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Huang H, Lin Z, He D, Hong L, Li Y. RiboDiffusion: tertiary structure-based RNA inverse folding with generative diffusion models. Bioinformatics 2024; 40:i347-i356. [PMID: 38940178 PMCID: PMC11211841 DOI: 10.1093/bioinformatics/btae259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024] Open
Abstract
MOTIVATION RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fundamental challenge is to find functional RNA sequences that satisfy given structural constraints, known as the inverse folding problem. Computational approaches have emerged to address this problem based on secondary structures. However, designing RNA sequences directly from 3D structures is still challenging, due to the scarcity of data, the nonunique structure-sequence mapping, and the flexibility of RNA conformation. RESULTS In this study, we propose RiboDiffusion, a generative diffusion model for RNA inverse folding that can learn the conditional distribution of RNA sequences given 3D backbone structures. Our model consists of a graph neural network-based structure module and a Transformer-based sequence module, which iteratively transforms random sequences into desired sequences. By tuning the sampling weight, our model allows for a trade-off between sequence recovery and diversity to explore more candidates. We split test sets based on RNA clustering with different cut-offs for sequence or structure similarity. Our model outperforms baselines in sequence recovery, with an average relative improvement of 11% for sequence similarity splits and 16% for structure similarity splits. Moreover, RiboDiffusion performs consistently well across various RNA length categories and RNA types. We also apply in silico folding to validate whether the generated sequences can fold into the given 3D RNA backbones. Our method could be a powerful tool for RNA design that explores the vast sequence space and finds novel solutions to 3D structural constraints. AVAILABILITY AND IMPLEMENTATION The source code is available at https://github.com/ml4bio/RiboDiffusion.
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Affiliation(s)
- Han Huang
- Department of Computer Science and Engineering, CUHK, Hong Kong SAR, 999077, China
- School of Computer Science and Engineering, Beihang University, Beijing, 100191, China
| | - Ziqian Lin
- Department of Computer Science and Engineering, CUHK, Hong Kong SAR, 999077, China
- School of Artificial Intelligence, Nanjing University, Nanjing, 210023, China
| | - Dongchen He
- Department of Computer Science and Engineering, CUHK, Hong Kong SAR, 999077, China
| | - Liang Hong
- Department of Computer Science and Engineering, CUHK, Hong Kong SAR, 999077, China
| | - Yu Li
- Department of Computer Science and Engineering, CUHK, Hong Kong SAR, 999077, China
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Ngo AD, Nguyen HL, Caglayan S, Chu DT. RNA therapeutics for the treatment of blood disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:273-286. [PMID: 38360003 DOI: 10.1016/bs.pmbts.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Blood disorders are defined as diseases related to the structure, function, and formation of blood cells. These diseases lead to increased years of life loss, reduced quality of life, and increased financial burden for social security systems around the world. Common blood disorder treatments such as using chemical drugs, organ transplants, or stem cell therapy have not yet approached the best goals, and treatment costs are also very high. RNA with a research history dating back several decades has emerged as a potential method to treat hematological diseases. A number of clinical trials have been conducted to pave the way for the use of RNA molecules to cure blood disorders. This novel approach takes advantage of regulatory mechanisms and the versatility of RNA-based oligonucleotides to target genes and cellular pathways involved in the pathogenesis of specific diseases. Despite positive results, currently, there is no RNA drug to treat blood-related diseases approved or marketed. Before the clinical adoption of RNA-based therapies, challenges such as safe delivery of RNA molecules to the target site and off-target effects of injected RNA in the body need to be addressed. In brief, RNA-based therapies open novel avenues for the treatment of hematological diseases, and clinical trials for approval and practical use of RNA-targeted are crucial.
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Affiliation(s)
- Anh Dao Ngo
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Hoang Lam Nguyen
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | | | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
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Lee SW, Frankston CM, Kim J. Epigenome editing in cancer: Advances and challenges for potential therapeutic options. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 383:191-230. [PMID: 38359969 DOI: 10.1016/bs.ircmb.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Cancers are diseases caused by genetic and non-genetic environmental factors. Epigenetic alterations, some attributed to non-genetic factors, can lead to cancer development. Epigenetic changes can occur in tumor suppressors or oncogenes, or they may contribute to global cell state changes, making cells abnormal. Recent advances in gene editing technology show potential for cancer treatment. Herein, we will discuss our current knowledge of epigenetic alterations occurring in cancer and epigenetic editing technologies that can be applied to developing therapeutic options.
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Affiliation(s)
- Seung-Won Lee
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Connor Mitchell Frankston
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Biomedical Engineering Graduate Program, Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Jungsun Kim
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR, United States; Cancer Biology Research Program, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States.
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Mehrabani M, Mohammadyar S, Rajizadeh MA, Bejeshk MA, Ahmadi B, Nematollahi MH, Mirtajaddini Goki M, Bahrampour Juybari K, Amirkhosravi A. Boosting therapeutic efficacy of mesenchymal stem cells in pulmonary fibrosis: The role of genetic modification and preconditioning strategies. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2023; 26:1001-1015. [PMID: 37605719 PMCID: PMC10440137 DOI: 10.22038/ijbms.2023.69023.15049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/14/2023] [Indexed: 08/23/2023]
Abstract
Pulmonary fibrosis (PF) is the end stage of severe lung diseases, in which the lung parenchyma is replaced by fibrous scar tissue. The result is a remarkable reduction in pulmonary compliance, which may lead to respiratory failure and even death. Idiopathic pulmonary fibrosis (IPF) is the most prevalent form of PF, with no reasonable etiology. However, some factors are believed to be behind the etiology of PF, including prolonged administration of several medications (e.g., bleomycin and amiodarone), environmental contaminant exposure (e.g., gases, asbestos, and silica), and certain systemic diseases (e.g., systemic lupus erythematosus). Despite significant developments in the diagnostic approach to PF in the last few years, efforts to find more effective treatments remain challenging. With their immunomodulatory, anti-inflammatory, and anti-fibrotic properties, stem cells may provide a promising approach for treating a broad spectrum of fibrotic conditions. However, they may lose their biological functions after long-term in vitro culture or exposure to harsh in vivo situations. To overcome these limitations, numerous modification techniques, such as genetic modification, preconditioning, and optimization of cultivation methods for stem cell therapy, have been adopted. Herein, we summarize the previous investigations that have been designed to assess the effects of stem cell preconditioning or genetic modification on the regenerative capacity of stem cells in PF.
