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Tang X, Ren H, Guo M, Qian J, Yang Y, Gu C. Review on circular RNAs and new insights into their roles in cancer. Comput Struct Biotechnol J 2021; 19:910-928. [PMID: 33598105 PMCID: PMC7851342 DOI: 10.1016/j.csbj.2021.01.018] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs (circRNAs) are a very interesting class of conserved single-stranded RNA molecules derived from exonic or intronic sequences by precursor mRNA back-splicing. Unlike canonical linear RNAs, circRNAs form covalently closed, continuous stable loops without a 5'end cap and 3'end poly(A) tail, and therefore are resistant to exonuclease digestion. The majority of circRNAs are highly abundant, and conserved across different species with a tissue or developmental-stage-specific expression. circRNAs have been shown to play important roles as microRNA sponges, regulators of gene splicing and transcription, RNA-binding protein sponges and protein/peptide translators. Emerging evidence reveals that circRNAs function in various human diseases, particularly cancers, and may function as better predictive biomarkers and therapeutic targets for cancer treatment. In consideration of their potential clinical relevance, circRNAs have become a new research hotspot in the field of tumor pathology. In the present study, the current understanding of the biogenesis, characteristics, databases, research methods, biological functions subcellular distribution, epigenetic regulation, extracellular transport and degradation of circRNAs was discussed. In particular, the multiple databases and methods involved in circRNA research were first summarized, and the recent advances in determining the potential roles of circRNAs in tumor growth, migration and invasion, which render circRNAs better predictive biomarkers, were described. Furthermore, future perspectives for the clinical application of circRNAs in the management of patients with cancer were proposed, which could provide new insights into circRNAs in the future.
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Key Words
- AML, acute myloid leukemia
- BSJ, back-splice junction
- Biomarker
- CLL, chronic lymphocytic leukemia
- CML, chronic myeloid leukemia
- CRC, colorectal cancer
- Cancer
- Circular RNAs
- EIciRNAs, exon–intron RNAs
- EMT, epithelial-mesenchymal transition
- Functions
- GC, gastric cancer
- HCC, hepatocellular carcinoma
- ISH, in situ hybridization
- LUAD, lung adenocarcinoma
- MER, miRNA response elements
- MM, multiple myeloma
- NSCLC, non-small cell lung cancer
- PCR, polymerase chain reaction
- PDAC, pancreatic ductal adenocarcinoma
- RBP, RNA-binding protein
- RNA, ribonucleic acid
- RNase, ribonuclease
- RT-PCR, reverse transcription-PCR
- TNM, tumor node metastases
- UTR, untranslated regions
- ccRCC, clear cell renal cell carcinoma
- ceRNAs, endogenous RNAs
- ciRNAs, circular intronic RNAs
- ciRS-7, circular RNA sponge for miR-7
- circRNAs, circular RNAs
- ecircRNAs, exonic circular RNAs
- lncRNAs, long ncRNA
- miRNAs, microRNAs
- ncRNAs, noncoding RNAs
- qPCR, quantitative PCR
- rRNA, ribosomal RNA
- siRNAs, small interfering RNAs
- snRNA, small nuclear RNA
- tricRNAs, tRNA intronic circRNAs
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Affiliation(s)
- Xiaozhu Tang
- The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210001, China
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Hongyan Ren
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Mengjie Guo
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jinjun Qian
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ye Yang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Chunyan Gu
- The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210001, China
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
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Yuan L, Chen L, Qian K, Qian G, Wu CL, Wang X, Xiao Y. Co-expression network analysis identified six hub genes in association with progression and prognosis in human clear cell renal cell carcinoma (ccRCC). Genom Data 2017; 14:132-140. [PMID: 29159069 PMCID: PMC5683669 DOI: 10.1016/j.gdata.2017.10.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/12/2017] [Accepted: 10/25/2017] [Indexed: 12/21/2022]
Abstract
Human clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignant adult kidney tumors. We constructed a weighted gene co-expression network to identify gene modules associated with clinical features of ccRCC (n = 97). Six hub genes (CCNB2, CDC20, CEP55, KIF20A, TOP2A and UBE2C) were identified in both co-expression and protein-protein interaction (PPI) networks, which were highly correlated with pathologic stage. The significance of expression of the hub genes in ccRCC was ranked top 4 among all cancers and correlated with poor prognosis. Functional analysis revealed that the hub genes were significantly enriched in cell cycle regulation and cell division. Gene set enrichment analysis suggested that the samples with highly expressed hub gene were correlated with cell cycle and p53 signaling pathway. Taken together, six hub genes were identified to be associated with progression and prognosis of ccRCC, and they might lead to poor prognosis by regulating p53 signaling pathway.
