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Vázquez-Domínguez I, Anido AA, Duijkers L, Hoppenbrouwers T, Hoogendoorn ADM, Koster C, Collin RWJ, Garanto A. Efficacy, biodistribution and safety comparison of chemically modified antisense oligonucleotides in the retina. Nucleic Acids Res 2024:gkae686. [PMID: 39119918 DOI: 10.1093/nar/gkae686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 06/25/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
Antisense oligonucleotides (AONs) are a versatile tool for treating inherited retinal diseases. However, little is known about how different chemical modifications of AONs can affect their biodistribution, toxicity, and uptake in the retina. Here, we addressed this question by comparing splice-switching AONs with three different chemical modifications commonly used in a clinical setting (2'O-methyl-phosphorothioate (2-OMe/PS), 2'O-methoxyethyl-phosphoriate (2-MOE/PS), and phosphorodiamidite morpholino oligomers (PMO)). These AONs targeted genes exclusively expressed in certain types of retinal cells. Overall, studies in vitro and in vivo in C57BL/6J wild-type mouse retinas showed that 2-OMe/PS and 2-MOE/PS AONs have comparable efficacy and safety profiles. In contrast, octa-guanidine-dendrimer-conjugated in vivo PMO-oligonucleotides (ivPMO) caused toxicity. This was evidenced by externally visible ocular phenotypes in 88.5% of all ivPMO-treated animals, accompanied by severe alterations at the morphological level. However, delivery of unmodified PMO-AONs did not cause any toxicity, although it clearly reduced the efficacy. We conducted the first systematic comparison of different chemical modifications of AONs in the retina. Our results showed that the same AON sequence with different chemical modifications displayed different splicing modulation efficacies, suggesting the 2'MOE/PS modification as the most efficacious in these conditions. Thereby, our work provides important insights for future clinical applications.
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Affiliation(s)
| | - Alejandro Allo Anido
- Radboud university medical center, Department of Human Genetics, Nijmegen, The Netherlands
| | - Lonneke Duijkers
- Radboud university medical center, Department of Human Genetics, Nijmegen, The Netherlands
| | - Tamara Hoppenbrouwers
- Radboud university medical center, Department of Human Genetics, Nijmegen, The Netherlands
| | - Anita D M Hoogendoorn
- Radboud university medical center, Amalia Children's Hospital, Department of Pediatrics, Nijmegen, The Netherlands
| | - Céline Koster
- Departments of Human Genetics and Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Rob W J Collin
- Radboud university medical center, Department of Human Genetics, Nijmegen, The Netherlands
| | - Alejandro Garanto
- Radboud university medical center, Department of Human Genetics, Nijmegen, The Netherlands
- Radboud university medical center, Amalia Children's Hospital, Department of Pediatrics, Nijmegen, The Netherlands
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2
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Lebenzon JE, Toxopeus J. Knock down to level up: Reframing RNAi for invertebrate ecophysiology. Comp Biochem Physiol A Mol Integr Physiol 2024; 297:111703. [PMID: 39029617 DOI: 10.1016/j.cbpa.2024.111703] [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: 02/21/2024] [Revised: 07/16/2024] [Accepted: 07/16/2024] [Indexed: 07/21/2024]
Abstract
Comparative ecophysiologists strive to understand physiological problems in non-model organisms, but molecular tools such as RNA interference (RNAi) are under-used in our field. Here, we provide a framework for invertebrate ecophysiologists to use RNAi to answer questions focused on physiological processes, rather than as a tool to investigate gene function. We specifically focus on non-model invertebrates, in which the use of other genetic tools (e.g., genetic knockout lines) is less likely. We argue that because RNAi elicits a temporary manipulation of gene expression, and resources to carry out RNAi are technically and financially accessible, it is an effective tool for invertebrate ecophysiologists. We cover the terminology and basic mechanisms of RNA interference as an accessible introduction for "non-molecular" physiologists, include a suggested workflow for identifying RNAi gene targets and validating biologically relevant gene knockdowns, and present a hypothesis-testing framework for using RNAi to answer common questions in the realm of invertebrate ecophysiology. This review encourages invertebrate ecophysiologists to use these tools and workflows to explore physiological processes and bridge genotypes to phenotypes in their animal(s) of interest.
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Affiliation(s)
- Jacqueline E Lebenzon
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4.
| | - Jantina Toxopeus
- Department of Biology, St. Francis Xavier University, 2321 Notre Dame Ave, Antigonish, NS, Canada B2G 2W5
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3
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Leckie J, Yokota T. Potential of Cell-Penetrating Peptide-Conjugated Antisense Oligonucleotides for the Treatment of SMA. Molecules 2024; 29:2658. [PMID: 38893532 PMCID: PMC11173757 DOI: 10.3390/molecules29112658] [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: 05/06/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Spinal muscular atrophy (SMA) is a severe neuromuscular disorder that is caused by mutations in the survival motor neuron 1 (SMN1) gene, hindering the production of functional survival motor neuron (SMN) proteins. Antisense oligonucleotides (ASOs), a versatile DNA-like drug, are adept at binding to target RNA to prevent translation or promote alternative splicing. Nusinersen is an FDA-approved ASO for the treatment of SMA. It effectively promotes alternative splicing in pre-mRNA transcribed from the SMN2 gene, an analog of the SMN1 gene, to produce a greater amount of full-length SMN protein, to compensate for the loss of functional protein translated from SMN1. Despite its efficacy in ameliorating SMA symptoms, the cellular uptake of these ASOs is suboptimal, and their inability to penetrate the CNS necessitates invasive lumbar punctures. Cell-penetrating peptides (CPPs), which can be conjugated to ASOs, represent a promising approach to improve the efficiency of these treatments for SMA and have the potential to transverse the blood-brain barrier to circumvent the need for intrusive intrathecal injections and their associated adverse effects. This review provides a comprehensive analysis of ASO therapies, their application for the treatment of SMA, and the encouraging potential of CPPs as delivery systems to improve ASO uptake and overall efficiency.
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Affiliation(s)
- Jamie Leckie
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- The Friends of Garrett Cumming Research & Muscular Dystrophy Canada HM Toupin Neurological Sciences Research, Edmonton, AB T6G 2H7, Canada
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4
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Yu S, Liao R, Bai L, Guo M, Zhang Y, Zhang Y, Yang Q, Song Y, Li Z, Meng Q, Wang S, Huang X. Anticancer effect of hUC-MSC-derived exosome-mediated delivery of PMO-miR-146b-5p in colorectal cancer. Drug Deliv Transl Res 2024; 14:1352-1369. [PMID: 37978163 PMCID: PMC10984892 DOI: 10.1007/s13346-023-01469-7] [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] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Antisense oligonucleotide (ASO) is a novel therapeutic platform for targeted cancer therapy. Previously, we have demonstrated that miR-146b-5p plays an important role in colorectal cancer progression. However, a safe and effective strategy for delivery of an ASO to its targeted RNA remains as a major hurdle in translational advances. Human umbilical cord mesenchymal cell (hUC-MSC)-derived exosomes were used as vehicles to deliver an anti-miR-146b-5p ASO (PMO-146b). PMO-146b was assembled onto the surface of exosomes (e) through covalent conjugation to an anchor peptide CP05 (P) that recognized an exosomal surface marker, CD63, forming a complex named ePPMO-146b. After ePPMO-146b treatment, cell proliferation, uptake ability, and migration assays were performed, and epithelial-mesenchymal transition progression was evaluated in vitro. A mouse xenograft model was used to determine the antitumor effect and distribution of ePPMO-146b in vivo. ePPMO-146b was taken up by SW620 cells and effectively inhibited cell proliferation and migration. The conjugate also exerted antitumor efficacy in a xenograft mouse model of colon cancer by systematic administration, where PPMO-146b was enriched in tumor tissue. Our study highlights the potential of hUC-MSC-derived exosomes anchored with PPMO-146b as a novel safe and effective approach for PMO backboned ASO delivery.
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Affiliation(s)
- Siming Yu
- Department of Pharmacy, Guangdong Province, Peking University Shenzhen Hospital, Shenzhen, 518036, People's Republic of China
- Department of Pharmacy, PKU-Shenzhen Clinical Institute of Shantou University Medical College, Shenzhen, People's Republic of China
| | - Ran Liao
- Biotherapy Center, Harbin Medical University Cancer Hospital, Heilongjiang Province, Harbin, 150081, People's Republic of China
| | - Lu Bai
- Department of Laboratory, Lianyungang Maternal and Child Health Care Hospital, Jiangsu Province, Lianyungang, 222000, People's Republic of China
| | - Madi Guo
- Biotherapy Center, Harbin Medical University Cancer Hospital, Heilongjiang Province, Harbin, 150081, People's Republic of China
| | - Yu Zhang
- Biotherapy Center, Harbin Medical University Cancer Hospital, Heilongjiang Province, Harbin, 150081, People's Republic of China
| | - Yumin Zhang
- Biotherapy Center, Harbin Medical University Cancer Hospital, Heilongjiang Province, Harbin, 150081, People's Republic of China
| | - Qi Yang
- Biotherapy Center, Harbin Medical University Cancer Hospital, Heilongjiang Province, Harbin, 150081, People's Republic of China
| | - Yushuai Song
- Department of Laboratory, Lianyungang Maternal and Child Health Care Hospital, Jiangsu Province, Lianyungang, 222000, People's Republic of China
| | - Zhiwei Li
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Heilongjiang Province, Harbin, 150081, People's Republic of China
| | - Qingwei Meng
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Heilongjiang Province, Harbin City, 150081, People's Republic of China
| | - Shubin Wang
- Department of Oncology, Guangdong Province, Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Cancer Institute, Peking University Shenzhen Hospital, Shenzhen-Peking University-Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, People's Republic of China
| | - Xiaoyi Huang
- Biotherapy Center, Harbin Medical University Cancer Hospital, Heilongjiang Province, Harbin, 150081, People's Republic of China.
- NHC Key Laboratory of Cell Transplantation, Harbin Medical University, Heilongjiang Province, Harbin, 150081, People's Republic of China.
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Das A, Gupta S, Shaw P, Sinha S. Synthesis of Self Permeable Antisense PMO Using C5-Guanidino-Functionalized Pyrimidines at the 5'-End Enables Sox2 Downregulation in Triple Negative Breast Cancer Cells. Mol Pharm 2024; 21:1256-1271. [PMID: 38324380 DOI: 10.1021/acs.molpharmaceut.3c00924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Delivery of macromolecular drugs inside cells has been a huge challenge in the field of oligonucleotide therapeutics for the past few decades. Earliest natural inspirations included the arginine rich stretch of cell permeable HIV-TAT peptide, which led to the design of several molecular transporters with varying numbers of rigid or flexible guanidinium units with different tethering groups. These transporters have been shown to efficiently deliver phosphorodiamidate morpholino oligonucleotides, which have a neutral backbone and cannot form lipoplexes. In this report, PMO based delivery agents having 3 or 4 guanidinium groups at the C5 position of the nucleobases of cytosine and uracil have been explored, which can be assimilated within the desired stretch of the antisense oligonucleotide. Guanidinium units have been connected by varying the flexibility with either a saturated (propyl) or an unsaturated (propargyl) spacer, which showed different serum dependency along with varied cytoplasmic distribution. The effect of cholesterol conjugation in the delivery agent as well as at the 5'-end of full length PMO in cellular delivery has also been studied. Finally, the efficacy of the delivery has been studied by the PMO mediated downregulation of the stemness marker Sox2 in the triple-negative breast cancer cell line MDA-MB 231. These results have validated the use of this class of delivery agents, which permit at a stretch PMO synthesis where the modified bases can also participate in Watson-Crick-Franklin base pairing for enhanced mRNA binding and protein downregulation and could solve the delivery problem of PMO.
