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Jaime-Casas S, Tripathi A, Pal SK, Yip W. Clinical Implications of the Molecular and Genomic Landscape of Upper Tract Urothelial Carcinoma. Curr Urol Rep 2024; 26:11. [PMID: 39379745 DOI: 10.1007/s11934-024-01245-1] [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] [Accepted: 09/27/2024] [Indexed: 10/10/2024]
Abstract
PURPOSE OF REVIEW Upper tract urothelial carcinoma (UTUC) is an aggressive entity with treatment strategies mirroring bladder cancer. Genomic and molecular profiling allows for a better characterization of this disease and allows for patient-tailored approaches. We aim to describe the genomic and molecular implications of this disease. RECENT FINDINGS Technological advances have the potential for early diagnosis and precise molecular analysis in patients with UTUC. Genomic profile clustering, specific mRNA signatures, and pathway-specific protein abundance tools have oncologic and clinical implications. We describe their utility in the context of this disease. In the era of precision medicine, designing clinical trials that explore the diagnostic and prognostic implications of biomolecular signatures in the context of UTUC is of utmost importance. Promising advances in this arena provide tools for physicians to avoid overtreatment in this patient population.
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Affiliation(s)
- Salvador Jaime-Casas
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Abhishek Tripathi
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Sumanta K Pal
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Wesley Yip
- Division of Urology and Urologic Oncology, City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA, 91010, USA.
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Walach MT, Nitschke K, Groß-Weege M, Großhans J, Wildner L, Pause L, Jarczyk J, Wessels F, Neuberger M, Kowalewski KF, Kriegmair MC, Popovic ZV, Gaiser T, Worst TS, Nuhn P. Cyclin A2 Expression as Predictive Biomarker in Muscle-Invasive Upper Tract Urothelial Carcinoma. Urol Int 2024; 108:128-136. [PMID: 38224675 DOI: 10.1159/000536184] [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: 03/25/2023] [Accepted: 01/03/2024] [Indexed: 01/17/2024]
Abstract
INTRODUCTION The aim was to evaluate the prognostic value of altered Cyclin A2 (CCNA2) gene expression in upper tract urothelial carcinoma (UTUC) and to assess its predictive potential as a prognostic factor for overall survival (OS) and disease-free survival. METHODS 62 patients who underwent surgical treatment for UTUC were included. Gene expression of CCNA2, MKI67, and p53 was analyzed by quantitative reverse transcriptase polymerase chain reaction. Survival analyses were performed using the Kaplan-Meier method and the log-rank test. For Cox regression analyses, uni- and multivariable hazard ratios were calculated. Spearman correlation was used to analyze correlation of CCNA2 expression with MKI67 and p53. RESULTS The median age of the cohort was 73 years, and it consisted of 48 males (77.4%) and 14 females (22.6%). Patients with high CCNA2 expression levels showed longer OS (HR 0.33; 95% CI: 0.15-0.74; p = 0.0073). Multivariable Cox regression analyses identified CCNA2 overexpression (HR 0.37; 95% CI: 0.16-0.85; p = 0.0189) and grading G2 (vs. G3) (HR 0.39; 95% CI: 0.17-0.87; p = 0.0168) to be independent predictors for longer OS. CCNA2 expression correlated positively with MKI67 expression (Rho = 0.4376, p = 0.0005). CONCLUSION Low CCNA2 expression is significantly associated with worse OS. Thus, CCNA2 might serve as a potential biomarker in muscle-invasive UTUC and may be used to characterize a subset of patients having an unfavorable outcome and for future risk assessment scores.
