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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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2
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An Updated Review of Contribution of Long Noncoding RNA-NEAT1 to the Progression of Human Cancers. Pathol Res Pract 2023; 245:154380. [PMID: 37043964 DOI: 10.1016/j.prp.2023.154380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/12/2023] [Accepted: 02/16/2023] [Indexed: 02/26/2023]
Abstract
Long non-coding RNAs (lncRNAs) present pivotal roles in cancer tumorigenesis and progression. Recently, nuclear paraspeckle assembly transcript 1 (NEAT1) as a lncRNA has been shown to mediate cell proliferation, migration, and EMT in tumor cells. NEAT1 by targeting several miRNAs/mRNA axes could regulate cancer cell behavior. Therefore, NEAT1 may function as a potent biomarker for the prediction and treatment of some human cancers. In this review, we summarized various NEAT1-related signaling pathways that are critical in cancer initiation and progression.
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3
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Li K, Raveendran A, Xie G, Zhang Y, Wu H, Huang Z, Jia Z, Yang J. Prediction for recurrent non-muscle invasive bladder cancer. Cancer Biomark 2023; 38:275-285. [PMID: 37661872 DOI: 10.3233/cbm-220373] [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] [Indexed: 09/05/2023]
Abstract
Non-muscle invasive bladder cancer (NMIBC) has a high recurrence rate, which places a significant burden on both patients and the healthcare system. Hence, it holds significant importance to predict the recurrence risk following treatment for individuals diagnosed with non-muscle invasive bladder cancer (NMIBC). As new generation technologies continue to emerge, an increasing number of recurrence risk prediction tools are being developed and discovered. This article provides an overview of the primary recurrence risk prediction tools currently available, including the liquid biopsy, tissue biopsy, and risk prediction tables. Each of these tools is described in detail and illustrated with relevant examples. Furthermore, we conduct an analysis of the advantages and disadvantages of these tools. This article aims to enhance the reader's understanding of the current progress in recurrence prediction tools and encourage their practical utilization in the fields of precision medicine and public health.
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Affiliation(s)
- Keqiang Li
- Laboratory Urology, Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Henan, China
| | - Aravind Raveendran
- Laboratory Urology, Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan, China
| | - Guoqing Xie
- Laboratory Urology, Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Henan, China
| | - Yu Zhang
- Laboratory Urology, Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Henan, China
| | - Haofan Wu
- Department of Gastrointestinal Surgery, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Zhenlin Huang
- Laboratory Urology, Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan, China
| | - Zhankui Jia
- Laboratory Urology, Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan, China
| | - Jinjian Yang
- Laboratory Urology, Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan, China
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Bhanvadia RR, Lotan Y. Progress in the development of tissue-based biomarkers for urothelial cancer. Expert Rev Anticancer Ther 2022; 22:605-619. [PMID: 35459430 DOI: 10.1080/14737140.2022.2070154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION As the understanding of molecular mechanisms of bladder cancer advances, molecularly-guided precision medicine becomes increasingly relevant. Biomarkers play a critical role in this setting, predicting treatment response and identifying candidates for targeted therapies. AREAS COVERED Current literature on biomarkers in their role in disease prognosis, and response to neoadjuvant and adjuvant therapies. In non-muscle invasive bladder cancer, particular focus is on markers of disease progression, and response to intravesical therapy. In muscle invasive and advanced bladder cancer, particular emphasis is on markers associated with neoadjuvant chemotherapy, as well as systemic immunotherapy. We discuss current shortcomings and pitfalls in contemporary markers, and future avenues of prospective research. EXPERT OPINION The focus on biomarkers has moved from immunohistochemical analysis and tumor-related phenotypic changes to examining genetic alterations. Single marker analysis has been shown to be insufficient in predicting both disease course and response to therapy, and studies have shifted towards examining marker combinations and genetic classifiers. Ultimately, significant progress in implementing biomarkers into clinical guidelines remains elusive, largely due to lack of prospective studies in well-defined patient cohorts and with clinically-meaningful endpoints. Until then, despite their promising value, tissue markers should be limited to experimental settings and clinical trials.