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Affiliation(s)
- Mehrnaz Mehrabani
- Physiology Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Sohaib Mohammadyar
- Department of Laboratory Hematology and Blood Banking, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Amin Rajizadeh
- Physiology Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
- Department of Physiology and Pharmacology, Afzalipour Medical Faculty, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Abbas Bejeshk
- Physiology Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
- Department of Physiology and Pharmacology, Afzalipour Medical Faculty, Kerman University of Medical Sciences, Kerman, Iran
| | - Bahareh Ahmadi
- Department of Laboratory Hematology and Blood Banking, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | | | | | - Kobra Bahrampour Juybari
- Abnormal Uterine Bleeding Research Center, Semnan University of Medical Sciences, Semnan, Iran
- School of Pharmacy, Semnan University of Medical Sciences, Semnan, Iran
| | - Arian Amirkhosravi
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
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RNA therapeutics: updates and future potential. SCIENCE CHINA. LIFE SCIENCES 2023; 66:12-30. [PMID: 36100838 PMCID: PMC9470505 DOI: 10.1007/s11427-022-2171-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/17/2022] [Indexed: 02/04/2023]
Abstract
Recent advancements in the production, modification, and cellular delivery of RNA molecules facilitated the expansion of RNA-based therapeutics. The increasing understanding of RNA biology initiated a corresponding growth in RNA therapeutics. In this review, the general concepts of five classes of RNA-based therapeutics, including RNA interference-based therapies, antisense oligonucleotides, small activating RNA therapies, circular RNA therapies, and messenger RNA-based therapeutics, will be discussed. Moreover, we also provide an overview of RNA-based therapeutics that have already received regulatory approval or are currently being evaluated in clinical trials, along with challenges faced by these technologies. RNA-based drugs demonstrated positive clinical trial results and have the ability to address previously "undruggable" targets, which delivers great promise as a disruptive therapeutic technology to fulfill its full clinical potentiality.
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Papolu PK, Ramakrishnan M, Mullasseri S, Kalendar R, Wei Q, Zou L, Ahmad Z, Vinod KK, Yang P, Zhou M. Retrotransposons: How the continuous evolutionary front shapes plant genomes for response to heat stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1064847. [PMID: 36570931 PMCID: PMC9780303 DOI: 10.3389/fpls.2022.1064847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/21/2022] [Indexed: 05/28/2023]
Abstract
Long terminal repeat retrotransposons (LTR retrotransposons) are the most abundant group of mobile genetic elements in eukaryotic genomes and are essential in organizing genomic architecture and phenotypic variations. The diverse families of retrotransposons are related to retroviruses. As retrotransposable elements are dispersed and ubiquitous, their "copy-out and paste-in" life cycle of replicative transposition leads to new genome insertions without the excision of the original element. The overall structure of retrotransposons and the domains responsible for the various phases of their replication is highly conserved in all eukaryotes. The two major superfamilies of LTR retrotransposons, Ty1/Copia and Ty3/Gypsy, are distinguished and dispersed across the chromosomes of higher plants. Members of these superfamilies can increase in copy number and are often activated by various biotic and abiotic stresses due to retrotransposition bursts. LTR retrotransposons are important drivers of species diversity and exhibit great variety in structure, size, and mechanisms of transposition, making them important putative actors in genome evolution. Additionally, LTR retrotransposons influence the gene expression patterns of adjacent genes by modulating potential small interfering RNA (siRNA) and RNA-directed DNA methylation (RdDM) pathways. Furthermore, comparative and evolutionary analysis of the most important crop genome sequences and advanced technologies have elucidated the epigenetics and structural and functional modifications driven by LTR retrotransposon during speciation. However, mechanistic insights into LTR retrotransposons remain obscure in plant development due to a lack of advancement in high throughput technologies. In this review, we focus on the key role of LTR retrotransposons response in plants during heat stress, the role of centromeric LTR retrotransposons, and the role of LTR retrotransposon markers in genome expression and evolution.
