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Sharma NK, Dwivedi P, Bhushan R, Maurya PK, Kumar A, Dakal TC. Engineering circular RNA for molecular and metabolic reprogramming. Funct Integr Genomics 2024; 24:117. [PMID: 38918231 DOI: 10.1007/s10142-024-01394-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/10/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024]
Abstract
The role of messenger RNA (mRNA) in biological systems is extremely versatile. However, it's extremely short half-life poses a fundamental restriction on its application. Moreover, the translation efficiency of mRNA is also limited. On the contrary, circular RNAs, also known as circRNAs, are a common and stable form of RNA found in eukaryotic cells. These molecules are synthesized via back-splicing. Both synthetic circRNAs and certain endogenous circRNAs have the potential to encode proteins, hence suggesting the potential of circRNA as a gene expression machinery. Herein, we aim to summarize all engineering aspects that allow exogenous circular RNA (circRNA) to prolong the time that proteins are expressed from full-length RNA signals. This review presents a systematic engineering approach that have been devised to efficiently assemble circRNAs and evaluate several aspects that have an impact on protein production derived from. We have also reviewed how optimization of the key components of circRNAs, including the topology of vector, 5' and 3' untranslated sections, entrance site of the internal ribosome, and engineered aptamers could be efficiently impacting the translation machinery for molecular and metabolic reprogramming. Collectively, molecular and metabolic reprogramming present a novel way of regulating distinctive cellular features, for instance growth traits to neoplastic cells, and offer new possibilities for therapeutic inventions.
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Affiliation(s)
- Narendra Kumar Sharma
- Department of Bioscience and Biotechnology, Banasthali Vidyapith (Deemed University), P.O. Banasthali Vidyapith Distt. Tonk, Rajasthan, 304 022, India.
| | - Pragya Dwivedi
- Department of Bioscience and Biotechnology, Banasthali Vidyapith (Deemed University), P.O. Banasthali Vidyapith Distt. Tonk, Rajasthan, 304 022, India
| | - Ravi Bhushan
- Department of Zoology, M.S. College, Motihari, Bihar, India
| | - Pawan Kumar Maurya
- Department of Biochemistry, Central University of Haryana, Mahendergarh, 123031, Haryana, India
| | - Abhishek Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Tikam Chand Dakal
- Genome and Computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India.
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2
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Yao S, Kasargod A, Chiu R, Torgerson TR, Kupiec-Weglinski JW, Dery KJ. The Coming Age of Antisense Oligos for the Treatment of Hepatic Ischemia/Reperfusion (IRI) and Other Liver Disorders: Role of Oxidative Stress and Potential Antioxidant Effect. Antioxidants (Basel) 2024; 13:678. [PMID: 38929116 DOI: 10.3390/antiox13060678] [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: 04/06/2024] [Revised: 05/21/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Imbalances in the redox state of the liver arise during metabolic processes, inflammatory injuries, and proliferative liver disorders. Acute exposure to intracellular reactive oxygen species (ROS) results from high levels of oxidative stress (OxS) that occur in response to hepatic ischemia/reperfusion injury (IRI) and metabolic diseases of the liver. Antisense oligonucleotides (ASOs) are an emerging class of gene expression modulators that target RNA molecules by Watson-Crick binding specificity, leading to RNA degradation, splicing modulation, and/or translation interference. Here, we review ASO inhibitor/activator strategies to modulate transcription and translation that control the expression of enzymes, transcription factors, and intracellular sensors of DNA damage. Several small-interfering RNA (siRNA) drugs with N-acetyl galactosamine moieties for the liver have recently been approved. Preclinical studies using short-activating RNAs (saRNAs), phosphorodiamidate morpholino oligomers (PMOs), and locked nucleic acids (LNAs) are at the forefront of proof-in-concept therapeutics. Future research targeting intracellular OxS-related pathways in the liver may help realize the promise of precision medicine, revolutionizing the customary approach to caring for and treating individuals afflicted with liver-specific conditions.
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Affiliation(s)
- Siyuan Yao
- The Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Aanchal Kasargod
- The Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Richard Chiu
- The Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Taylor R Torgerson
- The Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Jerzy W Kupiec-Weglinski
- The Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Kenneth J Dery
- The Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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3
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Ciucci G, Braga L, Zacchigna S. Discovery platforms for RNA therapeutics. Br J Pharmacol 2024. [PMID: 38760893 DOI: 10.1111/bph.16424] [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: 11/29/2023] [Revised: 04/14/2024] [Accepted: 04/19/2024] [Indexed: 05/20/2024] Open
Abstract
RNA therapeutics are emerging as a unique opportunity to drug currently "undruggable" molecules and diseases. While their advantages over conventional, small molecule drugs, their therapeutic implications and the tools for their effective in vivo delivery have been extensively reviewed, little attention has been so far paid to the technological platforms exploited for the discovery of RNA therapeutics. Here, we provide an overview of the existing platforms and ex vivo assays for RNA discovery, their advantages and disadvantages, as well as their main fields of application, with specific focus on RNA therapies that have reached either phase 3 or market approval.
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Affiliation(s)
- Giulio Ciucci
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Luca Braga
- Functional Cell Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Serena Zacchigna
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
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4
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Genna V, Reyes-Fraile L, Iglesias-Fernandez J, Orozco M. Nucleic acids in modern molecular therapies: A realm of opportunities for strategic drug design. Curr Opin Struct Biol 2024; 87:102838. [PMID: 38759298 DOI: 10.1016/j.sbi.2024.102838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/10/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024]
Abstract
RNA vaccines have made evident to society what was already known by the scientific community: nucleic acids will be the "drugs of the future." By modifying the genome, interfering in transcription or translation, and by introducing new catalysts into the cell or by mimicking antibody effects, nucleic acids can generate therapeutic activities that are not accessible by any other therapeutic agents. There are, however, challenges that need to be solved in the next few years to make nucleic acids usable in a wide range of therapeutic scenarios. This review illustrates how simulation methods can help achieve this goal.
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Affiliation(s)
- Vito Genna
- NBD|Nostrum Biodiscovery, Josep Tarradellas 8-10, Barcelona 08019, Spain. https://twitter.com/_VitoGenna_
| | - Laura Reyes-Fraile
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain; Sixfold Bioscience Ltd, Translational & Innovation Hub, 84 Wood Ln, London W12 0BZ, United Kingdom
| | | | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain; Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona 08028, Spain.
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5
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Seyhan AA. Trials and Tribulations of MicroRNA Therapeutics. Int J Mol Sci 2024; 25:1469. [PMID: 38338746 PMCID: PMC10855871 DOI: 10.3390/ijms25031469] [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: 12/22/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/12/2024] Open
Abstract
The discovery of the link between microRNAs (miRNAs) and a myriad of human diseases, particularly various cancer types, has generated significant interest in exploring their potential as a novel class of drugs. This has led to substantial investments in interdisciplinary research fields such as biology, chemistry, and medical science for the development of miRNA-based therapies. Furthermore, the recent global success of SARS-CoV-2 mRNA vaccines against the COVID-19 pandemic has further revitalized interest in RNA-based immunotherapies, including miRNA-based approaches to cancer treatment. Consequently, RNA therapeutics have emerged as highly adaptable and modular options for cancer therapy. Moreover, advancements in RNA chemistry and delivery methods have been pivotal in shaping the landscape of RNA-based immunotherapy, including miRNA-based approaches. Consequently, the biotechnology and pharmaceutical industry has witnessed a resurgence of interest in incorporating RNA-based immunotherapies and miRNA therapeutics into their development programs. Despite substantial progress in preclinical research, the field of miRNA-based therapeutics remains in its early stages, with only a few progressing to clinical development, none reaching phase III clinical trials or being approved by the US Food and Drug Administration (FDA), and several facing termination due to toxicity issues. These setbacks highlight existing challenges that must be addressed for the broad clinical application of miRNA-based therapeutics. Key challenges include establishing miRNA sensitivity, specificity, and selectivity towards their intended targets, mitigating immunogenic reactions and off-target effects, developing enhanced methods for targeted delivery, and determining optimal dosing for therapeutic efficacy while minimizing side effects. Additionally, the limited understanding of the precise functions of miRNAs limits their clinical utilization. Moreover, for miRNAs to be viable for cancer treatment, they must be technically and economically feasible for the widespread adoption of RNA therapies. As a result, a thorough risk evaluation of miRNA therapeutics is crucial to minimize off-target effects, prevent overdosing, and address various other issues. Nevertheless, the therapeutic potential of miRNAs for various diseases is evident, and future investigations are essential to determine their applicability in clinical settings.
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Affiliation(s)
- Attila A. Seyhan
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA;
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Joint Program in Cancer Biology, Lifespan Health System and Brown University, Providence, RI 02912, USA
- Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
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6
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Szymanowski W, Szymanowska A, Bielawska A, Lopez-Berestein G, Rodriguez-Aguayo C, Amero P. Aptamers as Potential Therapeutic Tools for Ovarian Cancer: Advancements and Challenges. Cancers (Basel) 2023; 15:5300. [PMID: 37958473 PMCID: PMC10647731 DOI: 10.3390/cancers15215300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Ovarian cancer (OC) is the most common lethal gynecologic cause of death in women worldwide, with a high mortality rate and increasing incidence. Despite advancements in the treatment, most OC patients still die from their disease due to late-stage diagnosis, the lack of effective diagnostic methods, and relapses. Aptamers, synthetic, short single-stranded oligonucleotides, have emerged as promising anticancer therapeutics. Their ability to selectively bind to target molecules, including cancer-related proteins and receptors, has revolutionized drug discovery and biomarker identification. Aptamers offer unique insights into the molecular pathways involved in cancer development and progression. Moreover, they show immense potential as drug delivery systems, enabling targeted delivery of therapeutic agents to cancer cells while minimizing off-target effects and reducing systemic toxicity. In the context of OC, the integration of aptamers with non-coding RNAs (ncRNAs) presents an opportunity for precise and efficient gene targeting. Additionally, the conjugation of aptamers with nanoparticles allows for accurate and targeted delivery of ncRNAs to specific cells, tissues, or organs. In this review, we will summarize the potential use and challenges associated with the use of aptamers alone or aptamer-ncRNA conjugates, nanoparticles, and multivalent aptamer-based therapeutics for the treatment of OC.
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Affiliation(s)
- Wojciech Szymanowski
- Department of Biotechnology, Medical University of Bialystok, 15-222 Bialystok, Poland; (W.S.); (A.B.)
| | - Anna Szymanowska
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.S.); (G.L.-B.); (C.R.-A.)
| | - Anna Bielawska
- Department of Biotechnology, Medical University of Bialystok, 15-222 Bialystok, Poland; (W.S.); (A.B.)
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.S.); (G.L.-B.); (C.R.-A.)
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.S.); (G.L.-B.); (C.R.-A.)
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Paola Amero
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.S.); (G.L.-B.); (C.R.-A.)
