected by the blood brain barrier, and this barrier blocks genes from traversing into the CNS if administered outside of the CNS. Viral and non-viral gene delivery vehicles, commonly referred to as vectors, are modified to enhance delivery efficiency to target locations in the CNS. Still, there are few gene therapy approaches approved by the FDA for CNS disease or injury treatment. The lack of viable clinical approaches is due, in part, to the unpredictable nature of many vector systems. In particular, safety concerns exist with the use of viral vectors for CNS gene delivery. To seek some alternatives to viral vectors, development of new non-viral, biomaterial vectors is occurring at a rapid rate. This review discusses the challenges of delivering various forms of genetic material to the CNS, the use and limitations of current viral vector delivery systems, and the use of non-viral, biomaterial vectors for CNS applications.
Collapse
|
38
|
Abstract
ABSTRACT
The spatial dimensions of host cells and bacterial microbes are perfectly suited to being studied by microscopy techniques. Therefore, cellular imaging has been instrumental in uncovering many paradigms of the intracellular lifestyle of microbes. Initially, microscopy was used as a qualitative, descriptive tool. However, with the onset of specific markers and the power of computer-assisted image analysis, imaging can now be used to gather quantitative data on biological processes. This makes imaging a driving force for the study of cellular phenomena. One particular imaging modality stands out, which is based on the physical principles of fluorescence. Fluorescence is highly specific and therefore can be exploited to label biomolecules of choice. It is also very sensitive, making it possible to follow individual molecules with this approach. Also, microscopy hardware has played an important role in putting microscopy in the spotlight for host-pathogen investigations. For example, microscopes have been automated for microscopy-based screenings. A new generation of microscopes and molecular probes are being used to image events below the resolution limit of light. Finally, workflows are being developed to link light microscopy with electron microscopy methods via correlative light electron microscopy. We are witnessing a golden age of cellular imaging in cellular microbiology.
Collapse
|
39
|
Perspectives on gene expression regulation techniques in Drosophila. J Genet Genomics 2019; 46:213-220. [DOI: 10.1016/j.jgg.2019.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/27/2019] [Accepted: 03/12/2019] [Indexed: 12/26/2022]
|
40
|
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.
Collapse
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
| |
Collapse
|
41
|
Shen Y, Kubben N, Candia J, Morozov AV, Misteli T, Losert W. RefCell: multi-dimensional analysis of image-based high-throughput screens based on 'typical cells'. BMC Bioinformatics 2018; 19:427. [PMID: 30445906 PMCID: PMC6240236 DOI: 10.1186/s12859-018-2454-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 10/31/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Image-based high-throughput screening (HTS) reveals a high level of heterogeneity in single cells and multiple cellular states may be observed within a single population. Currently available high-dimensional analysis methods are successful in characterizing cellular heterogeneity, but suffer from the "curse of dimensionality" and non-standardized outputs. RESULTS Here we introduce RefCell, a multi-dimensional analysis pipeline for image-based HTS that reproducibly captures cells with typical combinations of features in reference states and uses these "typical cells" as a reference for classification and weighting of metrics. RefCell quantitatively assesses heterogeneous deviations from typical behavior for each analyzed perturbation or sample. CONCLUSIONS We apply RefCell to the analysis of data from a high-throughput imaging screen of a library of 320 ubiquitin-targeted siRNAs selected to gain insights into the mechanisms of premature aging (progeria). RefCell yields results comparable to a more complex clustering-based single-cell analysis method; both methods reveal more potential hits than a conventional analysis based on averages.