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Key Words
- Clear cell renal cell carcinoma (ccRCC)
- Co-expression network analysis
- DAVID, Database for Annotation, Visualization and Integrated Discovery
- DEG, differentially expressed gene
- DEGs, differentially expressed genes
- GS, gene significance
- GSEA, enrichment analysis and gene set enrichment
- HPA, human protein atlas
- Hub genes
- MEs, module eigengenes
- MS, module significance
- PPI, protein-protein interaction
- Prognosis
- Progression
- SAM, significance analysis of microarrays
- STRING, search tool for the retrieval of interacting genes
- TCGA, the cancer genome atlas
- TOM, topological overlap matrix
- WGCNA, weighted gene co-expression network analysis
- ccRCC, clear cell renal cell carcinoma
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Affiliation(s)
- Lushun Yuan
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Liang Chen
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, The Fifth Hospital of Wuhan, Wuhan, China
| | - Guofeng Qian
- Department of Endocrinology, The First Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Chin-Lee Wu
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xinghuan Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Corresponding author.
| | - Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Correspondence to: Y. Xiao, Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.Department of Biological RepositoriesZhongnan Hospital of Wuhan UniversityWuhanChina
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Abstract
Tenascin-C is a large, multimodular, extracellular matrix glycoprotein that exhibits a very restricted pattern of expression but an enormously diverse range of functions. Here, we discuss the importance of deciphering the expression pattern of, and effects mediated by, different forms of this molecule in order to fully understand tenascin-C biology. We focus on both post transcriptional and post translational events such as splicing, glycosylation, assembly into a 3D matrix and proteolytic cleavage, highlighting how these modifications are key to defining tenascin-C function.
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Key Words
- AD1/AD2, additional domain 1/ additional domain 2
- ADAMTS, a disintegrin and metalloproteinase with thrombospondin motifs
- ASMCs, aortic smooth muscle cells
- BDNF, brain derived neurotrophic factor
- BHKs, baby hamster kidney cells
- BMP, bone morphogenetic protein
- CA19–9, carbohydrate antigen 19–9
- CALEB, chicken acidic leucine-rich EGF-like domain containing brain protein
- CEA, carcinoembryonic antigen
- CNS, central nervous system
- CRC, colorectal carcinomas
- CTGF, connective tissue growth factor
- DCIS, ductal carcinoma in-situ
- ECM, extracellular matrix
- EDA-FN, extra domain A containing fibronectin
- EDB-FN, extra domain B containing fibronectin
- EGF-L, epidermal growth factor-like
- EGF-R, epidermal growth factor receptor
- ELISPOT, enzyme-linked immunospot assay
- FBG, fibrinogen-like globe
- FGF2, fibroblast growth factor 2
- FGF4, fibroblast growth factor 4
- FN, fibronectin
- FNIII, fibronectin type III-like repeat
- GMEM, glioma-mesenchymal extracellular matrix antigen
- GPI, glycosylphosphatidylinositol
- HB-EGF, heparin-binding EGF-like growth factor
- HCEs, immortalized human corneal epithelial cell line
- HGF, hepatocyte growth factor
- HNK-1, human natural killer-1
- HSPGs, heparan sulfate proteoglycans
- HUVECs, human umbilical vein endothelial cells
- ICC, immunocytochemistry
- IF, immunofluorescence
- IFNγ, interferon gamma
- IGF, insulin-like growth factor
- IGF-BP, insulin-like growth factor-binding protein
- IHC, immunohistochemistry
- IL, interleukin
- ISH, in situ hybridization
- LPS, lipopolysaccharide
- MMP, matrix metalloproteinase
- MPNSTs, malignant peripheral nerve sheath tumors
- Mr, molecular mass
- NB, northern blot
- NF-kB, nuclear factor kappa-light-chain-enhancer of activated B cells
- NK, natural killer cells