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Affiliation(s)
- Margarete Teresa Walach
- Department of Urology and Urologic Surgery, University Medical Centre Mannheim (UMM), University of Heidelberg, Mannheim, Germany
| | - Katja Nitschke
- Department of Urology and Urologic Surgery, University Medical Centre Mannheim (UMM), University of Heidelberg, Mannheim, Germany
| | - Matthias Groß-Weege
- Department of Urology and Urologic Surgery, University Medical Centre Mannheim (UMM), University of Heidelberg, Mannheim, Germany
| | - Johannes Großhans
- Department of Urology and Urologic Surgery, University Medical Centre Mannheim (UMM), University of Heidelberg, Mannheim, Germany
| | - Lukas Wildner
- Department of Urology and Urologic Surgery, University Medical Centre Mannheim (UMM), University of Heidelberg, Mannheim, Germany
| | - Luca Pause
- Department of Urology and Urologic Surgery, University Medical Centre Mannheim (UMM), University of Heidelberg, Mannheim, Germany
| | - Jonas Jarczyk
- Department of Urology and Urologic Surgery, University Medical Centre Mannheim (UMM), University of Heidelberg, Mannheim, Germany
| | - Frederik Wessels
- Department of Urology and Urologic Surgery, University Medical Centre Mannheim (UMM), University of Heidelberg, Mannheim, Germany
| | - Manuel Neuberger
- Department of Urology and Urologic Surgery, University Medical Centre Mannheim (UMM), University of Heidelberg, Mannheim, Germany
| | - Karl-Friedrich Kowalewski
- Department of Urology and Urologic Surgery, University Medical Centre Mannheim (UMM), University of Heidelberg, Mannheim, Germany
| | - Maximilian Christian Kriegmair
- Department of Urology and Urologic Surgery, University Medical Centre Mannheim (UMM), University of Heidelberg, Mannheim, Germany
| | - Zoran V Popovic
- Institute of Pathology, University Medical Centre Mannheim (UMM), University of Heidelberg, Mannheim, Germany
| | - Timo Gaiser
- Institute of Pathology, University Medical Centre Mannheim (UMM), University of Heidelberg, Mannheim, Germany
| | - Thomas Stefan Worst
- Department of Urology and Urologic Surgery, University Medical Centre Mannheim (UMM), University of Heidelberg, Mannheim, Germany
| | - Philipp Nuhn
- Department of Urology and Urologic Surgery, University Medical Centre Mannheim (UMM), University of Heidelberg, Mannheim, Germany
- Department of Urology, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Kiel, Germany
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Wu S, Li R, Jiang Y, Yu J, Zheng J, Li Z, Li M, Xin K, Wang Y, Xu Z, Li S, Chen X. Liquid biopsy in urothelial carcinoma: Detection techniques and clinical applications. Biomed Pharmacother 2023; 165:115027. [PMID: 37354812 DOI: 10.1016/j.biopha.2023.115027] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/26/2023] Open
Abstract
The types of urothelial carcinoma (UC) include urothelial bladder cancer and upper tract urothelial carcinoma. Current diagnostic techniques cannot meet the needs of patients. Liquid biopsy is an accurate method of determining the molecular profile of UC and is a cutting-edge and popular technique that is expected to complement existing detection techniques and benefit patients with UC. Circulating tumor cells, cell-free DNA, cell-free RNA, extracellular vesicles, proteins, and metabolites can be found in the blood, urine, or other bodily fluids and are examined during liquid biopsies. This article focuses on the components of liquid biopsies and their clinical applications in UC. Liquid biopsies have tremendous potential in multiple aspects of precision oncology, from early diagnosis and treatment monitoring to predicting prognoses. They may therefore play an important role in the management of UC and precision medicine.
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Affiliation(s)
- Siyu Wu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Rong Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Yuanhong Jiang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Jiazheng Yu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Jianyi Zheng
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Zeyu Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Mingyang Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Kerong Xin
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Yang Wang
- Department of Gynecology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China.