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Affiliation(s)
- Raj R Bhanvadia
- Department of Urology, University of Texas Southwestern, Dallas, Texas 75390
| | - Yair Lotan
- Department of Urology, University of Texas Southwestern, Dallas, Texas 75390
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5
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Abedi Z, MotieGhader H, Hosseini SS, Sheikh Beig Goharrizi MA, Masoudi-Nejad A. mRNA-miRNA bipartite networks reconstruction in different tissues of bladder cancer based on gene co-expression network analysis. Sci Rep 2022; 12:5885. [PMID: 35393513 PMCID: PMC8991185 DOI: 10.1038/s41598-022-09920-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 03/24/2022] [Indexed: 12/14/2022] Open
Abstract
Bladder cancer (BC) is one of the most important cancers worldwide, and if it is diagnosed early, its progression in humans can be prevented and long-term survival will be achieved accordingly. This study aimed to identify novel micro-RNA (miRNA) and gene-based biomarkers for diagnosing BC. The microarray dataset of BC tissues (GSE13507) listed in the GEO database was analyzed for this purpose. The gene expression data from three BC tissues including 165 primary bladder cancer (PBC), 58 normal looking-bladder mucosae surrounding cancer (NBMSC), and 23 recurrent non-muscle invasive tumor tissues (RNIT) were used to reconstruct gene co-expression networks. After preprocessing and normalization, deferentially expressed genes (DEGs) were obtained and used to construct the weighted gene co-expression network (WGCNA). Gene co-expression modules and low-preserved modules were extracted among BC tissues using network clustering. Next, the experimentally validated mRNA-miRNA interaction information were used to reconstruct three mRNA-miRNA bipartite networks. Reactome pathway database and Gene ontology (GO) was subsequently performed for the extracted genes of three bipartite networks and miRNAs, respectively. To further analyze the data, ten hub miRNAs (miRNAs with the highest degree) were selected in each bipartite network to reconstruct three bipartite subnetworks. Finally, the obtained biomarkers were comprehensively investigated and discussed in authentic studies. The obtained results from our study indicated a group of genes including PPARD, CST4, CSNK1E, PTPN14, ETV6, and ADRM1 as well as novel miRNAs (e.g., miR-16-5p, miR-335-5p, miR-124-3p, and let-7b-5p) which might be potentially associated with BC and could be a potential biomarker. Afterward, three drug-gene interaction networks were reconstructed to explore candidate drugs for the treatment of BC. The hub miRNAs in the mRNA-miRNA bipartite network played a fundamental role in BC progression; however, these findings need further investigation.
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Affiliation(s)
- Zahra Abedi
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Habib MotieGhader
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran.
| | - Sahar Sadat Hosseini
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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Khashkhashi Moghadam S, Bakhshinejad B, Khalafizadeh A, Mahmud Hussen B, Babashah S. Non-coding RNA-associated competitive endogenous RNA regulatory networks: Novel diagnostic and therapeutic opportunities for hepatocellular carcinoma. J Cell Mol Med 2021; 26:287-305. [PMID: 34907642 PMCID: PMC8743668 DOI: 10.1111/jcmm.17126] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/09/2021] [Accepted: 12/03/2021] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC), as the most prevalent liver malignancy, is annually diagnosed in more than half a million people worldwide. HCC is strongly associated with hepatitis B and C viral infections as well as alcohol abuse. Obesity and nonalcoholic fatty liver disease (NAFLD) also significantly enhance the risk of liver cancer. Despite recent improvements in therapeutic approaches, patients diagnosed in advanced stages show poor prognosis. Accumulating evidence provides support for the regulatory role of non-coding RNAs (ncRNAs) in cancer. There are a variety of reports indicating the regulatory role of microRNAs (miRNAs) in different stages of HCC. Long non-coding RNAs (LncRNAs) exert their effects by sponging miRNAs and controlling the expression of miRNA-targeted genes. Circular RNAs (circRNAs) perform their biological functions by acting as transcriptional regulators, miRNA sponges and protein templates. Diverse studies have illustrated that dysregulation of competing endogenous RNA networks (ceRNETs) is remarkably correlated with HCC-causing diseases such as chronic viral infections, nonalcoholic steatohepatitis and liver fibrosis/cirrhosis. The aim of the current article was to provide an overview of the role and molecular mechanisms underlying the function of ceRNETs that modulate the characteristics of HCC such as uncontrolled cell proliferation, resistance to cell death, metabolic reprogramming, immune escape, angiogenesis and metastasis. The current knowledge highlights the potential of these regulatory RNA molecules as novel diagnostic biomarkers and therapeutic targets in HCC.
