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Lundstrom K. Trans-amplifying RNA hitting new grounds: Gene regulation by microRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102191. [PMID: 38725441 PMCID: PMC11078691 DOI: 10.1016/j.omtn.2024.102191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
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2
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Schlossbauer P, Naumann L, Klingler F, Burkhart M, Handrick R, Korff K, Neusüß C, Otte K, Hesse F. Stable overexpression of native and artificial miRNAs for the production of differentially fucosylated antibodies in CHO cells. Eng Life Sci 2024; 24:2300234. [PMID: 38845814 PMCID: PMC11151017 DOI: 10.1002/elsc.202300234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/04/2024] [Accepted: 03/17/2024] [Indexed: 06/09/2024] Open
Abstract
Cell engineering strategies typically rely on energy-consuming overexpression of genes or radical gene-knock out. Both strategies are not particularly convenient for the generation of slightly modulated phenotypes, as needed in biosimilar development of for example differentially fucosylated monoclonal antibodies (mAbs). Recently, transiently transfected small noncoding microRNAs (miRNAs), known to be regulators of entire gene networks, have emerged as potent fucosylation modulators in Chinese hamster ovary (CHO) production cells. Here, we demonstrate the applicability of stable miRNA overexpression in CHO production cells to adjust the fucosylation pattern of mAbs as a model phenotype. For this purpose, we applied a miRNA chaining strategy to achieve adjustability of fucosylation in stable cell pools. In addition, we were able to implement recently developed artificial miRNAs (amiRNAs) based on native miRNA sequences into a stable CHO expression system to even further fine-tune fucosylation regulation. Our results demonstrate the potential of miRNAs as a versatile tool to control mAb fucosylation in CHO production cells without adverse side effects on important process parameters.
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Affiliation(s)
- Patrick Schlossbauer
- Institute for Applied BiotechnologyUniversity of Applied Sciences BiberachBiberachGermany
| | | | - Florian Klingler
- Institute for Applied BiotechnologyUniversity of Applied Sciences BiberachBiberachGermany
| | - Madina Burkhart
- Institute for Applied BiotechnologyUniversity of Applied Sciences BiberachBiberachGermany
| | - René Handrick
- Institute for Applied BiotechnologyUniversity of Applied Sciences BiberachBiberachGermany
| | | | | | - Kerstin Otte
- Institute for Applied BiotechnologyUniversity of Applied Sciences BiberachBiberachGermany
| | - Friedemann Hesse
- Institute for Applied BiotechnologyUniversity of Applied Sciences BiberachBiberachGermany
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3
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Facal CL, Fernández Bessone I, Muñiz JA, Pereyra AE, Pedroncini O, Páez-Paz I, Clerici-Delville R, Arnaiz C, Urrutia L, Falasco G, Argañaraz CV, Saez T, Marin-Burgin A, Soiza-Reilly M, Falzone T, Avale ME. Tau reduction with artificial microRNAs modulates neuronal physiology and improves tauopathy phenotypes in mice. Mol Ther 2024; 32:1080-1095. [PMID: 38310353 PMCID: PMC11163272 DOI: 10.1016/j.ymthe.2024.01.033] [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: 08/02/2023] [Revised: 12/19/2023] [Accepted: 01/30/2024] [Indexed: 02/05/2024] Open
Abstract
Abnormal tau accumulation is the hallmark of several neurodegenerative diseases, named tauopathies. Strategies aimed at reducing tau in the brain are promising therapeutic interventions, yet more precise therapies would require targeting specific nuclei and neuronal subpopulations affected by disease while avoiding global reduction of physiological tau. Here, we developed artificial microRNAs directed against the human MAPT mRNA to dwindle tau protein by engaging the endogenous RNA interference pathway. In human differentiated neurons in culture, microRNA-mediated tau reduction diminished neuronal firing without affecting neuronal morphology or impairing axonal transport. In the htau mouse model of tauopathy, we locally expressed artificial microRNAs in the prefrontal cortex (PFC), an area particularly vulnerable to initiating tau pathology in this model. Tau knockdown prevented the accumulation of insoluble and hyperphosphorylated tau, modulated firing activity of putative pyramidal neurons, and improved glucose uptake in the PFC. Moreover, such tau reduction prevented cognitive decline in aged htau mice. Our results suggest target engagement of designed tau-microRNAs to effectively reduce tau pathology, providing a proof of concept for a potential therapeutic approach based on local tau knockdown to rescue tauopathy-related phenotypes.
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Affiliation(s)
- Carolina Lucía Facal
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), CONICET, Buenos Aires, Argentina
| | - Iván Fernández Bessone
- Instituto de Biología Celular y Neurociencias (IBCN), Universidad de Buenos Aires, CONICET-UBA, Buenos Aires, Argentina
| | - Javier Andrés Muñiz
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), CONICET, Buenos Aires, Argentina
| | - A Ezequiel Pereyra
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), CONICET, Buenos Aires, Argentina
| | - Olivia Pedroncini
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), Partner Institute of the Max Planck Society, CONICET-MPSP, Buenos Aires, Argentina
| | - Indiana Páez-Paz
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), CONICET, Buenos Aires, Argentina
| | - Ramiro Clerici-Delville
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), CONICET, Buenos Aires, Argentina
| | - Cayetana Arnaiz
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), Partner Institute of the Max Planck Society, CONICET-MPSP, Buenos Aires, Argentina
| | - Leandro Urrutia
- Centro de imágenes Moleculares, FLENI, Buenos Aires, Argentina
| | - Germán Falasco
- Centro de imágenes Moleculares, FLENI, Buenos Aires, Argentina
| | - Carla Verónica Argañaraz
- Instituto de Fisiología Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires, CONICET-UBA, Buenos Aires, Argentina
| | - Trinidad Saez
- Instituto de Biología Celular y Neurociencias (IBCN), Universidad de Buenos Aires, CONICET-UBA, Buenos Aires, Argentina
| | - Antonia Marin-Burgin
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), Partner Institute of the Max Planck Society, CONICET-MPSP, Buenos Aires, Argentina
| | - Mariano Soiza-Reilly
- Instituto de Fisiología Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires, CONICET-UBA, Buenos Aires, Argentina
| | - Tomás Falzone
- Instituto de Biología Celular y Neurociencias (IBCN), Universidad de Buenos Aires, CONICET-UBA, Buenos Aires, Argentina; Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), Partner Institute of the Max Planck Society, CONICET-MPSP, Buenos Aires, Argentina
| | - María Elena Avale
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), CONICET, Buenos Aires, Argentina.