| | - Zhenqun Xu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
| | - Shijie Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
| | - Xiaonan Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
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Fu T, Lin Y, Lin L, Yang Y, Guo Q, Long Y, He H, Bao Y, Lin T, Chen J, Chen Z, Du L, Liao G, Liao B, Huang J. Network architecture of non-coding RNAs provides insights into the pathogenesis of upper tract urothelial carcinoma. Urol Oncol 2022; 40:383.e11-383.e21. [DOI: 10.1016/j.urolonc.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/18/2022] [Accepted: 05/03/2022] [Indexed: 10/18/2022]
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Cinque A, Capasso A, Vago R, Floris M, Lee MW, Minnei R, Trevisani F. MicroRNA Signatures in the Upper Urinary Tract Urothelial Carcinoma Scenario: Ready for the Game Changer? Int J Mol Sci 2022; 23:2602. [PMID: 35269744 PMCID: PMC8910117 DOI: 10.3390/ijms23052602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/20/2022] [Accepted: 02/24/2022] [Indexed: 12/18/2022] Open
Abstract
Upper urinary tract urothelial carcinoma (UTUC) represents a minor subgroup of malignancies arising in the urothelium of the renal pelvis or ureter. The estimated annual incidence is around 2 cases per 100,000 people, with a mean age at diagnosis of 73 years. UTUC is more frequently diagnosed in an invasive or metastatic stage. However, even though the incidence of UTUC is not high, UTUC tends to be aggressive and rapidly progressing with a poor prognosis in some patients. A significant challenge in UTUC is ensuring accurate and timely diagnosis, which is complicated by the non-specific nature of symptoms seen at the onset of disease. Moreover, there is a lack of biomarkers capable of identifying the early presence of the malignancy and guide-tailored medical treatment. However, the growing understanding of the molecular biology underlying UTUC has led to the discovery of promising new biomarkers. Among these biomarkers, there is a class of small non-coding RNA biomarkers known as microRNAs (miRNAs) that are particularly promising. In this review, we will analyze the main characteristics of UTUC and focus on microRNAs as possible novel tools that could enter clinical practice in order to optimize the current diagnostic and prognostic algorithm.
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Affiliation(s)
- Alessandra Cinque
- Biorek S.r.l., San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Anna Capasso
- Department of Medical Oncology Livestrong Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, TX 78723, USA;
| | - Riccardo Vago
- Urological Research Institute, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
- Faculty of Medicine and Surgery,, Università Vita-Salute San Raffaele, 20132 Milan, Italy
| | - Matteo Floris
- Nephrology, Dialysis, and Transplantation, Università degli Studi di Cagliari, G. Brotzu Hospital, 09134 Cagliari, Italy; (M.F.); (R.M.)
| | - Michael W. Lee
- Department of Medical Oncology and Medical Education, Dell Medical School, Livestrong Cancer Institutes, University of Texas at Austin, Austin, TX 78723, USA;
| | - Roberto Minnei
- Nephrology, Dialysis, and Transplantation, Università degli Studi di Cagliari, G. Brotzu Hospital, 09134 Cagliari, Italy; (M.F.); (R.M.)
| | - Francesco Trevisani
- Biorek S.r.l., San Raffaele Scientific Institute, 20132 Milan, Italy;
- Urological Research Institute, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
- Unit of Urology, San Raffaele Scientific Institute, 20132 Milan, Italy
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Chen Y, Chen S, Lu J, Yuan D, He L, Qin P, Tan H, Xu L. MicroRNA-363-3p promote the development of acute myeloid leukemia with RUNX1 mutation by targeting SPRYD4 and FNDC3B. Medicine (Baltimore) 2021; 100:e25807. [PMID: 33950983 PMCID: PMC8104143 DOI: 10.1097/md.0000000000025807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/15/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Runt-related transcription factor 1 (RUNX1) is one of the most frequently mutated genes in most of hematological malignancies, especially in acute myeloid leukemia. In the present study, we aimed to identify the key genes and microRNAs based on acute myeloid leukemia with RUNX1 mutation. The newly finding targeted genes and microRNA associated with RUNX1 may benefit to the clinical treatment in acute myeloid leukemia. MATERIAL/METHODS The gene and miRNA expression data sets relating to RUNX1 mutation and wild-type adult acute myeloid leukemia (AML) patients were downloaded from The Cancer Genome Atlas database. Differentially