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Affiliation(s)
| | - Babak Bakhshinejad
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Khalafizadeh
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq.,Center of Research and Strategic Studies, Lebanese French University, Erbil, Kurdistan Region, Iraq
| | - Sadegh Babashah
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran.,Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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Dai R, Jiang Q, Zhou Y, Lin R, Lin H, Zhang Y, Zhang J, Gao X. Lnc-STYK1-2 regulates bladder cancer cell proliferation, migration, and invasion by targeting miR-146b-5p expression and AKT/STAT3/NF-kB signaling. Cancer Cell Int 2021; 21:408. [PMID: 34332611 PMCID: PMC8325849 DOI: 10.1186/s12935-021-02114-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/24/2021] [Indexed: 02/07/2023] Open
Abstract
Background Epigenetic modulation by noncoding RNAs substantially contributes to human cancer development, but noncoding RNAs involvement in bladder cancer remains poorly understood. This study investigated the role of long noncoding RNA (lncRNA) lnc-STYK1-2 in tumorigenesis in cancerous bladder cells. Methods Differential lncRNA and mRNA profiles were characterized by high-throughput RNA sequencing combined with validation via quantitative PCR. Bladder cancer cell proliferation was assessed through MTS, and bladder cancer cell migration and invasion were assessed through a Transwell system. The in vivo tumorigenesis of bladder cancer cells was evaluated using the cancer cell line-based xenograft model. The dual-luciferase reporter assay verified the association of miR-146b-5p with lnc-STYK1-2 and the target gene. Protein abundances and phosphorylation were detected by Western blotting. Results Alterations in lncRNA profiles, including decreased lnc-STYK1-2 expression, were detected in bladder cancer tissues compared with adjacent noncancerous tissues. lnc-STYK1-2 silencing effectively promoted proliferation, migration, and invasion in two bladder cancer cell lines, 5637 and T24, and their tumorigenesis in nude mice. lnc-STYK1-2 siRNA promoted miR-146b-5p and reduced ITGA2 expression in bladder cancer cells. Moreover, miR-146b-5p suppressed ITGA2 expression in bladder cancer cells through direct association. Also, lnc-STYK1-2 directly associated with miR-146b-5p. Finally, miR-146b-5p inhibitors abrogated the alterations in bladder cell functions, ITGA2 expression, and phosphorylation of AKT, STAT3, and P65 proteins in 5637 and T24 cells induced by lnc-STYK1-2 silencing. Conclusion lnc-STYK1-2 inhibited bladder cancer cell proliferation, migration, and tumorigenesis by targeting miR-146b-5p to regulate ITGA2 expression and AKT/STAT3/NF-kB signaling.
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Affiliation(s)
- Ranran Dai
- Guangdong Key Laboratory of Urology, Guangzhou Medical University, Guangzhou, China
| | - Qingping Jiang
- Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - You Zhou
- Guangdong Key Laboratory of Urology, Guangzhou Medical University, Guangzhou, China
| | - Ruifeng Lin
- Guangdong Key Laboratory of Urology, Guangzhou Medical University, Guangzhou, China
| | - Hai Lin
- Guangdong Key Laboratory of Urology, Guangzhou Medical University, Guangzhou, China
| | - Yumin Zhang
- Department of Children's Stomatology, Stomatology Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jinhu Zhang
- Guangdong Key Laboratory of Urology, Guangzhou Medical University, Guangzhou, China
| | - Xingcheng Gao
- Guangdong Key Laboratory of Urology, Guangzhou Medical University, Guangzhou, China. .,Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang road, Yuexiu district, Guangzhou, 510120, China.
