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Shihabeddin E, Santhanam A, Aronowitz AL, O’Brien J. Cost-effective strategies to knock down genes of interest in the retinas of adult zebrafish. Front Cell Neurosci 2024; 17:1321337. [PMID: 38322239 PMCID: PMC10845135 DOI: 10.3389/fncel.2023.1321337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/22/2023] [Indexed: 02/08/2024] Open
Abstract
High throughput sequencing has generated an enormous amount of information about the genes expressed in various cell types and tissues throughout the body, and about how gene expression changes over time and in diseased conditions. This knowledge has made targeted gene knockdowns an important tool in screening and identifying the roles of genes that are differentially expressed among specific cells of interest. While many approaches are available and optimized in mammalian models, there are still several limitations in the zebrafish model. In this article, we describe two approaches to target specific genes in the retina for knockdown: cell-penetrating, translation-blocking Vivo-Morpholino oligonucleotides and commercially available lipid nanoparticle reagents to deliver siRNA. We targeted expression of the PCNA gene in the retina of a P23H rhodopsin transgenic zebrafish model, in which rapidly proliferating progenitor cells replace degenerated rod photoreceptors. Retinas collected 48 h after intravitreal injections in adult zebrafish reveal that both Vivo-Morpholinos and lipid encapsulated siRNAs were able to successfully knock down expression of PCNA. However, only retinas injected with Vivo-Morpholinos showed a significant decrease in the formation of P23H rhodopsin-expressing rods, a downstream effect of PCNA inhibition. Surprisingly, Vivo-Morpholinos were able to exit the injected eye and enter the contralateral non-injected eye to inhibit PCNA expression. In this article we describe the techniques, concentrations, and considerations we found necessary to successfully target and inhibit genes through Vivo-Morpholinos and lipid encapsulated siRNAs.
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Affiliation(s)
- Eyad Shihabeddin
- Department of Ophthalmology and Visual Science, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
- MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Abirami Santhanam
- University of Houston College of Optometry, Houston, TX, United States
| | - Alexandra L. Aronowitz
- Department of Ophthalmology and Visual Science, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - John O’Brien
- Department of Ophthalmology and Visual Science, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
- MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
- University of Houston College of Optometry, Houston, TX, United States
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Lye LF, Owens KL, Jang S, Marcus JE, Brettmann EA, Beverley SM. An RNA Interference (RNAi) Toolkit and Its Utility for Functional Genetic Analysis of Leishmania (Viannia). Genes (Basel) 2022; 14. [PMID: 36672832 DOI: 10.3390/genes14010093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022] Open
Abstract
RNA interference (RNAi) is a powerful tool whose efficacy against a broad range of targets enables functional genetic tests individually or systematically. However, the RNAi pathway has been lost in evolution by a variety of eukaryotes including most Leishmania sp. RNAi was retained in species of the Leishmania subgenus Viannia, and here we describe the development, optimization, and application of RNAi tools to the study of L. (Viannia) braziliensis (Lbr). We developed vectors facilitating generation of long-hairpin or "stem-loop" (StL) RNAi knockdown constructs, using GatewayTM site-specific recombinase technology. A survey of applications of RNAi in L. braziliensis included genes interspersed within multigene tandem arrays such as quinonoid dihydropteridine reductase (QDPR), a potential target or modulator of antifolate sensitivity. Other tests include genes involved in cell differentiation and amastigote proliferation (A600), and essential genes of the intraflagellar transport (IFT) pathway. We tested a range of stem lengths targeting the L. braziliensis hypoxanthine-guanine phosphoribosyl transferase (HGPRT) and reporter firefly luciferase (LUC) genes and found that the efficacy of RNAi increased with stem length, and fell off greatly below about 128 nt. We used the StL length dependency to establish a useful 'hypomorphic' approach not possible with other gene ablation strategies, with shorter IFT140 stems yielding viable cells with compromised flagellar morphology. We showed that co-selection for RNAi against adenine phosphoryl transferase (APRT1) using 4-aminopyrazolpyrimidine (APP) could increase the efficacy of RNAi against reporter constructs, a finding that may facilitate improvements in future work. Thus, for many genes, RNAi provides a useful tool for studying Leishmania gene function with some unique advantages.
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Kang J, Joo J, Kwon EJ, Skalak M, Hussain S, She ZG, Ruoslahti E, Bhatia SN, Sailor MJ. Self-Sealing Porous Silicon-Calcium Silicate Core-Shell Nanoparticles for Targeted siRNA Delivery to the Injured Brain. Adv Mater 2016; 28:7962-7969. [PMID: 27383373 PMCID: PMC6274592 DOI: 10.1002/adma.201600634] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/06/2016] [Indexed: 05/04/2023]
Abstract
Calcium ions react with silicic acid released from dissolving porous silicon nanoparticles to create an insoluble calcium silicate shell. The calcium silicate shell traps and protects an siRNA payload, which can be delivered to neuronal tissues in vitro or in vivo. Gene delivery is enhanced by the action of targeting and cell-penetrating peptides attached to the calcium silicate shell.
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Affiliation(s)
- Jinyoung Kang
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, 92093-0358, USA
| | - Jinmyoung Joo
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093-0358, USA
| | - Ester J Kwon
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Matthew Skalak
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sazid Hussain
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Zhi-Gang She
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Erkki Ruoslahti
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
- Center for Nanomedicine and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106-9610, USA
| | - Sangeeta N Bhatia
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Electrical Engineering and Computer Science and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Division of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Cambridge, MA, 02139, USA
| | - Michael J Sailor
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, 92093-0358, USA.
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093-0358, USA.
- Department of Bioengineering, Materials Science and Engineering Program, University of California San Diego, 9500 Gilman Drive, m/c 0358, La Jolla, CA, 92093-0358, USA.
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