Collapse
Affiliation(s)
- Yang Shen
- Department of Physics and Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742 USA
| | - Nard Kubben
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Julián Candia
- Trans-NIH Center for Human Immunology (CHI), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Alexandre V. Morozov
- Department of Physics and Astronomy and Center for Quantitative Biology, Rutgers University, Piscataway, NJ 08854 USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Wolfgang Losert
- Department of Physics and Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742 USA
| |
Collapse
|
42
|
Parekh U, Wu Y, Zhao D, Worlikar A, Shah N, Zhang K, Mali P. Mapping Cellular Reprogramming via Pooled Overexpression Screens with Paired Fitness and Single-Cell RNA-Sequencing Readout. Cell Syst 2018; 7:548-555.e8. [PMID: 30448000 DOI: 10.1016/j.cels.2018.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 10/12/2018] [Accepted: 10/16/2018] [Indexed: 12/15/2022]
Abstract
Understanding the effects of genetic perturbations on the cellular state has been challenging using traditional pooled screens, which typically rely on the delivery of a single perturbation per cell and unidimensional phenotypic readouts. Here, we use barcoded open reading frame overexpression libraries coupled with single-cell RNA sequencing to assay cell state and fitness, a technique we call SEUSS (scalable functional screening by sequencing). Using SEUSS, we perturbed hPSCs with a library of developmentally critical transcription factors (TFs) and assayed the impact of TF overexpression on fitness and transcriptomic states. We further leveraged the versatility of the ORF library approach to assay mutant genes and whole gene families. From the transcriptomic responses, we built genetic co-regulatory networks to identify altered gene modules and found that KLF4 and SNAI2 drive opposing effects along the epithelial-mesenchymal transition axis. From the fitness responses, we identified ETV2 as a driver of reprogramming toward an endothelial-like state.
Collapse
Affiliation(s)
- Udit Parekh
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Yan Wu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Dongxin Zhao
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Atharv Worlikar
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Neha Shah
- Department of Nanoengineering, University of California, San Diego, La Jolla, CA, USA
| | - Kun Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
43
|
Bachas C, Hodzic J, van der Mijn JC, Stoepker C, Verheul HMW, Wolthuis RMF, Felley-Bosco E, van Wieringen WN, van Beusechem VW, Brakenhoff RH, de Menezes RX. Rscreenorm: normalization of CRISPR and siRNA screen data for more reproducible hit selection. BMC Bioinformatics 2018; 19:301. [PMID: 30126372 PMCID: PMC6102854 DOI: 10.1186/s12859-018-2306-z] [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: 05/14/2018] [Accepted: 07/30/2018] [Indexed: 11/10/2022] Open
Abstract
Background Reproducibility of hits from independent CRISPR or siRNA screens is poor. This is partly due to data normalization primarily addressing technical variability within independent screens, and not the technical differences between them. Results We present “rscreenorm”, a method that standardizes the functional data ranges between screens using assay controls, and subsequently performs a piecewise-linear normalization to make data distributions across all screens comparable. In simulation studies, rscreenorm reduces false positives. Using two multiple-cell lines siRNA screens, rscreenorm increased reproducibility between 27 and 62% for hits, and up to 5-fold for non-hits. Using publicly available CRISPR-Cas screen data, application of commonly used median centering yields merely 34% of overlapping hits, in contrast with rscreenorm yielding 84% of overlapping hits. Furthermore, rscreenorm yielded at most 8% discordant results, whilst median-centering yielded as much as 55%. Conclusions Rscreenorm yields more consistent results and keeps false positive rates under control, improving reproducibility of genetic screens data analysis from multiple cell lines. Electronic supplementary material The online version of this article (10.1186/s12859-018-2306-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Costa Bachas
- Department of Otolaryngology - Head and Neck Surgery, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, 1081, HV, The Netherlands.,Department of Epidemiology and Biostatistics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, 1007, MB, The Netherlands
| | - Jasmina Hodzic
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, 1081, HV, The Netherlands
| | - Johannes C van der Mijn
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, 1081, HV, The Netherlands
| | - Chantal Stoepker
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, 1081, HV, The Netherlands
| | - Rob M F Wolthuis
- Section of Oncogenetics, Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1118, Amsterdam, 1081, HV, The Netherlands
| | | | - Wessel N van Wieringen
- Department of Epidemiology and Biostatistics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, 1007, MB, The Netherlands.,Department of Mathematics, VU University, Amsterdam, The Netherlands
| | - Victor W van Beusechem
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, 1081, HV, The Netherlands
| | - Ruud H Brakenhoff
- Department of Otolaryngology - Head and Neck Surgery, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, 1081, HV, The Netherlands
| | - Renée X de Menezes
- Department of Epidemiology and Biostatistics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, 1007, MB, The Netherlands.
| |
Collapse
|
44
|
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.
Collapse
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:
| |
Collapse
|
45
|
RNA interference technology to improve the baculovirus-insect cell expression system. Biotechnol Adv 2018; 36:443-451. [DOI: 10.1016/j.biotechadv.2018.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/11/2017] [Accepted: 01/13/2018] [Indexed: 02/02/2023]
|
46
|
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.