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8
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Shee K, Seigne JD, Karagas MR, Marsit CJ, Hinds JW, Schned AR, Pettus JR, Armstrong DA, Miller TW, Andrew AS. Identification of Let-7f-5p as a novel biomarker of recurrence in non-muscle invasive bladder cancer. Cancer Biomark 2021; 29:101-110. [PMID: 32623385 DOI: 10.3233/cbm-191322] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Among patients diagnosed with non-muscle invasive bladder cancer (NMIBC), 30% to 70% experience recurrences within 6 to 12 years of diagnosis. The need to screen for these events every 3 to 6 months and ultimately annually by cystoscopy makes bladder cancer one of the most expensive malignancies to manage. OBJECTIVE The purpose of this study was to identify reproducible prognostic microRNAs in resected non-muscle invasive bladder tumor tissue that are predictive of the recurrent tumor phenotype as potential biomarkers and molecular therapeutic targets. METHODS Two independent cohorts of NMIBC patients were analyzed using a biomarker discovery and validation approach, respectively. RESULTS miRNA Let-7f-5p showed the strongest association with recurrence across both cohorts. Let-7f-5p levels in urine and plasma were both found to be significantly correlated with levels in tumor tissue. We assessed the therapeutic potential of targeting Lin28, a negative regulator of Let-7f-5p, with small-molecule inhibitor C1632. Lin28 inhibition significantly increased levels of Let-7f-5p expression and led to significant inhibition of viability and migration of HTB-2 cells. CONCLUSIONS We have identified Let-7f-5p as a miRNA biomarker of recurrence in NMIBC tumors. We further demonstrate that targeting Lin28, a negative regulator of Let-7f-5p, represents a novel potential therapeutic opportunity in NMIBC.
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Affiliation(s)
- Kevin Shee
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - John D Seigne
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Margaret R Karagas
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Carmen J Marsit
- Department of Environmental Health and of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - John W Hinds
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Alan R Schned
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Jason R Pettus
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - David A Armstrong
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Todd W Miller
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Angeline S Andrew
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
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Setti Boubaker N, Gurtner A, Trabelsi N, Manni I, Ayed H, Saadi A, Naimi Z, Ksontini M, Ayadi M, Blel A, Rammeh S, Chebil M, Piaggio G, Ouerhani S. Uncovering the expression patterns and the clinical significance of miR-182, miR-205, miR-27a and miR-369 in patients with urinary bladder cancer. Mol Biol Rep 2020; 47:8819-8830. [PMID: 33128684 DOI: 10.1007/s11033-020-05932-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/17/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Given the high recurrence and progression rates and the absence of reliable markers for early detection and prognosis prediction of patients with urothelial bladder cancer (BCa), the exploration of new biomarkers with high specificity is imperative. Mainly, microRNAs (miRNAs), which are involved in the initiation and the progression of BCa. Herein, the expression patterns of miR-182, miR-205, miR-27a and miR-369 were evaluated in patients with urothelial BCa. METHODS AND RESULTS The expression levels of the miRNAs were investigated in 90 FFPE tissue samples (23 LG NMIBC, 44 HG NMIBC, 23 MIBC) and 10 non tumoral bladder tissues using TaqMan based RT-qPCR. Data analysis was performed using 2-ΔΔCT method. Correlation to clinical characteristics of the patients was performed using descriptive statistics and the receiver operating characteristic (ROC) curve was performed to evaluate the diagnostic value of all miRNAs. MiR-27a, miR-205 and miR-369 were down-regulated whereas miR-182 was up-regulated in patients compared to controls (p < 0.001). MiR-205 and miR-182 positively segregate between NMIBC and MIBC (p = 0.002 and p = 0.000 respectively) whereas the distribution of miR-27a's expression among these tumor groups was almost significant (p = 0.05) and that of miR-369's expression was irrelevant (p = 0.618). Interestingly, miR-182 was discriminative between LG NMIBC and HG NMIBC (p < 0.001) and Ta/T1 tumors (p = 0.000). Furthermore, high levels of miR-182 were potentially predictive of progression in NMIBC patients (p = 0.01). CONCLUSION Collectively, a selection of miRNAs was found to be aberrantly expressed in BCa suggesting a potential diagnostic value in BCa. In addition, the clinical value of miR-182 and miR-205 as potential prognosis biomarkers was highlighted. Indeed, our data provide additional insights into cancer biology. Further functional or target studies are mandatory to strengthen these findings.
