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Lee DH, Bae WH, Ha H, Kim WR, Park EG, Lee YJ, Kim JM, Shin HJ, Kim HS. The human PTGR1 gene expression is controlled by TE-derived Z-DNA forming sequence cooperating with miR-6867-5p. Sci Rep 2024; 14:4723. [PMID: 38413664 PMCID: PMC10899170 DOI: 10.1038/s41598-024-55332-x] [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: 12/04/2023] [Accepted: 02/22/2024] [Indexed: 02/29/2024] Open
Abstract
Z-DNA, a well-known non-canonical form of DNA involved in gene regulation, is often found in gene promoters. Transposable elements (TEs), which make up 45% of the human genome, can move from one location to another within the genome. TEs play various biological roles in host organisms, and like Z-DNA, can influence transcriptional regulation near promoter regions. MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that play a critical role in the regulation of gene expression. Although TEs can generate Z-DNA and miRNAs can bind to Z-DNA, how these factors affect gene transcription has yet to be elucidated. Here, we identified potential Z-DNA forming sequence (ZFS), including TE-derived ZFS, in the promoter of prostaglandin reductase 1 (PTGR1) by data analysis. The transcriptional activity of these ZFS in PTGR1 was confirmed using dual-luciferase reporter assays. In addition, we discovered a novel ZFS-binding miRNA (miR-6867-5p) that suppressed PTGR1 expression by targeting to ZFS. In conclusion, these findings suggest that ZFS, including TE-derived ZFS, can regulate PTGR1 gene expression and that miR-6867-5p can suppress PTGR1 by interacting with ZFS.
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Affiliation(s)
- Du Hyeong Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Woo Hyeon Bae
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Hongseok Ha
- Institute of Endemic Diseases, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Woo Ryung Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Eun Gyung Park
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Yun Ju Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Jung-Min Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Hae Jin Shin
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea.
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea.
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Rezaei S, Jafari Najaf Abadi MH, Bazyari MJ, Jalili A, Kazemi Oskuee R, Aghaee-Bakhtiari SH. Dysregulated microRNAs in prostate cancer: In silico prediction and in vitro validation. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2024; 27:611-620. [PMID: 38629091 PMCID: PMC11017842 DOI: 10.22038/ijbms.2024.75164.16299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/04/2023] [Indexed: 04/19/2024]
Abstract
Objectives MicroRNAs, which are micro-coordinators of gene expression, have been recently investigated as a potential treatment for cancer. The study used computational techniques to identify microRNAs that could target a set of genes simultaneously. Due to their multi-target-directed nature, microRNAs have the potential to impact multiple key pathways and their pathogenic cross-talk. Materials and Methods We identified microRNAs that target a prostate cancer-associated gene set using integrated bioinformatics analyses and experimental validation. The candidate gene set included genes targeted by clinically approved prostate cancer medications. We used STRING, GO, and KEGG web tools to confirm gene-gene interactions and their clinical significance. Then, we employed integrated predicted and validated bioinformatics approaches to retrieve hsa-miR-124-3p, 16-5p, and 27a-3p as the top three relevant microRNAs. KEGG and DIANA-miRPath showed the related pathways for the candidate genes and microRNAs. Results The Real-time PCR results showed that miR-16-5p simultaneously down-regulated all genes significantly except for PIK3CA/CB in LNCaP; miR-27a-3p simultaneously down-regulated all genes significantly, excluding MET in LNCaP and PIK3CA in PC-3; and miR-124-3p could not down-regulate significantly PIK3CB, MET, and FGFR4 in LNCaP and FGFR4 in PC-3. Finally, we used a cell cycle assay to show significant G0/G1 arrest by transfecting miR-124-3p in LNCaP and miR-16-5p in both cell lines. Conclusion Our findings suggest that this novel approach may have therapeutic benefits and these predicted microRNAs could effectively target the candidate genes.
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Affiliation(s)
- Samaneh Rezaei
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Mohammad Javad Bazyari
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amin Jalili
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Kazemi Oskuee
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Hamid Aghaee-Bakhtiari
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Bioinformatics Research Center, Mashhad University of Medical Science, Mashhad, Iran
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In silico and in vitro analysis of microRNAs with therapeutic potential in atherosclerosis. Sci Rep 2022; 12:20334. [PMID: 36433987 PMCID: PMC9700707 DOI: 10.1038/s41598-022-24260-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022] Open
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.
