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Samara M, Vlachostergios PJ, Thodou E, Zachos I, Mitrakas L, Evmorfopoulos K, Tzortzis V, Giakountis A. Characterization of a miRNA Signature with Enhanced Diagnostic and Prognostic Power for Patients with Bladder Carcinoma. Int J Mol Sci 2023; 24:16243. [PMID: 38003433 PMCID: PMC10671612 DOI: 10.3390/ijms242216243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/04/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Bladder carcinoma is globally among the most prevalent cancers and is associated with a high mortality rate at advanced stages. Its detection relies on invasive diagnostic methods that are unpleasant for the patient. Non-invasive molecular biomarkers, such as miRNAs, could serve as alternatives for early detection and prognosis of this malignancy. We designed a computational approach that combines transcriptome profiling, survival analyses, and calculation of diagnostic power in order to isolate miRNA signatures with high diagnostic and prognostic utility. Our analysis of TCGA-BLCA data from 429 patients yielded one miRNA signature, consisting of five upregulated and three downregulated miRNAs with cumulative diagnostic power that outperforms current diagnostic methods. The same miRNAs have a strong prognostic significance since their expression is associated with the overall survival of bladder cancer patients. We evaluated the expression of this signature in 19 solid cancer types, supporting its unique diagnostic utility for bladder carcinoma. We provide computational evidence regarding the functional implications of this miRNA signature in cell cycle regulation, demonstrating its abundance in body fluids, including peripheral blood and urine. Our study characterized a novel miRNA signature with the potential to serve as a non-invasive method for bladder cancer diagnosis and prognosis.
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Affiliation(s)
- Maria Samara
- Department of Pathology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41335 Larissa, Greece
| | - Panagiotis J. Vlachostergios
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Eleni Thodou
- Department of Pathology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41335 Larissa, Greece
| | - Ioannis Zachos
- Department of Urology, Faculty of Medicine, School of Health Sciences, University of Thessaly, University Hospital of Larissa, 41335 Larissa, Greece
| | - Lampros Mitrakas
- Department of Urology, Faculty of Medicine, School of Health Sciences, University of Thessaly, University Hospital of Larissa, 41335 Larissa, Greece
| | - Konstantinos Evmorfopoulos
- Department of Urology, Faculty of Medicine, School of Health Sciences, University of Thessaly, University Hospital of Larissa, 41335 Larissa, Greece
| | - Vassilios Tzortzis
- Department of Urology, Faculty of Medicine, School of Health Sciences, University of Thessaly, University Hospital of Larissa, 41335 Larissa, Greece
| | - Antonis Giakountis
- Department of Biochemistry and Biotechnology, University of Thessaly, 41335 Larissa, Greece
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2
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Aveta A, Cilio S, Contieri R, Spena G, Napolitano L, Manfredi C, Franco A, Crocerossa F, Cerrato C, Ferro M, Del Giudice F, Verze P, Lasorsa F, Salonia A, Nair R, Walz J, Lucarelli G, Pandolfo SD. Urinary MicroRNAs as Biomarkers of Urological Cancers: A Systematic Review. Int J Mol Sci 2023; 24:10846. [PMID: 37446024 DOI: 10.3390/ijms241310846] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
MicroRNAs (miRNAs) are emerging as biomarkers for the detection and prognosis of cancers due to their inherent stability and resilience. To summarize the evidence regarding the role of urinary miRNAs (umiRNAs) in the detection, prognosis, and therapy of genitourinary cancers, we performed a systematic review of the most important scientific databases using the following keywords: (urinary miRNA) AND (prostate cancer); (urinary miRNA) AND (bladder cancer); (urinary miRNA) AND (renal cancer); (urinary miRNA) AND (testicular cancer); (urinary miRNA) AND (urothelial cancer). Of all, 1364 articles were screened. Only original studies in the English language on human specimens were considered for inclusion in our systematic review. Thus, a convenient sample of 60 original articles was identified. UmiRNAs are up- or downregulated in prostate cancer and may serve as potential non-invasive molecular biomarkers. Several umiRNAs have been identified as diagnostic biomarkers of urothelial carcinoma and bladder cancer (BC), allowing us to discriminate malignant from nonmalignant forms of hematuria. UmiRNAs could serve as therapeutic targets or recurrence markers of non-muscle-invasive BC and could predict the aggressivity and prognosis of muscle-invasive BC. In renal cell carcinoma, miRNAs have been identified as predictors of tumor detection, aggressiveness, and progression to metastasis. UmiRNAs could play an important role in the diagnosis, prognosis, and therapy of urological cancers.
