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Sharma V, Singh J, Kumar A, Kansara S, Akhtar MS, Khan MF, Aldosari SA, Mukherjee M, Sharma AK. Integrative experimental validation of concomitant miRNAs and transcription factors with differentially expressed genes in acute myocardial infarction. Eur J Pharmacol 2024; 971:176540. [PMID: 38552938 DOI: 10.1016/j.ejphar.2024.176540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/20/2024]
Abstract
Identification of concomitant miRNAs and transcription factors (TFs) with differential expression (DEGs) in MI is crucial for understanding holistic gene regulation, identifying key regulators, and precision in biomarker and therapeutic target discovery. We performed a comprehensive analysis using Affymetrix microarray data, advanced bioinformatic tools, and experimental validation to explore potential biomarkers associated with human pathology. The search strategy includes the identification of the GSE83500 dataset, comprising gene expression profiles from aortic wall punch biopsies of MI and non-MI patients, which were used in the present study. The analysis identified nine distinct genes exhibiting DEGs within the realm of MI. miRNA-gene/TF and TF-gene/miRNA regulatory relations were mapped to retrieve interacting hub genes to acquire an MI miRNA-TF co-regulatory network. Furthermore, an animal model of I/R-induced MI confirmed the involved gene based on quantitative RT-PCR and Western blot analysis. The consequences of the bioinformatic tool substantiate the inference regarding the presence of three key hub genes (UBE2N, TMEM106B, and CXADR), a central miRNA (hsa-miR-124-3p), and sixteen TFs. Animal studies support the involvement of predicted genes in the I/R-induced myocardial infarction assessed by RT-PCR and Western blotting. Thus, the final consequences suggest the involvement of promising molecular pathways regulated by TF (p53/NF-κB1), miRNA (hsa-miR-124-3p), and hub gene (UBE2N), which may play a key role in the pathogenesis of MI.
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Affiliation(s)
- Vikash Sharma
- Department of Pharmacology, Amity Institute of Pharmacy, Amity University Haryana, Gurugram, India
| | - Jitender Singh
- Department of Pharmacology, Amity Institute of Pharmacy, Amity University Haryana, Gurugram, India
| | - Ashish Kumar
- Department of Pharmacology, Amity Institute of Pharmacy, Amity University Haryana, Gurugram, India
| | - Samarth Kansara
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana, 122413, India
| | - Md Sayeed Akhtar
- Department of Clinical Pharmacy, College of Pharmacy, King Khalid University, Alfara, Abha, 62223, Saudi Arabia
| | - Mohd Faiyaz Khan
- Department of Clinical Pharmacy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Saad A Aldosari
- Department of Clinical Pharmacy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Monalisa Mukherjee
- Molecular Sciences and Engineering Laboratory, Amity Institute of Click Chemistry Research and Studies, Amity University, Noida, Uttar Pradesh, 201303, India
| | - Arun K Sharma
- Department of Pharmacology, Amity Institute of Pharmacy, Amity University Haryana, Gurugram, India.
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Zhang X, Xiao YL, Shi X, Shi HL, Dong ZX, Tang CD. The role of cellular senescence-related genes in Asthma: Insights from bioinformatics and animal experiments. Int Immunopharmacol 2024; 130:111770. [PMID: 38430806 DOI: 10.1016/j.intimp.2024.111770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/17/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND Asthma is a heterogeneous chronic respiratory disease, affecting about 10% of the global population. Cellular senescence is a multifaceted phenomenon defined as the irreversible halt of the cell cycle, commonly referred to as the senescence-associated secretory phenotype. Recent studies suggest that cellular senescence may play a role in asthma. This study aims to dissect the role and biological mechanisms of CSRGs in asthma, enhancing our understanding of the progression of asthma. METHODS The study utilized the GSE147878 dataset, employing methods like WGCNA, Differential analysis, Cibersort, GO, KEGG, unsupervised clustering, and GSVA to explore CSRGs functions and immune cell patterns in asthma. Machine learning identified key diagnostic genes, validated externally with the GSE165934 dataset and through qRT-PCR and WB experiments in animal models. RESULT From the GSE147878 dataset, 24 CSRGs were identified, highlighting their role in immune and inflammatory processes in asthma. Differences in CD4 naive T cells and activated dendritic cells between asthma and control groups underscored CSRGs' role in immune regulation. Cluster analysis revealed two distinct asthma patient groups with unique immune microenvironments. Machine learning identified five genes, leading to a TF-miRNA-mRNA network and singling out RHOA and RBM39 as key diagnostic genes, which were experimentally validated. Finally, a nomogram was created based on these genes. CONCLUSION This study, utilizing bioinformatics and animal experiments, identified RHOA and RBM39 as key diagnostic genes for asthma, providing new insights into the potential role and biological mechanisms of CSRGs in asthma.