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4
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Klingler F, Schlossbauer P, Naumann L, Handrick R, Hesse F, Neusüß C, Otte K. Developing microRNAs as engineering tools to modulate monoclonal antibody galactosylation. Biotechnol Bioeng 2024; 121:1355-1365. [PMID: 38079069 DOI: 10.1002/bit.28616] [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: 07/19/2023] [Revised: 11/24/2023] [Accepted: 11/25/2023] [Indexed: 04/01/2024]
Abstract
N-linked glycosylation is one of the most important post-translational modifications of monoclonal antibodies (mAbs) and is considered to be a critical quality attribute (CQA), as the glycan composition often has immunomodulatory effects. Since terminal galactose residues of mAbs can affect antibody-dependent cellular cytotoxicity (ADCC), complement-dependent cytolysis (CDC) activation, serum half-life, and antiviral activity it has to be monitored, controlled and modulated to ensure therapeutic effects. The ability of small noncoding microRNAs (miRNAs) to modulate glycosylation in Chinese hamster ovary (CHO) production cells was recently reported establishing miRNAs as engineering tools for modulation of protein glycosylation. In this study, we report the characterization and validation of miRNAs as engineering tools for increased (mmu-miR-452-5p, mmu-miR-193b-3p) or decreased (mmu-miR-7646-5p, mmu-miR-7243-3p, mmu-miR-1668, mmu-let-7c-1-3p, mmu-miR-7665-3p, mmu-miR-6403) degree of galactosylation. Furthermore, the biological mode of action regulating gene expression of the galactosylation pathway was characterized as well as their influence on bioprocess-related parameters. Most important, stable plasmid-based overexpression of these miRNAs represents a versatile tool for engineering N-linked galactosylation to achieve favorable phenotypes in cell lines for biopharmaceutical production.
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Affiliation(s)
- Florian Klingler
- Institute for Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Patrick Schlossbauer
- Institute for Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Lukas Naumann
- Department of Chemistry, Aalen University, Aalen, Germany
| | - René Handrick
- Institute for Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Friedemann Hesse
- Institute for Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | | | - Kerstin Otte
- Institute for Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
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5
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Rossi M, Steklov M, Huberty F, Nguyen T, Marijsse J, Jacques-Hespel C, Najm P, Lonez C, Breman E. Efficient shRNA-based knockdown of multiple target genes for cell therapy using a chimeric miRNA cluster platform. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102038. [PMID: 37799328 PMCID: PMC10548280 DOI: 10.1016/j.omtn.2023.102038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/15/2023] [Indexed: 10/07/2023]
Abstract
Genome engineering technologies are powerful tools in cell-based immunotherapy to optimize or fine-tune cell functionalities. However, their use for multiple gene edits poses relevant biological and technical challenges. Short hairpin RNA (shRNA)-based cell engineering bypasses these criticalities and represents a valid alternative to CRISPR-based gene editing. Here, we describe a microRNA (miRNA)-based multiplex shRNA platform obtained by combining highly efficient miRNA scaffolds into a chimeric cluster, to deliver up to four shRNA-like sequences. Thanks to its limited size, our cassette could be deployed in a one-step process along with all the CAR components, streamlining the generation of engineered CAR T cells. The plug-and-play design of the shRNA platform allowed us to swap each shRNA-derived guide sequence without affecting the system performance. Appropriately choosing the target sequences, we were able to either achieve a functional KO, or fine-tune the expression levels of the target genes, all without the need for gene editing. Through our strategy we achieved easy, safe, efficient, and tunable modulation of multiple target genes simultaneously. This approach allows for the effective introduction of multiple functionally relevant tweaks in the transcriptome of the engineered cells, which may lead to increased performance in challenging environments, e.g., solid tumors.
