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Yi SA, Pongkulapa T, Nevins S, Goldston LL, Chen M, Lee KB. Developing MiR-133a Zipper Nanoparticles for Targeted Enhancement of Thermogenic Adipocyte Generation. Adv Healthc Mater 2024:e2400654. [PMID: 38795000 DOI: 10.1002/adhm.202400654] [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: 02/20/2024] [Revised: 05/17/2024] [Indexed: 05/27/2024]
Abstract
Existing delivery methods for RNAi therapeutics encounter challenges, including stability, specificity, and off-target effects, which restrict their clinical effectiveness. In this study, a novel miR-133a zipper nanoparticle (NP) system that integrates miRNA zipper technology with rolling circle transcription (RCT) to achieve targeted delivery and specific regulation of miR-133a in adipocytes, is presented. This innovative approach can greatly enhance the delivery and release of miR-133a zippers, increasing the expression of thermogenic genes and mitochondrial biogenesis. he miR-133a zipper NP is utilized for the delivery of miRNA zipper-blocking miR-133a, an endogenous inhibitor of Prdm16 expression, to enhance the thermogenic activity of adipocytes by modulating their transcriptional program. Inhibition of miR-133a through the miR-133a zipper NP leads to more significant upregulation of thermogenic gene expression (Prdm16 and Ucp1) than with the free miR-133a zipper strand. Furthermore, miR-133a zipper NPs increase the number of mitochondria and induce heat production, reducing the size of 3D adipose spheroids. In short, this study emphasizes the role of RNA NPs in improving RNAi stability and specificity and paves the way for broader applications in gene therapy. Moreover, this research represents a significant advancement in RNAi-based treatments, pointing toward a promising direction for future therapeutic strategies.
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Affiliation(s)
- Sang Ah Yi
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Thanapat Pongkulapa
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Sarah Nevins
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Li Ling Goldston
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Meizi Chen
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
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2
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Gonzalez-Candia A, Figueroa EG, Krause BJ. Pharmacological and molecular mechanisms of miRNA-based therapies for targeting cardiovascular dysfunction. Biochem Pharmacol 2024:116318. [PMID: 38801924 DOI: 10.1016/j.bcp.2024.116318] [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: 04/09/2024] [Revised: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
Advances in understanding gene expression regulation through epigenetic mechanisms have contributed to elucidating the regulatory mechanisms of noncoding RNAs as pharmacological targets in several diseases. MicroRNAs (miRs) are a class of evolutionarily conserved, short, noncoding RNAs regulating in a concerted manner gene expression at the post-transcriptional level by targeting specific sequences of the 3'-untranslated region of mRNA. Conversely, mechanisms of cardiovascular disease (CVD) remain largely elusive due to their life-course origins, multifactorial pathophysiology, and co-morbidities. In this regard, CVD treatment with conventional medications results in therapeutic failure due to progressive resistance to monotherapy, which overlooks the multiple factors involved, and reduced adherence to poly-pharmacology approaches. Consequently, considering its role in regulating complete gene pathways, miR-based drugs have appreciably progressed into preclinical and clinical testing. This review summarizes the current knowledge about the mechanisms of miRs in cardiovascular disease, focusing specifically on describing how clinical chemistry and physics have improved the stability of the miR molecule. In addition, a comprehensive review of the main miRs involved in cardiovascular disease and the clinical trials in which these molecules are used as active pharmacological molecules is provided.
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Affiliation(s)
- Alejandro Gonzalez-Candia
- Laboratory of Fetal Neuroprogramming (www.neurofetal-lab.cl), Institute of Health Sciences, Universidad de O'Higgins, Rancagua, Chile
| | - Esteban G Figueroa
- Laboratory of Fetal Neuroprogramming (www.neurofetal-lab.cl), Institute of Health Sciences, Universidad de O'Higgins, Rancagua, Chile
| | - Bernardo J Krause
- Institute of Health Sciences, Universidad de O'Higgins, Rancagua, Chile.
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3
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Brown SD, Klimi E, Bakker WAM, Beqqali A, Baker AH. Non-coding RNAs to treat vascular smooth muscle cell dysfunction. Br J Pharmacol 2024. [PMID: 38773733 DOI: 10.1111/bph.16409] [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: 11/17/2023] [Revised: 02/19/2024] [Accepted: 03/14/2024] [Indexed: 05/24/2024] Open
Abstract
Vascular smooth muscle cell (vSMC) dysfunction is a critical contributor to cardiovascular diseases, including atherosclerosis, restenosis and vein graft failure. Recent advances have unveiled a fascinating range of non-coding RNAs (ncRNAs) that play a pivotal role in regulating vSMC function. This review aims to provide an in-depth analysis of the mechanisms underlying vSMC dysfunction and the therapeutic potential of various ncRNAs in mitigating this dysfunction, either preventing or reversing it. We explore the intricate interplay of microRNAs, long-non-coding RNAs and circular RNAs, shedding light on their roles in regulating key signalling pathways associated with vSMC dysfunction. We also discuss the prospects and challenges associated with developing ncRNA-based therapies for this prevalent type of cardiovascular pathology.
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Affiliation(s)
- Simon D Brown
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Eftychia Klimi
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | | | - Abdelaziz Beqqali
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew H Baker
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, Maastricht, The Netherlands
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Emami Nejad A, Mostafavi Zadeh SM, Nickho H, Sadoogh Abbasian A, Forouzan A, Ahmadlou M, Nedaeinia R, Shaverdi S, Manian M. The role of microRNAs involved in the disorder of blood-brain barrier in the pathogenesis of multiple sclerosis. Front Immunol 2023; 14:1281567. [PMID: 38193092 PMCID: PMC10773759 DOI: 10.3389/fimmu.2023.1281567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/30/2023] [Indexed: 01/10/2024] Open
Abstract
miRNAs are involved in various vital processes, including cell growth, development, apoptosis, cellular differentiation, and pathological cellular activities. Circulating miRNAs can be detected in various body fluids including serum, plasma, saliva, and urine. It is worth mentioning that miRNAs remain stable in the circulation in biological fluids and are released from membrane-bound vesicles called exosomes, which protect them from RNase activity. It has been shown that miRNAs regulate blood-brain barrier integrity by targeting both tight junction and adherens junction molecules and can also influence the expression of inflammatory cytokines. Some recent studies have examined the impact of certain commonly used drugs in Multiple Sclerosis on miRNA levels. In this review, we will focus on the recent findings on the role of miRNAs in multiple sclerosis, including their role in the cause of MS and molecular mechanisms of the disease, utilizing miRNAs as diagnostic and clinical biomarkers, using miRNAs as a therapeutic modality or target for Multiple Sclerosis and drug responses in patients, elucidating their importance as prognosticators of disease progression, and highlighting their potential as a future treatment for MS.
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Affiliation(s)
| | - Seyed Mostafa Mostafavi Zadeh
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Nickho
- Department of Immunology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Sadoogh Abbasian
- Department of Internal Medicine, School of Medicine, Amiralmomenin Hospital, Arak University of Medical Sciences, Arak, Iran
| | - Azim Forouzan
- Department of Internal Medicine, School of Medicine, Amiralmomenin Hospital, Arak University of Medical Sciences, Arak, Iran
| | - Mojtaba Ahmadlou
- Department of Biostatistics, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Reza Nedaeinia
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Saham Shaverdi
- Department of Biology, Payame Noor University (PNU), Tehran, Iran
| | - Mostafa Manian
- Department of Medical Laboratory Science, Faculty of Medicine, Islamic Azad University, Kermanshah, Iran
- Neurosciences Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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5
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Alves-Vale C, Capela AM, Tavares-Marcos C, Domingues-Silva B, Pereira B, Santos F, Gomes CP, Espadas G, Vitorino R, Sabidó E, Borralho P, Nóbrega-Pereira S, Bernardes de Jesus B. Expression of NORAD correlates with breast cancer aggressiveness and protects breast cancer cells from chemotherapy. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:910-924. [PMID: 37680988 PMCID: PMC10480464 DOI: 10.1016/j.omtn.2023.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/16/2023] [Indexed: 09/09/2023]
Abstract
The recently discovered human lncRNA NORAD is induced after DNA damage in a p53-dependent manner. It plays a critical role in the maintenance of genomic stability through interaction with Pumilio proteins, limiting the repression of their target mRNAs. Therefore, NORAD inactivation causes chromosomal instability and aneuploidy, which contributes to the accumulation of genetic abnormalities and tumorigenesis. NORAD has been detected in several types of cancer, including breast cancer, which is the most frequently diagnosed and the second-leading cause of cancer death in women. In the present study, we confirmed upregulated NORAD expression levels in a set of human epithelial breast cancer cell lines (MDA-MB-231, MDA-MB-436, and MDA-MB-468), which belong to the most aggressive subtypes (triple-negative breast cancer). These results are in line with previous data showing that high NORAD expression levels in basal-like tumors were associated with poor prognosis. Here, we demonstrate that NORAD downregulation sensitizes triple-negative breast cancer cells to chemotherapy, through a potential accumulation of genomic aberrations and an impaired capacity to signal DNA damage. These results show that NORAD may represent an unexploited neoadjuvant therapeutic target for chemotherapy-unresponsive breast cancer.
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Affiliation(s)
- Catarina Alves-Vale
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Hospital CUF Descobertas, CUF Oncologia, 1998-018 Lisbon, Portugal
| | - Ana Maria Capela
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carlota Tavares-Marcos
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Beatriz Domingues-Silva
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Bruno Pereira
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP – Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Francisco Santos
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carla Pereira Gomes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Guadalupe Espadas
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Rui Vitorino
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Eduard Sabidó
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Paula Borralho
- Hospital CUF Descobertas, CUF Oncologia, 1998-018 Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Sandrina Nóbrega-Pereira
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Bruno Bernardes de Jesus
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
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Herrera BS, Henz SL, Dua S, Martin L, Teles RP, Patel M, Teles FRF. Pursuing new periodontal pathogens with an improved RNA-oligonucleotide quantification technique (ROQT). Arch Oral Biol 2023; 152:105721. [PMID: 37196563 DOI: 10.1016/j.archoralbio.2023.105721] [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: 03/02/2023] [Revised: 04/22/2023] [Accepted: 05/09/2023] [Indexed: 05/19/2023]
Abstract
OBJECTIVE The aim of this study was to optimize the sensitivity, specificity and cost-effectiveness of the RNA-Oligonucleotide Quantification Technique (ROQT) in order to identify periodontal pathogens that remain unrecognized or uncultured in the oral microbiome. DESIGN Total nucleic acids (TNA) were extracted from subgingival biofilm samples using an automated process. RNA, DNA and Locked Nucleic Acid (LNA) digoxigenin-labeled oligonucleotide probes targeting 5 cultivated/named species and 16 uncultivated or unnamed bacterial taxa were synthesized. Probe specificity was determined by targeting 96 oral bacterial species; sensitivity was assessed using serial dilutions of reference bacterial strains. Different stringency temperatures were compared and new standards were tested. The tested conditions were evaluated analyzing samples from periodontally healthy individuals, and patients with moderate or severe periodontitis. RESULTS The automated extraction method at 63⁰C along with LNA-oligunucleotides probes, and use of reverse RNA sequences for standards yielded stronger signals without cross-reactions. In the pilot clinical study, the most commonly detected uncultivated/unrecognized species were Selenomonas sp. HMT 134, Prevotella sp. HMT 306, Desulfobulbus sp. HMT 041, Synergistetes sp. HMT 360 and Bacteroidetes HMT 274. In the cultivated segment of the microbiota, the most abundant taxa were T. forsythia HMT 613 and Fretibacterium fastidiosum (formerly Synergistetes) HMT 363. CONCLUSIONS In general, samples from severe patients had the greatest levels of organisms. Classic (T. forsythia, P. gingivalis) and newly proposed (F. alocis and Desulfobulbus sp. HMT 041) pathogens were present in greater amounts in samples from severe periodontitis sites, followed by moderate periodontitis sites.