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Affiliation(s)
- Xiang Zhang
- Henan Provincial Engineering Laboratory of Insect Bio-reactor, Henan International Joint Laboratory of Insect Biology and Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China; College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, People's Republic of China
| | - Ya-Li Xiao
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, People's Republic of China
| | - Xin Shi
- Department of College English Teaching and Studies, Nanyang Normal University, Nanyang, 473061, People's Republic of China
| | - Hong-Ling Shi
- Henan Provincial Engineering Laboratory of Insect Bio-reactor, Henan International Joint Laboratory of Insect Biology and Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China; College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, People's Republic of China
| | - Zi-Xing Dong
- Henan Provincial Engineering Laboratory of Insect Bio-reactor, Henan International Joint Laboratory of Insect Biology and Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China; College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, People's Republic of China
| | - Cun-Duo Tang
- Henan Provincial Engineering Laboratory of Insect Bio-reactor, Henan International Joint Laboratory of Insect Biology and Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China; College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, People's Republic of China.
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Zheng J, Wang R, Wang Y. New concepts drive the development of delivery tools for sustainable treatment of diabetic complications. Biomed Pharmacother 2024; 171:116206. [PMID: 38278022 DOI: 10.1016/j.biopha.2024.116206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024] Open
Abstract
Diabetic complications, especially diabetic retinopathy, diabetic nephropathy and painful diabetic neuropathy, account for a large portion of patients with diabetes and display rising global prevalence. They are the leading causes of blindness, kidney failure and hypersensitivity to pain caused by diabetes. Current approved therapeutics against the diabetic complications are few and exhibit limited efficacy. The enhanced cell-specificity, stability, biocompatibility, and loading capacity of drugs are essential for the mitigation of diabetic complications. In the article, we have critically discussed the recent studies over the past two years in material sciences and biochemistry. The insightful concepts in these studies drive the development of novel nanoparticles and mesenchymal stem cells-derived extracellular vesicles to meet the need for treatment of diabetic complications. Their underlying biochemical principles, advantages and limitations have been in-depth analyzed. The nanoparticles discussed in the article include double-headed nanodelivery system, nanozyme, ESC-HCM-B system, soft polymer nanostars, tetrahedral DNA nanostructures and hydrogels. They ameliorate the diabetic complication through attenuation of inflammation, apoptosis and restoration of metabolic homeostasis. Moreover, mesenchymal stem cell-derived extracellular vesicles efficiently deliver therapeutic proteins to the retinal cells to suppress the angiogenesis, inflammation, apoptosis and oxidative stress to reverse diabetic retinopathy. Collectively, we provide a critical discussion on the concept, mechanism and therapeutic applicability of new delivery tools to treat these three devastating diabetic complications.
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Affiliation(s)
- Jianan Zheng
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Ru Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China; Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, China.
| | - Yibing Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China; Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, China.
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Totoń-Żurańska J, Sulicka-Grodzicka J, Seweryn MT, Pitera E, Kapusta P, Konieczny P, Drabik L, Kołton-Wróż M, Chyrchel B, Nowak E, Surdacki A, Grodzicki T, Wołkow PP. MicroRNA composition of plasma extracellular vesicles: a harbinger of late cardiotoxicity of doxorubicin. Mol Med 2022; 28:156. [PMID: 36517751 PMCID: PMC9753431 DOI: 10.1186/s10020-022-00588-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 11/09/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The use of doxorubicin is associated with an increased risk of acute and long-term cardiomyopathy. Despite the constantly growing number of cancer survivors, little is known about the transcriptional mechanisms which progress in the time leading to a severe cardiac outcome. It is also unclear whether long-term transcriptomic alterations related to doxorubicin use are similar to transcriptomic patterns present in patients suffering from other cardiomyopathies. METHODS We have sequenced miRNA from total plasma and extracellular vesicles (EVs) from 66 acute lymphoblastic leukemia (ALL) survivors and 61 healthy controls (254 samples in total). We then analyzed processes regulated by differentially expressed circulating miRNAs and cross-validated results with the data of patients with clinically manifested cardiomyopathies. RESULTS We found that especially miRNAs contained within EVs may be informative in terms of cardiomyopathy development and may regulate pathways related to neurotrophin signaling, transforming growth factor beta (TGFβ) or epidermal growth factor receptors (ErbB). We identified vesicular miR-144-3p and miR-423-3p as the most variable between groups and significantly correlated with echocardiographic parameters and, respectively, for plasma: let-7g-5p and miR-16-2-3p. Moreover, vesicular miR-144-3p correlates with the highest number of echocardiographic parameters and is differentially expressed in the circulation of patients with dilated cardiomyopathy. We also found that distribution of particular miRNAs between of plasma and EVs (proportion between compartments) e.g., miR-184 in ALL, is altered, suggesting changes within secretory and miRNA sorting mechanisms. CONCLUSIONS Our results show that transcriptomic changes resulting from doxorubicin induced myocardial injury are reflected in circulating miRNA levels and precede development of the late onset cardiomyopathy phenotype. Among miRNAs related to cardiac function, we found vesicular miR-144-3p and miR-423-3p, as well as let-7g-5p and miR-16-2-3p contained in the total plasma. Selection of source for such studies (plasma or EVs) is of critical importance, as distribution of some miRNA between plasma and EVs is altered in ALL survivors, in comparison to healthy people, which suggests that doxorubicin-induced changes include miRNA sorting and export to extracellular space.