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Affiliation(s)
- Nouha Setti Boubaker
- Laboratory of proteins engineering and bioactive molecules (LIP-MB), INSAT, University of Tunis Carthage, Tunis, Tunisia.
- UOSD SAFU, Department of Research, Diagnosis and Innovative Technologies, IRCCS-Regina Elena National Cancer Institute, Rome, Italy.
| | - Aymone Gurtner
- UOSD SAFU, Department of Research, Diagnosis and Innovative Technologies, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
- Institute of Translational Pharmacology, National Research Council, Rome, Italy
| | - Nesrine Trabelsi
- Laboratory of proteins engineering and bioactive molecules (LIP-MB), INSAT, University of Tunis Carthage, Tunis, Tunisia
| | - Isabella Manni
- UOSD SAFU, Department of Research, Diagnosis and Innovative Technologies, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Haroun Ayed
- Laboratory of proteins engineering and bioactive molecules (LIP-MB), INSAT, University of Tunis Carthage, Tunis, Tunisia
- Urology Department, Charles Nicolle Hospital, Faculty of Medicine, University of Tunis-El Manar, Tunis, Tunisia
| | - Ahmed Saadi
- Laboratory of proteins engineering and bioactive molecules (LIP-MB), INSAT, University of Tunis Carthage, Tunis, Tunisia
- Urology Department, Charles Nicolle Hospital, Faculty of Medicine, University of Tunis-El Manar, Tunis, Tunisia
| | - Zeineb Naimi
- Medical Oncology Department, Salah Azaiez Institute, Faculty of Medicine, University of Tunis-El Manar, Tunis, Tunisia
| | - Meriem Ksontini
- Pathology Department, Charles Nicolle Hospital, Faculty of Medicine, University of Tunis-El Manar, Tunis, Tunisia
| | - Mouna Ayadi
- Medical Oncology Department, Salah Azaiez Institute, Faculty of Medicine, University of Tunis-El Manar, Tunis, Tunisia
| | - Ahlem Blel
- Pathology Department, Charles Nicolle Hospital, Faculty of Medicine, University of Tunis-El Manar, Tunis, Tunisia
| | - Soumaya Rammeh
- Pathology Department, Charles Nicolle Hospital, Faculty of Medicine, University of Tunis-El Manar, Tunis, Tunisia
| | - Mohamed Chebil
- Urology Department, Charles Nicolle Hospital, Faculty of Medicine, University of Tunis-El Manar, Tunis, Tunisia
| | - Giulia Piaggio
- UOSD SAFU, Department of Research, Diagnosis and Innovative Technologies, IRCCS-Regina Elena National Cancer Institute, Rome, Italy.