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Affiliation(s)
- Bruno S Herrera
- Department of Periodontology, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sandra L Henz
- Department of Periodontology, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Preventive and Social Dentistry, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Shawn Dua
- Department of Periodontology, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lynn Martin
- Department of Basic and Translational Sciences, University of Pennsylvania, School of Dental Medicine, Philadelphia, PA, USA
| | - Ricardo P Teles
- Department of Periodontics, University of Pennsylvania, School of Dental Medicine, Philadelphia, PA, USA
| | - Michele Patel
- Department of Applied Oral Sciences, The Forsyth Institute, Cambridge, MA, USA.
| | - Flavia R F Teles
- Department of Basic and Translational Sciences, University of Pennsylvania, School of Dental Medicine, Philadelphia, PA, USA
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7
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Anwar S, Mir F, Yokota T. Enhancing the Effectiveness of Oligonucleotide Therapeutics Using Cell-Penetrating Peptide Conjugation, Chemical Modification, and Carrier-Based Delivery Strategies. Pharmaceutics 2023; 15:pharmaceutics15041130. [PMID: 37111616 PMCID: PMC10140998 DOI: 10.3390/pharmaceutics15041130] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
Oligonucleotide-based therapies are a promising approach for treating a wide range of hard-to-treat diseases, particularly genetic and rare diseases. These therapies involve the use of short synthetic sequences of DNA or RNA that can modulate gene expression or inhibit proteins through various mechanisms. Despite the potential of these therapies, a significant barrier to their widespread use is the difficulty in ensuring their uptake by target cells/tissues. Strategies to overcome this challenge include cell-penetrating peptide conjugation, chemical modification, nanoparticle formulation, and the use of endogenous vesicles, spherical nucleic acids, and smart material-based delivery vehicles. This article provides an overview of these strategies and their potential for the efficient delivery of oligonucleotide drugs, as well as the safety and toxicity considerations, regulatory requirements, and challenges in translating these therapies from the laboratory to the clinic.
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Affiliation(s)
- Saeed Anwar
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Farin Mir
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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8
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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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Schmitz U. Overview of Computational and Experimental Methods to Identify Tissue-Specific MicroRNA Targets. Methods Mol Biol 2023; 2630:155-177. [PMID: 36689183 DOI: 10.1007/978-1-0716-2982-6_12] [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: 01/24/2023]
Abstract
As ubiquitous posttranscriptional regulators of gene expression, microRNAs (miRNAs) play key roles in cell physiology and function across taxa. In the last two decades, we have gained a good understanding about miRNA biogenesis pathways, modes of action, and consequences of miRNA-mediated gene regulation. More recently, research has focused on exploring causes for miRNA dysregulation, miRNA-mediated crosstalk between genes and signaling pathways, and the role of miRNAs in disease.This chapter discusses methods for the identification of miRNA-target interactions and causes for tissue-specific miRNA-target regulation. Computational approaches for predicting miRNA target sites and assessing tissue-specific target regulation are discussed. Moreover, there is an emphasis on features that affect miRNA target recognition and how high-throughput sequencing protocols can help in assessing miRNA-mediated gene regulation on a genome-wide scale. In addition, this chapter introduces some experimental approaches for the validation of miRNA targets as well as web-based resources sharing predicted and validated miRNA-target interactions.
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Affiliation(s)
- Ulf Schmitz
- Department of Molecular & Cell Biology, College of Public Health, Medical & Vet Sciences, James Cook University, Douglas, Australia.
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia.
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Abstract
The highly specific induction of RNA interference-mediated gene knockdown, based on the direct application of small interfering RNAs (siRNAs), opens novel avenues towards innovative therapies. Two decades after the discovery of the RNA interference mechanism, the first siRNA drugs received approval for clinical use by the US Food and Drug Administration and the European Medicines Agency between 2018 and 2022. These are mainly based on an siRNA conjugation with a targeting moiety for liver hepatocytes, N-acetylgalactosamine, and cover the treatment of acute hepatic porphyria, transthyretin-mediated amyloidosis, hypercholesterolemia, and primary hyperoxaluria type 1. Still, the development of siRNA therapeutics faces several challenges and issues, including the definition of optimal siRNAs in terms of target, sequence, and chemical modifications, siRNA delivery to its intended site of action, and the absence of unspecific off-target effects. Further siRNA drugs are in clinical studies, based on different delivery systems and covering a wide range of different pathologies including metabolic diseases, hematology, infectious diseases, oncology, ocular diseases, and others. This article reviews the knowledge on siRNA design and chemical modification, as well as issues related to siRNA delivery that may be addressed using different delivery systems. Details on the mode of action and clinical status of the various siRNA therapeutics are provided, before giving an outlook on issues regarding the future of siRNA drugs and on their potential as one emerging standard modality in pharmacotherapy. Notably, this may also cover otherwise un-druggable diseases, the definition of non-coding RNAs as targets, and novel concepts of personalized and combination treatment regimens.
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Affiliation(s)
- Maik Friedrich
- Faculty of Leipzig, Institute of Clinical Immunology, Max-Bürger-Forschungszentrum (MBFZ), University of Leipzig, Leipzig, Germany.,Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Achim Aigner
- Rudolf-Boehm Institute for Pharmacology and Toxicology, Clinical Pharmacology, University of Leipzig, Haertelstrasse 16-18, 04107, Leipzig, Germany.
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11
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El-Desoky AM, Ali YBM, Talaat RM. Cytotoxic effect of combining two antisense oligonucleotides against telomerase rna component (hTR and mRNA of centromere protein B (CENP-B) in hepatocellular carcinoma cells. AN ACAD BRAS CIENC 2022; 94:e20200573. [PMID: 35894385 DOI: 10.1590/0001-3765202120200573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/03/2020] [Indexed: 11/22/2022] Open
Abstract
Telomerase is a ribonucleoprotein enzyme that plays a crucial role in maintaining the malignancy and is responsible for cellular immortality and tumorigenesis. On another hand, Centromere protein B (CENP-B) plays an important role in cell cycle regulation and helping in the high rate proliferation of cancer cells. Our study is designed to evaluate the effect of using combined antisense oligonucleotides (ASOs) targeting (hTR) and mRNA of CENP-B on liver cancer cells. Compared with a single treatment, combination treatment with Locked Nucleic Acid (LNA) ASO (hTR) and (CENP-B) (6.25 nM from each) exhibit the maximum synergistic cytotoxic effect. hTR and CENP-B mRNA was abrogated while hTERT expression was disappeared. Caspase-3, Bax, and Bcl-2 were not detected, indicating caspase-independent cell death. A significant reduction in [Tumor necrosis factor (TNF-α) and Transforming growth factor (TGF-β)] coincides with elevation in Nitric oxide (NO) secretions was observed. Taken together; our data suggest that combination treatment with LNA ASO (hTR) and (CENP-B) could provide a promising strategy for cancer treatment by controlling many pathways concurrently. This might open a new prospective application of antisense in cancer therapy.
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Affiliation(s)
- Ahmed M El-Desoky
- University of Sadat City (USC), Genetic Engineering and Biotechnology Research Institute (GEBRI), Department of Molecular Biology, PO Box 79 / 22857 Sadat City, Egypt
| | - Yasser B M Ali
- University of Sadat City (USC), Genetic Engineering and Biotechnology Research Institute (GEBRI), Department of Molecular Biology, PO Box 79 / 22857 Sadat City, Egypt
| | - Roba M Talaat
- University of Sadat City (USC), Genetic Engineering and Biotechnology Research Institute (GEBRI), Department of Molecular Biology, PO Box 79 / 22857 Sadat City, Egypt
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12
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Yang K, Schuder DN, Ngor AK, Chaput JC. REVEALR-Based Genotyping of SARS-CoV-2 Variants of Concern in Clinical Samples. J Am Chem Soc 2022; 144:11685-11692. [PMID: 35729726 PMCID: PMC9236216 DOI: 10.1021/jacs.2c03420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Indexed: 11/29/2022]
Abstract
The SARS-CoV-2 virus has evolved into new strains that increase viral transmissibility and reduce vaccine protection. The rapid circulation of these more harmful strains across the globe has created a pressing need for alternative public health screening tools. REVEALR (RNA-encoded viral nucleic acid analytic reporter), a rapid and highly sensitive DNAzyme-based detection system, functions with perfect accuracy against patient-derived clinical samples. Here, we design REVEALR into a novel genotyping assay that detects single-base mismatches corresponding to each of the major SARS-CoV-2 strains found in the United States. Of 34 sequence-verified patient samples collected in early, mid, and late 2021 at the UCI Medical Center in Orange, California, REVEALR identified the correct variant [Wuhan-Hu-1, alpha (B.1.1.7), gamma (P.1), epsilon (B.1.427/9), delta (B.1.617.2), and omicron (B.1.1.529)] with 100% accuracy. The assay, which is programmable and amenable to multiplexing, offers an important new approach to personalized diagnostics.
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Affiliation(s)
- Kefan Yang
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697-3958, United States
| | - Daniel N. Schuder
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3958, United States
| | - Arlene K. Ngor
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, United States
| | - John C. Chaput
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, United States
- Department of Chemistry, University of California, Irvine, CA 92697-3958, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3958, United States
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697-3958, United States
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13
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Ahamad S, Mathew S, Khan WA, Mohanan K. Development of small-molecule PCSK9 inhibitors for the treatment of hypercholesterolemia. Drug Discov Today 2022; 27:1332-1349. [PMID: 35121175 DOI: 10.1016/j.drudis.2022.01.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/28/2021] [Accepted: 01/26/2022] [Indexed: 12/23/2022]
Abstract
When secreted into the circulation, proprotein convertase subtilisin kexin type 9 (PCSK9) blocks the low-density lipoprotein receptors (LDL-R) and, as a consequence, low-density lipoprotein cholesterol (LDL-C) levels increase. Therefore, PCSK9 has emerged as a potential therapeutic target for lowering LDL-C levels and preventing atherosclerosis. The US Food and Drug Administration (FDA) has approved two monoclonal antibodies (mAbs) against PCSK9, but the expensive manufacturing process limits their use. Subsequently, there have been tremendous efforts to develop cost-effective small molecules specific to PCSK9 over the past few years. These small molecules are promising therapeutics that act by preventing the synthesis of PCSK9, its secretion from cells, or the PCSK9-LDRL interaction. In this review, we summarize recent developments in the discovery of small-molecule PCSK9 inhibitors, focusing on their design, therapeutic effects, specific targets, and mechanisms of action.
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Affiliation(s)
- Shakir Ahamad
- Department of Chemistry, Aligarh Muslim University, Aligarh, 202002 UP, India.
| | - Shintu Mathew
- Medicinal and Process Chemistry Division CSIR-Central Drug Research Institute Lucknow, 226031 UP, India
| | - Waqas A Khan
- Department of Chemistry, Aligarh Muslim University, Aligarh, 202002 UP, India
| | - Kishor Mohanan
- Medicinal and Process Chemistry Division CSIR-Central Drug Research Institute Lucknow, 226031 UP, India.