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Affiliation(s)
- Arnab Das
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Shalini Gupta
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Pallab Shaw
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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6
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Deng L, Gao R, Chen H, Jiao B, Zhang C, Wei L, Yan C, Ye-Lehmann S, Zhu T, Chen C. Let-7b-TLR7 Signaling Axis Contributes to the Anesthesia/Surgery-Induced Cognitive Impairment. Mol Neurobiol 2024; 61:1818-1832. [PMID: 37782443 DOI: 10.1007/s12035-023-03658-4] [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: 04/10/2023] [Accepted: 09/15/2023] [Indexed: 10/03/2023]
Abstract
Perioperative neurocognitive disorders (PNDs) are severe and common neurological complications among elderly patients following anesthesia and surgery. As the first line of defense of the innate immune system, Toll-like receptors (TLRs) have been found to be involved in the occurrence of neurodegenerative diseases in recent years. However, the role of TLR7 in the pathology and development of PNDs remains largely unclear. In our current study, we hypothesized that increased microRNA let-7b (let-7b) during anesthesia and surgical operation would activate TLR7 signaling pathways and mediate PNDs. Using a mouse model of PNDs, 18-20 months wild-type (WT) mice were undergoing unilateral nephrectomy, and increased TLR7 and let-7b expression levels were found in the surgery group compared with the Sham group. Of note, increased TLR7 was found to be co-localized with let-7b in the hippocampal area CA1 in the PNDs model. In addition, TLR7 and let-7b inhibition could improve hippocampus-dependent memory and attenuate the production of inflammatory cytokines. Together, our results indicated that TLR7 activation and up-regulation might be triggered by increased let-7b under stressful conditions and initiated the downstream inflammatory signaling, playing a substantial role in the development of PNDs.
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Affiliation(s)
- Liyun Deng
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu, China
| | - Rui Gao
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu, China
| | - Hai Chen
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Bo Jiao
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu, China
| | - Changteng Zhang
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu, China
| | - Liuxing Wei
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu, China
| | - Caiyi Yan
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu, China
| | - Shixin Ye-Lehmann
- Unité INSERM U1195, Diseases and Hormones of the Nervous System, University of Paris-Scalay, Bicêtre Hosptial, Bât. Grégory Pincus, Le Kremlin-Bicêtre, France
| | - Tao Zhu
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu, China
| | - Chan Chen
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China.
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu, China.
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7
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Kawamoto Y, Wu Y, Takahashi Y, Takakura Y. Development of nucleic acid medicines based on chemical technology. Adv Drug Deliv Rev 2023; 199:114872. [PMID: 37244354 DOI: 10.1016/j.addr.2023.114872] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - You Wu
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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8
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Das U, Kundu J, Shaw P, Bose C, Ghosh A, Gupta S, Sarkar S, Bhadra J, Sinha S. Self-transfecting GMO-PMO chimera targeting Nanog enable gene silencing in vitro and suppresses tumor growth in 4T1 allografts in mouse. MOLECULAR THERAPY - NUCLEIC ACIDS 2023; 32:203-228. [PMID: 37078062 PMCID: PMC10106836 DOI: 10.1016/j.omtn.2023.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 03/16/2023] [Indexed: 04/05/2023]
Abstract
Phosphorodiamidate morpholino oligonucleotide (PMO)-based antisense reagents cannot enter cells without the help of a delivery technique, which limits their clinical applications. To overcome this problem, self-transfecting guanidinium-linked morpholino (GMO)-PMO or PMO-GMO chimeras have been explored as antisense agents. GMO facilitates cellular internalization and participates in Watson-Crick base pairing. Targeting NANOG in MCF7 cells resulted in decline of the whole epithelial to mesenchymal transition (EMT) and stemness pathway, evident through its phenotypic manifestations, all of which were promulgated in combination with Taxol due to downregulation of MDR1 and ABCG2. GMO-PMO-mediated knockdown of no tail gene resulted in desired phenotypes in zebrafish even upon delivery after 16-cell stages. In BALB/c mice, 4T1 allografts were found to regress via intra-tumoral administration of NANOG GMO-PMO antisense oligonucleotides (ASOs), which was associated with occurrence of necrotic regions. GMO-PMO-mediated tumor regression restored histopathological damage in liver, kidney, and spleen caused by 4T1 mammary carcinoma. Serum parameters of systemic toxicity indicated that GMO-PMO chimeras are safe. To the best of our knowledge, self-transfecting antisense reagent is the first report since the discovery of guanidinium-linked DNA (DNG), which could be useful as a combination cancer therapy and, in principle, can render inhibition of any target gene without using any delivery vehicle.
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Maksudov F, Kliuchnikov E, Pierson D, Ujwal M, Marx KA, Chanda A, Barsegov V. Therapeutic phosphorodiamidate morpholino oligonucleotides: Physical properties, solution structures, and folding thermodynamics. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:631-647. [PMID: 36910708 PMCID: PMC9996446 DOI: 10.1016/j.omtn.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
Elucidating the structure-function relationships for therapeutic RNA mimicking phosphorodiamidate morpholino oligonucleotides (PMOs) is challenging due to the lack of information about their structures. While PMOs have been approved by the US Food and Drug Administration for treatment of Duchenne muscular dystrophy, no structural information on these unique, charge-neutral, and stable molecules is available. We performed circular dichroism and solution viscosity measurements combined with molecular dynamics simulations and machine learning to resolve solution structures of 22-mer, 25-mer, and 30-mer length PMOs. The PMO conformational dynamics are defined by the competition between non-polar nucleobases and uncharged phosphorodiamidate groups for shielding from solvent exposure. PMO molecules form non-canonical, partially helical, stable folded structures with a small 1.4- to 1.7-nm radius of gyration, low count of three to six base pairs and six to nine base stacks, characterized by -34 to -51 kcal/mol free energy, -57 to -103 kcal/mol enthalpy, and -23 to -53 kcal/mol entropy for folding. The 4.5- to 6.2-cm3/g intrinsic viscosity and Huggins constant of 4.5-9.9 are indicative of extended and aggregating systems. The results obtained highlight the importance of the conformational ensemble view of PMO solution structures, thermodynamic stability of their non-canonical structures, and concentration-dependent viscosity properties. These principles form a paradigm to understand the structure-properties-function relationship for therapeutic PMOs to advance the design of new RNA-mimic-based drugs.
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Affiliation(s)
- Farkhad Maksudov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
| | | | - Daniel Pierson
- Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA
| | | | - Kenneth A. Marx
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
- Inciton, Inc., Andover, MA 01854, USA
| | - Arani Chanda
- Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA
- Corresponding author: Arani Chanda, Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA.
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
- Inciton, Inc., Andover, MA 01854, USA
- Corresponding author: Valeri Barsegov, Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA.
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10
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Menon D, Singh R, Joshi KB, Gupta S, Bhatia D. Designer, Programmable DNA-peptide hybrid materials with emergent properties to probe and modulate biological systems. Chembiochem 2023; 24:e202200580. [PMID: 36468492 DOI: 10.1002/cbic.202200580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/07/2022]
Abstract
The chemistry of DNA endows it with certain functional properties that facilitate the generation of self-assembled nanostructures, offering precise control over their geometry and morphology, that can be exploited for advanced biological applications. Despite the structural promise of these materials, their applications are limited owing to lack of functional capability to interact favourably with biological systems, which has been achieved by functional proteins or peptides. Herein, we outline a strategy for functionalizing DNA structures with short-peptides, leading to the formation of DNA-peptide hybrid materials. This proposition offers the opportunity to leverage the unique advantages of each of these bio-molecules, that have far reaching emergent properties in terms of better cellular interactions and uptake, better stability in biological media, an acceptable and programmable immune response and high bioactive molecule loading capacities. We discuss the synthetic strategies for the formation of these materials, namely, solid-phase functionalization and solution-coupling functionalization. We then proceed to highlight selected biological applications of these materials in the domains of cell instruction & molecular recognition, gene delivery, drug delivery and bone & tissue regeneration. We conclude with discussions shedding light on the challenges that these materials pose and offer our insights on future directions of peptide-DNA research for targeted biomedical applications.
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Affiliation(s)
- Dhruv Menon
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE, United Kingdom
| | - Ramesh Singh
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
| | - Kashti B Joshi
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, India
| | - Sharad Gupta
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
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11
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Ghosh U, Gupta S, Sinha S. Synthesis of 5'-Thiol Functionalized Morpholino Oligo-Nucleotide and Subsequent Conjugation with IGT to Improve Delivery and Antisense Efficacy In Vitro. Bioconjug Chem 2023; 34:174-180. [PMID: 36538654 DOI: 10.1021/acs.bioconjchem.2c00587] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Thiol functionalized oligonucleotides are useful intermediates for a wide range of applications including DNA nanobiotechnology field through conjugation with various types of probes and cargos. Due to the limitation of synthetic process, phosphorodiamidate morpholino oligonucleotides (PMOs) have not been explored like other oligonucleotides through SH conjugation as mentioned above. In this paper, we report the synthesis of 5'-SH functionalized PMO using a solid support synthesis protocol with an optimized cysteine derived linker so that loading and coupling efficiency of morpholino monomers were effective enough to get a 25-mer 5'-SH functionalized PMO against human Nanog. The PMO with SH functionality was subsequently conjugated with our previously reported Internal Oligo-guanidinium Transporter (IGT) in solution phase to obtain the IGT-PMO conjugate. Interestingly, 5'-conjugated PMO (IGT-PMO) showed 2.5 times better antisense efficacy than 3'-conjugated PMO with IGT (PMO-IGT). 5'-Conjugation enables us to use IGT-PMO for further conjugation at the 3'-N terminal of PMO which was not possible earlier with 5'-OH-PMO-IGT. PMO has become an important class of antisense reagents because four PMO-based drugs have been approved for the treatment of Duchenne muscular dystrophy; hence such an improved result with 5'-modified PMO could be useful for enhancing the therapeutic efficacy of DMD drugs. Similarly, thiol-modified PMO could also be explored like other thiol-containing oligonucleotides for various other applications.
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Affiliation(s)
- Ujjwal Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India
| | - Shalini Gupta
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India
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12
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Kundu J, Ghosh A, Ghosh U, Das A, Nagar D, Pattanayak S, Ghose A, Sinha S. Synthesis of Phosphorodiamidate Morpholino Oligonucleotides Using Trityl and Fmoc Chemistry in an Automated Oligo Synthesizer. J Org Chem 2022; 87:9466-9478. [PMID: 35839125 DOI: 10.1021/acs.joc.2c00265] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphorodiamidate morpholino oligonucleotides (PMOs) constitute 3 out of the 11 FDA-approved oligonucleotide-based drugs in the last 6 years. PMOs can effectively silence disease-causing genes and modify splicing. However, PMO synthesis has remained challenging for a variety of reasons: inefficient deprotection and coupling methods and instability of monomers. Here, we report the development of a suitable combination of resin supports, deblocking and coupling reagents for synthesizing PMOs using either trityl or Fmoc-protected chlorophosphoramidate monomers. The synthesized PMOs using both the methods on a solid support have been validated for gene silencing in a zebrafish model. The protocol was successfully transferred into an automated DNA synthesizer to make several sequences of PMOs, demonstrating for the first time the adaptation of regular PMOs in a commercial DNA synthesizer. Moreover, PMOs with longer than 20-mer sequences, including FDA-approved Eteplirsen (30-mer), were achieved in >20% overall yield that is superior to previous reports. Hybridization study shows that PMOs exhibit a higher binding affinity toward complementary DNA relative to the DNA/DNA duplex (>6 °C). Additionally, the introduction of Fmoc chemistry into PMOs opens up the possibility for PMO synthesis in commercial peptide synthesizers for future development.