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Prosser O, Stonehouse NJ, Tuplin A. Inhibition of Chikungunya virus genome replication by targeting essential RNA structures within the virus genome. Antiviral Res 2023; 211:105523. [PMID: 36603772 DOI: 10.1016/j.antiviral.2023.105523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/22/2022] [Accepted: 01/02/2023] [Indexed: 01/04/2023]
Abstract
Chikungunya virus (CHIKV) is a pathogenic arbovirus spread by Aedes spp. mosquitos. CHIKV has a wide global prevalence and represents a significant health burden in affected populations. Symptoms of CHIKV infection include fever, rashes and debilitating joint and muscle pain, which can persist for several months to years in some patients. To date, there remains no vaccine or specific antiviral therapy against this important human pathogen. Based on our previously published structural and phenotypic analysis of the 5' region of the CHIKV genome, we designed a panel of locked nucleic acid oligonucleotides to bind structured RNA replication elements within the virus genome, which are essential for efficient CHIKV replication. Using electromobility shift assays, we confirmed the relative binding efficiencies of each LNA to target CHIKV genomic RNA. We then went on to demonstrate, using both sub-genomic replicon and infectious virus systems, that targeting individual RNA replication elements inhibits CHIKV genome replication and production of infectious virus. Time course assays demonstrated that LNAs can access the CHIKV replication complex and virus genome, during active virus replication. For the first time, these findings show that functional RNA elements can be specifically targeted during the CHIKV lifecycle and consequently represent potential novel antiviral targets.
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Affiliation(s)
- Oliver Prosser
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Nicola J Stonehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Andrew Tuplin
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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8
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Li J, Qu X, Guan C, Luo N, Chen H, Li A, Zhuang H, Yang J, Diao H, Zeng S, Wang Q, Fan J, Jiang M, Bai X, Ye Z, Jiang X, Chen W, Nikolic-Paterson DJ, Yu X. Mitochondrial micropeptide MOXI promotes fibrotic gene transcription by translocation to the nucleus and bridging N-acetyltransferase 14 with transcription factor c-Jun. Kidney Int 2023; 103:886-902. [PMID: 36804379 DOI: 10.1016/j.kint.2023.01.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 01/04/2023] [Accepted: 01/20/2023] [Indexed: 02/17/2023]
Abstract
Progressive fibrosis is a hallmark of chronic kidney disease, but we lack effective treatments to halt this destructive process. Micropeptides (peptides of no more than 100 amino acids) encoded by small open reading frames represent a new class of eukaryotic regulators. Here, we describe that the micropeptide regulator of β-oxidation (MOXI) regulates kidney fibrosis. MOXI expression was found to be up-regulated in human fibrotic kidney disease, and this correlated with the degree of fibrosis and loss of kidney function. MOXI was expressed in the cytoplasm and mitochondria of cultured tubular epithelial cells and translocated to the nucleus upon Transforming Growth Factor-β1 stimulation. Deletion of Moxi protected mice against fibrosis and inflammation in the folic acid and unilateral ureteral obstruction models. As a potential molecular therapy, treatment with an antisense MOXI oligonucleotide effectively knocked-down MOXI expression and protected against kidney fibrosis in both models. Bimolecular fluorescence complementation identified the enzyme N-acetyltransferase 14 (Nat14) and transcription factor c-Jun as MOXI binding partners. The MOXI/Nat14/c-Jun complex enhances basal and Transforming Growth Factor-β1 induced collagen I gene promoter activity. Phosphorylation at T49 is required for MOXI nuclear localization and for complex formation with Nat14 and c-Jun. Furthermore, mice with a MoxiT49A point mutation were protected in the models of kidney fibrosis. Thus, our studies demonstrate a key role for the micropeptide MOXI in kidney fibrosis and identify a new function of MOXI in forming a transcriptional complex with Nat14 and c-Jun.
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Affiliation(s)
- Jinhua Li
- The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China; Department of Nephrology, Monash Health and Monash University Department of Medicine, Clayton, Victoria, Australia; Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China; Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| | - Xinli Qu
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Chengnong Guan
- The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China
| | - Ning Luo
- Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Huiting Chen
- The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China
| | - Andy Li
- Department of Nephrology, Monash Health and Monash University Department of Medicine, Clayton, Victoria, Australia
| | - Hongjie Zhuang
- Department of Paediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiayi Yang
- Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Hui Diao
- Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Shuhan Zeng
- Department of Paediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qing Wang
- The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China
| | - Jinjin Fan
- Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Mengjie Jiang
- Department of Paediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyan Bai
- Department of Nephrology, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China; Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhiming Ye
- Department of Nephrology, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China; Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiaoyun Jiang
- Department of Paediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wei Chen
- Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - David J Nikolic-Paterson
- Department of Nephrology, Monash Health and Monash University Department of Medicine, Clayton, Victoria, Australia
| | - Xueqing Yu
- Department of Nephrology, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China; Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China.
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9
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Kamali MJ, Salehi M, Fatemi S, Moradi F, Khoshghiafeh A, Ahmadifard M. Locked nucleic acid (LNA): A modern approach to cancer diagnosis and treatment. Exp Cell Res 2023; 423:113442. [PMID: 36521777 DOI: 10.1016/j.yexcr.2022.113442] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 12/04/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
Cancer is responsible for about one in six deaths in the world. Conventional cancer treatments like chemotherapy, radiotherapy, and surgery are associated with drug poisoning and poor prognosis. Thanks to advances in RNA delivery and target selection, new cancer medicines are now conceivable to improve the quality of life and extend the lives of cancer patients. Antisense oligonucleotides (ASOs) and siRNAs are the most important tools in RNA therapies. Locked Nucleic Acids (LNAs) are one of the newest RNA analogs, exhibiting more affinity to binding, sequence specificity, thermal stability, and nuclease resistance due to their unique properties. Assays using LNA are also used in molecular diagnostic methods and provide accurate and rapid mutation detection that improves specificity and sensitivity. This study aims to review the special properties of LNA oligonucleotides that make them safe and effective antisense drugs for cancer treatment by controlling gene expression. Following that, we go over all of the molecular detection methods and cancer treatment antisense tactics that are possible with LNA technology.
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Affiliation(s)
- Mohammad Javad Kamali
- Department of Medical Genetics, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Mohammad Salehi
- School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Somayeh Fatemi
- Department of Medical Genetics, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Fereshteh Moradi
- Department of Medical Genetics, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Azin Khoshghiafeh
- Department of Medical Genetics, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Mohamadreza Ahmadifard
- Department of Medical Genetics, School of Medicine, Babol University of Medical Sciences, Babol, Iran.
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10
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Probst V, Simonyan A, Pacheco F, Guo Y, Nielsen FC, Bagger FO. Benchmarking full-length transcript single cell mRNA sequencing protocols. BMC Genomics 2022; 23:860. [PMID: 36581800 PMCID: PMC9801581 DOI: 10.1186/s12864-022-09014-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 11/14/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Single cell mRNA sequencing technologies have transformed our understanding of cellular heterogeneity and identity. For sensitive discovery or clinical marker estimation where high transcript capture per cell is needed only plate-based techniques currently offer sufficient resolution. RESULTS Here, we present a performance evaluation of four different plate-based scRNA-seq protocols. Our evaluation is aimed towards applications taxing high gene detection sensitivity, reproducibility between samples, and minimum hands-on time, as is required, for example, in clinical use. We included two commercial kits, NEBNext® Single Cell/ Low Input RNA Library Prep Kit (NEB®), SMART-seq® HT kit (Takara®), and the non-commercial protocols Genome & Transcriptome sequencing (G&T) and SMART-seq3 (SS3). G&T delivered the highest detection of genes per single cell. SS3 presented the highest gene detection per single cell at the lowest price. Takara® kit presented similar high gene detection per single cell, and high reproducibility between samples, but at the absolute highest price. NEB® delivered a lower detection of genes but remains an alternative to more expensive commercial kits. CONCLUSION For the tested kits we found that ease-of-use came at higher prices. Takara can be selected for its ease-of-use to analyse a few samples, but we recommend the cheaper G&T-seq or SS3 for laboratories where a substantial sample flow can be expected.
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Affiliation(s)
- Victoria Probst
- grid.475435.4Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Arman Simonyan
- grid.475435.4Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Felix Pacheco
- grid.475435.4Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Yuliu Guo
- grid.475435.4Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Finn Cilius Nielsen
- grid.475435.4Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Frederik Otzen Bagger
- grid.475435.4Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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11
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Okuyan HM, Begen MA. LncRNAs in Osteoarthritis. Clin Chim Acta 2022; 532:145-163. [PMID: 35667478 DOI: 10.1016/j.cca.2022.05.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/29/2022] [Accepted: 05/31/2022] [Indexed: 11/27/2022]
Abstract
Osteoarthritis (OA) is a progressive joint disease that affects millions of older adults around the world. With increasing rates of incidence and prevalence worldwide, OA has become an enormous global socioeconomic burden on healthcare systems. Long non-coding ribonucleic acids (lncRNAs), essential functional molecules in many biological processes, are a group of non-coding RNAs that are greater than approximately 200 nucleotides in length. Fast-growing and recent developments in lncRNA research are captivating and represent a novel and promising field in understanding the complexity of OA pathogenesis. The involvement of lncRNAs in OA's pathological processes and their altered expressions in joint tissues, blood and synovial fluid make them attractive candidates for the diagnosis and treatment of OA. We focus on the recent advances in major regulator mechanisms of lncRNAs in the pathophysiology of OA and discuss potential diagnostic and therapeutic uses of lncRNAs for OA. We investigate how upregulation or downregulation of lncRNAs influences the pathogenesis of OA and how we can use lncRNAs to elucidate the molecular mechanism of OA. Furthermore, we evaluate how we can use lncRNAs as a diagnostic marker or therapeutic target for OA. Our study not only provides a comprehensive review of lncRNAs regarding OA's pathogenesis but also contributes to the elucidation of its molecular mechanisms and to the development of diagnostic and therapeutic approaches for OA.
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Affiliation(s)
- Hamza Malik Okuyan
- Biomedical Engineering, Physiotherapy and Rehabilitation, Faculty of Health Sciences, Sakarya University of Applied Sciences, Sakarya, Turkey; Ivey Business School, Epidemiology and Biostatistics - Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada.
| | - Mehmet A Begen
- Ivey Business School, Epidemiology and Biostatistics - Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada.
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12
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Diener C, Keller A, Meese E. Emerging concepts of miRNA therapeutics: from cells to clinic. Trends Genet 2022; 38:613-626. [PMID: 35303998 DOI: 10.1016/j.tig.2022.02.006] [Citation(s) in RCA: 220] [Impact Index Per Article: 110.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are very powerful genetic regulators, as evidenced by the fact that a single miRNA can direct entire cellular pathways via interacting with a broad spectrum of target genes. This property renders miRNAs as highly interesting therapeutic tools to restore cell functions that are altered as part of a disease phenotype. However, this strength of miRNAs is also a weakness because their cellular effects are so numerous that off-target effects can hardly be avoided. In this review, we point out the main challenges and the strategies to specifically address the problems that need to be surmounted in the push toward a therapeutic application of miRNAs. Particular emphasis is given to approaches that have already found their way into clinical studies.
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Affiliation(s)
- Caroline Diener
- Institute of Human Genetics, Medical Faculty, Saarland University, 66421 Homburg, Germany
| | - Andreas Keller
- Center for Bioinformatics, Medical Faculty, Saarland University, 66123 Saarbrücken, Germany; Department of Neurology and Neurological Sciences, Stanford University, School of Medicine, Stanford, CA 94305, USA.
| | - Eckart Meese
- Institute of Human Genetics, Medical Faculty, Saarland University, 66421 Homburg, Germany
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13
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miRNAs in Cancer (Review of Literature). Int J Mol Sci 2022; 23:ijms23052805. [PMID: 35269947 PMCID: PMC8910953 DOI: 10.3390/ijms23052805] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are short, noncoding, single-stranded RNA molecules that regulate gene expression at the post-transcriptional level by binding to mRNAs. miRNAs affect the course of processes of fundamental importance for the proper functioning of the organism. These processes include cell division, proliferation, differentiation, cell apoptosis and the formation of blood vessels. Altered expression of individual miRNAs has been shown in numerous cancers, which may indicate the oncogenic or suppressor potential of the molecules in question. This paper discusses the current knowledge about the possibility of using miRNA as a diagnostic marker and a potential target in modern anticancer therapies.