| | - Slah Ouerhani
- Laboratory of proteins engineering and bioactive molecules (LIP-MB), INSAT, University of Tunis Carthage, Tunis, Tunisia
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Amanullah M, Yu M, Sun X, Luo A, Zhou Q, Zhou L, Hou L, Wang W, Lu W, Liu P, Lu Y. MDEHT: a multivariate approach for detecting differential expression of microRNA isoform data in RNA-sequencing studies. Bioinformatics 2020; 36:2657-2664. [PMID: 31930386 PMCID: PMC7203753 DOI: 10.1093/bioinformatics/btaa015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 12/15/2019] [Accepted: 01/09/2020] [Indexed: 12/13/2022] Open
Abstract
Motivation miRNA isoforms (isomiRs) are produced from the same arm as the archetype miRNA with a few nucleotides different at 5 and/or 3 termini. These well-conserved isomiRs are functionally important and have contributed to the evolution of miRNA genes. Accurate detection of differential expression of miRNAs can bring new insights into the cellular function of miRNA and a further improvement in miRNA-based diagnostic and prognostic applications. However, very few methods take isomiR variations into account in the analysis of miRNA differential expression. Results To overcome this challenge, we developed a novel approach to take advantage of the multidimensional structure of isomiR data from the same miRNAs, termed as a multivariate differential expression by Hotelling’s T2 test (MDEHT). The utilization of the information hidden in isomiRs enables MDEHT to increase the power of identifying differentially expressed miRNAs that are not marginally detectable in univariate testing methods. We conducted rigorous and unbiased comparisons of MDEHT with seven commonly used tools in simulated and real datasets from The Cancer Genome Atlas. Our comprehensive evaluations demonstrated that the MDEHT method was robust among various datasets and outperformed other commonly used tools in terms of Type I error rate, true positive rate and reproducibility. Availability and implementation The source code for identifying and quantifying isomiRs and performing miRNA differential expression analysis is available at https://github.com/amanzju/MDEHT. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Md Amanullah
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province and Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China
| | - Mengqian Yu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Xiwei Sun
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China.,Institute for Advanced Research, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Aoran Luo
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province and Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China
| | - Qing Zhou
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province and Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China
| | - Liyuan Zhou
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Ling Hou
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province and Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China
| | - Wei Wang
- Institute for Advanced Research, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.,Department of Pathology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China
| | - Weiguo Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province and Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China
| | - Pengyuan Liu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China.,Department of Pathology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China.,Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Yan Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province and Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China
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11
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Taheri M, Shirvani-Farsani Z, Ghafouri-Fard S, Omrani MD. Expression profile of microRNAs in bladder cancer and their application as biomarkers. Biomed Pharmacother 2020; 131:110703. [PMID: 32890965 DOI: 10.1016/j.biopha.2020.110703] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/21/2020] [Accepted: 08/28/2020] [Indexed: 12/24/2022] Open
Abstract
Bladder cancer (BC) comprises 3% of all cancers and is particularly common in the developed countries. Early diagnosis is an important necessity in improvement of BC prognosis, as patients' outcome is significantly different between muscle invasive BC (MIBC) and non-muscle invasive BC cases. This cancer is resulted from an intricate interaction between genetic and environmental factors. Recent studies have identified microRNAs (miRNAs) as potential modulators of carcinogenic potential of BC cells. These small transcripts regulate expression of target genes mostly through binding with their 3' untranslated regions. Expression of several oncomiRs has been increased in BC tissues, peripheral blood or urine samples of these patients. These miRNAs promote oncogenic potential of BC through modulation of epithelial-mesenchymal transition or PI3K/AKT, JAK/STAT and NF-κB/Snail signaling pathways. Besides, a number of tumor suppressive miRNAs have been down-regulated in BC samples leading to enhanced proliferation, invasiveness and metastasis of these cells. TGFβ1, Akt, MAPK, MET/SMAD3/SNAIL, MAPK1/Slug/vimentin and Wnt7a/β-catenin pathways and axes are among molecular targets of these miRNAs. Aberrant expressions of miRNAs in biofluids of patients with BC have potentiated them as molecular markers for prediction of disease course. In the current review, we provided a summary of studies which reported aberrant expression of miRNAs and their implications in the diagnosis or prognosis of patients with BC.