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14
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Ferenczi A, Chew YP, Kroll E, von Koppenfels C, Hudson A, Molnar A. Mechanistic and genetic basis of single-strand templated repair at Cas12a-induced DNA breaks in Chlamydomonas reinhardtii. Nat Commun 2021; 12:6751. [PMID: 34799578 PMCID: PMC8604939 DOI: 10.1038/s41467-021-27004-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/26/2021] [Indexed: 12/12/2022] Open
Abstract
Single-stranded oligodeoxynucleotides (ssODNs) are widely used as DNA repair templates in CRISPR/Cas precision genome editing. However, the underlying mechanisms of single-strand templated DNA repair (SSTR) are inadequately understood, constraining rational improvements to precision editing. Here we study SSTR at CRISPR/Cas12a-induced DNA double-strand breaks (DSBs) in the eukaryotic model green microalga Chlamydomonas reinhardtii. We demonstrate that ssODNs physically incorporate into the genome during SSTR at Cas12a-induced DSBs. This process is genetically independent of the Rad51-dependent homologous recombination and Fanconi anemia pathways, is strongly antagonized by non-homologous end-joining, and is mediated almost entirely by the alternative end-joining enzyme polymerase θ. These findings suggest differences in SSTR between C. reinhardtii and animals. Our work illustrates the promising potentially of C. reinhardtii as a model organism for studying nuclear DNA repair.
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Affiliation(s)
- Aron Ferenczi
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Yen Peng Chew
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Erika Kroll
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | | | - Andrew Hudson
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Attila Molnar
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
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15
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Panda S, Poudel TN, Hegde P, Aldrich CC. Innovative Strategies for the Construction of Diverse 1'-Modified C-Nucleoside Derivatives. J Org Chem 2021; 86:16625-16640. [PMID: 34756029 DOI: 10.1021/acs.joc.1c01920] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modified C-nucleosides have proven to be enormously successful as chemical probes to understand fundamental biological processes and as small-molecule drugs for cancer and infectious diseases. Historically, the modification of the glycosyl unit has focused on the 2'-, 3'-, and 4'-positions as well as the ribofuranosyl ring oxygen. By contrast, the 1'-position has rarely been studied due to the labile nature of the anomeric position. However, the improved chemical stability of C-nucleosides allows the modification of the 1'-position with substituents not found in conventional N-nucleosides. Herein, we disclose new chemistry for the installation of diverse substituents at the 1'-position of C-nucleosides, including alkyl, alkenyl, difluoromethyl, and fluoromethyl substituents, using the 4-amino-7-(1'-hydroxy-d-ribofuranosyl)pyrrolo[2,1-f][1,2,4]triazine scaffold as a representative purine nucleoside mimetic.
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Affiliation(s)
- Subhankar Panda
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Tej Narayan Poudel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Pooja Hegde
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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16
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Li J, Wang L, Hua X, Tang H, Chen R, Yang T, Das S, Xiao J. CRISPR/Cas9-Mediated miR-29b Editing as a Treatment of Different Types of Muscle Atrophy in Mice. Mol Ther 2020; 28:1359-1372. [PMID: 32222157 PMCID: PMC7210721 DOI: 10.1016/j.ymthe.2020.03.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 03/06/2020] [Indexed: 02/07/2023] Open
Abstract
Muscle atrophy is the loss of skeletal muscle mass and strength in response to diverse catabolic stimuli. At present, no effective treatments except exercise have been shown to reduce muscle atrophy clinically. Here, we report that CRISPR/Cas9-mediated genome editing through local injection into gastrocnemius muscles or tibialis anterior muscle efficiently targets the biogenesis processing sites in pre-miR-29b. In vivo, this CRISPR-based treatment prevented the muscle atrophy induced by angiotensin II (AngII), immobilization, and denervation via activation of the AKT-FOXO3A-mTOR signaling pathway and protected against AngII-induced myocyte apoptosis in mice, leading to significantly increased exercise capacity. Our work establishes CRISPR/Cas9-based gene targeting on miRNA as a potential durable therapy for the treatment of muscle atrophy and expands the strategies available interrogating miRNA function in vivo.
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Affiliation(s)
- Jin Li
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Lijun Wang
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Xuejiao Hua
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Haifei Tang
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Rui Chen
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Tingting Yang
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Saumya Das
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Junjie Xiao
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai 200444, China; School of Medicine, Shanghai University, Shanghai 200444, China.
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17
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Böhm A, Vachalcova M, Snopek P, Bacharova L, Komarova D, Hatala R. Molecular Mechanisms, Diagnostic Aspects and Therapeutic Opportunities of Micro Ribonucleic Acids in Atrial Fibrillation. Int J Mol Sci 2020; 21:ijms21082742. [PMID: 32326592 PMCID: PMC7215603 DOI: 10.3390/ijms21082742] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/13/2020] [Accepted: 04/13/2020] [Indexed: 12/22/2022] Open
Abstract
Micro ribonucleic acids (miRNAs) are short non-coding RNA molecules responsible for regulation of gene expression. They are involved in many pathophysiological processes of a wide spectrum of diseases. Recent studies showed their involvement in atrial fibrillation. They seem to become potential screening biomarkers for atrial fibrillation and even treatment targets for this arrhythmia. The aim of this review article was to summarize the latest knowledge about miRNA and their molecular relation to the pathophysiology, diagnosis and treatment of atrial fibrillation.
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Affiliation(s)
- Allan Böhm
- National Cardiovascular Institute, 831 01 Bratislava, Slovakia;
- Faculty of Medicine, Slovak Medical University, 831 01 Bratislava, Slovakia
- Academy—Research Organization, 811 02 Bratislava, Slovakia; (M.V.); (P.S.); (D.K.)
- Correspondence:
| | - Marianna Vachalcova
- Academy—Research Organization, 811 02 Bratislava, Slovakia; (M.V.); (P.S.); (D.K.)
- East-Slovak Institute of Cardiovascular Diseases, 040 11 Kosice, Slovakia
| | - Peter Snopek
- Academy—Research Organization, 811 02 Bratislava, Slovakia; (M.V.); (P.S.); (D.K.)
- Cardiology Clinic Faculty Hospital, 950 01 Nitra, Slovakia
- Saint Elisabeth University of Health and Social work, 811 02 Bratislava, Slovakia
| | - Ljuba Bacharova
- Faculty of Medicine, Comenius University, 813 72 Bratislava, Slovakia;
- International Laser Center, 841 04 Bratislava, Slovakia
| | - Dominika Komarova
- Academy—Research Organization, 811 02 Bratislava, Slovakia; (M.V.); (P.S.); (D.K.)
| | - Robert Hatala
- National Cardiovascular Institute, 831 01 Bratislava, Slovakia;
- Faculty of Medicine, Slovak Medical University, 831 01 Bratislava, Slovakia
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18
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Ferreira D, Escudeiro A, Adega F, Anjo SI, Manadas B, Chaves R. FA-SAT ncRNA interacts with PKM2 protein: depletion of this complex induces a switch from cell proliferation to apoptosis. Cell Mol Life Sci 2020; 77:1371-1386. [PMID: 31346634 PMCID: PMC11104958 DOI: 10.1007/s00018-019-03234-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 01/11/2023]
Abstract
FA-SAT is a highly conserved satellite DNA sequence transcribed in many Bilateria species. To disclose the cellular and functional profile of FA-SAT non-coding RNAs, a comprehensive experimental approach, including the transcripts location in the cell and in the cell cycle, the identification of its putative protein interactors, and silencing/ectopic expression phenotype analysis, was performed. FA-SAT non-coding RNAs play a nuclear function at the G1 phase of the cell cycle and the interactomic assay showed that the PKM2 protein is the main interactor. The disruption of the FA-SAT non-coding RNA/PKM2 protein complex, by the depletion of either FA-SAT or PKM2, results in the same phenotype-apoptosis, and the ectopic overexpression of FA-SAT did not affect the cell-cycle progression, but promotes the PKM2 nuclear accumulation. Overall, our data first describe the importance of this ribonucleoprotein complex in apoptosis and cell-cycle progression, what foresees a promising novel candidate molecular target for cancer therapy and diagnosis.
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Affiliation(s)
- Daniela Ferreira
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Ana Escudeiro
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Filomena Adega
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Sandra I Anjo
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
- Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal.
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisbon, Portugal.
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19
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Pendergraff H, Schmidt S, Vikeså J, Weile C, Øverup C, W. Lindholm M, Koch T. Nuclear and Cytoplasmatic Quantification of Unconjugated, Label-Free Locked Nucleic Acid Oligonucleotides. Nucleic Acid Ther 2020; 30:4-13. [PMID: 31618108 PMCID: PMC6987631 DOI: 10.1089/nat.2019.0810] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/28/2019] [Indexed: 12/23/2022] Open
Abstract
Methods for the quantification of antisense oligonucleotides (AONs) provide insightful information on biodistribution and intracellular trafficking. However, the established methods have not provided information on the absolute number of molecules in subcellular compartments or about how many AONs are needed for target gene reduction for unconjugated AONs. We have developed a new method for nuclear AON quantification that enables us to determine the absolute number of AONs per nucleus without relying on AON conjugates such as fluorophores that may alter AON distribution. This study describes an alternative and label-free method using subcellular fractionation, nucleus counting, and locked nucleic acid (LNA) sandwich enzyme-linked immunosorbent assay to quantify absolute numbers of oligonucleotides in nuclei. Our findings show compound variability (diversity) by which 247,000-693,000 LNAs/nuclei results in similar target reduction for different compounds. This method can be applied to any antisense drug discovery platform providing information on specific and clinically relevant AONs. Finally, this method can directly compare nuclear entry of AON with target gene knockdown for any compound design and nucleobase sequence, gene target, and phosphorothioate stereochemistry.
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Affiliation(s)
- Hannah Pendergraff
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Steffen Schmidt
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Jonas Vikeså
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Christian Weile
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Charlotte Øverup
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Marie W. Lindholm
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Troels Koch
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
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20
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Uemura Y, Kobayashi K. Targeting murine alveolar macrophages by the intratracheal administration of locked nucleic acid containing antisense oligonucleotides. Drug Deliv 2020; 26:803-811. [PMID: 31385541 PMCID: PMC6713109 DOI: 10.1080/10717544.2019.1648589] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The pulmonary delivery of locked nucleic acid containing antisense oligonucleotides (LNA-ASOs) is expected to be a novel therapeutic approach for lung diseases. However, there are two concerns to be considered: immune responses, as the lung has a distinct immune mechanism to protect it from inhaled pathogens; and leakage into blood, since the lung is permeable to small molecules. As phagocytic alveolar macrophages reside in the alveolar space, it is hypothesized that inhaled LNA-ASOs effectively accumulate and exert a knockdown (KD) effect on these cells at low doses. Thus, targeting alveolar macrophages by inhaled LNA-ASOs may reduce these risks. To test this hypothesis, LNA-ASOs targeting Scarb1 or Hprt1 were intratracheally administered to mice. We confirmed the remarkable accumulation of intratracheally administered LNA-ASOs in murine alveolar macrophages and found that they exerted a significant and sequence-dependent KD effect. The dose required for KD in alveolar macrophages was lower than that required to induce KD in the whole lung. Furthermore, when a KD effect was observed in alveolar macrophages, no KD effect was observed in the liver or kidney; however, several inflammatory cytokines were increased in the lung. These results suggest the potential application of LNA-ASOs as an inhaled drug specific to alveolar macrophages. However, further studies on the immuno-stimulatory effects of LNA-ASOs will be necessary for the development of novel inhaled therapeutic agents.