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Affiliation(s)
- Pradeep K. Papolu
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Sileesh Mullasseri
- Department of Zoology, St. Albert’s College (Autonomous), Kochi, Kerala, India
| | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, Biocenter 3, University of Helsinki, Helsinki, Finland
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Long−Hai Zou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Zishan Ahmad
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | | | - Ping Yang
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, Zhejiang, China
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Miguel Pereira Souza L, Camacho Lima M, Filipe Silva Bezerra L, Silva Pimentel A. Transposition of polymer-encapsulated small interfering RNA through lung surfactant models at the air-water interface. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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8
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Panagopoulos A, Samant S, Bakhos JJ, Liu M, Khan B, Makadia J, Muhammad F, Kievit FM, Agrawal DK, Chatzizisis YS. Triggering receptor expressed on myeloid cells-1 (TREM-1) inhibition in atherosclerosis. Pharmacol Ther 2022; 238:108182. [DOI: 10.1016/j.pharmthera.2022.108182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 03/14/2022] [Accepted: 03/30/2022] [Indexed: 11/29/2022]
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Hussain S, Tulsyan S, Dar SA, Sisodiya S, Abiha U, Kumar R, Mishra BN, Haque S. Role of epigenetics in carcinogenesis: Recent advancements in anticancer therapy. Semin Cancer Biol 2022; 83:441-451. [PMID: 34182144 DOI: 10.1016/j.semcancer.2021.06.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 04/29/2021] [Accepted: 06/23/2021] [Indexed: 02/08/2023]
Abstract
The role of epigenetics in the etiology of cancer progression is being emphasized for the past two decades to check the impact of chromatin modifiers and remodelers. Histone modifications, DNA methylation, chromatin remodeling, nucleosome positioning, regulation by non-coding RNAs and precisely microRNAs are influential epigenetic marks in the field of progressive cancer sub-types. Furthermore, constant epigenetic changes due to hyper or hypomethylation could efficiently serve as effective biomarkers of cancer diagnosis and therapeutic development. Ongoing research in the field of epigenetics has resulted in the resolutory role of various epigenetic markers and their inhibition using specific inhibitors to arrest their key cellular functions in in-vitro and pre-clinical studies. Although, the mechanism of epigenetics in cancer largely remains unexplored. Nevertheless, various advancements in the field of epigenetics have been made through transcriptome analysis and in-vitro genome targeting technologies to unravel the applicability of epigenetic markers for future cancer therapeutics and management. Therefore, this review emphasizes on recent advances in epigenetic landscapes that could be targeted/explored using novel approaches as personalized treatment modalities for cancer containment.
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Affiliation(s)
- Showket Hussain
- Division of Molecular Oncology & Molecular Diagnostics, ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Sonam Tulsyan
- Division of Molecular Oncology & Molecular Diagnostics, ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Sajad Ahmad Dar
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Sandeep Sisodiya
- Division of Molecular Oncology & Molecular Diagnostics, ICMR-National Institute of Cancer Prevention and Research, Noida, India; Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Umme Abiha
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Rakesh Kumar
- Dr. B.R.A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Bhartendu Nath Mishra
- Department of Biotechnology, Institute of Engineering and Technology, Lucknow, India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia; Bursa Uludağ University Faculty of Medicine, Görükle Campus, Nilüfer, Bursa, Turkey.
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Zhang C, Ma Y, Zhang J, Kuo JCT, Zhang Z, Xie H, Zhu J, Liu T. Modification of Lipid-Based Nanoparticles: An Efficient Delivery System for Nucleic Acid-Based Immunotherapy. Molecules 2022; 27:molecules27061943. [PMID: 35335310 PMCID: PMC8949521 DOI: 10.3390/molecules27061943] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 02/05/2023] Open
Abstract
Lipid-based nanoparticles (LBNPs) are biocompatible and biodegradable vesicles that are considered to be one of the most efficient drug delivery platforms. Due to the prominent advantages, such as long circulation time, slow drug release, reduced toxicity, high transfection efficiency, and endosomal escape capacity, such synthetic nanoparticles have been widely used for carrying genetic therapeutics, particularly nucleic acids that can be applied in the treatment for various diseases, including congenital diseases, cancers, virus infections, and chronic inflammations. Despite great merits and multiple successful applications, many extracellular and intracellular barriers remain and greatly impair delivery efficacy and therapeutic outcomes. As such, the current state of knowledge and pitfalls regarding the gene delivery and construction of LBNPs will be initially summarized. In order to develop a new generation of LBNPs for improved delivery profiles and therapeutic effects, the modification strategies of LBNPs will be reviewed. On the basis of these developed modifications, the performance of LBNPs as therapeutic nanoplatforms have been greatly improved and extensively applied in immunotherapies, including infectious diseases and cancers. However, the therapeutic applications of LBNPs systems are still limited due to the undesirable endosomal escape, potential aggregation, and the inefficient encapsulation of therapeutics. Herein, we will review and discuss recent advances and remaining challenges in the development of LBNPs for nucleic acid-based immunotherapy.
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Affiliation(s)
- Chi Zhang
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (C.Z.); (J.C.-T.K.); (Z.Z.)
| | - Yifan Ma
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA; (Y.M.); (J.Z.)
| | - Jingjing Zhang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA; (Y.M.); (J.Z.)
| | - Jimmy Chun-Tien Kuo
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (C.Z.); (J.C.-T.K.); (Z.Z.)
| | - Zhongkun Zhang
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (C.Z.); (J.C.-T.K.); (Z.Z.)
| | - Haotian Xie
- Department of Statistics, The Ohio State University, Columbus, OH 43210, USA;
| | - Jing Zhu
- College of Nursing and Health Innovation, The University of Texas Arlington, Arlington, TX 76010, USA
- Correspondence: (J.Z.); (T.L.); Tel.: +1-614-570-1164 (J.Z.); +86-186-6501-3854 (T.L.)
| | - Tongzheng Liu
- College of Pharmacy, Jinan University, Guangzhou 511443, China
- Correspondence: (J.Z.); (T.L.); Tel.: +1-614-570-1164 (J.Z.); +86-186-6501-3854 (T.L.)
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Kuo FC, Chao CT, Lin SH. The Dynamics and Plasticity of Epigenetics in Diabetic Kidney Disease: Therapeutic Applications Vis-à-Vis. Int J Mol Sci 2022; 23:ijms23020843. [PMID: 35055027 PMCID: PMC8777872 DOI: 10.3390/ijms23020843] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 02/01/2023] Open
Abstract
Chronic kidney disease (CKD) refers to the phenomenon of progressive decline in the glomerular filtration rate accompanied by adverse consequences, including fluid retention, electrolyte imbalance, and an increased cardiovascular risk compared to those with normal renal function. The triggers for the irreversible renal function deterioration are multifactorial, and diabetes mellitus serves as a major contributor to the development of CKD, namely diabetic kidney disease (DKD). Recently, epigenetic dysregulation emerged as a pivotal player steering the progression of DKD, partly resulting from hyperglycemia-associated metabolic disturbances, rising oxidative stress, and/or uncontrolled inflammation. In this review, we describe the major epigenetic molecular mechanisms, followed by summarizing current understandings of the epigenetic alterations pertaining to DKD. We highlight the epigenetic regulatory processes involved in several crucial renal cell types: Mesangial cells, podocytes, tubular epithelia, and glomerular endothelial cells. Finally, we highlight epigenetic biomarkers and related therapeutic candidates that hold promising potential for the early detection of DKD and the amelioration of its progression.
