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Abrego-Guandique DM, Ilori OA, Caroleo MC, Cannataro R, Cione E, Tucci P. Differential Digestive Stability of Food-Derived microRNAs: The Case of miR-30c-5p and miR-92a-3p in Polyfloral Honey. Curr Issues Mol Biol 2024; 46:7473-7485. [PMID: 39057084 PMCID: PMC11276035 DOI: 10.3390/cimb46070443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Dietary microRNAs (miRs) represent a new area in food science. Although they have been found in many foods, including honey, more research is needed about their stability and fate during digestion. Hence, this study aimed to analyze the digestive stability of two selected miRs in honey. We extracted miR-92a-3p and miR-30c-5p from pasteurized and unpasteurized forms of polyfloral honey using two different methods and kits: a column-based manual method and a phenol-free semi-automated magnetic-bead-based method. The latter option was used for the subsequent analysis of samples according to the INFOGEST static in vitro digestion protocol. Also, the honey samples were examined for exosome-like particles using dynamic light scattering. Although the expression levels of both miRs were significantly lower following intestinal digestion, we found a difference in the resilience of the miRs to gastrointestinal conditions, with miR-30c-5p being relatively stable compared to miR-92a-3p following digestion, regardless of the honey's pasteurization treatment. Moreover, there was marked heterogeneity in the extracellular vesicle profile of the pasteurized sample. We identified the presence of two broadly conserved miRs in honey: miR-92a-3p and miR-30c-5p. Despite honey exhibiting high digestibility, miR-92a-3p was less resilient than miR-30c-5p, demonstrating considerable resistance under gastrointestinal conditions. Although further research is needed, the results obtained from this study may represent a starting point for utilizing honey as a source of exogenous miRNAs for preventive strategies and more "natural" treatments.
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Affiliation(s)
| | - Olubukunmi Amos Ilori
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (O.A.I.); (P.T.)
| | - Maria Cristina Caroleo
- Department of Health Sciences, University of Magna Graecia Catanzaro, 88100 Catanzaro, Italy; (D.M.A.-G.); (M.C.C.)
- Galascreen Laboratories, University of Calabria, 87036 Rende, Italy;
| | - Roberto Cannataro
- Galascreen Laboratories, University of Calabria, 87036 Rende, Italy;
- Research Division, Dynamical Business & Science Society, DBSS International SAS, Bogota 110861, Colombia
| | - Erika Cione
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (O.A.I.); (P.T.)
- Galascreen Laboratories, University of Calabria, 87036 Rende, Italy;
| | - Paola Tucci
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (O.A.I.); (P.T.)
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Pesta M, Travnicek I, Kulda V, Ostasov P, Windrichova J, Houfkova K, Knizkova T, Bendova B, Hes O, Hora M, Topolcan O, Polivka J. Prognostic Value of Tumor Tissue Up-regulated microRNAs in Clear Cell Renal Cell Carcinoma (ccRCC). In Vivo 2024; 38:1799-1805. [PMID: 38936941 PMCID: PMC11215600 DOI: 10.21873/invivo.13631] [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: 01/23/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND/AIM The management of patients with clear cell renal cell carcinoma (ccRCC) includes prognosis assessment based on TNM classification and biochemical markers. This approach stratifies patients with advanced ccRCC into groups of favorable, intermediate, and poor prognosis. The aim of the study was to improve prognosis estimation using microRNAs involved in the pathogenesis of ccRCC. PATIENTS AND METHODS The study was based on a histologically-verified set of matched ccRCC FFPE tissue samples (normal renal tissue, primary tumor, metastasis, n=20+20+20). The expression of 2,549 microRNAs was analyzed using the SurePrint G3 Human miRNA microarray kit (Agilent Technologies). Prognostic value of significantly deregulated microRNAs was further evaluated on microRNA expression and clinical data of 475 patients obtained from TCGA Kidney Clear Cell Carcinoma (KIRC) database. RESULTS There were 13 up-regulated and 6 down-regulated microRNAs in tumor tissues compared to control tissues. Among them, survival analysis revealed those with prognostic significance. Patients with high expression of miR-21, miR-27a, miR-34a, miR-106b, miR-210, and miR-342 showed significantly unfavorable outcome. The opposite was observed for miR-30e, patients with low expression had significantly shorter survival. CONCLUSION The inclusion of these microRNAs in a prognostic panel holds the potential to enhance stratification scoring systems, on which the treatment of ccRCC patients is based.