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Affiliation(s)
- Yasunori Uemura
- a Immunology & Allergy Research Laboratories, Immunology & Allergy R&D Unit, R&D Division, Kyowa Kirin Co., Ltd , Nagaizumi-cho , Japan
| | - Katsuya Kobayashi
- a Immunology & Allergy Research Laboratories, Immunology & Allergy R&D Unit, R&D Division, Kyowa Kirin Co., Ltd , Nagaizumi-cho , Japan
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21
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Christou M, Wengel J, Sokratous K, Kyriacou K, Nikolaou G, Phylactou LA, Mastroyiannopoulos NP. Systemic Evaluation of Chimeric LNA/2'-O-Methyl Steric Blockers for Myotonic Dystrophy Type 1 Therapy. Nucleic Acid Ther 2019; 30:80-93. [PMID: 31873063 PMCID: PMC7133450 DOI: 10.1089/nat.2019.0811] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a dominantly inherited, multisystemic disorder characterized clinically by delayed muscle relaxation and weakness. The disease is caused by a CTG repeat expansion in the 3′ untranslated region (3′ UTR) of the DMPK gene, which leads to the expression of a toxic gain-of-function mRNA. The expanded CUG repeat mRNA sequesters the MBNL1 splicing regulator in nuclear-retained foci structures, resulting in loss of protein function and disruption of alternative splicing homeostasis. In this study, we used CAG repeat antisense oligonucleotides (ASOs), composed of locked nucleic acid (LNA)- and 2′-O-methyl (2′OMe)-modified bases in a chimeric design, to alleviate CUGexpanded-mediated toxicity. Chimeric 14–18mer LNA/2′OMe oligonucleotides, exhibiting an LNA incorporation of ∼33%, significantly ameliorated the misregulated alternative splicing of Mbnl1-dependent exons in primary DM1 mouse myoblasts and tibialis anterior muscles of DM1 mice. Subcutaneous delivery of 14mer and 18mer LNA/2′OMe chimeras in DM1 mice resulted in high levels of accumulation in all tested skeletal muscles, as well as in the diaphragm and heart tissue. Despite the efficient delivery, chimeric LNA/2′OMe oligonucleotides were not able, even at a high-dosage regimen (400 mg/kg/week), to correct the misregulated splicing of Serca1 exon 22 in skeletal muscles. Nevertheless, oligonucleotide doses were well-tolerated as determined by histological and plasma biochemistry analyses. Our results provide proof of concept that inhibition of MBNL1 sequestration by systemic delivery of a steric-blocking ASO is extremely challenging, considering the large number of target sites that need to be occupied per RNA molecule. Although not suitable for DM1 therapy, chimeric LNA/2′OMe oligonucleotides could prove to be highly beneficial for other diseases, such as Duchenne muscular dystrophy, that require inhibition of a single target site per RNA molecule.
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Affiliation(s)
- Melina Christou
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense M, Denmark
| | - Kleitos Sokratous
- Department of Electron Microscopy and Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Bioinformatics Group, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kyriacos Kyriacou
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Department of Electron Microscopy and Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Georgios Nikolaou
- Veterinary Diagnostic Laboratory, Vet Ex Machina Ltd, Nicosia, Cyprus
| | - Leonidas A Phylactou
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Nikolaos P Mastroyiannopoulos
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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22
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Optimization of 2',4'-BNA/LNA-Based Oligonucleotides for Splicing Modulation In Vitro. Methods Mol Biol 2019; 1828:395-411. [PMID: 30171556 DOI: 10.1007/978-1-4939-8651-4_25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Antisense oligonucleotide-mediated splicing modulation is an attractive strategy for treating genetic disorders. In 2016, two splice-switching oligonucleotides (SSOs) were approved by the FDA. To date, various types of novel artificial nucleic acids have been developed, and their potential for splicing modulations has been demonstrated. To apply these novel chemistries to SSOs, it is necessary to determine the appropriate design for each artificial nucleic acid such as the length of the SSO and number of modifications. In this protocol, we focus on SSOs modified with 2'-O,4'-methylene-bridged nucleic acid (2',4'-BNA)/locked nucleic acid (LNA), which is an artificial nucleic acid that shows extremely high binding affinity to target RNA strands. We describe our typical protocol for the optimization of 2',4'-BNA-based SSOs.
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23
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Khatib H, Gross N. Symposium review: Embryo survival-A genomic perspective of the other side of fertility. J Dairy Sci 2018; 102:3744-3753. [PMID: 30293848 DOI: 10.3168/jds.2018-15252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 07/31/2018] [Indexed: 01/13/2023]
Abstract
The majority of embryonic loss in cattle occurs within the first 3 to 4 wk of pregnancy, and there are currently no accurate predictors of pregnancy outcome. Existing embryo quality assessment methods include morphological evaluation and embryo biopsy. These methods are not accurate and carry some health risks to the developing embryo, respectively. Therefore, there is need to identify noninvasive biomarkers such as microRNA that can predict embryo quality and pregnancy outcome. Furthermore, researchers need a better understanding of the dynamic interaction between the mother and the embryo. The transcriptome of the uterus shows plasticity that depends on the embryo type so that the expression level of some genes for in vivo embryos would be different from that of in vitro-produced embryos. Similarly, the embryonic transcriptome and epigenome change in response to different environmental factors such as stress, diet, disease, and physiological status of the mother. This embryo-mother crosstalk could be better understood by investigating the molecular signaling that occurs at different stages of embryonic development. Although transcriptomics is a useful tool to assess the roles of genes and pathways in embryo quality and maternal receptivity, it does not provide the exact functions of these genes, and it shows correlation rather than causality. Therefore, an in-depth functional genomic analysis is needed for better understanding of the molecular mechanisms controlling embryo development. In this review, we discuss recent genomic technologies such as RNA interference, gapmer technology, and genome editing techniques used in humans and livestock to elucidate the molecular mechanisms of genes affecting embryo development.
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Affiliation(s)
- H Khatib
- Department of Animal Sciences, University of Wisconsin, Madison 53706.
| | - N Gross
- Department of Animal Sciences, University of Wisconsin, Madison 53706
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24
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Miettinen HM, Gripentrog JM, Lord CI, Nagy JO. CD177-mediated nanoparticle targeting of human and mouse neutrophils. PLoS One 2018; 13:e0200444. [PMID: 29990379 PMCID: PMC6039027 DOI: 10.1371/journal.pone.0200444] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 06/26/2018] [Indexed: 12/23/2022] Open
Abstract
Neutrophils are the most abundant white blood cells, with a vital role in innate immune defense against bacterial and fungal pathogens. Although mostly associated with pathological processes directly related to immune defense, they can also play a detrimental role in inflammatory conditions and have been found to have a pro-metastatic role in the spread of cancer cells. Here, we explore ways to temporarily suppress these detrimental activities. We first examined the possibility of using siRNA and antisense oligonucleotides (ASOs) for transient knockdown of the human and mouse C5a receptor, an important chemoattractant receptor involved in neutrophil-mediated injury that is associated with myocardial infarction, sepsis, and neurodegenerative diseases. We found that siRNAs and ASOs transfected into cultured cell lines can eliminate 70–90% of C5a receptor mRNA and protein within 72 h of administration, a clinically relevant time frame after a cardiovascular event. Targeted drug delivery to specific cells or tissues of interest in a mammalian host, however, remains a major challenge. Here, using phage display technology, we have identified peptides that bind specifically to CD177, a neutrophil-specific surface molecule. We have attached these peptides to fluorescent, lipid-based nanoparticles and confirmed targeting and delivery to cultured cells ectopically presenting either human or mouse CD177. In addition, we have shown peptide-nanoparticle binding specifically to neutrophils in human and mouse blood. We anticipate that these or related tagged nanoparticles may be therapeutically useful for delivery of siRNAs or ASOs to neutrophils for transient knockdown of pro-inflammatory proteins such as the C5a receptor.
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Affiliation(s)
- Heini M. Miettinen
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States of America
- * E-mail:
| | - Jeannie M. Gripentrog
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States of America
| | - Connie I. Lord
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States of America
| | - Jon O. Nagy
- NanoValent Pharmaceuticals, Inc., Bozeman, MT, United States of America
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25
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Xie JJ, Jiang YY, Jiang Y, Li CQ, Lim MC, An O, Mayakonda A, Ding LW, Long L, Sun C, Lin LH, Chen L, Wu JY, Wu ZY, Cao Q, Fang WK, Yang W, Soukiasian H, Meltzer SJ, Yang H, Fullwood M, Xu LY, Li EM, Lin DC, Koeffler HP. Super-Enhancer-Driven Long Non-Coding RNA LINC01503, Regulated by TP63, Is Over-Expressed and Oncogenic in Squamous Cell Carcinoma. Gastroenterology 2018; 154:2137-2151.e1. [PMID: 29454790 DOI: 10.1053/j.gastro.2018.02.018] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 02/06/2018] [Accepted: 02/08/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS Long non-coding RNAs (lncRNAs) are expressed in tissue-specific pattern, but it is not clear how these are regulated. We aimed to identify squamous cell carcinoma (SCC)-specific lncRNAs and investigate mechanisms that control their expression and function. METHODS We studied expression patterns and functions of 4 SCC-specific lncRNAs. We obtained 113 esophageal SCC (ESCC) and matched non-tumor esophageal tissues from a hospital in Shantou City, China, and performed quantitative reverse transcription polymerase chain reaction assays to measure expression levels of LINC01503. We collected clinical data from patients and compared expression levels with survival times. LINC01503 was knocked down using small interfering RNAs and oligonucleotides in TE7, TE5, and KYSE510 cell lines and overexpressed in KYSE30 cells. Cells were analyzed by chromatin immunoprecipitation sequencing, luciferase reporter assays, colony formation, migration and invasion, and mass spectrometry analyses. Cells were injected into nude mice and growth of xenograft tumors was measured. LINC01503 interaction with proteins was studied using fluorescence in situ hybridization, RNA pulldown, and RNA immunoprecipitation analyses. RESULTS We identified a lncRNA, LINC01503, which is regulated by a super enhancer and is expressed at significantly higher levels in esophageal and head and neck SCCs than in non-tumor tissues. High levels in SCCs correlated with shorter survival times of patients. The transcription factor TP63 bound to the super enhancer at the LINC01503 locus and activated its transcription. Expression of LINC01503 in ESCC cell lines increased their proliferation, colony formation, migration, and invasion. Knockdown of LINC01503 in SCC cells reduced their proliferation, colony formation, migration, and invasion, and the growth of xenograft tumors in nude mice. Expression of LINC01503 in ESCC cell lines reduced ERK2 dephosphorylation by DUSP6, leading to activation of ERK signaling via MAPK. LINC01503 disrupted the interaction between EBP1 and the p85 subunit of PI3K, increasing AKT signaling. CONCLUSIONS We identified an lncRNA, LINC01503, which is increased in SCC cells compared with non-tumor cells. Increased expression of LINC01503 promotes ESCC cell proliferation, migration, invasion, and growth of xenograft tumors. It might be developed as a biomarker of aggressive SCCs in patients.
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Affiliation(s)
- Jian-Jun Xie
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China; Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California.
| | - Yan-Yi Jiang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yuan Jiang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Chun-Quan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Mei-Chee Lim
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Lin Long
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - Chun Sun
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - Le-Hang Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Li Chen
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jian-Yi Wu
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - Zhi-Yong Wu
- Department of Oncologic Surgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-Sen University, Shantou, China
| | - Qi Cao
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Wang-Kai Fang
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - Wei Yang
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Harmik Soukiasian
- Division of Thoracic Surgery, Cedars-Sinai Medical Center, Los Angeles, California
| | - Stephen J Meltzer
- Departments of Medicine and Oncology, the Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Melissa Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore
| | - Li-Yan Xu
- Institute of Oncologic Pathology, Medical College of Shantou University, Shantou, China.
| | - En-Min Li
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China.