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Affiliation(s)
- Matteo Rossi
- Celyad Oncology, 1435 Mont-Saint-Guibert, Belgium
| | | | | | - Thuy Nguyen
- Celyad Oncology, 1435 Mont-Saint-Guibert, Belgium
| | | | | | - Paul Najm
- Celyad Oncology, 1435 Mont-Saint-Guibert, Belgium
| | | | - Eytan Breman
- Celyad Oncology, 1435 Mont-Saint-Guibert, Belgium
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6
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McNicholas M, De Cola A, Bashardanesh Z, Foss A, Lloyd CB, Hébert S, Faury D, Andrade AF, Jabado N, Kleinman CL, Pathania M. A Compendium of Syngeneic, Transplantable Pediatric High-Grade Glioma Models Reveals Subtype-Specific Therapeutic Vulnerabilities. Cancer Discov 2023; 13:1592-1615. [PMID: 37011011 PMCID: PMC10326601 DOI: 10.1158/2159-8290.cd-23-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/20/2023] [Accepted: 03/29/2023] [Indexed: 04/04/2023]
Abstract
Pediatric high-grade gliomas (pHGG) are lethal, incurable brain tumors frequently driven by clonal mutations in histone genes. They often harbor a range of additional genetic alterations that correlate with different ages, anatomic locations, and tumor subtypes. We developed models representing 16 pHGG subtypes driven by different combinations of alterations targeted to specific brain regions. Tumors developed with varying latencies and cell lines derived from these models engrafted in syngeneic, immunocompetent mice with high penetrance. Targeted drug screening revealed unexpected selective vulnerabilities-H3.3G34R/PDGFRAC235Y to FGFR inhibition, H3.3K27M/PDGFRAWT to PDGFRA inhibition, and H3.3K27M/PDGFRAWT and H3.3K27M/PPM1DΔC/PIK3CAE545K to combined inhibition of MEK and PIK3CA. Moreover, H3.3K27M tumors with PIK3CA, NF1, and FGFR1 mutations were more invasive and harbored distinct additional phenotypes, such as exophytic spread, cranial nerve invasion, and spinal dissemination. Collectively, these models reveal that different partner alterations produce distinct effects on pHGG cellular composition, latency, invasiveness, and treatment sensitivity. SIGNIFICANCE Histone-mutant pediatric gliomas are a highly heterogeneous tumor entity. Different histone mutations correlate with different ages of onset, survival outcomes, brain regions, and partner alterations. We have developed models of histone-mutant gliomas that reflect this anatomic and genetic heterogeneity and provide evidence of subtype-specific biology and therapeutic targeting. See related commentary by Lubanszky and Hawkins, p. 1516. This article is highlighted in the In This Issue feature, p. 1501.
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Affiliation(s)
- Michael McNicholas
- Department of Oncology and Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
- CRUK Children's Brain Tumour Centre of Excellence, University of Cambridge, Cambridge, United Kingdom
| | - Antonella De Cola
- Department of Oncology and Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
- CRUK Children's Brain Tumour Centre of Excellence, University of Cambridge, Cambridge, United Kingdom
| | - Zahedeh Bashardanesh
- Lady Davis Research Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Amelia Foss
- Department of Oncology and Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
- CRUK Children's Brain Tumour Centre of Excellence, University of Cambridge, Cambridge, United Kingdom
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Cameron B. Lloyd
- Department of Oncology and Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
- CRUK Children's Brain Tumour Centre of Excellence, University of Cambridge, Cambridge, United Kingdom
| | - Steven Hébert
- Lady Davis Research Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Damien Faury
- Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | | | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Claudia L. Kleinman
- Lady Davis Research Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Manav Pathania
- Department of Oncology and Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
- CRUK Children's Brain Tumour Centre of Excellence, University of Cambridge, Cambridge, United Kingdom
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7
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Gupta S, Aggarwal S, Munde M. New Insights into the Role of Ligand-Binding Modes in GC-DNA Condensation through Thermodynamic and Spectroscopic Studies. ACS OMEGA 2023; 8:4554-4565. [PMID: 36777612 PMCID: PMC9909821 DOI: 10.1021/acsomega.2c01557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 09/20/2022] [Indexed: 06/18/2023]
Abstract
In biological systems, the unprompted assembly of DNA molecules by cationic ligands into condensed structures is ubiquitous. The ability of ligands to provoke DNA packaging is crucial to the molecular organization and functional control of DNA, yet their underlined physical roles have remained elusive. Here, we have examined the DNA condensation mechanism of four cationic ligands, including their primary DNA-binding modes through extensive biophysical studies. We observed contrasting changes for these ligands binding to poly[dGdC]:poly[dGdC] (GC-DNA) and poly[dAdT]:poly[dAdT] (AT-DNA). Based on a CD spectroscopic study, it was confirmed that only GC-DNA undergoes B- to Ψ-type DNA transformation in the presence of ligands. In the fluorescence displacement assay (FDA), the ability of ligands to displace GC-DNA-bound EtBr follows the order: protamine21+ > cohex3+ > Ni2+ > spermine4+, which indicates that there is no direct correlation between the ligand charge and its ability to displace the drug from the DNA, indicating that GC-DNA condensation is not just influenced by electrostatic interaction but ligand-specific interactions may also have played a crucial role. Furthermore, the detailed ITC-binding studies suggested that DNA-ligand interactions are generally driven by unfavorable enthalpy and favorable entropy. The correlations from various studies insinuate that cationic ligands show major groove binding as one of the preferred binding modes during GC-DNA condensation.
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Affiliation(s)
- Sakshi Gupta
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Department
of Applied Science, The NorthCap University, Sector 23-A, Gurgaon, Haryana 122017, India
| | - Soumya Aggarwal
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manoj Munde
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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8
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Bagchi A, Devaraju N, Chambayil K, Rajendiran V, Venkatesan V, Sayed N, Pai AA, Nath A, David E, Nakamura Y, Balasubramanian P, Srivastava A, Thangavel S, Mohankumar KM, Velayudhan SR. Erythroid lineage-specific lentiviral RNAi vectors suitable for molecular functional studies and therapeutic applications. Sci Rep 2022; 12:14033. [PMID: 35982069 PMCID: PMC9388678 DOI: 10.1038/s41598-022-13783-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 05/27/2022] [Indexed: 12/02/2022] Open
Abstract
Numerous genes exert multifaceted roles in hematopoiesis. Therefore, we generated novel lineage-specific RNA interference (RNAi) lentiviral vectors, H23B-Ery-Lin-shRNA and H234B-Ery-Lin-shRNA, to probe the functions of these genes in erythroid cells without affecting other hematopoietic lineages. The lineage specificity of these vectors was confirmed by transducing multiple hematopoietic cells to express a fluorescent protein. Unlike the previously reported erythroid lineage RNAi vector, our vectors were designed for cloning the short hairpin RNAs (shRNAs) for any gene, and they also provide superior knockdown of the target gene expression with a single shRNA integration per cell. High-level lineage-specific downregulation of BCL11A and ZBTB7A, two well-characterized transcriptional repressors of HBG in adult erythroid cells, was achieved with substantial induction of fetal hemoglobin with a single-copy lentiviral vector integration. Transduction of primary healthy donor CD34+ cells with these vectors resulted in >80% reduction in the target protein levels and up to 40% elevation in the γ-chain levels in the differentiated erythroid cells. Xenotransplantation of the human CD34+ cells transduced with H23B-Ery-Lin-shBCL11A LV in immunocompromised mice showed ~ 60% reduction in BCL11A protein expression with ~ 40% elevation of γ-chain levels in the erythroid cells derived from the transduced CD34+ cells. Overall, the novel erythroid lineage-specific lentiviral RNAi vectors described in this study provide a high-level knockdown of target gene expression in the erythroid cells, making them suitable for their use in gene therapy for hemoglobinopathies. Additionally, the design of these vectors also makes them ideal for high-throughput RNAi screening for studying normal and pathological erythropoiesis.
