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Bereczki Z, Benczik B, Balogh OM, Marton S, Puhl E, Pétervári M, Váczy-Földi M, Papp ZT, Makkos A, Glass K, Locquet F, Euler G, Schulz R, Ferdinandy P, Ágg B. Mitigating off-target effects of small RNAs: conventional approaches, network theory and artificial intelligence. Br J Pharmacol 2024. [PMID: 39293936 DOI: 10.1111/bph.17302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/07/2024] [Accepted: 06/17/2024] [Indexed: 09/20/2024] Open
Abstract
Three types of highly promising small RNA therapeutics, namely, small interfering RNAs (siRNAs), microRNAs (miRNAs) and the RNA subtype of antisense oligonucleotides (ASOs), offer advantages over small-molecule drugs. These small RNAs can target any gene product, opening up new avenues of effective and safe therapeutic approaches for a wide range of diseases. In preclinical research, synthetic small RNAs play an essential role in the investigation of physiological and pathological pathways as silencers of specific genes, facilitating discovery and validation of drug targets in different conditions. Off-target effects of small RNAs, however, could make it difficult to interpret experimental results in the preclinical phase and may contribute to adverse events of small RNA therapeutics. Out of the two major types of off-target effects we focused on the hybridization-dependent, especially on the miRNA-like off-target effects. Our main aim was to discuss several approaches, including sequence design, chemical modifications and target prediction, to reduce hybridization-dependent off-target effects that should be considered even at the early development phase of small RNA therapy. Because there is no standard way of predicting hybridization-dependent off-target effects, this review provides an overview of all major state-of-the-art computational methods and proposes new approaches, such as the possible inclusion of network theory and artificial intelligence (AI) in the prediction workflows. Case studies and a concise survey of experimental methods for validating in silico predictions are also presented. These methods could contribute to interpret experimental results, to minimize off-target effects and hopefully to avoid off-target-related adverse events of small RNA therapeutics.
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Affiliation(s)
- Zoltán Bereczki
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
| | - Bettina Benczik
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Olivér M Balogh
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
| | - Szandra Marton
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
| | - Eszter Puhl
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
| | - Mátyás Pétervári
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Sanovigado Kft, Budapest, Hungary
| | - Máté Váczy-Földi
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
| | - Zsolt Tamás Papp
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
| | - András Makkos
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Kimberly Glass
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Fabian Locquet
- Physiologisches Institut, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Gerhild Euler
- Physiologisches Institut, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Rainer Schulz
- Physiologisches Institut, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Péter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Bence Ágg
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
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Saade J, Mestre TA. Huntington's Disease: Latest Frontiers in Therapeutics. Curr Neurol Neurosci Rep 2024; 24:255-264. [PMID: 38861215 DOI: 10.1007/s11910-024-01345-y] [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] [Accepted: 05/21/2024] [Indexed: 06/12/2024]
Abstract
PURPOSE OF REVIEW Huntington's disease (HD) is an autosomal-dominant disorder caused by a pathological expansion of a trinucleotide repeat (CAG) on exon 1 of the huntingtin (HTT) gene. HD is characterized by the presence of chorea, alongside other hyperkinesia, parkinsonism and a combination of cognitive and behavioural features. Currently, there are no disease-modifying therapies (DMTs) for HD, and the only intervention(s) with approved indication target the treatment of chorea. This article reviews recent research on the clinical development of DMTs and newly developed tools that enhance clinical trial design towards a successful DMT in the future. RECENT FINDINGS HD is living in an era of target-specific drug development with emphasis on the mechanisms related to mutant Huntingtin (HTT) protein. Examples include antisense oligonucleotides (ASO), splicing modifiers and microRNA molecules that aim to reduce the levels of mutant HTT protein. After initial negative results with ASO molecules Tominersen and WVE-120101/ WVE-120102, the therapeutic landscape continues to expand, with various trials currently under development to document proof-of-concept and safety/tolerability. Immune-targeted therapies have also been evaluated in early-phase clinical trials, with promising preliminary findings. The possibility of quantifying mHTT in CSF, along with the development of an integrated biological staging system in HD are important innovations applicable to clinical trial design that enhance the drug development process. Although a future in HD with DMTs remains a hope for those living with HD, care partners and care providers, the therapeutic landscape is promising, with various drug development programs underway following a targeted approach supported by disease-specific biomarkers and staging frameworks.
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Affiliation(s)
- Joseph Saade
- The Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Tiago A Mestre
- The Ottawa Hospital Research Institute, Ottawa, ON, Canada.
- The University of Ottawa Brain and Research Institute, Ottawa, ON, Canada.
- Parkinson's Disease and Movement Disorder Clinic, Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada.
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Kong C, Yin G, Wang X, Sun Y. In Utero Gene Therapy and its Application in Genetic Hearing Loss. Adv Biol (Weinh) 2024:e2400193. [PMID: 39007241 DOI: 10.1002/adbi.202400193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/03/2024] [Indexed: 07/16/2024]
Abstract
For monogenic genetic diseases, in utero gene therapy (IUGT) shows the potential for early prevention against irreversible and lethal pathological changes. Moreover, animal models have also demonstrated the effectiveness of IUGT in the treatment of coagulation disorders, hemoglobinopathies, neurogenetic disorders, and metabolic and pulmonary diseases. For major alpha thalassemia and severe osteogenesis imperfecta, in utero stem cell transplantation has entered the phase I clinical trial stage. Within the realm of the inner ear, genetic hearing loss significantly hampers speech, cognitive, and intellectual development in children. Nowadays, gene therapies offer substantial promise for deafness, with the success of clinical trials in autosomal recessive deafness 9 using AAV-OTOF gene therapy. However, the majority of genetic mutations that cause deafness affect the development of cochlear structures before the birth of fetuses. Thus, gene therapy before alterations in cochlear structure leading to hearing loss has promising applications. In this review, addressing advances in various fields of IUGT, the progress, and application of IUGT in the treatment of genetic hearing loss are focused, in particular its implementation methods and unique advantages.
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Affiliation(s)
- Chenyang Kong
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Ge Yin
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiaohui Wang
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yu Sun
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Otorhinolaryngology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
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Zhang C, Rehman M, Tian X, Pei SLC, Gu J, Bell TA, Dong K, Tham MS, Cai Y, Wei Z, Behrens F, Jetten AM, Zhao H, Lek M, Somlo S. Glis2 is an early effector of polycystin signaling and a target for therapy in polycystic kidney disease. Nat Commun 2024; 15:3698. [PMID: 38693102 PMCID: PMC11063051 DOI: 10.1038/s41467-024-48025-6] [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: 06/02/2023] [Accepted: 04/15/2024] [Indexed: 05/03/2024] Open
Abstract
Mouse models of autosomal dominant polycystic kidney disease (ADPKD) show that intact primary cilia are required for cyst growth following the inactivation of polycystin-1. The signaling pathways underlying this process, termed cilia-dependent cyst activation (CDCA), remain unknown. Using translating ribosome affinity purification RNASeq on mouse kidneys with polycystin-1 and cilia inactivation before cyst formation, we identify the differential 'CDCA pattern' translatome specifically dysregulated in kidney tubule cells destined to form cysts. From this, Glis2 emerges as a candidate functional effector of polycystin signaling and CDCA. In vitro changes in Glis2 expression mirror the polycystin- and cilia-dependent changes observed in kidney tissue, validating Glis2 as a cell culture-based indicator of polycystin function related to cyst formation. Inactivation of Glis2 suppresses polycystic kidney disease in mouse models of ADPKD, and pharmacological targeting of Glis2 with antisense oligonucleotides slows disease progression. Glis2 transcript and protein is a functional target of CDCA and a potential therapeutic target for treating ADPKD.
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Affiliation(s)
- Chao Zhang
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Michael Rehman
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Xin Tian
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Steven Lim Cho Pei
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jianlei Gu
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | | | - Ke Dong
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ming Shen Tham
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Yiqiang Cai
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Zemeng Wei
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Felix Behrens
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Anton M Jetten
- Cell Biology Section, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Stefan Somlo
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA.
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
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Qin B, Peng Q, Dong H, Lei L, Wu S. Non-coding RNAs in diabetic foot ulcer- a focus on infected wounds. Diabetes Metab Res Rev 2024; 40:e3740. [PMID: 37839046 DOI: 10.1002/dmrr.3740] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 07/19/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023]
Abstract
Diabetes mellitus is associated with a wide range of neuropathies, vasculopathies, and immunopathies, resulting in many complications. More than 30% of diabetic patients risk developing diabetic foot ulcers (DFUs). Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), play essential roles in various biological functions in the hyperglycaemic environment that determines the development of DFU. Ulceration results in tissue breakdown and skin barrier scavenging, thereby facilitating bacterial infection and biofilm formation. Many bacteria contribute to diabetic foot infection (DFI), including Staphylococcus aureus (S. aureus) et al. A heterogeneous group of "ncRNAs," termed small RNAs (sRNAs), powerfully regulates biofilm formation and DFI healing. Multidisciplinary foot care interventions have been identified for nonhealing ulcers. With an appreciation of the link between disease processes and ncRNAs, a novel therapeutic model of bioactive materials loaded with ncRNAs has been developed to prevent and manage diabetic foot complications.
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Affiliation(s)
- Boquan Qin
- Department of Orthopedic Surgery and Orthopedic Research Institute, Laboratory of Stem Cell and Tissue Engineering, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Qi Peng
- Department of Orthopedic Surgery and Orthopedic Research Institute, Laboratory of Stem Cell and Tissue Engineering, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hongxian Dong
- Department of Orthopedic Surgery and Orthopedic Research Institute, Laboratory of Stem Cell and Tissue Engineering, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Lei Lei
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shizhou Wu
- Department of Orthopedic Surgery and Orthopedic Research Institute, Laboratory of Stem Cell and Tissue Engineering, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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Suryawanshi YN, Warbhe RA. Familial Hypercholesterolemia: A Literature Review of the Pathophysiology and Current and Novel Treatments. Cureus 2023; 15:e49121. [PMID: 38125244 PMCID: PMC10732334 DOI: 10.7759/cureus.49121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Familial hypercholesterolemia (FH) is a genetically transmitted disorder. It shows an autosomal dominant mode of inheritance. It is a metabolic disorder. Mutation in chromosome 19 leads to this disorder. Chromosome 19 codes data for low-density lipoprotein (LDL) receptor (LDLR). LDLR either reduces increased LDL levels from the circulation or maintains a normal level of LDL. It precipitates the risk of cardiovascular disease at an early age. Characteristic features of FH are elevated levels of LDL in the blood because of sudden changes in LDLR, which causes a decrease in the clearance of LDL from the blood. Plaque gets deposited in the lumen of the arteries, called atherosclerosis, which occurs at an early young age. If both genes are affected then it is homozygous FH (HoFH); such a case is very rare. When a single gene is affected then that condition is known as heterozygous FH (HeFH). HoFH comes up with more severe cardiac disease than HeFH at an early age. The major cause of FH is a mutation in the LDLR gene while other causes include mutation in various genes like apolipoprotein B (apo B), proprotein convertase subtilisin/kexin type 9 (PCSK9), LDLR adaptor protein 1 (LDLRAP 1). In order to prevent cardiovascular crises due to FH, it must be diagnosed early and treated effectively. With increasing research and advances in medical sciences, many kinds of current and novel therapies are emerging that aim to reduce the level of LDL in blood.