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Affiliation(s)
- Martin Pesta
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Laboratory of Immunoanalysis, University Hospital in Pilsen, Pilsen, Czech Republic
| | - Ivan Travnicek
- Department of Urology, University Hospital in Pilsen, Pilsen, Czech Republic
| | - Vlastimil Kulda
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic;
| | - Pavel Ostasov
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Jindra Windrichova
- Laboratory of Immunoanalysis, University Hospital in Pilsen, Pilsen, Czech Republic
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Katerina Houfkova
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Tereza Knizkova
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Barbora Bendova
- Department of Urology, University Hospital in Pilsen, Pilsen, Czech Republic
| | - Ondrej Hes
- Department of Pathology, University Hospital in Pilsen, Pilsen, Czech Republic
| | - Milan Hora
- Department of Urology, University Hospital in Pilsen, Pilsen, Czech Republic
| | - Ondrej Topolcan
- Laboratory of Immunoanalysis, University Hospital in Pilsen, Pilsen, Czech Republic
| | - Jiri Polivka
- Laboratory of Immunoanalysis, University Hospital in Pilsen, Pilsen, Czech Republic
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
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Takeda M, Akamatsu S, Kita Y, Goto T, Kobayashi T. The Roles of Extracellular Vesicles in the Progression of Renal Cell Carcinoma and Their Potential for Future Clinical Application. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:nano13101611. [PMID: 37242027 DOI: 10.3390/nano13101611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023]
Abstract
Renal cell carcinoma (RCC) is the most common type of kidney cancer and is thought to originate from renal tubular epithelial cells. Extracellular vesicles (EVs) are nanosized lipid bilayer vesicles that are secreted into extracellular spaces by nearly all cell types, including cancer cells and non-cancerous cells. EVs are involved in multiple steps of RCC progression, such as local invasion, host immune modulation, drug resistance, and metastasis. Therefore, EVs secreted from RCC are attracting rapidly increasing attention from researchers. In this review, we highlight the mechanism by which RCC-derived EVs lead to disease progression as well as the potential and challenges related to the clinical implications of EV-based diagnostics and therapeutics.
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Affiliation(s)
- Masashi Takeda
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Shusuke Akamatsu
- Department of Urology, Graduate School of Medicine, Nagoya University, Nagoya 466-8550, Japan
| | - Yuki Kita
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Takayuki Goto
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Takashi Kobayashi
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
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Todorović L, Stanojević B. VHL tumor suppressor as a novel potential candidate biomarker in papillary thyroid carcinoma. BIOMOLECULES AND BIOMEDICINE 2023; 23:26-36. [PMID: 36036061 PMCID: PMC9901892 DOI: 10.17305/bjbms.2022.7850] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/12/2022] [Indexed: 02/03/2023]
Abstract
Papillary thyroid carcinoma (PTC) is the most common type of endocrine cancer, with an increasing incidence worldwide. The treatment of PTC is currently the subject of clinical controversy, making it critically important to identify molecular markers that would help improve the risk stratification of PTC patients and optimize the therapeutic approach. The VHL tumor suppressor gene has been implicated in tumorigenesis of various types of carcinoma and linked with their aggressive biological behavior. The role of VHL in the origin and development of PTC has only recently begun to be revealed. In this narrative review we attempt to summarize the existing knowledge that implicates VHL in PTC pathogenesis and to outline its potential significance as a candidate molecular biomarker for the grouping of PTC patients into high and low risk groups.
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Affiliation(s)
- Lidija Todorović
- Laboratory for Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia,Correspondence to Lidija Todorović:
| | - Boban Stanojević
- Laboratory for Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia,Department of Haematological Medicine, Division of Cancer Studies, Leukemia and Stem Cell Biology Team, King’s College London, London, UK,Virocell Biologics, Department of Cell and Gene Therapy, Great Ormond Street Hospital for Children, Zayed Centre for Research into Rare Disease in Children, London, UK
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Molina-Cerrillo J, Santoni M, Ruiz Á, Massari F, Pozas J, Ortego I, Gómez V, Grande E, Alonso-Gordoa T. Epigenetics in advanced renal cell carcinoma: Potential new targets. Crit Rev Oncol Hematol 2022; 180:103857. [DOI: 10.1016/j.critrevonc.2022.103857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/06/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
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Diagnostic Strategies for Urologic Cancer Using Expression Analysis of Various Oncogenic Surveillance Molecules—From Non-Coding Small RNAs to Cancer-Specific Proteins. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12157390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Urinary-tract-related tumors are prone to simultaneous or heterogeneous multiple tumor development within the primary organ. Urologic tumors have a very high risk of recurrence in the long and short term. This may be related to the disruption of homeostasis on the genetic level, such as the induction of genetic mutations due to exposure to various carcinogenic factors and the disruption of cancer suppressor gene functions. It is essential to detect the cancer progression signals caused by genetic abnormalities and find treatment therapies. In this review, we discuss the usefulness of tumor-expressing clinical biomarkers for predicting cancer progression. Furthermore, we discuss various factors associated with disturbed intracellular signals and those targeted by microRNAs, which are representative of non-coding small RNAs.