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Affiliation(s)
- Feng-Chih Kuo
- National Defense Medical Center, Department of Internal Medicine, Division of Endocrinology and Metabolism, Tri-Service General Hospital, Taipei 114, Taiwan
| | - Chia-Ter Chao
- Department of Internal Medicine, Nephrology Division, National Taiwan University Hospital, Taipei 100, Taiwan
- Graduate Institute of Toxicology, National Taiwan University College of Medicine, Taipei 100, Taiwan
- Department of Internal Medicine, Nephrology Division, National Taiwan University College of Medicine, Taipei 100, Taiwan
| | - Shih-Hua Lin
- National Defense Medical Center, Graduate Institute of Medical Sciences, Taipei 114, Taiwan
- National Defense Medical Center, Department of Internal Medicine, Nephrology Division, Taipei 114, Taiwan
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Islam F, Zhou Y, Lam AK. Liposomal siRNA Delivery in Papillary Thyroid Carcinoma Cells. Methods Mol Biol 2022; 2534:121-133. [PMID: 35670972 DOI: 10.1007/978-1-0716-2505-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The discovery of RNA interference (RNAi) has opened a new strategy in cancer therapy, especially by silencing target genes. Pharmacologically it can be achieved by introducing of small (19-21 base pairs) dsRNA molecules known as small interfering RNA (siRNA) targeting interested genes. siRNA mediated gene has been widely investigated for its utility in treating various diseases including cancer. However, the systemic delivery of interested siRNA via non-viral methods remains a major challenge with large numbers of polymeric and liposomal systems being tested. The most effective methods involving cationic liposomes delivery to cells. Nonetheless, systemic delivery of siRNA via cationic lipid particles is often poor due to rapid uptake by reticuloendothelial organs, resulting in decreased delivery of these particles to the site of interest. Polyethylene glycol (PEG) has been used in siRNA-liposomes formulation to minimize reticuloendothelial uptake. Also, PEGylation permits the accumulation of the liposomes-loaded siRNA at the tumor sites with defective vasculatures such as enhanced permeability and retention phenomena. Thus, a simple method to prepare stable PEGylated siRNA-loaded lipid particles could provide better systemic delivery system in treating various cancers, including papillary thyroid carcinoma. Here we illustrate a simple protocol for the formulation of siRNA-loaded lipid particles by hydration of freeze-dried matrix (HFDM) method for effective delivery of target specific siRNA to papillary thyroid carcinoma cells.
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Affiliation(s)
- Farhadul Islam
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh.
- Cancer Molecular Pathology of School of Medicine and Dentistry, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia.
| | - Yaoqi Zhou
- Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Alfred K Lam
- Cancer Molecular Pathology of School of Medicine and Dentistry, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia.
- Pathology Queensland, Gold Coast University Hospital, Southport, QLD, Australia.
- Faculty of Medicine, University of Queensland, Herston, QLD, Australia.
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Mousavi SR, Sajjadi MS, Khosravian F, Feizbakhshan S, Salmanizadeh S, Esfahani ZT, Beni FA, Arab A, Kazemi M, Shahzamani K, Sami R, Hosseinzadeh M, Salehi M, Lotfi H. Dysregulation of RNA interference components in COVID-19 patients. BMC Res Notes 2021; 14:401. [PMID: 34715923 PMCID: PMC8554738 DOI: 10.1186/s13104-021-05816-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/19/2021] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the novel coronavirus causing severe respiratory illness (COVID-19). This virus was initially identified in Wuhan city, a populated area of the Hubei province in China, and still remains one of the major global health challenges. RNA interference (RNAi) is a mechanism of post-transcriptional gene silencing that plays a crucial role in innate viral defense mechanisms by inhibiting the virus replication as well as expression of various viral proteins. Dicer, Drosha, Ago2, and DGCR8 are essential components of the RNAi system, which is supposed to be dysregulated in COVID-19 patients. This study aimed to assess the expression level of the mentioned mRNAs in COVID-19patients compared to healthy individuals. RESULTS Our findings demonstrated that the expression of Dicer, Drosha, and Ago2 was statistically altered in COVID-19 patients compared to healthy subjects. Ultimately, the RNA interference mechanism as a crucial antiviral defense system was suggested to be dysregulated in COVID-19 patients.
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Affiliation(s)
- Seyyed Reza Mousavi
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, 8175954319, Isfahan, Iran
- Medical Genetics Research Center of Genome, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Sadat Sajjadi
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Farinaz Khosravian
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, 8175954319, Isfahan, Iran
- Medical Genetics Research Center of Genome, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sara Feizbakhshan
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, 8175954319, Isfahan, Iran
- Medical Genetics Research Center of Genome, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sharareh Salmanizadeh
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, 8175954319, Isfahan, Iran
- Medical Genetics Research Center of Genome, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Zahra Taherian Esfahani
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Faeze Ahmadi Beni
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, 8175954319, Isfahan, Iran
- Medical Genetics Research Center of Genome, Isfahan University of Medical Sciences, Isfahan, Iran
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ameneh Arab
- Noor Educational and Medical Center،Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Kazemi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Kiana Shahzamani
- Isfahan Gastroenterology and Hepatology Research Center (lGHRC), Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ramin Sami
- Department of Pulmonology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Majid Hosseinzadeh
- Craniofacial and Cleft Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mansoor Salehi
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, 8175954319, Isfahan, Iran.