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Affiliation(s)
- Yasha N Suryawanshi
- Department of Physiology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Rupesh A Warbhe
- Department of Pharmacology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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Buthelezi LA, Pillay S, Ntuli NN, Gcanga L, Guler R. Antisense Therapy for Infectious Diseases. Cells 2023; 12:2119. [PMID: 37626929 PMCID: PMC10453568 DOI: 10.3390/cells12162119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Infectious diseases, particularly Tuberculosis (TB) caused by Mycobacterium tuberculosis, pose a significant global health challenge, with 1.6 million reported deaths in 2021, making it the most fatal disease caused by a single infectious agent. The rise of drug-resistant infectious diseases adds to the urgency of finding effective and safe intervention therapies. Antisense therapy uses antisense oligonucleotides (ASOs) that are short, chemically modified, single-stranded deoxyribonucleotide molecules complementary to their mRNA target. Due to their designed target specificity and inhibition of a disease-causing gene at the mRNA level, antisense therapy has gained interest as a potential therapeutic approach. This type of therapy is currently utilized in numerous diseases, such as cancer and genetic disorders. Currently, there are limited but steadily increasing studies available that report on the use of ASOs as treatment for infectious diseases. This review explores the sustainability of FDA-approved and preclinically tested ASOs as a treatment for infectious diseases and the adaptability of ASOs for chemical modifications resulting in reduced side effects with improved drug delivery; thus, highlighting the potential therapeutic uses of ASOs for treating infectious diseases.
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Affiliation(s)
- Lwanda Abonga Buthelezi
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa; (L.A.B.); (S.P.); (N.N.N.); (L.G.)
- Department of Pathology, Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Shandre Pillay
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa; (L.A.B.); (S.P.); (N.N.N.); (L.G.)
- Department of Pathology, Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Noxolo Nokukhanya Ntuli
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa; (L.A.B.); (S.P.); (N.N.N.); (L.G.)
- Department of Pathology, Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lorna Gcanga
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa; (L.A.B.); (S.P.); (N.N.N.); (L.G.)
- Department of Pathology, Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa; (L.A.B.); (S.P.); (N.N.N.); (L.G.)
- Department of Pathology, Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- Faculty of Health Sciences, Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
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Friedman L, Avitzur OB, Galai EO, Ferrari N, Choen A, Dahan S, Mordechai T, Hart G. The safety and toxicity profile of SPL84, an inhaled antisense oligonucleotide for treatment of cystic fibrosis patients with the 3849 +10kb C->T mutation, supports a Phase 1/2 clinical study. Expert Opin Drug Metab Toxicol 2023; 19:709-720. [PMID: 37799089 DOI: 10.1080/17425255.2023.2266361] [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: 06/13/2023] [Accepted: 09/15/2023] [Indexed: 10/07/2023]
Abstract
INTRODUCTION SPL84 is an inhaled antisense oligonucleotide (ASO) in development for the treatment of cystic fibrosis (CF) patients carrying the 3849 + 10kb C->T (3849) mutation. To support the initiation of the first clinical study, a full battery of safety and toxicology studies were performed. RESEARCH DESIGN AND METHODS SPL84 was administered by inhalation to mice and monkeys to determine the no observed adverse effect level (NOAEL) and establish sufficient safety margins for the starting clinical dose. RESULTS There were no preclinical safety findings with SPL84; no related clinical signs, nor any effect on body weight, food consumption, or clinical pathology. The microscopic changes in the lungs were regarded as non-adverse and reflected a normal clearance process for inhaled compounds. Systemic exposure in both species was low. The NOAEL for mice and monkeys was the highest administered dose in both species, resulting in safety margins ~ 40X the proposed starting clinical dose. CONCLUSION These successful results supported the initiation of a phase 1/2 clinical study of SPL84 (ongoing), assessing the safety, tolerability, and pharmacokinetics of a single ascending dose in healthy subjects to be followed by assessment of safety, tolerability, pharmacokinetics, and preliminary efficacy of multiple ascending doses in CF patients carrying the 3849 mutation.
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Affiliation(s)
- Lital Friedman
- SpliSense, BiohouseLabs, Haddasah Ein Kerem, Jerusalem, Israel
| | | | | | | | - Asa Choen
- SpliSense, BiohouseLabs, Haddasah Ein Kerem, Jerusalem, Israel
| | - Sara Dahan
- SpliSense, BiohouseLabs, Haddasah Ein Kerem, Jerusalem, Israel
| | - Tamar Mordechai
- SpliSense, BiohouseLabs, Haddasah Ein Kerem, Jerusalem, Israel
| | - Gili Hart
- SpliSense, BiohouseLabs, Haddasah Ein Kerem, Jerusalem, Israel
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Fan S, Jiang T, Lv T, Liu J, Wang X. Synthesis of the Disaccharide Core of Ezomycin Nucleosides. Org Lett 2023; 25:4355-4358. [PMID: 37267119 DOI: 10.1021/acs.orglett.3c01494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The ezomycins make up a class of complex nucleoside antibiotics that share a common disaccharide core. Herein we present an efficient synthesis of this core from diacetone-d-allose, using a ruthenium-catalyzed asymmetric allylic etherification and a de novo carbohydrate synthesis based on the diastereoselective Henry reaction. Our strategy overcomes several challenges, such as introducing a dense array of functional groups and creating consecutive stereocenters with high selectivity. This approach enables the rapid preparation of disaccharides and paves the way for the total synthesis of ezomycins.
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Affiliation(s)
- Shuai Fan
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
| | - Tai Jiang
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
| | - Tinghong Lv
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
| | - Jian Liu
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
| | - Xiaolei Wang
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou 730000, P. R. China
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Vasilyeva SV, Baranovskaya EE, Dyudeeva ES, Lomzov AA, Pyshnyi DV. Synthesis of Oligonucleotides Carrying Inter-nucleotide N-(Benzoazole)-phosphoramide Moieties. ACS OMEGA 2023; 8:1556-1566. [PMID: 36643477 PMCID: PMC9835791 DOI: 10.1021/acsomega.2c07083] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
In this work, we present new oligonucleotide derivatives containing inter-nucleotide N-benzimidazole, N-benzoxazole, N-benzothiazole, and 1,3-dimethyl-N-benzimidazole (benzoazoles) phosphoramide groups. These modifications were introduced via the Staudinger reaction with appropriate azides during standard automated solid-phase oligonucleotide synthesis. The principal structural difference between the new azido modifiers and those already known is that they are bulk heterocyclic structures, similar to purine nucleoside bases. Modified oligonucleotides with one and two modifications at different positions and multiple modified heteronucleotide sequences were obtained with high yields. The possibility of multiple modifications in the process of automatic DNA synthesis is fundamental and critical for further application of our oligonucleotide derivatives. Initial studies on the properties of new oligonucleotides were carried out. The stability of the oligodeoxyribonucleotide duplex containing phosphoramide groups of N-benzoazoles with complementary DNA or RNA is slightly lower than that of native complexes.
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Affiliation(s)
| | | | - Evgeniya S. Dyudeeva
- Institute of Chemical Biology and Fundamental
Medicine, SB of RAS, pr. Lavrent’eva 8, 630090 Novosibirsk, Russia
| | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental
Medicine, SB of RAS, pr. Lavrent’eva 8, 630090 Novosibirsk, Russia
| | - Dmitrii V. Pyshnyi
- Institute of Chemical Biology and Fundamental
Medicine, SB of RAS, pr. Lavrent’eva 8, 630090 Novosibirsk, Russia
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Lee SH, Ng CX, Wong SR, Chong PP. MiRNAs Overexpression and Their Role in Breast Cancer: Implications for Cancer Therapeutics. Curr Drug Targets 2023; 24:484-508. [PMID: 36999414 DOI: 10.2174/1389450124666230329123409] [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: 09/22/2022] [Revised: 12/20/2022] [Accepted: 01/30/2023] [Indexed: 04/01/2023]
Abstract
MicroRNAs have a plethora of roles in various biological processes in the cells and most human cancers have been shown to be associated with dysregulation of the expression of miRNA genes. MiRNA biogenesis involves two alternative pathways, the canonical pathway which requires the successful cooperation of various proteins forming the miRNA-inducing silencing complex (miRISC), and the non-canonical pathway, such as the mirtrons, simtrons, or agotrons pathway, which bypasses and deviates from specific steps in the canonical pathway. Mature miRNAs are secreted from cells and circulated in the body bound to argonaute 2 (AGO2) and miRISC or transported in vesicles. These miRNAs may regulate their downstream target genes via positive or negative regulation through different molecular mechanisms. This review focuses on the role and mechanisms of miRNAs in different stages of breast cancer progression, including breast cancer stem cell formation, breast cancer initiation, invasion, and metastasis as well as angiogenesis. The design, chemical modifications, and therapeutic applications of synthetic anti-sense miRNA oligonucleotides and RNA mimics are also discussed in detail. The strategies for systemic delivery and local targeted delivery of the antisense miRNAs encompass the use of polymeric and liposomal nanoparticles, inorganic nanoparticles, extracellular vesicles, as well as viral vectors and viruslike particles (VLPs). Although several miRNAs have been identified as good candidates for the design of antisense and other synthetic modified oligonucleotides in targeting breast cancer, further efforts are still needed to study the most optimal delivery method in order to drive the research beyond preclinical studies.