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14
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Dedeoğlu BG, Noyan S. Experimental MicroRNA Targeting Validation. Methods Mol Biol 2022; 2257:79-90. [PMID: 34432274 DOI: 10.1007/978-1-0716-1170-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
microRNAs (miRNAs) have recently been recognized as a new dimension of posttranscriptional regulation. It is well defined that most human protein-coding genes are regulated by one or more miRNAs. Therefore, it is crucial to identify genes targeted by the miRNAs to better understand their functions. Although bioinformatics tools have the ability to identify target candidates it is still essential to identify physiological targets by experimental approaches. Currently, the majority of miRNA-target experimental validation approaches assess the changes in target expression in mRNA or protein level upon miRNA upregulation or downregulation. Additionally, finding out direct physical interactions between miRNAs and their targets is also among the experimental techniques. In this chapter we reviewed the existing experimental techniques for miRNA target identification by considering their advantages and potential drawbacks.
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Affiliation(s)
| | - Senem Noyan
- Biotechnology Institute, Ankara University, Ankara, Turkey
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15
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Edelmann MR, Husser C, Duschmalé MB, Fischer G, Senn C, Koller E, Brink A. Tritium labeling of antisense oligonucleotides via different conjugation agents. AAPS OPEN 2021. [DOI: 10.1186/s41120-021-00040-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractA novel approach to tritium-labeled antisense oligonucleotides (ASO) was established by conjugating N-succinimidyl propionate, as well as maleimide-derivatives, to the 3′-end of ASOs targeting metastasis-associated lung adenocarcinoma transcript 1 (Malat1) containing amino- or sulfhydryl-linkers. In vitro stability and Malat1 RNA reduction studies demonstrated that N-ethylmaleimide (NEM) could be used as a stable tag while maintaining the desired target interaction. The corresponding radioactive label conjugation using [3H]-NEM resulted in tritium-labeled ASOs with a high molar specific activity of up to 17 Ci/mmol. Single-dose in vivo studies in mice were carried out to compare [3H]-ASOs with their unlabeled counterpart ASOs, with and without conjugation to N-acetylgalactosamine (GalNAc), for tissue and plasma concentrations time profiles. Despite the structural modification of the labeled ASOs, in vitro target interaction and in vivo pharmacokinetic behaviors were similar to that of the unlabeled ASOs. In conclusion, this new method provides a powerful technique for fast and safe access to tritium-labeled oligonucleotides, e.g., for pharmacokinetic, mass balance, or autoradiography studies.
Graphical abstract
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16
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Small RNAs Asserting Big Roles in Mycobacteria. Noncoding RNA 2021; 7:ncrna7040069. [PMID: 34842799 PMCID: PMC8628891 DOI: 10.3390/ncrna7040069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023] Open
Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb), with 10.4 million new cases per year reported in the human population. Recent studies on the Mtb transcriptome have revealed the abundance of noncoding RNAs expressed at various phases of mycobacteria growth, in culture, in infected mammalian cells, and in patients. Among these noncoding RNAs are both small RNAs (sRNAs) between 50 and 350 nts in length and smaller RNAs (sncRNA) < 50 nts. In this review, we provide an up-to-date synopsis of the identification, designation, and function of these Mtb-encoded sRNAs and sncRNAs. The methodological advances including RNA sequencing strategies, small RNA antagonists, and locked nucleic acid sequence-specific RNA probes advancing the studies on these small RNA are described. Initial insights into the regulation of the small RNA expression and putative processing enzymes required for their synthesis and function are discussed. There are many open questions remaining about the biological and pathogenic roles of these small non-coding RNAs, and potential research directions needed to define the role of these mycobacterial noncoding RNAs are summarized.
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17
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Markati T, Duis J, Servais L. Therapies in preclinical and clinical development for Angelman syndrome. Expert Opin Investig Drugs 2021; 30:709-720. [PMID: 34112038 DOI: 10.1080/13543784.2021.1939674] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Angelman syndrome is a rare genetic neurodevelopmental disorder, caused by deficiency or abnormal function of the maternal ubiquitin protein-ligase E3A, known as UBE3A, in the central nervous system. There is no disease-modifying treatment available, but the therapeutic pipeline of Angelman syndrome includes at least 15 different approaches at preclinical or clinical development. In the coming years, several clinical trials will be enrolling patients, which prompted this comprehensive review.Areas covered: We summarize and critically review the different therapeutic approaches. Some approaches attempt to restore the missing or nonfunctional UBE3A protein in the neurons via gene replacement or enzyme replacement therapies. Other therapies aim to induce expression of the normal paternal copy of the UBE3A gene by targeting a long non-coding RNA, the UBE3A-ATS, which interferes with its own expression. Another therapeutic category includes compounds that target molecular pathways and effector proteins known to be involved in Angelman syndrome pathophysiology.Expert opinion: We believe that by 2022-2023, more than five disease-modifying treatments will be simultaneously at clinical testing. However, the are several challenges with regards to safety and efficacy, which need to be addressed. Additionally, there is still a significant unmet need for clinical trial readiness.
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Affiliation(s)
- Theodora Markati
- MDUK Oxford Neuromuscular Center, University of Oxford, Oxford, UK.,Department of Paediatrics, University of Oxford, Oxford, UK
| | - Jessica Duis
- Section of Genetics & Inherited Metabolic Disease, Department of Pediatrics, Children's Hospital Colorado, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Laurent Servais
- MDUK Oxford Neuromuscular Center, University of Oxford, Oxford, UK.,Department of Paediatrics, University of Oxford, Oxford, UK.,Division of Child Neurology, Centre De Références Des Maladies Neuromusculaires, Department of Pediatrics, University Hospital Liège & University of Liège, Belgium
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18
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Romero-Palomo F, Festag M, Lenz B, Schadt S, Brink A, Kipar A, Steinhuber B, Husser C, Koller E, Sewing S, Tessier Y, Dzygiel P, Fischer G, Winter M, Hetzel U, Mihatsch MJ, Braendli-Baiocco A. Safety, Tissue Distribution, and Metabolism of LNA-Containing Antisense Oligonucleotides in Rats. Toxicol Pathol 2021; 49:1174-1192. [PMID: 34060347 DOI: 10.1177/01926233211011615] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Antisense oligonucleotides (ASOs) are chemically modified nucleic acids with therapeutic potential, some of which have been approved for marketing. We performed a study in rats to investigate mechanisms of toxicity after administration of 3 tool locked nucleic acid (LNA)-containing ASOs with differing established safety profiles. Four male rats per group were dosed once, 3, or 6 times subcutaneously, with 7 days between dosing, and sacrificed 3 days after the last dose. These ASOs were either unconjugated (naked) or conjugated with N-acetylgalactosamine for hepatocyte-targeted delivery. The main readouts were in-life monitoring, clinical and anatomic pathology, exposure assessment and metabolite identification in liver and kidney by liquid chromatography coupled to tandem mass spectrometry, ASO detection in liver and kidney by immunohistochemistry, in situ hybridization, immune electron microscopy, and matrix-assisted laser desorption/ionization mass spectrometry imaging. The highly toxic compounds showed the greatest amount of metabolites and a low degree of tissue accumulation. This study reveals different patterns of cell death associated with toxicity in liver (apoptosis and necrosis) and kidney (necrosis only) and provides new ultrastructural insights on the tissue accumulation of ASOs. We observed that the immunostimulatory properties of ASOs can be either primary from sequence-dependent properties or secondary to cell necrosis.
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Affiliation(s)
- Fernando Romero-Palomo
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, 1529Roche Innovation Center Basel, Switzerland
| | - Matthias Festag
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, 1529Roche Innovation Center Basel, Switzerland
| | - Barbara Lenz
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, 1529Roche Innovation Center Basel, Switzerland
| | - Simone Schadt
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, 1529Roche Innovation Center Basel, Switzerland
| | - Andreas Brink
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, 1529Roche Innovation Center Basel, Switzerland
| | - Anja Kipar
- Laboratory for Animal Model Pathology (LAMP), Institute of Veterinary Pathology, 30843Vetsuisse Faculty, University of Zürich, Switzerland
| | - Bernd Steinhuber
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, 1529Roche Innovation Center Basel, Switzerland
| | - Christophe Husser
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, 1529Roche Innovation Center Basel, Switzerland
| | - Erich Koller
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, 1529Roche Innovation Center Basel, Switzerland
| | - Sabine Sewing
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, 1529Roche Innovation Center Basel, Switzerland
| | - Yann Tessier
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, 1529Roche Innovation Center Basel, Switzerland
| | - Pawel Dzygiel
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, 1529Roche Innovation Center Basel, Switzerland
| | - Guy Fischer
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, 1529Roche Innovation Center Basel, Switzerland
| | - Michael Winter
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, 1529Roche Innovation Center Basel, Switzerland
| | - Udo Hetzel
- Electron Microscopy Unit, Institute of Veterinary Pathology, 27217Vetsuisse Faculty, University of Zürich, Switzerland
| | - Michael J Mihatsch
- 361703Institute for Pathology, University Hospital of Basel, Switzerland
| | - Annamaria Braendli-Baiocco
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, 1529Roche Innovation Center Basel, Switzerland
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19
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Ferrara B, Belbekhouche S, Habert D, Houppe C, Vallée B, Bourgoin-Voillard S, Cohen JL, Cascone I, Courty J. Cell surface nucleolin as active bait for nanomedicine in cancer therapy: a promising option. NANOTECHNOLOGY 2021; 32:322001. [PMID: 33892482 DOI: 10.1088/1361-6528/abfb30] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Conventional chemotherapy used against cancer is mostly limited due to their non-targeted nature, affecting normal tissue and causing undesirable toxic effects to the affected tissue. With the aim of improving these treatments both therapeutically and in terms of their safety, numerous studies are currently being carried out using nanoparticles (NPs) as a vector combining tumor targeting and carrying therapeutic tools. In this context, it appears that nucleolin, a molecule over-expressed on the surface of tumor cells, is an interesting therapeutic target. Several ligands, antagonists of nucleolin of various origins, such as AS1411, the F3 peptide and the multivalent pseudopeptide N6L have been developed and studied as therapeutic tools against cancer. Over the last ten years or so, numerous studies have been published demonstrating that these antagonists can be used as tumor targeting agents with NPs from various origins. Focusing on nucleolin ligands, the aim of this article is to review the literature recently published or under experimentation in our research team to evaluate the efficacy and future development of these tools as anti-tumor agents.