Collapse
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
| |
Collapse
|
47
|
Schaefer C, Mallela N, Seggewiß J, Lechtape B, Omran H, Dirksen U, Korsching E, Potratz J. Target discovery screens using pooled shRNA libraries and next-generation sequencing: A model workflow and analytical algorithm. PLoS One 2018; 13:e0191570. [PMID: 29385199 PMCID: PMC5792015 DOI: 10.1371/journal.pone.0191570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 01/08/2018] [Indexed: 11/28/2022] Open
Abstract
In the search for novel therapeutic targets, RNA interference screening has become a valuable tool. High-throughput technologies are now broadly accessible but their assay development from baseline remains resource-intensive and challenging. Focusing on this assay development process, we here describe a target discovery screen using pooled shRNA libraries and next-generation sequencing (NGS) deconvolution in a cell line model of Ewing sarcoma. In a strategy designed for comparative and synthetic lethal studies, we screened for targets specific to the A673 Ewing sarcoma cell line. Methods, results and pitfalls are described for the entire multi-step screening procedure, from lentiviral shRNA delivery to bioinformatics analysis, illustrating a complete model workflow. We demonstrate that successful studies are feasible from the first assay performance and independent of specialized screening units. Furthermore, we show that a resource-saving screen depth of 100-fold average shRNA representation can suffice to generate reproducible target hits despite heterogeneity in the derived datasets. Because statistical analysis methods are debatable for such datasets, we created ProFED, an analysis package designed to facilitate descriptive data analysis and hit calling using an aim-oriented profile filtering approach. In its versatile design, this open-source online tool provides fast and easy analysis of shRNA and other count-based datasets to complement other analytical algorithms.
Collapse
Affiliation(s)
- Christiane Schaefer
- Pediatric Hematology and Oncology, University Hospital Münster, Münster, Germany
| | - Nikhil Mallela
- Institute of Bioinformatics, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Jochen Seggewiß
- Institute of Human Genetics, University Hospital Münster, Münster, Germany
| | - Birgit Lechtape
- Pediatric Hematology and Oncology, University Hospital Münster, Münster, Germany
| | - Heymut Omran
- General Pediatrics, University Hospital Münster, Münster, Germany
| | - Uta Dirksen
- Department of Hematology and Oncology, Pediatrics III, West German Cancer Center, German Cancer Consortium (DKTK) Center Essen, University Hospital Essen, Essen, Germany
| | - Eberhard Korsching
- Institute of Bioinformatics, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Jenny Potratz
- Pediatric Hematology and Oncology, University Hospital Münster, Münster, Germany
- General Pediatrics, University Hospital Münster, Münster, Germany
- * E-mail:
| |
Collapse
|
48
|
Horváth B, Kalinka AT. The genetics of egg retention and fertilization success in Drosophila: One step closer to understanding the transition from facultative to obligate viviparity. Evolution 2018; 72:318-336. [PMID: 29265369 DOI: 10.1111/evo.13411] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 10/16/2017] [Accepted: 11/14/2017] [Indexed: 12/17/2022]
Abstract
Oviparous, facultative egg retention enables Drosophila females to withhold fertilized eggs in their reproductive tracts until circumstances favor oviposition. The propensity to retain fertilized eggs varies greatly between species, and is correlated with other reproductive traits, such as egg size and ovariole number. While previous studies have described the phenomenon, no study to date has characterized within-species variation or the genetic basis of the trait. Here, we develop a novel microscope-based method for measuring egg retention in Drosophila females and determine the range of phenotypic variation in mated female egg retention in a subset of 91 Drosophila Genetic Reference Panel (DGRP) lines. We inferred the genetic basis of egg retention using a genome-wide association study (GWAS). Further, the scoring of more than 95,000 stained, staged eggs enabled estimates of fertilization success for each line. We found evidence that ovary- and spermathecae-related genes as well as genes affecting olfactory behavior, male mating behavior, male-female attraction and sperm motility may play a crucial role in post-mating physiology. Based on our findings we also propose potential evolutionary routes toward obligate viviparity. In particular, we propose that the loss of fecundity incurred by viviparity could be offset by benefits arising from enhanced mate discrimination, resource specialization, or modified egg morphology.