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Affiliation(s)
- Abhirup Bagchi
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Vellore, Tamil Nadu, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Nivedhitha Devaraju
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Vellore, Tamil Nadu, 632002, India
- Manipal Academy of Higher Education, Manipal, Karnataka, 576119, India
| | - Karthik Chambayil
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Vellore, Tamil Nadu, 632002, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
| | - Vignesh Rajendiran
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Vellore, Tamil Nadu, 632002, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
| | - Vigneshwaran Venkatesan
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Vellore, Tamil Nadu, 632002, India
- Manipal Academy of Higher Education, Manipal, Karnataka, 576119, India
| | - Nilofer Sayed
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Vellore, Tamil Nadu, 632002, India
| | - Aswin Anand Pai
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India
| | - Aneesha Nath
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Vellore, Tamil Nadu, 632002, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
| | - Ernest David
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Ibaraki, 3050074, Japan
| | - Poonkuzhali Balasubramanian
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India
| | - Alok Srivastava
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Vellore, Tamil Nadu, 632002, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India
| | - Saravanabhavan Thangavel
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Vellore, Tamil Nadu, 632002, India
- Manipal Academy of Higher Education, Manipal, Karnataka, 576119, India
| | - Kumarasamypet M Mohankumar
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Vellore, Tamil Nadu, 632002, India.
- Manipal Academy of Higher Education, Manipal, Karnataka, 576119, India.
| | - Shaji R Velayudhan
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Vellore, Tamil Nadu, 632002, India.
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India.
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India.
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9
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Mao Y, Wang X, Hu W, Li A, Li Y, Huang H, Yan R, Zhang Y, Li J, Li H, Wang S. Long-term and efficient inhibition of hepatitis B virus replication by AAV8-delivered artificial microRNAs. Antiviral Res 2022; 204:105366. [PMID: 35732226 DOI: 10.1016/j.antiviral.2022.105366] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/28/2022] [Accepted: 06/15/2022] [Indexed: 11/02/2022]
Abstract
Chronic hepatitis B virus (HBV) infection remains a global health problem and current treatments are insufficient due to immune tolerance to hepatitis B surface antigen (HBsAg). RNA interference (RNAi) is a more promising approach for antiviral therapy. Here, 17 single artificial microRNAs (amiRNAs) targeting the highly conserved regions of HBV genome were screened to inhibit HBV replication. In addition, we compared three tandem amiRNAs, each containing 3 different amiRNAs, out of which amiRNA135 was selected to be studied in detail. In vitro data showed that amiRNA135 significantly inhibited the replication of different HBV genotypes (including resistant and mutant). In vivo study was carried out by adeno-associated virus 8-mediated gene delivery, we found that the anti-HBV effects of AAV8-amiRNA135 were time and dose-dependent. Serum HBsAg and HBeAg in high dose groups were significantly reduced at 7 days after a single intravenous vector injection, and maintained at low levels throughout a 15-month experiment. Immunohistochemical staining and HBV core particle DNA analysis confirmed that HBV replication in the liver was strongly inhibited by AAV8-amiRNA135. Taken together, our data suggest that AAV8-mediated trimeric amiRNA expression is a promising therapeutic approach for chronic HBV infection.
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Affiliation(s)
- Yingying Mao
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Xuejun Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
| | - Wei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Andrew Li
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, USA
| | - Ying Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hai Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Renhe Yan
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Yanling Zhang
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Jinlong Li
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Hongwei Li
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China.
| | - Shengqi Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
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10
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Calumenin knockdown, by intronic artificial microRNA, to improve expression efficiency of the recombinant human coagulation factor IX. Biotechnol Lett 2022; 44:713-728. [PMID: 35412165 DOI: 10.1007/s10529-022-03249-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/25/2022] [Indexed: 11/02/2022]
Abstract
OBJECTIVES To improve the expression efficiency of recombinant hFIX, by enhancing its γ-carboxylation, which is inhibited by Calumenin (CALU), we used intronic artificial microRNAs (amiRNAs) for the CALU downregulation. METHODS Two human CALU (hCALU)-specific amiRNAs were designed, validated and inserted within a truncated form of the hFIX intron 1, in either 3'- or 5'-untranslated regions of the hFIX cDNA, in an expression vector. After transfections of a human cell line with the recombinant constructs, processing of the miRNAs confirmed by RT-PCR, using stem-loop primers. The hFIX and hCALU expression assessments were done based on RT-PCR results. The Gamma(γ)-carboxylation of the expressed hFIX was examined by a barium citrate precipitation method, followed by Enzyme-Linked Immunosorbent Assay. RESULTS Efficient CALU down regulations, with more than 30-fold decrease, occurred in the cells carrying either of the two examined the 3'-located amiRNAs. The CALU downregulation in the same cells doubled the FIX γ-carboxylation, although the transcription of the FIX decreased significantly. On the other hand, while the expression of the amiRNAs from the 5'-located intron had no decreasing effect on the expression level of CALU, the level of hFIX transcription in these cells increased almost twofold compared to the construct without amiRNA. CONCLUSION The CALU downregulation, consistent with efficient hFIX γ-carboxylation, occurred in the cells carrying either of the two amiRNAs containing constructs, although it was affected by the locations of the amiRNA carrying introns, suggesting a possible need to optimize the conditions for the amiRNAs expression.