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Affiliation(s)
- Benedetta Ferrara
- Université Paris-Est Creteil, Immunorégulation et Biothérapie, INSERM U955, Hôpital Henri Mondor, F-94010 Créteil, France
| | - Sabrina Belbekhouche
- Université Paris-Est Creteil, CNRS, Institut Chimie et Matériaux Paris Est, UMR 7182, 2 Rue Henri Dunant, F-94320 Thiais, France
| | - Damien Habert
- Université Paris-Est Creteil, Immunorégulation et Biothérapie, INSERM U955, Hôpital Henri Mondor, F-94010 Créteil, France
| | - Claire Houppe
- Université Paris-Est Creteil, Immunorégulation et Biothérapie, INSERM U955, Hôpital Henri Mondor, F-94010 Créteil, France
| | - Benoit Vallée
- Université Paris-Est Creteil, Immunorégulation et Biothérapie, INSERM U955, Hôpital Henri Mondor, F-94010 Créteil, France
| | - Sandrine Bourgoin-Voillard
- Université Paris-Est Creteil, Immunorégulation et Biothérapie, INSERM U955, Hôpital Henri Mondor, F-94010 Créteil, France
- Université Grenoble Alpes, Laboratory of Fundamental and Applied Bioenergetics/Prométhée Proteomic Platform, UGA-INSERM U1055-CHUGA, Grenoble, France
- Université Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC, PROMETHEE Proteomic Platform, Grenoble, France
| | - José L Cohen
- Université Paris-Est Creteil, Immunorégulation et Biothérapie, INSERM U955, Hôpital Henri Mondor, F-94010 Créteil, France
| | - Ilaria Cascone
- Université Paris-Est Creteil, Immunorégulation et Biothérapie, INSERM U955, Hôpital Henri Mondor, F-94010 Créteil, France
| | - José Courty
- Université Paris-Est Creteil, Immunorégulation et Biothérapie, INSERM U955, Hôpital Henri Mondor, F-94010 Créteil, France
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20
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Chong ZX, Yeap SK, Ho WY. Transfection types, methods and strategies: a technical review. PeerJ 2021; 9:e11165. [PMID: 33976969 PMCID: PMC8067914 DOI: 10.7717/peerj.11165] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/05/2021] [Indexed: 12/17/2022] Open
Abstract
Transfection is a modern and powerful method used to insert foreign nucleic acids into eukaryotic cells. The ability to modify host cells’ genetic content enables the broad application of this process in studying normal cellular processes, disease molecular mechanism and gene therapeutic effect. In this review, we summarized and compared the findings from various reported literature on the characteristics, strengths, and limitations of various transfection methods, type of transfected nucleic acids, transfection controls and approaches to assess transfection efficiency. With the vast choices of approaches available, we hope that this review will help researchers, especially those new to the field, in their decision making over the transfection protocol or strategy appropriate for their experimental aims.
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Affiliation(s)
- Zhi Xiong Chong
- School of Pharmacy, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Selangor, Malaysia
| | - Wan Yong Ho
- School of Pharmacy, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
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21
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Watanabe A, Katsube T. Pharmacokinetic-pharmacodynamic modeling for hepatic delivery and efficacy of antisense oligonucleotides with lipophilic ligands in mice. Biopharm Drug Dispos 2021; 42:178-187. [PMID: 33724506 DOI: 10.1002/bdd.2271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/09/2021] [Accepted: 02/21/2021] [Indexed: 11/11/2022]
Abstract
Conjugation with lipophilic ligands such as cholesterol and α-tocopherol dramatically improves the delivery and efficacy of antisense oligonucleotides (ASOs) in the liver. To estimate the hepatic ASO concentration and the efficacy of ASOs conjugated with lipophilic ligands in mice, we constructed a pharmacokinetic-pharmacodynamic (PK-PD) model that consisted of a two-linear compartment model for the plasma and the hepatic ASO concentration, and two indirect response models for the hepatic apolipoprotein B (Apo-B) mRNA and plasma total cholesterol. The model provided a good fit of the hepatic ASO concentration although it showed an overprediction of Apo-B mRNA and an underprediction of the plasma total cholesterol within 2-fold at a later time after single intravenous administration of ASOs conjugated with lipophilic ligands. In addition, the model simulations indicated that the efficacy at a dose regimen of ASOs conjugated with lipophilic ligands (0.2 mg/kg, once a week) in mice was comparable to that at an effective dose of unchanged ASO (2.5 mg/kg, once a week). Although further studies are required to refine the parameters of the PK-PD model, this approach could be used to guide dose-ranging pharmacological studies for ASOs conjugated with lipophilic ligands in mice.
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Affiliation(s)
- Ayahisa Watanabe
- Pharmaceutical Research Division, Biologics 1, Laboratory for Advanced Medicine Research, Shionogi & Co., Ltd, Toyonaka, Japan
| | - Takayuki Katsube
- Project Management Department, Clinical Pharmacology & Pharmacokinetics, Shionogi & Co., Ltd, Toyonaka, Japan
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22
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Abstract
Long noncoding RNAs (lncRNAs) are a class of RNA with 200 nucleotides or longer that are not translated into protein. lncRNAs are highly abundant; a study estimates that at least four times more lncRNAs are typically present than coding RNAs in humans. However, function of more than 95% of human lncRNAs are still unknown. Synthetic antisense oligonucleotides called gapmers are powerful tools for lncRNA loss-of-function studies. Gapmers contain a central DNA part, which activates RNase H-mediated RNA degradation, flanked by modified oligonucleotides, such as 2'-O-methyl RNA (2'OMe), 2'-O-methoxyethyl RNA (2'MOE), constrained ethyl nucleosides (cEt), and locked nucleic acids (LNAs). In contrast to siRNA or RNAi-based methods, antisense oligonucleotide gapmer-based knockdown is often more effective against nuclear-localized lncRNA targets, since RNase H is mainly localized in nuclei. As such, gapmers are also potentially a powerful tool for therapeutics targeting lncRNAs in various diseases, including cancer, cardiovascular diseases, lung fibrosis, and neurological/neuromuscular diseases. This chapter will discuss the development and applications of gapmers for lncRNA loss-of-function studies and tips to design effective antisense oligonucleotides.
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23
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Diggins NL, Crawford LB, Struthers HM, Hook LM, Landais I, Skalsky RL, Hancock MH. Techniques for Characterizing Cytomegalovirus-Encoded miRNAs. Methods Mol Biol 2021; 2244:301-342. [PMID: 33555594 DOI: 10.1007/978-1-0716-1111-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
microRNAs (miRNAs) are small noncoding RNAs that regulate gene expression at the posttranscriptional level by binding to sites within the 3' untranslated regions of messenger RNA (mRNA) transcripts. The discovery of this completely new mechanism of gene regulation necessitated the development of a variety of techniques to further characterize miRNAs, their expression, and function. In this chapter, we will discuss techniques currently used in the miRNA field to detect, express and inhibit miRNAs, as well as methods used to identify and validate their targets, specifically with respect to the miRNAs encoded by human cytomegalovirus.
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Affiliation(s)
- Nicole L Diggins
- Vaccine and Gene Therapy Institute, Oregon Health and Sciences University, Beaverton, OR, USA
| | - Lindsey B Crawford
- Vaccine and Gene Therapy Institute, Oregon Health and Sciences University, Beaverton, OR, USA
| | - Hillary M Struthers
- Vaccine and Gene Therapy Institute, Oregon Health and Sciences University, Beaverton, OR, USA
| | - Lauren M Hook
- Vaccine and Gene Therapy Institute, Oregon Health and Sciences University, Beaverton, OR, USA
| | - Igor Landais
- Vaccine and Gene Therapy Institute, Oregon Health and Sciences University, Beaverton, OR, USA
| | - Rebecca L Skalsky
- Vaccine and Gene Therapy Institute, Oregon Health and Sciences University, Beaverton, OR, USA
| | - Meaghan H Hancock
- Vaccine and Gene Therapy Institute, Oregon Health and Sciences University, Beaverton, OR, USA.
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24
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Zhang W, Guan X, Tang J. The long non-coding RNA landscape in triple-negative breast cancer. Cell Prolif 2020; 54:e12966. [PMID: 33314471 PMCID: PMC7848969 DOI: 10.1111/cpr.12966] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/03/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023] Open
Abstract
Triple‐negative breast cancer (TNBC) is a type of breast cancer that has a higher risk of distant recurrence and metastasis, leading to a relatively aggressive biological behaviour and poor outcome. So far, the clinical management of TNBC is challenging because of its heterogeneity and paucity of specific targeted therapy. Recently, various studies have identified a lot of differently expressed long non‐coding RNAs (lncRNAs) in TNBC. Those lncRNAs have been reported to play important roles in the multistep process of TNBC tumorigenesis. Here, we review the biological characteristics of lncRNAs, and present the current state of knowledge concerning the expression, function and regulation of lncRNAs in TNBC. Accumulating studies explored the potential lncRNAs‐based therapeutics in TNBC, including the techniques of genetic modification using antisense oligonucleotides, locked nucleic acid and RNA nanotechnology. In current review, we also discuss the future prospects of studies about lncRNAs in TNBC and development of lncRNA‐based strategies for clinical TNBC patients.
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Affiliation(s)
- Wenwen Zhang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xiaoxiang Guan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jinhai Tang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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25
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Bach S, Demper JC, Biedenkopf N, Becker S, Hartmann RK. RNA secondary structure at the transcription start site influences EBOV transcription initiation and replication in a length- and stability-dependent manner. RNA Biol 2020; 18:523-536. [PMID: 32882148 DOI: 10.1080/15476286.2020.1818459] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Ebola virus (EBOV) RNA has the potential to form hairpin structures at the transcription start sequence (TSS) and reinitiation sites of internal genes, both on the genomic and antigenomic/mRNA level. Hairpin formation involving the TSS and the spacer sequence between promotor elements (PE) 1 and 2 was suggested to regulate viral transcription. Here, we provide evidence that such RNA structures form during RNA synthesis by the viral polymerase and affect its activity. This was analysed using monocistronic minigenomes carrying hairpin structure variants in the TSS-spacer region that differ in length and stability. Transcription and replication were measured via reporter activity and by qRT-PCR quantification of the distinct viral RNA species. We demonstrate that viral RNA synthesis is remarkably tolerant to spacer extensions of up to ~54 nt, but declines beyond this length limit (~25% residual activity for a 66-nt extension). Minor incremental stabilizations of hairpin structures in the TSS-spacer region and on the mRNA/antigenomic level were found to rapidly abolish viral polymerase activity, which may be exploited for antisense strategies to inhibit viral RNA synthesis. Finally, balanced viral transcription and replication can still occur when any RNA structure formation potential at the TSS is eliminated, provided that hexamer phasing in the promoter region is maintained. Altogether, the findings deepen and refine our insight into structure and length constraints within the EBOV transcription and replication promoter and suggest a remarkable flexibility of the viral polymerase in recognition of PE1 and PE2.
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Affiliation(s)
- Simone Bach
- Institut fuür Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Jana-Christin Demper
- Institut fuür Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Nadine Biedenkopf
- Institut fuü;r Virologie, Philipps-Universität Marburg, Marburg, Germany
| | - Stephan Becker
- Institut fuü;r Virologie, Philipps-Universität Marburg, Marburg, Germany
| | - Roland K Hartmann
- Institut fuür Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
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26
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MicroRNA-221: A Fine Tuner and Potential Biomarker of Chronic Liver Injury. Cells 2020; 9:cells9081767. [PMID: 32717951 PMCID: PMC7464779 DOI: 10.3390/cells9081767] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/10/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
The last decade has witnessed significant advancements in our understanding of how small noncoding RNAs, such as microRNAs (miRNAs), regulate disease progression. One such miRNA, miR-221, has been shown to play a key role in the progression of liver fibrosis, a common feature of most liver diseases. Many reports have demonstrated the upregulation of miR-221 in liver fibrosis caused by multiple etiologies such as viral infections and nonalcoholic steatohepatitis. Inhibition of miR-221 via different strategies has shown promising results in terms of the suppression of fibrogenic gene signatures in vitro, as well as in vivo, in independent mouse models of liver fibrosis. In addition, miR-221 has also been suggested as a noninvasive serum biomarker for liver fibrosis and cirrhosis. In this review, we discuss the biology of miR-221, its significance and use as a biomarker during progression of liver fibrosis, and finally, potential and robust approaches that can be utilized to suppress liver fibrosis via inhibition of miR-221.