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Affiliation(s)
- Jayanta Kundu
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Ujjwal Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Arnab Das
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Dhriti Nagar
- Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Sankha Pattanayak
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Aurnab Ghose
- Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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13
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Yang L, Ye X, Li X, Huang Z, Chen F, Yang W, Wang Z. Colorimetric aptasensor for sensitive detection of quinclorac based on exonuclease III-assisted cyclic release of phosphorodiamidate morpholino oligomer mimic enzyme strategy. Anal Chim Acta 2022; 1207:339815. [DOI: 10.1016/j.aca.2022.339815] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 11/01/2022]
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14
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Pan S, Cesarek M, Godoy C, Co CM, Schindler C, Padilla K, Haskell A, Barreda H, Story C, Poole R, Dabney A, Gregory CA. Morpholino-driven blockade of Dkk-1 in osteosarcoma inhibits bone damage and tumour expansion by multiple mechanisms. Br J Cancer 2022; 127:43-55. [PMID: 35277659 PMCID: PMC9276700 DOI: 10.1038/s41416-022-01764-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 02/02/2022] [Accepted: 02/15/2022] [Indexed: 11/09/2022] Open
Abstract
Abstract
Background
Osteosarcoma (OS) is the most common primary bone malignancy. Chemotherapy plays an essential role in OS treatment, potentially doubling 5-year event-free survival if tumour necrosis can be stimulated. The canonical Wnt inhibitor Dickkopf-1 (Dkk-1) enhances OS survival in part through upregulation of aldehyde-dehydrogenase-1A1 which neutralises reactive oxygen species originating from nutritional stress and chemotherapeutic challenge.
Methods
A vivo morpholino (DkkMo) was employed to block the expression of Dkk-1 in OS cells. Cell mitosis, gene expression and bone destruction were measured in vitro and in vivo in the presence and absence of doxorubicin (DRB).
Results
DkkMo reduced the expression of Dkk-1 and Aldh1a1, reduced expansion of OS tumours, preserved bone volume and architecture and stimulated tumour necrosis. This was observed in the presence or absence of DRB.
Conclusion
These results indicate that administration of DkkMo with or without chemotherapeutics can substantially improve OS outcome with respect to tumour expansion and osteolytic corruption of bone in experimental OS model.
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15
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Schissel CK, Mohapatra S, Wolfe JM, Fadzen CM, Bellovoda K, Wu CL, Wood JA, Malmberg AB, Loas A, Gómez-Bombarelli R, Pentelute BL. Deep learning to design nuclear-targeting abiotic miniproteins. Nat Chem 2021; 13:992-1000. [PMID: 34373596 PMCID: PMC8819921 DOI: 10.1038/s41557-021-00766-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 07/05/2021] [Indexed: 02/08/2023]
Abstract
There are more amino acid permutations within a 40-residue sequence than atoms on Earth. This vast chemical search space hinders the use of human learning to design functional polymers. Here we show how machine learning enables the de novo design of abiotic nuclear-targeting miniproteins to traffic antisense oligomers to the nucleus of cells. We combined high-throughput experimentation with a directed evolution-inspired deep-learning approach in which the molecular structures of natural and unnatural residues are represented as topological fingerprints. The model is able to predict activities beyond the training dataset, and simultaneously deciphers and visualizes sequence-activity predictions. The predicted miniproteins, termed 'Mach', reach an average mass of 10 kDa, are more effective than any previously known variant in cells and can also deliver proteins into the cytosol. The Mach miniproteins are non-toxic and efficiently deliver antisense cargo in mice. These results demonstrate that deep learning can decipher design principles to generate highly active biomolecules that are unlikely to be discovered by empirical approaches.
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Affiliation(s)
- Carly K. Schissel
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Somesh Mohapatra
- Massachusetts Institute of Technology, Department of Materials Science and Engineering, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Justin M. Wolfe
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Colin M. Fadzen
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Kamela Bellovoda
- Sarepta Therapeutics, 215 First Street, Cambridge, MA 02142, USA
| | - Chia-Ling Wu
- Sarepta Therapeutics, 215 First Street, Cambridge, MA 02142, USA
| | - Jenna A. Wood
- Sarepta Therapeutics, 215 First Street, Cambridge, MA 02142, USA
| | | | - Andrei Loas
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rafael Gómez-Bombarelli
- Massachusetts Institute of Technology, Department of Materials Science and Engineering, 77 Massachusetts Avenue, Cambridge, MA 02139, USA,Correspondence to: ,
| | - Bradley L. Pentelute
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Avenue, Cambridge, MA 02139, USA,The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA,Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA,Correspondence to: ,
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16
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Cale JM, Greer K, Fletcher S, Wilton SD. Proof-of-Concept: Antisense Oligonucleotide Mediated Skipping of Fibrillin-1 Exon 52. Int J Mol Sci 2021; 22:ijms22073479. [PMID: 33801742 PMCID: PMC8037683 DOI: 10.3390/ijms22073479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 11/16/2022] Open
Abstract
Marfan syndrome is one of the most common dominantly inherited connective tissue disorders, affecting 2–3 in 10,000 individuals, and is caused by one of over 2800 unique FBN1 mutations. Mutations in FBN1 result in reduced fibrillin-1 expression, or the production of two different fibrillin-1 monomers unable to interact to form functional microfibrils. Here, we describe in vitro evaluation of antisense oligonucleotides designed to mediate exclusion of FBN1 exon 52 during pre-mRNA splicing to restore monomer homology. Antisense oligonucleotide sequences were screened in healthy control fibroblasts. The most effective sequence was synthesised as a phosphorodiamidate morpholino oligomer, a chemistry shown to be safe and effective clinically. We show that exon 52 can be excluded in up to 100% of FBN1 transcripts in healthy control fibroblasts transfected with PMO52. Immunofluorescent staining revealed the loss of fibrillin 1 fibres with ~50% skipping and the subsequent re-appearance of fibres with >80% skipping. However, the effect of exon skipping on the function of the induced fibrillin-1 isoform remains to be explored. Therefore, these findings demonstrate proof-of-concept that exclusion of an exon from FBN1 pre-mRNA can result in internally truncated but identical monomers capable of forming fibres and lay a foundation for further investigation to determine the effect of exon skipping on fibrillin-1 function.
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Affiliation(s)
- Jessica M. Cale
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (J.M.C.); (K.G.); (S.F.)
| | - Kane Greer
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (J.M.C.); (K.G.); (S.F.)
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (J.M.C.); (K.G.); (S.F.)
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Nedlands, WA 6009, Australia
- PYC Therapeutics, Nedlands, WA 6009, Australia
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (J.M.C.); (K.G.); (S.F.)
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Nedlands, WA 6009, Australia
- Correspondence: ; Tel.: +61-8-9360-2305
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17
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Dastpeyman M, Sharifi R, Amin A, Karas JA, Cuic B, Pan Y, Nicolazzo JA, Turner BJ, Shabanpoor F. Endosomal escape cell-penetrating peptides significantly enhance pharmacological effectiveness and CNS activity of systemically administered antisense oligonucleotides. Int J Pharm 2021; 599:120398. [PMID: 33640427 DOI: 10.1016/j.ijpharm.2021.120398] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/11/2021] [Accepted: 02/14/2021] [Indexed: 12/19/2022]
Abstract
Antisense oligonucleotides (ASOs) are an emerging class of gene-specific therapeutics for diseases associated with the central nervous system (CNS). However, ASO delivery across the blood-brain barrier (BBB) to their CNS target cells remains a major challenge. Since ASOs are mainly taken up into the brain capillary endothelial cells interface through endosomal routes, entrapment in the endosomal compartment is a major obstacle for efficient CNS delivery of ASOs. Therefore, we evaluated the effectiveness of a panel of cell-penetrating peptides (CPPs) bearing several endosomal escape domains for the intracellular delivery, endosomal release and antisense activity of FDA-approved Spinraza (Nusinersen), an ASO used to treat spinal muscular atrophy (SMA). We identified a CPP, HA2-ApoE(131-150), which, when conjugated to Nusinersen, showed efficient endosomal escape capability and significantly increased the level of full-length functional mRNA of the survival motor neuron 2 (SMN2) gene in SMA patient-derived fibroblasts. Treatment of SMN2 transgenic adult mice with this CPP-PMO conjugate resulted in a significant increase in the level of full-length SMN2 in the brain and spinal cord. This work provides proof-of-principle that integration of endosomal escape domains with CPPs enables higher cytosolic delivery of ASOs, and more importantly enhances the efficiency of BBB-permeability and CNS activity of systemically administered ASOs.
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Affiliation(s)
- Mohadeseh Dastpeyman
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3010, VIC, Australia
| | - Ramin Sharifi
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3010, VIC, Australia
| | - Azin Amin
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3010, VIC, Australia
| | - John A Karas
- School of Chemistry, The University of Melbourne, VIC 3010, Australia; The Bio21 Institute, University of Melbourne, 30 Flemington Rd., VIC 3010, Australia
| | - Brittany Cuic
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3010, VIC, Australia
| | - Yijun Pan
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Joseph A Nicolazzo
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Bradley J Turner
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3010, VIC, Australia; The Perron Institute for Neurological and Translational Science, Queen Elizabeth Medical Centre, Nedlands, Western Australia 6150, Australia
| | - Fazel Shabanpoor
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3010, VIC, Australia.
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18
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Kundu J, Banerjee P, Bose C, Das U, Ghosh U, Sinha S. Internal Oligoguanidinium Transporter: Mercury-Free Scalable Synthesis, Improvement of Cellular Localization, Endosomal Escape, Mitochondrial Localization, and Conjugation with Antisense Morpholino for NANOG Inhibition to Induce Chemosensitization of Taxol in MCF-7 Cells. Bioconjug Chem 2020; 31:2367-2382. [PMID: 32986398 DOI: 10.1021/acs.bioconjchem.0c00444] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A nontoxic delivery vehicle is essential for the therapeutic applications of antisense phosphorodiamidate morpholino oligonucleotides (PMOs). Though guanidinium-rich or arginine-rich cellular transporter conjugated Vivo-PMO or PPMO has been developed for in vivo application, however, either their toxicity or stability has become an issue. Previously, we reported nonpeptidic internal guanidinium transporter (IGT) mediated delivery of PMO for gene silencing and got encouraging results. In this paper, we report the synthesis of IGT using a Hg-free method for scale up and N-terminal modification of IGT with a suitable hydrophobic or lipophilic group to improve the cell permeability, endosomal escape, and mitochondrial localization and to reduce toxicity in the MTT assay. For the delivery of PMO, IGT-PMO conjugate was synthesized to target NANOG in cells, a transcription factor required for cancer stem cell proliferation and embryonic development and is involved in many cancers. Our data shows IGT-PMO-facilitated NANOG inhibition, and thereby the prevention of EpCAM-N-Cadherin-Vimentin axis mediated epithelial to mesenchymal transition (EMT) in MCF-7 cells. Moreover, unlike taxol, NANOG inhibition influences the expression of stemness factor c-Myc, Hh-Gli signaling proteins, other cancer related factors, and their respective phenotypes in cancer cells. To the best of our knowledge, this is the first report to illustrate that the IGT-PMO-mediated NANOG inhibition increases the therapeutic potential of taxol and induces G0-G1 arrest in cancer cells to prevent cancer progression. However, it warrants further investigation in other cancer cells and preclinical platforms.