- Medical Genetics Research Center of Genome, Isfahan University of Medical Sciences, Isfahan, Iran.
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Hajie Lotfi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
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Adam RD, Coriu D, Jercan A, Bădeliţă S, Popescu BA, Damy T, Jurcuţ R. Progress and challenges in the treatment of cardiac amyloidosis: a review of the literature. ESC Heart Fail 2021; 8:2380-2396. [PMID: 34089308 PMCID: PMC8318516 DOI: 10.1002/ehf2.13443] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/04/2021] [Accepted: 05/12/2021] [Indexed: 12/19/2022] Open
Abstract
Cardiac amyloidosis is a restrictive cardiomyopathy determined by the accumulation of amyloid, which is represented by misfolded protein fragments in the cardiac extracellular space. The main classification of systemic amyloidosis is determined by the amyloid precursor proteins causing a very heterogeneous disease spectrum, but the main types of amyloidosis involving the heart are light chain (AL) and transthyretin amyloidosis (ATTR). AL, in which the amyloid precursor is represented by misfolded immunoglobulin light chains, can involve almost any system carrying the worst prognosis among amyloidosis patients. This has however dramatically improved in the last few years with the increased usage of the novel therapies such as proteasome inhibitors and haematopoietic cell transplantation, in the case of timely diagnosis and initiation of treatment. The treatment for AL is directed by the haematologist working closely with the cardiologist when there is a significant cardiac involvement. Transthyretin (TTR) is a protein that is produced by the liver and is involved in the transportation of thyroid hormones, especially thyroxine and retinol binding protein. ATTR results from the accumulation of transthyretin amyloid in the extracellular space of different organs and systems, especially the heart and the nervous system. Specific therapies for ATTR act at various levels of TTR, from synthesis to deposition: TTR tetramer stabilization, oligomer aggregation inhibition, genetic therapy, amyloid fibre degradation, antiserum amyloid P antibodies, and antiserum TTR antibodies. Treatment of systemic amyloidosis has dramatically evolved over the last few years in both AL and ATTR, improving disease prognosis. Moreover, recent studies revealed that timely treatment can lead to an improvement in clinical status and in a regression of amyloid myocardial infiltration showed by imaging, especially by cardiac magnetic resonance, in both AL and ATTR. However, treating cardiac amyloidosis is a complex task due to the frequent association between systemic congestion and low blood pressure, thrombo-embolic and haemorrhagic risk balance, patient frailty, and generally poor prognosis. The aim of this review is to describe the current state of knowledge regarding cardiac amyloidosis therapy in this constantly evolving field, classified as treatment of the cardiac complications of amyloidosis (heart failure, rhythm and conduction disturbances, and thrombo-embolic risk) and the disease-modifying therapy.
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Affiliation(s)
- Robert Daniel Adam
- Department of CardiologyEmergency Institute for Cardiovascular Diseases ‘Prof. Dr. C. C. Iliescu’3rd Cardiology Department, 258 Fundeni StreetBucharest022328Romania
- University of Medicine and Pharmacy ‘Carol Davila’BucharestRomania
| | - Daniel Coriu
- University of Medicine and Pharmacy ‘Carol Davila’BucharestRomania
- Department of HematologyFundeni Clinical InstituteBucharestRomania
| | - Andreea Jercan
- University of Medicine and Pharmacy ‘Carol Davila’BucharestRomania
| | - Sorina Bădeliţă
- Department of HematologyFundeni Clinical InstituteBucharestRomania
| | - Bogdan A. Popescu
- Department of CardiologyEmergency Institute for Cardiovascular Diseases ‘Prof. Dr. C. C. Iliescu’3rd Cardiology Department, 258 Fundeni StreetBucharest022328Romania
- University of Medicine and Pharmacy ‘Carol Davila’BucharestRomania
| | - Thibaud Damy
- French Referral Center for Cardiac AmyloidosisAmyloidosis Mondor NetworkCréteilFrance
- Department of CardiologyHenri Mondor Hospital/AP‐HPCréteilFrance
| | - Ruxandra Jurcuţ
- Department of CardiologyEmergency Institute for Cardiovascular Diseases ‘Prof. Dr. C. C. Iliescu’3rd Cardiology Department, 258 Fundeni StreetBucharest022328Romania
- University of Medicine and Pharmacy ‘Carol Davila’BucharestRomania
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IKBKB siRNA-Encapsulated Poly (Lactic- co-Glycolic Acid) Nanoparticles Diminish Neuropathic Pain by Inhibiting Microglial Activation. Int J Mol Sci 2021; 22:ijms22115657. [PMID: 34073390 PMCID: PMC8203094 DOI: 10.3390/ijms22115657] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 01/08/2023] Open
Abstract
Activation of nuclear factor-kappa B (NF-κB) in microglia plays a decisive role in the progress of neuropathic pain, and the inhibitor of kappa B (IκB) is a protein that blocks the activation of NF-κB and is degraded by the inhibitor of NF-κB kinase subunit beta (IKBKB). The role of IKBKB is to break down IκB, which blocks the activity of NF-kB. Therefore, it prevents the activity of NK-kB. This study investigated whether neuropathic pain can be reduced in spinal nerve ligation (SNL) rats by reducing the activity of microglia by delivering IKBKB small interfering RNA (siRNA)-encapsulated poly (lactic-co-glycolic acid) (PLGA) nanoparticles. PLGA nanoparticles, as a carrier for the delivery of IKBKB genes silencer, were used because they have shown potential to enhance microglial targeting. SNL rats were injected with IKBKB siRNA-encapsulated PLGA nanoparticles intrathecally for behavioral tests on pain response. IKBKB siRNA was delivered for suppressing the expression of IKBKB. In rats injected with IKBKB siRNA-encapsulated PLGA nanoparticles, allodynia caused by mechanical stimulation was reduced, and the secretion of pro-inflammatory mediators due to NF-κB was reduced. Delivering IKBKB siRNA through PLGA nanoparticles can effectively control the inflammatory response and is worth studying as a treatment for neuropathic pain.
