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Torres-Bustamante MI, Vazquez-Urrutia JR, Solorzano-Ibarra F, Ortiz-Lazareno PC. The Role of miRNAs to Detect Progression, Stratify, and Predict Relevant Clinical Outcomes in Bladder Cancer. Int J Mol Sci 2024; 25:2178. [PMID: 38396855 PMCID: PMC10889402 DOI: 10.3390/ijms25042178] [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: 12/18/2023] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Bladder cancer (BC) is one of the most common types of cancer worldwide, with significant differences in survival depending on the degree of muscle and surrounding tissue invasion. For this reason, the timely detection and monitoring of the disease are important. Surveillance cystoscopy is an invasive, costly, and uncomfortable procedure to monitor BC, raising the need for new, less invasive alternatives. In this scenario, microRNAs (miRNAs) represent attractive prognostic tools given their role as gene regulators in different biological processes, tissue expression, and their ease of evaluation in liquid samples. In cancer, miRNA expression is dynamically modified depending on the tumor type and cancer staging, making them potential biomarkers. This review describes the most recent studies in the last five years exploring the utility of miRNA-based strategies to monitor progression, stratify, and predict relevant clinical outcomes of bladder cancer. Several studies have shown that multimarker miRNA models can better predict overall survival, recurrence, and progression in BC patients than traditional strategies, especially when combining miRNA expression with clinicopathological variables. Future studies should focus on validating their use in different cohorts and liquid samples.
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Affiliation(s)
| | - Jorge Raul Vazquez-Urrutia
- Department of Medicine, The Pennsylvania State University College of Medicine, The Pennsylvania State University, Hershey, PA 17033, USA;
| | - Fabiola Solorzano-Ibarra
- Instituto de Investigación en Enfermedades Crónico Degenerativas, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Guadalajara 44340, Mexico;
- Estancias Posdoctorales por México, Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONACYT), México City 03940, Mexico
| | - Pablo Cesar Ortiz-Lazareno
- División de Inmunología, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara 44340, Mexico
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Xv Y, Qiu M, Liu Z, Xiao M, Wang F. Development of a 7-miRNA prognostic signature for patients with bladder cancer. Aging (Albany NY) 2022; 14:10093-10106. [PMID: 36566019 PMCID: PMC9831742 DOI: 10.18632/aging.204447] [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: 08/20/2021] [Accepted: 02/12/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Bladder carcinoma (BC) represents one of the most prevalent malignant cancers, while predicting its clinical outcomes using traditional indicators is difficult. This study aimed to develop a miRNA signature for the prognostic prediction of patients with BC. MATERIALS AND METHODS MiRNAs that expressed differentially were identified between 413 BC and 19 non-tumor patients, whose prognostic values were evaluated using univariate and multivariate Cox regression analyses. The independent prognostic factors were screened out and were used to establish a signature. The risk score of the signature was calculated. Receiver operating characteristic (ROC) curves and Kaplan-Meier curves were used to verify the predictive performance of the miRNA signature and the risk score. A nomogram was constructed which integrated with the miRNA signature and clinical parameters. Experiments were performed. RESULTS 7 prognosis related miRNAs were selected as independent risk factors, and a 7-miRNA signature was constructed, with an area under ROC (AUC) of 0.721. The 7-miRNA-signature based risk score acts as an independent prognostic factor, with satisfactory predictive performance (AUC = 0.744). Increased miR-337-3p expressions were detected in tumor samples and BC cell lines than in non-tumorigenic tissues and cell lines. Experiments suggested that miR-337-3p induces the proliferation, migration, and invasion of BC cells. CONCLUSION The constructed 7-miRNA signature is a promising biomarker for predicting the prognosis of patients with BC, and miR-337-3p may act as a candidate therapeutic target in BC treatments.