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11
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Wang W, Zhou P, Wang X, Chen F, Christensen E, Thompson J, Ren X, Kells A, Stanek L, Carter T, Hou J, Sah D. Efficient and Precise Processing of the Optimized Pri-amiRNA in a Huntingtin-Lowering AAV Gene Therapy in Vitro and in Mice and Nonhuman Primates. Hum Gene Ther 2021; 33:37-60. [PMID: 34806402 PMCID: PMC10112875 DOI: 10.1089/hum.2021.221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Huntington's Disease is a fatal neurodegenerative disorder caused by an inherited mutation in the huntingtin gene (HTT) comprising an expanded cytosine-adenine-guanine (CAG) trinucleotide repeat sequence that results in a pathogenic huntingtin protein. AAV gene therapy containing a primary artificial microRNA (pri-amiRNA) specifically targeting HTT mRNA has the potential to provide long-lasting therapeutic benefit, via durable reduction of mutant HTT expression after a single administration. The efficiency and precision of processing of the pri-amiRNA precursor to the mature guide strand by transduced cells is critical for specific and potent HTT lowering. The selection of the optimized pri-amiRNA comprised a series of in vitro studies followed by in vivo studies in small and then large mammals. Our studies demonstrate the predictivity of certain cell culture systems and rodent models for nonhuman primates (NHP) with respect to some, but not all key features of pri-amiRNA processing. In addition, our results show that the processing of pri-amiRNAs to the mature guide strand can differ greatly across different scaffolds and sequences while providing the same levels of target lowering. Importantly, our data demonstrate that there is a combinatorial effect of guide and passenger strand sequences, together with the scaffold, on pri-amiRNA processing, with different guide and passenger strand sequences within the same scaffold dramatically altering pri-amiRNA processing. Taken together, our results highlight the importance of optimizing not only target lowering, but also the efficiency and precision of pri-amiRNA processing in vitro, in rodents and in large mammals to identify the most potent and selective AAV gene therapy that harnesses the endogenous miRNA biogenesis pathway for target lowering without perturbing the endogenous cellular miRNA profile. The optimized pri-amiRNA was selected with this focus on efficiency and precision of pri-amiRNA processing in addition to its pharmacological activity on HTT lowering, and general tolerability in vivo.
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Affiliation(s)
- Wei Wang
- Voyager Therapeutics Inc, 461444, Cambridge, Massachusetts, United States;
| | - Pengcheng Zhou
- Voyager Therapeutics Inc, 461444, Cambridge, Massachusetts, United States;
| | - Xin Wang
- Voyager Therapeutics Inc, 461444, Cambridge, Massachusetts, United States;
| | - Fen Chen
- Voyager Therapeutics Inc, 461444, Cambridge, Massachusetts, United States;
| | - Emily Christensen
- Voyager Therapeutics Inc, 461444, Cambridge, Massachusetts, United States;
| | - Jeffrey Thompson
- Voyager Therapeutics Inc, 461444, Cambridge, Massachusetts, United States;
| | - Xiaoqin Ren
- Voyager Therapeutics Inc, 461444, Cambridge, Massachusetts, United States;
| | - Adrian Kells
- Voyager Therapeutics Inc, 461444, Cambridge, Massachusetts, United States;
| | - Lisa Stanek
- Sanofi Genzyme, 2194, Cambridge, Massachusetts, United States;
| | - Todd Carter
- Voyager Therapeutics Inc, 461444, Cambridge, Massachusetts, United States;
| | - Jay Hou
- Voyager Therapeutics Inc, 461444, Cambridge, Massachusetts, United States;
| | - Dinah Sah
- Voyager Therapeutics Inc, 461444, 75 Sidney Street, Cambridge, Massachusetts, United States, 02139;
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12
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Sasaki K, Takaoka S, Obata Y. Oocyte-specific gene knockdown by intronic artificial microRNAs driven by Zp3 transcription in mice. J Reprod Dev 2021; 67:229-234. [PMID: 33716236 PMCID: PMC8238676 DOI: 10.1262/jrd.2020-146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Conditional knockout technology is a powerful tool for investigating the spatiotemporal functions of target genes. However, generation of conditional knockout
mice involves complicated breeding programs and considerable time. A recent study has shown that artificially designed microRNAs (amiRNAs), inserted into an
intron of the constitutively expressed gene, induce knockdown of the targeted gene in mice, thus creating a simpler method to analyze the functions of target
genes in oocytes. Here, to establish an oocyte-specific knockdown system, amiRNA sequences against enhanced green fluorescent protein (EGFP) were knocked into
the intronic sites of the Zp3 gene. Knock-in mice were then bred with EGFP transgenic mice. Our results showed that
Zp3-derived amiRNA successfully reduced EGFP fluorescence in the oocytes in a size-dependent manner. Importantly, knockdown of EGFP did not
occur in somatic cells. Thus, we present our knockdown system as a tool for screening gene functions in mouse oocytes.