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Affiliation(s)
- Achille Aveta
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, Urology Unit, University of Naples "Federico II", 80138 Naples, Italy
- Department of Urology, Institut Paoli-Calmettes Cancer Centre, 13055 Marseille, France
| | - Simone Cilio
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, Urology Unit, University of Naples "Federico II", 80138 Naples, Italy
- Division of Experimental Oncology/Unit of Urology, URI, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | - Roberto Contieri
- Department of Biomedical Sciences, Humanitas University, 20072 Pieve Emanuele, Italy
| | - Gianluca Spena
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, Urology Unit, University of Naples "Federico II", 80138 Naples, Italy
| | - Luigi Napolitano
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, Urology Unit, University of Naples "Federico II", 80138 Naples, Italy
| | - Celeste Manfredi
- Unit of Urology, Department of Woman, Child and General and Specialized Surgery, University of Campania "Luigi Vanvitelli", 80131 Naples, Italy
| | - Antonio Franco
- Department of Urology, Sant'Andrea Hospital, "La Sapienza" University, 00189 Rome, Italy
| | - Fabio Crocerossa
- Department of Urology, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Clara Cerrato
- Urology Unit, University Hospital Southampton NHS Trust, Southampton SO16 6YD, UK
| | - Matteo Ferro
- Division of Urology, European Institute of Oncology, 20122 Milan, Italy
| | | | - Paolo Verze
- Department of Medicine and Surgery, Scuola Medica Salernitana, University of Salerno, 84081 Fisciano, Italy
| | - Francesco Lasorsa
- Urology, Andrology and Kidney Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Andrea Salonia
- Division of Experimental Oncology/Unit of Urology, URI, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | - Rajesh Nair
- The Urology Centre, Guy's and St. Thomas' NHS Foundation Trust, Guy's Hospital, London SE1 9RT, UK
| | - Jochen Walz
- Department of Urology, Institut Paoli-Calmettes Cancer Centre, 13055 Marseille, France
| | - Giuseppe Lucarelli
- Urology, Andrology and Kidney Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Savio Domenico Pandolfo
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, Urology Unit, University of Naples "Federico II", 80138 Naples, Italy
- Department of Medicine and Surgery, Scuola Medica Salernitana, University of Salerno, 84081 Fisciano, Italy
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3
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Tantray I, Ojha R, Sharma AP. Non-coding RNA and autophagy: Finding novel ways to improve the diagnostic management of bladder cancer. Front Genet 2023; 13:1051762. [PMID: 36685879 PMCID: PMC9845264 DOI: 10.3389/fgene.2022.1051762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/07/2022] [Indexed: 01/06/2023] Open
Abstract
Major fraction of the human genome is transcribed in to the RNA but is not translated in to any specific functional protein. These transcribed but not translated RNA molecules are called as non-coding RNA (ncRNA). There are thousands of different non-coding RNAs present inside the cells, each regulating different cellular pathway/pathways. Over the last few decades non-coding RNAs have been found to be involved in various diseases including cancer. Non-coding RNAs are reported to function both as tumor enhancer and/or tumor suppressor in almost each type of cancer. Urothelial carcinoma of the urinary bladder is the second most common urogenital malignancy in the world. Over the last few decades, non-coding RNAs were demonstrated to be linked with bladder cancer progression by modulating different signalling pathways and cellular processes such as autophagy, metastasis, drug resistance and tumor proliferation. Due to the heterogeneity of bladder cancer cells more in-depth molecular characterization is needed to identify new diagnostic and treatment options. This review emphasizes the current findings on non-coding RNAs and their relationship with various oncological processes such as autophagy, and their applicability to the pathophysiology of bladder cancer. This may offer an understanding of evolving non-coding RNA-targeted diagnostic tools and new therapeutic approaches for bladder cancer management in the future.