expressed miRNAs and differentially expressed genes (DEGs) were identified by edgeR of R platform. Gene ontology and the Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed by Metascape and Gene set enrichment analysis. The protein-protein interaction network and miRNA-mRNA regulatory network were performed by Search Tool for the Retrieval of Interacting Genes database and Cytoscape software. RESULTS A total of 27 differentially expressed miRNAs (25 upregulated and 2 downregulated) and 561 DEGs (429 upregulated and 132 downregulated) were identified. Five miRNAs (miR-151b, miR-151a-5p, let-7a-2-3p, miR-363-3p, miR-20b-5p) had prognostic significance in AML. The gene ontology analysis showed that upregulated DEGs suggested significant enrichment in MHC class II protein complex, extracellular structure organization, blood vessel development, cell morphogenesis involved in differentiation, embryonic morphogenesis, regulation of cell adhesion, and so on. Similarly, the downregulated DEGs were mainly enriched in secretory granule lumen, extracellular structure organization. In the gene set enrichment analysis of Kyoto Encyclopedia of Genes and Genomes pathways, the RUNX1 mutation was associated with adherent junction, WNT signaling pathway, JAK-STAT signaling pathway, pathways in cancer, cell adhesion molecules CAMs, MAPK signaling pathway. Eleven genes (PPBP, APP, CCR5, HLA-DRB1, GNAI1, APLNR, P2RY14, C3AR1, HTR1F, CXCL12, GNG11) were simultaneously identified by hub gene analysis and module analysis. MicroRNA-363-3p may promote the development of RUNX1 mutation AML, targeting SPRYD4 and FNDC3B. In addition, the RUNX1 mutation rates in patient were obviously correlated with age, white blood cell, FAB type, risk(cyto), and risk(molecular) (P < .05). CONCLUSION Our findings have indicated that multiple genes and microRNAs may play a crucial role in RUNX1 mutation AML. MicroRNA-363-3p may promote the development of RUNX1 mutation AML by targeting SPRYD4 and FNDC3B.
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Affiliation(s)
- Yimin Chen
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University
- Department of Urology and Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong Key Laboratory of Urology, Guangzhou Institute of Urology
| | - Shuyi Chen
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University
- Department of Urology and Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong Key Laboratory of Urology, Guangzhou Institute of Urology
| | - Jielun Lu
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Danyun Yuan
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University
- Department of Urology and Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong Key Laboratory of Urology, Guangzhou Institute of Urology
| | - Lang He
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University
- Department of Urology and Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong Key Laboratory of Urology, Guangzhou Institute of Urology
| | - Pengfei Qin
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University
| | - Huo Tan
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University
| | - Lihua Xu
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University
- Department of Urology and Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong Key Laboratory of Urology, Guangzhou Institute of Urology
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Systematic evaluation of multiple qPCR platforms, NanoString and miRNA-Seq for microRNA biomarker discovery in human biofluids. Sci Rep 2021; 11:4435. [PMID: 33627690 PMCID: PMC7904811 DOI: 10.1038/s41598-021-83365-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/02/2021] [Indexed: 02/06/2023] Open
Abstract
Aberrant miRNA expression has been associated with many diseases, and extracellular miRNAs that circulate in the bloodstream are remarkably stable. Recently, there has been growing interest in identifying cell-free circulating miRNAs that can serve as non-invasive biomarkers for early detection of disease or selection of treatment options. However, quantifying miRNA levels in biofluids is technically challenging due to their low abundance. Using reference samples, we performed a cross-platform evaluation in which miRNA profiling was performed on four different qPCR platforms (MiRXES, Qiagen, Applied Biosystems, Exiqon), nCounter technology (NanoString), and miRNA-Seq. Overall, our results suggest that using miRNA-Seq for discovery and targeted qPCR for validation is a rational strategy for miRNA biomarker development in clinical samples that involve limited amounts of biofluids.