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Affiliation(s)
- Keisuke Sasaki
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan.,Research Fellow of Japan Society for the Promotion of Science, Tokyo 102-0083, Japan
| | - Saaya Takaoka
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Yayoi Obata
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
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13
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Effective and Accurate Gene Silencing by a Recombinant AAV-Compatible MicroRNA Scaffold. Mol Ther 2019; 28:422-430. [PMID: 31843447 DOI: 10.1016/j.ymthe.2019.11.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 11/11/2019] [Accepted: 11/21/2019] [Indexed: 01/13/2023] Open
Abstract
Short hairpin RNAs that are delivered by recombinant adeno-associated virus (rAAV) have the potential to elicit long-term RNAi therapy for human disease. However, the discovery that short hairpin sequences can cause truncation of the rAAV genome calls into question the efficiency and gene-silencing specificity of this strategy in humans. Here, we report that embedding the guide strand of a small silencing RNA into an artificial microRNA (miRNA) scaffold derived from mouse miRNA-33 ensures rAAV genomic integrity and reduces off-targeting by 10-fold, while maintaining effective in vivo target gene repression in mice.
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14
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Rousset F, Salmon P, Bredl S, Cherpin O, Coelho M, Myburgh R, Alessandrini M, Perny M, Roccio M, Speck RF, Senn P, Krause KH. Optimizing Synthetic miRNA Minigene Architecture for Efficient miRNA Hairpin Concatenation and Multi-target Gene Knockdown. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 14:351-363. [PMID: 30665184 PMCID: PMC6350225 DOI: 10.1016/j.omtn.2018.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 11/30/2018] [Accepted: 12/01/2018] [Indexed: 12/20/2022]
Abstract
Synthetic microRNA (miRNA) minigenes (SMIGs) have a major potential for molecular therapy; however, their optimal architecture still needs to be determined. We have previously optimized the stem structure of miRNA hairpins for efficient gene knockdown. Here, we investigate the overall architecture of SMIGs driven by polymerase II-dependent promoters. When miRNA hairpins were placed directly behind the promoter, gene knockdown was inefficient as compared with constructs containing an intercalated sequence (“spacer”). Spacer sequence was relevant for knockdown efficiency and concatenation potential: GFP-based sequences (even when truncated or including stop codons) were particularly efficient. In contrast, a spacer of similar length based on a CD4 intronic sequence was entirely inefficient. Spacer sequences influenced miRNA steady-state levels without affecting transcript stability. We demonstrate that with an optimized spacer, up to five concatenated hairpins targeting two different genes are efficiently expressed and able to knock down their respective targets. Transplantation of hematopoietic stem cells containing a CCR5 knockdown SMIG demonstrated a sustained in vivo efficacy of our approach. In summary, we have defined features that optimize SMIG efficiency. Based on these results, optimized knockdown of genes of interest, such as the HIV co-receptor CCR5 and the NADPH oxidase subunit p22phox, was achieved.
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Affiliation(s)
- Francis Rousset
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
| | - Patrick Salmon
- Department of Neurosciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Simon Bredl
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, Zurich, Switzerland
| | - Ophélie Cherpin
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Marta Coelho
- Department of Neurosciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Renier Myburgh
- Division of Hematology, University Hospital of Zurich, Zurich, Switzerland
| | - Marco Alessandrini
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Michael Perny
- Department of Otorhinolaryngology, Inselspital and University of Bern, Bern, Switzerland
| | - Marta Roccio
- Department of Otorhinolaryngology, Inselspital and University of Bern, Bern, Switzerland
| | - Roberto F Speck
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, Zurich, Switzerland
| | - Pascal Senn
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Department of Head and Neck Surgery, University Hospital of Geneva, Geneva, Switzerland
| | - Karl Heinz Krause
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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15
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Yu R, Chen C, Cao W, Liu H, Zhou S, Song Y, Zhu C. High-degree and broad-spectrum resistance mediated by a combination of NIb siRNA and miRNA suppresses replication of necrotic and common strains of potato virus Y. Arch Virol 2018; 163:3073-3081. [PMID: 30097746 DOI: 10.1007/s00705-018-3969-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/14/2018] [Indexed: 11/29/2022]
Abstract
In plants, viral replication can be inhibited through gene silencing, which is mediated by short interfering RNA (siRNA) or microRNA (miRNA). However, under natural conditions, viruses are extremely susceptible to mutations that may decrease the efficiency of cleavage of these small RNAs (sRNAs). Therefore, a single sRNA may not provide a sufficient degree of viral resistance to transgenic plants. Potato virus Y necrotic strain (PVYN) and Potato virus Y common strain (PVYO) are the two major PVY strains that cause systemic necrosis and mottling, respectively, in tobacco. In this study, we designed specific siRNAs and miRNAs to target two regions of the PVYO replicase gene (NIb). Eight plant expression vectors containing one or two sRNAs were constructed. Luciferase activity assays showed that the designed sRNAs successfully cleaved the NIb gene of PVYO and PVYN, and the vector carrying a combined siRNA- and miRNA-based short hairpin RNA (shRNA) demonstrated the strongest inhibitory effect. These effects were confirmed through the acquisition of PVYO and PVYN resistance in transgenic sRNA-expressing Nicotiana tabacum plants. This phenomenon could be related to a plant defense mechanism in which siRNA and miRNA pathways are complementary and interact to achieve gene silencing. Furthermore, there is a tendency for the homologous small RNA sequences (PVYO) to be more effective in conferring resistance than those with imperfect homology (PVYN). Overall, these findings confirm that the use of a combined siRNA- and miRNA-based shRNAs is a promising approach for introducing viral resistance to plants through genetic engineering.
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Affiliation(s)
- Ru Yu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Caixia Chen
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Weilin Cao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Hongmei Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Shumei Zhou
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Yunzhi Song
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China.
| | - Changxiang Zhu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China.