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Romano G, Acunzo M, Nana-Sinkam P. microRNAs as Novel Therapeutics in Cancer. Cancers (Basel) 2021; 13:cancers13071526. [PMID: 33810332 PMCID: PMC8037786 DOI: 10.3390/cancers13071526] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Over the last few years, we have witnessed incredible advancements in anti-tumor drug development. microRNAs, a class of small non-coding RNAs dysregulated in all cancers, have been recently elected as candidate therapeutics for treating a variety of diseases, including cancer. The scope of this review is to give some insight into the role of the most relevant microRNAs in cancer. We will focus on examining their biological role in tumor development while also providing a broad overview of microRNAs as therapeutics. There is a dedicated focus on the different methods available for microRNA delivery in addition to the efforts being made to increase the specificity of these delivery methods. Finally, we discuss the ongoing clinical trials that are using microRNAs for cancer treatment. Abstract In the last 20 years, the functional roles for miRNAs in gene regulation have been well established. MiRNAs act as regulators in virtually all biological pathways and thus have been implicated in numerous diseases, including cancer. They are particularly relevant in regulating the basic hallmarks of cancer, including apoptosis, proliferation, migration, and invasion. Despite the substantial progress made in identifying the molecular mechanisms driving the deregulation of miRNAs in cancer, the clinical translation of these important molecules to therapy remains in its infancy. The paucity of vehicles available for the safe and efficient delivery of miRNAs and ongoing concerns for toxicity remain major obstacles to clinical application. Novel formulations and the development of new vectors have significantly improved the stability of oligonucleotides, increasing the effectiveness of therapy. Furthermore, the use of specific moieties for delivery in target tissues or cells has increased the specificity of treatment. The use of new technologies has allowed small but important steps toward more specific therapeutic delivery in tumor tissues and cells. Although a long road remains, the path ahead holds great potential. Currently, a few miRNA drugs are under investigation in human clinical trials with promising results ahead.
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Kwon S, Shin S, Do M, Oh BH, Song Y, Bui VD, Lee ES, Jo DG, Cho YW, Kim DH, Park JH. Engineering approaches for effective therapeutic applications based on extracellular vesicles. J Control Release 2020; 330:15-30. [PMID: 33278480 DOI: 10.1016/j.jconrel.2020.11.062] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/24/2020] [Accepted: 11/30/2020] [Indexed: 12/18/2022]
Abstract
The biological significance of extracellular vesicles (EVs) as intercellular communication mediators has been increasingly revealed in a wide range of normal physiological processes and disease pathogenesis. In particular, regenerative and immunomodulatory EVs hold potential as innate biotherapeutics, whereas pathological EVs are considered therapeutic targets for inhibiting their bioactivity. Given their ability to transport functional cargos originating from the source cells to target cells, EVs can also be used as a therapeutic means to deliver drug molecules. This review aims to provide an updated overview of the key engineering approaches for better exploiting EVs in disease intervention. The emphasis is lying on the preconditioning methods for therapeutic EVs, drug loading and targeting technologies for carrier EVs, and activity control strategies for pathological EVs.
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Affiliation(s)
- Seunglee Kwon
- School of Chemical Engineering, College of Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sol Shin
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Republic of Korea
| | - Minjae Do
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Byeong Hoon Oh
- School of Chemical Engineering, College of Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Yeari Song
- School of Chemical Engineering, College of Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Van Dat Bui
- School of Chemical Engineering, College of Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Eun Sook Lee
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Republic of Korea
| | - Dong-Gyu Jo
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Republic of Korea; Biomedical Institute for Convergence at SKKU, Sungkyunkwan University, Suwon 16419, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea; ExoStemTech Inc., Ansan 15588, Republic of Korea
| | - Yong Woo Cho
- ExoStemTech Inc., Ansan 15588, Republic of Korea; Department of Chemical Engineering, Hanyang University, Ansan 15588, Republic of Korea
| | - Deok-Ho Kim
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Jae Hyung Park
- School of Chemical Engineering, College of Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea; Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Republic of Korea; Biomedical Institute for Convergence at SKKU, Sungkyunkwan University, Suwon 16419, Republic of Korea; ExoStemTech Inc., Ansan 15588, Republic of Korea.
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Krivosheeva IA, Filatova AY, Moshkovskii SA, Baranova AV, Skoblov MY. Analysis of candidate genes expected to be essential for melanoma surviving. Cancer Cell Int 2020; 20:488. [PMID: 33041669 PMCID: PMC7541296 DOI: 10.1186/s12935-020-01584-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/28/2020] [Indexed: 11/10/2022] Open
Abstract
Introduction Cancers may be treated by selective targeting of the genes vital for their survival. A number of attempts have led to discovery of several genes essential for surviving of tumor cells of different types. In this work, we tried to analyze genes that were previously predicted to be essential for melanoma surviving. Here we present the results of transient siRNA-mediated knockdown of the four of such genes, namely, UNC45A, STK11IP, RHPN2 and ZNFX1, in melanoma cell line A375, then assayed the cells for their viability, proliferation and ability to migrate in vitro. In our study, the knockdown of the genes predicted as essential for melanoma survival does not lead to statistically significant changes in cell viability. On the other hand, for each of the studied genes, mobility assays showed that the knockdown of each of the target genes accelerates the speed of cells migrating. Possible explanation for such counterintuitive results may include insufficiency of the predicting computational models or the necessity of a multiplex knockdown of the genes. Aims To examine the hypothesis of essentiality of hypomutated genes for melanoma surviving we have performed knockdown of several genes in melanoma cell line and analyzed cell viability and their ability to migrate. Methods Knockdown was performed by siRNAs transfected by Metafectene PRO. The levels of mRNAs before and after knockdown were evaluated by RT-qPCR analysis. Cell viability and proliferation were assessed by MTT assay. Cell migration was assessed by wound healing assay. Results The knockdown of the genes predicted as essential for melanoma survival does not lead to statistically significant changes in cell viability. On the other hand, for each of the studied genes, mobility assays showed that the knockdown of each of the target genes accelerates the speed of cells migrating. Conclusion Our results do not confirm initial hypothesis that the genes predicted essential for melanoma survival as a matter of fact support the survival of melanoma cells.