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Affiliation(s)
- Yingjie Xv
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, Yuzhong 400016, China
| | - Ming Qiu
- Department of Urology, The People’s Hospital of Dazu, Chongqing, Dazu 402360, China
| | - Zhaojun Liu
- Department of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, Yuzhong 400016, China
| | - Mingzhao Xiao
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, Yuzhong 400016, China
| | - Fen Wang
- Department of Pathology, The People’s Hospital of Dazu, Chongqing, Dazu 402360, China
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Development of a 3-MicroRNA Signature and Nomogram for Predicting the Survival of Patients with Uveal Melanoma Based on TCGA and GEO Databases. J Ophthalmol 2022; 2022:9724160. [DOI: 10.1155/2022/9724160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/02/2022] [Accepted: 11/12/2022] [Indexed: 11/24/2022] Open
Abstract
Background. The aim of this study was to apply bioinformatic analysis to develop a robust miRNA signature and construct a nomogram model in uveal melanoma (UM) to improve prognosis prediction. Methods. miRNA and mRNA sequencing data for 80 UM patients were obtained from The Cancer Genome Atlas (TCGA) database. The patients were further randomly assigned to a training set (n = 40, used to identify key miRNAs) and a testing set (n = 40, used to internally verify the signature). Then, miRNAs data of GSE84976 and GSE68828 were downloaded from Gene Expression Omnibus (GEO) database for outside verification. Combining univariate analysis and LASSO methods for identifying a robust miRNA biomarker in training set and the signature was validated in testing set and outside dataset. A prognostic nomogram was constructed and combined with decision curve as well as reduction curve analyses to assess the application of clinical usefulness. Finally, we constructed a miRNA-mRNA regulator network in UM and conducted pathway enrichment analysis according to the mRNAs in the network. Results. In total, a 3-miRNA was identified and validated that can robustly predict UM patients’ survival. According to univariate and multivariate cox analyses, age at diagnosis, tumor node metastasis (TNM) classification, stage, and the 3-miRNA signature significantly correlated with the survival outcomes. These characteristics were used to establish nomogram. The nomogram worked well for predicting 1 and 3 years of overall survival time. The decision curve of nomogram revealed a good clinical usefulness of our nomogram. What’s more, a miRNA-mRNA network was constructed. Pathway enrichment showed that this network was largely involved in mRNA processing, the mRNA surveillance pathway, the spliceosome, and so on. Conclusions. We developed a 3-miRNA biomarker and constructed a prognostic nomogram, which may afford a quantitative tool for predicting the survival of UM. Our finding also provided some new potential targets for the treatment of UM.
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Predictive and Prognostic Value of Non-Coding RNA in Breast Cancer. Cancers (Basel) 2022; 14:cancers14122952. [PMID: 35740618 PMCID: PMC9221286 DOI: 10.3390/cancers14122952] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 12/21/2022] Open
Abstract
For decades since the central dogma, cancer biology research has been focusing on the involvement of genes encoding proteins. It has been not until more recent times that a new molecular class has been discovered, named non-coding RNA (ncRNA), which has been shown to play crucial roles in shaping the activity of cells. An extraordinary number of studies has shown that ncRNAs represent an extensive and prevalent group of RNAs, including both oncogenic or tumor suppressive molecules. Henceforth, various clinical trials involving ncRNAs as extraordinary biomarkers or therapies have started to emerge. In this review, we will focus on the prognostic and diagnostic role of ncRNAs for breast cancer.
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Liu P, Luo J, Chen X. miRCom: Tensor Completion Integrating Multi-View Information to Deduce the Potential Disease-Related miRNA-miRNA Pairs. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1747-1759. [PMID: 33180730 DOI: 10.1109/tcbb.2020.3037331] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
MicroRNAs (miRNAs) are consistently capable of regulating gene expression synergistically in a combination mode and play a key role in various biological processes associated with the initiation and development of human diseases, which indicate that comprehending the synergistic molecular mechanism of miRNAs may facilitate understanding the pathogenesis of diseases or even overcome it. However, most existing computational methods had an incomprehensive acknowledge of the miRNA synergistic effect on the pathogenesis of complex diseases, or were hard to be extended to a large-scale prediction task of miRNA synergistic combinations for different diseases. In this article, we propose a novel tensor completion framework integrating multi-view miRNAs and diseases information, called miRCom, for the discovery of potential disease-associated miRNA-miRNA pairs. We first construct an incomplete three-order association tensor and several types of similarity matrices based on existing biological knowledge. Then, we formulate an objective function via performing the factorizations of coupled tensor and matrices simultaneously. Finally, we build an optimization schema by adopting the ADMM algorithm. After that, we obtain the prediction of miRNA-miRNA pairs for different diseases from the full tensor. The contrastive experimental results with other approaches verified that miRCom effectively identify the potential disease-related miRNA-miRNA pairs. Moreover, case study results further illustrated that miRNA-miRNA pairs have more biologically significance and prognostic value than single miRNAs.