- NSCLC, non-small cell lung carcinoma
- NSCs, neural stem cells
- NT, neurotrophin
- PAMPs, pathogen-associated molecular patterns
- PDGF, platelet derived growth factor
- PDGF-Rβ, platelet derived growth factor receptor β
- PIGF, phosphatidylinositol-glycan biosynthesis class F protein
- PLCγ, phospholipase-C gamma
- PNS, peripheral nervous system
- PTPRζ1, receptor-type tyrosine-protein phosphatase zeta
- RA, rheumatoid arthritis
- RCC, renal cell carcinoma
- RD, rhabdomyosarcoma
- RGD, arginylglycylaspartic acid
- RT-PCR, real-time polymerase chain reaction
- SB, Southern blot
- SCC, squamous cell carcinoma
- SMCs, smooth muscle cells
- SVZ, sub-ventricular zone
- TA, tenascin assembly domain
- TGFβ, transforming growth factor β
- TIMP, tissue inhibitor of metalloproteinases
- TLR4, toll-like receptor 4
- TNFα, tumor necrosis factor α
- TSS, transcription start site
- UBC, urothelial bladder cancer
- UCC, urothelial cell carcinoma
- VEGF, vascular endothelial growth factor
- VSMCs, vascular smooth muscle cells
- VZ, ventricular zone
- WB, immunoblot/ western blot
- bFGF, basic fibroblast growth factor
- biosynthesis
- c, charged
- cancer
- ccRCC, clear cell renal cell carcinoma
- chRCC, chromophobe-primary renal cell carcinoma
- development
- glycosylation
- mAb, monoclonal antibody
- matrix assembly
- mitogen-activated protein kinase, MAPK
- pHo, extracellular pH
- pRCC, papillary renal cell carcinoma
- proteolytic cleavage
- siRNA, small interfering RNA
- splicing
- tenascin-C
- therapeutics
- transcription
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Affiliation(s)
- Sean P Giblin
- a Nuffield Department of Orthopaedics; Rheumatology and Musculoskeletal Sciences ; Kennedy Institute of Rheumatology; University of Oxford ; Oxford , UK
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Toma M, Wehner R, Kloß A, Hübner L, Fodelianaki G, Erdmann K, Füssel S, Zastrow S, Meinhardt M, Seliger B, Brech D, Noessner E, Tonn T, Schäkel K, Bornhäuser M, Bachmann MP, Wirth MP, Baretton G, Schmitz M. Accumulation of tolerogenic human 6-sulfo LacNAc dendritic cells in renal cell carcinoma is associated with poor prognosis. Oncoimmunology 2015; 4:e1008342. [PMID: 26155414 DOI: 10.1080/2162402x.2015.1008342] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 12/24/2022] Open
Abstract
Dendritic cells (DCs) essentially contribute to the induction and regulation of innate and adaptive immunity. Based on these important properties, DCs may profoundly influence tumor progression in patients. However, little is known about the role of distinct human DC subsets in primary tumors and their impact on clinical outcome. In the present study, we investigated the characteristics of human 6-sulfo LacNAc (slan) DCs in clear cell renal cell carcinoma (ccRCC). slanDCs have been shown to display various tumor-directed properties and to accumulate in tumor-draining lymph nodes from patients. When evaluating 263 ccRCC and 227 tumor-free tissue samples, we found increased frequencies of slanDCs in ccRCC tissues compared to tumor-free tissues. slanDCs were also detectable in the majority of 24 metastatic lymph nodes and 67 distant metastases from ccRCC patients. Remarkably, a higher density of slanDCs was significantly associated with a reduced progression-free, tumor-specific or overall survival of ccRCC patients. Tumor-infiltrating slanDCs displayed an immature phenotype expressing interleukin-10. ccRCC cells efficiently impaired slanDC-induced T-cell proliferation and programming as well as natural killer (NK) cell activation. In conclusion, these findings indicate that higher slanDC numbers in ccRCC tissues are associated with poor prognosis. The induction of a tolerogenic phenotype in slanDCs leading to an insufficient activation of innate and adaptive antitumor immunity may represent a novel immune escape mechanism of ccRCC. These observations may have implications for the design of therapeutic strategies that harness tumor-directed functional properties of DCs against ccRCC.