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Affiliation(s)
- Irina A Krivosheeva
- Laboratory of Functional Genomics, Research Centre of Medical Genetics, Erevanskaya Street, 10 building 2, Floor 44, Moscow, 115304 Russia
| | - Alexandra Yu Filatova
- Laboratory of Functional Genomics, Research Centre of Medical Genetics, Erevanskaya Street, 10 building 2, Floor 44, Moscow, 115304 Russia
| | - Sergei A Moshkovskii
- Laboratory of Medical Proteomics, Institute of Biomedical Chemistry, Moscow, Russia
| | - Ancha V Baranova
- School of Systems Biology, George Mason University, Fairfax, VA USA.,Laboratory of Functional Genomics, Research Centre of Medical Genetics, Erevanskaya Street, 10 building 2, Floor 44, Moscow, 115304 Russia
| | - Mikhail Yu Skoblov
- Laboratory of Functional Genomics, Research Centre of Medical Genetics, Erevanskaya Street, 10 building 2, Floor 44, Moscow, 115304 Russia
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Hu B, Boakye‐Yiadom KO, Yu W, Yuan Z, Ho W, Xu X, Zhang X. Nanomedicine Approaches for Advanced Diagnosis and Treatment of Atherosclerosis and Related Ischemic Diseases. Adv Healthc Mater 2020; 9:e2000336. [PMID: 32597562 DOI: 10.1002/adhm.202000336] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/30/2020] [Indexed: 12/16/2022]
Abstract
Cardiovascular diseases (CVDs) remain one of the major causes of mortality worldwide. In response to this and other worldwide health epidemics, nanomedicine has emerged as a rapidly evolving discipline that involves the development of innovative nanomaterials and nanotechnologies and their applications in therapy and diagnosis. Nanomedicine presents unique advantages over conventional medicines due to the superior properties intrinsic to nanoscopic therapies. Once used mainly for cancer therapies, recently, tremendous progress has been made in nanomedicine that has led to an overall improvement in the treatment and diagnosis of CVDs. This review elucidates the pathophysiology and potential targets of atherosclerosis and associated ischemic diseases. It may be fruitful to pursue future work in the nanomedicine-mediated treatment of CVDs based on these targets. A comprehensive overview is then provided featuring the latest preclinical and clinical outcomes in cardiovascular imaging, biomarker detection, tissue engineering, and nanoscale delivery, with specific emphasis on nanoparticles, nanostructured scaffolds, and nanosensors. Finally, the challenges and opportunities regarding the future development and clinical translation of nanomedicine in related fields are discussed. Overall, this review aims to provide a deep and thorough understanding of the design, application, and future development of nanomedicine for atherosclerosis and related ischemic diseases.
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Affiliation(s)
- Bin Hu
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of PharmacyShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 P. R. China
| | - Kofi Oti Boakye‐Yiadom
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of PharmacyShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 P. R. China
| | - Wei Yu
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of PharmacyShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 P. R. China
| | - Zi‐Wei Yuan
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of PharmacyShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 P. R. China
| | - William Ho
- Department of Chemical and Materials EngineeringNew Jersey Institute of Technology Newark NJ 07102 USA
| | - Xiaoyang Xu
- Department of Chemical and Materials EngineeringNew Jersey Institute of Technology Newark NJ 07102 USA
| | - Xue‐Qing Zhang
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of PharmacyShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 P. R. China
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Yu S, Yan C, Wu W, He S, Liu M, Liu J, Yang X, Ma J, Lu Y, Jia L. RU486 Metabolite Inhibits CCN1/Cyr61 Secretion by MDA-MB-231-Endothelial Adhesion. Front Pharmacol 2019; 10:1296. [PMID: 31824306 PMCID: PMC6880622 DOI: 10.3389/fphar.2019.01296] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/10/2019] [Indexed: 12/26/2022] Open
Abstract
Successful adhesion of circulating tumor cells (CTCs) to microvascular endothelium of distant metastatic tissue is the key starting step of metastatic cascade that could be effectively chemoprevented as we demonstrated previously. Here, we hypothesize that the hetero-adhesion may produce secretory biomarkers that may be important for both premetastatic diagnosis and chemoprevention. We show that co-incubation of triple-negative breast cancer (TNBC) cell line MDA-MB-231 with human pulmonary microvascular endothelial monolayers (HPMEC) secretes Cyr61 (CCN1), primarily from MDA-MB-231. However, addition of metapristone (RU486 metabolite) to the co-incubation system inhibits Cyr61 secretion probably via the Cyr61/integrin αvβ1 signaling pathway without significant cytotoxicity on both MDA-MB-231 and HPMEC. Transfection of MDA-MB-231 with Cyr61-related recombinant plasmid or siRNA enhances or reduces Cyr61 expression, accordingly. The transfection significantly changes hetero-adhesion and migration of MDA-MB-231, and the changed bioactivities by overexpressed CYR61 could be antagonized by metapristone in vitro. Moreover, the circulating MDA-MB-231 develops lung metastasis in mice, which could be effectively prevented by oral metapristone without significant toxicity. The present study, for the first time, demonstrates that co-incubation of MDA-MB-231 with HPMEC secrets CYR61 probably via the CYR61/integrin αvβ1 signaling pathway to promote adhesion-invasion of TNBC (early metastatic step). Metapristone, by interfering the adhesion-invasion process, prevents metastasis from happening.