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Hassler MR, Bray F, Catto JWF, Grollman AP, Hartmann A, Margulis V, Matin SF, Roupret M, Sfakianos JP, Shariat SF, Faltas BM. Molecular Characterization of Upper Tract Urothelial Carcinoma in the Era of Next-generation Sequencing: A Systematic Review of the Current Literature. Eur Urol 2020; 78:209-220. [PMID: 32571725 DOI: 10.1016/j.eururo.2020.05.039] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 05/27/2020] [Indexed: 12/25/2022]
Abstract
CONTEXT While upper tract urothelial carcinoma (UTUC) share histological appearance with bladder cancer (BC), the former has differences in etiology and clinical phenotype consistent with characteristic molecular alterations. OBJECTIVE To systematically evaluate current genomic sequencing and proteomic data examining molecular alterations in UTUC. EVIDENCE ACQUISITION A systematic review using PubMed, Scopus, and Web of Science was performed in December 2019 according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses statement. EVIDENCE SYNTHESIS A total of 46 publications were selected for inclusion in this report, including 13 studies assessing genome-wide alterations, 18 studies assessing gene expression or microRNA expression profiles, three studies assessing proteomics, one study assessing genome-wide DNA methylation, and 14 studies evaluating distinct pathway alteration patterns. Differences between sporadic and hereditary UTUC, and between UTUC and BC, as well as molecular profiles associated with exposure to aristolochic acid are highlighted. Molecular pathways relevant to UTUC biology, such as alterations in FGFR3, TP53, or microsatellite instability, are discussed. Our findings are limited by tumor and patient heterogeneity and different platforms used in the studies. CONCLUSIONS Molecular events in UTUC and BC can be shared or distinct. Consequently, molecular subtypes differ according to location. Further work is needed to define the epigenomic and proteomic features of UTUC, and understand the mechanisms by which they shape the clinical behavior of UTUC. PATIENT SUMMARY We report the current data on the molecular alterations specific to upper tract urothelial carcinoma (UTUC), resulting from novel genomic and proteomic technologies. Although UTUC biology is comparable with that of bladder cancer, the rates and UTUC-enriched alterations support its uniqueness and the need for precision medicine strategies for this rare tumor type.
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Affiliation(s)
- Melanie R Hassler
- Department of Urology, Medical University of Vienna, Vienna, Austria
| | - Freddie Bray
- Section of Cancer Surveillance, International Agency for Research on Cancer, Lyon, France
| | - James W F Catto
- Academic Urology Unit, University of Sheffield, Sheffield, UK
| | - Arthur P Grollman
- Department of Pharmacological Sciences and Department of Medicine, Stony Brook University, Stony Brook, New York, NY, USA
| | - Arndt Hartmann
- Institute of Pathology, Friedrich-Alexander Universität, Erlangen, Germany
| | - Vitaly Margulis
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Surena F Matin
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Morgan Roupret
- Urology, GRC n°5, Predictive Onco-Uro, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne University, Paris, France
| | - John P Sfakianos
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shahrokh F Shariat
- Department of Urology, Medical University of Vienna, Vienna, Austria; Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Karl Landsteiner Institute of Urology and Andrology, Vienna, Austria; Department of Urology, Weill Cornell Medical College, New York-Presbyterian Hospital, New York, NY, USA; Department of Urology, Second Faculty of Medicine, Charles University, Prague, Czech Republic; Institute for Urology and Reproductive Health, I.M. Sechenov First Moscow State Medical University, Moscow, Russia; Division of Urology, Department of Special Surgery, Jordan University Hospital, The University of Jordan, Amman, Jordan; European Association of Urology research foundation, Arnhem, Netherlands.