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Chen Y, Liu W, Li D, Cao Y, Wang W, Li C, An R. MiRNA-148a inhibits cell growth and drug resistance by regulating WNT10a expression in renal cell carcinoma. Transl Androl Urol 2022; 11:996-1006. [PMID: 35958896 PMCID: PMC9360522 DOI: 10.21037/tau-22-464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 07/14/2022] [Indexed: 12/05/2022] Open
Abstract
Background We aimed to explore miR-148a exerts a tumor suppressor effect and arsenic trioxide (As2O3) sensitivity on renal cell carcinoma (RCC). Methods We performed polymerase chain reaction (PCR) on 42 pairs of tumor and paracancerous samples collected from RCC patients to investigate the miR-148a expression; meanwhile, we analyzed the interplay between clinical indicators and miR-148a expression of RCC. Then, the influence of miR-148a overexpression on the functions of RCC cells were analyze using transwell migration assay, Cell Counting Kit-8 (CCK-8), and cell wound healing assay. Furthermore, the ability of miR-148a to sensitize Caki-1 cells treated with As2O3 were detected using flow cytometry. Finally, the relevant mechanism of miR-148a on the downstream gene Wnt family member 10A (WNT10a) was explored by cell reverse method. Results The results from RCC patients indicated a significantly lower miR-148a level than adjacent tissues. The low miR-148a expression increased prevalence of distant metastasis and decreased survival rate compared to those with high expression in patients. In the RCC cell lines, the proliferation and metastasis ability of the miR-148a mimic group was remarkably lower than the miR-NC group. At the same time, it was verified that WNT10a was remarkably higher cell lines and RCC tissues; and negatively related to miR-148a expression. In addition, miR-148a mimics were found to remarkably reduce the protein expression of WNT10a. In the cell reverse experiment, overexpression of WNT10a was confirmed to offset the miR-148a mimics effect on metastasis and proliferation of RCC cells. In addition, an increase in relative apoptosis was detected in As2O3 treated with/without miR-148a mimics for 48 hours, and apoptosis was significantly reduced after transfection with WNT10a in the Caki-1 cell line and significantly reduced after combined treatment. Conclusions The study revealed that miR-148a is associated with distant metastases and leads to poor prognosis in RCC patients. Moreover, miR-148a inhibit the malignant progression and increase the sensitivity of RCC cells to As2O3 by regulating WNT10a.
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Affiliation(s)
- Yongsheng Chen
- Department of Urology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Wenhua Liu
- Intensive Care Unit (ICU) Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Dechao Li
- Department of Urology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yan Cao
- Department of Urology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Wentao Wang
- Department of Urology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Changfu Li
- Department of Urology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Ruihua An
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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Giubellino A, Ricketts CJ, Moreno V, Linehan WM, Merino MJ. MicroRNA Profiling of Morphologically Heterogeneous Clear Cell Renal Cell Carcinoma. J Cancer 2021; 12:5375-5384. [PMID: 34405000 PMCID: PMC8364632 DOI: 10.7150/jca.52310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 12/26/2020] [Indexed: 01/05/2023] Open
Abstract
Intratumoral heterogeneity (IH) has been recently described as an important contributor to tumor growth through a branched rather than a linear pattern of tumor evolution for renal cell carcinoma. As to whether the miRNA profiling of the different and heterogeneous areas is the same or not, it is not known. This study analyzed the differences and similarities of the miRNA profiles in histologically distinct regions within several RCC tumors. The observed differences may have great implications for the development of predictive biomarkers and the identification of druggable targets with improvement of combinatorial therapeutic approaches for the effective treatment of kidney cancer, as well as for the identification of circulating malignant cells that can be useful to detect tumor recurrences.
