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Diener C, Keller A, Meese E. The miRNA-target interactions: An underestimated intricacy. Nucleic Acids Res 2024; 52:1544-1557. [PMID: 38033323 PMCID: PMC10899768 DOI: 10.1093/nar/gkad1142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/23/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023] Open
Abstract
MicroRNAs (miRNAs) play indispensable roles in posttranscriptional gene regulation. Their cellular regulatory impact is determined not solely by their sheer number, which likely amounts to >2000 individual miRNAs in human, than by the regulatory effectiveness of single miRNAs. Although, one begins to develop an understanding of the complex mechanisms underlying miRNA-target interactions (MTIs), the overall knowledge of MTI functionality is still rather patchy. In this critical review, we summarize key features of mammalian MTIs. We especially highlight latest insights on (i) the dynamic make-up of miRNA binding sites including non-canonical binding sites, (ii) the cooperativity between miRNA binding sites, (iii) the adaptivity of MTIs through sequence modifications, (iv) the bearing of intra-cellular miRNA localization changes and (v) the role of cell type and cell status specific miRNA interaction partners. The MTI biology is discussed against the background of state-of-the-art approaches with particular emphasis on experimental strategies for evaluating miRNA functionality.
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Affiliation(s)
- Caroline Diener
- Saarland University (USAAR), Institute of Human Genetics, 66421 Homburg, Germany
| | - Andreas Keller
- Saarland University (USAAR), Chair for Clinical Bioinformatics, 66123 Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)–Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Saarland University (USAAR), Institute of Human Genetics, 66421 Homburg, Germany
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Kimura Y, Ohzawa H, Miyato H, Kaneko Y, Kuchimaru T, Takahashi R, Yamaguchi H, Kurashina K, Saito S, Hosoya Y, Lefor AK, Sata N, Kitayama J. Intraperitoneal transfer of microRNA-29b-containing small extracellular vesicles can suppress peritoneal metastases of gastric cancer. Cancer Sci 2023; 114:2939-2950. [PMID: 36939028 PMCID: PMC10323101 DOI: 10.1111/cas.15793] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 03/21/2023] Open
Abstract
Small extracellular vesicles (sEV) contain various microRNAs (miRNAs) and play crucial roles in the tumor metastatic process. Although miR-29b levels in peritoneal exosomes were markedly reduced in patients with peritoneal metastases (PM), their role has not been fully clarified. In this study, we asked whether the replacement of miR-29b can affect the development of PM in a murine model. UE6E7T-12, human bone marrow-derived mesenchymal stem cells (BMSCs), were transfected with miR-29b-integrating recombinant lentiviral vector and sEV were isolated from culture supernatants using ultracentrifugation. The sEV contained markedly increased amounts of miR-29b compared with negative controls. Treatment with transforming growth factor-β1 decreased the expression of E-cadherin and calretinin with increased expression of vimentin and fibronectin on human omental tissue-derived mesothelial cells (HPMCs). However, the effects were totally abrogated by adding miR-29b-rich sEV. The sEV inhibited proliferation and migration of HPMCs by 15% (p < 0.005, n = 6) and 70% (p < 0.005, n = 6), respectively, and inhibited adhesion of NUGC-4 and MKN45 to HPMCs by 90% (p < 0.0001, n = 5) and 77% (p < 0.0001, n = 5), respectively. MicroRNA-29b-rich murine sEV were similarly obtained using mouse BMSCs and examined for in vivo effects with a syngeneic murine model using YTN16P, a highly metastatic clone of gastric cancer cell. Intraperitoneal (IP) transfer of the sEV every 3 days markedly reduced the number of PM from YTN16P in the mesentery (p < 0.05, n = 6) and the omentum (p < 0.05, n = 6). Bone marrow mesenchymal stem cell-derived sEV are a useful carrier for IP administration of miR-29b, which can suppress the development of PM of gastric cancer.