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Affiliation(s)
- Jayanta Kundu
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, West Bengal, India
| | - Priyanjalee Banerjee
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, West Bengal, India
| | - Chandra Bose
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, West Bengal, India
| | - Ujjal Das
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, West Bengal, India
| | - Ujjwal Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, West Bengal, India
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, West Bengal, India
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19
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Tsoumpra MK, Fukumoto S, Matsumoto T, Takeda S, Wood MJA, Aoki Y. Peptide-conjugate antisense based splice-correction for Duchenne muscular dystrophy and other neuromuscular diseases. EBioMedicine 2019; 45:630-645. [PMID: 31257147 PMCID: PMC6642283 DOI: 10.1016/j.ebiom.2019.06.036] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/31/2019] [Accepted: 06/18/2019] [Indexed: 12/14/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked disorder characterized by progressive muscle degeneration, caused by the absence of dystrophin. Exon skipping by antisense oligonucleotides (ASOs) has recently gained recognition as therapeutic approach in DMD. Conjugation of a peptide to the phosphorodiamidate morpholino backbone (PMO) of ASOs generated the peptide-conjugated PMOs (PPMOs) that exhibit a dramatically improved pharmacokinetic profile. When tested in animal models, PPMOs demonstrate effective exon skipping in target muscles and prolonged duration of dystrophin restoration after a treatment regime. Herein we summarize the main pathophysiological features of DMD and the emergence of PPMOs as promising exon skipping agents aiming to rescue defective gene expression in DMD and other neuromuscular diseases. The listed PPMO laboratory findings correspond to latest trends in the field and highlight the obstacles that must be overcome prior to translating the animal-based research into clinical trials tailored to the needs of patients suffering from neuromuscular diseases.
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Key Words
- aso, antisense oligonucleotides
- cns, central nervous system
- cpp, cell penetrating peptide
- dgc, dystrophin glyco-protein complex
- dmd, duchenne muscular dystrophy
- fda, us food and drug administration
- pmo, phosphorodiamidate morpholino
- ppmo, peptide-conjugated pmos
- ps, phosphorothioate
- sma, spinal muscular atrophy
- 2ʹ-ome, 2ʹ-o-methyl
- 2ʹ-moe, 2ʹ-o-methoxyethyl
- 6mwt, 6-minute walk test
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Affiliation(s)
- Maria K Tsoumpra
- Department of Molecular Therapy, National Institute of Neuroscience, National Centre of Neurology and Psychiatry, Kodaira-shi, Tokyo, Japan
| | - Seiji Fukumoto
- Fujii Memorial Institute of Medical Sciences, University of Tokushima, Tokushima, Japan
| | - Toshio Matsumoto
- Fujii Memorial Institute of Medical Sciences, University of Tokushima, Tokushima, Japan
| | - Shin'ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Centre of Neurology and Psychiatry, Kodaira-shi, Tokyo, Japan
| | | | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Centre of Neurology and Psychiatry, Kodaira-shi, Tokyo, Japan.
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20
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Zimmer AM, Pan YK, Chandrapalan T, Kwong RWM, Perry SF. Loss-of-function approaches in comparative physiology: is there a future for knockdown experiments in the era of genome editing? ACTA ACUST UNITED AC 2019; 222:222/7/jeb175737. [PMID: 30948498 DOI: 10.1242/jeb.175737] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Loss-of-function technologies, such as morpholino- and RNAi-mediated gene knockdown, and TALEN- and CRISPR/Cas9-mediated gene knockout, are widely used to investigate gene function and its physiological significance. Here, we provide a general overview of the various knockdown and knockout technologies commonly used in comparative physiology and discuss the merits and drawbacks of these technologies with a particular focus on research conducted in zebrafish. Despite their widespread use, there is an ongoing debate surrounding the use of knockdown versus knockout approaches and their potential off-target effects. This debate is primarily fueled by the observations that, in some studies, knockout mutants exhibit phenotypes different from those observed in response to knockdown using morpholinos or RNAi. We discuss the current debate and focus on the discrepancies between knockdown and knockout phenotypes, providing literature and primary data to show that the different phenotypes are not necessarily a direct result of the off-target effects of the knockdown agents used. Nevertheless, given the recent evidence of some knockdown phenotypes being recapitulated in knockout mutants lacking the morpholino or RNAi target, we stress that results of knockdown experiments need to be interpreted with caution. We ultimately argue that knockdown experiments should not be discontinued if proper control experiments are performed, and that with careful interpretation, knockdown approaches remain useful to complement the limitations of knockout studies (e.g. lethality of knockout and compensatory responses).
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Affiliation(s)
- Alex M Zimmer
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Yihang K Pan
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | | | | | - Steve F Perry
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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21
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Kicsák M, Mándi A, Varga S, Herczeg M, Batta G, Bényei A, Borbás A, Herczegh P. Tricyclanos: conformationally constrained nucleoside analogues with a new heterotricycle obtained from a d-ribofuranose unit. Org Biomol Chem 2019; 16:393-401. [PMID: 29090729 DOI: 10.1039/c7ob02296d] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A novel type of nucleoside analogue in which the sugar part is replaced by a new tricycle, 3,7,10-trioxa-11-azatricyclo[5.3.1.05,11]undecane has been prepared by substrate-controlled asymmetric synthesis. 1,5-Dialdehydes obtained from properly protected or unprotected uridine, ribothymidine, cytidine, inosine, adenosine and guanosine by metaperiodate oxidation reacted readily with tris(hydroxymethyl)aminomethane to provide the corresponding tricyclic derivatives with three new stereogenic centers. Through a double cyclisation cascade process the tricyclic compounds were obtained in good to high yields, with very high diastereoselectivity. Formation of one stereoisomer, out of the eight possible, was observed in all cases. The absolute configuration of the new stereotriad-containing tricyclic systems was aided by conventional NMR experiments followed by chemical shift calculations using an X-ray crystal structure as reference that was in good agreement with H-H distances obtained from a new ROESY NMR method. The synthesis was compatible with silyl, trityl and dimethoxytrityl protecting groups. A new reagent mixture containing ZnCl2, Et3SiH and hexafluoroisopropanol was developed for detritylation of the acid-sensitive tricyclano nucleosides.
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Affiliation(s)
- Máté Kicsák
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary.
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22
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Multiple Exon Skipping in the Duchenne Muscular Dystrophy Hot Spots: Prospects and Challenges. J Pers Med 2018; 8:jpm8040041. [PMID: 30544634 PMCID: PMC6313462 DOI: 10.3390/jpm8040041] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/24/2018] [Accepted: 12/04/2018] [Indexed: 12/19/2022] Open
Abstract
Duchenne muscular dystrophy (DMD), a fatal X-linked recessive disorder, is caused mostly by frame-disrupting, out-of-frame deletions in the dystrophin (DMD) gene. Antisense oligonucleotide-mediated exon skipping is a promising therapy for DMD. Exon skipping aims to convert out-of-frame mRNA to in-frame mRNA and induce the production of internally-deleted dystrophin as seen in the less severe Becker muscular dystrophy. Currently, multiple exon skipping has gained special interest as a new therapeutic modality for this approach. Previous retrospective database studies represented a potential therapeutic application of multiple exon skipping. Since then, public DMD databases have become more useful with an increase in patient registration and advances in molecular diagnosis. Here, we provide an update on DMD genotype-phenotype associations using a global DMD database and further provide the rationale for multiple exon skipping development, particularly for exons 45–55 skipping and an emerging therapeutic concept, exons 3–9 skipping. Importantly, this review highlights the potential of multiple exon skipping for enabling the production of functionally-corrected dystrophin and for treating symptomatic patients not only with out-of-frame deletions but also those with in-frame deletions. We will also discuss prospects and challenges in multiple exon skipping therapy, referring to recent progress in antisense chemistry and design, as well as disease models.
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23
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Phumesin P, Junking M, Panya A, Yongpitakwattana P, Noisakran S, Limjindaporn T, Yenchitsomanus PT. Inhibition of dengue virus replication in monocyte-derived dendritic cells by vivo-morpholino oligomers. Virus Res 2018; 260:123-128. [PMID: 30503719 DOI: 10.1016/j.virusres.2018.11.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/17/2018] [Accepted: 11/28/2018] [Indexed: 12/24/2022]
Abstract
Skin dendritic cells (DCs) are primary target cells of dengue virus (DENV) infection and they play an important role in its immunopathogenesis. Monocyte-derived dendritic cells (MDDCs) represent dermal and bloodstream DCs that serve as human primary cells for ex vivo studies of DENV infection. Improved understanding of the mechanisms that effectuate the inhibition of DENV replication in MDDCs will accelerate the development of antiviral drugs to treat DENV infection. In this study, we investigated whether or not vivo-morpholino oligomer (vivo-MO), which was designed to target the top of the 3' stem-loop (3' SL) at the 3' UTR of the DENV genome, could inhibit DENV infection and replication in MDDCs. The findings of this study revealed that vivo-MO-1 could inhibit DENV-2 infection in MDDCs, and that it could significantly reduce DENV RNA, protein, and viral production in a dose-dependent manner. Treatment of MDDCs with 4 μM of vivo-MO-1 decreased DENV production by more than 1,000-fold, when compared to that of the vivo-MO-NC control. Thus, vivo-MO-1 targeting of DENV RNA demonstrates potential for further development into an anti-DENV agent.
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Affiliation(s)
- Patta Phumesin
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Mutita Junking
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Aussara Panya
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Petlada Yongpitakwattana
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Sansanee Noisakran
- Medical Biotechnology Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok 10700, Thailand
| | - Thawornchai Limjindaporn
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; Department of Anatomy, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Pa-Thai Yenchitsomanus
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
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24
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Tsai CR, Lee HF, Chi CS, Yang MT, Hsu CC. Antisense oligonucleotides modulate dopa decarboxylase function in aromatic l-amino acid decarboxylase deficiency. Hum Mutat 2018; 39:2072-2082. [PMID: 30260058 DOI: 10.1002/humu.23659] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 08/22/2018] [Accepted: 09/25/2018] [Indexed: 12/24/2022]
Abstract
Aromatic l-amino acid decarboxylase deficiency (AADCD), attributed to mutations in the dopa decarboxylase (DDC) gene, is a rare neurometabolic disease resulting from a defect in the biosynthesis of dopamine and serotonin. The DDC c.714+4A>T mutation is the most prevalent mutation among patients with AADCD, and is also a founder mutation among Taiwanese patients. In this study, the molecular consequences and function of this mutation were examined in AADCD patient-derived lymphoblastoid cells. We identified novel DDC mRNA isoforms spliced with a new exon (exon 6a) in normal and c.714+4A>T lymphoblastoid cells. In addition, we identified the SR proteins (SRSF9 and SRSF6), as well as cis-elements involved in modulating the splicing of this mutated transcript. Notably, we demonstrated that antisense oligonucleotides (ASOs) were able to restore the normal mRNA splicing and increase the level of DDC protein, as well as its downstream product serotonin, in lymphoblastoid cells derived from the patient with AADCD, suggesting that these ASOs might represent a feasible alternative strategy for gene therapy of AADCD in patients with the common c.714+4A>T mutation.