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Samanta D, Ebrahimi SB, Mirkin CA. Nucleic-Acid Structures as Intracellular Probes for Live Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1901743. [PMID: 31271253 PMCID: PMC6942251 DOI: 10.1002/adma.201901743] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/08/2019] [Indexed: 05/02/2023]
Abstract
The chemical composition of cells at the molecular level determines their growth, differentiation, structure, and function. Probing this composition is powerful because it provides invaluable insight into chemical processes inside cells and in certain cases allows disease diagnosis based on molecular profiles. However, many techniques analyze fixed cells or lysates of bulk populations, in which information about dynamics and cellular heterogeneity is lost. Recently, nucleic-acid-based probes have emerged as a promising platform for the detection of a wide variety of intracellular analytes in live cells with single-cell resolution. Recent advances in this field are described and common strategies for probe design, types of targets that can be identified, current limitations, and future directions are discussed.
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Affiliation(s)
- Devleena Samanta
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Sasha B Ebrahimi
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Chad A Mirkin
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
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Li J, Sun YBY, Chen W, Fan J, Li S, Qu X, Chen Q, Chen R, Zhu D, Zhang J, Wu Z, Chi H, Crawford S, Oorschot V, Puelles VG, Kerr PG, Ren Y, Nilsson SK, Christian M, Tang H, Chen W, Bertram JF, Nikolic-Paterson DJ, Yu X. Smad4 promotes diabetic nephropathy by modulating glycolysis and OXPHOS. EMBO Rep 2020; 21:e48781. [PMID: 31916354 DOI: 10.15252/embr.201948781] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/31/2019] [Accepted: 11/18/2019] [Indexed: 02/06/2023] Open
Abstract
Diabetic nephropathy (DN) is the leading cause of end-stage kidney disease. TGF-β1/Smad3 signalling plays a major pathological role in DN; however, the contribution of Smad4 has not been examined. Smad4 depletion in the kidney using anti-Smad4 locked nucleic acid halted progressive podocyte damage and glomerulosclerosis in mouse type 2 DN, suggesting a pathogenic role of Smad4 in podocytes. Smad4 is upregulated in human and mouse podocytes during DN. Conditional Smad4 deletion in podocytes protects mice from type 2 DN, independent of obesity. Mechanistically, hyperglycaemia induces Smad4 localization to mitochondria in podocytes, resulting in reduced glycolysis and oxidative phosphorylation and increased production of reactive oxygen species. This operates, in part, via direct binding of Smad4 to the glycolytic enzyme PKM2 and reducing the active tetrameric form of PKM2. In addition, Smad4 interacts with ATPIF1, causing a reduction in ATPIF1 degradation. In conclusion, we have discovered a mitochondrial mechanism by which Smad4 causes diabetic podocyte injury.
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Affiliation(s)
- Jinhua Li
- Shunde Women and Children Hospital, Guangdong Medical University, Shunde, Guangdong, China.,The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China.,Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Vic., Australia.,Department of Physiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Vic., Australia.,Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Yu Bo Yang Sun
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Vic., Australia
| | - Weiyi Chen
- Department of Physiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Vic., Australia
| | - Jinjin Fan
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Songhui Li
- Biomedical Manufacturing Commonwealth Scientific and Industrial Research Organisation (CSIRO), Melbourne, Vic., Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Vic., Australia
| | - Xinli Qu
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Vic., Australia
| | - Qikang Chen
- Shunde Women and Children Hospital, Guangdong Medical University, Shunde, Guangdong, China
| | - Riling Chen
- Shunde Women and Children Hospital, Guangdong Medical University, Shunde, Guangdong, China
| | - Dajian Zhu
- Shunde Women and Children Hospital, Guangdong Medical University, Shunde, Guangdong, China
| | - Jinfeng Zhang
- Shunde Women and Children Hospital, Guangdong Medical University, Shunde, Guangdong, China
| | - Zhuguo Wu
- The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China
| | - Honggang Chi
- The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China
| | - Simon Crawford
- Monash Ramaciotti Cryo EM Platform, Monash Biomedicine Discovery Institute, Clayton, Vic., Australia
| | - Viola Oorschot
- Monash Ramaciotti Cryo EM Platform, Monash Biomedicine Discovery Institute, Clayton, Vic., Australia
| | - Victor G Puelles
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Vic., Australia.,III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Departments of Nephrology and Medicine, Monash Health and Monash University, Clayton, Vic., Australia
| | - Peter G Kerr
- Departments of Nephrology and Medicine, Monash Health and Monash University, Clayton, Vic., Australia
| | - Yi Ren
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, USA
| | - Susan K Nilsson
- Biomedical Manufacturing Commonwealth Scientific and Industrial Research Organisation (CSIRO), Melbourne, Vic., Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Vic., Australia
| | - Mark Christian
- School of Science and Technology, Nottingham Trent University, Clifton, Nottingham, UK
| | - Huanwen Tang
- Dongguan Key Laboratory of Environmental Medicine, Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, Guangdong, China
| | - Wei Chen
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - John F Bertram
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Vic., Australia
| | - David J Nikolic-Paterson
- Departments of Nephrology and Medicine, Monash Health and Monash University, Clayton, Vic., Australia
| | - Xueqing Yu
- Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
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Vandghanooni S, Eskandani M, Barar J, Omidi Y. Antisense LNA-loaded nanoparticles of star-shaped glucose-core PCL-PEG copolymer for enhanced inhibition of oncomiR-214 and nucleolin-mediated therapy of cisplatin-resistant ovarian cancer cells. Int J Pharm 2020; 573:118729. [PMID: 31705975 DOI: 10.1016/j.ijpharm.2019.118729] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/17/2019] [Accepted: 09/21/2019] [Indexed: 02/07/2023]
Abstract
We aimed to inhibit overexpressed oncomiR-214 in cisplatin (CIS)-resistant ovarian cancer (OC) and perform targeted therapy of sensitized cells using a novel polymeric drug delivery system (DDS). A system of nanoparticles (NPs) of star-shaped glucose-core polycaprolactone-polyethylene glycol (Glu-PCL-PEG) block copolymer containing cisplatin (CIS-PCL NPs) and locked nucleic acid (LNA) anti-miR-214 (LNA-PCL NPs) were prepared and anti-nucleolin aptamer was conjugated to the surface of prepared NPs to prepare Ap-CIS-PCL NPs and Ap-LNA-PCL NPs, respectively. The cancer-targeting ability of the NPs was confirmed and the CIS-resistant A2780 (A2780 R) cells were transfected with Ap-LNA-PCL NPs to inhibit oncomiR-214 and sensitize the cells to CIS. Next, the miR-214-inhibited cells were exposed to the Ap-CIS-NPs and the deracination efficiency of targeted DDS was evaluated. The oncomiR-214 in A2780 R cells were harnessed by Ap-LNA-PCL NPs, and nucleolin-mediated endocytosis of targeted polymeric DDSs containing CIS into miR-214-inhibited A2780 R cells caused enhanced apoptosis, which was further confirmed by apoptosis detection and evaluation of downstream genes expression. Targeted inhibition of miR-214 using the developed NPs containing LNA can decrease drug-resistant properties of cancer cells and may enhance the efficiency of targeted DDSs.
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Affiliation(s)
- Somayeh Vandghanooni
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Morteza Eskandani
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jaleh Barar
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran,; Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran,; Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
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Bagger FO, Probst V. Single Cell Sequencing in Cancer Diagnostics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:175-193. [PMID: 32949400 DOI: 10.1007/978-981-15-4494-1_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Personalized medicine has been driven by improvements in genomic sequencing and analysis. For several diseases, in particular cancers, it has for nearly a decade been standard clinical practice to analyze the genome and expression of the genes of patients. The results are reflected directly in the treatment plan for the patient, in targeted medical inventions. This specialized mode of diagnostics has been restricted to account for averaged trends in the tumor. The approach sharply contrasts our knowledge on heterogeneity within tumors. Several studies further describe how treatment against one tumor subclone in some cases merely serves to provide space and support for uncontrolled growth of more aggressive subclones. In this chapter, we describe current possibilities for implementation of single cell sequencing of malignomas in clinic, as well as discuss hands-on practical advice for single cell routine diagnostics that allows for full delineation of tumor clonality.
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Affiliation(s)
- Frederik Otzen Bagger
- Department of Genomic Medicine, Rigshospitalet, Centre of Diagnostics, Section 4113, Copenhagen, Denmark.
| | - Victoria Probst
- Department of Genomic Medicine, Rigshospitalet, Centre of Diagnostics, Section 4113, Copenhagen, Denmark
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31
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Soler-Bistué A, Zorreguieta A, Tolmasky ME. Bridged Nucleic Acids Reloaded. Molecules 2019; 24:E2297. [PMID: 31234313 PMCID: PMC6630285 DOI: 10.3390/molecules24122297] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/18/2022] Open
Abstract
Oligonucleotides are key compounds widely used for research, diagnostics, and therapeutics. The rapid increase in oligonucleotide-based applications, together with the progress in nucleic acids research, has led to the design of nucleotide analogs that, when part of these oligomers, enhance their efficiency, bioavailability, or stability. One of the most useful nucleotide analogs is the first-generation bridged nucleic acids (BNA), also known as locked nucleic acids (LNA), which were used in combination with ribonucleotides, deoxyribonucleotides, or other analogs to construct oligomers with diverse applications. However, there is still room to improve their efficiency, bioavailability, stability, and, importantly, toxicity. A second-generation BNA, BNANC (2'-O,4'-aminoethylene bridged nucleic acid), has been recently made available. Oligomers containing these analogs not only showed less toxicity when compared to LNA-containing compounds but, in some cases, also exhibited higher specificity. Although there are still few applications where BNANC-containing compounds have been researched, the promising results warrant more effort in incorporating these analogs for other applications. Furthermore, newer BNA compounds will be introduced in the near future, offering great hope to oligonucleotide-based fields of research and applications.
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Affiliation(s)
- Alfonso Soler-Bistué
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, Instituto Tecnológico de Chascomús, CONICET, Universidad Nacional de San Martín, San Martín 1650, Argentina.
| | - Angeles Zorreguieta
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires C1405BWE, Argentina.
| | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92834-6850, USA.
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32
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Cao Q, Chen X, Huang C, Pollock CA. MicroRNA as novel biomarkers and therapeutic targets in diabetic kidney disease: An update. FASEB Bioadv 2019; 1:375-388. [PMID: 32123840 PMCID: PMC6996361 DOI: 10.1096/fba.2018-00064] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 11/28/2018] [Accepted: 03/22/2019] [Indexed: 02/06/2023] Open
Abstract
Diabetic kidney disease (DKD) is a life-limiting condition characterized by progressive and irreversible loss of renal function. Currently, the estimated glomerular filtration rate (eGFR) and albuminuria are used as key markers to define DKD. However, they may not accurately indicate the degree of renal dysfunction and injury. Current therapeutic approaches for DKD, including attainment of blood pressure goals, optimal control of blood glucose and lipid levels, and the use of agents to block the renin-angiotensin-aldosterone system (RAAS) can only slow the progression of DKD. Hence, early diagnosis and innovative strategies are needed to both prevent and treat DKD. In recent years, a novel class of noncoding RNA, microRNAs (miRNAs) are reported to be involved in all biological processes, including cellular proliferation, apoptosis, and differentiation. miRNAs are small noncoding RNAs that regulate gene expression by posttranscriptional and epigenetic mechanisms. They are found to be in virtually all body fluids and used successfully as biomarkers for various diseases. Urinary miRNAs correlate with clinical and histologic parameters in DKD and differential urinary miRNA expression patterns have been reported. Kidney fibrosis is the common end stage of various CKD including DKD. Transforming growth factor-β(TGF-β) is regarded as the master regulator of kidney fibrosis, which is likely at least in part through regulating miRNA expression. miRNA are widely involved in the progression of DKD via many molecular mechanisms. In this review, the involvement of miRNA in fibrosis, inflammation, hypertrophy, autophagy, endoplasmic reticulum (ER) stress, oxidative stress, insulin resistance, and podocyte injury will be discussed, as these mechanisms are believed to offer new therapeutic targets that can be exploited to develop important treatments for DKD over the next decade.