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Key Words
- CTLs, cytotoxic T cells
- DCs, dendritic cells
- FCS, fetal calf serum
- HLA, human leukocyte antigen
- IFNγ, interferonγ
- IL, interleukin
- ILT, immunoglobulin-like transcript
- LPS, lipopolysaccharide
- NK cells, natural killer cells
- PBMCs, peripheral blood mononuclear cells
- PMA, phorbol myristate acetate
- T cells
- TMAs, tissue microarrays
- TNF-α, tumor necrosis factor-α
- Th1 cells, T helper type I cells
- ccRCC, clear cell renal cell carcinoma
- dendritic cells
- renal cell carcinoma
- slan, 6-sulfo LacNAc
- tumor immunology
- tumor microenvironment
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Affiliation(s)
- Marieta Toma
- Institute of Pathology; University Hospital of Dresden ; Dresden, Germany
| | - Rebekka Wehner
- Institute of Immunology; Medical Faculty; TU Dresden ; Dresden, Germany
| | - Anja Kloß
- Institute of Immunology; Medical Faculty; TU Dresden ; Dresden, Germany
| | - Linda Hübner
- Institute of Immunology; Medical Faculty; TU Dresden ; Dresden, Germany
| | - Georgia Fodelianaki
- Institute of Immunology; Medical Faculty; TU Dresden ; Dresden, Germany ; Center for Regenerative Therapies Dresden ; Dresden, Germany
| | - Kati Erdmann
- Department of Urology; University Hospital of Dresden ; Dresden, Germany
| | - Susanne Füssel
- Department of Urology; University Hospital of Dresden ; Dresden, Germany
| | - Stefan Zastrow
- Department of Urology; University Hospital of Dresden ; Dresden, Germany
| | - Matthias Meinhardt
- Institute of Pathology; University Hospital of Dresden ; Dresden, Germany
| | - Barbara Seliger
- Institute for Medical Immunology; Martin Luther University Halle-Wittenberg ; Halle (Saale), Germany
| | - Dorothee Brech
- Institute of Molecular Immunology; Helmholtz Center Munich; German Research Center for Environmental Health Munich ; Munich, Germany
| | - Elfriede Noessner
- Institute of Molecular Immunology; Helmholtz Center Munich; German Research Center for Environmental Health Munich ; Munich, Germany
| | - Torsten Tonn
- Center for Regenerative Therapies Dresden ; Dresden, Germany ; German Red Cross Blood Service ; Dresden, Germany ; German Cancer Consortium (DKTK) ; Dresden, Germany ; German Cancer Research Center (DKFZ) ; Heidelberg, Germany
| | - Knut Schäkel
- Department of Dermatology; University Hospital of Heidelberg ; Heidelberg, Germany
| | - Martin Bornhäuser
- Center for Regenerative Therapies Dresden ; Dresden, Germany ; German Cancer Consortium (DKTK) ; Dresden, Germany ; German Cancer Research Center (DKFZ) ; Heidelberg, Germany ; Department of Medicine I; University Hospital of Dresden ; Dresden, Germany
| | - Michael P Bachmann
- Center for Regenerative Therapies Dresden ; Dresden, Germany ; German Cancer Consortium (DKTK) ; Dresden, Germany ; German Cancer Research Center (DKFZ) ; Heidelberg, Germany ; Department of Radioimmunology; Institute of Radiopharmaceutical Cancer Research; Helmholtz Center Dresden-Rossendorf ; Dresden, Germany
| | - Manfred P Wirth
- Department of Urology; University Hospital of Dresden ; Dresden, Germany ; German Cancer Consortium (DKTK) ; Dresden, Germany ; German Cancer Research Center (DKFZ) ; Heidelberg, Germany
| | - Gustavo Baretton
- Institute of Pathology; University Hospital of Dresden ; Dresden, Germany ; German Cancer Consortium (DKTK) ; Dresden, Germany ; German Cancer Research Center (DKFZ) ; Heidelberg, Germany
| | - Marc Schmitz
- Institute of Immunology; Medical Faculty; TU Dresden ; Dresden, Germany ; Center for Regenerative Therapies Dresden ; Dresden, Germany ; German Cancer Consortium (DKTK) ; Dresden, Germany ; German Cancer Research Center (DKFZ) ; Heidelberg, Germany
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5
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Mangolini A, Bonon A, Volinia S, Lanza G, Gambari R, Pinton P, Russo GR, del Senno L, Dell’Atti L, Aguiari G. Differential expression of microRNA501-5p affects the aggressiveness of clear cell renal carcinoma. FEBS Open Bio 2014; 4:952-65. [PMID: 25426415 PMCID: PMC4241533 DOI: 10.1016/j.fob.2014.10.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 10/09/2014] [Accepted: 10/28/2014] [Indexed: 12/18/2022] Open
Abstract
Low expression of miR501-5p correlates with good prognosis for patients with ccRCC. miRNA501-5p downregulation stimulates apoptosis by p53 activation. miR501-5p upregulation promotes cell proliferation and survival. Increased cell growth occurs by activation of mTOR kinase and MDM2 expression. This miRNA modulates apoptosis/cell growth, making it a prognostic biomarker for ccRCC.