| | - Bishoy M Faltas
- Department of Urology, Weill Cornell Medical College, New York-Presbyterian Hospital, New York, NY, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA; Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA; Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine, New York, NY, USA; Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
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Lopez-Rincon A, Martinez-Archundia M, Martinez-Ruiz GU, Schoenhuth A, Tonda A. Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection. BMC Bioinformatics 2019; 20:480. [PMID: 31533612 PMCID: PMC6751684 DOI: 10.1186/s12859-019-3050-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/22/2019] [Indexed: 12/16/2022] Open
Abstract
Background MicroRNAs (miRNAs) are noncoding RNA molecules heavily involved in human tumors, in which few of them circulating the human body. Finding a tumor-associated signature of miRNA, that is, the minimum miRNA entities to be measured for discriminating both different types of cancer and normal tissues, is of utmost importance. Feature selection techniques applied in machine learning can help however they often provide naive or biased results. Results An ensemble feature selection strategy for miRNA signatures is proposed. miRNAs are chosen based on consensus on feature relevance from high-accuracy classifiers of different typologies. This methodology aims to identify signatures that are considerably more robust and reliable when used in clinically relevant prediction tasks. Using the proposed method, a 100-miRNA signature is identified in a dataset of 8023 samples, extracted from TCGA. When running eight-state-of-the-art classifiers along with the 100-miRNA signature against the original 1046 features, it could be detected that global accuracy differs only by 1.4%. Importantly, this 100-miRNA signature is sufficient to distinguish between tumor and normal tissues. The approach is then compared against other feature selection methods, such as UFS, RFE, EN, LASSO, Genetic Algorithms, and EFS-CLA. The proposed approach provides better accuracy when tested on a 10-fold cross-validation with different classifiers and it is applied to several GEO datasets across different platforms with some classifiers showing more than 90% classification accuracy, which proves its cross-platform applicability. Conclusions The 100-miRNA signature is sufficiently stable to provide almost the same classification accuracy as the complete TCGA dataset, and it is further validated on several GEO datasets, across different types of cancer and platforms. Furthermore, a bibliographic analysis confirms that 77 out of the 100 miRNAs in the signature appear in lists of circulating miRNAs used in cancer studies, in stem-loop or mature-sequence form. The remaining 23 miRNAs offer potentially promising avenues for future research. Electronic supplementary material The online version of this article (10.1186/s12859-019-3050-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alejandro Lopez-Rincon
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, David de Wied building,Universiteitsweg 99, Utrecht, 3584 CG, The Netherlands.
| | - Marlet Martinez-Archundia
- Laboratorio de Modelado Molecular, Bioinformática y diseño de fármacos. Departamento de Posgrado. Escuela Superior de Medicina del Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - Gustavo U Martinez-Ruiz
- Faculty of Medicine, National Autonomous University of Mexico; Federico Gomez Children's Hospital of Mexico, Mexico City, Mexico
| | | | - Alberto Tonda
- UMR 782 GMPA, Université Paris-Saclay, INRA, AgroParisTech, Thiverval-Grignon, France
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Zeuschner P, Linxweiler J, Junker K. Non-coding RNAs as biomarkers in liquid biopsies with a special emphasis on extracellular vesicles in urological malignancies. Expert Rev Mol Diagn 2019; 20:151-167. [DOI: 10.1080/14737159.2019.1665998] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Philip Zeuschner
- Department of Urology and Pediatric Urology, Saarland University, Homburg, Germany
| | - Johannes Linxweiler
- Department of Urology and Pediatric Urology, Saarland University, Homburg, Germany
| | - Kerstin Junker
- Department of Urology and Pediatric Urology, Saarland University, Homburg, Germany
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Xu J, Chen Z, Wang Y, Wang X, Chen L, Yuan T, Tang X, Lu Y, Chen H, Chen M, Duan Z, Fan J, Liang J, Zhang X. Several circulating miRNAs related to hyperlipidemia and atherosclerotic cardiovascular diseases. Lipids Health Dis 2019; 18:104. [PMID: 31010436 PMCID: PMC6477752 DOI: 10.1186/s12944-019-1046-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 04/08/2019] [Indexed: 12/19/2022] Open
Abstract