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Affiliation(s)
- Sau Har Lee
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
- Centre for Drug Discovery and Molecular Pharmacology (CDDMP), Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Chu Xin Ng
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Sharon Rachel Wong
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Pei Pei Chong
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
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12
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Tian B, Bian Y, Bian DJ, Gao Y, Zhang X, Zhou SW, Zhang YH, Pang YN, Li ZS, Wang LW. Knowledge mapping of alternative splicing of cancer from 2012 to 2021: A bibliometric analysis. Front Oncol 2022; 12:1068805. [PMID: 36591484 PMCID: PMC9795218 DOI: 10.3389/fonc.2022.1068805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/24/2022] [Indexed: 12/15/2022] Open
Abstract
Background As a processing method of RNA precursors, alternative splicing (AS) is critical to normal cellular activities. Aberrant AS events are associated with cancer development and can be promising targets to treat cancer. However, no detailed and unbiased study describes the current state of AS of cancer research. We aim to measure and recognize the current state and trends of AS cancer research in this study. Methods The Web of Science Core Collection was used to acquire the articles. Utilizing three bibliometric tools (CiteSpace, VOSviewer, R-bibliometrix), we were able to measure and recognize the influence and collaboration data of individual articles, journals, and co-citations. Analysis of co-occurrence and burst information helped us identify the trending research areas related to AS of cancer. Results From 2012 to 2021, the total number of papers on AS of cancer published in 766 academic journals was 3,507, authored by 20,406 researchers in 405 institutions from 80 countries/regions. Research involving AS of cancer genes was primarily conducted in the United States and China; simultaneously, the Chinese Academy of Sciences, Fudan University, and National Cancer Institute were the institutions with strong research capabilities. Scorilas Andreas is the scholar with the most publications, while the most co-citations were generated by Wang, Eric T. Plos One published the most papers on AS of cancer, while J Biol Chem was the most co-cited academic journal in this field. The results of keyword co-occurrence analysis can be divided into three types: molecular (P53, CD44, androgen receptor, srsf3, esrp1), pathological process (apoptosis, EMT, metastasis, angiogenesis, proliferation), and disease (breast cancer, colorectal cancer, prostate cancer, hepatocellular carcinoma, gastric cancer). Conclusion Research on AS of cancer has been increasing in intensity over the past decade. Current AS of cancer studies focused on the hallmarks of AS in cancer and AS signatures including diagnostic and therapeutic targets. Among them, the current trends are splicing factors regulating epithelial-mesenchymal transition and other hallmarks, aberrant splicing events in tumors, and further mechanisms. These might give researchers interested in this field a forward-looking perspective and inform further research.
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Affiliation(s)
- Bo Tian
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yan Bian
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - De-Jian Bian
- Department of Emergency, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Ye Gao
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xun Zhang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Si-Wei Zhou
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yan-Hui Zhang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Ya-Nan Pang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China,Shanghai Institute of Pancreatic Diseases, Shanghai, China,*Correspondence: Ya-Nan Pang, ; Zhao-Shen Li, ; Luo-Wei Wang,
| | - Zhao-Shen Li
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China,*Correspondence: Ya-Nan Pang, ; Zhao-Shen Li, ; Luo-Wei Wang,
| | - Luo-Wei Wang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China,*Correspondence: Ya-Nan Pang, ; Zhao-Shen Li, ; Luo-Wei Wang,
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Abstract
Acromegaly is a systemic disease associated with increased morbidity and mortality that can be prevented with adequate disease control. Three modalities of treatment (surgery, medical treatment, and radiotherapy) are available; however, a significant proportion of patients still maintain disease activity despite treatment. Therefore, there is a need for innovations in the treatment of acromegaly that include changes in the current trial and error approach and the development of new drugs. In this review, we summarize the recent innovations in the treatment of acromegaly and address the future perspectives in this field.
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Affiliation(s)
- Leandro Kasuki
- Neuroendocrinology Research Center/Endocrinology Division, Medical School and Hospital Universitário Clementino Fraga Filho, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil; Neuroendocrinology Division, Instituto Estadual Do Cérebro Paulo Niemeyer, Secretaria Estadual de Saúde, Rio de Janeiro, Brazil; Endocrinology Division, Hospital Federal de Bonsucesso, Rio de Janeiro, Brazil
| | - Mônica R Gadelha
- Neuroendocrinology Research Center/Endocrinology Division, Medical School and Hospital Universitário Clementino Fraga Filho, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil; Neuroendocrinology Division, Instituto Estadual Do Cérebro Paulo Niemeyer, Secretaria Estadual de Saúde, Rio de Janeiro, Brazil; Neuropathology and Molecular Genetics Laboratory, Instituto Estadual Do Cérebro Paulo Niemeyer, Secretaria Estadual de Saúde, Rio de Janeiro, Brazil.
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14
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Viegas JSR, Bentley MVLB, Vicentini FTMDC. Challenges to perform an efficiently gene therapy adopting non-viral vectors: Melanoma landscape. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Chen R, Lin S, Chen X. The promising novel therapies for familial hypercholesterolemia. J Clin Lab Anal 2022; 36:e24552. [PMID: 35712827 PMCID: PMC9279988 DOI: 10.1002/jcla.24552] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 02/06/2023] Open
Abstract
Background The incidence of premature atherosclerotic cardiovascular disease in familial hypercholesterolemia (FH) is high. In recent years, novel therapeutic modalities have shown significant lipid‐lowering ability. In this paper, we summarize the recent developments in novel therapies for FH via the treatment of different targets and discuss the characteristics of each targeted therapy. Based on the process of protein synthesis, we attempt to summarize the direct‐effect targets including protein, RNA, and DNA. Methods For this systematic review, relevant studies are assessed by searching in several databases including PubMed, Web of Science, Scopus, and Google Scholar. The publications of original researches are considered for screening. Results Most drugs are protein‐targeted such as molecule‐based and monoclonal antibodies, including statins, ezetimibe, alirocumab, evolocumab, and evinacumab. Both antisense oligonucleotide (ASO) and small interfering RNA (siRNA) approaches, such as mipomersen, vupanorsen, inclisiran, and ARO‐ANG3, are designed to reduce the number of mRNA transcripts and then degrade proteins. DNA‐targeted therapies such as adeno‐associated virus or CRISPR–Cas9 modification could be used to deliver or edit genes to address a genetic deficiency and improve the related phenotype. Conclusion While the therapies based on different targets including protein, RNA, and DNA are on different stages of development, the mechanisms of these novel therapies may provide new ideas for precision medicine.
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Affiliation(s)
- Ruoyu Chen
- School of Medicine of Ningbo University, Ningbo, China
| | - Shaoyi Lin
- The Affiliated Ningbo First Hospital, School of Medicine of Ningbo University, Ningbo, China
| | - Xiaomin Chen
- The Affiliated Ningbo First Hospital, School of Medicine of Ningbo University, Ningbo, China.,Ningbo First Hospital Affiliated to School of Medicine of Zhejiang University, Ningbo, China
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16
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Taheri F, Taghizadeh E, Baniamerian F, Rostami D, Rozeian A, Mohammad Gheibi Hayat S, Jamialahmadi T, Reiner Ž, Sahebkar A. Cellular and Molecular Aspects of Managing Familial Hypercholesterolemia: Recent and Emerging Therapeutic Approaches. Endocr Metab Immune Disord Drug Targets 2022; 22:1018-1028. [PMID: 35532248 DOI: 10.2174/1871530322666220509040844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/08/2022] [Accepted: 03/18/2022] [Indexed: 11/22/2022]
Abstract
Familial hypercholesterolemia (FH) as a high-frequency genetic disorder is diagnosed based on family and/or patient's history of coronary heart disease (CHD) or some other atherosclerotic disease, LDL-C levels and/or clinical signs such as tendonous xantomata, arcus cornealis before age 45 years as well as functional mutation in the LDLR, apoB or PCSK9 gene. Its clinical features are detectable since early childhood. Early diagnosis and timely treatment increase life expectancy in most patients with FH. Current FH therapies decrease the level of low-density lipoprotein up to ≥50% from baseline with diet, pharmacotherapeutic treatment, lipid apheresis, and liver transplantation. The cornerstone of medical therapy is the use of more potent statins in higher doses, to which often ezetimibe has to be added, but some FH patients do not achieve the target LDL-C with this therapy Therefore, besides these and the most recent but already established therapeutic approaches including PCSK9 inhibitors, inclisiran, and bempedoic acid, new therapies are on the horizon such as gene therapy, CRISPR/Cas9 strategy etc. This paper focuses on cellular and molecular potential strategies for the treatment of FH.
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Affiliation(s)
- Forough Taheri
- Sharekord Branch, Islamic Azad University, Sharekord, Iran
| | - Eskandar Taghizadeh
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Fatemeh Baniamerian
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Daryoush Rostami
- Department of Anesthesia, school of Paramedical Sciences, Zabol University of Medical Sciences, Zabol, Iran
| | - Ahmad Rozeian
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Seyed Mohammad Gheibi Hayat
- Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Tannaz Jamialahmadi
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Željko Reiner
- Department of Internal Medicine, University Hospital Center Zagreb, School of Medicine University of Zagreb, Croatia
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,School of Medicine, The University of Western Australia, Perth, Australia.,Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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17
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Takahashi M, Cawrse BM, Grajkowski A, Beaucage SL. Use of Arabinonucleosides for Development and Implementation of a Novel 2'-O-Protecting Group for Efficient Solid-Phase Synthesis and 2'-O-Deprotection of RNA Sequences. Curr Protoc 2022; 2:e346. [PMID: 35030289 DOI: 10.1002/cpz1.346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The implementation of protecting groups for 2'-hydroxyl function of ribonucleosides is very demanding in that synthetic RNA sequences must be highly pure to ensure the safety and efficacy of nucleic acid-based drugs for treatment of human diseases. A synthetic approach consisting of a condensation reaction between 2'-O-aminoribonucleosides with ethyl pyruvate has been employed to provide stable 2'-O-imino-2-methyl propanoic acid ethyl esters. Conversion of these esters to fully protected ribonucleoside phosphoramidite monomers has allowed rapid and efficient incorporation of 2'-O-protected ribonucleosides into RNA sequences while minimizing the formation of process-related impurities during solid-phase synthesis. Two chimeric 20-mer RNA sequences have been synthesized and then exposed to a solution of sodium hydroxide to saponify the 2'-O-imino-2-methyl propanoic acid ethyl ester protecting groups to their sodium salts. When subjected to ion-exchange conditions at 65°C and near neutral pH, fully deprotected RNA sequences are isolated without production of alkylating side-products and/or formation of mutagenic nucleobase adducts. © 2022 Wiley Periodicals LLC. This article has been contributed to by US Government employees and their work is in the public domain in the USA. Basic Protocol 1: Synthesis of uridine 2'-O-imino-2-propanoic acid ethyl ester and its fully protected 3'-O-phosphoramidite Basic Protocol 2: Synthesis of N6 -protected adenosine 2'-O-imino-2-propanoic acid ethyl ester and its fully protected 3'-O-phosphoramidite Basic Protocol 3: Synthesis of N4 -protected cytidine 2'-O-imino-2-propanoic acid ethyl ester and its fully protected 3'-O-phosphoramidite Basic Protocol 4: Synthesis of N2 -protected guanosine 2'-O-imino-2-propanoic acid ethyl ester and its fully protected 3'-O-phosphoramidite Basic Protocol 5: Automated solid-phase RNA synthesis and deprotection using 2'-O-imino-2-proponate-protected phosphoramidites.