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California.
| | - H Phillip Koeffler
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California; Cancer Science Institute of Singapore, National University of Singapore, Singapore; National University Cancer Institute, National University Hospital Singapore, Singapore
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Chapman SD, Farina L, Kronforst K, Dizon M. MicroRNA Profile Differences in Neonates at Risk for Cerebral Palsy. PHYSICAL MEDICINE AND REHABILITATION INTERNATIONAL 2018; 5:1148. [PMID: 30740584 PMCID: PMC6364989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
BACKGROUND MicroRNAs; miRs are used as biomarkers in the diagnosis of several diseases. Cerebral palsy; CP, resulting from perinatal brain injury, cannot be diagnosed until 18-24 months old. Biomarkers to predict CP and assess response to investigational therapies are needed. We hypothesized that miRs expressed in neonates with the CP risk factors of abnormal tone and/or intraventricular hemorrhage; IVH differ from those without risk factors. METHODS This was a cohort study of neonates at risk for CP. Subjects <32 weeks gestation and <1500 grams were recruited from neonatal intensive care units at a large urban delivery hospital and an adjacent children's hospital. Thirty-one plasma samples were evaluated. An unbiased examination was performed by locked nucleic acid quantitative real time - polymerase chain reaction; qRT-PCR. Results were evaluated in the context of IVH and abnormal tone. RESULTS Plasma miR profiles in neonates at risk for CP differ when comparing those with and without IVH, and with and without abnormal tone. Restricted profiles were found in each condition with greater differences in the tone comparison than the IVH comparison. CONCLUSION Plasma miR profiles show potential in predicting CP. This study also suggests biologically plausible candidates for future studies.
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Affiliation(s)
- S D Chapman
- United States Naval Hospital Okinawa, 18 Medical Group, Kadena Air Base, Okinawa, Japan
| | - L Farina
- Department of Medicine, Northwestern University, USA
| | - K Kronforst
- Department of Pediatrics, Northwestern University, USA
| | - Mlv Dizon
- Department of Pediatrics, Northwestern University, USA
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Locked Nucleic Acid Technology for Highly Sensitive Detection of Somatic Mutations in Cancer. Adv Clin Chem 2017; 83:53-72. [PMID: 29304903 DOI: 10.1016/bs.acc.2017.10.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The molecular diagnosis of the cancer mutational status is essential for modern clinical laboratory medicine. Mutations in EGFR, KRAS, BRAF, and PIK3CA genes are widely analyzed in solid tumors such as lung cancer, colorectal cancer, breast cancer, and melanoma. The allele-specific polymerase chain reaction, high-resolution melting, and Sanger sequencing are used for detecting and identifying gene mutations in many clinical laboratories. The locked nucleic acid (LNA) is a class of nucleic acid analogs that contain a methylene bridge connecting the 2' oxygen and 4' carbon in the ribose moiety. This methylene bridge locks the ribose group into a C3'-endo conformation. LNA, including an oligonucleotide, increases the thermal stability of hybrid strands. The use of LNA technology in molecular diagnostic methods improves the specificity and sensitivity of assays. This review describes routinely analyzed mutations and molecular diagnostic methods used in the clinical laboratory along with the performance improvement of mutational analysis with LNA.
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Uemura Y, Hagiwara K, Kobayashi K. The intratracheal administration of locked nucleic acid containing antisense oligonucleotides induced gene silencing and an immune-stimulatory effect in the murine lung. PLoS One 2017; 12:e0187286. [PMID: 29107995 PMCID: PMC5673232 DOI: 10.1371/journal.pone.0187286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 10/17/2017] [Indexed: 12/21/2022] Open
Abstract
Locked nucleic acid containing antisense oligonucleotides (LNA-ASOs) have the potential to modulate the disease-related gene expression by the RNaseH-dependent degradation of mRNAs. Pulmonary drug delivery has been widely used for the treatment of lung disease. Thus, the inhalation of LNA-ASOs is expected to be an efficient therapy that can be applied to several types of lung disease. Because the lung has a distinct immune system against pathogens, the immune-stimulatory effect of LNA-ASOs should be considered for the development of novel inhaled LNA-ASOs therapies. However, there have been no reports on the relationship between knock-down (KD) and the immune-stimulatory effects of inhaled LNA-ASOs in the lung. In this report, LNA-ASOs targeting Scarb1 (Scarb1-ASOs) or negative control LNA-ASOs targeting ApoB (ApoB-ASOs) were intratracheally administered to mice to investigate the KD of the gene expression and the immune-stimulatory effects in the lung. We confirmed that the intratracheal administration of Scarb1-ASOs exerted a KD effect in the lung without a drug delivery system. On the other hand, both Scarb1-ASOs and ApoB-ASOs induced neutrophilic infiltration in the alveoli and increased the expression levels of G-CSF and CXCL1 in the lung. The dose required for KD was the same as the dose that induced the neutrophilic immune response. In addition, in our in vitro experiments, Scarb1-ASOs did not increase the G-CSF or CXCL1 expression in primary lung cells, even though Scarb1-ASOs exerted a strong KD effect. Hence, we hypothesize that inhaled LNA-ASOs have the potential to exert a KD effect in the lung, but that they may be associated with a risk of immune stimulation. Further studies about the mechanism underlying the immune-stimulatory effect of LNA-ASOs is necessary for the development of novel inhaled LNA-ASO therapies.
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Affiliation(s)
- Yasunori Uemura
- Immunology & Allergy R&D Unit, R&D Division, Kyowa Hakko Kirin Co., Ltd., Nagaizumi-cho, Shizuoka, Japan
- * E-mail:
| | - Kenji Hagiwara
- Innovative Technology Labs, Research Functions Unit, R&D Division, Kyowa Hakko Kirin Co., Ltd., Machida, Tokyo, Japan
| | - Katsuya Kobayashi
- Immunology & Allergy R&D Unit, R&D Division, Kyowa Hakko Kirin Co., Ltd., Nagaizumi-cho, Shizuoka, Japan
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Physiological and therapeutic regulation of PCSK9 activity in cardiovascular disease. Basic Res Cardiol 2017; 112:32. [PMID: 28439730 PMCID: PMC5403857 DOI: 10.1007/s00395-017-0619-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/07/2017] [Indexed: 12/14/2022]
Abstract
Ischemic heart disease is the main cause of death worldwide and is accelerated by increased levels of low-density lipoprotein cholesterol (LDL-C). Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a potent circulating regulator of LDL-C through its ability to induce degradation of the LDL receptor (LDLR) in the lysosome of hepatocytes. Only in the last few years, a number of breakthroughs in the understanding of PCSK9 biology have been reported illustrating how PCSK9 activity is tightly regulated at several levels by factors influencing its transcription, secretion, or by extracellular inactivation and clearance. Two humanized antibodies directed against the LDLR-binding site in PCSK9 received approval by the European and US authorities and additional PCSK9 directed therapeutics are climbing up the phases of clinical trials. The first outcome data of the PCSK9 inhibitor evolocumab reported a significant reduction in the composite endpoint (cardiovascular death, myocardial infarction, or stroke) and further outcome data are awaited. Meanwhile, it became evident that PCSK9 has (patho)physiological roles in several cardiovascular cells. In this review, we summarize and discuss the recent biological and clinical data on PCSK9, the regulation of PCSK9, its extra-hepatic activities focusing on cardiovascular cells, molecular concepts to target PCSK9, and finally briefly summarize the data of recent clinical studies.
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Kropp J, Carrillo JA, Namous H, Daniels A, Salih SM, Song J, Khatib H. Male fertility status is associated with DNA methylation signatures in sperm and transcriptomic profiles of bovine preimplantation embryos. BMC Genomics 2017; 18:280. [PMID: 28381255 PMCID: PMC5382486 DOI: 10.1186/s12864-017-3673-y] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 03/31/2017] [Indexed: 11/12/2022] Open
Abstract
Background Infertility in dairy cattle is a concern where reduced fertilization rates and high embryonic loss are contributing factors. Studies of the paternal contribution to reproductive performance are limited. However, recent discoveries have shown that, in addition to DNA, sperm delivers transcription factors and epigenetic components that are required for fertilization and proper embryonic development. Hence, characterization of the paternal contribution at the time of fertilization is warranted. We hypothesized that sire fertility is associated with differences in DNA methylation patterns in sperm and that the embryonic transcriptomic profiles are influenced by the fertility status of the bull. Embryos were generated in vitro by fertilization with either a high or low fertility Holstein bull. Blastocysts derived from each high and low fertility bulls were evaluated for morphology, development, and transcriptomic analysis using RNA-Sequencing. Additionally, DNA methylation signatures of sperm from high and low fertility sires were characterized by performing whole-genome DNA methylation binding domain sequencing. Results Embryo morphology and developmental capacity did not differ between embryos generated from either a high or low fertility bull. However, RNA-Sequencing revealed 98 genes to be differentially expressed at a false discovery rate < 1%. A total of 65 genes were upregulated in high fertility bull derived embryos, and 33 genes were upregulated in low fertility derived embryos. Expression of the genes CYCS, EEA1, SLC16A7, MEPCE, and TFB2M was validated in three new pairs of biological replicates of embryos. The role of the differentially expressed gene TFB2M in embryonic development was further assessed through expression knockdown at the zygotic stage, which resulted in decreased development to the blastocyst stage. Assessment of the epigenetic signature of spermatozoa between high and low fertility bulls revealed 76 differentially methylated regions. Conclusions Despite similar morphology and development to the blastocyst stage, preimplantation embryos derived from high and low fertility bulls displayed significant transcriptomic differences. The relationship between the paternal contribution and the embryonic transcriptome is unclear, although differences in methylated regions were identified which could influence the reprogramming of the early embryo. Further characterization of paternal factors delivered to the oocyte could lead to the identification of biomarkers for better selection of sires to improve reproductive efficiency. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3673-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jenna Kropp
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - José A Carrillo
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Hadjer Namous
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alyssa Daniels
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sana M Salih
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, 53792, USA.,Present address: Department of Obstetrics and Gynecology, West Virginia University, Morgantown, WV, 26508, USA
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Hasan Khatib
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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Abstract
Ischemic heart disease is the main cause of death worldwide and it is accelerated by increased low-density lipoprotein (LDL) cholesterol (LDL-C) and/or lipoprotein (a) (Lp(a)) concentrations. Proprotein convertase subtilisin/kexin type 9 (PCSK9) alters both LDL-C and in part Lp(a) concentrations through its ability to induce degradation of the LDL receptor (LDLR). PCSK9, however, has additional targets which are potentially involved in lipid metabolism regulation such as the very low density lipoprotein receptor (VLDL), CD36 (cluster of differentiation 36) and the epithelial cholesterol transporter (NPC1L1) and it affects expression of apolipoprotein B48. The PCSK9 activity is tightly regulated at several levels by factors influencing its transcription, secretion, or by extracellular inactivation and clearance. Many comorbidities (kidney insufficiency, hypothyreoidism, hyperinsulinemia, inflammation) modify PCSK9 expression and release. Two humanized antibodies directed against extracellular PCSK9 received approval by the European and US authorities and additional PCSK9 directed therapeutics (such as silencing RNA) are already in clinical trials. Their results demonstrate a significant reduction in both LDL-C and Lp(a) concentrations – independent of the concomitant medication – and one of them reduced plaque size in high risk cardiovascular patients; results of two ongoing large clinical endpoints studies are awaited. In this review, we summarize and discuss the recent biological data on PCSK9, the regulation of PCSK9, and finally briefly summarize the data of recent clinical studies in the context of lipid metabolism.
