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Karagianni K, Bibi A, Madé A, Acharya S, Parkkonen M, Barbalata T, Srivastava PK, de Gonzalo-Calvo D, Emanueli C, Martelli F, Devaux Y, Dafou D, Nossent AY. Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseases. Mol Ther Nucleic Acids 2024; 35:102085. [PMID: 38192612 PMCID: PMC10772297 DOI: 10.1016/j.omtn.2023.102085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
RNA editing, a common and potentially highly functional form of RNA modification, encompasses two different RNA modifications, namely adenosine to inosine (A-to-I) and cytidine to uridine (C-to-U) editing. As inosines are interpreted as guanosines by the cellular machinery, both A-to-I and C-to-U editing change the nucleotide sequence of the RNA. Editing events in coding sequences have the potential to change the amino acid sequence of proteins, whereas editing events in noncoding RNAs can, for example, affect microRNA target binding. With advancing RNA sequencing technology, more RNA editing events are being discovered, studied, and reported. However, RNA editing events are still often overlooked or discarded as sequence read quality defects. With this position paper, we aim to provide guidelines and recommendations for the detection, validation, and follow-up experiments to study RNA editing, taking examples from the fields of cardiovascular and brain disease. We discuss all steps, from sample collection, storage, and preparation, to different strategies for RNA sequencing and editing-sensitive data analysis strategies, to validation and follow-up experiments, as well as potential pitfalls and gaps in the available technologies. This paper may be used as an experimental guideline for RNA editing studies in any disease context.
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Affiliation(s)
- Korina Karagianni
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Alessia Bibi
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Alisia Madé
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, Italy
| | - Shubhra Acharya
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-alzette, Luxembourg
| | - Mikko Parkkonen
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - Teodora Barbalata
- Lipidomics Department, Institute of Cellular Biology and Pathology “Nicolae Simionescu” of the Romanian Academy, 8, B. P. Hasdeu Street, 050568 Bucharest, Romania
| | | | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | | | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, Italy
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Dimitra Dafou
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - A. Yaël Nossent
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
- Department of Nutrition, Exercise and Sports (NEXS), University of Copenhagen, Copenhagen, Denmark
| | - on behalf of EU-CardioRNA COST Action CA17129
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-alzette, Luxembourg
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
- Lipidomics Department, Institute of Cellular Biology and Pathology “Nicolae Simionescu” of the Romanian Academy, 8, B. P. Hasdeu Street, 050568 Bucharest, Romania
- National Heart & Lung Institute, Imperial College London, London, UK
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
- Department of Nutrition, Exercise and Sports (NEXS), University of Copenhagen, Copenhagen, Denmark
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He J, Gao Y, Yang C, Guo Y, Liu L, Lu S, He H. Navigating the landscape: Prospects and hurdles in targeting vascular smooth muscle cells for atherosclerosis diagnosis and therapy. J Control Release 2024; 366:261-281. [PMID: 38161032 DOI: 10.1016/j.jconrel.2023.12.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/02/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Vascular smooth muscle cells (VSMCs) have emerged as pivotal contributors throughout all phases of atherosclerotic plaque development, effectively dispelling prior underestimations of their prevalence and significance. Recent lineage tracing studies have unveiled the clonal nature and remarkable adaptability inherent to VSMCs, thereby illuminating their intricate and multifaceted roles in the context of atherosclerosis. This comprehensive review provides an in-depth exploration of the intricate mechanisms and distinctive characteristics that define VSMCs across various physiological processes, firmly underscoring their paramount importance in shaping the course of atherosclerosis. Furthermore, this review offers a thorough examination of the significant strides made over the past two decades in advancing imaging techniques and therapeutic strategies with a precise focus on targeting VSMCs within atherosclerotic plaques, notably spotlighting meticulously engineered nanoparticles as a promising avenue. We envision the potential of VSMC-targeted nanoparticles, thoughtfully loaded with medications or combination therapies, to effectively mitigate pro-atherogenic VSMC processes. These advancements are poised to contribute significantly to the pivotal objective of modulating VSMC phenotypes and enhancing plaque stability. Moreover, our paper also delves into recent breakthroughs in VSMC-targeted imaging technologies, showcasing their remarkable precision in locating microcalcifications, dynamically monitoring plaque fibrous cap integrity, and assessing the therapeutic efficacy of medical interventions. Lastly, we conscientiously explore the opportunities and challenges inherent in this innovative approach, providing a holistic perspective on the potential of VSMC-targeted strategies in the evolving landscape of atherosclerosis research and treatment.
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Affiliation(s)
- Jianhua He
- School of Pharmacy, Research Center for Pharmaceutical Preparations, Hubei University of Chinese Medicine, Wuhan 430065, People's Republic of China.
| | - Yu Gao
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Can Yang
- School of Pharmacy, Research Center for Pharmaceutical Preparations, Hubei University of Chinese Medicine, Wuhan 430065, People's Republic of China
| | - Yujie Guo
- School of Pharmacy, Research Center for Pharmaceutical Preparations, Hubei University of Chinese Medicine, Wuhan 430065, People's Republic of China
| | - Lisha Liu
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China.
| | - Shan Lu
- School of Pharmacy, Research Center for Pharmaceutical Preparations, Hubei University of Chinese Medicine, Wuhan 430065, People's Republic of China.
| | - Hongliang He
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Sciences & Medical Engineering, Southeast University, Nanjing 210009, People's Republic of China.
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Genkel V, Dolgushin I, Savochkina A, Nikushkina K, Baturina I, Minasova A, Sumerkina V, Pykhova L, Kupriyanov S, Kuznetsova A, Shaposhnik I. Innate and Adaptive Immunity-Related Markers as Predictors of the Short-Term Progression of Subclinical Atherosclerosis in Middle-Aged Patients. Int J Mol Sci 2023; 24:12205. [PMID: 37569579 PMCID: PMC10419170 DOI: 10.3390/ijms241512205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/26/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
Assessment of inflammation is a promising approach to monitoring the progression of asymptomatic atherosclerosis. The aim of the present study was to investigate the predictive value of innate and adaptive immunity-related markers, in relation to the short-term progression of subclinical atherosclerosis. The study included 183 patients aged 40-64 years who underwent duplex scanning of the carotid and lower limb arteries at two visits with an interval of 12-24 months between examinations. Phenotyping of circulating lymphocytes and monocytes subpopulations were performed through flow cytometry. An increase in the number of circulating TLR4-positive intermediate monocytes (>447.0-467.0 cells/μL) was an independent predictor of the short-term progression of lower limb artery atherosclerosis (p < 0.0001) and polyvascular atherosclerosis (p = 0.003). The assessment of TLR4-positive monocytes significantly improved the prognostic model for the progression of lower limb arterial atherosclerosis (C-index 0.728 (0.642-0.815) versus 0.637 (0.539-0.735); p = 0.038). An increase in the number of circulating TLR4-positive intermediate monocytes was an independent predictor of the short-term progression of lower limb artery and polyvascular atherosclerosis. Their inclusion into models containing conventional risk factors significantly improved their prognostic effectiveness regarding lower limb artery atherosclerosis progression.
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Affiliation(s)
- Vadim Genkel
- Federal State Budgetary Educational Institution of Higher Education “South-Ural State Medical University” of the Ministry of Healthcare of the Russian Federation, 454092 Chelyabinsk, Russia; (I.D.); (A.S.); (K.N.); (I.B.); (A.M.); (V.S.); (L.P.); (S.K.); (A.K.); (I.S.)
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