Background In recent years, an increasing number of studies have proved that circulating miRNAs could be used for the early diagnosis of cardiovascular diseases and even play vital roles in the evaluation of therapeutic effects or prognosis. This study was conducted to examine the correlation between serum microRNAs and hyperlipidemia to provide a theoretical basis for the early screening and intervention of atherosclerotic cardiovascular diseases (ASCVD). Methods The serum samples and clinical data of 122 patients with hyperlipidemia and 168 healthy subjects were collected. Related clinical information was statistically analyzed for the two groups. Expression of circulating miRNAs was detected by miRNA microarray analysis and further verified by reverse transcription-quantitative PCR (RT-qPCR). Results Statistical analysis of clinical information revealed a significant difference in the incidence of ASCVD between the two groups. The MiRNA microarray analysis (n = 10) showed 22 miRNAs with significantly different expression, among which 12 showed upregulation, and the others showed downregulation. Those possessing obvious differences and stable expression in the miRNA microarray, including miRNA-191-3p, miRNA-933, and miRNA-425-3p, were chosen for further investigation using RT-qPCR. The results demonstrated that several miRNAs were related to lipid metabolism disorders, especially miRNA-933. The area under the curve (AUC) of miRNA-933 in distinguishing the hyperlipidemia and ASCVD patients was 0.739 (95% CI, 0.682–0.795; P < 0.01) and 0.703 (95% CI, 0.643–0.763, P < 0.01), respectively. Conclusions In conclusion, miRNA-191-3p, miRNA-933, and miRNA-425-3p may be depressed in the peripheral circulation of patients with lipid metabolism disorders (mainly LDL). Circulating miRNA-933 could be a feasible predictor for ASCVD at the early stage. Electronic supplementary material The online version of this article (10.1186/s12944-019-1046-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiang Xu
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou, 225009, China.,Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225009, China
| | - Zixuan Chen
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225009, China
| | - Yingge Wang
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou, 225009, China
| | - Xiaohong Wang
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225009, China
| | - Lu Chen
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225009, China
| | - Tingting Yuan
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225009, China
| | - Xiangming Tang
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou, 225009, China.,Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225009, China
| | - Yaoyao Lu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225009, China
| | - Hongmei Chen
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225009, China
| | - Miaolei Chen
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225009, China
| | - Zuowei Duan
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou, 225009, China
| | - Jianglin Fan
- Department of Molecular Pathology, Faculty of Medicine, Graduate School of Medical Sciences, University of Yamanashi, Yamanashi, 409-3898, Japan
| | - Jingyan Liang
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225009, China. .,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, 225001, China. .,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, 225009, China.
| | - Xinjiang Zhang
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou, 225009, China.
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Miyake M, Owari T, Hori S, Nakai Y, Fujimoto K. Emerging biomarkers for the diagnosis and monitoring of urothelial carcinoma. Res Rep Urol 2018; 10:251-261. [PMID: 30588457 PMCID: PMC6299471 DOI: 10.2147/rru.s173027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Urothelial carcinoma (UC) arises extensively from the renal pelvis, ureter, urinary bladder, and urethra. UC represents a clinical and social challenge because of its incidence, post-treatment recurrence rate, and prognosis. Combinations of urine cytology, cystoscopy, and conventional imaging such as computed tomography are currently used for diagnosis and monitoring modalities of UC. Both the poor diagnostic accuracy of urine cytology and poor cost performance of cystoscopy and conventional imaging modalities emphasize the urgent need for advancement in clinical guidance for UC. Urine- and blood-based biomarkers for detection of UC of the bladder and upper urinary tract represent a considerable research area. Biomarkers can help to improve UC diagnosis with the aim of replacing cystoscopy and other imaging examinations in future and may enable individualizing risk stratification regarding therapy and follow-up. Over the decades, numerous studies have focused on the potential application of biomarkers for UC, including urine, circulating tumor DNA, RNAs, proteins, and extracellular vesicles. Although some biomarkers such as ImmunoCyt/uCyt+, UroVysion, NMP-22, bladder tumor antigen, CxBladder, and Xpert Bladder Cancer are currently available in clinical practice, few biomarkers achieve high sensitivity and specificity. Emerging biomarkers are continuously developed and reported in medical journals. However, there is a significant lack on following external validation using different cohorts. The positive results are needed to be confirmed by more studies with large-scale cohorts and long follow-up periods to prove the true value of novel biomarkers, followed by their adoption in clinical practice. The present paper provides an overview of the evidence based on high-impact studies regarding urine- and blood-based biomarkers and their clinical applications in bladder cancer and upper tract UC.
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Affiliation(s)
- Makito Miyake
- Department of Urology, Nara Medical University, Kashihara-shi, Nara 634-8522, Japan,
| | - Takuya Owari
- Department of Urology, Nara Medical University, Kashihara-shi, Nara 634-8522, Japan,
| | - Shunta Hori
- Department of Urology, Nara Medical University, Kashihara-shi, Nara 634-8522, Japan,
| | - Yasushi Nakai
- Department of Urology, Nara Medical University, Kashihara-shi, Nara 634-8522, Japan,
| | - Kiyohide Fujimoto
- Department of Urology, Nara Medical University, Kashihara-shi, Nara 634-8522, Japan,
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