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Affiliation(s)
- Ishaq Tantray
- School of Medicine, Department of Pathology, Stanford University, Stanford, CA, United States
| | - Rani Ojha
- Department of Urology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India,*Correspondence: Rani Ojha, ; Aditya P. Sharma,
| | - Aditya P. Sharma
- Department of Urology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India,*Correspondence: Rani Ojha, ; Aditya P. Sharma,
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Martin-Way D, Puche-Sanz I, Cozar JM, Zafra-Gomez A, Gomez-Regalado MDC, Morales-Alvarez CM, Hernandez AF, Martinez-Gonzalez LJ, Alvarez-Cubero MJ. Genetic variants of antioxidant enzymes and environmental exposures as molecular biomarkers associated with the risk and aggressiveness of bladder cancer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:156965. [PMID: 35764155 DOI: 10.1016/j.scitotenv.2022.156965] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Bladder cancer (BC) is one of the top 10 most common tumours worldwide; however, no molecular markers are currently available for tumour management and follow-up. BC could benefit from molecular biomarkers in environmental disease, which provide mechanistic understanding of individual susceptibility to exposure-related cancers and allow characterizing genetic alterations in the molecular pathway for malignancy. This case-control study performed a molecular analysis in 99 BC and 125 controls. Buccal swabs were collected to assess SNPs in eleven genes coding for xenobiotic detoxification enzymes, cellular antioxidant defences, and hormone synthesis and signalling (NAT2 (rs1801280), GPX1 (rs1050450 and rs17650792), TXNRD1 (rs7310505), PRDX3 (rs3740562), PON1 (rs662), SOD1 (rs10432782), SOD2 (rs4880), CAT (rs1001179), CYP17A1 (rs743572) and ESR1 (rs746432)). A structured questionnaire was administered to study participants to assess environmental and dietary chemical exposures. Several miRNAs associated with BC and detoxification/antioxidant pathways were analysed in a subsample of the study population, including miR-93-5p, miR-221-3p, miR-126, miR-27a-3p, miR-193b, and miR-193a-5p. Levels of selected environmental pollutants (polycyclic aromatic hydrocarbons and endocrine disrupting chemicals) were determined in urine from a subsample of BC cases and controls. We found that CYP17A1, CAT, SOD1, ESR1, PON1, and GPX1 (rs17650792) were associated with BC risk. Furthermore, exposure to smoke and/or dust, and alcohol intake were identified as risk factors for BC. Increased urinary levels of benzo[a]pyrene and bisphenol A were observed in BC patients relative to controls, along with an increased expression of miR-193b, miR-27a and miR-93-5p in BC. Nevertheless, further studies with a larger sample size are warranted to confirm these exploratory results. This study also shows that the combination of genetic markers (PON1 and CYP17A1) and miRNA (miR-221-3p and miR-93-5p) open a new scenario in the use of non-invasive biomarkers in the stratification of BC to guide personalized medicine, which is extremely urged in the current clinical setting.
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Affiliation(s)
- D Martin-Way
- Urology Department, University Hospital Fuenlabrada, Fuenlabrada, Madrid, Spain
| | - I Puche-Sanz
- Urology Department, University Hospital Virgen de las Nieves, Av. de las Fuerzas Armadas 2, 18014 Granada, Spain
| | - J M Cozar
- Urology Department, University Hospital Virgen de las Nieves, Av. de las Fuerzas Armadas 2, 18014 Granada, Spain
| | - A Zafra-Gomez
- University of Granada, Department of Analytical Chemistry, Campus of Fuentenueva, 18071 Granada, Spain
| | - M D C Gomez-Regalado
- University of Granada, Department of Analytical Chemistry, Campus of Fuentenueva, 18071 Granada, Spain
| | - C M Morales-Alvarez
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Granada, Spain; University of Granada, Department of Biochemistry and Molecular Biology III, Faculty of Medicine, PTS, Granada, Spain
| | - A F Hernandez
- University of Granada, Legal Medicine and Toxicology Department, Faculty of Medicine, PTS, Granada, Spain; Instituto de Investigación Biosanitaria ibs. GRANADA, 18014 Granada, Spain; Consortium for Biomedical Research in Epidemiology & Public Health (CIBER en Epidemiología y Salud Pública - CIBERESP), Spain
| | - L J Martinez-Gonzalez
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Granada, Spain.