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Affiliation(s)
- Rainer Schulz
- Department of Physiology, Justus-Liebig-Universität, Aulweg 129, 35392, Giessen, Germany.
| | - Klaus-Dieter Schlüter
- Department of Physiology, Justus-Liebig-Universität, Aulweg 129, 35392, Giessen, Germany
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Rebustini IT. A Functional MicroRNA Screening Method for Organ Morphogenesis. CURRENT PROTOCOLS IN CELL BIOLOGY 2017; 74:19.19.1-19.19.17. [PMID: 28256721 DOI: 10.1002/cpcb.15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The increasing repertoire of microRNAs expressed during organ development and their role in regulating organ morphogenesis provide a compelling need to develop methods to assess microRNA function using various in vitro and in vivo experimental models. Methods to assess microRNA function during organ morphogenesis include transfection of microRNA inhibitors (antagomirs) and activators (mimics) into mouse embryonic explanted organs using liposomes, which can potentially result in low efficiency of transfection and off-target effects. We devised a method to assess microRNA function in explanted organs by transfecting antagomirs and mimics using peptide-based nanoparticles, increasing functional microRNA targeting efficiency, and decreasing off-target effects. Our method can be applied to a variety of embryonic organs that can be explanted and provides an alternative to efficiently and functionally prioritize microRNAs during organ morphogenesis for further in vivo genetic approaches. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Ivan T Rebustini
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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He NY, Li Q, Wu CY, Ren Z, Gao Y, Pan LH, Wang MM, Wen HY, Jiang ZS, Tang ZH, Liu LS. Lowering serum lipids via PCSK9-targeting drugs: current advances and future perspectives. Acta Pharmacol Sin 2017; 38:301-311. [PMID: 28112180 PMCID: PMC5342665 DOI: 10.1038/aps.2016.134] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/18/2016] [Indexed: 12/12/2022] Open
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9), also known as neural apoptosis regulated convertase (NARC1), is a key modulator of cholesterol metabolism. PCSK9 increases the serum concentration of low-density lipoprotein cholesterol by escorting low-density lipoprotein receptors (LDLRs) from the membrane of hepatic cells into lysosomes, where the LDLRs are degraded. Owing to the importance of PCSK9 in lipid metabolism, considerable effort has been made over the past decade in developing drugs targeting PCSK9 to lower serum lipid levels. Nevertheless, some problems and challenges remain. In this review we first describes the structure and function of PCSK9 and its gene polymorphisms. We then discuss the various designs of pharmacological targets of PCSK9, including those that block the binding of PCSK9 to hepatic LDLRs (mimetic peptides, adnectins, and monoclonal antibodies), inhibit PCSK9 expression (the clustered regularly interspaced short palindromic repeats/Cas9 platform, small molecules, antisense oligonucleotides, and small interfering RNAs), and interfere with PCSK9 secretion. Finally, this review highlights future challenges in this field, including safety concerns associated with PCSK9 monoclonal antibodies, the limited utility of PCSK9 inhibitors in the central nervous system, and the cost-effectiveness of PCSK9 inhibitors.
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Affiliation(s)
- Ni-ya He
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, University of South China, Hengyang 421001, China
| | - Qing Li
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, University of South China, Hengyang 421001, China
| | - Chun-yan Wu
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, University of South China, Hengyang 421001, China
| | - Zhong Ren
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, University of South China, Hengyang 421001, China
| | - Ya Gao
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, University of South China, Hengyang 421001, China
| | - Li-hong Pan
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, University of South China, Hengyang 421001, China
| | - Mei-mei Wang
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, University of South China, Hengyang 421001, China
| | - Hong-yan Wen
- Medical College, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Zhi-sheng Jiang
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, University of South China, Hengyang 421001, China
| | - Zhi-han Tang
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, University of South China, Hengyang 421001, China
| | - Lu-shan Liu
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, University of South China, Hengyang 421001, China
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Gene activation of SMN by selective disruption of lncRNA-mediated recruitment of PRC2 for the treatment of spinal muscular atrophy. Proc Natl Acad Sci U S A 2017; 114:E1509-E1518. [PMID: 28193854 DOI: 10.1073/pnas.1616521114] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a neurodegenerative disease characterized by progressive motor neuron loss and caused by mutations in SMN1 (Survival Motor Neuron 1). The disease severity inversely correlates with the copy number of SMN2, a duplicated gene that is nearly identical to SMN1. We have delineated a mechanism of transcriptional regulation in the SMN2 locus. A previously uncharacterized long noncoding RNA (lncRNA), SMN-antisense 1 (SMN-AS1), represses SMN2 expression by recruiting the Polycomb Repressive Complex 2 (PRC2) to its locus. Chemically modified oligonucleotides that disrupt the interaction between SMN-AS1 and PRC2 inhibit the recruitment of PRC2 and increase SMN2 expression in primary neuronal cultures. Our approach comprises a gene-up-regulation technology that leverages interactions between lncRNA and PRC2. Our data provide proof-of-concept that this technology can be used to treat disease caused by epigenetic silencing of specific loci.
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Antimisiaris S, Mourtas S, Papadia K. Targeted si-RNA with liposomes and exosomes (extracellular vesicles): How to unlock the potential. Int J Pharm 2017; 525:293-312. [PMID: 28163221 DOI: 10.1016/j.ijpharm.2017.01.056] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 01/25/2017] [Accepted: 01/27/2017] [Indexed: 12/17/2022]
Abstract
The concept of RNA interference therapeutics has been initiated 18 years ago, and the main bottleneck for translation of the technology into therapeutic products remains the delivery of functional RNA molecules into the cell cytoplasm. In the present review article after an introduction about the theoretical basis of RNAi therapy and the main challenges encountered for its realization, an overview of the different types of delivery systems or carriers, used as potential systems to overcome RNAi delivery issues, will be provided. Characteristic examples or results obtained with the most promising systems will be discussed. Focus will be given mostly on the applications of liposomes or other types of lipid carriers, such as exosomes, towards improved delivery of RNAi to therapeutic targets. Finally the approach of integrating the advantages of these two vesicular systems, liposomes and exosomes, as a potential solution to realize RNAi therapy, will be proposed.
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Affiliation(s)
- Sophia Antimisiaris
- Laboratory of Pharmaceutical Technology, Department of Pharmacy, University of Patras, Rio 26504, Greece; Institute of Chemical Engineering, FORTH/ICE-HT, Rio 26504, Greece.
| | - Spyridon Mourtas
- Laboratory of Pharmaceutical Technology, Department of Pharmacy, University of Patras, Rio 26504, Greece
| | - Konstantina Papadia
- Laboratory of Pharmaceutical Technology, Department of Pharmacy, University of Patras, Rio 26504, Greece
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Parlea L, Puri A, Kasprzak W, Bindewald E, Zakrevsky P, Satterwhite E, Joseph K, Afonin KA, Shapiro BA. Cellular Delivery of RNA Nanoparticles. ACS COMBINATORIAL SCIENCE 2016; 18:527-47. [PMID: 27509068 PMCID: PMC6345529 DOI: 10.1021/acscombsci.6b00073] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
RNA nanostructures can be programmed to exhibit defined sizes, shapes and stoichiometries from naturally occurring or de novo designed RNA motifs. These constructs can be used as scaffolds to attach functional moieties, such as ligand binding motifs or gene expression regulators, for nanobiology applications. This review is focused on four areas of importance to RNA nanotechnology: the types of RNAs of particular interest for nanobiology, the assembly of RNA nanoconstructs, the challenges of cellular delivery of RNAs in vivo, and the delivery carriers that aid in the matter. The available strategies for the design of nucleic acid nanostructures, as well as for formulation of their carriers, make RNA nanotechnology an important tool in both basic research and applied biomedical science.
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Affiliation(s)
- Lorena Parlea
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Anu Puri
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Wojciech Kasprzak
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Eckart Bindewald
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Paul Zakrevsky
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Emily Satterwhite
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kenya Joseph
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kirill A. Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, University of North Carolina at Charlotte, Charlotte North Carolina 28223, United States
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte North Carolina 28223, United States
| | - Bruce A. Shapiro
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
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Chang H, Yi B, Ma R, Zhang X, Zhao H, Xi Y. CRISPR/cas9, a novel genomic tool to knock down microRNA in vitro and in vivo. Sci Rep 2016; 6:22312. [PMID: 26924382 PMCID: PMC4770416 DOI: 10.1038/srep22312] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 02/12/2016] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs are small and non-coding RNA molecules with the master role in regulation of gene expression at post-transcriptional/translational levels. Many methods have been developed for microRNA loss-of-function study, such as antisense inhibitors and sponges; however, the robustness, specificity, and stability of these traditional strategies are not highly satisfied. CRISPR/cas9 system is emerging as a novel genome editing tool in biology/medicine research, but its indication in microRNA research has not been studied exclusively. In this study, we clone CRISPR/cas9 constructs with single-guide RNAs specifically targeting biogenesis processing sites of selected microRNAs; and we find that CRISPR/cas9 can robustly and specifically reduce the expression of these microRNAs up to 96%. CRISPR/cas9 also shows an exclusive benefit in control of crossing off-target effect on microRNAs in the same family or with highly conserved sequences. More significantly, for the first time, we demonstrate the long term stability of microRNA knockdown phenotype by CRISPR/cas9 in both in vitro and in vivo models.
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Affiliation(s)
- Hong Chang
- Mitchell Cancer Institute, University of South Alabama, USA
| | - Bin Yi
- Mitchell Cancer Institute, University of South Alabama, USA
| | - Ruixia Ma
- Mitchell Cancer Institute, University of South Alabama, USA
| | - Xiaoguo Zhang
- Mitchell Cancer Institute, University of South Alabama, USA
| | - Hongyou Zhao
- Mitchell Cancer Institute, University of South Alabama, USA
| | - Yaguang Xi
- Mitchell Cancer Institute, University of South Alabama, USA
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Bergeron N, Phan BAP, Ding Y, Fong A, Krauss RM. Proprotein convertase subtilisin/kexin type 9 inhibition: a new therapeutic mechanism for reducing cardiovascular disease risk. Circulation 2016; 132:1648-66. [PMID: 26503748 DOI: 10.1161/circulationaha.115.016080] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays an important role in the regulation of cholesterol homeostasis. By binding to hepatic low-density lipoprotein (LDL) receptors and promoting their lysosomal degradation, PCSK9 reduces LDL uptake, leading to an increase in LDL cholesterol concentrations. Gain-of-function mutations in PCSK9 associated with high LDL cholesterol and premature cardiovascular disease have been causally implicated in the pathophysiology of autosomal-dominant familial hypercholesterolemia. In contrast, the more commonly expressed loss-of-function mutations in PCSK9 are associated with reduced LDL cholesterol and cardiovascular disease risk. The development of therapeutic approaches that inhibit PCSK9 function has therefore attracted considerable attention from clinicians and the pharmaceutical industry for the management of hypercholesterolemia and its associated cardiovascular disease risk. This review summarizes the effects of PCSK9 on hepatic and intestinal lipid metabolism and the more recently explored functions of PCSK9 in extrahepatic tissues. Therapeutic approaches that prevent interaction of PCSK9 with hepatic LDL receptors (monoclonal antibodies, mimetic peptides), inhibit PCSK9 synthesis in the endoplasmic reticulum (antisense oligonucleotides, siRNAs), and interfere with PCSK9 function (small molecules) are also described. Finally, clinical trials testing the safety and efficacy of monoclonal antibodies to PCSK9 are reviewed. These have shown dose-dependent decreases in LDL cholesterol (44%-65%), apolipoprotein B (48%-59%), and lipoprotein(a) (27%-50%) without major adverse effects in various high-risk patient categories, including those with statin intolerance. Initial reports from 2 of these trials have indicated the expected reduction in cardiovascular events. Hence, inhibition of PCSK9 holds considerable promise as a therapeutic option for decreasing cardiovascular disease risk.
