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Mata-Ventosa A, Vila-Planas A, Solsona-Pujol A, Dueña JDL, Torrents M, Izquierdo-García E, Pastor-Anglada M, Pérez-Torras S, Terrazas M. RNase H-sensitive multifunctional ASO-based constructs as promising tools for the treatment of multifactorial complex pathologies. Bioorg Chem 2024; 150:107595. [PMID: 38968904 DOI: 10.1016/j.bioorg.2024.107595] [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: 05/08/2024] [Revised: 06/13/2024] [Accepted: 06/24/2024] [Indexed: 07/07/2024]
Abstract
Combined therapies play a key role in the fight against complex pathologies, such as cancer and related drug-resistance issues. This is particularly relevant in targeted therapies where inhibition of the drug target can be overcome by cross-activating complementary pathways. Unfortunately, the drug combinations approved to date -mostly based on small molecules- face several problems such as toxicity effects, which limit their clinical use. To address these issues, we have designed a new class of RNase H-sensitive construct (3ASO) that can be disassembled intracellularly upon cell entry, leading to the simultaneous release of three different therapeutic oligonucleotides (ONs), tackling each of them the mRNA of a different protein. Here, we used Escherichia coli RNase H1 as a model to study an unprecedented mode of recognition and cleavage, that is mainly dictated by the topology of our RNA·DNA-based hybrid construct. As a model system for our technology we have created 3ASO constructs designed to specifically inhibit the expression of HER2, Akt and Hsp27 in HER2+ breast cancer cells. These trifunctional ON tools displayed very low toxicity and good levels of antiproliferative activity in HER2+ breast cancer cells. The present study will be of great potential in the fight against complex pathologies involving multiple mRNA targets, as the proposed cleavable designs will allow the efficient single-dose administration of different ON drugs simultaneously.
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Affiliation(s)
- Aida Mata-Ventosa
- Molecular Pharmacology and Experimental Therapeutics, Department of Biochemistry and Molecular Biomedicine, Institute of Biomedicine, University of Barcelona (IBUB), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBER EHD), Instituto de Salud Carlos III, Madrid, Spain; Institut de Recerca Sant Joan de Déu (IR SJD-CERCA), Esplugues de Llobregat, Barcelona, Spain
| | - Ariadna Vila-Planas
- Department of Inorganic and Organic Chemistry, Organic Chemistry Section, Institute of Biomedicine, University of Barcelona (IBUB), Barcelona, Spain
| | - Aina Solsona-Pujol
- Department of Inorganic and Organic Chemistry, Organic Chemistry Section, Institute of Biomedicine, University of Barcelona (IBUB), Barcelona, Spain; BioFrontiers Institute, University of Colorado, Boulder, CO, United States; Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, United States
| | - Jordi de la Dueña
- Department of Inorganic and Organic Chemistry, Organic Chemistry Section, Institute of Biomedicine, University of Barcelona (IBUB), Barcelona, Spain
| | - Maria Torrents
- Department of Inorganic and Organic Chemistry, Organic Chemistry Section, Institute of Biomedicine, University of Barcelona (IBUB), Barcelona, Spain
| | - Eduardo Izquierdo-García
- Department of Inorganic and Organic Chemistry, Organic Chemistry Section, Institute of Biomedicine, University of Barcelona (IBUB), Barcelona, Spain
| | - Marçal Pastor-Anglada
- Molecular Pharmacology and Experimental Therapeutics, Department of Biochemistry and Molecular Biomedicine, Institute of Biomedicine, University of Barcelona (IBUB), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBER EHD), Instituto de Salud Carlos III, Madrid, Spain; Institut de Recerca Sant Joan de Déu (IR SJD-CERCA), Esplugues de Llobregat, Barcelona, Spain
| | - Sandra Pérez-Torras
- Molecular Pharmacology and Experimental Therapeutics, Department of Biochemistry and Molecular Biomedicine, Institute of Biomedicine, University of Barcelona (IBUB), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBER EHD), Instituto de Salud Carlos III, Madrid, Spain; Institut de Recerca Sant Joan de Déu (IR SJD-CERCA), Esplugues de Llobregat, Barcelona, Spain.
| | - Montserrat Terrazas
- Department of Inorganic and Organic Chemistry, Organic Chemistry Section, Institute of Biomedicine, University of Barcelona (IBUB), Barcelona, Spain.