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Affiliation(s)
- Qinghua Cao
- Renal Research LaboratoryKolling Institute of Medical Research, The University of Sydney, Royal North Shore hospitalSt Leonards, SydneyNew South WalesAustralia
| | - Xin‐Ming Chen
- Renal Research LaboratoryKolling Institute of Medical Research, The University of Sydney, Royal North Shore hospitalSt Leonards, SydneyNew South WalesAustralia
| | - Chunling Huang
- Renal Research LaboratoryKolling Institute of Medical Research, The University of Sydney, Royal North Shore hospitalSt Leonards, SydneyNew South WalesAustralia
| | - Carol A. Pollock
- Renal Research LaboratoryKolling Institute of Medical Research, The University of Sydney, Royal North Shore hospitalSt Leonards, SydneyNew South WalesAustralia
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Antisense Oligonucleotide-Based Downregulation of the G56R Pathogenic Variant Causing NR2E3-Associated Autosomal Dominant Retinitis Pigmentosa. Genes (Basel) 2019; 10:genes10050363. [PMID: 31083481 PMCID: PMC6562693 DOI: 10.3390/genes10050363] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/28/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022] Open
Abstract
The recurrent missense variant in Nuclear Receptor Subfamily 2 Group E Member 3 (NR2E3), c.166G>A, p.(Gly56Arg) or G56R, underlies 1%–2% of cases with autosomal dominant retinitis pigmentosa (adRP), a frequent, genetically heterogeneous inherited retinal disease (IRD). The mutant NR2E3 protein has a presumed dominant negative effect (DNE) by competition for dimer formation with Cone-Rod Homeobox (CRX) but with abolishment of DNA binding, acting as a repressor in trans. Both the frequency and DNE of G56R make it an interesting target for allele-specific knock-down of the mutant allele using antisense oligonucleotides (AONs), an emerging therapeutic strategy for IRD. Here, we designed gapmer AONs with or without a locked nucleic acid modification at the site of the mutation, which were analyzed for potential off-target effects. Next, we overexpressed wild type (WT) or mutant NR2E3 in RPE-1 cells, followed by AON treatment. Transcript and protein levels of WT and mutant NR2E3 were detected by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and Western blot respectively. All AONs showed a general knock-down of mutant and WT NR2E3 on RNA and protein level, showing the accessibility of the region for AON-induced knockdown. Further modifications are needed however to increase allele-specificity. In conclusion, we propose the first proof-of-concept for AON-mediated silencing of a single nucleotide variation with a dominant negative effect as a therapeutic approach for NR2E3-associated adRP.
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Whole mount in situ localization of miRNAs and target mRNA transcripts in plants. 3 Biotech 2019; 9:193. [PMID: 31065493 DOI: 10.1007/s13205-019-1704-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/03/2019] [Indexed: 12/13/2022] Open
Abstract
The functional characterization of miRNAs often involves understanding of their spatiotemporal expression, which mostly relies on reporter-based or in situ hybridization studies. The available in situ localization methods follow separate protocols for pre-hybridization, hybridization, post-hybridization, and detection steps for both miRNA and mRNA transcripts in plants. In this study, we present a single method which can be used for whole mount in situ localization of both miRNAs and mRNAs in different plant tissues. Our modified method provides enhanced sensitivity for the localization of miRNA and their target transcripts. Consequently, a less laborious, time-saving, economic and efficient method has been proposed by the modification of pre-hybridization, hybridization, post-hybridization and detection steps.
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Hillebrand F, Ostermann PN, Müller L, Degrandi D, Erkelenz S, Widera M, Pfeffer K, Schaal H. Gymnotic Delivery of LNA Mixmers Targeting Viral SREs Induces HIV-1 mRNA Degradation. Int J Mol Sci 2019; 20:ijms20051088. [PMID: 30832397 PMCID: PMC6429378 DOI: 10.3390/ijms20051088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 02/07/2023] Open
Abstract
Transcription of the HIV-1 provirus generates a viral pre-mRNA, which is alternatively spliced into more than 50 HIV-1 mRNAs encoding all viral proteins. Regulation of viral alternative splice site usage includes the presence of splicing regulatory elements (SREs) which can dramatically impact RNA expression and HIV-1 replication when mutated. Recently, we were able to show that two viral SREs, GI3-2 and ESEtat, are important players in the generation of viral vif, vpr and tat mRNAs. Furthermore, we demonstrated that masking these SREs by transfected locked nucleic acid (LNA) mixmers affect the viral splicing pattern and viral particle production. With regard to the development of future therapeutic LNA mixmer-based antiretroviral approaches, we delivered the GI3-2 and the ESEtat LNA mixmers “nakedly”, without the use of transfection reagents (gymnosis) into HIV-1 infected cells. Surprisingly, we observed that gymnotically-delivered LNA mixmers accumulated in the cytoplasm, and seemed to co-localize with GW bodies and induced degradation of mRNAs containing their LNA target sequence. The GI3-2 and the ESEtat LNA-mediated RNA degradation resulted in abrogation of viral replication in HIV-1 infected Jurkat and PM1 cells as well as in PBMCs.
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Affiliation(s)
- Frank Hillebrand
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
| | - Philipp Niklas Ostermann
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
| | - Lisa Müller
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
| | - Daniel Degrandi
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
| | - Steffen Erkelenz
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
| | - Marek Widera
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
| | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
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Kicsák M, Mándi A, Varga S, Herczeg M, Batta G, Bényei A, Borbás A, Herczegh P. Tricyclanos: conformationally constrained nucleoside analogues with a new heterotricycle obtained from a d-ribofuranose unit. Org Biomol Chem 2019; 16:393-401. [PMID: 29090729 DOI: 10.1039/c7ob02296d] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A novel type of nucleoside analogue in which the sugar part is replaced by a new tricycle, 3,7,10-trioxa-11-azatricyclo[5.3.1.05,11]undecane has been prepared by substrate-controlled asymmetric synthesis. 1,5-Dialdehydes obtained from properly protected or unprotected uridine, ribothymidine, cytidine, inosine, adenosine and guanosine by metaperiodate oxidation reacted readily with tris(hydroxymethyl)aminomethane to provide the corresponding tricyclic derivatives with three new stereogenic centers. Through a double cyclisation cascade process the tricyclic compounds were obtained in good to high yields, with very high diastereoselectivity. Formation of one stereoisomer, out of the eight possible, was observed in all cases. The absolute configuration of the new stereotriad-containing tricyclic systems was aided by conventional NMR experiments followed by chemical shift calculations using an X-ray crystal structure as reference that was in good agreement with H-H distances obtained from a new ROESY NMR method. The synthesis was compatible with silyl, trityl and dimethoxytrityl protecting groups. A new reagent mixture containing ZnCl2, Et3SiH and hexafluoroisopropanol was developed for detritylation of the acid-sensitive tricyclano nucleosides.
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Affiliation(s)
- Máté Kicsák
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary.
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Yokoi H, Kasahara Y, Obika S, Doi T, Kamada H. Development of a detection method for antisense oligonucleotides in mouse kidneys by matrix-assisted laser desorption/ionization imaging mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1984-1990. [PMID: 30152908 DOI: 10.1002/rcm.8274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Oligonucleotide therapeutics have recently gained much attention, but its pharmacokinetic evaluation methods are still not sufficient, and, in particular, more tools are needed to evaluate their tissue distribution and metabolites. We developed a matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS)-based method to evaluate the tissue distribution of oligonucleotide therapeutics. METHODS We used an antisense oligonucleotide containing locked nucleic acids (LNA-A). Various washing protocols were examined using mouse kidney homogenate sections. Next, we applied a two-step matrix preparation strategy. As a first step, 3-hydroxypicolinic acid (3-HPA) matrix containing citrate and amines was sprayed using an airbrush and subsequently 3-HPA matrix containing citrate only was sprayed using the ImagePrep. Finally, kidney sections prepared from LNA-A-dosed mice were treated with our optimized method and analyzed with MALDI-IMS. RESULTS The selected washing method made it possible to detect LNA-A with MALDI-IMS and, furthermore, our developed matrix pretreatment method enhanced signal intensity approximately two-fold. MALDI-IMS revealed that LNA-A localized in a portion presumed to be the renal cortex. We also obtained information on LNA-A metabolites, which showed the same distribution profile as LNA-A in kidneys. CONCLUSIONS This study shows that MALDI-IMS can be applied to evaluate the tissue distribution of oligonucleotide therapeutics. Our method can evaluate the tissue distribution along with metabolites and has the potential to help the development of novel oligonucleotide therapeutics.
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Affiliation(s)
- Hiroyuki Yokoi
- Otsuka Pharmaceutical Co., Ltd, Tokushima Research Institute, Tokushima, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Yuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Takefumi Doi
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Haruhiko Kamada
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
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Vandghanooni S, Eskandani M, Barar J, Omidi Y. AS1411 aptamer-decorated cisplatin-loaded poly(lactic-co-glycolic acid) nanoparticles for targeted therapy of miR-21-inhibited ovarian cancer cells. Nanomedicine (Lond) 2018; 13:2729-2758. [PMID: 30394201 DOI: 10.2217/nnm-2018-0205] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
AIM The overexpression of miRNA-21 correlates with the cisplatin (CIS) resistance in the ovarian cancers. METHODS AS1411 antinucleolin aptamer-decorated PEGylated poly(lactic-co-glycolic acid) nanoparticles containing CIS (Ap-CIS-NPs) and anti-miR-21 (Ap-anti-miR-21-NPs) were prepared, physicochemically investigated and their cancer-targeting ability was confirmed. CIS-resistant A2780 cells (A2780 R) were infected with anti-miR-21 using Ap-anti-miR-21-NPs to decrease the drug resistance and sensitize the cells to CIS. Afterward, miR-21-inhibited cells were exposed to the Ap-CIS-NPs. RESULTS Ap-anti-miR-21-NPs could infect the A2780 R cells mainly through nucleolin-mediated endocytosis and inhibit the endogenous miR-21. Targeted delivery of CIS using Ap-CIS-NPs into the miR-21-inhibited cells caused an enhanced mortality. CONCLUSION The targeted delivery of chemotherapeutics to the oncomiR-inhibited cells may find a robust application in cancer chemo/gene therapy.