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Affiliation(s)
- Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zeinab Shirvani-Farsani
- Department of Cellular and Molecular Biology, Faculty of Life Sciences and Technology, Shahid Beheshti University G.C., Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mir Davood Omrani
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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12
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Yang ZH, Li J, Chen WZ, Kong FS. Oncogenic gene RGC-32 is a direct target of miR-26b and facilitates tongue squamous cell carcinoma aggressiveness through EMT and PI3K/AKT signalling. Cell Biochem Funct 2020; 38:943-954. [PMID: 32325539 DOI: 10.1002/cbf.3520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 02/08/2020] [Accepted: 02/12/2020] [Indexed: 11/12/2022]
Abstract
Growing data have recognized the significance of Response Gene to Complement (RGC)-32 in numerous tumour developments. Notwithstanding, the functional role and underlying mechanism of it in tongue squamous cell carcinoma (TSCC) remain enigmatic. Here, to identify the impact of RGC-32 in TSCC, its expression in multiple TSCC cells was measured and loss-of-function experiments in cell lines were performed to illuminate the function of it induced TSCC progression, via si-RNA knockdown, CCK-8, colony formation, wound-healing, transwell, flow cytometry and western blot assays. To clarify potential mechanism, expressions of hallmarks in epithelial-mesenchymal transition (EMT) process and PI3K/AKT signalling were assessed, and the upstream miR regulator of RGC-32 was predicted and verified by applying bioinformatic approaches and dual-luciferase reporter assay, respectively. Finally, the rescue experiments were applied to better elucidate the effect of miR-26b/RGC-32 axis in TSCC behaviours. As a result, RGC-32 was upregulated in TSCC cells and knocking down of it abrogated cell proliferation, trans-migration and invasion, whilst promoted apoptosis in TSCC, which was regulated through repressing EMT and inactivation of PI3K/AKT signalling. Subsequently, miR-26b was predicted and identified as an upstream regulator of RGC-32, and the pro-tumorigenic effect of RGC-32 was reversed by miR-26b overexpression. Collectively, our results demonstrated that RGC-32 facilitated TSCC progression, which was modulated by activations of PI3K/AKT pathway and EMT process, and reduction of its negative regulator of miR-26b. These findings highlight a novel role of miR-26b/RGC-32 axis in TSCC and underlying mechanism, encouraging a potent usage in TSCC treatment. SIGNIFICANCE OF THE STUDY: We first uncovered that Response Gene to Complement-32 played a significantly pro-tumorigenic role in tongue squamous cell carcinoma (TSCC), which was closely regulated by downregulation of miR-26b and activations of epithelial-mesenchymal transition process and PI3K/AKT signalling. These findings contribute to better understand the molecular mechanism in carcinogenesis of TSCC, and shed some light on promising strategy for TSCC therapeutics.
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Affiliation(s)
- Zhong-Heng Yang
- Department of Stomatology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Juan Li
- Department of Pathology, The Fourth Hospital of Jinan, Jinan, Shandong, China
| | - Wei-Zhi Chen
- Department of Radiology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Fan-Shuang Kong
- Department of General Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
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13
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Hou G, Xu W, Jin Y, Wu J, Pan Y, Zhou F. MiRNA-217 accelerates the proliferation and migration of bladder cancer via inhibiting KMT2D. Biochem Biophys Res Commun 2019; 519:747-753. [PMID: 31547991 DOI: 10.1016/j.bbrc.2019.09.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 12/22/2022]
Abstract
To uncover the biological function of miRNA-217 in the progression of bladder cancer and the underlying mechanism. Potential miRNAs binding KMT2D were predicted through online bioinformatics. Their expression levels in bladder cancer tissues and adjacent ones were determined. Through Pearson correlation analysis and survival analysis, the most potential miRNA candidate (miRNA-217) that targets and regulates KMT2D in bladder cancer was selected. Subsequently, expression levels of miRNA-217 and KMT2D in non-muscle invasive bladder cancer (NMIBC) and muscle invasive bladder cancer (MIBC) were detected. MiRNA-217 level in bladder cancer cell lines was determined as well. The interaction between KMT2D and miRNA-217 was verified by dual-luciferase reporter gene assay. Finally, regulatory effect of miRNA-217 on viability and migration in T24 and UMUC-3 cells were investigated. Five potential candidates that were upstream genes binding KMT2D were searched by bioinformatics. Among them, miRNA-217 was remarkably upregulated in bladder cancer tissues and closely linked to poor prognosis of affected patients. Moreover, dual-luciferase reporter gene assay verified the interaction between miRNA-217 and KMT2D. MiRNA-217 was able to downregulate mRNA and protein levels of KMT2D. Furthermore, knockdown of miRNA-217 attenuated viability and migration in bladder cancer cells. MiRNA-217 accelerates proliferative and migratory abilities in bladder cancer via inhibiting the level of tumor suppressor KMT2D, thereafter leading to the poor prognosis in bladder cancer patients.