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Affiliation(s)
- Chi-Ren Tsai
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 402, Taiwan.,Department of Pediatrics, Taichung Veterans General Hospital, Taichung, 407, Taiwan
| | - Hsiu-Fen Lee
- Department of Pediatrics, Taichung Veterans General Hospital, Taichung, 407, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, 402, Taiwan
| | - Ching-Shiang Chi
- School of Medicine, Chung Shan Medical University, Taichung, 402, Taiwan.,Department of Pediatrics, Tung's Taichung Metroharbor Hospital, Taichung, 435, Taiwan
| | - Ming-Te Yang
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Chia-Chi Hsu
- Department of Pediatrics, Taichung Veterans General Hospital, Taichung, 407, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, 112, Taiwan
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25
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Nan Y, Zhang YJ. Antisense Phosphorodiamidate Morpholino Oligomers as Novel Antiviral Compounds. Front Microbiol 2018; 9:750. [PMID: 29731743 PMCID: PMC5920040 DOI: 10.3389/fmicb.2018.00750] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/03/2018] [Indexed: 01/23/2023] Open
Abstract
Phosphorodiamidate morpholino oligomers (PMO) are short single-stranded DNA analogs that are built upon a backbone of morpholine rings connected by phosphorodiamidate linkages. As uncharged nucleic acid analogs, PMO bind to complementary sequences of target mRNA by Watson–Crick base pairing to block protein translation through steric blockade. PMO interference of viral protein translation operates independently of RNase H. Meanwhile, PMO are resistant to a variety of enzymes present in biologic fluids, a characteristic that makes them highly suitable for in vivo applications. Notably, PMO-based therapy for Duchenne muscular dystrophy (DMD) has been approved by the United States Food and Drug Administration which is now a hallmark for PMO-based antisense therapy. In this review, the development history of PMO, delivery methods for improving cellular uptake of neutrally charged PMO molecules, past studies of PMO antagonism against RNA and DNA viruses, PMO target selection, and remaining questions of PMO antiviral strategies are discussed in detail and new insights are provided.
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Affiliation(s)
- Yuchen Nan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China.,Virginia-Maryland College of Veterinary Medicine and Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States
| | - Yan-Jin Zhang
- Virginia-Maryland College of Veterinary Medicine and Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States
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26
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Phumesin P, Junking M, Panya A, Yongpitakwattana P, Noisakran S, Limjindaporn T, Yenchitsomanus PT. Vivo-morpholino oligomers strongly inhibit dengue virus replication and production. Arch Virol 2017; 163:867-876. [PMID: 29260328 DOI: 10.1007/s00705-017-3666-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/16/2017] [Indexed: 01/07/2023]
Abstract
Dengue virus (DENV) infection is a worldwide public health problem, which can cause severe dengue hemorrhagic fever (DHF) and life-threatening dengue shock syndrome (DSS). There are currently no anti-DENV drugs available, and there has been an intensive search for effective anti-DENV agents that can inhibit all four DENV serotypes. In this study, we tested whether vivo-morpholino oligomers (vivo-MOs), whose effect on DENV infection has not previously been studied, can inhibit DENV infection. Vivo-MOs were designed to target the top of 3' stem-loop (3' SL) in the 3' UTR of the DENV genome and tested for inhibition of DENV infection in monkey kidney epithelial (Vero) cells and human lung epithelial carcinoma (A549) cells. The results showed that vivo-MOs could bind to a DENV RNA sequence and markedly reduce DENV-RNA, protein, and virus production in infected Vero and A549 cells. Vivo-MOs at a concentration of 4 µM could inhibit DENV production by more than 104-fold when compared to that of an untreated control. In addition, vivo-MOs also inhibited DENV production in U937 cells and primary human monocytes. Therefore, vivo-MOs targeting to the 3' SL in the 3' UTR of DENV genomes are effective and have the potential to be developed as anti-DENV agents.
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Affiliation(s)
- Patta Phumesin
- Siriraj Center of Research Excellence for Molecular Medicine (SiCORE-MM), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Mutita Junking
- Siriraj Center of Research Excellence for Molecular Medicine (SiCORE-MM), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Aussara Panya
- Siriraj Center of Research Excellence for Molecular Medicine (SiCORE-MM), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Petlada Yongpitakwattana
- Siriraj Center of Research Excellence for Molecular Medicine (SiCORE-MM), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Sansanee Noisakran
- Medical Biotechnology Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok, 10700, Thailand
| | - Thawornchai Limjindaporn
- Department of Anatomy, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Pa-Thai Yenchitsomanus
- Siriraj Center of Research Excellence for Molecular Medicine (SiCORE-MM), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
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27
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Goikoetxea A, Todd EV, Gemmell NJ. Stress and sex: does cortisol mediate sex change in fish? Reproduction 2017; 154:R149-R160. [PMID: 28890443 DOI: 10.1530/rep-17-0408] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/24/2017] [Accepted: 09/08/2017] [Indexed: 12/30/2022]
Abstract
Cortisol is the main glucocorticoid (GC) in fish and the hormone most directly associated with stress. Recent research suggests that this hormone may act as a key factor linking social environmental stimuli and the onset of sex change by initiating a shift in steroidogenesis from estrogens to androgens. For many teleost fish, sex change occurs as a usual part of the life cycle. Changing sex is known to enhance the lifetime reproductive success of these fish and the modifications involved (behavioral, gonadal and morphological) are well studied. However, the exact mechanism behind the transduction of the environmental signals into the molecular cascade that underlies this singular process remains largely unknown. We here synthesize current knowledge regarding the role of cortisol in teleost sex change with a focus on two well-described transformations: temperature-induced masculinization and socially regulated sex change. Three non-mutually exclusive pathways are considered when describing the potential role of cortisol in mediating teleost sex change: cross-talk between GC and androgen pathways, inhibition of aromatase expression and upregulation of amh (the gene encoding anti-Müllerian hormone). We anticipate that understanding the role of cortisol in the initial stages of sex change will further improve our understanding of sex determination and differentiation across vertebrates, and may lead to new tools to control fish sex ratios in aquaculture.
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Affiliation(s)
| | - Erica V Todd
- Department of AnatomyUniversity of Otago, Dunedin, New Zealand
| | - Neil J Gemmell
- Department of AnatomyUniversity of Otago, Dunedin, New Zealand
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28
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Neuromuscular NMDA Receptors Modulate Developmental Synapse Elimination. J Neurosci 2017; 36:8783-9. [PMID: 27559162 DOI: 10.1523/jneurosci.1181-16.2016] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/27/2016] [Indexed: 02/03/2023] Open
Abstract
UNLABELLED At birth, each mammalian skeletal muscle fiber is innervated by multiple motor neurons, but in a few weeks, all but one of those axons retracts (Redfern, 1970) and differential activity between inputs controls this phenomenon (Personius and Balice-Gordon, 2001; Sanes and Lichtman, 2001; Personius et al., 2007; Favero et al., 2012). Acetylcholine, the primary neuromuscular transmitter, has long been presumed to mediate this activity-dependent process (O'Brien et al., 1978), but glutamatergic transmission also occurs at the neuromuscular junction (Berger et al., 1995; Grozdanovic and Gossrau, 1998; Mays et al., 2009). To test the role of neuromuscular NMDA receptors, we assessed their contribution to muscle calcium fluxes in mice and tested whether they influence removal of excess innervation at the end plate. Developmental synapse pruning was slowed by reduction of NMDA receptor activation or expression and by reduction of glutamate production. Conversely, pruning is accelerated by application of exogenous NMDA. We also found that NMDA induced increased muscle calcium only during the first 2 postnatal weeks. Therefore, neuromuscular NMDA receptors play previously unsuspected roles in neuromuscular activity and synaptic pruning during development. SIGNIFICANCE STATEMENT In normal adult muscle, each muscle fiber is innervated by a single axon, but at birth, fibers are multiply innervated. Elimination of excess connections requires neural activity; because the neuromuscular junction (NMJ) is a cholinergic synapse, acetylcholine has been assumed to be the critical mediator of activity. However, glutamate receptors are also expressed at the NMJ. We found that axon removal in mice is slowed by pharmacological and molecular manipulations that decrease signaling through neuromuscular NMDA receptors, whereas application of exogenous NMDA at the NMJ accelerates synapse elimination and increases muscle calcium levels during the first 2 postnatal weeks. Therefore, neuromuscular NMDA receptors play previously unsuspected roles in neuromuscular activity and elimination of excess synaptic input during development.
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29
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Nandi B, Khatra H, Khan PP, Bhadra J, Pattanayak S, Sinha S. Cationic Cytosine Morpholino-Based Transporters: Synthesis and Regulation of Intracellular Localization. ChemistrySelect 2017. [DOI: 10.1002/slct.201700238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Bappaditya Nandi
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata 700032 India
| | - Harleen Khatra
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata 700032 India
| | - Pragya Paramita Khan
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata 700032 India
| | - Jhuma Bhadra
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata 700032 India
| | - Sankha Pattanayak
- Department of Chemical and Systems Biology; Stanford University; Stanford, California, CA 94305-5174
| | - Surajit Sinha
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata 700032 India
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30
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Wang M, Wu B, Lu P, Shah SN, Tucker JD, Bollinger LE, Lu Q. Evaluation of Amphiphilic Peptide Modified Antisense Morpholino Oligonucleotides In Vitro and in Dystrophic mdx Mice. Polymers (Basel) 2017; 9:E177. [PMID: 30970855 PMCID: PMC6432210 DOI: 10.3390/polym9050177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/28/2017] [Accepted: 05/08/2017] [Indexed: 01/16/2023] Open
Abstract
A series of amphiphilic peptides modified PMO (Pt-PMO) were prepared, and their antisense effect and toxicity were evaluated both in vitro and in mdx mice. The results showed that the exon-skipping performance of Pt-PMO are relative to the structure of the conjugated peptide: the Pt3/Pt4 composed of six/seven arginines and one myristoylation modified PMO showed more efficacy and with less toxicity as compared to others, confirming that appropriate hydrophilic-lipophilic balance (HLB) and cationic sequence numbers play a crucial role in improving cell uptake and corresponding exon-skipping efficiency. This was observed particularly in enhanced delivery efficiency of PMO comparable to B-PMO in vitro, while 6-fold improved exon-skipping was achieved against naked PMO in vivo. The multi-PMO modified Pt8-PMO also showed improved exon-skipping both in vitro and in vivo, though there is lower efficiency in systemic delivery as compared to Pt4-PMO. These data suggest that with optimization of peptide in component, charge density has clear potential for exploration towards achieving higher efficiency of antisense oligonucleotide systemic delivery, and thus is more applicable for clinical application.