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Köditz B, Heidenreich A, von Brandenstein M. The Current Status of Kidney Cancer Urine Markers – A Systematic Review. KIDNEY CANCER 2022. [DOI: 10.3233/kca-220005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND: Renal cell carcinoma is the 9th most common malignant disease in the Western World. Typically, patients develop symptoms in a late stage of the disease and most of them are diagnosed by chance. Up to 30% of the patients at the time of diagnosis had metastatic disease. Therefore, highly specific and sensitive biomarkers for the detection and progression of kidney cancer are of great importance. Here, urine markers can be a major advantage and can have a huge clinical impact on the diagnosis, differentiation and prognosis of kidney cancer. At the moment there are several approaches to improve these conditions.. METHODS: A systematic literature research was performed according to the PRISMA guidelines to identify studies reporting urine markers for kidney cancer between 2012 and 2021. A two-step process for the selection of the studies was initiated. In total 287 studies were considering for the final analysis. In total, 6 studies, which presented potential urinary biomarker were analyzed in depth. RESULTS: The major focus was on urinary markers for the detection, progression and differentiation of renal cell carcinoma. In total, a study population of 1099 patients were investigated in the different studies that were analyzed in depth. The median patient sample size of the different studies was 157 patients. The focus was based on the investigation of different microRNAs and proteins as urinary marker for kidney cancer detection. CONCLUSION: Overall, there are different approaches present for the detection, prognosis and differentiation of kidney cancer in urine but most of the studies are based on a small sample size and need to be validated in a greater collective. Furthermore, the standard should be improved to bring these biomarkers into routine clinical practice.
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Affiliation(s)
- Barbara Köditz
- Department of Urology, Facility of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Axel Heidenreich
- Department of Urology, Facility of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Melanie von Brandenstein
- Department of Urology, Facility of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
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Roganović J, Petrović N. Clinical Perspectives of Non-Coding RNA in Oral Inflammatory Diseases and Neuropathic Pain: A Narrative Review. Int J Mol Sci 2022; 23:ijms23158278. [PMID: 35955417 PMCID: PMC9368403 DOI: 10.3390/ijms23158278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 02/07/2023] Open
Abstract
Non-coding RNAs (ncRNAs) represent a research hotspot by playing a key role in epigenetic and transcriptional regulation of diverse biological functions and due to their involvement in different diseases, including oral inflammatory diseases. Based on ncRNAs’ suitability for salivary biomarkers and their involvement in neuropathic pain and tissue regeneration signaling pathways, the present narrative review aims to highlight the potential clinical applications of ncRNAs in oral inflammatory diseases, with an emphasis on salivary diagnostics, regenerative dentistry, and precision medicine for neuropathic orofacial pain.
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Affiliation(s)
- Jelena Roganović
- Department of Pharmacology in Dentistry, School of Dental Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Correspondence: ; Tel.: +381-641976330
| | - Nina Petrović
- Department of Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia;
- Institute for Oncology and Radiology of Serbia, 11000 Belgrade, Serbia
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Renner AM, Derichsweiler C, Ilyas S, Gessner I, Fries JWU, Mathur S. High efficiency capture of biomarker miRNA15a for noninvasive diagnosis of malignant kidney tumors. Biomater Sci 2022; 10:1113-1122. [PMID: 35048092 DOI: 10.1039/d1bm01737c] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
To date, there are no preoperative and quantitative dynamics in clinical practice that can reliably differentiate between a benign and malignant renal cell carcinoma (RCC). For monitoring different analytes in body fluids, more than 40 different molecular biomarkers have been identified, however, they are associated with limited clinical sensitivity and/or non-optimal specificity due to their leaky nature. Previous work on RCC demonstrated the miRNA15a to be reliable and novel biomarker with 98.1% specificity and 100% sensitivity. Despite the high potential of miRNA15a biomarker, its clinical application is considerably hampered by the insensitive nature of the detection methods and low concentration of biomarker in samples that is aggravated by the high level of contamination due to other solutes present in body fluids. In this work, a non-invasive quantitative approach is demonstrated to overcome such diagnostics issues through biotin-streptavidin binding and fluorescence active magnetic nanocarriers that ensured prompt isolation, enrichment and purification of the biomarker miRNA15a from urine. The study demonstrates that detectable low levels of these miRNAs through miRNA capturing nanocarriers can potentially function as advanced diagnostic markers for the non-invasive investigation and early detection of renal cancer.