Renal cell carcinoma is a common neoplasia of the adult kidney that accounts for about 3% of adult malignancies. Clear cell renal carcinoma is the most frequent subtype of kidney cancer and 20–40% of patients develop metastases. The absence of appropriate biomarkers complicates diagnosis and prognosis of this disease. In this regard, small noncoding RNAs (microRNAs), which are mutated in several neoplastic diseases including kidney carcinoma, may be optimal candidates as biomarkers for diagnosis and prognosis of this kind of cancer. Here we show that patients with clear cell kidney carcinoma that express low levels of miR501-5p exhibited a good prognosis compared with patients with unchanged or high levels of this microRNA. Consistently, in kidney carcinoma cells the downregulation of miR501-5p induced an increased caspase-3 activity, p53 expression as well as decreased mTOR activation, leading to stimulation of the apoptotic pathway. Conversely, miR501-5p upregulation enhanced the activity of mTOR and promoted both cell proliferation and survival. These biological processes occurred through p53 inactivation by proteasome degradation in a mechanism involving MDM2-mediated p53 ubiquitination. Our results support a role for miR501-5p in balancing apoptosis and cell survival in clear cell renal carcinoma. In particular, the downregulation of microRNA501-5p promotes a good prognosis, while its upregulation contributes to a poor prognosis, in particular, if associated with p53 and MDM2 overexpression and mTOR activation. Thus, the expression of miR501-5p is a possible biomarker for the prognosis of clear cell renal carcinoma.
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Affiliation(s)
- Alessandra Mangolini
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, University of Ferrara, Via Fossato di Mortara 64/b, 44121 Ferrara, Italy
| | - Anna Bonon
- Department of Biomedical and Specialty Surgical Sciences, Section of Biochemistry, Molecular Biology and Medical Genetics, University of Ferrara, Via Fossato di Mortara 74, 44121 Ferrara, Italy
| | - Stefano Volinia
- Department of Morphology, Surgery and Experimental Medicine, Section of Anatomy and Histology, University of Ferrara, Via Fossato di Mortara 64/b, 44121 Ferrara, Italy
| | - Giovanni Lanza
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathological Anatomy and Biomolecular Diagnostic, Azienda Ospedaliero Universitaria, Via Aldo Moro 8, 44124 Ferrara, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnologies, Section of Molecular Biology, University of Ferrara, Via Fossato di Mortara 74, 44121 Ferrara, Italy
| | - Paolo Pinton
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, University of Ferrara, Via Fossato di Mortara 64/b, 44121 Ferrara, Italy
| | - Gian Rosario Russo
- Unit of Urology, St. Anna Hospital, Via Aldo Moro 8, 44124 Ferrara, Italy
| | - Laura del Senno
- Department of Biomedical and Specialty Surgical Sciences, Section of Biochemistry, Molecular Biology and Medical Genetics, University of Ferrara, Via Fossato di Mortara 74, 44121 Ferrara, Italy
| | - Lucio Dell’Atti
- Unit of Urology, St. Anna Hospital, Via Aldo Moro 8, 44124 Ferrara, Italy
| | - Gianluca Aguiari
- Department of Biomedical and Specialty Surgical Sciences, Section of Biochemistry, Molecular Biology and Medical Genetics, University of Ferrara, Via Fossato di Mortara 74, 44121 Ferrara, Italy
- Corresponding author. Tel.: +39 0532974460; fax: +39 0532974484.
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