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Affiliation(s)
- Suhong Yu
- Cancer Metastasis Alert and Prevention Center, and Biopharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, Fuzhou, China
| | - Cuicui Yan
- Cancer Metastasis Alert and Prevention Center, and Biopharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, Fuzhou, China
| | - Wenjing Wu
- Cancer Metastasis Alert and Prevention Center, and Biopharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, Fuzhou, China
| | - Sudan He
- Cancer Metastasis Alert and Prevention Center, and Biopharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, Fuzhou, China
| | - Min Liu
- Cancer Metastasis Alert and Prevention Center, and Biopharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, Fuzhou, China
| | - Jian Liu
- Cancer Metastasis Alert and Prevention Center, and Biopharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, Fuzhou, China
| | - Xingtian Yang
- Cancer Metastasis Alert and Prevention Center, and Biopharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, Fuzhou, China
| | - Ji Ma
- Cancer Metastasis Alert and Prevention Center, and Biopharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, Fuzhou, China
| | - Yusheng Lu
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Lee Jia
- Cancer Metastasis Alert and Prevention Center, and Biopharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, Fuzhou, China.,Institute of Oceanography, Minjiang University, Fuzhou, China
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21
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Brodskaia AV, Timin AS, Gorshkov AN, Muslimov AR, Bondarenko AB, Tarakanchikova YV, Zabrodskaya YA, Baranovskaya IL, Il'inskaja EV, Sakhenberg EI, Sukhorukov GB, Vasin AV. Inhibition of influenza A virus by mixed siRNAs, targeting the PA, NP, and NS genes, delivered by hybrid microcarriers. Antiviral Res 2018; 158:147-160. [PMID: 30092251 DOI: 10.1016/j.antiviral.2018.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 07/02/2018] [Accepted: 08/03/2018] [Indexed: 12/28/2022]
Abstract
In the present study, a highly effective carrier system has been developed for the delivery of antiviral siRNA mixtures. The developed hybrid microcarriers, made of biodegradable polymers and SiO2 nanostructures, more efficiently mediate cellular uptake of siRNA than commercially available liposome-based reagents and polyethyleneimine (PEI); they also demonstrate low in vitro toxicity and protection of siRNA from RNase degradation. A series of siRNA designs (targeting the most conserved regions of three influenza A virus (IAV) genes: NP, NS, and PA) were screened in vitro using RT-qPCR, ELISA analysis, and hemagglutination assay. Based on the results of screening, the three most effective siRNAs (PA-1630, NP-717, and NS-777) were selected for in situ encapsulation into hybrid microcarriers. It was revealed that pre-treatment of cells with a mixture of PA-1630, NP-717, and NS-777 siRNAs, delivered by hybrid microcarriers, provided stronger inhibition of viral M1 mRNA expression and control of NP protein level, after viral infection, than single pre-treatment by any of three encapsulated siRNAs used in the study. Moreover, the effective inhibition of replication in several IAV subtypes (H1N1, H1N1pdm, H5N2, and H7N9) using a cocktail of the three selected siRNAs, delivered by our hybrid capsules to the cells, was achieved. In conclusion, we have developed a proof-of-principle which shows that our hybrid microcarrier technology (utilizing a therapeutic siRNA cocktail) may represent a promising approach in anti-influenza therapy.
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Affiliation(s)
- Aleksandra V Brodskaia
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, 197376, St. Petersburg, Russian Federation; Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251, St. Petersburg, Russian Federation.
| | - Alexander S Timin
- RASA Center, National Research Tomsk Polytechnic University, Lenin Avenue, 30, 634050, Tomsk, Russian Federation; First I. P. Pavlov State Medical University of St. Petersburg, Lev Tolstoy str., 6/8, 197022, St. Petersburg, Russian Federation.
| | - Andrey N Gorshkov
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, 197376, St. Petersburg, Russian Federation; Institute of Cytology, Russian Academy of Sciences, Tikhoretsky ave. 4, 194064, St. Petersburg, Russian Federation
| | - Albert R Muslimov
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, 197376, St. Petersburg, Russian Federation; First I. P. Pavlov State Medical University of St. Petersburg, Lev Tolstoy str., 6/8, 197022, St. Petersburg, Russian Federation
| | - Andrei B Bondarenko
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, 197376, St. Petersburg, Russian Federation; St. Petersburg State University, Vasilyevsky Island, Liniya 16-ya, 29, 199178, St. Petersburg, Russian Federation
| | - Yana V Tarakanchikova
- Saratov State University, Astrakhanskaya Street 83, 410012, Saratov, Russian Federation
| | - Yana A Zabrodskaya
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, 197376, St. Petersburg, Russian Federation; Petersburg Nuclear Physics Institute in Honor of B. P. Konstantinov, National Research Center "Kurchatov Institute", 188300, Gatchina, Russian Federation
| | - Irina L Baranovskaya
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, 197376, St. Petersburg, Russian Federation; Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251, St. Petersburg, Russian Federation
| | - Eugenia V Il'inskaja
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, 197376, St. Petersburg, Russian Federation
| | - Elena I Sakhenberg
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, 197376, St. Petersburg, Russian Federation; Institute of Cytology, Russian Academy of Sciences, Tikhoretsky ave. 4, 194064, St. Petersburg, Russian Federation
| | - Gleb B Sukhorukov
- Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251, St. Petersburg, Russian Federation; School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom
| | - Andrey V Vasin
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, 197376, St. Petersburg, Russian Federation; Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251, St. Petersburg, Russian Federation; St. Petersburg State Chemical Pharmaceutical Academy, Prof. Popova str., 14 A, 197376, St. Petersburg, Russian Federation.
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