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Zhang Y, Yu Y, Yang Y, Wang Y, Yu C. Engineered Silica Nanoparticles for Nucleic Acid Delivery. SMALL METHODS 2024; 8:e2300812. [PMID: 37906035 DOI: 10.1002/smtd.202300812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/14/2023] [Indexed: 11/02/2023]
Abstract
The development of nucleic acid-based drugs holds great promise for therapeutic applications, but their effective delivery into cells is hindered by poor cellular membrane permeability and inherent instability. To overcome these challenges, delivery vehicles are required to protect and deliver nucleic acids efficiently. Silica nanoparticles (SiNPs) have emerged as promising nanovectors and recently bioregulators for gene delivery due to their unique advantages. In this review, a summary of recent advancements in the design of SiNPs for nucleic acid delivery and their applications is provided, mainly according to the specific type of nucleic acids. First, the structural characteristics and working mechanisms of various types of nucleic acids are introduced and classified according to their functions. Subsequently, for each nucleic acid type, the use of SiNPs for enhancing delivery performance and their biomedical applications are summarized. The tailored design of SiNPs for selected type of nucleic acid delivery will be highlighted considering the characteristics of nucleic acids. Lastly, the limitations in current research and personal perspectives on future directions in this field are presented. It is expected this opportune review will provide insights into a burgeoning research area for the development of next-generation SiNP-based nucleic acid delivery systems.
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Affiliation(s)
- Yue Zhang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Yingjie Yu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Yannan Yang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, 4072, Australia
- Shanghai Frontiers Science Research Base of Intelligent Optoelectronics and Perception, Institute of Optoelectronics, Fudan University, Shanghai, 200433, P. R. China
| | - Yue Wang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Chengzhong Yu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, 4072, Australia
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China
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Hunt JP, Wilding KM, Barnett RJ, Robinson H, Soltani M, Cho JE, Bundy BC. Engineering Cell‐Free Protein Synthesis for High‐Yield Production and Human Serum Activity Assessment of Asparaginase: Toward On‐Demand Treatment of Acute Lymphoblastic Leukemia. Biotechnol J 2020; 15:e1900294. [DOI: 10.1002/biot.201900294] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/13/2019] [Indexed: 12/22/2022]
Affiliation(s)
- J. Porter Hunt
- Department of Chemical Engineering Brigham Young University Provo UT 84602 USA
| | - Kristen M. Wilding
- Department of Chemical Engineering Brigham Young University Provo UT 84602 USA
| | - R. Jordan Barnett
- Department of Chemical Engineering Brigham Young University Provo UT 84602 USA
| | - Hannah Robinson
- Department of Chemical Engineering Brigham Young University Provo UT 84602 USA
| | - Mehran Soltani
- Department of Chemical Engineering Brigham Young University Provo UT 84602 USA
| | - Jae Eun Cho
- Department of Chemical Engineering Brigham Young University Provo UT 84602 USA
| | - Bradley C. Bundy
- Department of Chemical Engineering Brigham Young University Provo UT 84602 USA
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Kim SK, Yoon PK, Kim SJ, Woo SG, Rha E, Lee H, Yeom SJ, Kim H, Lee DH, Lee SG. CRISPR interference-mediated gene regulation in Pseudomonas putida KT2440. Microb Biotechnol 2019; 13:210-221. [PMID: 30793496 PMCID: PMC6922533 DOI: 10.1111/1751-7915.13382] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 01/08/2023] Open
Abstract
Targeted gene regulation is indispensable for reprogramming a cellular network to modulate a microbial phenotype. Here, we adopted the type II CRISPR interference (CRISPRi) system for simple and efficient regulation of target genes in Pseudomonas putida KT2440. A single CRISPRi plasmid was generated to express a nuclease-deficient Cas9 gene and a designed single guide RNA, under control of l-rhamnose-inducible Prha BAD and the constitutive Biobrick J23119 promoter respectively. Two target genes were selected to probe the CRISPRi-mediated gene regulation: exogenous green fluorescent protein on the multicopy plasmid and endogenous glpR on the P. putida KT2440 chromosome, encoding GlpR, a transcriptional regulator that represses expression of the glpFKRD gene cluster for glycerol utilization. The CRISPRi system successfully repressed the two target genes, as evidenced by a reduction in the fluorescence intensity and the lag phase of P. putida KT2440 cell growth on glycerol. Furthermore, CRISPRi-mediated repression of glpR improved both the cell growth and glycerol utilization, resulting in the enhanced production of mevalonate in an engineered P. putida KT2440 harbouring heterologous genes for the mevalonate pathway. CRISPRi is expected to become a robust tool to reprogram P. putida KT2440 for the development of microbial cell factories producing industrially valuable products.
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Affiliation(s)
- Seong Keun Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Paul K Yoon
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Soo-Jung Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Seung-Gyun Woo
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Eugene Rha
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Hyewon Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Soo-Jin Yeom
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Haseong Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Dae-Hee Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Korea
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Jang YJ, Lee KH, Yoo TH, Kim DM. Interfacing a Personal Glucose Meter with Cell-Free Protein Synthesis for Rapid Analysis of Amino Acids. Anal Chem 2019; 91:2531-2535. [DOI: 10.1021/acs.analchem.8b05526] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yeon-Jae Jang
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Kyung-Ho Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 Worldcup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
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Kim SK, Han GH, Seong W, Kim H, Kim SW, Lee DH, Lee SG. CRISPR interference-guided balancing of a biosynthetic mevalonate pathway increases terpenoid production. Metab Eng 2016; 38:228-240. [DOI: 10.1016/j.ymben.2016.08.006] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/10/2016] [Accepted: 08/24/2016] [Indexed: 11/26/2022]
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