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Affiliation(s)
- Mayumi Takahashi
- Laboratory of Biological Chemistry, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Brian M Cawrse
- Laboratory of Biological Chemistry, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Andrzej Grajkowski
- Laboratory of Biological Chemistry, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Serge L Beaucage
- Laboratory of Biological Chemistry, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
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18
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Abstract
The Human Genome Project marked a major milestone in the scientific community as it unravelled the ~3 billion bases that are central to crucial aspects of human life. Despite this achievement, it only scratched the surface of understanding how each nucleotide matters, both individually and as part of a larger unit. Beyond the coding genome, which comprises only ~2% of the whole genome, scientists have realized that large portions of the genome, not known to code for any protein, were crucial for regulating the coding genes. These large portions of the genome comprise the 'non-coding genome'. The history of gene regulation mediated by proteins that bind to the regulatory non-coding genome dates back many decades to the 1960s. However, the original definition of 'enhancers' was first used in the early 1980s. In this Review, we summarize benchmark studies that have mapped the role of cardiac enhancers in disease and development. We highlight instances in which enhancer-localized genetic variants explain the missing link to cardiac pathogenesis. Finally, we inspire readers to consider the next phase of exploring enhancer-based gene therapy for cardiovascular disease.
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19
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Kozlovskii I, Popov P. Structure-based deep learning for binding site detection in nucleic acid macromolecules. NAR Genom Bioinform 2021; 3:lqab111. [PMID: 34859211 PMCID: PMC8633674 DOI: 10.1093/nargab/lqab111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/14/2021] [Accepted: 11/09/2021] [Indexed: 12/30/2022] Open
Abstract
Structure-based drug design (SBDD) targeting nucleic acid macromolecules, particularly RNA, is a gaining momentum research direction that already resulted in several FDA-approved compounds. Similar to proteins, one of the critical components in SBDD for RNA is the correct identification of the binding sites for putative drug candidates. RNAs share a common structural organization that, together with the dynamic nature of these molecules, makes it challenging to recognize binding sites for small molecules. Moreover, there is a need for structure-based approaches, as sequence information only does not consider conformation plasticity of nucleic acid macromolecules. Deep learning holds a great promise to resolve binding site detection problem, but requires a large amount of structural data, which is very limited for nucleic acids, compared to proteins. In this study we composed a set of ∼2000 nucleic acid-small molecule structures comprising ∼2500 binding sites, which is ∼40-times larger than previously used one, and demonstrated the first structure-based deep learning approach, BiteNetN, to detect binding sites in nucleic acid structures. BiteNetN operates with arbitrary nucleic acid complexes, shows the state-of-the-art performance, and can be helpful in the analysis of different conformations and mutant variants, as we demonstrated for HIV-1 TAR RNA and ATP-aptamer case studies.
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Affiliation(s)
- Igor Kozlovskii
- iMolecule, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Petr Popov
- iMolecule, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
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20
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Targeting RNA structures in diseases with small molecules. Essays Biochem 2021; 64:955-966. [PMID: 33078198 PMCID: PMC7724634 DOI: 10.1042/ebc20200011] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/16/2020] [Accepted: 09/30/2020] [Indexed: 01/08/2023]
Abstract
RNA is crucial for gene expression and regulation. Recent advances in understanding of RNA biochemistry, structure and molecular biology have revealed the importance of RNA structure in cellular processes and diseases. Various approaches to discovering drug-like small molecules that target RNA structure have been developed. This review provides a brief introduction to RNA structural biology and how RNA structures function as disease regulators. We summarize approaches to targeting RNA with small molecules and highlight their advantages, shortcomings and therapeutic potential.
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21
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Pereira S, Santos RS, Moreira L, Guimarães N, Gomes M, Zhang H, Remaut K, Braeckmans K, De Smedt S, Azevedo NF. Lipoplexes to Deliver Oligonucleotides in Gram-Positive and Gram-Negative Bacteria: Towards Treatment of Blood Infections. Pharmaceutics 2021; 13:pharmaceutics13070989. [PMID: 34210111 PMCID: PMC8309032 DOI: 10.3390/pharmaceutics13070989] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 11/16/2022] Open
Abstract
Bacterial resistance to antibiotics threatens the ability to treat life-threatening bloodstream infections. Oligonucleotides (ONs) composed of nucleic acid mimics (NAMs) able to inhibit essential genes can become an alternative to traditional antibiotics, as long as they are safely transported in human serum upon intravenous administration and they are carried across the multilayered bacterial envelopes, impermeable to ONs. In this study, fusogenic liposomes were considered to transport the ONs and promote their internalization in clinically relevant bacteria. Locked nucleic acids and 2′-OMethyl RNA were evaluated as model NAMs and formulated into DOTAP–DOPE liposomes followed by post-PEGylation. Our data showed a complexation stability between the post-PEGylated liposomes and the ONs of over 82%, during 24 h in native human serum, as determined by fluorescence correlation spectroscopy. Quantification by a lipid-mixing assay showed that liposomes, with and without post-PEGylation, fused with all bacteria tested. Such fusion promoted the delivery of a fraction of the ONs into the bacterial cytosol, as observed by fluorescence in situ hybridization and bacterial fractionation. In short, we demonstrated for the first time that liposomes can safely transport ONs in human serum and intracellularly deliver them in both Gram-negative and -positive bacteria, which holds promise towards the treatment of bloodstream infections.
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Affiliation(s)
- Sara Pereira
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal; (S.P.); (L.M.); (N.G.); (M.G.); (N.F.A.)
| | - Rita Sobral Santos
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal; (S.P.); (L.M.); (N.G.); (M.G.); (N.F.A.)
- Correspondence: ; Tel.: +351-225-08-48-71
| | - Luís Moreira
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal; (S.P.); (L.M.); (N.G.); (M.G.); (N.F.A.)
| | - Nuno Guimarães
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal; (S.P.); (L.M.); (N.G.); (M.G.); (N.F.A.)
| | - Mariana Gomes
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal; (S.P.); (L.M.); (N.G.); (M.G.); (N.F.A.)
| | - Heyang Zhang
- Ghent Research Group on Nanomedicine, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (H.Z.); (K.R.); (K.B.); (S.D.S.)
| | - Katrien Remaut
- Ghent Research Group on Nanomedicine, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (H.Z.); (K.R.); (K.B.); (S.D.S.)
| | - Kevin Braeckmans
- Ghent Research Group on Nanomedicine, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (H.Z.); (K.R.); (K.B.); (S.D.S.)
- Centre for Advanced Light Microscopy, Ghent University, 9000 Ghent, Belgium
| | - Stefaan De Smedt
- Ghent Research Group on Nanomedicine, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (H.Z.); (K.R.); (K.B.); (S.D.S.)
- Centre for Advanced Light Microscopy, Ghent University, 9000 Ghent, Belgium
| | - Nuno Filipe Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal; (S.P.); (L.M.); (N.G.); (M.G.); (N.F.A.)
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22
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Lin M, Hu X, Chang S, Chang Y, Bian W, Hu R, Wang J, Zhu Q, Qiu J. Advances of Antisense Oligonucleotide Technology in the Treatment of Hereditary Neurodegenerative Diseases. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2021; 2021:6678422. [PMID: 34211575 PMCID: PMC8211492 DOI: 10.1155/2021/6678422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 05/13/2021] [Accepted: 05/29/2021] [Indexed: 12/11/2022]
Abstract
Antisense nucleic acids are single-stranded oligonucleotides that have been specially chemically modified, which can bind to RNA expressed by target genes through base complementary pairing and affect protein synthesis at the level of posttranscriptional processing or protein translation. In recent years, the application of antisense nucleic acid technology in the treatment of neuromuscular diseases has made remarkable progress. In 2016, the US FDA approved two antisense nucleic acid drugs for the treatment of Duchenne muscular dystrophy (DMD) and spinal muscular atrophy (SMA), and the development to treat other neurodegenerative diseases has also entered the clinical stage. Therefore, ASO represents a treatment with great potential. The article will summarize ASO therapies in terms of mechanism of action, chemical modification, and administration methods and analyze their role in several common neurodegenerative diseases, such as SMA, DMD, and amyotrophic lateral sclerosis (ALS). This article systematically summarizes the great potential of antisense nucleic acid technology in the treatment of hereditary neurodegenerative diseases.
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Affiliation(s)
- Mengsi Lin
- Department of Prenatal Screening and Diagnosis Center, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, Jiangsu Province 226001, China
| | - Xinyi Hu
- Department of Prenatal Screening and Diagnosis Center, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, Jiangsu Province 226001, China
| | - Shiyi Chang
- School of Medicine, Nantong University, Nantong, Jiangsu Province 226001, China
| | - Yan Chang
- School of Life Sciences, Nantong University, Nantong, Jiangsu Province 226001, China
| | - Wenjun Bian
- Department of Prenatal Screening and Diagnosis Center, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, Jiangsu Province 226001, China
| | - Ruikun Hu
- Department of Prenatal Screening and Diagnosis Center, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, Jiangsu Province 226001, China
| | - Jing Wang
- Department of Prenatal Screening and Diagnosis Center, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, Jiangsu Province 226001, China
| | - Qingwen Zhu
- Department of Prenatal Screening and Diagnosis Center, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, Jiangsu Province 226001, China
| | - Jiaying Qiu
- Department of Prenatal Screening and Diagnosis Center, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, Jiangsu Province 226001, China
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Kadbhane A, Patel M, Srivastava S, Singh PK, Madan J, Singh SB, Khatri DK. Perspective insights and application of exosomes as a novel tool against neurodegenerative disorders: An expository appraisal. J Drug Deliv Sci Technol 2021. [DOI: 10.1016/j.jddst.2021.102526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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24
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Grajkowski A, Takahashi M, Cawrse BM, Beaucage SL. An Improved PEG-Linked Solid Support for Minimizing Process-Related Impurities During Solid-Phase Synthesis of DNA and RNA Sequences. Curr Protoc 2021; 1:e108. [PMID: 33945676 DOI: 10.1002/cpz1.108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The preparation of controlled pore glass (CPG) supports, functionalized with several hexaethylene glycol spacers, to alleviate the problems associated with the porosity of commercial CPG supports is described in this article. The pore size of CPG restricts the diffusion of reagents to the leader nucleoside embedded in porous supports; this inhibits efficient solid-phase syntheses of DNA and RNA sequences and, by default, the purity of those sequences through formation of a shorter than full-length oligonucleotide. Functionalization of a CPG support with five hexaethylene glycol spacers led to a 42% reduction in process-related impurities contaminating oligonucleotide sequences, compared to that obtained using the commercial long-chain alkylamine (LCAA) CPG support. © 2021 Wiley Periodicals LLC. This article has been contributed to by US Government employees and their work is in the public domain in the USA. Basic Protocol 1: Preparation of the hydroxylated CPG support 3 Basic Protocol 2: Automated preparation of the CPG support 6 Basic Protocol 3: Automated preparation of the poly(hexaethylene glycol)-derived CPG 7 Basic Protocol 4: Automated functionalization of the poly(hexaethylene glycol)-derived CPG support 7 with leader deoxyribo- and ribonucleosides to provide the CPG support 9 Basic Protocol 5: Automated syntheses of DNA and RNA sequences on poly(hexaethylene glycol)-derived CPG support 9 and on a commercial long-chain alkylamine (LCAA) CPG support Support Protocol: Release and deprotection of the DNA and RNA sequences linked to the poly(hexaethylene glycol)-derived CPG support 10 and commercial LCAA-CPG support Basic Protocol 6: Comparative RP-HPLC analyses of crude, fully deprotected DNA or RNA sequences released from the poly(hexaethylene glycol)-derived CPG support 10 and from a commercial LCAA-CPG support.