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16
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Thalhammer A, Jaudon F, Cingolani LA. Combining Optogenetics with Artificial microRNAs to Characterize the Effects of Gene Knockdown on Presynaptic Function within Intact Neuronal Circuits. J Vis Exp 2018. [PMID: 29608168 PMCID: PMC5931759 DOI: 10.3791/57223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The purpose of this protocol is to characterize the effect of gene knockdown on presynaptic function within intact neuronal circuits. We describe a workflow on how to combine artificial microRNA (miR)-mediated RNA interference with optogenetics to achieve selective stimulation of manipulated presynaptic boutons in acute brain slices. The experimental approach involves the use of a single viral construct and a single neuron-specific promoter to drive the expression of both an optogenetic probe and artificial miR(s) against presynaptic gene(s). When stereotactically injected in the brain region of interest, the expressed construct makes it possible to stimulate with light exclusively the neurons with reduced expression of the gene(s) under investigation. This strategy does not require the development and maintenance of genetically modified mouse lines and can in principle be applied to other organisms and to any neuronal gene of choice. We have recently applied it to investigate how the knockdown of alternative splice isoforms of presynaptic P/Q-type voltage-gated calcium channels (VGCCs) regulates short-term synaptic plasticity at CA3 to CA1 excitatory synapses in acute hippocampal slices. A similar approach could also be used to manipulate and probe the neuronal circuitry in vivo.
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Affiliation(s)
- Agnes Thalhammer
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia
| | - Fanny Jaudon
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia
| | - Lorenzo A Cingolani
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia;
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17
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Du X, Cai Y, Xi W, Zhang R, Jia L, Yang A, Zhao J, Yan B. Multi‑target inhibition by four tandem shRNAs embedded in homo‑ or hetero‑miRNA backbones. Mol Med Rep 2017; 17:307-314. [PMID: 29115602 DOI: 10.3892/mmr.2017.7854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/02/2017] [Indexed: 11/06/2022] Open
Abstract
The functional influence of microRNA (miRNA)backbone selection remains unclear with respect to multiplexing miRNA‑based short hairpin RNAs (shRNAmiRs), due to a lack of comparative studies. To this end, a pair of shRNAmiR tetramers were designed in the present study that targeted four genes with a shared miR30a backbone (homo‑BB) or four miRNA backbones (hetero‑BB). A PBLT+ 293A cell line overexpressing four targets was established, which permitted simultaneous dissection of individual gene knockdown. Multi‑target inhibition was confirmed by a decrease in positive cell populations of the relative gene and mean fluorescence intensities, with almost comparable activities of homo‑ and hetero‑BB tetramers. Of note, this multi‑inhibition was sustained over a 1‑month period, with no notable difference, particularly in the late‑phased inhibitory effects between homo‑ and hetero‑BB tetra‑shRNA miRs. These preliminary data may indicate little influence of scaffold substitution in the functionalities of multiplexed shRNAmiRs and little recombination‑depleted risk of repetitively adopting the same miRNA backbone in this artificial in vitro system. More comparative studies are further required to explore extended repertoires of scaffold‑paralleled multi‑shRNAmiRs in more physiologically relevant models.
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Affiliation(s)
- Xiao Du
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yanhui Cai
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Wenjin Xi
- Department of Immunology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Rui Zhang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Lintao Jia
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Angang Yang
- Department of Immunology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Jing Zhao
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Bo Yan
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
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18
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Fowler DK, Peters JH, Williams C, Washbourne P. Redundant Postsynaptic Functions of SynCAMs 1-3 during Synapse Formation. Front Mol Neurosci 2017; 10:24. [PMID: 28197078 PMCID: PMC5281628 DOI: 10.3389/fnmol.2017.00024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 01/17/2017] [Indexed: 01/13/2023] Open
Abstract
Investigating the roles of synaptogenic adhesion molecules during synapse formation has proven challenging, often due to compensatory functions between additional family members. The synaptic cell adhesion molecules 1–3 (SynCAM1–3) are expressed both pre- and postsynaptically, share highly homologous domains and are synaptogenic when ectopically presented to neurons; yet their endogenous functions during synaptogenesis are unclear. Here we report that SynCAM1–3 are functionally redundant and collectively necessary for synapse formation in cultured hippocampal neurons. Only triple knockdown (KD) of SynCAM1–3 using highly efficient, chained artificial microRNAs (amiRNAs) reduced synapse density and increased synapse area. Electrophysiological recordings of quantal release events supported an increase in synapse size caused by SynCAM1–3 depletion. Furthermore, a combinatorial, mosaic lentiviral approach comparing wild type (WT) and SynCAM1–3 KD neurons in the same culture demonstrate that SynCAM1–3 set synapse number and size through postsynaptic mechanisms. The results demonstrate that the redundancy between SynCAM1–3 has concealed their synaptogenic function at the postsynaptic terminal.
