In silico and in vitro analysis of microRNAs with therapeutic potential in atherosclerosis
Abstract Atherosclerosis is a chronic inflammatory disease in which aberrant lipid metabolism plays a key role. MicroRNAs (miRNAs), micro-coordinators of gene expression, have been recently proposed as novel clinical biomarkers and potential therapeutic tools for a broad spectrum of diseases. This s...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-11-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-24260-z |
| _version_ | 1797986728866217984 |
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| author | Maryam Mahjoubin-Tehran Seyed Hamid Aghaee-Bakhtiari Amirhossein Sahebkar Alexandra E. Butler Reza Kazemi Oskuee Amin Jalili |
| author_facet | Maryam Mahjoubin-Tehran Seyed Hamid Aghaee-Bakhtiari Amirhossein Sahebkar Alexandra E. Butler Reza Kazemi Oskuee Amin Jalili |
| author_sort | Maryam Mahjoubin-Tehran |
| collection | DOAJ |
| description | Abstract Atherosclerosis is a chronic inflammatory disease in which aberrant lipid metabolism plays a key role. MicroRNAs (miRNAs), micro-coordinators of gene expression, have been recently proposed as novel clinical biomarkers and potential therapeutic tools for a broad spectrum of diseases. This study aimed to identify miRNAs with therapeutic potential in atherosclerosis. Bioinformatic databases, including experimentally validated and computational prediction tools as well as a novel combination method, were used to identify miRNAs that are able to simultaneously inhibit key genes related to the pathogenesis of atherosclerosis. Further validation of genes and miRNAs was conducted using the STRING online tool, KEGG pathway analysis and DIANA-miRPath. The inhibitory effects of the identified miRNAs in HepG2 and Huh7 cells were verified by real-time PCR. The MTT assay was utilized to evaluate cell cytotoxicity effects of miRNAs. Atherosclerotic drug-targeted genes were selected as key genes. Strong interactions between genes were confirmed using STRING. These genes were shown to be integral to critical pathological processes involved in atherosclerosis. A novel combined method of validated and predicted tools for the identification of effective miRNAs was defined as the combination score (C-Score). Bioinformatic analysis showed that hsa-miR-124-3p and hsa-miR-16-5p possessed the best C-Score (0.68 and 0.62, respectively). KEGG and DIANA-miRPath analysis showed that selected genes and identified miRNAs were involved in atherosclerosis-related pathways. Compared with the controls in both HepG2 and Huh7 cell lines, miR-124 significantly reduced the expression of CETP, PCSK9, MTTP, and APOB, and miR-16 significantly reduced the expression of APOCIII, CETP, HMGCR, PCSK9, MTTP, and APOB, respectively. The cytotoxicity assay showed that miR-124 reduced cell viability, especially after 72 h; however, miR-16 did not show any significant cytotoxicity in either cell line. Our findings indicate that hsa-miR-124 and miR-16 have potential for use as therapeutic candidates in the treatment of atherosclerosis. |
| first_indexed | 2024-04-11T07:36:39Z |
| format | Article |
| id | doaj.art-888e3233bb9b41a08cb25e4192aa1c9b |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-11T07:36:39Z |
| publishDate | 2022-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-888e3233bb9b41a08cb25e4192aa1c9b2022-12-22T04:36:43ZengNature PortfolioScientific Reports2045-23222022-11-0112111610.1038/s41598-022-24260-zIn silico and in vitro analysis of microRNAs with therapeutic potential in atherosclerosisMaryam Mahjoubin-Tehran0Seyed Hamid Aghaee-Bakhtiari1Amirhossein Sahebkar2Alexandra E. Butler3Reza Kazemi Oskuee4Amin Jalili5Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical SciencesDepartment of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical SciencesApplied Biomedical Research Center, Mashhad University of Medical SciencesResearch Department, Royal College of Surgeons in Ireland, BahrainBiotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical SciencesDepartment of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical SciencesAbstract Atherosclerosis is a chronic inflammatory disease in which aberrant lipid metabolism plays a key role. MicroRNAs (miRNAs), micro-coordinators of gene expression, have been recently proposed as novel clinical biomarkers and potential therapeutic tools for a broad spectrum of diseases. This study aimed to identify miRNAs with therapeutic potential in atherosclerosis. Bioinformatic databases, including experimentally validated and computational prediction tools as well as a novel combination method, were used to identify miRNAs that are able to simultaneously inhibit key genes related to the pathogenesis of atherosclerosis. Further validation of genes and miRNAs was conducted using the STRING online tool, KEGG pathway analysis and DIANA-miRPath. The inhibitory effects of the identified miRNAs in HepG2 and Huh7 cells were verified by real-time PCR. The MTT assay was utilized to evaluate cell cytotoxicity effects of miRNAs. Atherosclerotic drug-targeted genes were selected as key genes. Strong interactions between genes were confirmed using STRING. These genes were shown to be integral to critical pathological processes involved in atherosclerosis. A novel combined method of validated and predicted tools for the identification of effective miRNAs was defined as the combination score (C-Score). Bioinformatic analysis showed that hsa-miR-124-3p and hsa-miR-16-5p possessed the best C-Score (0.68 and 0.62, respectively). KEGG and DIANA-miRPath analysis showed that selected genes and identified miRNAs were involved in atherosclerosis-related pathways. Compared with the controls in both HepG2 and Huh7 cell lines, miR-124 significantly reduced the expression of CETP, PCSK9, MTTP, and APOB, and miR-16 significantly reduced the expression of APOCIII, CETP, HMGCR, PCSK9, MTTP, and APOB, respectively. The cytotoxicity assay showed that miR-124 reduced cell viability, especially after 72 h; however, miR-16 did not show any significant cytotoxicity in either cell line. Our findings indicate that hsa-miR-124 and miR-16 have potential for use as therapeutic candidates in the treatment of atherosclerosis.https://doi.org/10.1038/s41598-022-24260-z |
| spellingShingle | Maryam Mahjoubin-Tehran Seyed Hamid Aghaee-Bakhtiari Amirhossein Sahebkar Alexandra E. Butler Reza Kazemi Oskuee Amin Jalili In silico and in vitro analysis of microRNAs with therapeutic potential in atherosclerosis Scientific Reports |
| title | In silico and in vitro analysis of microRNAs with therapeutic potential in atherosclerosis |
| title_full | In silico and in vitro analysis of microRNAs with therapeutic potential in atherosclerosis |
| title_fullStr | In silico and in vitro analysis of microRNAs with therapeutic potential in atherosclerosis |
| title_full_unstemmed | In silico and in vitro analysis of microRNAs with therapeutic potential in atherosclerosis |
| title_short | In silico and in vitro analysis of microRNAs with therapeutic potential in atherosclerosis |
| title_sort | in silico and in vitro analysis of micrornas with therapeutic potential in atherosclerosis |
| url | https://doi.org/10.1038/s41598-022-24260-z |
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