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Yıldırım Akdeniz G, Timuçin AC. Structure based computational RNA design towards MafA transcriptional repressor implicated in multiple myeloma. J Mol Graph Model 2024; 132:108839. [PMID: 39096645 DOI: 10.1016/j.jmgm.2024.108839] [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: 04/27/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024]
Abstract
Multiple myeloma is recognized as the second most common hematological cancer. MafA transcriptional repressor is an established mediator of myelomagenesis. While there are multitude of drugs available for targeting various effectors in multiple myeloma, current literature lacks a candidate RNA based MafA modulator. Thus, using the structure of MafA homodimer-consensus target DNA, a computational effort was implemented to design a novel RNA based chemical modulator against MafA. First, available MafA-consensus DNA structure was employed to generate an RNA library. This library was further subjected to global docking to select the most plausible RNA candidates, preferring to bind DNA binding region of MafA. Following global docking, MD-ready complexes that were prepared via local docking program, were subjected to 500 ns of MD simulations. First, each of these MD simulations were analyzed for relative binding free energy through MM-PBSA method, which pointed towards a strong RNA based MafA binder, RNA1. Second, through a detailed MD analysis, RNA1 was shown to prefer binding to a single monomer of the dimeric DNA binding domain of MafA using higher number of hydrophobic interactions compared with positive control MafA-DNA complex. At the final phase, a principal component analyses was conducted, which led us to identify the actual interaction region of RNA1 and MafA monomer. Overall, to our knowledge, this is the first computational study that presents an RNA molecule capable of potentially targeting MafA protein. Furthermore, limitations of our study together with possible future implications of RNA1 in multiple myeloma were also discussed.
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Affiliation(s)
- Güneş Yıldırım Akdeniz
- Department of Molecular Biology, Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, Sabancı University, 34956, Tuzla, İstanbul, Turkey.
| | - Ahmet Can Timuçin
- Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Acıbadem Mehmet Ali Aydınlar University, 34752, Ataşehir, İstanbul, Turkey.
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Peterson CW, Venkataraman R, Reddy SS, Pande D, Enstrom MR, Radtke S, Humbert O, Kiem HP. Intracellular RNase activity dampens zinc finger nuclease-mediated gene editing in hematopoietic stem and progenitor cells. Mol Ther Methods Clin Dev 2022; 24:30-39. [PMID: 34977270 PMCID: PMC8671732 DOI: 10.1016/j.omtm.2021.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/19/2021] [Indexed: 12/21/2022]
Abstract
Over the past decade, numerous gene-editing platforms which alter host DNA in a highly specific and targeted fashion have been described. Two notable examples are zinc finger nucleases (ZFNs), the first gene-editing platform to be tested in clinical trials, and more recently, CRISPR/Cas9. Although CRISPR/Cas9 approaches have become arguably the most popular platform in the field, the therapeutic advantages and disadvantages of each strategy are only beginning to emerge. We have established a nonhuman primate (NHP) model that serves as a strong predictor of successful gene therapy and gene-editing approaches in humans; our recent work shows that ZFN-edited hematopoietic stem and progenitor cells (HSPCs) engraft at lower levels than CRISPR/Cas9-edited cells. Here, we investigate the mechanisms underlying this difference. We show that optimized culture conditions, including defined serum-free media, augment engraftment of gene-edited NHP HSPCs in a mouse xenograft model. Furthermore, we identify intracellular RNases as major barriers for mRNA-encoded nucleases relative to preformed enzymatically active CRISPR/Cas9 ribonucleoprotein (RNP) complexes. We conclude that CRISPR/Cas9 RNP gene editing is more stable and efficient than ZFN mRNA-based delivery and identify co-delivered RNase inhibitors as a strategy to enhance the expression of gene-editing proteins from mRNA intermediates.
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Affiliation(s)
- Christopher W. Peterson
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Rasika Venkataraman
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Sowmya S. Reddy
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Dnyanada Pande
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Mark R. Enstrom
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Stefan Radtke
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Olivier Humbert
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Hans-Peter Kiem
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
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Garcia A, Dunoyer-Geindre S, Fish RJ, Neerman-Arbez M, Reny JL, Fontana P. Methods to Investigate miRNA Function: Focus on Platelet Reactivity. Thromb Haemost 2021; 121:409-421. [PMID: 33124028 PMCID: PMC8263142 DOI: 10.1055/s-0040-1718730] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs modulating protein production. They are key players in regulation of cell function and are considered as biomarkers in several diseases. The identification of the proteins they regulate, and their impact on cell physiology, may delineate their role as diagnostic or prognostic markers and identify new therapeutic strategies. During the last 3 decades, development of a large panel of techniques has given rise to multiple models dedicated to the study of miRNAs. Since plasma samples are easily accessible, circulating miRNAs can be studied in clinical trials. To quantify miRNAs in numerous plasma samples, the choice of extraction and purification techniques, as well as normalization procedures, are important for comparisons of miRNA levels in populations and over time. Recent advances in bioinformatics provide tools to identify putative miRNAs targets that can then be validated with dedicated assays. In vitro and in vivo approaches aim to functionally validate candidate miRNAs from correlations and to understand their impact on cellular processes. This review describes the advantages and pitfalls of the available techniques for translational research to study miRNAs with a focus on their role in regulating platelet reactivity.