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Affiliation(s)
- Justyna Totoń-Żurańska
- grid.5522.00000 0001 2162 9631Center for Medical Genomics OMICRON, Jagiellonian University Medical College, ul. Kopernika 7C, 31-034 Krakow, Poland
| | - Joanna Sulicka-Grodzicka
- grid.5522.00000 0001 2162 9631Department of Rheumatology, Jagiellonian University Medical College, Krakow, Poland
| | - Michał T. Seweryn
- grid.5522.00000 0001 2162 9631Center for Medical Genomics OMICRON, Jagiellonian University Medical College, ul. Kopernika 7C, 31-034 Krakow, Poland ,grid.261331.40000 0001 2285 7943Department of Cancer Biology and Genetics, Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus, OH USA
| | - Ewelina Pitera
- grid.5522.00000 0001 2162 9631Center for Medical Genomics OMICRON, Jagiellonian University Medical College, ul. Kopernika 7C, 31-034 Krakow, Poland
| | - Przemysław Kapusta
- grid.5522.00000 0001 2162 9631Center for Medical Genomics OMICRON, Jagiellonian University Medical College, ul. Kopernika 7C, 31-034 Krakow, Poland
| | - Paweł Konieczny
- grid.5522.00000 0001 2162 9631Center for Medical Genomics OMICRON, Jagiellonian University Medical College, ul. Kopernika 7C, 31-034 Krakow, Poland
| | - Leszek Drabik
- grid.5522.00000 0001 2162 9631Medical College and John Paul II Hospital, Jagiellonian University, Krakow, Poland ,grid.5522.00000 0001 2162 9631Department of Pharmacology, Jagiellonian University Medical College, Krakow, Poland
| | - Maria Kołton-Wróż
- grid.5522.00000 0001 2162 9631Center for Medical Genomics OMICRON, Jagiellonian University Medical College, ul. Kopernika 7C, 31-034 Krakow, Poland
| | - Bernadeta Chyrchel
- grid.5522.00000 0001 2162 9631Second Department of Cardiology, Jagiellonian University Medical College, Krakow, Poland
| | - Ewelina Nowak
- grid.5522.00000 0001 2162 9631Department of Internal Medicine and Gerontology, Jagiellonian University Medical College, Krakow, Poland
| | - Andrzej Surdacki
- grid.5522.00000 0001 2162 9631Second Department of Cardiology, Jagiellonian University Medical College, Krakow, Poland
| | - Tomasz Grodzicki
- grid.5522.00000 0001 2162 9631Department of Internal Medicine and Gerontology, Jagiellonian University Medical College, Krakow, Poland
| | - Paweł P. Wołkow
- grid.5522.00000 0001 2162 9631Center for Medical Genomics OMICRON, Jagiellonian University Medical College, ul. Kopernika 7C, 31-034 Krakow, Poland ,grid.5522.00000 0001 2162 9631Department of Pharmacology, Jagiellonian University Medical College, Krakow, Poland
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Current Status and Trends of Research on Anthracycline-Induced Cardiotoxicity from 2002 to 2021: A Twenty-Year Bibliometric and Visualization Analysis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:6260243. [PMID: 35993025 PMCID: PMC9388240 DOI: 10.1155/2022/6260243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/21/2022] [Accepted: 07/24/2022] [Indexed: 12/30/2022]
Abstract
Anthracyclines constitute the cornerstone of numerous chemotherapy regimens for various cancers. However, the clinical application of anthracyclines is significantly limited to their dose-dependent cardiotoxicity. A comprehensive understanding of the current status of anthracycline-induced cardiotoxicity is necessary for in-depth research and optimal clinical protocols. Bibliometric analysis is widely applied in depicting development trends and tracking frontiers of a specific field. The present study is aimed at revealing the status and trends of anthracycline-induced cardiotoxicity during the past two decades by employing bibliometric software including R-bibliometric, VOSviewer, and CiteSpace. A total of 3504 publications concerning anthracycline-induced cardiotoxicity from 2002 to 2021 were collected from the Web of Science Core Collection database. Results showed significant growth in annual yields from 90 records in 2002 to 304 papers in 2021. The United States was the most productive country with the strongest collaboration worldwide in the field. Charles University in the Czech Republic was the institution that contributed the most papers, while 7 of the top 10 productive institutions were from the United States. The United States Department of Health and Human Services and the National Institutes of Health are the two agencies that provide financial support for more than 50% of sponsored publications. The research categories of included publications mainly belong to Oncology and Cardiac Cardiovascular Systems. The Journal of Clinical Oncology had a comprehensive impact on this research field with the highest IF value and many publications. Simunek Tomas from Charles University contributed the most publications, while Lipshultz Steven E. from the State University of New York possessed the highest H-index. In addition, the future research frontiers of anthracycline-induced cardiotoxicity might include early detection, pharmacogenomics, molecular mechanism, and cardiooncology. The present bibliometric analysis may provide a valuable reference for researchers and practitioners in future research directions.
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