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Affiliation(s)
- Andrzej Grajkowski
- Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Mayumi Takahashi
- Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Brian M Cawrse
- Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Serge L Beaucage
- Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
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Martínez-Guitián M, Vázquez-Ucha JC, Álvarez-Fraga L, Conde-Pérez K, Bou G, Poza M, Beceiro A. Antisense inhibition of lpxB gene expression in Acinetobacter baumannii by peptide-PNA conjugates and synergy with colistin. J Antimicrob Chemother 2021; 75:51-59. [PMID: 31586411 DOI: 10.1093/jac/dkz409] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 08/28/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND LpxB is an enzyme involved in the biosynthesis pathway of lipid A, a component of LPS. OBJECTIVES To evaluate the lpxB gene in Acinetobacter baumannii as a potential therapeutic target and to propose antisense agents such as peptide nucleic acids (PNAs) as a tool to combat bacterial infection, either alone or in combination with known antimicrobial therapies. METHODS RNA-seq analysis of the A. baumannii ATCC 17978 strain in a murine pneumonia model was performed to study the in vivo expression of lpxB. Protein expression was studied in the presence or absence of anti-lpxB (KFF)3K-PNA (pPNA). Time-kill curve analyses and protection assays of infected A549 cells were performed. The chequerboard technique was used to test for synergy between pPNA and colistin. A Galleria mellonella infection model was used to test the in vivo efficacy of pPNA. RESULTS The lpxB gene was overexpressed during pneumonia. Treatment with a specific pPNA inhibited LpxB expression in vitro, decreased survival of the ATCC 17978 strain and increased the survival rate of infected A549 cells. Synergy was observed between pPNA and colistin in colistin-susceptible strains. In vivo assays confirmed that a combination treatment of anti-lpxB pPNA and colistin was more effective than colistin in monotherapy. CONCLUSIONS The lpxB gene is essential for A. baumannii survival. Anti-lpxB pPNA inhibits LpxB expression, causing bacterial death. This pPNA showed synergy with colistin and increased the survival rate in G. mellonella. The data suggest that antisense pPNA molecules blocking the lpxB gene could be used as antibacterial agents.
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Affiliation(s)
- Marta Martínez-Guitián
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Juan Carlos Vázquez-Ucha
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Laura Álvarez-Fraga
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Kelly Conde-Pérez
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Germán Bou
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Margarita Poza
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Alejandro Beceiro
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
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26
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Chen Y, Wang S, Yang S, Li R, Yang Y, Chen Y, Zhang W. Inhibitory role of ginsenoside Rb2 in endothelial senescence and inflammation mediated by microRNA‑216a. Mol Med Rep 2021; 23:415. [PMID: 33786633 PMCID: PMC8025470 DOI: 10.3892/mmr.2021.12054] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/09/2021] [Indexed: 01/02/2023] Open
Abstract
Targeting microRNAs (miRs) using small chemical molecules has become a promising strategy for disease treatment. miR‑216a has been reported to be a potential therapeutic target in endothelial senescence and atherosclerosis via the Smad3/NF‑κB signaling pathway. Ginsenoside Rb2 (Rb2) is the main bioactive component extracted from the plant Panax ginseng, and is a widely used traditional Chinese medicine. In the present study, Rb2 was identified to have a high score for miR‑216a via bioinformatics analysis based on its sequence and structural features. The microscale thermophoresis experiment further demonstrated that Rb2 had a specific binding affinity for miR‑216a and the dissociation constant was 17.6 µM. In both young and senescent human umbilical vein endothelial cells (HUVECs), as well as human aortic endothelial cells, Rb2 decreased the expression of endogenous miR‑216a. Next, a replicative endothelial senescence model of HUVECs was established by infection with pre‑miR‑216a recombinant lentiviruses (Lv‑miR‑216a) and the number of population‑doubling level (PDL) was calculated. Stable overexpression of miR‑216a induced a premature senescent‑like phenotype, whereas the senescent features and increased activity of senescence‑associated β‑galactosidase (SA‑β‑gal) were reversed after Rb2 treatment. The percentage of SA‑β‑gal‑positive cells in senescent PDL25 cells transfected with Lv‑miR‑216a was decreased 76% by Rb2 treatment compared with the Lv‑miR‑216a group without Rb2 treatment (P=0.01). Mechanistically, miR‑216a inhibited Smad3 protein expression, promoted IκBα degradation and activated NF‑κB‑responsive genes, such as vascular cell adhesion molecule 1 (VCAM1), which promoted the adhesiveness of endothelial cells to monocytes. These pro‑inflammatory effects of miR‑216a were significantly suppressed by Rb2 treatment. When Smad3 was suppressed by small interfering RNA, the elevated expression levels of intercellular adhesion molecule 1 and VCAM1 induced by miR‑216a were significantly reversed. Collectively, to the best of our knowledge, the present study demonstrated for the first time that Rb2 exerted an anti‑inflammation effect on the process of endothelial cell senescence and could be a potential therapeutic drug by targeting miR‑216a.
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Affiliation(s)
- Yutong Chen
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing 100069, P.R. China
| | - Shuting Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100037, P.R. China
| | - Shujun Yang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100037, P.R. China
| | - Rongxia Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100037, P.R. China
| | - Yunyun Yang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100037, P.R. China
| | - Yu Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100037, P.R. China
| | - Weili Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100037, P.R. China
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Genetic Drivers of Head and Neck Squamous Cell Carcinoma: Aberrant Splicing Events, Mutational Burden, HPV Infection and Future Targets. Genes (Basel) 2021; 12:genes12030422. [PMID: 33804181 PMCID: PMC7998272 DOI: 10.3390/genes12030422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/16/2021] [Accepted: 03/11/2021] [Indexed: 12/15/2022] Open
Abstract
Head and neck cancers include cancers that originate from a variety of locations. These include the mouth, nasal cavity, throat, sinuses, and salivary glands. These cancers are the sixth most diagnosed cancers worldwide. Due to the tissues they arise from, they are collectively named head and neck squamous cell carcinomas (HNSCC). The most important risk factors for head and neck cancers are infection with human papillomavirus (HPV), tobacco use and alcohol consumption. The genetic basis behind the development and progression of HNSCC includes aberrant non-coding RNA levels. However, one of the most important differences between healthy tissue and HNSCC tissue is changes in the alternative splicing of genes that play a vital role in processes that can be described as the hallmarks of cancer. These changes in the expression profile of alternately spliced mRNA give rise to various protein isoforms. These protein isoforms, alternate methylation of proteins, and changes in the transcription of non-coding RNAs (ncRNA) can be used as diagnostic or prognostic markers and as targets for the development of new therapeutic agents. This review aims to describe changes in alternative splicing and ncRNA patterns that contribute to the development and progression of HNSCC. It will also review the use of the changes in gene expression as biomarkers or as the basis for the development of new therapies.
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28
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Takahashi M, Grajkowski A, Cawrse BM, Beaucage SL. Innovative 2'- O-Imino-2-propanoate-Protecting Group for Effective Solid-Phase Synthesis and 2'- O-Deprotection of RNA Sequences. J Org Chem 2021; 86:4944-4956. [PMID: 33706514 DOI: 10.1021/acs.joc.0c02773] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The implementation of protecting groups for the 2'-hydroxyl function of ribonucleosides is still challenging, particularly when RNA sequences must be of the highest purity for therapeutic applications as nucleic acid-based drugs. A 2'-hydroxyl-protecting group should optimally (i) be easy to install; (ii) allow rapid and efficient incorporation of the 2'-O-protected ribonucleosides into RNA sequences to minimize, to the greatest extent possible, the formation of process-related impurities (e.g., shorter than full-length sequences) during solid-phase synthesis; and (iii) be completely cleaved from RNA sequences without the production of alkylating side products and/or formation of mutagenic nucleobase adducts. The reaction of 2'-O-aminoribonucleosides with ethyl pyruvate results in the formation of stable 2'-O-imino-2-methyl propanoic acid ethyl esters and, subsequently, of the fully protected ribonucleoside phosphoramidite monomers, which are required for the solid-phase synthesis of two chimeric RNA sequences (20-mers) containing the four canonical ribonucleosides. Upon treatment of the RNA sequences with a solution of sodium hydroxide, the 2'-O-imino-2-methyl propanoic acid ethyl ester-protecting groups are saponified to their sodium salts, which after ion exchange underwent quantitative intramolecular decarboxylation under neutral conditions at 65 °C to provide fully deprotected RNA sequences in marginally better yields than those obtained from commercial 2'-O-tert-butyldimethylsilyl ribonucleoside phosphoramidites under highly similar conditions.
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Affiliation(s)
- Mayumi Takahashi
- Laboratory of Biological Chemistry, Division of Biotechnology Review and Research IV, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Andrzej Grajkowski
- Laboratory of Biological Chemistry, Division of Biotechnology Review and Research IV, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Brian M Cawrse
- Laboratory of Biological Chemistry, Division of Biotechnology Review and Research IV, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Serge L Beaucage
- Laboratory of Biological Chemistry, Division of Biotechnology Review and Research IV, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
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29
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Liang XH, De Hoyos CL, Shen W, Zhang L, Fazio M, Crooke ST. Solid-Phase Separation of Toxic Phosphorothioate Antisense Oligonucleotide-Protein Nucleolar Aggregates Is Cytoprotective. Nucleic Acid Ther 2021; 31:126-144. [PMID: 33534636 DOI: 10.1089/nat.2020.0923] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Phosphorothioate antisense oligonucleotides (PS-ASOs) interact with proteins and can localize to or induce the formation of a variety of subcellular PS-ASO-protein or PS-ASO-ribonucleoprotein aggregates. In this study, we show that these different aggregates that form with varying compositions at various concentrations in the cytosol, nucleus, and nucleolus may undergo phase separations in cells. Some aggregates can form with both nontoxic and toxic PS-ASOs, such as PS bodies, paraspeckles, and nuclear filaments. However, toxic PS-ASOs have been shown to form unique nucleolar aggregates that result in nucleolar dysfunction and apoptosis. These include liquid-like aggregates that we labeled "cloudy nucleoli" and solid-like perinucleolar filaments. Toxic nucleolar aggregates may undergo solid-phase separation and in the solid phase, protein mobility in and out of the aggregates is limited. Other aggregates appear to undergo liquid-phase separation, including paraspeckles and perinucleolar caps, in which protein mobility is negatively correlated with the binding affinity of the proteins to PS-ASOs. However, PS bodies and nuclear filaments are solid-like aggregates. Importantly, in cells that survived treatment with toxic PS-ASOs, solid-like PS-ASO aggregates accumulated, especially Hsc70-containing nucleolus-like structures, in which modest pre-rRNA transcriptional activity was retained and appeared to mitigate the nucleolar toxicity. This is the first demonstration that exogenous drugs, PS-ASOs, can form aggregates that undergo phase separations and that solid-phase separation of toxic PS-ASO-induced nucleolar aggregates is cytoprotective.