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Affiliation(s)
- Guoliang Hou
- Department of Urology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, Guangdong, China; Department of Urology, The First People's Hospital of Foshan (Affiliated Foshan Hospital of Sun Yat-sen University), Foshan, 528000, Guangdong, China
| | - Wenfeng Xu
- Department of Urology, The First People's Hospital of Foshan (Affiliated Foshan Hospital of Sun Yat-sen University), Foshan, 528000, Guangdong, China
| | - Yabin Jin
- Clinical Research Institute, The First People's Hospital of Foshan (Affiliated Foshan Hospital of Sun Yat-sen University), Foshan, 528000, Guangdong, China
| | - Jialing Wu
- Clinical Research Institute, The First People's Hospital of Foshan (Affiliated Foshan Hospital of Sun Yat-sen University), Foshan, 528000, Guangdong, China
| | - Yingming Pan
- Clinical Research Institute, The First People's Hospital of Foshan (Affiliated Foshan Hospital of Sun Yat-sen University), Foshan, 528000, Guangdong, China
| | - Fangjian Zhou
- Department of Urology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, Guangdong, China.
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14
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Snyder-Talkington BN, Dong C, Singh S, Raese R, Qian Y, Porter DW, Wolfarth MG, Guo NL. Multi-Walled Carbon Nanotube-Induced Gene Expression Biomarkers for Medical and Occupational Surveillance. Int J Mol Sci 2019; 20:E2635. [PMID: 31146342 PMCID: PMC6600433 DOI: 10.3390/ijms20112635] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/21/2019] [Accepted: 05/24/2019] [Indexed: 12/19/2022] Open
Abstract
As the demand for multi-walled carbon nanotube (MWCNT) incorporation into industrial and biomedical applications increases, so does the potential for unintentional pulmonary MWCNT exposure, particularly among workers during manufacturing. Pulmonary exposure to MWCNTs raises the potential for development of lung inflammation, fibrosis, and cancer among those exposed; however, there are currently no effective biomarkers for detecting lung fibrosis or predicting the risk of lung cancer resulting from MWCNT exposure. To uncover potential mRNAs and miRNAs that could be used as markers of exposure, this study compared in vivo mRNA and miRNA expression in lung tissue and blood of mice exposed to MWCNTs with in vitro mRNA and miRNA expression from a co-culture model of human lung epithelial and microvascular cells, a system previously shown to have a higher overall genome-scale correlation with mRNA expression in mouse lungs than either cell type grown separately. Concordant mRNAs and miRNAs identified by this study could be used to drive future studies confirming human biomarkers of MWCNT exposure. These potential biomarkers could be used to assess overall worker health and predict the occurrence of MWCNT-induced diseases.
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Affiliation(s)
| | - Chunlin Dong
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA.
| | - Salvi Singh
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA.
| | - Rebecca Raese
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA.
| | - Yong Qian
- National Institute for Occupational and Environmental Safety and Health, 1095 Willowdale Rd., Morgantown, WV 26505, USA.
| | - Dale W Porter
- National Institute for Occupational and Environmental Safety and Health, 1095 Willowdale Rd., Morgantown, WV 26505, USA.
| | - Michael G Wolfarth
- National Institute for Occupational and Environmental Safety and Health, 1095 Willowdale Rd., Morgantown, WV 26505, USA.
| | - Nancy L Guo
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA.
- Department of Occupational and Environmental Health Sciences, School of Public Health, West Virginia University, Morgantown, WV 26506, USA.
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