| | - M J Alvarez-Cubero
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Granada, Spain; University of Granada, Department of Biochemistry and Molecular Biology III, Faculty of Medicine, PTS, Granada, Spain; Instituto de Investigación Biosanitaria ibs. GRANADA, 18014 Granada, Spain
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Koguchi D, Matsumoto K, Shiba I, Harano T, Okuda S, Mori K, Hirano S, Kitajima K, Ikeda M, Iwamura M. Diagnostic Potential of Circulating Tumor Cells, Urinary MicroRNA, and Urinary Cell-Free DNA for Bladder Cancer: A Review. Int J Mol Sci 2022; 23:9148. [PMID: 36012417 PMCID: PMC9409245 DOI: 10.3390/ijms23169148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/02/2022] [Accepted: 08/14/2022] [Indexed: 12/15/2022] Open
Abstract
Early detection of primary bladder cancer (BCa) is vital, because stage and grade have been generally accepted not only as categorical but also as prognostic factors in patients with BCa. The widely accepted screening methods for BCa, cystoscopy and urine cytology, have unsatisfactory diagnostic accuracy, with high rates of false negatives, especially for flat-type BCa with cystoscopy and for low-risk disease with urine cytology. Currently, liquid biopsy has attracted much attention as being compensatory for that limited diagnostic power. In this review, we survey the literature on liquid biopsy for the detection of BCa, focusing on circulating tumor cells (CTCs), urinary cell-free DNA (ucfDNA), and urinary microRNA (umiRNA). In diagnostic terms, CTCs and umiRNA are determined by quantitative analysis, and ucfDNA relies on finding genetic and epigenetic changes. The ideal biomarkers should be highly sensitive in detecting BCa. Currently, CTCs produce an unfavorable result; however, umiRNA and ucfDNA, especially when analyzed using a panel of genes, produce promising results. However, given the small cohort size in most studies, no conclusions can yet be drawn about liquid biopsy's immediate application to clinical practice. Further large studies to validate the diagnostic value of liquid biopsy for clinical use are mandatory.
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Affiliation(s)
| | - Kazumasa Matsumoto
- Department of Urology, Kitasato University School of Medicine, 1-15-1 Kitasato Minami-ku Sagamihara, Sagamihara 252-0374, Kanagawa, Japan
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Wang Y, Han Y, Jin Y, He Q, Wang Z. The Advances in Epigenetics for Cancer Radiotherapy. Int J Mol Sci 2022; 23:ijms23105654. [PMID: 35628460 PMCID: PMC9145982 DOI: 10.3390/ijms23105654] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 02/08/2023] Open
Abstract
Cancer is an important factor threatening human life and health; in recent years, its morbidity and mortality remain high and demosntrate an upward trend. It is of great significance to study its pathogenesis and targeted therapy. As the complex mechanisms of epigenetic modification has been increasingly discovered, they are more closely related to the occurrence and development of cancer. As a reversible response, epigenetic modification is of great significance for the improvement of classical therapeutic measures and the discovery of new therapeutic targets. It has become a research focusto explore the multi-level mechanisms of RNA, DNA, chromatin and proteins. As an important means of cancer treatment, radiotherapy has made great progress in technology, methods, means and targeted sensitization after years of rapid development, and even research on radiotherapy based on epigenetic modification is rampant. A series of epigenetic effects of radiation on DNA methylation, histone modification, chromosome remodeling, RNA modification and non-coding RNA during radiotherapy affects the therapeutic effects and prognosis. Starting from the epigenetic mechanism of tumorigenesis, this paper reviews the latest progress in the mechanism of interaction between epigenetic modification and cancer radiotherapy and briefly introduces the main types, mechanisms and applications of epigenetic modifiers used for radiotherapy sensitization in order to explore a more individual and dynamic approach of cancer treatment based on epigenetic mechanism. This study strives to make a modest contribution to the progress of human disease research.
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Affiliation(s)
| | | | | | - Qiang He
- Correspondence: (Q.H.); (Z.W.); Tel.: +86-431-85619443 (Z.W.)
| | - Zhicheng Wang
- Correspondence: (Q.H.); (Z.W.); Tel.: +86-431-85619443 (Z.W.)