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Affiliation(s)
- Alexander M Renner
- Institute of Inorganic Chemistry, University of Cologne, Greinstr. 6, 50939 Cologne, Germany.
| | - Christina Derichsweiler
- Institute of Inorganic Chemistry, University of Cologne, Greinstr. 6, 50939 Cologne, Germany.
| | - Shaista Ilyas
- Institute of Inorganic Chemistry, University of Cologne, Greinstr. 6, 50939 Cologne, Germany.
| | - Isabel Gessner
- Institute of Inorganic Chemistry, University of Cologne, Greinstr. 6, 50939 Cologne, Germany.
| | - Jochen W U Fries
- Institute of Urology/Pathology, University Hospital of Cologne, Kerpenerstr. 62, 50924 Cologne, Germany
| | - Sanjay Mathur
- Institute of Inorganic Chemistry, University of Cologne, Greinstr. 6, 50939 Cologne, Germany.
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Kretschmer M, Gapp K. Deciphering the RNA universe in sperm in its role as a vertical information carrier. ENVIRONMENTAL EPIGENETICS 2022; 8:dvac011. [PMID: 35633894 PMCID: PMC9134061 DOI: 10.1093/eep/dvac011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/11/2022] [Accepted: 04/13/2022] [Indexed: 05/21/2023]
Abstract
The inheritance of neurophysiologic and neuropsychologic complex diseases can only partly be explained by the Mendelian concept of genetic inheritance. Previous research showed that both psychological disorders like post-traumatic stress disorder and metabolic diseases are more prevalent in the progeny of affected parents. This could suggest an epigenetic mode of transmission. Human studies give first insight into the scope of intergenerational influence of stressors but are limited in exploring the underlying mechanisms. Animal models have elucidated the mechanistic underpinnings of epigenetic transmission. In this review, we summarize progress on the mechanisms of paternal intergenerational transmission by means of sperm RNA in mouse models. We discuss relevant details for the modelling of RNA-mediated transmission, point towards currently unanswered questions and propose experimental considerations for tackling these questions.
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Affiliation(s)
- Miriam Kretschmer
- Department of Health Sciences and Technology, ETH Zurich, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Winterthurerstrasse 190, Zurich 8057, Switzerland
- Neuroscience Centre Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Katharina Gapp
- *Correspondence address. Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Y36 M 12, Winterthurerstrasse 190, Zurich 8057, Switzerland. Tel: +0041 44 633 85 89; E-mail:
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ÖZZENGİN B, ERGÜN S. Role of miR-6814-5p for the formation of T5, a heparanase variant, in renal cell carcinoma. CUKUROVA MEDICAL JOURNAL 2021. [DOI: 10.17826/cumj.984271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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von Brandenstein M, Herden J, Köditz B, Huerta M, Nestler T, Heidenreich A, Fries JWU. Non-invasive urine markers for the differentiation between RCCs and oncocytoma. J Clin Lab Anal 2021; 35:e23762. [PMID: 33960011 PMCID: PMC8128285 DOI: 10.1002/jcla.23762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 11/09/2022] Open
Abstract
Background Recently, our group showed that Vim3 is overexpressed in tissue samples of renal oncocytomas and Mxi‐2 in clear cell renal carcinoma (ccRCC). The mechanism leading to the truncation of both proteins is known and involves with two miRs, both detectable in urine. Since the analysis of miRs is time‐consuming, our aim was to identify the truncated proteins in urine instead. Furthermore, urine samples from small renal masses (SRMs) (n = 45, <4 cm) were analyzed to get a pre‐surgical differentiation of the cancer subtypes. Methods Urines were accessed from the urological biobank (n = 350). Proteins were isolated from urine samples, and Western blots were performed. Each sample was analyzed with ELISA for the expression of Vim3 and Mxi‐2. A lateral flow assay was established. For the detection of SRMs, the miRs were isolated and qRT‐PCR was performed. Results A significant increase of Vim3 in urines from patients with oncocytoma (n = 20) was detectable with ELISA compared to all other subtypes of RCCs (chromophobe (n = 50), papillary (n = 40), ccRCC (n = 200), and controls (n = 40) (***p < 0.0001)). Mxi‐2 was predominantly overexpressed in ccRCCs (***p < 0.0001). Lateral flow assay of Vim3 and Mxi‐2 shows two bands in the case of oncocytoma and ccRCC indicating the specificity of this test. For SRMs, an overexpression of miR‐15a/Mxi2 was detectable in urine samples from ccRCC and chromoRCC patients. In contrast to that, miR‐498/Vim3 were predominantly overexpressed in oncocytoma patients. Conclusion Both proteins (Vim3 and Mxi‐2) were detectable in patients’ urines and can be used for the non‐invasive differentiation of kidney cancers.