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Affiliation(s)
- Nathalie Bergeron
- From Children's Hospital Oakland Research Institute, CA (N.B., R.M.K.); Touro University, College of Pharmacy, Vallejo, CA (N.B., Y.D., A.F.); and University of California, San Francisco (B.A.P.P., R.M.K.).
| | - Binh An P Phan
- From Children's Hospital Oakland Research Institute, CA (N.B., R.M.K.); Touro University, College of Pharmacy, Vallejo, CA (N.B., Y.D., A.F.); and University of California, San Francisco (B.A.P.P., R.M.K.)
| | - Yunchen Ding
- From Children's Hospital Oakland Research Institute, CA (N.B., R.M.K.); Touro University, College of Pharmacy, Vallejo, CA (N.B., Y.D., A.F.); and University of California, San Francisco (B.A.P.P., R.M.K.)
| | - Aleyna Fong
- From Children's Hospital Oakland Research Institute, CA (N.B., R.M.K.); Touro University, College of Pharmacy, Vallejo, CA (N.B., Y.D., A.F.); and University of California, San Francisco (B.A.P.P., R.M.K.)
| | - Ronald M Krauss
- From Children's Hospital Oakland Research Institute, CA (N.B., R.M.K.); Touro University, College of Pharmacy, Vallejo, CA (N.B., Y.D., A.F.); and University of California, San Francisco (B.A.P.P., R.M.K.).
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Clauss S, Sinner MF, Kääb S, Wakili R. The Role of MicroRNAs in Antiarrhythmic Therapy for Atrial Fibrillation. Arrhythm Electrophysiol Rev 2015; 4:146-55. [PMID: 26835117 DOI: 10.15420/aer.2015.4.3.146] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/23/2015] [Indexed: 12/19/2022] Open
Abstract
Atrial fibrillation (AF) is the most common arrhythmia worldwide and has an enormous impact on our healthcare system as it is a major contributor of morbidity and mortality. Although there are several therapeutic options available, treatment of AF still remains challenging. AF pathophysiology is complex and still incompletely understood. In general, our understanding of AF is based on two mechanistic paradigms as functional hallmarks of AF: ectopic activity and reentry. Both ectopic activity and reentry are the result of remodelling processes. Functional and/or expressional changes in ion channels, connexins or calcium-handling proteins are important factors in electrical remodelling, whereas signalling processes leading to atrial dilatation and atrial fibrosis are key factors of structural remodelling. In recent years, new intriguing key players in AF pathophysiology have been identified: microRNAs (miRNAs). MiRNAs are short, non-coding RNA fragments that can regulate gene expression and have been demonstrated as important modifiers in signalling cascades leading to electrical and structural remodelling. In this article we review the miRNA-mediated molecular mechanisms underlying AF with special emphasis on the perspective of miRNAs as potential therapeutic targets for AF treatment.
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Affiliation(s)
- Sebastian Clauss
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, US; University Hospital Munich, Ludwig-Maximilians University Munich; DZHK (German Centre for Cardiovascular Research), Partner Site Munich, Germany
| | - Moritz F Sinner
- University Hospital Munich, Ludwig-Maximilians University Munich
| | - Stefan Kääb
- University Hospital Munich, Ludwig-Maximilians University Munich; DZHK (German Centre for Cardiovascular Research), Partner Site Munich, Germany
| | - Reza Wakili
- University Hospital Munich, Ludwig-Maximilians University Munich; DZHK (German Centre for Cardiovascular Research), Partner Site Munich, Germany
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Kropp J, Khatib H. mRNA fragments in in vitro culture media are associated with bovine preimplantation embryonic development. Front Genet 2015; 6:273. [PMID: 26379701 PMCID: PMC4547040 DOI: 10.3389/fgene.2015.00273] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/10/2015] [Indexed: 11/13/2022] Open
Abstract
In vitro production (IVP) systems have been used to bypass problems of fertilization and early embryonic development. However, embryos produced by IVP are commonly selected for implantation based on morphological assessment, which is not a strong indicator of establishment and maintenance of pregnancy. Thus, there is a need to identify additional indicators of embryonic developmental potential. Previous studies have identified microRNA expression in in vitro culture media to be indicative of embryo quality in both bovine and human embryos. Like microRNAs, mRNAs have been shown to be secreted from cells into the extracellular environment, but it is unknown whether or not these RNAs are secreted by embryos. Thus, the objective of the present study was to determine whether mRNAs are secreted into in vitro culture media and if their expression in the media is indicative of embryo quality. In vitro culture medium was generated and collected from both blastocyst and degenerate (those which fail to develop from the morula to blastocyst stage) embryos. Small-RNA sequencing revealed that many mRNA fragments were present in the culture media. A total of 17 mRNA fragments were differentially expressed between blastocyst and degenerate conditioned media. Differential expression was confirmed by quantitative real-time PCR for fragments of mRNA POSTN and VSNL-1, in four additional biological replicates of media. To better understand the mechanisms of mRNA secretion into the media, the expression of a predicted RNA binding protein of POSTN, PUM2, was knocked down using an antisense oligonucleotide gapmer. Supplementation of a PUM2 gapmer significantly reduced blastocyst development and decreased secretion of POSTN mRNA into the media. Overall, differential mRNA expression in the media was repeatable and sets the framework for future study of mRNA biomarkers in in vitro culture media to improve predictability of reproductive performance.
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Affiliation(s)
| | - Hasan Khatib
- Department of Animal Sciences, University of Wisconsin–Madison, MadisonWI, USA
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Hřebabecký H, Procházková E, Šála M, Plačková P, Tloušťová E, Barauskas O, Lee YJ, Tian Y, Mackman R, Nencka R. Synthesis and biological evaluation of conformationally restricted adenine bicycloribonucleosides. Org Biomol Chem 2015; 13:9300-13. [PMID: 26239898 DOI: 10.1039/c5ob00987a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We prepared a novel series of conformationally restricted bicyclonucleosides and nucleotides. The synthetic approach employed a ring closing metathesis to provide access to both 6 and 7 membered saturated and unsaturated rings linking the 3' to 5' methylene groups of the sugar. The bicyclonucleosides were also transformed to the corresponding phosphoramidate prodrugs by an innovative one-pot protocol of boronate ester protection, coupling of the phosphoryl chloridate and deprotection of the boronate. A similar strategy was also employed for the synthesis of the corresponding monophosphates as crucial intermediates for the synthesis of selected triphosphates. The biological properties of the nucleosides and monophosphate prodrugs were assessed for antiviral and cytostatic activities in cell based assays whilst the triphosphates were evaluated in enzymatic assays. The lack of significant effects suggests that the linkage of the 3' to 5'via a ring system and the subsequent conformational restriction of the ribose ring to the South conformation are incompatible with the kinases and polymerases that recognize nucleosides and their metabolites.
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Affiliation(s)
- Hubert Hřebabecký
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Gilead Sciences & IOCB Research Centre, 166 10 Prague 6, Czech Republic.
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42
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Suresh G, Priyakumar UD. Inclusion of methoxy groups inverts the thermodynamic stabilities of DNA-RNA hybrid duplexes: A molecular dynamics simulation study. J Mol Graph Model 2015; 61:150-9. [PMID: 26254870 DOI: 10.1016/j.jmgm.2015.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/22/2015] [Accepted: 07/27/2015] [Indexed: 11/30/2022]
Abstract
Modified nucleic acids have found profound applications in nucleic acid based technologies such as antisense and antiviral therapies. Previous studies on chemically modified nucleic acids have suggested that modifications incorporated in furanose sugar especially at 2'-position attribute special properties to nucleic acids when compared to other modifications. 2'-O-methyl modification to deoxyribose sugars of DNA-RNA hybrids is one such modification that increases nucleic acid stability and has become an attractive class of compounds for potential antisense applications. It has been reported that modification of DNA strands with 2'-O-methyl group reverses the thermodynamic stability of DNA-RNA hybrid duplexes. Molecular dynamics simulations have been performed on two hybrid duplexes (DR and RD) which differ from each other and 2'-O-methyl modified counterparts to investigate the effect of 2'-O-methyl modification on their duplex stability. The results obtained suggest that the modification drives the conformations of both the hybrid duplexes towards A-RNA like conformation. The modified hybrid duplexes exhibit significantly contrasting dynamics and hydration patterns compared to respective parent duplexes. In line with the experimental results, the relative binding free energies suggest that the introduced modifications stabilize the less stable DR hybrid, but destabilize the more stable RD duplex. Binding free energy calculations suggest that the increased hydrophobicity is primarily responsible for the reversal of thermodynamic stability of hybrid duplexes. Free energy component analysis further provides insights into the stability of modified duplexes.
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Affiliation(s)
- Gorle Suresh
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India.
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43
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Inhibition of AAC(6')-Ib-mediated resistance to amikacin in Acinetobacter baumannii by an antisense peptide-conjugated 2',4'-bridged nucleic acid-NC-DNA hybrid oligomer. Antimicrob Agents Chemother 2015; 59:5798-803. [PMID: 26169414 DOI: 10.1128/aac.01304-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/08/2015] [Indexed: 01/08/2023] Open
Abstract
Multiresistant Acinetobacter baumannii, a common etiologic agent of severe nosocomial infections in compromised hosts, usually harbors aac(6')-Ib. This gene specifies resistance to amikacin and other aminoglycosides, seriously limiting the effectiveness of these antibiotics. An antisense oligodeoxynucleotide (ODN4) that binds to a duplicated sequence on the aac(6')-Ib mRNA, one of the copies overlapping the initiation codon, efficiently inhibited translation in vitro. An isosequential nuclease-resistant hybrid oligomer composed of 2',4'-bridged nucleic acid-NC (BNA(NC)) residues and deoxynucleotides (BNA(NC)-DNA) conjugated to the permeabilizing peptide (RXR)4XB ("X" and "B" stand for 6-aminohexanoic acid and β-alanine, respectively) (CPPBD4) inhibited translation in vitro at the same levels observed in testing ODN4. Furthermore, CPPBD4 in combination with amikacin inhibited growth of a clinical A. baumannii strain harboring aac(6')-Ib in liquid cultures, and when both compounds were used as combination therapy to treat infected Galleria mellonella organisms, survival was comparable to that seen with uninfected controls.
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44
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Šála M, Dejmek M, Procházková E, Hřebabecký H, Rybáček J, Dračínský M, Novák P, Rosenbergová Š, Fukal J, Sychrovský V, Rosenberg I, Nencka R. Synthesis of locked cyclohexene and cyclohexane nucleic acids (LCeNA and LCNA) with modified adenosine units. Org Biomol Chem 2015; 13:2703-15. [DOI: 10.1039/c4ob02193b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We designed novel conformationally locked cyclohexene nucleic acid and studied their properties.