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7
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Wen Z, Huang G, Lai Y, Xiao L, Peng X, Liu K, Zhang C, Chen X, Li R, Li X, Lai Y, Ni L. Diagnostic panel of serum miR-125b-5p, miR-182-5p, and miR-200c-3p as non-invasive biomarkers for urothelial bladder cancer. Clin Transl Oncol 2022; 24:909-918. [PMID: 35028929 DOI: 10.1007/s12094-021-02741-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/23/2021] [Indexed: 02/05/2023]
Abstract
PURPOSE This study aimed to identify a diagnostic panel of serum microRNAs (miRNAs) for the early detection of bladder cancer (BC). METHODS Serum samples were collected from 112 BC patients and 112 normal controls (NCs). A three-stage selection was conducted to identify differentially expressed miRNAs as candidates to construct the diagnostic panel. Further, to explore their potential roles in urothelial BC, bioinformatics analyses, including target genes prediction and functional annotation, were used. RESULTS Six downregulated miRNAs (miR-1-3p, miR-30a-5p, miR-100-5p, miR-125b-5p, miR-143-3p, and miR-200c-3p) and one upregulated, miR-182-5p, in BC patients' serum were detected compared to NCs and were selected to establish the diagnostic panel. Based on a backward stepwise logistic regression analysis, miR-125b-5p, miR-182-5p, and miR-200c-3p comprehended the diagnostic panel [area under the curve (AUC) = 0.959, sensitivity = 91.67%, specificity = 92.5%]. CONCLUSION The panel of three miRNAs had an excellent diagnostic capability, representing a potential non-invasive method for early BC detection.
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Affiliation(s)
- Z Wen
- Shantou University Medical College, Shantou, Guangdong, 515041, People's Republic of China
- Department of Urology, Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen, Guangdong, 518036, People's Republic of China
| | - G Huang
- Shantou University Medical College, Shantou, Guangdong, 515041, People's Republic of China
- Department of Urology, Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen, Guangdong, 518036, People's Republic of China
| | - Y Lai
- Department of Urology, People's Hospital of Longhua, Shenzhen, Guangdong, 518109, People's Republic of China
| | - L Xiao
- Department of Urology, Shenzhen University General Hospital, Shenzhen, Guangdong, 518109, People's Republic of China
| | - X Peng
- Shantou University Medical College, Shantou, Guangdong, 515041, People's Republic of China
- Department of Urology, Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen, Guangdong, 518036, People's Republic of China
| | - K Liu
- Department of Urology, Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen, Guangdong, 518036, People's Republic of China
- Anhui Medical University, Hefei, Anhui, 230032, People's Republic of China
| | - C Zhang
- Department of Urology, Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen, Guangdong, 518036, People's Republic of China
| | - X Chen
- Shantou University Medical College, Shantou, Guangdong, 515041, People's Republic of China
- Department of Urology, Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen, Guangdong, 518036, People's Republic of China
| | - R Li
- Department of Urology, Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen, Guangdong, 518036, People's Republic of China
- Anhui Medical University, Hefei, Anhui, 230032, People's Republic of China
| | - X Li
- Shantou University Medical College, Shantou, Guangdong, 515041, People's Republic of China
- Department of Urology, Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen, Guangdong, 518036, People's Republic of China
| | - Y Lai
- Shantou University Medical College, Shantou, Guangdong, 515041, People's Republic of China
- Department of Urology, Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen, Guangdong, 518036, People's Republic of China
| | - L Ni
- Shantou University Medical College, Shantou, Guangdong, 515041, People's Republic of China
- Department of Urology, Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen, Guangdong, 518036, People's Republic of China
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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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9
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Wang C, Jiang H. Long non-coding RNA PCAT19 regulates the malignant progression of bladder cancer through the miR-335-5p/IER2 axis. Crit Rev Eukaryot Gene Expr 2022; 32:81-94. [DOI: 10.1615/critreveukaryotgeneexpr.2022043175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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10