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Affiliation(s)
- Melanie von Brandenstein
- Department of Urology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Jan Herden
- Department of Urology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Barbara Köditz
- Department of Urology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Manuel Huerta
- Department of Urology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Tim Nestler
- Department of Urology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Axel Heidenreich
- Department of Urology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Jochen W U Fries
- Department of Urology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
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Reches A, Berhani O, Mandelboim O. A Unique Regulation Region in the 3' UTR of HLA-G with a Promising Potential. Int J Mol Sci 2020; 21:ijms21030900. [PMID: 32019184 PMCID: PMC7037441 DOI: 10.3390/ijms21030900] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 01/26/2020] [Accepted: 01/28/2020] [Indexed: 12/28/2022] Open
Abstract
Human leukocyte antigen G (HLA-G) is a non-classical human leukocyte antigen (HLA) class I protein that interacts with inhibitory receptors and is commonly overexpressed in various cancers, thereby establishing itself as an inhibitory checkpoint immune ligand. It is also expressed in trophoblast cells during pregnancy and protects the fetus from immune rejection. Despite its crucial role and its intriguing expression pattern, the regulation of HLA-G’s expression is only partially understood. HLA-G’s mRNA is expressed in many tissues but the protein expression is restricted only to the cells mentioned above. Therefore, we suggest that HLA-G is post-transcriptionally regulated. Here, we reveal a distinctive site present only in the 3′ Untranslated region (UTR) of HLA-G, which might explain its unique expression pattern. Consequently, we attempted to find binding factors such as RNA binding proteins (RBPs) and microRNAS (miRs) that regulate HLA-G expression by interacting with this distinct site present in its 3′ UTR. Our research indicates that this site should be further studied in order to reveal its significance.
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Ashrafizadeh M, Ahmadi Z, Samarghandian S, Mohammadinejad R, Yaribeygi H, Sathyapalan T, Sahebkar A. MicroRNA-mediated regulation of Nrf2 signaling pathway: Implications in disease therapy and protection against oxidative stress. Life Sci 2020; 244:117329. [PMID: 31954747 DOI: 10.1016/j.lfs.2020.117329] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/12/2020] [Accepted: 01/15/2020] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRs) are small non-coding pieces of RNA that are involved in a variety of physiologic processes such as apoptosis, cell proliferation, cell differentiation, cell cycle and cell survival. These multifunctional nucleotides are also capable of preventing oxidative damages by modulating antioxidant defense systems in a variety of milieu, such as in diabetes. Although the exact molecular mechanisms by which miRs modulate the antioxidant defense elements are unclear, some evidence suggests that they may exert these effects via nuclear factor erythroid 2-related factor 2 (Nrf2) signaling pathway. This intracellular mechanism is crucial in the maintenance of the physiologic redox balance by regulating the expression and activity of various cellular antioxidative defense elements and thereby plays a pivotal role in the development of oxidative stress. Any impairment in the Nrf2 signaling pathway may result in oxidative damage-dependent complications such as various diabetic complications, neurological disorders and cancer. In the current review, we discuss the modulatory effects of miRs on the Nrf2 signaling pathway, which can potentially be novel therapeutic targets.