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Affiliation(s)
- Mingxing Wang
- McColl-Lockwood Laboratory for Muscular Dystrophy Research, Carolinas Medical Center, 1000 Blythe Blvd, Charlotte, NC 28231, USA.
| | - Bo Wu
- McColl-Lockwood Laboratory for Muscular Dystrophy Research, Carolinas Medical Center, 1000 Blythe Blvd, Charlotte, NC 28231, USA.
| | - Peijuan Lu
- McColl-Lockwood Laboratory for Muscular Dystrophy Research, Carolinas Medical Center, 1000 Blythe Blvd, Charlotte, NC 28231, USA.
| | - Sapana N Shah
- McColl-Lockwood Laboratory for Muscular Dystrophy Research, Carolinas Medical Center, 1000 Blythe Blvd, Charlotte, NC 28231, USA.
| | - Jason D Tucker
- McColl-Lockwood Laboratory for Muscular Dystrophy Research, Carolinas Medical Center, 1000 Blythe Blvd, Charlotte, NC 28231, USA.
| | - Lauren E Bollinger
- McColl-Lockwood Laboratory for Muscular Dystrophy Research, Carolinas Medical Center, 1000 Blythe Blvd, Charlotte, NC 28231, USA.
| | - Qilong Lu
- McColl-Lockwood Laboratory for Muscular Dystrophy Research, Carolinas Medical Center, 1000 Blythe Blvd, Charlotte, NC 28231, USA.
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31
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Villegas-Pineda JC, Toledo-Leyva A, Osorio-Trujillo JC, Hernández-Ramírez VI, Talamás-Rohana P. The translational blocking of α5 and α6 integrin subunits affects migration and invasion, and increases sensitivity to carboplatin of SKOV-3 ovarian cancer cell line. Exp Cell Res 2017; 351:127-134. [PMID: 28131812 DOI: 10.1016/j.yexcr.2017.01.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/05/2017] [Accepted: 01/21/2017] [Indexed: 01/02/2023]
Abstract
Epithelial ovarian cancer is the most lethal gynecologic malignancy. Integrins, overexpressed in cancer, are involved in various processes that favor the development of the disease. This study focused on determining the degree of involvement of α5, α6 and β3 integrin subunits in the establishment/development of epithelial ovarian cancer (EOC), such as proliferation, migration, invasion, and response to carboplatin. The translation of the α5, α6 and β3 integrins was blocked using morpholines, generating morphant cells for these proteins, which were corroborated by immunofluorescence assays. WST-1 proliferation assay showed that silencing of α5, α6, and β3 integrins does not affect the survival of morphants. Wound healing and transwell chamber assays showed that blocking α5 and α6 integrins decrease, in lesser and greater level respectively, the migratory and the invasive capacity of SKOV-3 cells. Finally, blocking α5 and α6 integrins partially sensitized the cells response to carboplatin, while blocking integrin β3 generated resistance to this drug. Statistical analyses were performed with the GraphPad Prism 5.0 software employing one way and two-way ANOVA tests; data are shown as average±SD. Results suggest that α5 and α6 integrins could become good candidates for chemotherapy targets in EOC.
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Affiliation(s)
- Julio César Villegas-Pineda
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, Ciudad de México 07360, Mexico.
| | - Alfredo Toledo-Leyva
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, Ciudad de México 07360, Mexico.
| | - Juan Carlos Osorio-Trujillo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, Ciudad de México 07360, Mexico.
| | - Verónica Ivonne Hernández-Ramírez
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, Ciudad de México 07360, Mexico.
| | - Patricia Talamás-Rohana
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, Ciudad de México 07360, Mexico.
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32
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Bhadra J, Pattanayak S, Khan PP, Kundu J, Sinha S. Internal Oligoguanidinium-Based Cellular Transporter Enhances Antisense Efficacy of Morpholinos in In Vitro and Zebrafish Model. Bioconjug Chem 2016; 27:2254-2259. [PMID: 27625020 DOI: 10.1021/acs.bioconjchem.6b00252] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
An efficient cellular transporter is highly desirable for the therapeutic applications of antisense phosphorodiamidate morpholino oligonucleotides (PMOs) as Vivo-PMO and PPMO have limitations for in vivo study. We report here a novel internally tetraguanidinium-linked nonpeptidic cellular transporter having a conformationally rigid backbone composed of pharmacologically compatible heterocyclic six-membered rings which internalizes efficiently into cells in full growth medium and ubiquitously distributed into zebrafish embryos. It efficiently transports antisense PMO in vitro and in vivo zebrafish embryos. Comparative study with Gene Tools Vivo-PMO revealed that our cellular-transporter conjugated PMO shows better antisense efficacy.
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Affiliation(s)
- Jhuma Bhadra
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Sankha Pattanayak
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Pragya Paramita Khan
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Jayanta Kundu
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Surajit Sinha
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
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33
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Havens MA, Hastings ML. Splice-switching antisense oligonucleotides as therapeutic drugs. Nucleic Acids Res 2016; 44:6549-63. [PMID: 27288447 PMCID: PMC5001604 DOI: 10.1093/nar/gkw533] [Citation(s) in RCA: 290] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/02/2016] [Indexed: 01/09/2023] Open
Abstract
Splice-switching oligonucleotides (SSOs) are short, synthetic, antisense, modified nucleic acids that base-pair with a pre-mRNA and disrupt the normal splicing repertoire of the transcript by blocking the RNA–RNA base-pairing or protein–RNA binding interactions that occur between components of the splicing machinery and the pre-mRNA. Splicing of pre-mRNA is required for the proper expression of the vast majority of protein-coding genes, and thus, targeting the process offers a means to manipulate protein production from a gene. Splicing modulation is particularly valuable in cases of disease caused by mutations that lead to disruption of normal splicing or when interfering with the normal splicing process of a gene transcript may be therapeutic. SSOs offer an effective and specific way to target and alter splicing in a therapeutic manner. Here, we discuss the different approaches used to target and alter pre-mRNA splicing with SSOs. We detail the modifications to the nucleic acids that make them promising therapeutics and discuss the challenges to creating effective SSO drugs. We highlight the development of SSOs designed to treat Duchenne muscular dystrophy and spinal muscular atrophy, which are currently being tested in clinical trials.
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Affiliation(s)
- Mallory A Havens
- Department of Biology, Lewis University, Romeoville, IL 60446, USA
| | - Michelle L Hastings
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
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34
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Jain HV, Beaucage SL. An Amphipathic trans-Acting Phosphorothioate DNA Element Delivers Uncharged PNA and PMO Nucleic Acid Sequences in Mammalian Cells. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2016; 64:4.69.1-4.69.22. [PMID: 27516815 PMCID: PMC4976944 DOI: 10.1002/0471142700.nc0469s64] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An innovative approach to the delivery of uncharged peptide nucleic acids (PNAs) and phosphorodiamidate morpholino (PMO) oligomers in mammalian cells is described and consists of extending the sequence of those oligomers with a short PNA-polyA or PMO-polyA tail. Recognition of the polyA-tailed PNA or PMO oligomers by an amphipathic trans-acting polythymidylic thiophosphate triester element (dTtaPS) results in efficient internalization of those oligomers in several cell lines. The authors' findings indicate that cellular uptake of the oligomers occurs through an energy-dependent mechanism and macropinocytosis appears to be the predominant endocytic pathway used for internalization. The functionality of the internalized oligomers is demonstrated by alternate splicing of the pre-mRNA encoding luciferase in HeLa pLuc 705 cells. Amphipathic phosphorothioate DNA elements may represent a unique class of cellular transporters for robust delivery of uncharged nucleic acid sequences in live mammalian cells. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Harsh V Jain
- Laboratory of Biological Chemistry, Food and Drug Administration, Silver Spring, Maryland
| | - Serge L Beaucage
- Laboratory of Biological Chemistry, Food and Drug Administration, Silver Spring, Maryland
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35
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Subbotina E, Koganti SRK, Hodgson-Zingman DM, Zingman LV. Morpholino-driven gene editing: A new horizon for disease treatment and prevention. Clin Pharmacol Ther 2015; 99:21-5. [PMID: 26474085 DOI: 10.1002/cpt.276] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 09/22/2015] [Accepted: 10/09/2015] [Indexed: 11/10/2022]
Affiliation(s)
- E Subbotina
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - S R K Koganti
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - D M Hodgson-Zingman
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa, USA.,François Abboud Cardiovascular Research Center, University of Iowa, Iowa City, Iowa, USA
| | - L V Zingman
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa, USA.,François Abboud Cardiovascular Research Center, University of Iowa, Iowa City, Iowa, USA.,Veterans Affairs Medical Center, Iowa City, Iowa, USA
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36
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Reinardy HC, Emerson CE, Manley JM, Bodnar AG. Tissue regeneration and biomineralization in sea urchins: role of Notch signaling and presence of stem cell markers. PLoS One 2015; 10:e0133860. [PMID: 26267358 PMCID: PMC4534296 DOI: 10.1371/journal.pone.0133860] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/02/2015] [Indexed: 11/30/2022] Open
Abstract
Echinoderms represent a phylum with exceptional regenerative capabilities that can reconstruct both external appendages and internal organs. Mechanistic understanding of the cellular pathways involved in regeneration in these animals has been hampered by the limited genomic tools and limited ability to manipulate regenerative processes. We present a functional assay to investigate mechanisms of tissue regeneration and biomineralization by measuring the regrowth of amputated tube feet (sensory and motor appendages) and spines in the sea urchin, Lytechinus variegatus. The ability to manipulate regeneration was demonstrated by concentration-dependent inhibition of regrowth of spines and tube feet by treatment with the mitotic inhibitor, vincristine. Treatment with the gamma-secretase inhibitor DAPT resulted in a concentration-dependent inhibition of regrowth, indicating that both tube feet and spine regeneration require functional Notch signaling. Stem cell markers (Piwi and Vasa) were expressed in tube feet and spine tissue, and Vasa-positive cells were localized throughout the epidermis of tube feet by immunohistochemistry, suggesting the existence of multipotent progenitor cells in these highly regenerative appendages. The presence of Vasa protein in other somatic tissues (e.g. esophagus, radial nerve, and a sub-population of coelomocytes) suggests that multipotent cells are present throughout adult sea urchins and may contribute to normal homeostasis in addition to regeneration. Mechanistic insight into the cellular pathways governing the tremendous regenerative capacity of echinoderms may reveal processes that can be modulated for regenerative therapies, shed light on the evolution of regeneration, and enable the ability to predict how these processes will respond to changing environmental conditions.
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Affiliation(s)
- Helena C. Reinardy
- Molecular Discovery Laboratory, Bermuda Institute of Ocean Sciences, St. George’s GE 01, Bermuda
| | - Chloe E. Emerson
- Molecular Discovery Laboratory, Bermuda Institute of Ocean Sciences, St. George’s GE 01, Bermuda
| | - Jason M. Manley
- Molecular Discovery Laboratory, Bermuda Institute of Ocean Sciences, St. George’s GE 01, Bermuda
| | - Andrea G. Bodnar
- Molecular Discovery Laboratory, Bermuda Institute of Ocean Sciences, St. George’s GE 01, Bermuda
- * E-mail:
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37
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Martínez T, Jiménez AI, Pañeda C. Short-interference RNAs: becoming medicines. EXCLI JOURNAL 2015; 14:714-46. [PMID: 26648823 PMCID: PMC4669907 DOI: 10.17179/excli2015-297] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 05/12/2015] [Indexed: 12/30/2022]
Abstract
RNA interference is a cellular mechanism by which small molecules of double stranded RNA modulate gene expression acting on the concentration and/or availability of a given messenger RNA. Almost 10 years after Fire and Mello received the Nobel Prize for the discovery of this mechanism in flat worms, RNA interference is on the edge of becoming a new class of therapeutics. With various phase III studies underway, the following years will determine whether RNAi-therapeutics can rise up to the challenge and become mainstream medicines. The present review gives a thorough overview of the current status of this technology focusing on the path to the clinic of this new class of compounds.