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Olgun G, Tastan O. miRCoop: Identifying Cooperating miRNAs via Kernel Based Interaction Tests. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1760-1771. [PMID: 33382660 DOI: 10.1109/tcbb.2020.3047901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Although miRNAs can cause widespread changes in expression programs, single miRNAs typically induce mild repression on their targets. Cooperativity among miRNAs is reported as one strategy to overcome this constraint. Expanding the catalog of synergistic miRNAs is critical for understanding gene regulation and for developing miRNA-based therapeutics. In this study, we develop miRCoop to identify synergistic miRNA pairs that have weak or no repression on the target mRNA individually, but when act together, induce strong repression. miRCoop uses kernel-based statistical interaction tests, together with miRNA and mRNA target information. We apply our approach to patient data of two different cancer types. In kidney cancer, we identify 66 putative triplets. For 64 of these triplets, there is at least one common transcription factor that potentially regulates all participating RNAs of the triplet, supporting a functional association among them. Furthermore, we find that identified triplets are enriched for certain biological processes that are relevant to kidney cancer. Some of the synergistic miRNAs are very closely encoded in the genome, hinting a functional association among them. In applying the method on tumor data with the primary liver site, we find 3105 potential triplet interactions. We believe miRCoop can aid our understanding of the complex regulatory interactions in different health and disease states of the cell and can help in designing miRNA-based therapies. Matlab code for the methodology is provided in https://github.com/guldenolgun/miRCoop.
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Downregulated KIF3B Induced by miR-605-3p Inhibits the Progression of Colon Cancer via Inactivating Wnt/ β-Catenin. JOURNAL OF ONCOLOGY 2021; 2021:5046981. [PMID: 34422048 PMCID: PMC8373513 DOI: 10.1155/2021/5046981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/04/2021] [Indexed: 11/18/2022]
Abstract
Colon cancer is a common malignant disease with high morbidity and mortality, and miRNA dysfunction has been confirmed as an important reason for cancer development. Several studies have verified miR-605-3p as a tumor inhibitor while its roles in colon cancer remain uncertain. In this study, the specimen of the patients and the cell lines of colon cancer were used to observe the expression of miR-605-3p, and the CCK-8, Transwell assay, and flow cytometry assay were used to observe the functions of miR-605-3p in colon cancer cells. The downstream factors of miR-605-3p were predicted by TargetScan and then were verified by dual-luciferase reporter assay. Moreover, western blot was used to investigate the effect of miR-605-3p on Wnt/β-catenin signal pathway. The result showed that miR-605-3p was extremely downregulated in the pathological tissues and tumor cells, and miR-605-3p could effectively induce the apoptosis and impede the proliferation and invasion of the tumor cells. It was found that KIF3B was a target of KIF3B; decreased KIF3B could reverse the effects of miR-605-3p on colon cancer. Besides, the inactivated Wnt/β-catenin pathway was also observed in colon cells when miR-605-3p was upregulated, and the phenomenon could be rescued by KIF3B upregulation. In conclusion, miR-605-3p could inactivate the Wnt/β-catenin pathway induced via promoting KIF3B expression.
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Shen C, Luo J, Ouyang W, Ding P, Wu H. Identification of Small Molecule–miRNA Associations with Graph Regularization Techniques in Heterogeneous Networks. J Chem Inf Model 2020; 60:6709-6721. [DOI: 10.1021/acs.jcim.0c00975] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Cong Shen
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410083, China
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410083, China
| | - Wenjue Ouyang
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410083, China
| | - Pingjian Ding
- School of Computer Science, University of South China, Hengyang 421001, China
| | - Hao Wu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410083, China
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Shen C, Luo J, Lai Z, Ding P. Multiview Joint Learning-Based Method for Identifying Small-Molecule-Associated MiRNAs by Integrating Pharmacological, Genomics, and Network Knowledge. J Chem Inf Model 2020; 60:4085-4097. [DOI: 10.1021/acs.jcim.0c00244] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Cong Shen
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410083, China
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410083, China
| | - Zihan Lai
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410083, China
| | - Pingjian Ding
- School of Computer Science, University of South China, Hengyang 421001, China
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