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Alterations of Chromatin Regulators in the Pathogenesis of Urinary Bladder Urothelial Carcinoma. Cancers (Basel) 2021; 13:cancers13236040. [PMID: 34885146 PMCID: PMC8656749 DOI: 10.3390/cancers13236040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Urinary bladder cancer is one of the ten major cancers worldwide, with higher incidences in males, in smokers, and in highly industrialized countries. New therapies beyond cytotoxic chemotherapy are urgently needed to improve treatment of these tumors. A better understanding of the mechanisms underlying their development may help in this regard. Recently, it was discovered that a group of proteins regulating the state of chromatin and thus gene expression is exceptionally and frequently affected by gene mutations in bladder cancers. Altered function of these mutated chromatin regulators must therefore be fundamental in their development, but how and why is poorly understood. Here we review the current knowledge on changes in chromatin regulators and discuss their possible consequences for bladder cancer development and options for new therapies. Abstract Urothelial carcinoma (UC) is the most frequent histological type of cancer in the urinary bladder. Genomic changes in UC activate MAPK and PI3K/AKT signal transduction pathways, which increase cell proliferation and survival, interfere with cell cycle and checkpoint control, and prevent senescence. A more recently discovered additional category of genetic changes in UC affects chromatin regulators, including histone-modifying enzymes (KMT2C, KMT2D, KDM6A, EZH2), transcription cofactors (CREBBP, EP300), and components of the chromatin remodeling complex SWI/SNF (ARID1A, SMARCA4). It is not yet well understood how these changes contribute to the development and progression of UC. Therefore, we review here the emerging knowledge on genomic and gene expression alterations of chromatin regulators and their consequences for cell differentiation, cellular plasticity, and clonal expansion during UC pathogenesis. Our analysis identifies additional relevant chromatin regulators and suggests a model for urothelial carcinogenesis as a basis for further mechanistic studies and targeted therapy development.
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Identification of the circRNA-miRNA-mRNA Regulatory Network in Bladder Cancer by Bioinformatics Analysis. Int J Genomics 2021; 2021:9935986. [PMID: 34824999 PMCID: PMC8610721 DOI: 10.1155/2021/9935986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/01/2021] [Accepted: 10/26/2021] [Indexed: 01/05/2023] Open
Abstract
In recent years, increasing evidence shows that circular RNA (circRNA) disorder is closely related to tumorigenesis and cancer progression. However, the regulatory functions of most circRNAs in bladder cancer (BCa) remain unclear. This study was aimed at exploring the molecular regulatory mechanism of circRNAs in BCa. We obtained four datasets of circRNA, microRNA (miRNA), and messenger (mRNA) expression profiles from the Gene Expression Omnibus and The Cancer Genome Atlas microarray databases and identified 434, 367, and 4799/4841 differentially expressed circRNAs, miRNAs, and mRNAs, respectively. With these differentially expressed RNAs, we established a circRNA-miRNA-mRNA targeted interaction network. A total of 18, 24, and 51 central circRNAs, miRNAs, and mRNAs were identified, respectively. Among them, the top 10 mRNAs that had high connectivity with other circRNAs and miRNAs were regarded as hub genes. We detected the expression levels of these 10 mRNAs in 16 pairs of BCa tissues and adjacent normal tissues through quantitative real-time polymerase chain reaction. The differentially expressed mRNAs and central mRNAs were enriched in the processes and pathways that are associated with the growth, differentiation, proliferation, and apoptosis of tumor cells. The outstanding genes (CDCA4, GATA6, LATS2, RHOB, ZBTB4, and ZFPM2) also interacted with numerous drugs, indicating their potency as biomarkers and drug targets. The findings of this study provide a deep understanding of the circRNA-related competitive endogenous RNA regulatory mechanism in BCa pathogenesis.
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Kashani B, Zandi Z, Kaveh V, Pourbagheri-Sigaroodi A, Ghaffari SH, Bashash D. Small molecules with huge impacts: the role of miRNA-regulated PI3K pathway in human malignancies. Mol Biol Rep 2021; 48:8045-8059. [PMID: 34689281 DOI: 10.1007/s11033-021-06739-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/15/2021] [Indexed: 11/28/2022]
Abstract
Along with evolution, a considerable number of signaling cascades have evolved within cells to meet their multifaceted needs. Among transmitting molecules, phosphoinositide 3-kinase (PI3K), Akt, and mammalian target of rapamycin (mTOR) have teamed up to build a signaling axis that effectively regulates various cellular processes including cell proliferation and migration. Given the extensive output of the PI3K/Akt/mTOR signaling axis, its aberrancy could subsequently lead to the formation of a wide range of human cancers spanning from hematologic malignancies to different types of solid tumors. Despite the high frequency of the PI3K pathway over-activation in most malignancies, mutations in the DNA sequence are not equally common. Such incompatibility sheds light on the possible effects of post-translational modification mechanisms that may take control of this pathway, some of the most important ones of which are through microRNAs (miRNAs or miRs). The present review is designed to take off the veil from the regulatory role of these small non-coding RNAs on the PI3K/Akt/mTOR signaling axis in carcinogenesis.