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Affiliation(s)
- Somayeh Vandghanooni
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Morteza Eskandani
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jaleh Barar
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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Dash S, Balasubramaniam M, Dash C, Pandhare J. Biotin-based Pulldown Assay to Validate mRNA Targets of Cellular miRNAs. J Vis Exp 2018. [PMID: 29985341 DOI: 10.3791/57786] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNAs that post-transcriptionally regulate cellular gene expression. MiRNAs bind to the 3' untranslated region (UTR) of target mRNA to inhibit protein translation or in some instances cause mRNA degradation. The binding of the miRNA to the 3' UTR of the target mRNA is mediated by a 2-8 nucleotide seed sequence at the 5' end of miRNA. While the role of miRNAs as cellular regulatory molecules is well established, identification of the target mRNAs with functional relevance remains a challenge. Bioinformatic tools have been employed to predict sequences within the 3' UTR of mRNAs as potential targets for miRNA binding. These tools have also been utilized to determine the evolutionary conservation of such sequences among related species in an attempt to predict functional role. However, these computational methods often generate false positive results and are limited to predicting canonical interaction between miRNA and mRNA. Therefore, experimental procedures that measure direct binding of miRNA to its mRNA target are necessary to establish functional interaction. In this report, we describe a sensitive method for validating direct interaction between the cellular miRNA miR-125b and the 3' UTR of PARP-1 mRNA. We elaborate a protocol in which synthetic biotinylated-miRNA mimics were transfected into mammalian cells and the miRNA-mRNA complex in the cellular lysate was pulled down with streptavidin-coated magnetic beads. Finally, the target mRNA in the pulled-down nucleic acid complex was quantified using a qPCR-based strategy.
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Affiliation(s)
- Sabyasachi Dash
- School of Biotechnology, Kalinga Institute of Industrial Technology University; 1. Center for AIDS Health Disparities Research Department of Biochemistry and Cancer Biology, Meharry Medical College; Kalinga Institute of Industrial Technology University
| | - Muthukumar Balasubramaniam
- 1. Center for AIDS Health Disparities Research Department of Biochemistry and Cancer Biology, Meharry Medical College
| | - Chandravanu Dash
- 1. Center for AIDS Health Disparities Research Department of Biochemistry and Cancer Biology, Meharry Medical College;
| | - Jui Pandhare
- 1. Center for AIDS Health Disparities Research Department of Biochemistry and Cancer Biology, Meharry Medical College;
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Sertznig H, Hillebrand F, Erkelenz S, Schaal H, Widera M. Behind the scenes of HIV-1 replication: Alternative splicing as the dependency factor on the quiet. Virology 2018; 516:176-188. [PMID: 29407375 DOI: 10.1016/j.virol.2018.01.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 01/31/2023]
Abstract
Alternative splicing plays a key role in the HIV-1 life cycle and is essential to maintain an equilibrium of mRNAs that encode viral proteins and polyprotein-isoforms. In particular, since all early HIV-1 proteins are expressed from spliced intronless and late enzymatic and structural proteins from intron containing, i.e. splicing repressed viral mRNAs, cellular splicing factors and splicing regulatory proteins are crucial for the replication capacity. In this review, we will describe the complex network of cis-acting splicing regulatory elements (SREs), which are mainly localized in the neighbourhoods of all HIV-1 splice sites and warrant the proper ratio of individual transcript isoforms. Since SREs represent binding sites for trans-acting cellular splicing factors interacting with the cellular spliceosomal apparatus we will review the current knowledge of interactions between viral RNA and cellular proteins as well as their impact on viral replication. Finally, we will discuss potential therapeutic approaches targeting HIV-1 alternative splicing.
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Affiliation(s)
- Helene Sertznig
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Frank Hillebrand
- Institute of Virology, Heinrich Heine University, University Hospital, Düsseldorf, Germany
| | - Steffen Erkelenz
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany
| | - Heiner Schaal
- Institute of Virology, Heinrich Heine University, University Hospital, Düsseldorf, Germany
| | - Marek Widera
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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41
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Oberemok VV, Laikova KV, Repetskaya AI, Kenyo IM, Gorlov MV, Kasich IN, Krasnodubets AM, Gal'chinsky NV, Fomochkina II, Zaitsev AS, Bekirova VV, Seidosmanova EE, Dydik KI, Meshcheryakova AO, Nazarov SA, Smagliy NN, Chelengerova EL, Kulanova AA, Deri K, Subbotkin MV, Useinov RZ, Shumskykh MN, Kubyshkin AV. A Half-Century History of Applications of Antisense Oligonucleotides in Medicine, Agriculture and Forestry: We Should Continue the Journey. Molecules 2018; 23:E1302. [PMID: 29844255 PMCID: PMC6099785 DOI: 10.3390/molecules23061302] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 05/25/2018] [Accepted: 05/27/2018] [Indexed: 02/07/2023] Open
Abstract
Antisense oligonucleotides (ASO), short single-stranded polymers based on DNA or RNA chemistries and synthesized in vitro, regulate gene expression by binding in a sequence-specific manner to an RNA target. The functional activity and selectivity in the action of ASOs largely depends on the combination of nitrogenous bases in a target sequence. This simple and natural property of nucleic acids provides an attractive route by which scientists can create different ASO-based techniques. Over the last 50 years, planned and realized applications in the field of antisense and nucleic acid nanotechnologies have produced astonishing results and posed new challenges for further developments, exemplifying the essence of the post-genomic era. Today the majority of ASOs are chemically modified and/or incorporated within nanoparticles to enhance their stability and cellular uptake. This review critically analyzes some successful cases using the antisense approach in medicine to address severe diseases, such as Duchenne muscular dystrophy and spinal muscular atrophy, and suggests some prospective directions for future research. We also examine in detail the elaboration of unmodified insect-specific DNA insecticides and RNA preparations in the areas of agriculture and forestry, a relatively new branch of ASO that allows circumvention of the use of non-selective chemical insecticides. When considering the variety of successful ASO modifications with an efficient signal-to-noise ratio of action, coupled with the affordability of in vitro oligonucleotide synthesis and post-synthesis procedures, we predict that the next half-century will produce a fruitful yield of tools created from effective ASO-based end products.
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MESH Headings
- Agriculture/methods
- Animals
- Biological Control Agents/chemical synthesis
- Biological Control Agents/history
- Biological Control Agents/pharmacology
- DNA/antagonists & inhibitors
- DNA/genetics
- DNA/metabolism
- Forestry/methods
- Gene Expression Regulation/drug effects
- History, 20th Century
- History, 21st Century
- Humans
- Larva/drug effects
- Larva/genetics
- Larva/metabolism
- Moths/drug effects
- Moths/genetics
- Moths/growth & development
- Moths/metabolism
- Muscular Atrophy, Spinal/genetics
- Muscular Atrophy, Spinal/metabolism
- Muscular Atrophy, Spinal/pathology
- Muscular Atrophy, Spinal/therapy
- Muscular Dystrophy, Duchenne/genetics
- Muscular Dystrophy, Duchenne/metabolism
- Muscular Dystrophy, Duchenne/pathology
- Muscular Dystrophy, Duchenne/therapy
- Nanoparticles/administration & dosage
- Nanoparticles/chemistry
- Neuromuscular Agents/chemical synthesis
- Neuromuscular Agents/history
- Neuromuscular Agents/therapeutic use
- Oligonucleotides, Antisense/chemical synthesis
- Oligonucleotides, Antisense/genetics
- Oligonucleotides, Antisense/metabolism
- RNA, Messenger/antagonists & inhibitors
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
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Affiliation(s)
- Volodymyr V Oberemok
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Kateryna V Laikova
- Medical Academy named after S.I. Georgievsky, V.I. Vernadsky Crimean Federal University, Lenin Avenue 5/7, 295051 Simferopol, Crimea.
| | - Anna I Repetskaya
- Botanical Garden named after N.V. Bagrov, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 29500 Simferopol, Crimea.
| | - Igor M Kenyo
- Academy of Bioresources and Environmental Management of V.I. Vernadsky Crimean Federal University, 95492 Agrarnoye, Crimea.
| | - Mikhail V Gorlov
- D. Mendeleev University of Chemical Technology of Russia, Miusskaya sq. 9, 125047 Moscow, Russia.
| | - Igor N Kasich
- Rostov State Medical University, Nakhchivan Lane 29, 344022 Rostov-on-Don, Russia.
| | - Alisa M Krasnodubets
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Nikita V Gal'chinsky
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Iryna I Fomochkina
- Medical Academy named after S.I. Georgievsky, V.I. Vernadsky Crimean Federal University, Lenin Avenue 5/7, 295051 Simferopol, Crimea.
| | - Aleksei S Zaitsev
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Viktoriya V Bekirova
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Eleonora E Seidosmanova
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Ksenia I Dydik
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Anna O Meshcheryakova
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Sergey A Nazarov
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Natalya N Smagliy
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Edie L Chelengerova
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Alina A Kulanova
- Medical Academy named after S.I. Georgievsky, V.I. Vernadsky Crimean Federal University, Lenin Avenue 5/7, 295051 Simferopol, Crimea.
| | - Karim Deri
- Medical Academy named after S.I. Georgievsky, V.I. Vernadsky Crimean Federal University, Lenin Avenue 5/7, 295051 Simferopol, Crimea.
| | - Mikhail V Subbotkin
- Medical Academy named after S.I. Georgievsky, V.I. Vernadsky Crimean Federal University, Lenin Avenue 5/7, 295051 Simferopol, Crimea.
| | - Refat Z Useinov
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Maksym N Shumskykh
- Taurida Academy, V.I. Vernadsky Crimean Federal University, Vernadsky Avenue 4, 295007 Simferopol, Crimea.
| | - Anatoly V Kubyshkin
- Medical Academy named after S.I. Georgievsky, V.I. Vernadsky Crimean Federal University, Lenin Avenue 5/7, 295051 Simferopol, Crimea.
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42
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Najem D, Rennie K, Ribecco-Lutkiewicz M, Ly D, Haukenfrers J, Liu Q, Nzau M, Fraser DD, Bani-Yaghoub M. Traumatic brain injury: classification, models, and markers. Biochem Cell Biol 2018; 96:391-406. [PMID: 29370536 DOI: 10.1139/bcb-2016-0160] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Traumatic brain injury (TBI) is a leading cause of morbidity and mortality worldwide. Due to its high incidence rate and often long-term sequelae, TBI contributes significantly to increasing costs of health care expenditures annually. Unfortunately, advances in the field have been stifled by patient and injury heterogeneity that pose a major challenge in TBI prevention, diagnosis, and treatment. In this review, we briefly discuss the causes of TBI, followed by its prevalence, classification, and pathophysiology. The current imaging detection methods and animal models used to study brain injury are examined. We discuss the potential use of molecular markers in detecting and monitoring the progression of TBI, with particular emphasis on microRNAs as a novel class of molecular modulators of injury and its repair in the neural tissue.
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Affiliation(s)
- Dema Najem
- a Department of Translational Bioscience, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
| | - Kerry Rennie
- a Department of Translational Bioscience, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
| | - Maria Ribecco-Lutkiewicz
- a Department of Translational Bioscience, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
| | - Dao Ly
- a Department of Translational Bioscience, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
| | - Julie Haukenfrers
- a Department of Translational Bioscience, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
| | - Qing Liu
- a Department of Translational Bioscience, National Research Council Canada, Ottawa, ON K1A 0R6, Canada.,b Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Munyao Nzau
- c Paediatric Neurosurgery, Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | - Douglas D Fraser
- d Children's Health Research Institute, London, ON N6C 2V5, Canada.,e Departments of Pediatrics and Clinical Neurological Sciences, Western University, London, ON N6A 3K7, Canada
| | - Mahmud Bani-Yaghoub
- a Department of Translational Bioscience, National Research Council Canada, Ottawa, ON K1A 0R6, Canada.,f Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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43
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Fernández Fernández E, Santos-Carballal B, de Santi C, Ramsey JM, MacLoughlin R, Cryan SA, Greene CM. Biopolymer-Based Nanoparticles for Cystic Fibrosis Lung Gene Therapy Studies. MATERIALS 2018; 11:ma11010122. [PMID: 29342838 PMCID: PMC5793620 DOI: 10.3390/ma11010122] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/04/2018] [Accepted: 01/08/2018] [Indexed: 12/14/2022]
Abstract
Lung gene therapy for cystic fibrosis disease has not been successful due to several challenges such as the absence of an appropriate vector. Therefore, optimal delivery of emerging therapeutics to airway epithelial cells demands suitable non-viral systems. In this work, we describe the formulation and the physicochemical investigation of biocompatible and biodegradable polymeric nanoparticles (NPs), including PLGA and chitosan (animal and non-animal), as novel methods for the safe and efficient delivery of CFTR-specific locked nucleic acids (LNAs).