Collapse
Affiliation(s)
- Barbara Horváth
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 1, Vienna A-1210, Austria.,Vienna Graduate School of Population Genetics, Veterinärmedizinische Universität Wien, Veterinärplatz 1, Vienna A-1210, Austria.,Current Address: Barbara Ellis, Institutionen för ekologi och genetik, Evolutionsbiologiskt Centrum (EBC), Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Alex T Kalinka
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 1, Vienna A-1210, Austria
| |
Collapse
|
49
|
Haney SA. High-Content Screening Approaches That Minimize Confounding Factors in RNAi, CRISPR, and Small Molecule Screening. Methods Mol Biol 2018; 1683:113-130. [PMID: 29082490 DOI: 10.1007/978-1-4939-7357-6_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Screening arrayed libraries of reagents, particularly small molecules began as a vehicle for drug discovery, but the in last few years it has become a cornerstone of biological investigation, joining RNAi and CRISPR as methods for elucidating functional relationships that could not be anticipated, and illustrating the mechanisms behind basic and disease biology, and therapeutic resistance. However, these approaches share some common challenges, especially with respect to specificity or selectivity of the reagents as they are scaled to large protein families or the genome. High-content screening (HCS) has emerged as an important complement to screening, mostly the result of a wide array of specific molecular events, such as protein kinase and transcription factor activation, morphological changes associated with stem cell differentiation or the epithelial-mesenchymal transition of cancer cells. Beyond the range of cellular events that can be screened by HCS, image-based screening introduces new processes for differentiating between specific and nonspecific effects on cells. This chapter introduces these complexities and discusses strategies available in image-based screening that can mitigate the challenges they can bring to screening.
Collapse
Affiliation(s)
- Steven A Haney
- Cancer Biology and the Tumor Microenvironment, Discovery Oncology, Lilly Research Laboratories/Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN, 46285, USA.
| |
Collapse
|
50
|
Identification of Rab18 as an Essential Host Factor for BK Polyomavirus Infection Using a Whole-Genome RNA Interference Screen. mSphere 2017; 2:mSphere00291-17. [PMID: 28815213 PMCID: PMC5555678 DOI: 10.1128/mspheredirect.00291-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 07/12/2017] [Indexed: 11/20/2022] Open
Abstract
Polyomaviruses bind to a group of specific gangliosides on the plasma membrane of the cell prior to being endocytosed. They then follow a retrograde trafficking pathway to reach the endoplasmic reticulum (ER). The viruses begin to disassemble in the ER and then exit the ER and move to the nucleus. However, the details of intracellular trafficking between the endosome and the ER are largely unknown. By implementing a whole human genome small interfering RNA screen, we identified Rab18, syntaxin 18, and the NRZ complex as key components in endosome-ER trafficking of the human polyomavirus BKPyV. These results serve to further elucidate the route BKPyV takes from outside the cell to its site of replication in the nucleus. BK polyomavirus (BKPyV) is a human pathogen first isolated in 1971. BKPyV infection is ubiquitous in the human population, with over 80% of adults worldwide being seropositive for BKPyV. BKPyV infection is usually asymptomatic; however, BKPyV reactivation in immunosuppressed transplant patients causes two diseases, polyomavirus-associated nephropathy and hemorrhagic cystitis. To establish a successful infection in host cells, BKPyV must travel in retrograde transport vesicles to reach the nucleus. To make this happen, BKPyV requires the cooperation of host cell proteins. To further identify host factors associated with BKPyV entry and intracellular trafficking, we performed a whole-genome small interfering RNA screen on BKPyV infection of primary human renal proximal tubule epithelial cells. The results revealed the importance of Ras-related protein Rab18 and syntaxin 18 for BKPyV infection. Our subsequent experiments implicated additional factors that interact with this pathway and suggest a more detailed model of the intracellular trafficking process, indicating that BKPyV reaches the endoplasmic reticulum (ER) lumen through a retrograde transport pathway between the late endosome and the ER. IMPORTANCE Polyomaviruses bind to a group of specific gangliosides on the plasma membrane of the cell prior to being endocytosed. They then follow a retrograde trafficking pathway to reach the endoplasmic reticulum (ER). The viruses begin to disassemble in the ER and then exit the ER and move to the nucleus. However, the details of intracellular trafficking between the endosome and the ER are largely unknown. By implementing a whole human genome small interfering RNA screen, we identified Rab18, syntaxin 18, and the NRZ complex as key components in endosome-ER trafficking of the human polyomavirus BKPyV. These results serve to further elucidate the route BKPyV takes from outside the cell to its site of replication in the nucleus.
Collapse
|