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Affiliation(s)
- Milad Ashrafizadeh
- Department of Basic Science, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Zahra Ahmadi
- Department of Basic Science, Shoushtar Branch, Islamic Azad University, Shoushtar, Iran
| | - Saeed Samarghandian
- Department of Basic Medical Sciences, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Reza Mohammadinejad
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Habib Yaribeygi
- Research Center of Physiology, Semnan University of Medical Sciences, Semnan, Iran.
| | - Thozhukat Sathyapalan
- Department of Academic Diabetes, Endocrinology and Metabolism, Hull York Medical School, University of Hull, Hull, UK
| | - Amirhossein Sahebkar
- Halal Research Center of IRI, FDA, Tehran, Iran; Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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12
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Vimentin 3 Allows Differentiation between Normozoospermia and Oligoasthenoteratozoospermia. DISEASE MARKERS 2019; 2019:9803498. [PMID: 31885747 PMCID: PMC6925920 DOI: 10.1155/2019/9803498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/07/2019] [Accepted: 11/26/2019] [Indexed: 11/18/2022]
Abstract
Vimentin is a structural protein predominantly located in the head of sperms. The function and localization of the previously identified truncated version, Vimentin 3 (Vim3), are still unknown. To investigate whether the expression of Vim3 can be used as a reliable marker for the differentiation of sperm quality, we analyzed ejaculates from patients with oligoasthenoteratozoospermia (OAT) syndrome and normozoospermia. We identified sperms with head, neck, and tail changes, which were less positive for Vim3 in OAT syndrome compared to normozoospermia. The expression of Vim3 was significantly downregulated in patients with OAT syndrome compared to sperms from patients with normozoospermia (∗∗ p < 0.01). The ELISA analysis showed similar results as ejaculates from normozoospermic patients showed a significantly higher Vim3 concentration than patients with OAT syndrome (∗∗∗ p < 0.001). This study demonstrates that Vim3 is more highly expressed in ejaculates from patients with normozoospermia compared to ejaculates from patients with OAT syndrome. Therefore, we postulate that Vim3 can be used to determine ejaculate quality. Furthermore, we identified the marker, Vim3, to differentiate between mature sperms with no morphological changes and sperms with head, neck, and tail changes. A lateral flow assay that allows quick analysis is currently under development.
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Turunen TA, Roberts TC, Laitinen P, Väänänen MA, Korhonen P, Malm T, Ylä-Herttuala S, Turunen MP. Changes in nuclear and cytoplasmic microRNA distribution in response to hypoxic stress. Sci Rep 2019; 9:10332. [PMID: 31316122 PMCID: PMC6637125 DOI: 10.1038/s41598-019-46841-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 07/05/2019] [Indexed: 02/08/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that have well-characterized roles in cytoplasmic gene regulation, where they act by binding to mRNA transcripts and inhibiting their translation (i.e. post-transcriptional gene silencing, PTGS). However, miRNAs have also been implicated in transcriptional gene regulation and alternative splicing, events that are restricted to the cell nucleus. Here we performed nuclear-cytoplasmic fractionation in a mouse endothelial cell line and characterized the localization of miRNAs in response to hypoxia using small RNA sequencing. A highly diverse population of abundant miRNA species was detected in the nucleus, of which the majority (56%) was found to be preferentially localized in one compartment or the other. Induction of hypoxia resulted in changes in miRNA levels in both nuclear and cytoplasmic compartments, with the majority of changes being restricted to one location and not the other. Notably, the classical hypoxamiR (miR-210-3p) was highly up-regulated in the nuclear compartment after hypoxic stimulus. These findings reveal a previously unappreciated level of molecular complexity in the physiological response occurring in ischemic tissue. Furthermore, widespread differential miRNA expression in the nucleus strongly suggests that these small RNAs are likely to perform extensive nuclear regulatory functions in the general case.
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Affiliation(s)
- Tiia A Turunen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Yliopistonranta 1E, 70210, Kuopio, Finland
| | - Thomas C Roberts
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford, OX1 3QX, UK.,Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Pia Laitinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Yliopistonranta 1E, 70210, Kuopio, Finland
| | - Mari-Anna Väänänen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Yliopistonranta 1E, 70210, Kuopio, Finland
| | - Paula Korhonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Yliopistonranta 1E, 70210, Kuopio, Finland
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Yliopistonranta 1E, 70210, Kuopio, Finland
| | - Seppo Ylä-Herttuala
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Yliopistonranta 1E, 70210, Kuopio, Finland.,Heart Center and Gene Therapy Unit, Kuopio University Hospital, PO Box 100, 70029 KUH, Kuopio, Finland
| | - Mikko P Turunen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Yliopistonranta 1E, 70210, Kuopio, Finland.