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Affiliation(s)
- Bahareh Kashani
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Zandi
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahid Kaveh
- Department of Medical Oncology and Hematology, Iran University of Medical Sciences, Tehran, Iran
| | - Atieh Pourbagheri-Sigaroodi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed H Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Rascio F, Spadaccino F, Rocchetti MT, Castellano G, Stallone G, Netti GS, Ranieri E. The Pathogenic Role of PI3K/AKT Pathway in Cancer Onset and Drug Resistance: An Updated Review. Cancers (Basel) 2021; 13:3949. [PMID: 34439105 PMCID: PMC8394096 DOI: 10.3390/cancers13163949] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 07/30/2021] [Indexed: 12/12/2022] Open
Abstract
The PI3K/AKT pathway is one of the most frequently over-activated intracellular pathways in several human cancers. This pathway, acting on different downstream target proteins, contributes to the carcinogenesis, proliferation, invasion, and metastasis of tumour cells. A multi-level impairment, involving mutation and genetic alteration, aberrant regulation of miRNAs sequences, and abnormal phosphorylation of cascade factors, has been found in multiple cancer types. The deregulation of this pathway counteracts common therapeutic strategies and contributes to multidrug resistance. In this review, we underline the involvement of this pathway in patho-physiological cell survival mechanisms, emphasizing its key role in the development of drug resistance. We also provide an overview of the potential inhibition strategies currently available.
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Affiliation(s)
- Federica Rascio
- Nephrology Dialysis and Transplantation Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (G.C.); (G.S.)
| | - Federica Spadaccino
- Clinical Pathology Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (F.S.); (G.S.N.); (E.R.)
| | - Maria Teresa Rocchetti
- Cell Biology Unit, Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy;
| | - Giuseppe Castellano
- Nephrology Dialysis and Transplantation Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (G.C.); (G.S.)
| | - Giovanni Stallone
- Nephrology Dialysis and Transplantation Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (G.C.); (G.S.)
| | - Giuseppe Stefano Netti
- Clinical Pathology Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (F.S.); (G.S.N.); (E.R.)
| | - Elena Ranieri
- Clinical Pathology Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (F.S.); (G.S.N.); (E.R.)
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Ang X, Zhang Z, Xu Z, Zhou Q, You J, Li M, Zhou F, Chen W. Establishment and analysis of a novel miRNA prognostic risk model for bladder cancer based on TCGA database. ALL LIFE 2021. [DOI: 10.1080/26895293.2021.1944327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Xiaojie Ang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
| | - Zhiyu Zhang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
| | - Zekun Xu
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
| | - Qi Zhou
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
| | - Jiawei You
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
| | - Miao Li
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
| | - Feng Zhou
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
| | - Weiguo Chen
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
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Sulforaphane Impact on Reactive Oxygen Species (ROS) in Bladder Carcinoma. Int J Mol Sci 2021; 22:ijms22115938. [PMID: 34073079 PMCID: PMC8197880 DOI: 10.3390/ijms22115938] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 02/06/2023] Open
Abstract
Sulforaphane (SFN) is a natural glucosinolate found in cruciferous vegetables that acts as a chemopreventive agent, but its mechanism of action is not clear. Due to antioxidative mechanisms being thought central in preventing cancer progression, SFN could play a role in oxidative processes. Since redox imbalance with increased levels of reactive oxygen species (ROS) is involved in the initiation and progression of bladder cancer, this mechanism might be involved when chemoresistance occurs. This review summarizes current understanding regarding the influence of SFN on ROS and ROS-related pathways and appraises a possible role of SFN in bladder cancer treatment.
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