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Affiliation(s)
- Daniel K Fowler
- Department of Biology, Institute of Neuroscience, University of OregonEugene, OR, USA; Department of Integrative Physiology and Neuroscience, Washington State UniversityPullman, WA, USA
| | - James H Peters
- Department of Integrative Physiology and Neuroscience, Washington State University Pullman, WA, USA
| | - Carly Williams
- Department of Biology, Institute of Neuroscience, University of Oregon Eugene, OR, USA
| | - Philip Washbourne
- Department of Biology, Institute of Neuroscience, University of Oregon Eugene, OR, USA
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19
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Tian B, Li J, Oakley TR, Todd TC, Trick HN. Host-Derived Artificial MicroRNA as an Alternative Method to Improve Soybean Resistance to Soybean Cyst Nematode. Genes (Basel) 2016; 7:E122. [PMID: 27941644 PMCID: PMC5192498 DOI: 10.3390/genes7120122] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/17/2016] [Accepted: 12/01/2016] [Indexed: 11/23/2022] Open
Abstract
The soybean cyst nematode (SCN), Heterodera glycines, is one of the most important pests limiting soybean production worldwide. Novel approaches to managing this pest have focused on gene silencing of target nematode sequences using RNA interference (RNAi). With the discovery of endogenous microRNAs as a mode of gene regulation in plants, artificial microRNA (amiRNA) methods have become an alternative method for gene silencing, with the advantage that they can lead to more specific silencing of target genes than traditional RNAi vectors. To explore the application of amiRNAs for improving soybean resistance to SCN, three nematode genes (designated as J15, J20, and J23) were targeted using amiRNA vectors. The transgenic soybean hairy roots, transformed independently with these three amiRNA vectors, showed significant reductions in SCN population densities in bioassays. Expression of the targeted genes within SCN eggs were downregulated in populations feeding on transgenic hairy roots. Our results provide evidence that host-derived amiRNA methods have great potential to improve soybean resistance to SCN. This approach should also limit undesirable phenotypes associated with off-target effects, which is an important consideration for commercialization of transgenic crops.
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Affiliation(s)
- Bin Tian
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
| | - Jiarui Li
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
- Bayer CropScience, 3500 Paramount Pkwy, Morrisville, NC 27560, USA.
| | - Thomas R Oakley
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
| | - Timothy C Todd
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
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20
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Zhang ZQ, Cao Z, Liu C, Li R, Wang WD, Wang XY. MiRNA-Embedded ShRNAs for Radiation-Inducible LGMN Knockdown and the Antitumor Effects on Breast Cancer. PLoS One 2016; 11:e0163446. [PMID: 27656894 PMCID: PMC5033420 DOI: 10.1371/journal.pone.0163446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/08/2016] [Indexed: 11/18/2022] Open
Abstract
Legumain (LGMN) is highly expressed in breast cancer (BC) and other solid tumors and is a potential anticancer target. Here we investigate the anti-tumor effects of short hairpin RNAs (shRNAs) targeting LGMN embedded in a microRNA-155 (miR-155) architecture, which is driven by a radiation-inducible chimeric RNA polymerase II (Pol II) promoter. Lentiviral vectors were generated with the chimeric promoter which controlled the expression of downstream shRNA-miR-155 cassette. Fluorescence was observed by using confocal microscopy. Real-time quantitative PCR and Western blotting were used to determine the expression level of LGMN, MMP2, and MMP9. Furthermore, the proliferation and invasive ability of BC cells was analyzed via plate colony formation and invasion assays. Here we demonstrated that the chimeric promoter could be effectively induced by radiation treatment. Furthermore, the shRNA-miR-155 cassette targeting LGMN could be effectively activated by the chimeric promoter. Radiation plus knockdown of LGMN impairs colony formation and dampens cell migration and invasion in BC cells. Inhibition of LGMN downregulates MMP2 and MMP9 expression in BC cells. Pol II-driven shRNA-miR-155 could effectively suppress the growth and invasiveness of BC cells, and that the interference effects could be regulated by radiation doses. Moreover, knockdown of LGMN alleviates the aggressive phenotype of BC cells through modulating MMPs expression.
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Affiliation(s)
- Zhi-Qiang Zhang
- Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, 400014, China
- Key Laboratory of Pediatrics in Chongqing, Chongqing, 400014, China
- Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, 400014, China
- Department of Critical Care Medicine, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Zhi Cao
- Department of Radiation Oncology, Sichuan Cancer Hospital, Chengdu, 610041, China
| | - Cong Liu
- Institute of Combined Injury, State Key Laboratory of Trauma, Burns and Combined Injury, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Rong Li
- Institute of Combined Injury, State Key Laboratory of Trauma, Burns and Combined Injury, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Wei-Dong Wang
- Department of Radiation Oncology, Sichuan Cancer Hospital, Chengdu, 610041, China
- * E-mail: (WW); (XW)
| | - Xing-Yong Wang
- Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, 400014, China
- Key Laboratory of Pediatrics in Chongqing, Chongqing, 400014, China
- Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, 400014, China
- Department of Critical Care Medicine, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
- * E-mail: (WW); (XW)
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21
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Fowler DK, Stewart S, Seredick S, Eisen JS, Stankunas K, Washbourne P. A MultiSite Gateway Toolkit for Rapid Cloning of Vertebrate Expression Constructs with Diverse Research Applications. PLoS One 2016; 11:e0159277. [PMID: 27500400 PMCID: PMC4976983 DOI: 10.1371/journal.pone.0159277] [Citation(s) in RCA: 8] [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: 05/13/2016] [Accepted: 06/29/2016] [Indexed: 11/19/2022] Open
Abstract
Recombination-based cloning is a quick and efficient way to generate expression vectors. Recent advancements have provided powerful recombinant DNA methods for molecular manipulations. Here, we describe a novel collection of three-fragment MultiSite Gateway cloning system-compatible vectors providing expanded molecular tools for vertebrate research. The components of this toolkit encompass a broad range of uses such as fluorescent imaging, dual gene expression, RNA interference, tandem affinity purification, chemically-inducible dimerization and lentiviral production. We demonstrate examples highlighting the utility of this toolkit for producing multi-component vertebrate expression vectors with diverse primary research applications. The vectors presented here are compatible with other Gateway toolkits and collections, facilitating the rapid generation of a broad range of innovative DNA constructs for biological research.
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Affiliation(s)
- Daniel K. Fowler
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Scott Stewart
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Steve Seredick
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Judith S. Eisen
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Kryn Stankunas
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
- * E-mail: (PW); (KS)
| | - Philip Washbourne
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
- * E-mail: (PW); (KS)
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