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Affiliation(s)
- Yuki Kimura
- Department of SurgeryJichi Medical University HospitalShimotsukeJapan
| | - Hideyuki Ohzawa
- Department of Clinical OncologyJichi Medical University HospitalShimotsukeJapan
| | - Hideyo Miyato
- Department of SurgeryJichi Medical University HospitalShimotsukeJapan
| | - Yuki Kaneko
- Department of SurgeryJichi Medical University HospitalShimotsukeJapan
| | | | - Rei Takahashi
- Department of SurgeryJichi Medical University HospitalShimotsukeJapan
| | - Hironori Yamaguchi
- Department of Clinical OncologyJichi Medical University HospitalShimotsukeJapan
| | - Kentaro Kurashina
- Department of SurgeryJichi Medical University HospitalShimotsukeJapan
| | - Shin Saito
- Department of SurgeryJichi Medical University HospitalShimotsukeJapan
| | - Yoshinori Hosoya
- Department of SurgeryJichi Medical University HospitalShimotsukeJapan
| | | | - Naohiro Sata
- Department of SurgeryJichi Medical University HospitalShimotsukeJapan
| | - Joji Kitayama
- Department of SurgeryJichi Medical University HospitalShimotsukeJapan
- Center for Clinical ResearchJichi Medical University HospitalShimotsukeJapan
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Kobelyatskaya AA, Kudryavtsev AA, Kudryavtseva AV, Snezhkina AV, Fedorova MS, Kalinin DV, Pavlov VS, Guvatova ZG, Naberezhnev PA, Nyushko KM, Alekseev BY, Krasnov GS, Bulavkina EV, Pudova EA. ALDH3A2, ODF2, QSOX2, and MicroRNA-503-5p Expression to Forecast Recurrence in TMPRSS2-ERG-Positive Prostate Cancer. Int J Mol Sci 2022; 23:ijms231911695. [PMID: 36232996 PMCID: PMC9569942 DOI: 10.3390/ijms231911695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022] Open
Abstract
Following radical surgery, patients may suffer a relapse. It is important to identify such patients so that therapy tactics can be modified appropriately. Existing stratification schemes do not display the probability of recurrence with enough precision since locally advanced prostate cancer (PCa) is classified as high-risk but is not ranked in greater detail. Between 40 and 50% of PCa cases belong to the TMPRSS2-ERG subtype that is a sufficiently homogeneous group for high-precision prognostic marker search to be possible. This study includes two independent cohorts and is based on high throughput sequencing and qPCR data. As a result, we have been able to suggest a perspective-trained model involving a deep neural network based on both qPCR data for mRNA and miRNA and clinicopathological criteria that can be used for recurrence risk forecasts in patients with TMPRSS2-ERG-positive, locally advanced PCa (the model uses ALDH3A2 + ODF2 + QSOX2 + hsa-miR-503-5p + ISUP + pT, with an AUC = 0.944). In addition to the prognostic model’s use of identified differentially expressed genes and miRNAs, miRNA–target pairs were found that correlate with the prognosis and can be presented as an interactome network.
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Affiliation(s)
- Anastasiya A. Kobelyatskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Correspondence:
| | | | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anastasiya V. Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Maria S. Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Dmitry V. Kalinin
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, 117997 Moscow, Russia
| | - Vladislav S. Pavlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Zulfiya G. Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Pavel A. Naberezhnev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Kirill M. Nyushko
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, 125284 Moscow, Russia
| | - Boris Y. Alekseev
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, 125284 Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elizaveta V. Bulavkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena A. Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Diener C, Keller A, Meese E. Emerging concepts of miRNA therapeutics: from cells to clinic. Trends Genet 2022; 38:613-626. [PMID: 35303998 DOI: 10.1016/j.tig.2022.02.006] [Citation(s) in RCA: 247] [Impact Index Per Article: 123.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are very powerful genetic regulators, as evidenced by the fact that a single miRNA can direct entire cellular pathways via interacting with a broad spectrum of target genes. This property renders miRNAs as highly interesting therapeutic tools to restore cell functions that are altered as part of a disease phenotype. However, this strength of miRNAs is also a weakness because their cellular effects are so numerous that off-target effects can hardly be avoided. In this review, we point out the main challenges and the strategies to specifically address the problems that need to be surmounted in the push toward a therapeutic application of miRNAs. Particular emphasis is given to approaches that have already found their way into clinical studies.
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Affiliation(s)
- Caroline Diener
- Institute of Human Genetics, Medical Faculty, Saarland University, 66421 Homburg, Germany
| | - Andreas Keller
- Center for Bioinformatics, Medical Faculty, Saarland University, 66123 Saarbrücken, Germany; Department of Neurology and Neurological Sciences, Stanford University, School of Medicine, Stanford, CA 94305, USA.
| | - Eckart Meese
- Institute of Human Genetics, Medical Faculty, Saarland University, 66421 Homburg, Germany
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