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45
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Borkowski R, Du L, Zhao Z, McMillan E, Kosti A, Yang CR, Suraokar M, Wistuba II, Gazdar AF, Minna JD, White MA, Pertsemlidis A. Genetic mutation of p53 and suppression of the miR-17∼92 cluster are synthetic lethal in non-small cell lung cancer due to upregulation of vitamin D Signaling. Cancer Res 2014; 75:666-75. [PMID: 25519225 DOI: 10.1158/0008-5472.can-14-1329] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lung cancer is the leading cause of cancer-related fatalities. Recent success developing genotypically targeted therapies, with potency only in well-defined subpopulations of tumors, suggests a path to improving patient survival. We used a library of oligonucleotide inhibitors of microRNAs, a class of posttranscriptional gene regulators, to identify novel synthetic lethal interactions between miRNA inhibition and molecular mechanisms in non-small cell lung cancer (NSCLC). Two inhibitors, those for miR-92a and miR-1226*, produced a toxicity distribution across a panel of 27 cell lines that correlated with loss of p53 protein expression. Notably, depletion of p53 was sufficient to confer sensitivity to otherwise resistant telomerase-immortalized bronchial epithelial cells. We found that both miR inhibitors cause sequence-specific downregulation of the miR-17∼92 polycistron, and this downregulation was toxic only in the context of p53 loss. Mechanistic studies indicated that the selective toxicity of miR-17∼92 polycistron inactivation was the consequence of derepression of vitamin D signaling via suppression of CYP24A1, a rate-limiting enzyme in the 1α,25-dihydroxyvitamin D3 metabolic pathway. Of note, high CYP24A1 expression significantly correlated with poor patient outcome in multiple lung cancer cohorts. Our results indicate that the screening approach used in this study can identify clinically relevant synthetic lethal interactions and that vitamin D receptor agonists may show enhanced efficacy in p53-negative lung cancer patients.
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Affiliation(s)
- Robert Borkowski
- Division of Basic Sciences, Southwestern Graduate School of Biomedical Sciences, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Liqin Du
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas. Department of Cellular and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Zhenze Zhao
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Elizabeth McMillan
- Division of Basic Sciences, Southwestern Graduate School of Biomedical Sciences, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Adam Kosti
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Chin-Rang Yang
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Milind Suraokar
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Adi F Gazdar
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas. Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas. Department of Pathology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - John D Minna
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas. Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas. Department of Pharmacology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas. Department of Internal Medicine, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Michael A White
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas. Department of Cell Biology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.
| | - Alexander Pertsemlidis
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas. Department of Cellular and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas. Department of Pediatrics, The University of Texas Health Science Center at San Antonio, San Antonio, Texas.
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Rošić S, Köhler F, Erhardt S. Repetitive centromeric satellite RNA is essential for kinetochore formation and cell division. ACTA ACUST UNITED AC 2014; 207:335-49. [PMID: 25365994 PMCID: PMC4226727 DOI: 10.1083/jcb.201404097] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
SAT III RNA binds to the kinetochore component CENP-C and is required for correct assembly and function of the kinetochore at centromeres. Chromosome segregation requires centromeres on every sister chromatid to correctly form and attach the microtubule spindle during cell division. Even though centromeres are essential for genome stability, the underlying centromeric DNA is highly variable in sequence and evolves quickly. Epigenetic mechanisms are therefore thought to regulate centromeres. Here, we show that the 359-bp repeat satellite III (SAT III), which spans megabases on the X chromosome of Drosophila melanogaster, produces a long noncoding RNA that localizes to centromeric regions of all major chromosomes. Depletion of SAT III RNA causes mitotic defects, not only of the sex chromosome but also in trans of all autosomes. We furthermore find that SAT III RNA binds to the kinetochore component CENP-C, and is required for correct localization of the centromere-defining proteins CENP-A and CENP-C, as well as outer kinetochore proteins. In conclusion, our data reveal that SAT III RNA is an integral part of centromere identity, adding RNA to the complex epigenetic mark at centromeres in flies.
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Affiliation(s)
- Silvana Rošić
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Alliance, and CellNetworks Excellence Cluster, University of Heidelberg, 69120 Heidelberg, Germany Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Alliance, and CellNetworks Excellence Cluster, University of Heidelberg, 69120 Heidelberg, Germany Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Alliance, and CellNetworks Excellence Cluster, University of Heidelberg, 69120 Heidelberg, Germany
| | - Florian Köhler
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Alliance, and CellNetworks Excellence Cluster, University of Heidelberg, 69120 Heidelberg, Germany Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Alliance, and CellNetworks Excellence Cluster, University of Heidelberg, 69120 Heidelberg, Germany Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Alliance, and CellNetworks Excellence Cluster, University of Heidelberg, 69120 Heidelberg, Germany
| | - Sylvia Erhardt
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Alliance, and CellNetworks Excellence Cluster, University of Heidelberg, 69120 Heidelberg, Germany Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Alliance, and CellNetworks Excellence Cluster, University of Heidelberg, 69120 Heidelberg, Germany Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Alliance, and CellNetworks Excellence Cluster, University of Heidelberg, 69120 Heidelberg, Germany
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Giza DE, Vasilescu C, Calin GA. Key principles of miRNA involvement in human diseases. Discoveries (Craiova) 2014; 2:e34. [PMID: 26317116 PMCID: PMC4547364 DOI: 10.15190/d.2014.26] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 12/29/2014] [Accepted: 12/30/2014] [Indexed: 12/12/2022] Open
Abstract
Although rapid progress in our understanding of the functions of miRNA has been made by experimentation and computational approach, a considerable effort still has to be done in determining the general principles that govern the miRNA's mode of action in human diseases. We will further discuss how these principles are being progressively approached by molecular studies, as well as the importance of miRNA in regulating different target genes and functions in specific biological contexts. There is a great demand to understand the principles of context - specific miRNA target recognition in order to design future experiments and models of normal developmental and disease states.
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Affiliation(s)
- Dana Elena Giza
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Hematology, Fundeni Clinical Hospital, Bucharest, Romania
| | - Catalin Vasilescu
- Department of Surgery, Fundeni Clinical Hospital, Bucharest, Romania
- UMF Carol Davila, Bucharest, Romania
| | - George A. Calin
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Adachi S, Homoto M, Tanaka R, Hioki Y, Murakami H, Suga H, Matsumoto M, Nakayama KI, Hatta T, Iemura SI, Natsume T. ZFP36L1 and ZFP36L2 control LDLR mRNA stability via the ERK-RSK pathway. Nucleic Acids Res 2014; 42:10037-49. [PMID: 25106868 PMCID: PMC4150769 DOI: 10.1093/nar/gku652] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Low-density lipoprotein receptor (LDLR) mRNA is unstable, but is stabilized upon extracellular signal-regulated kinase (ERK) activation, possibly through the binding of certain proteins to the LDLR mRNA 3′-untranslated region (UTR), although the detailed mechanism underlying this stability control is unclear. Here, using a proteomic approach, we show that proteins ZFP36L1 and ZFP36L2 specifically bind to the 3′-UTR of LDLR mRNA and recruit the CCR4-NOT-deadenylase complex, resulting in mRNA destabilization. We also show that the C-terminal regions of ZFP36L1 and ZFP36L2 are directly phosphorylated by p90 ribosomal S6 kinase, a kinase downstream of ERK, resulting in dissociation of the CCR4-NOT-deadenylase complex and stabilization of LDLR mRNA. We further demonstrate that targeted disruption of the interaction between LDLR mRNA and ZFP36L1 and ZFP36L2 using antisense oligonucleotides results in upregulation of LDLR mRNA and protein. These results indicate that ZFP36L1 and ZFP36L2 regulate LDLR protein levels downstream of ERK. Our results also show the usefulness of our method for identifying critical regulators of specific RNAs and the potency of antisense oligonucleotide-based therapeutics.
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Affiliation(s)
- Shungo Adachi
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan Galaxy Pharma Inc., Akita 010-0951, Japan
| | - Masae Homoto
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Rikou Tanaka
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan Galaxy Pharma Inc., Akita 010-0951, Japan
| | - Yusaku Hioki
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Hiroshi Murakami
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Tomohisa Hatta
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Shun-ichiro Iemura
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
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49
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Suresh G, Priyakumar UD. Atomistic investigation of the effect of incremental modification of deoxyribose sugars by locked nucleic acid (β-D-LNA and α-L-LNA) moieties on the structures and thermodynamics of DNA-RNA hybrid duplexes. J Phys Chem B 2014; 118:5853-63. [PMID: 24845216 DOI: 10.1021/jp5014779] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chemically modified oligonucleotides offer many possibilities in utilizing their special features for a vast number of applications in nucleic acid based therapies and synthetic molecular biology. Locked nucleic acid analogues (α-/β-LNA) are modifications having an extra ring of 2'-O,4'-C-methylene group in the furanose sugar. LNA strands have been shown to exhibit high binding affinity toward RNA and DNA strands, and the resultant duplexes show significantly high melting temperatures. In the present study, molecular dynamics (MD) simulations were performed on DNA-RNA hybrid duplexes by systematically modifying their deoxyribose sugars with locked nucleic acid analogues. Several geometrical and energetic analyses were performed using principal component (PCA) analysis and binding free energy methods to understand the consequence of incorporated isomeric LNA modifications on the structure, dynamics, and stability of DNA-RNA hybrid duplex. The β-modification systematically changes the conformation of the DNA-RNA hybrid duplex whereas drastic changes are observed for α-modification. The fully modified duplexes have distinct properties compared to partial and unmodified duplexes, and the partly modified duplexes have properties intermediate to full strand and unmodified duplexes. The distribution of BI versus BII populations suggests that backbone rearrangement is minimal for β-LNA modification in order to accommodate it in duplexes whereas extensive backbone rearrangement is necessary in order to incorporate α-LNA modification which subsequently alters the energetic and structural properties of the duplexes. The simulation results also suggest that the alteration of DNA-RNA hybrid properties depends on the position of modification and the gap between the modifications.
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Affiliation(s)
- Gorle Suresh
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500 032, India
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Fernandes SA, Douglas AGL, Varela MA, Wood MJA, Aoki Y. Oligonucleotide-Based Therapy for FTD/ALS Caused by the C9orf72 Repeat Expansion: A Perspective. J Nucleic Acids 2013; 2013:208245. [PMID: 24349764 PMCID: PMC3855979 DOI: 10.1155/2013/208245] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 09/19/2013] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive and lethal disease of motor neuron degeneration, leading to paralysis of voluntary muscles and death by respiratory failure within five years of onset. Frontotemporal dementia (FTD) is characterised by degeneration of frontal and temporal lobes, leading to changes in personality, behaviour, and language, culminating in death within 5-10 years. Both of these diseases form a clinical, pathological, and genetic continuum of diseases, and this link has become clearer recently with the discovery of a hexanucleotide repeat expansion in the C9orf72 gene that causes the FTD/ALS spectrum, that is, c9FTD/ALS. Two basic mechanisms have been proposed as being potentially responsible for c9FTD/ALS: loss-of-function of the protein encoded by this gene (associated with aberrant DNA methylation) and gain of function through the formation of RNA foci or protein aggregates. These diseases currently lack any cure or effective treatment. Antisense oligonucleotides (ASOs) are modified nucleic acids that are able to silence targeted mRNAs or perform splice modulation, and the fact that they have proved efficient in repeat expansion diseases including myotonic dystrophy type 1 makes them ideal candidates for c9FTD/ALS therapy. Here, we discuss potential mechanisms and challenges for developing oligonucleotide-based therapy for c9FTD/ALS.
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Affiliation(s)
- Stephanie A. Fernandes
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
- Institute of Biosciences, University of Sao Paulo, Rua do Matao, 05508-090 Sao Paulo, SP, Brazil
| | - Andrew G. L. Douglas
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Miguel A. Varela
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Matthew J. A. Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Yoshitsugu Aoki
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
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