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Affiliation(s)
- Tamara Martínez
- Sylentis, R&D department c/Santiago Grisolía, Tres Cantos, Madrid, Spain
| | - Ana Isabel Jiménez
- Sylentis, R&D department c/Santiago Grisolía, Tres Cantos, Madrid, Spain
| | - Covadonga Pañeda
- Sylentis, R&D department c/Santiago Grisolía, Tres Cantos, Madrid, Spain
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Lamm MS, Liu H, Gemmell NJ, Godwin JR. The Need for Speed: Neuroendocrine Regulation of Socially-controlled Sex Change. Integr Comp Biol 2015; 55:307-22. [DOI: 10.1093/icb/icv041] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Looking to the horizon: the role of bilirubin in the development and prevention of age-related chronic diseases. Clin Sci (Lond) 2015; 129:1-25. [DOI: 10.1042/cs20140566] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Bilirubin, the principal tetrapyrrole, bile pigment and catabolite of haem, is an emerging biomarker of disease resistance, which may be related to several recently documented biological functions. Initially believed to be toxic in infants, the perception of bilirubin has undergone a transformation: it is now considered to be a molecule that may promote health in adults. Data from the last decade demonstrate that mildly elevated serum bilirubin levels are strongly associated with reduced prevalence of chronic diseases, particularly cardiovascular diseases (CVDs), as well as CVD-related mortality and risk factors. Recent data also link bilirubin to other chronic diseases, including cancer and Type 2 diabetes mellitus, and to all-cause mortality. Therefore, there is evidence to suggest that bilirubin is a biomarker for reduced chronic disease prevalence and a predictor of all-cause mortality, which is of important clinical significance. In the present review, detailed information on the association between bilirubin and all-cause mortality, as well as the pathological conditions of CVD, cancer, diabetes and neurodegenerative diseases, is provided. The mechanistic background concerning how bilirubin and its metabolism may influence disease prevention and its clinical relevance is also discussed. Given that the search for novel biomarkers of these diseases, as well as for novel therapeutic modalities, is a key research objective for the near future, bilirubin represents a promising candidate, meeting the criteria of a biomarker, and should be considered more carefully in clinical practice as a molecule that might provide insights into disease resistance. Clearly, however, greater molecular insight is warranted to support and strengthen the conclusion that bilirubin can prevent disease, with future research directions also proposed.
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Koganti SRK, Zhu Z, Subbotina E, Gao Z, Sierra A, Proenza M, Yang L, Alekseev A, Hodgson-Zingman D, Zingman L. Disruption of KATP channel expression in skeletal muscle by targeted oligonucleotide delivery promotes activity-linked thermogenesis. Mol Ther 2015; 23:707-16. [PMID: 25648265 DOI: 10.1038/mt.2015.21] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 01/19/2015] [Indexed: 12/18/2022] Open
Abstract
Despite the medical, social, and economic impact of obesity, only a few therapeutic options, focused largely on reducing caloric intake, are currently available and these have limited success rates. A major impediment is that any challenge by caloric restriction is counterbalanced by activation of systems that conserve energy to prevent body weight loss. Therefore, targeting energy-conserving mechanisms to promote energy expenditure is an attractive strategy for obesity treatment. Here, in order to suppress muscle energy efficiency, we target sarcolemmal ATP-sensitive potassium (KATP) channels which have previously been shown to be important in maintaining muscle energy economy. Specifically, we employ intramuscular injections of cell-penetrating vivo-morpholinos to prevent translation of the channel pore-forming subunit. This intervention results in significant reduction of KATP channel expression and function in treated areas, without affecting the channel expression in nontargeted tissues. Furthermore, suppression of KATP channel function in a group of hind limb muscles causes a substantial increase in activity-related energy consumption, with little effect on exercise tolerance. These findings establish a proof-of-principle that selective skeletal muscle targeting of sarcolemmal KATP channel function is possible and that this intervention can alter overall bodily energetics without a disabling impact on muscle mechanical function.
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Affiliation(s)
- Siva Rama Krishna Koganti
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Zhiyong Zhu
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Ekaterina Subbotina
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Zhan Gao
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Ana Sierra
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Manuel Proenza
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Liping Yang
- Veterans Affairs Medical Center, Iowa City, Iowa, USA
| | - Alexey Alekseev
- Department of Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Denice Hodgson-Zingman
- 1] Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA [2] Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa, USA [3] François Abboud Cardiovascular Research Center, University of Iowa, Iowa City, Iowa, USA
| | - Leonid Zingman
- 1] Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA [2] Veterans Affairs Medical Center, Iowa City, Iowa, USA [3] Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa, USA [4] François Abboud Cardiovascular Research Center, University of Iowa, Iowa City, Iowa, USA
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Rapid screening of gene function by systemic delivery of morpholino oligonucleotides to live mouse embryos. PLoS One 2015; 10:e0114932. [PMID: 25629157 PMCID: PMC4309589 DOI: 10.1371/journal.pone.0114932] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 11/16/2014] [Indexed: 11/19/2022] Open
Abstract
Traditional gene targeting methods in mice are complex and time consuming, especially when conditional deletion methods are required. Here, we describe a novel technique for assessing gene function by injection of modified antisense morpholino oligonucleotides (MOs) into the heart of mid-gestation mouse embryos. After allowing MOs to circulate through the embryonic vasculature, target tissues were explanted, cultured and analysed for expression of key markers. We established proof-of-principle by partially phenocopying known gene knockout phenotypes in the fetal gonads (Stra8, Sox9) and pancreas (Sox9). We also generated a novel double knockdown of Gli1 and Gli2, revealing defects in Leydig cell differentiation in the fetal testis. Finally, we gained insight into the roles of Adamts19 and Ctrb1, genes of unknown function in sex determination and gonadal development. These studies reveal the utility of this method as a means of first-pass analysis of gene function during organogenesis before committing to detailed genetic analysis.
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Jain HV, Verthelyi D, Beaucage SL. Amphipathic trans-acting phosphorothioate DNA elements mediate the delivery of uncharged nucleic acid sequences in mammalian cells. RSC Adv 2015. [DOI: 10.1039/c5ra12038a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Amphipathic trans-acting phosphorothioate DNA elements deliver PNA and PMO oligomers in mammalian cells.
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Affiliation(s)
- H. V. Jain
- Division of Biotechnology Review and Research IV
- CDER
- FDA
- Maryland 20933
- USA
| | - D. Verthelyi
- Division of Biotechnology Review and Research III
- CDER
- FDA
- Maryland 20933
- USA
| | - S. L. Beaucage
- Division of Biotechnology Review and Research IV
- CDER
- FDA
- Maryland 20933
- USA
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Clinical implications of miRNAs in the pathogenesis, diagnosis and therapy of pancreatic cancer. Adv Drug Deliv Rev 2015; 81:16-33. [PMID: 25453266 DOI: 10.1016/j.addr.2014.10.020] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 10/12/2014] [Accepted: 10/15/2014] [Indexed: 02/06/2023]
Abstract
Despite considerable progress being made in understanding pancreatic cancer (PC) pathogenesis, it still remains the 10th most often diagnosed malignancy in the world and 4th leading cause of cancer related deaths in the United States with a five year survival rate of only 6%. The aggressive nature, lack of early diagnostic and prognostic markers, late clinical presentation, and limited efficacy of existing treatment regimens make PC a lethal cancer with high mortality and poor prognosis. Therefore, novel reliable biomarkers and molecular targets are urgently needed to combat this deadly disease. MicroRNAs (miRNAs) are short (19-24 nucleotides) non-coding RNA molecules implicated in the regulation of gene expression at post-transcriptional level and play significant roles in various physiological and pathological conditions. Aberrant expression of miRNAs has been reported in several cancers including PC and is implicated in PC pathogenesis and progression, suggesting their utility in diagnosis, prognosis and therapy. In this review, we summarize the role of several miRNAs that regulate various oncogenes (KRAS) and tumor suppressor genes (p53, p16, SMAD4, etc.) involved in PC development, their prospective roles as diagnostic and prognostic markers and as a therapeutic targets.
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Rigo F, Seth PP, Bennett CF. Antisense oligonucleotide-based therapies for diseases caused by pre-mRNA processing defects. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:303-52. [PMID: 25201110 DOI: 10.1007/978-1-4939-1221-6_9] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Before a messenger RNA (mRNA) is translated into a protein in the cytoplasm, its pre-mRNA precursor is extensively processed through capping, splicing and polyadenylation in the nucleus. Defects in the processing of pre-mRNAs due to mutations in RNA sequences often cause disease. Traditional small molecules or protein-based therapeutics are not well suited for correcting processing defects by targeting RNA. However, antisense oligonucleotides (ASOs) designed to bind RNA by Watson-Crick base pairing can target most RNA transcripts and have emerged as the ideal therapeutic agents for diseases that are caused by pre-mRNA processing defects. Here we review the diverse ASO-based mechanisms that can be exploited to modulate the expression of RNA. We also discuss how advancements in medicinal chemistry and a deeper understanding of the pharmacokinetic and toxicological properties of ASOs have enabled their use as therapeutic agents. We end by describing how ASOs have been used successfully to treat various pre-mRNA processing diseases in animal models.
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Affiliation(s)
- Frank Rigo
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA, USA,
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Clayton NP, Nelson CA, Weeden T, Taylor KM, Moreland RJ, Scheule RK, Phillips L, Leger AJ, Cheng SH, Wentworth BM. Antisense Oligonucleotide-mediated Suppression of Muscle Glycogen Synthase 1 Synthesis as an Approach for Substrate Reduction Therapy of Pompe Disease. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e206. [PMID: 25350581 PMCID: PMC4217081 DOI: 10.1038/mtna.2014.57] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/16/2014] [Indexed: 01/10/2023]
Abstract
Pompe disease is an autosomal recessive disorder caused by a deficiency of acid α-glucosidase (GAA; EC 3.2.1.20) and the resultant progressive lysosomal accumulation of glycogen in skeletal and cardiac muscles. Enzyme replacement therapy using recombinant human GAA (rhGAA) has proven beneficial in addressing several aspects of the disease such as cardiomyopathy and aberrant motor function. However, residual muscle weakness, hearing loss, and the risks of arrhythmias and osteopenia persist despite enzyme therapy. Here, we evaluated the relative merits of substrate reduction therapy (by inhibiting glycogen synthesis) as a potential adjuvant strategy. A phosphorodiamidate morpholino oligonucleotide (PMO) designed to invoke exon skipping and premature stop codon usage in the transcript for muscle specific glycogen synthase (Gys1) was identified and conjugated to a cell penetrating peptide (GS-PPMO) to facilitate PMO delivery to muscle. GS-PPMO systemic administration to Pompe mice led to a dose-dependent decrease in glycogen synthase transcripts in the quadriceps, and the diaphragm but not the liver. An mRNA response in the heart was seen only at the higher dose tested. Associated with these decreases in transcript levels were correspondingly lower tissue levels of muscle specific glycogen synthase and activity. Importantly, these reductions resulted in significant decreases in the aberrant accumulation of lysosomal glycogen in the quadriceps, diaphragm, and heart of Pompe mice. Treatment was without any overt toxicity, supporting the notion that substrate reduction by GS-PPMO-mediated inhibition of muscle specific glycogen synthase represents a viable therapeutic strategy for Pompe disease after further development.