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Affiliation(s)
- Xue-Hai Liang
- Core Antisense Research and Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Cheryl Li De Hoyos
- Core Antisense Research and Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Wen Shen
- Core Antisense Research and Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Lingdi Zhang
- Core Antisense Research and Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Michael Fazio
- Medicinal Chemistry, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Stanley T Crooke
- Core Antisense Research and Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
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30
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Louie W, Shen MW, Tahiry Z, Zhang S, Worstell D, Cassa CA, Sherwood RI, Gifford DK. Machine learning based CRISPR gRNA design for therapeutic exon skipping. PLoS Comput Biol 2021; 17:e1008605. [PMID: 33417623 PMCID: PMC7819613 DOI: 10.1371/journal.pcbi.1008605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 01/21/2021] [Accepted: 12/03/2020] [Indexed: 12/26/2022] Open
Abstract
Restoring gene function by the induced skipping of deleterious exons has been shown to be effective for treating genetic disorders. However, many of the clinically successful therapies for exon skipping are transient oligonucleotide-based treatments that require frequent dosing. CRISPR-Cas9 based genome editing that causes exon skipping is a promising therapeutic modality that may offer permanent alleviation of genetic disease. We show that machine learning can select Cas9 guide RNAs that disrupt splice acceptors and cause the skipping of targeted exons. We experimentally measured the exon skipping frequencies of a diverse genome-integrated library of 791 splice sequences targeted by 1,063 guide RNAs in mouse embryonic stem cells. We found that our method, SkipGuide, is able to identify effective guide RNAs with a precision of 0.68 (50% threshold predicted exon skipping frequency) and 0.93 (70% threshold predicted exon skipping frequency). We anticipate that SkipGuide will be useful for selecting guide RNA candidates for evaluation of CRISPR-Cas9-mediated exon skipping therapy.
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Affiliation(s)
- Wilson Louie
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Max W. Shen
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Zakir Tahiry
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sophia Zhang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Daniel Worstell
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Christopher A. Cassa
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richard I. Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands
| | - David K. Gifford
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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31
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Abstract
Acromegaly is a systemic disease associated with increased morbidity and mortality. Most of these comorbidities can be prevented or delayed with adequate disease treatment. Although three modalities of treatment (surgery, medical treatment, and radiotherapy) are available and new drugs were approved in the last decades, there are still some patients that maintain disease activity despite treatment. Therefore, there is a need for novel therapies for acromegaly and for that purpose new formulations of currently used drugs and also new drugs are currently under study. In this review, we summarize the novel therapies for acromegaly.
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Affiliation(s)
- Bernardo Maia
- Neuroendocrinology Research Center/Endocrinology Division – Medical School and Hospital Universitário Clementino Fraga Filho – Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leandro Kasuki
- Neuroendocrinology Research Center/Endocrinology Division – Medical School and Hospital Universitário Clementino Fraga Filho – Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Neuroendocrinology Division – Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
- Endocrinology Division – Hospital Federal de Bonsucesso, Rio de Janeiro Brazil
| | - Mônica R Gadelha
- Neuroendocrinology Research Center/Endocrinology Division – Medical School and Hospital Universitário Clementino Fraga Filho – Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Neuroendocrinology Division – Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
- Neuropatology and Molecular Genetics Laboratory – Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
- Correspondence should be addressed to M R Gadelha:
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Abstract
Objective Alternative splicing can generate various structural and functional protein isoforms. Recently, accumulating evidence shows a relationship between alternative splicing and cancer. Cancer is a complex and chronic disease that involves malignant transformation. In this review, we consider alternative splicing events in relation to the hallmarks of cancer cells, and discuss current therapies to treat cancer-related to alternative splicing. Data sources Data cited in this article are from the PubMed and Embase database, primarily focusing on research published from 2000 to 2018. Study selection Articles were selected with the search terms “alternative splicing,” “cancer cell,” “tumor microenvironment,” and “therapy.” Results Alternative splicing plays an important role in tumorigenesis, development, and escape from cell death. Taking this trait of cancer cells into consideration will allow more definite diagnoses of cancer, and allow the development of more effective medicines to intervene in cancer that could focus on controlling alternative splicing or competitively binding to the final products. Conclusions Alternative splicing is common in cancer cells. Consideration of alternative splicing may allow different strategies for cancer therapy or the identification of novel biomarkers for cancer diagnosis.
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Grajkowski A, Takahashi M, Cawrse BM, Beaucage SL. An expedient process for reducing the formation of process-related impurities during solid-phase synthesis of potential nucleic acid-based drugs. Bioorg Med Chem 2020; 28:115779. [PMID: 33007546 DOI: 10.1016/j.bmc.2020.115779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022]
Abstract
With the intent of mitigating the formation of process-related impurities during solid-phase synthesis of DNA or RNA sequences, a hydroxylated controlled-pore glass support conjugated to three, five or seven hexaethylene glycol spacers was prepared and demonstrated to provide a more efficient and robust synthesis process. Indeed, the use of a support conjugated to five hexaethylene glycol spacers led to a 19% up to 42% reduction of process-related impurities contaminating synthetic nucleic acid sequences, when compared to that obtained from the same DNA/RNA sequences synthesized using a commercial long-chain alkylamine controlled-pore glass support under highly similar conditions.
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Affiliation(s)
- Andrzej Grajkowski
- Laboratory of Biological Chemistry, Division of Biotechnology Review and Research IV, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20933, United States
| | - Mayumi Takahashi
- Laboratory of Biological Chemistry, Division of Biotechnology Review and Research IV, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20933, United States
| | - Brian M Cawrse
- Laboratory of Biological Chemistry, Division of Biotechnology Review and Research IV, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20933, United States
| | - Serge L Beaucage
- Laboratory of Biological Chemistry, Division of Biotechnology Review and Research IV, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20933, United States.
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Therapeutic efficacy of antisense oligonucleotides in mouse models of CLN3 Batten disease. Nat Med 2020; 26:1444-1451. [PMID: 32719489 DOI: 10.1038/s41591-020-0986-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 06/19/2020] [Indexed: 02/07/2023]
Abstract
CLN3 Batten disease is an autosomal recessive, neurodegenerative, lysosomal storage disease caused by mutations in CLN3, which encodes a lysosomal membrane protein1-3. There are no disease-modifying treatments for this disease that affects up to 1 in 25,000 births, has an onset of symptoms in early childhood and typically is fatal by 20-30 years of life4-7. Most patients with CLN3 Batten have a deletion encompassing exons 7 and 8 (CLN3∆ex7/8), creating a reading frameshift7,8. Here we demonstrate that mice with this deletion can be effectively treated using an antisense oligonucleotide (ASO) that induces exon skipping to restore the open reading frame. A single treatment of neonatal mice with an exon 5-targeted ASO-induced robust exon skipping for more than a year, improved motor coordination, reduced histopathology in Cln3∆ex7/8 mice and increased survival in a new mouse model of the disease. ASOs also induced exon skipping in cell lines derived from patients with CLN3 Batten disease. Our findings demonstrate the utility of ASO-based reading-frame correction as an approach to treat CLN3 Batten disease and broaden the therapeutic landscape for ASOs in the treatment of other diseases using a similar strategy.
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35
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Rahman MA, Nasrin F, Bhattacharjee S, Nandi S. Hallmarks of Splicing Defects in Cancer: Clinical Applications in the Era of Personalized Medicine. Cancers (Basel) 2020; 12:cancers12061381. [PMID: 32481522 PMCID: PMC7352608 DOI: 10.3390/cancers12061381] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/25/2020] [Accepted: 05/25/2020] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing promotes proteome diversity by using limited number of genes, a key control point of gene expression. Splicing is carried out by large macromolecular machineries, called spliceosome, composed of small RNAs and proteins. Alternative splicing is regulated by splicing regulatory cis-elements in RNA and trans-acting splicing factors that are often tightly regulated in a tissue-specific and developmental stage-specific manner. The biogenesis of ribonucleoprotein (RNP) complexes is strictly regulated to ensure that correct complements of RNA and proteins are coordinated in the right cell at the right time to support physiological functions. Any perturbations that impair formation of functional spliceosomes by disrupting the cis-elements, or by compromising RNA-binding or function of trans-factors can be deleterious to cells and result in pathological consequences. The recent discovery of oncogenic mutations in splicing factors, and growing evidence of the perturbed splicing in multiple types of cancer, underscores RNA processing defects as a critical driver of oncogenesis. These findings have resulted in a growing interest in targeting RNA splicing as a therapeutic approach for cancer treatment. This review summarizes our current understanding of splicing alterations in cancer, recent therapeutic efforts targeting splicing defects in cancer, and future potentials to develop novel cancer therapies.
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36
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Shandilya S, Rani P, Onteru SK, Singh D. Natural ligand-receptor mediated loading of siRNA in milk derived exosomes. J Biotechnol 2020; 318:1-9. [PMID: 32361020 DOI: 10.1016/j.jbiotec.2020.04.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/17/2020] [Accepted: 04/26/2020] [Indexed: 12/16/2022]
Abstract
siRNA based therapeutics have become the next frontier in molecular medicine. Though exosomes emerge as a promising drug delivery vehicle for siRNAs, significant hurdle remains in finding safe and effective loading methods. Traditional methods of loading exogenous siRNAs in exosomes are marked by certain limitations like siRNA aggregation, toxicity to the cells and their high experimental cost. As an electroporation and lipofection free approach, we show that the molecular conjugate of bovine lactoferrin with polyl-l-ysine electrostatically interacts with negatively charged siRNA, wherein lactoferrin as a ligand is captured by the GAPDH present in exosomes, loading siRNA in an effortless manner. This method exhibited transfection efficiency, colocalization percentage and colocalization threshold similar to electroporation. Furthermore, efficient uptake of exosomes loaded with siRNA via conjugate in recipient cells was observed. Our current study univocally establishes chemical free and non-mechanical method for the encapsulation and intercellular delivery of siRNA for wider therapeutic applications.