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Affiliation(s)
- Alix Garcia
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Richard J. Fish
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Marguerite Neerman-Arbez
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- iGE3, Institute of Genetics and Genomics in Geneva, Geneva, Switzerland
| | - Jean-Luc Reny
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of General Internal Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Pierre Fontana
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Angiology and Haemostasis, Geneva University Hospitals, Geneva, Switzerland
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Tarakanchikova Y, Alzubi J, Pennucci V, Follo M, Kochergin B, Muslimov A, Skovorodkin I, Vainio S, Antipina MN, Atkin V, Popov A, Meglinski I, Cathomen T, Cornu TI, Gorin DA, Sukhorukov GB, Nazarenko I. Biodegradable Nanocarriers Resembling Extracellular Vesicles Deliver Genetic Material with the Highest Efficiency to Various Cell Types. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1904880. [PMID: 31840408 DOI: 10.1002/smll.201904880] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/31/2019] [Indexed: 05/11/2023]
Abstract
Efficient delivery of genetic material to primary cells remains challenging. Here, efficient transfer of genetic material is presented using synthetic biodegradable nanocarriers, resembling extracellular vesicles in their biomechanical properties. This is based on two main technological achievements: generation of soft biodegradable polyelectrolyte capsules in nanosize and efficient application of the nanocapsules for co-transfer of different RNAs to tumor cell lines and primary cells, including hematopoietic progenitor cells and primary T cells. Near to 100% efficiency is reached using only 2.5 × 10-4 pmol of siRNA, and 1 × 10-3 nmol of mRNA per cell, which is several magnitude orders below the amounts reported for any of methods published so far. The data show that biodegradable nanocapsules represent a universal and highly efficient biomimetic platform for the transfer of genetic material with the utmost potential to revolutionize gene transfer technology in vitro and in vivo.
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Affiliation(s)
- Yana Tarakanchikova
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
- Opto-Electronics and Measurement Techniques Research Unit, P.O. Box 4500, University of Oulu, Oulu, 90014, Finland
- Nanobiotechnology Laboratory, St. Petersburg Academic University, St. Petersburg, 194021, Russia
- RASA center in St. Petersburg, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Jamal Alzubi
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
| | - Valentina Pennucci
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
| | - Marie Follo
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, 153000, Germany
| | - Boris Kochergin
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
- Department of Inorganic Chemistry, Ivanovo State University of Chemistry and Technology, Sheremetievskiy Avenue 7, 153000, Ivanovo, Russia
| | - Albert Muslimov
- Nanobiotechnology Laboratory, St. Petersburg Academic University, St. Petersburg, 194021, Russia
| | - Ilya Skovorodkin
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, Laboratory of Developmental Biology, Infotech Oulu, University of Oulu, Borealis Biobank of Northern Finland, 138634, Oulu, Finland
| | - Seppo Vainio
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, Laboratory of Developmental Biology, Infotech Oulu, University of Oulu, Borealis Biobank of Northern Finland, 138634, Oulu, Finland
| | - Maria N Antipina
- Institute of Materials Research and Engineering, A*STAR, Singapore, 138634, Singapore
| | - Vsevolod Atkin
- Educational Research Institute of Nanostructures and Biosystems, Saratov State University, Saratov, Astrakhanskaya 83, 410012, Saratov, Russia
| | - Alexey Popov
- Opto-Electronics and Measurement Techniques Research Unit, P.O. Box 4500, University of Oulu, Oulu, 90014, Finland
| | - Igor Meglinski
- Opto-Electronics and Measurement Techniques Research Unit, P.O. Box 4500, University of Oulu, Oulu, 90014, Finland
- Aston Institute of Materials Research, School of Engineering and Applied Science, Aston University, Birmingham, B4 7ET, UK
- School of Life and Health Sciences, Aston University, Birmingham, B4 7ET, UK
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
| | - Tatjana I Cornu
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
| | - Dmitry A Gorin
- Skoltech center of Photonics & Quantum Materials, Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Building 3, Moscow, 143026, Russia
| | - Gleb B Sukhorukov
- Educational Research Institute of Nanostructures and Biosystems, Saratov State University, Saratov, Astrakhanskaya 83, 410012, Saratov, Russia
- School of Engineering and Material Science, Queen Mary University of London, London, B47ET, UK
| | - Irina Nazarenko
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, B47ET, Germany
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