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Affiliation(s)
- Elena Fernández Fernández
- Lung Biology Group, Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin 9, Ireland.
| | | | - Chiara de Santi
- Lung Biology Group, Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin 9, Ireland.
| | - Joanne M Ramsey
- School of Pharmacy, Royal College of Surgeons in Ireland, Dublin 2, Ireland.
| | - Ronan MacLoughlin
- School of Pharmacy, Royal College of Surgeons in Ireland, Dublin 2, Ireland.
- School of Pharmacy and Pharmaceutical Sciences, Trinity College, Dublin 2, Ireland.
- Aerogen Ltd., Galway Business Park, Dangan, Galway H91 HE94, Ireland.
| | - Sally-Ann Cryan
- School of Pharmacy, Royal College of Surgeons in Ireland, Dublin 2, Ireland.
| | - Catherine M Greene
- Lung Biology Group, Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin 9, Ireland.
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44
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Abstract
With the advent of next-generation sequencing (NGS) and the demand for a personalized healthcare system, the fields of precision medicine and gene therapy are advancing in new directions. There is a push to identify genes that contribute to disease development, either alone or in conjunction with other genes or environmental factors, and then design targeted therapies based on this knowledge, rather than the traditional approach of treating generalized symptoms with pharmaceuticals in a one-size-fits-all manner. Identification of genes that contribute to disease pathogenesis and progression is critical for the maturation of the precision medicine field. Concomitant with a better understanding of disease pathology, precision medicine approaches can be adopted with greater confidence and are expected to lead to a new standard for clinical practice. In this chapter, we provide a brief introduction to precision medicine, discuss the importance of identifying genes and genetic variants that contribute to disease development and progression, offer examples of approaches that can be applied to treat specific diseases, and present some of the current challenges and limitations of precision medicine.
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Affiliation(s)
- Taylor M Benson
- Department of Biomedical Research, Center for Genes, Environment, and Health, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, USA
| | - Fatjon Leti
- Department of Biomedical Research, Center for Genes, Environment, and Health, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, USA
| | - Johanna K DiStefano
- Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, 85004, USA.
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45
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Bohr HG, Shim I, Stein C, Ørum H, Hansen HF, Koch T. Electronic Structures of LNA Phosphorothioate Oligonucleotides. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 8:428-441. [PMID: 28918042 PMCID: PMC5537454 DOI: 10.1016/j.omtn.2017.05.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 05/29/2017] [Accepted: 05/29/2017] [Indexed: 01/08/2023]
Abstract
Important oligonucleotides in anti-sense research have been investigated in silico and experimentally. This involves quantum mechanical (QM) calculations and chromatography experiments on locked nucleic acid (LNA) phosphorothioate (PS) oligonucleotides. iso-potential electrostatic surfaces are essential in this study and have been calculated from the wave functions derived from the QM calculations that provide binding information and other properties of these molecules. The QM calculations give details of the electronic structures in terms of e.g., energy and bonding, which make them distinguish or differentiate between the individual PS diastereoisomers determined by the position of sulfur atoms. Rules are derived from the electronic calculations of these molecules and include the effects of the phosphorothioate chirality and formation of electrostatic potential surfaces. Physical and electrochemical descriptors of the PS oligonucleotides are compared to the experiments in which chiral states on these molecules can be distinguished. The calculations demonstrate that electronic structure, electrostatic potential, and topology are highly sensitive to single PS configuration changes and can give a lead to understanding the activity of the molecules.
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Affiliation(s)
- Henrik G Bohr
- Department of Chemistry, B-206-DTU, The Technical University of Denmark, 2800 Lyngby, Denmark.
| | - Irene Shim
- Department of Chemistry, B-206-DTU, The Technical University of Denmark, 2800 Lyngby, Denmark
| | - Cy Stein
- Department of Medical Oncology and Experimental Therapeutics and Molecular and Cellular Biology, City of Hope Medical Center, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Henrik Ørum
- Anemonevej 4, Hareskov, 3500 Værløse, Denmark
| | - Henrik F Hansen
- Roche Innovation Center Copenhagen, Fremtidsvej 3, 2970, Denmark
| | - Troels Koch
- Roche Innovation Center Copenhagen, Fremtidsvej 3, 2970, Denmark
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46
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Icli B, Feinberg MW. MicroRNAs in dysfunctional adipose tissue: cardiovascular implications. Cardiovasc Res 2017; 113:1024-1034. [PMID: 28505257 PMCID: PMC5852642 DOI: 10.1093/cvr/cvx098] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/20/2017] [Accepted: 05/12/2017] [Indexed: 12/16/2022] Open
Abstract
In this review, we focus on the emerging role of microRNAs, non-coding RNAs that regulate gene expression and signaling pathways, in dysfunctional adipose tissue. We highlight current paradigms of microRNAs involved in adipose differentiation and function in depots such as white, brown, and beige adipose tissues and potential implications of microRNA dysregulation in human disease such as obesity, inflammation, microvasculature dysfunction, and related cardiovascular diseases. We highlight accumulating studies indicating that adipocyte-derived microRNAs may not only serve as biomarkers of cardiometabolic disease, but also may directly regulate gene expression of other tissues. Finally, we discuss the future prospects, challenges, and emerging strategies for microRNA delivery and targeting for therapeutic applications in cardiovascular disease states associated with adipocyte dysfunction.
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Affiliation(s)
- Basak Icli
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, NRB-742F, Boston, MA 02115, USA
| | - Mark W. Feinberg
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, NRB-742F, Boston, MA 02115, USA
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47
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Evich M, Spring-Connell AM, Germann MW. Impact of modified ribose sugars on nucleic acid conformation and function. HETEROCYCL COMMUN 2017. [DOI: 10.1515/hc-2017-0056] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
AbstractThe modification of the ribofuranose in nucleic acids is a widespread method of manipulating the activity of nucleic acids. These alterations, however, impact the local conformation and chemical reactivity of the sugar. Changes in the conformation and dynamics of the sugar moiety alter the local and potentially global structure and plasticity of nucleic acids, which in turn contributes to recognition, binding of ligands and enzymatic activity of proteins. This review article introduces the conformational properties of the (deoxy)ribofuranose ring and then explores sugar modifications and how they impact local and global structure and dynamics in nucleic acids.
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Affiliation(s)
- Marina Evich
- Georgia State University, Department of Chemistry, 50 Decatur St. SE, Atlanta, GA 30303, USA
| | | | - Markus W. Germann
- Georgia State University, Department of Chemistry, 50 Decatur St. SE, Atlanta, GA 30303, USA
- Georgia State University, Department of Biology, P.O. 4010, Atlanta, GA 30303, USA
- Georgia State University, Neuroscience Institute, P.O. 5030, Atlanta, GA 30303, USA
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48
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Srishylam P, Raji Reddy A, Banerjee S, Penta S, Sanghvi YS. DDQ mediated regiospecific protection of primary alcohol and deprotection under neutral conditions: Application of new p -methoxy benzyl-pixyl ether as reagent of choice for nucleoside protection. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.05.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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49
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Kumar R, Ries A, Wengel J. Synthesis and Excellent Duplex Stability of Oligonucleotides Containing 2'-Amino-LNA Functionalized with Galactose Units. Molecules 2017; 22:molecules22050852. [PMID: 28531137 PMCID: PMC6153924 DOI: 10.3390/molecules22050852] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 05/17/2017] [Accepted: 05/17/2017] [Indexed: 02/07/2023] Open
Abstract
A convenient method for the preparation of oligonucleotides containing internally-attached galactose and triantennary galactose units has been developed based on click chemistry between 2′-N-alkyne 2′-amino-LNA nucleosides and azido-functionalized galactosyl building blocks. The synthesized oligonucleotides show excellent binding affinity and selectivity towards complementary DNA/RNA strands with an increase in the melting temperature of up to +23.5 °C for triply-modified variants.
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Affiliation(s)
- Rajesh Kumar
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
- Department of Chemistry, University of Delhi, Delhi 110007, India.
| | - Annika Ries
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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50
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Friese OV, Sperry JB, He Y, Joseph L, Carroll JA, Rouse JC. Characterization of Apolipoprotein C3 (Apo C3) LNA/DNA Impurities and Degradation Products by LC-MS/MS. AAPS JOURNAL 2017; 19:1735-1744. [PMID: 28488174 DOI: 10.1208/s12248-017-0088-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/07/2017] [Indexed: 01/22/2023]
Abstract
Apolipoprotein C3 (Apo C3) LNA/DNA gapmer was evaluated under various stress and formulation conditions for the purpose of its development as a potential biotherapeutic for low density lipoprotein (LDL) lowering. Using ion-pairing (IP) reversed-phase (RP) liquid chromatography ultra-high resolution (UHR) tandem mass spectrometry (IP-RPLC-MS/MS), a combination of accurate mass measurements and collision-induced dissociation enabled in-depth characterization of Apo C3 LNA/DNA oligonucleotide, in particular the inherent impurities following synthesis and degradation products after exposure to stress conditions. In this study, oligonucleotide samples were stressed under different pH and UV exposure conditions. The primary impurities in Apo C3 LNA/DNA were losses of nucleotide moieties from both the 5'- and 3'-terminus leading to n-1, n-2, etc. species. Desulfurization and depurination were observed in Apo C3 LNA/DNA after a week under UV light stress conditions at low pH. Guanine oxidation and dimerization were the primary degradation products detected under UV light exposure for 1 week at high pH. The effect of antioxidants on the levels of these degradation products was evaluated under neutral pH conditions. In the presence of all antioxidants, levels of guanine oxidation and desulfurization under tested conditions were the same as those in the unstressed sample, except for sodium ascorbate. The thorough understanding of the Apo C3 LNA/DNA oligonucleotide structure, its impurities, and degradation products laid the foundation for the successful formulation development of this novel biotherapeutic modality.
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Affiliation(s)
- Olga V Friese
- Biotherapeutics Pharmaceutical Sciences, Pfizer WRD, St. Louis, Missouri, USA.
| | - Justin B Sperry
- Biotherapeutics Pharmaceutical Sciences, Pfizer WRD, St. Louis, Missouri, USA
| | - Yan He
- Biotherapeutics Pharmaceutical Sciences, Pfizer WRD, St. Louis, Missouri, USA
| | - Liji Joseph
- Biotherapeutics Pharmaceutical Sciences, Pfizer WRD, St. Louis, Missouri, USA
| | - James A Carroll
- Biotherapeutics Pharmaceutical Sciences, Pfizer WRD, St. Louis, Missouri, USA
| | - Jason C Rouse
- Biotherapeutics Pharmaceutical Sciences, Pfizer WRD, Andover, Massachusetts, USA
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