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Affiliation(s)
- Shruti Shandilya
- Molecular Endocrinology, Functional Genomics and Systems Biology Laboratory, Animal Biochemistry Division, National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Payal Rani
- Molecular Endocrinology, Functional Genomics and Systems Biology Laboratory, Animal Biochemistry Division, National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Suneel Kumar Onteru
- Molecular Endocrinology, Functional Genomics and Systems Biology Laboratory, Animal Biochemistry Division, National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Dheer Singh
- Molecular Endocrinology, Functional Genomics and Systems Biology Laboratory, Animal Biochemistry Division, National Dairy Research Institute, Karnal, 132001, Haryana, India.
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Hibino M, Aiba Y, Shoji O. Cationic guanine: positively charged nucleobase with improved DNA affinity inhibits self-duplex formation. Chem Commun (Camb) 2020; 56:2546-2549. [PMID: 32040115 DOI: 10.1039/d0cc00169d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oligonucleotides represent powerful DNA-recognition tools, but the formation of undesirable "self-duplexes" becomes more probable with increasing DNA affinity. Herein, we have developed a modified nucleobase with "self-avoiding" properties. Facile methylation of guanine yields a cationic N7-methylguanine, which suppresses the formation of self-duplexes whilst improving DNA affinity through electrostatic interaction.
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Affiliation(s)
- Masaki Hibino
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Yuichiro Aiba
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
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38
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Uveal melanoma: Towards a molecular understanding. Prog Retin Eye Res 2019; 75:100800. [PMID: 31563544 DOI: 10.1016/j.preteyeres.2019.100800] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 02/08/2023]
Abstract
Uveal melanoma is an aggressive malignancy that originates from melanocytes in the eye. Even if the primary tumor has been successfully treated with radiation or surgery, up to half of all UM patients will eventually develop metastatic disease. Despite the common origin from neural crest-derived cells, uveal and cutaneous melanoma have few overlapping genetic signatures and uveal melanoma has been shown to have a lower mutational burden. As a consequence, many therapies that have proven effective in cutaneous melanoma -such as immunotherapy- have little or no success in uveal melanoma. Several independent studies have recently identified the underlying genetic aberrancies in uveal melanoma, which allow improved tumor classification and prognostication of metastatic disease. In most cases, activating mutations in the Gα11/Q pathway drive uveal melanoma oncogenesis, whereas mutations in the BAP1, SF3B1 or EIF1AX genes predict progression towards metastasis. Intriguingly, the composition of chromosomal anomalies of chromosome 3, 6 and 8, shown to correlate with an adverse outcome, are distinctive in the BAP1mut, SF3B1mut and EIF1AXmut uveal melanoma subtypes. Expression profiling and epigenetic studies underline this subdivision in high-, intermediate-, or low-metastatic risk subgroups and suggest a different approach in the future towards prevention and/or treatment based on the specific mutation present in the tumor of the patients. In this review we discuss the current knowledge of the underlying genetic events that lead to uveal melanoma, their implication for the disease course and prognosis, as well as the therapeutic possibilities that arise from targeting these different aberrant pathways.
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Coutinho MF, Matos L, Santos JI, Alves S. RNA Therapeutics: How Far Have We Gone? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:133-177. [PMID: 31342441 DOI: 10.1007/978-3-030-19966-1_7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In recent years, the RNA molecule became one of the most promising targets for therapeutic intervention. Currently, a large number of RNA-based therapeutics are being investigated both at the basic research level and in late-stage clinical trials. Some of them are even already approved for treatment. RNA-based approaches can act at pre-mRNA level (by splicing modulation/correction using antisense oligonucleotides or U1snRNA vectors), at mRNA level (inhibiting gene expression by siRNAs and antisense oligonucleotides) or at DNA level (by editing mutated sequences through the use of CRISPR/Cas). Other RNA approaches include the delivery of in vitro transcribed (IVT) mRNA or the use of oligonucleotides aptamers. Here we review these approaches and their translation into clinics trying to give a brief overview also on the difficulties to its application as well as the research that is being done to overcome them.
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Affiliation(s)
- Maria Francisca Coutinho
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal
| | - Liliana Matos
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal
| | - Juliana Inês Santos
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal
| | - Sandra Alves
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal.
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Qadir MI, Bukhat S, Rasul S, Manzoor H, Manzoor M. RNA therapeutics: Identification of novel targets leading to drug discovery. J Cell Biochem 2019; 121:898-929. [DOI: 10.1002/jcb.29364] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/20/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Muhammad Imran Qadir
- Institute of Molecular Biology and Biotechnology Bahauddin Zakariya University Multan Pakistan
| | - Sherien Bukhat
- Institute of Molecular Biology and Biotechnology Bahauddin Zakariya University Multan Pakistan
| | - Sumaira Rasul
- Institute of Molecular Biology and Biotechnology Bahauddin Zakariya University Multan Pakistan
| | - Hamid Manzoor
- Institute of Molecular Biology and Biotechnology Bahauddin Zakariya University Multan Pakistan
| | - Majid Manzoor
- College of Pharmaceutical Sciences Zhejiang University Hangzhou China
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41
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Perrone B, La Cognata V, Sprovieri T, Ungaro C, Conforti FL, Andò S, Cavallaro S. Alternative Splicing of ALS Genes: Misregulation and Potential Therapies. Cell Mol Neurobiol 2019; 40:1-14. [PMID: 31385134 DOI: 10.1007/s10571-019-00717-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/31/2019] [Indexed: 12/12/2022]
Abstract
Neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA), Parkinson's, Alzheimer's, and Huntington's disease affect a rapidly increasing population worldwide. Although common pathogenic mechanisms have been identified (e.g., protein aggregation or dysfunction, immune response alteration and axonal degeneration), the molecular events underlying timing, dosage, expression, and location of RNA molecules are still not fully elucidated. In particular, the alternative splicing (AS) mechanism is a crucial player in RNA processing and represents a fundamental determinant for brain development, as well as for the physiological functions of neuronal circuits. Although in recent years our knowledge of AS events has increased substantially, deciphering the molecular interconnections between splicing and ALS remains a complex task and still requires considerable efforts. In the present review, we will summarize the current scientific evidence outlining the involvement of AS in the pathogenic processes of ALS. We will also focus on recent insights concerning the tuning of splicing mechanisms by epigenomic and epi-transcriptomic regulation, providing an overview of the available genomic technologies to investigate AS drivers on a genome-wide scale, even at a single-cell level resolution. In the future, gene therapy strategies and RNA-based technologies may be utilized to intercept or modulate the splicing mechanism and produce beneficial effects against ALS.
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Affiliation(s)
- Benedetta Perrone
- Institute for Biomedical Research and Innovation, National Research Council, Mangone, Cosenza, Italy
| | - Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council, Catania, Italy
| | - Teresa Sprovieri
- Institute for Biomedical Research and Innovation, National Research Council, Mangone, Cosenza, Italy
| | - Carmine Ungaro
- Institute for Biomedical Research and Innovation, National Research Council, Mangone, Cosenza, Italy
| | - Francesca Luisa Conforti
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, Cosenza, Italy
| | - Sebastiano Andò
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, Cosenza, Italy.,Centro Sanitario, University of Calabria, Arcavacata di Rende, Cosenza, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council, Catania, Italy.
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Kim BS, Kim HJ, Osawa S, Hayashi K, Toh K, Naito M, Min HS, Yi Y, Kwon IC, Kataoka K, Miyata K. Dually Stabilized Triblock Copolymer Micelles with Hydrophilic Shell and Hydrophobic Interlayer for Systemic Antisense Oligonucleotide Delivery to Solid Tumor. ACS Biomater Sci Eng 2019; 5:5770-5780. [DOI: 10.1021/acsbiomaterials.9b00384] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Beob Soo Kim
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | | | - Shigehito Osawa
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Kotaro Hayashi
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Kazuko Toh
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | | | - Hyun Su Min
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yu Yi
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ick Chan Kwon
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Kazunori Kataoka
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Kanjiro Miyata
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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Oligonucleotide therapy: An emerging focus area for drug delivery in chronic inflammatory respiratory diseases. Chem Biol Interact 2019; 308:206-215. [PMID: 31136735 PMCID: PMC7094617 DOI: 10.1016/j.cbi.2019.05.028] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 04/30/2019] [Accepted: 05/15/2019] [Indexed: 02/07/2023]
Abstract
Oligonucleotide-based therapies are advanced novel interventions used in the management of various respiratory diseases such as asthma and Chronic Obstructive Pulmonary Disease (COPD). These agents primarily act by gene silencing or RNA interference. Better methodologies and techniques are the need of the hour that can deliver these agents to tissues and cells in a target specific manner by which their maximum potential can be reached in the management of chronic inflammatory diseases. Nanoparticles play an important role in the target-specific delivery of drugs. In addition, oligonucleotides also are extensively used for gene transfer in the form of polymeric, liposomal and inorganic carrier materials. Therefore, the current review focuses on various novel dosage forms like nanoparticles, liposomes that can be used efficiently for the delivery of various oligonucleotides such as siRNA and miRNA. We also discuss the future perspectives and targets for oligonucleotides in the management of respiratory diseases.
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Unveiling the druggable RNA targets and small molecule therapeutics. Bioorg Med Chem 2019; 27:2149-2165. [PMID: 30981606 PMCID: PMC7126819 DOI: 10.1016/j.bmc.2019.03.057] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/25/2019] [Accepted: 03/29/2019] [Indexed: 12/15/2022]
Abstract
The increasing appreciation for the crucial roles of RNAs in infectious and non-infectious human diseases makes them attractive therapeutic targets. Coding and non-coding RNAs frequently fold into complex conformations which, if effectively targeted, offer opportunities to therapeutically modulate numerous cellular processes, including those linked to undruggable protein targets. Despite the considerable skepticism as to whether RNAs can be targeted with small molecule therapeutics, overwhelming evidence suggests the challenges we are currently facing are not outside the realm of possibility. In this review, we highlight the most recent advances in molecular techniques that have sparked a revolution in understanding the RNA structure-to-function relationship. We bring attention to the application of these modern techniques to identify druggable RNA targets and to assess small molecule binding specificity. Finally, we discuss novel screening methodologies that support RNA drug discovery and present examples of therapeutically valuable RNA targets.