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Di Mauro V, Crasto S, Colombo FS, Di Pasquale E, Catalucci D. Wnt signalling mediates miR-133a nuclear re-localization for the transcriptional control of Dnmt3b in cardiac cells. Sci Rep 2019; 9:9320. [PMID: 31249372 PMCID: PMC6597717 DOI: 10.1038/s41598-019-45818-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 06/14/2019] [Indexed: 12/14/2022] Open
Abstract
MiR-133a is a muscle-enriched miRNA, which plays a key role for proper skeletal and cardiac muscle function via regulation of transduction cascades, including the Wnt signalling. MiR-133a modulates its targets via canonical mRNA repression, a process that has been largely demonstrated to occur within the cytoplasm. However, recent evidence has shown that miRNAs play additional roles in other sub-cellular compartments, such as nuclei. Here, we show that miR-133a translocates to the nucleus of cardiac cells following inactivation of the canonical Wnt pathway. The nuclear miR-133a/AGO2 complex binds to a complementary miR-133a target site within the promoter of the de novo DNA methyltransferase 3B (Dnmt3b) gene, leading to its transcriptional repression, which is mediated by DNMT3B itself. Altogether, these data show an unconventional role of miR-133a that upon its relocalization to the nucleus is responsible for epigenetic repression of its target gene Dnmt3b via a DNMT3B self-regulatory negative feedback loop.
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Affiliation(s)
- Vittoria Di Mauro
- University of Milan Bicocca, Piazza dell'Ateneo Nuovo 1, 20126, Milan, Italy
- CNR-IRGB UOS Milan, Via Fantoli 15/16, 20138, Milan, Italy
- Humanitas Clinical and Research Center, via Alessandro Manzoni 113, 20089, Rozzano, Milan, Italy
| | - Silvia Crasto
- CNR-IRGB UOS Milan, Via Fantoli 15/16, 20138, Milan, Italy
- Humanitas Clinical and Research Center, via Alessandro Manzoni 113, 20089, Rozzano, Milan, Italy
| | - Federico Simone Colombo
- Humanitas Clinical and Research Center, via Alessandro Manzoni 113, 20089, Rozzano, Milan, Italy
| | - Elisa Di Pasquale
- CNR-IRGB UOS Milan, Via Fantoli 15/16, 20138, Milan, Italy
- Humanitas Clinical and Research Center, via Alessandro Manzoni 113, 20089, Rozzano, Milan, Italy
| | - Daniele Catalucci
- CNR-IRGB UOS Milan, Via Fantoli 15/16, 20138, Milan, Italy.
- Humanitas Clinical and Research Center, via Alessandro Manzoni 113, 20089, Rozzano, Milan, Italy.
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Fries JWU. MicroRNAs as markers to monitor endothelin-1 signalling and potential treatment in renal disease: Carcinoma - proteinuric damage - toxicity. Biol Cell 2019; 111:169-186. [PMID: 30866090 DOI: 10.1111/boc.201800059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 01/01/2019] [Accepted: 02/25/2019] [Indexed: 12/11/2022]
Abstract
This review highlights new developments in miRNA as diagnostic and surveillance tools in diseases damaging the renal proximal tubule mediated by endothelin in the field of renal carcinoma, proteinuric kidney disease and tubulotoxicity. A new mechanism in the miRNA regulation of proteins leads to the binding of the miRNA directly to the DNA with premature transcriptional termination and hence the formation of truncated protein isoforms (Mxi2, Vim3). These isoforms are mediated through miRNA15a or miRNA 498, respectively. ET-1 can activate a cytoplasmic complex consisting of NF-κB p65, MAPK p38α, and PKCα. Consequently, PKCα does not transmigrate into the nucleus, which leads to the loss of suppression of a primiRNA15a, maturation of this miRNA in the cytoplasm, tubular secretion and detectability in the urine. This mechanism has been shown in renal cell carcinoma and in proteinuric disease as a biomarker for the activation of the signalling pathway. Similarly, ET-1 induced miRNA 498 transmigrates into the nucleus to form the truncated protein Vim3, which is a biomarker for the benign renal cell tumour, oncocytoma. In tubulotoxicity, ET-1 induced miRNa133a down-regulating multiple-drug-resistant related protein-2, relevant for proteinuric and cisplatin/cyclosporine A toxicity. Current advantages and limitations of miRNAs as urinary biomarkers are discussed.
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Affiliation(s)
- Jochen W U Fries
- Department of Pathology, University Hospital of Koeln, 50931, Koeln, Germany
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