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Affiliation(s)
| | - Carol A Nelson
- Translational Medicine Consulting, Westford, Massachusetts, USA
| | - Timothy Weeden
- Genzyme, A Sanofi Company, Framingham, Massachusetts, USA
| | | | | | | | - Lucy Phillips
- Genzyme, A Sanofi Company, Framingham, Massachusetts, USA
| | - Andrew J Leger
- Genzyme, A Sanofi Company, Framingham, Massachusetts, USA
| | - Seng H Cheng
- Genzyme, A Sanofi Company, Framingham, Massachusetts, USA
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Sun X, Marque LO, Cordner Z, Pruitt JL, Bhat M, Li PP, Kannan G, Ladenheim EE, Moran TH, Margolis RL, Rudnicki DD. Phosphorodiamidate morpholino oligomers suppress mutant huntingtin expression and attenuate neurotoxicity. Hum Mol Genet 2014; 23:6302-17. [PMID: 25035419 DOI: 10.1093/hmg/ddu349] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by a CAG trinucleotide repeat expansion in the huntingtin (HTT) gene. Disease pathogenesis derives, at least in part, from the long polyglutamine tract encoded by mutant HTT. Therefore, considerable effort has been dedicated to the development of therapeutic strategies that significantly reduce the expression of the mutant HTT protein. Antisense oligonucleotides (ASOs) targeted to the CAG repeat region of HTT transcripts have been of particular interest due to their potential capacity to discriminate between normal and mutant HTT transcripts. Here, we focus on phosphorodiamidate morpholino oligomers (PMOs), ASOs that are especially stable, highly soluble and non-toxic. We designed three PMOs to selectively target expanded CAG repeat tracts (CTG22, CTG25 and CTG28), and two PMOs to selectively target sequences flanking the HTT CAG repeat (HTTex1a and HTTex1b). In HD patient-derived fibroblasts with expanded alleles containing 44, 77 or 109 CAG repeats, HTTex1a and HTTex1b were effective in suppressing the expression of mutant and non-mutant transcripts. CTGn PMOs also suppressed HTT expression, with the extent of suppression and the specificity for mutant transcripts dependent on the length of the targeted CAG repeat and on the CTG repeat length and concentration of the PMO. PMO CTG25 reduced HTT-induced cytotoxicity in vitro and suppressed mutant HTT expression in vivo in the N171-82Q transgenic mouse model. Finally, CTG28 reduced mutant HTT expression and improved the phenotype of Hdh(Q7/Q150) knock-in HD mice. These data demonstrate the potential of PMOs as an approach to suppressing the expression of mutant HTT.
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Affiliation(s)
- Xin Sun
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences
| | - Leonard O Marque
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences
| | - Zachary Cordner
- Behavioral Neuroscience Laboratory, Department of Psychiatry and Behavioral Sciences
| | - Jennifer L Pruitt
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences
| | - Manik Bhat
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences
| | - Pan P Li
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences
| | - Geetha Kannan
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences
| | - Ellen E Ladenheim
- Behavioral Neuroscience Laboratory, Department of Psychiatry and Behavioral Sciences
| | - Timothy H Moran
- Behavioral Neuroscience Laboratory, Department of Psychiatry and Behavioral Sciences
| | - Russell L Margolis
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Department of Neurology, and Program of Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Dobrila D Rudnicki
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Program of Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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Kroeger PT, Wingert RA. Using zebrafish to study podocyte genesis during kidney development and regeneration. Genesis 2014; 52:771-92. [PMID: 24920186 DOI: 10.1002/dvg.22798] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 06/08/2014] [Accepted: 06/09/2014] [Indexed: 12/21/2022]
Abstract
During development, vertebrates form a progression of up to three different kidneys that are comprised of functional units termed nephrons. Nephron composition is highly conserved across species, and an increasing appreciation of the similarities between zebrafish and mammalian nephron cell types has positioned the zebrafish as a relevant genetic system for nephrogenesis studies. A key component of the nephron blood filter is a specialized epithelial cell known as the podocyte. Podocyte research is of the utmost importance as a vast majority of renal diseases initiate with the dysfunction or loss of podocytes, resulting in a condition known as proteinuria that causes nephron degeneration and eventually leads to kidney failure. Understanding how podocytes develop during organogenesis may elucidate new ways to promote nephron health by stimulating podocyte replacement in kidney disease patients. In this review, we discuss how the zebrafish model can be used to study kidney development, and how zebrafish research has provided new insights into podocyte lineage specification and differentiation. Further, we discuss the recent discovery of podocyte regeneration in adult zebrafish, and explore how continued basic research using zebrafish can provide important knowledge about podocyte genesis in embryonic and adult environments. genesis 52:771-792, 2014. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Paul T Kroeger
- Department of Biological Sciences and Center for Zebrafish Research, University of Notre Dame, Notre Dame, Indiana, 46556
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Suresh G, Priyakumar UD. Atomistic investigation of the effect of incremental modification of deoxyribose sugars by locked nucleic acid (β-D-LNA and α-L-LNA) moieties on the structures and thermodynamics of DNA-RNA hybrid duplexes. J Phys Chem B 2014; 118:5853-63. [PMID: 24845216 DOI: 10.1021/jp5014779] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chemically modified oligonucleotides offer many possibilities in utilizing their special features for a vast number of applications in nucleic acid based therapies and synthetic molecular biology. Locked nucleic acid analogues (α-/β-LNA) are modifications having an extra ring of 2'-O,4'-C-methylene group in the furanose sugar. LNA strands have been shown to exhibit high binding affinity toward RNA and DNA strands, and the resultant duplexes show significantly high melting temperatures. In the present study, molecular dynamics (MD) simulations were performed on DNA-RNA hybrid duplexes by systematically modifying their deoxyribose sugars with locked nucleic acid analogues. Several geometrical and energetic analyses were performed using principal component (PCA) analysis and binding free energy methods to understand the consequence of incorporated isomeric LNA modifications on the structure, dynamics, and stability of DNA-RNA hybrid duplex. The β-modification systematically changes the conformation of the DNA-RNA hybrid duplex whereas drastic changes are observed for α-modification. The fully modified duplexes have distinct properties compared to partial and unmodified duplexes, and the partly modified duplexes have properties intermediate to full strand and unmodified duplexes. The distribution of BI versus BII populations suggests that backbone rearrangement is minimal for β-LNA modification in order to accommodate it in duplexes whereas extensive backbone rearrangement is necessary in order to incorporate α-LNA modification which subsequently alters the energetic and structural properties of the duplexes. The simulation results also suggest that the alteration of DNA-RNA hybrid properties depends on the position of modification and the gap between the modifications.
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Affiliation(s)
- Gorle Suresh
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500 032, India
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Tan CW, Chan YF, Quah YW, Poh CL. Inhibition of enterovirus 71 infection by antisense octaguanidinium dendrimer-conjugated morpholino oligomers. Antiviral Res 2014; 107:35-41. [PMID: 24769243 PMCID: PMC7118997 DOI: 10.1016/j.antiviral.2014.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/25/2014] [Accepted: 04/13/2014] [Indexed: 12/11/2022]
Abstract
Enterovirus 71 (EV-71) infections are generally manifested as mild hand, foot and mouth disease, but have been reported to cause severe neurological complications with high mortality rates. Treatment options remain limited due to the lack of antivirals. Octaguanidinium-conjugated morpholino oligomers (vivo-MOs) are single-stranded DNA-like antisense agents that can readily penetrate cells and reduce gene expression by steric blocking of complementary RNA sequences. In this study, inhibitory effects of three vivo-MOs that are complementary to the EV-71 internal ribosome entry site (IRES) and the RNA-dependent RNA polymerase (RdRP) were tested in RD cells. Vivo-MO-1 and vivo-MO-2 targeting the EV-71 IRES showed significant viral plaque reductions of 2.5 and 3.5 log10PFU/ml, respectively. Both vivo-MOs reduced viral RNA copies and viral capsid expression in RD cells in a dose-dependent manner. In contrast, vivo-MO-3 targeting the EV-71 RdRP exhibited less antiviral activity. Both vivo-MO-1 and 2 remained active when administered either 4h before or within 6h after EV-71 infection. Vivo-MO-2 exhibited antiviral activities against poliovirus (PV) and coxsackievirus A16 but vivo-MO-1 showed no antiviral activities against PV. Both the IRES-targeting vivo-MO-1 and vivo-MO-2 inhibit EV-71 RNA translation. Resistant mutants arose after serial passages in the presence of vivo-MO-1, but none were isolated against vivo-MO-2. A single T to C substitution at nucleotide position 533 was sufficient to confer resistance to vivo-MO-1. Our findings suggest that IRES-targeting vivo-MOs are good antiviral candidates for treating early EV-71 infection, and vivo-MO-2 is a more favorable candidate with broader antiviral spectrum against enteroviruses and are refractory to antiviral resistance.
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Affiliation(s)
- Chee Wah Tan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia; Tropical Infectious Disease Research and Education Center, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yi Wan Quah
- Faculty of Science and Technology, Sunway University, 46150 Petaling Jaya, Selangor, Malaysia
| | - Chit Laa Poh
- Faculty of Science and Technology, Sunway University, 46150 Petaling Jaya, Selangor, Malaysia.
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50
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Amin NM, Tandon P, Osborne Nishimura E, Conlon FL. RNA-seq in the tetraploid Xenopus laevis enables genome-wide insight in a classic developmental biology model organism. Methods 2014; 66:398-409. [PMID: 23792920 PMCID: PMC3884041 DOI: 10.1016/j.ymeth.2013.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/07/2013] [Accepted: 06/13/2013] [Indexed: 01/08/2023] Open
Abstract
Advances in sequencing technology have significantly advanced the landscape of developmental biology research. The dissection of genetic networks in model and non-model organisms has been greatly enhanced with high-throughput sequencing technologies. RNA-seq has revolutionized the ability to perform developmental biology research in organisms without a published genome sequence. Here, we describe a protocol for developmental biologists to perform RNA-seq on dissected tissue or whole embryos. We start with the isolation of RNA and generation of sequencing libraries. We further show how to interpret and analyze the large amount of sequencing data that is generated in RNA-seq. We explore the abilities to examine differential expression, gene duplication, transcript assembly, alternative splicing and SNP discovery. For the purposes of this article, we use Xenopus laevis as the model organism to discuss uses of RNA-seq in an organism without a fully annotated genome sequence.
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Affiliation(s)
- Nirav M Amin
- University of North Carolina, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA; Department of Genetics, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Panna Tandon
- University of North Carolina, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA; Department of Genetics, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | | | - Frank L Conlon
- University of North Carolina, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA; Department of Biology, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA; Department of Genetics, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA.
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