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45
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Liang XH, Shen W, Crooke ST. Specific Increase of Protein Levels by Enhancing Translation Using Antisense Oligonucleotides Targeting Upstream Open Frames. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019. [PMID: 28639196 DOI: 10.1007/978-981-10-4310-9_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A number of diseases are caused by low levels of key proteins; therefore, increasing the amount of specific proteins in human bodies is of therapeutic interest. Protein expression is downregulated by some structural or sequence elements present in the 5' UTR of mRNAs, such as upstream open reading frames (uORF). Translation initiation from uORF(s) reduces translation from the downstream primary ORF encoding the main protein product in the same mRNA, leading to a less efficient protein expression. Therefore, it is possible to use antisense oligonucleotides (ASOs) to specifically inhibit translation of the uORF by base-pairing with the uAUG region of the mRNA, redirecting translation machinery to initiate from the primary AUG site. Here we review the recent findings that translation of specific mRNAs can be enhanced using ASOs targeting uORF regions. Appropriately designed and optimized ASOs are highly specific, and they act in a sequence- and position-dependent manner, with very minor off-target effects. Protein levels can be increased using this approach in different types of human and mouse cells, and, importantly, also in mice. Since uORFs are present in around half of human mRNAs, the uORF-targeting ASOs may thus have valuable potential as research tools and as therapeutics to increase the levels of proteins for a variety of genes.
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Affiliation(s)
- Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA, 92010, USA.
| | - Wen Shen
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA, 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA, 92010, USA
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46
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Zakrevsky P, Bindewald E, Humbertson H, Viard M, Dorjsuren N, Shapiro BA. A Suite of Therapeutically-Inspired Nucleic Acid Logic Systems for Conditional Generation of Single-Stranded and Double-Stranded Oligonucleotides. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E615. [PMID: 30991728 PMCID: PMC6526476 DOI: 10.3390/nano9040615] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/15/2019] [Accepted: 03/25/2019] [Indexed: 01/16/2023]
Abstract
Several varieties of small nucleic acid constructs are able to modulate gene expression via one of a number of different pathways and mechanisms. These constructs can be synthesized, assembled and delivered to cells where they are able to impart regulatory functions, presenting a potential avenue for the development of nucleic acid-based therapeutics. However, distinguishing aberrant cells in need of therapeutic treatment and limiting the activity of deliverable nucleic acid constructs to these specific cells remains a challenge. Here, we designed and characterized a collection of nucleic acids systems able to generate and/or release sequence-specific oligonucleotide constructs in a conditional manner based on the presence or absence of specific RNA trigger molecules. The conditional function of these systems utilizes the implementation of AND and NOT Boolean logic elements, which could ultimately be used to restrict the release of functionally relevant nucleic acid constructs to specific cellular environments defined by the high or low expression of particular RNA biomarkers. Each system is generalizable and designed with future therapeutic development in mind. Every construct assembles through nuclease-resistant RNA/DNA hybrid duplex formation, removing the need for additional 2'-modifications, while none contain any sequence restrictions on what can define the diagnostic trigger sequence or the functional oligonucleotide output.
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Affiliation(s)
- Paul Zakrevsky
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Eckart Bindewald
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
| | - Hadley Humbertson
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
| | - Nomongo Dorjsuren
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Bruce A Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
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Abstract
Antisense oligonucleotides (AONs) have been actively developed for more than 30 years as a form of molecular medicine and represent promising therapeutic tools for many disorders. Significant progress has been made toward their clinical development in particular for splice switching AONs for the treatment of neuromuscular disorders such as Duchenne muscular dystrophy (DMD). Many different chemistries of AONs can be used for splice switching modulation, and some of them have now reached regulatory approval. However, despite advances in AON chemistry and design, systemic use of AONs is limited due to poor tissue uptake and sufficient therapeutic efficacy is difficult to achieve. Therefore, there is still a critical need to develop efficient AONs able to target all relevant tissues and international efforts are currently on going to advance new compounds or alternative chemistries with higher therapeutic potential. Here we describe the methods to evaluate the potency of tricyclo-DNA (tcDNA)-AONs, a novel class of AONs which displays unique pharmacological properties and unprecedented uptake in many tissues after systemic administration (Goyenvalle et al., Nat Med 21:270-275, 2015; Goyenvalle et al., J Neuromuscul Dis 3:157-167, 2016; Relizani et al., Mol Ther Nucleic Acids 8:144-157, 2017; Robin et al., Mol Ther Nucleic Acids 7:81-89, 2017). We will focus on the preclinical evaluation of these tcDNA for DMD, specifically targeting the exon 51 of the human dystrophin gene. We will first detail methods to analyze their efficacy both in vitro in human myoblasts and in vivo in the hDMD and mdx52 mouse models and then describe means to evaluate their potential renal toxicity.
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48
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Le BT, Raguraman P, Kosbar TR, Fletcher S, Wilton SD, Veedu RN. Antisense Oligonucleotides Targeting Angiogenic Factors as Potential Cancer Therapeutics. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 14:142-157. [PMID: 30594893 PMCID: PMC6307321 DOI: 10.1016/j.omtn.2018.11.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 02/07/2023]
Abstract
Cancer is one of the leading causes of death worldwide, and conventional cancer therapies such as surgery, chemotherapy, and radiotherapy do not address the underlying molecular pathologies, leading to inadequate treatment and tumor recurrence. Angiogenic factors, such as EGF, PDGF, bFGF, TGF-β, TGF-α, VEGF, endoglin, and angiopoietins, play important roles in regulating tumor development and metastasis, and they serve as potential targets for developing cancer therapeutics. Nucleic acid-based therapeutic strategies have received significant attention in the last two decades, and antisense oligonucleotide-mediated intervention is a prominent therapeutic approach for targeted manipulation of gene expression. Clinical benefits of antisense oligonucleotides have been recognized by the U.S. Food and Drug Administration, with full or conditional approval of Vitravene, Kynamro, Exondys51, and Spinraza. Herein we review the scope of antisense oligonucleotides that target angiogenic factors toward tackling solid cancers.
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Affiliation(s)
- Bao T Le
- Centre for Comparative Genomics, Murdoch University, Murdoch, WA 6150, Australia; Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Prithi Raguraman
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Tamer R Kosbar
- Centre for Comparative Genomics, Murdoch University, Murdoch, WA 6150, Australia; Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Susan Fletcher
- Centre for Comparative Genomics, Murdoch University, Murdoch, WA 6150, Australia; Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Steve D Wilton
- Centre for Comparative Genomics, Murdoch University, Murdoch, WA 6150, Australia; Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Rakesh N Veedu
- Centre for Comparative Genomics, Murdoch University, Murdoch, WA 6150, Australia; Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia.
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49
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Yuan L, Li JY. Exosomes in Parkinson's Disease: Current Perspectives and Future Challenges. ACS Chem Neurosci 2019; 10:964-972. [PMID: 30664350 DOI: 10.1021/acschemneuro.8b00469] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Exosomes, which are lipid bilayer membrane vesicles, have been implicated as carriers of biological macromolecules. In recent years, the functions of exosomes in the spreading of pathological conversion of proteins among neurons have drawn particular attention in Parkinson's disease research. Extracellular α-synuclein is proven to be associated with exosomes in vivo and in vitro. The contents of these exosomes may be altered during the pathological and clinical processes, serving as a potential target for biomarker development in Parkinson's disease. This Review highlights the current understanding of biogenesis and pathophysiological roles of exosomes. Meanwhile, exosomes are promising delivery vehicles. Artificial exosomes can be loaded with defined therapeutically active molecules, such as drugs, small interfering RNAs, long noncoding RNAs, and proteins to the brain, ensuring the site-specific targeting strategy to the recipient cells. Therefore, we will also discuss the potential applications of exosomes in developing modified exosome-based drug carrier systems to halt the pathologic propagation of Parkinson's disease.
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Affiliation(s)
- Lin Yuan
- Institute of Health Science, China Medical University, Shenyang 110122, China
| | - Jia-Yi Li
- Institute of Health Science, China Medical University, Shenyang 110122, China
- Neural Plasticity and Repair Unit, Wallenberg Neuroscience Center, Department of Experimental Medical Science, Lund University, BMC A10, 22184 Lund, Sweden
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50
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Uvarova V, Nizamov T, Abakumov M, Vodopyanov S, Abakumova T, Saltykova I, Mogilnikov P, Shchetinin I, Majouga A. Lipidoid iron oxide nanoparticles are a platform for nucleic acid delivery to the liver. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2019. [DOI: 10.24075/brsmu.2018.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Targeted delivery of antisense drugs is a promising technology which can provide a platform for the development of highly effective therapeuticals against a broad range of diseases. Insufficient stability of RNA in biological media coupled with hydrophilicity that prevents the molecule from penetrating cell membranes considerably limit RNA application in clinical practice. The aim of this work was to design a system for antisense drug delivery to liver hepatocytes using lipidoid magnetic nanoparticles (LNP). Nanocubes (NC) with average sizes of 16 and 27 nm were synthesized through decomposition of iron (III) oleate under high temperature conditions and functionalized with a cationic lipidoid С12-200. Magnetic NC demonstrated good MR-contrasting properties. Biodistribution of LNP was studied in vivo in BALB/c mice using the MR scanner. Additionally, liver sections obtained from the mice were subjected to histological examination. Nanoparticles of smaller size did not have a cytotoxic effect on HepG2 and Huh7 cell lines, whereas for larger NC, IC50 was 21.5 μg/ml and 126 μg/ml for HepG2 and Huh7 cells, respectively. Smaller particles tended to accumulate in hepatocytes. Bigger NC mainly accumulated in the spleen but also ended up in liver macrophages. This fact can be explained by a bigger hydrodynamic size of nanoparticles with a bigger magnetic core. Particles with smaller cores are a more effective platform for the delivery of antisense drugs to hepatocytes.
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Affiliation(s)
- V.I. Uvarova
- Laboratory of Biomedical Nanomaterials, National University of Science and Technology MISiS, Moscow; Laboratory of Tissue Specific Ligands Investigation, Lomonosov Moscow State University, Moscow
| | - T.R. Nizamov
- Laboratory of Biomedical Nanomaterials, National University of Science and Technology MISiS, Moscow
| | - M.A. Abakumov
- Laboratory of Biomedical Nanomaterials, National University of Science and Technology MISiS, Moscow
| | - S.S. Vodopyanov
- Laboratory of Biomedical Nanomaterials, National University of Science and Technology MISiS, Moscow
| | - T.O. Abakumova
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow
| | - I.V. Saltykova
- Laboratory of Tissue Specific Ligands Investigation, Lomonosov Moscow State University, Moscow
| | - P.S. Mogilnikov
- Department of Physical Materials Science, National University of Science and Technology MISiS, Moscow
| | - I.V. Shchetinin
- Department of Physical Materials Science, National University of Science and Technology MISiS, Moscow
| | - A.M. Majouga
- Mendeleev University of Chemical Technology of Russia, Moscow
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