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Affiliation(s)
- Alessio Giubellino
- Translational Surgical Pathology, Laboratory of Pathology, National Institutes of health, Bethesda, MD
| | - Christopher J Ricketts
- Urologic Oncology Branch National Cancer Institute, National Institutes of health, Bethesda, MD
| | - Vanessa Moreno
- Translational Surgical Pathology, Laboratory of Pathology, National Institutes of health, Bethesda, MD
| | - W Marston Linehan
- Urologic Oncology Branch National Cancer Institute, National Institutes of health, Bethesda, MD
| | - Maria J Merino
- Translational Surgical Pathology, Laboratory of Pathology, National Institutes of health, Bethesda, MD
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The Role of Epigenetics in the Progression of Clear Cell Renal Cell Carcinoma and the Basis for Future Epigenetic Treatments. Cancers (Basel) 2021; 13:cancers13092071. [PMID: 33922974 PMCID: PMC8123355 DOI: 10.3390/cancers13092071] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The accumulated evidence on the role of epigenetic markers of prognosis in clear cell renal cell carcinoma (ccRCC) is reviewed, as well as state of the art on epigenetic treatments for this malignancy. Several epigenetic markers are likely candidates for clinical use, but still have not passed the test of prospective validation. Development of epigenetic therapies, either alone or in combination with tyrosine-kinase inhibitors of immune-checkpoint inhibitors, are still in their infancy. Abstract Clear cell renal cell carcinoma (ccRCC) is curable when diagnosed at an early stage, but when disease is non-confined it is the urologic cancer with worst prognosis. Antiangiogenic treatment and immune checkpoint inhibition therapy constitute a very promising combined therapy for advanced and metastatic disease. Many exploratory studies have identified epigenetic markers based on DNA methylation, histone modification, and ncRNA expression that epigenetically regulate gene expression in ccRCC. Additionally, epigenetic modifiers genes have been proposed as promising biomarkers for ccRCC. We review and discuss the current understanding of how epigenetic changes determine the main molecular pathways of ccRCC initiation and progression, and also its clinical implications. Despite the extensive research performed, candidate epigenetic biomarkers are not used in clinical practice for several reasons. However, the accumulated body of evidence of developing epigenetically-based biomarkers will likely allow the identification of ccRCC at a higher risk of progression. That will facilitate the establishment of firmer therapeutic decisions in a changing landscape and also monitor active surveillance in the aging population. What is more, a better knowledge of the activities of chromatin modifiers may serve to develop new therapeutic opportunities. Interesting clinical trials on epigenetic treatments for ccRCC associated with well established antiangiogenic treatments and immune checkpoint inhibitors are revisited.
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Fang P, Zhou L, Lim LY, Fu H, Yuan ZX, Lin J. Targeting Strategies for Renal Cancer Stem Cell Therapy. Curr Pharm Des 2020; 26:1964-1978. [PMID: 32188377 DOI: 10.2174/1381612826666200318153106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/27/2020] [Indexed: 12/24/2022]
Abstract
Renal cell carcinoma (RCC) is an intractable genitourinary malignancy that accounts for approximately 4% of adult malignancies. Currently, there is no approved targeted therapy for RCC that has yielded durable remissions, and they remain palliative in intent. Emerging evidence has indicated that renal tumorigenesis and RCC treatment-resistance may originate from renal cancer stem cells (CSCs) with tumor-initiating capacity (CSC hypothesis). A better understanding of the mechanism underlying renal CSCs will help to dissect RCC heterogeneity and drug treatment efficiency, to promote more personalized and targeted therapies. In this review, we summarized the stem cell characteristics of renal CSCs. We outlined the targeting strategies and challenges associated with developing therapies that target renal CSCs angiogenesis, immunosuppression, signaling pathways, surface biomarkers, microRNAs and nanomedicine. In conclusion, CSCs are an important role in renal carcinogenesis and represent a valid target for treatment of RCC patients.
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Affiliation(s)
- Pengchao Fang
- Department of Pharmacy, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Liuting Zhou
- Department of Pharmacy, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Lee Y Lim
- Department of Pharmacy, School of Medicine and Pharmacology, The University of Western Australia, Crawley WA 6009, Perth, Australia
| | - Hualin Fu
- Department of Pharmacy, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhi-Xiang Yuan
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Juchun Lin
- Department of Pharmacy, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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Hadj-Moussa H, Storey KB. The OxymiR response to oxygen limitation: a comparative microRNA perspective. J Exp Biol 2020; 223:223/10/jeb204594. [DOI: 10.1242/jeb.204594] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
ABSTRACT
From squid at the bottom of the ocean to humans at the top of mountains, animals have adapted to diverse oxygen-limited environments. Surviving these challenging conditions requires global metabolic reorganization that is orchestrated, in part, by microRNAs that can rapidly and reversibly target all biological functions. Herein, we review the involvement of microRNAs in natural models of anoxia and hypoxia tolerance, with a focus on the involvement of oxygen-responsive microRNAs (OxymiRs) in coordinating the metabolic rate depression that allows animals to tolerate reduced oxygen levels. We begin by discussing animals that experience acute or chronic periods of oxygen deprivation at the ocean's oxygen minimum zone and go on to consider more elevated environments, up to mountain plateaus over 3500 m above sea level. We highlight the commonalities and differences between OxymiR responses of over 20 diverse animal species, including invertebrates and vertebrates. This is followed by a discussion of the OxymiR adaptations, and maladaptations, present in hypoxic high-altitude environments where animals, including humans, do not enter hypometabolic states in response to hypoxia. Comparing the OxymiR responses of evolutionarily disparate animals from diverse environments allows us to identify species-specific and convergent microRNA responses, such as miR-210 regulation. However, it also sheds light on the lack of a single unified response to oxygen limitation. Characterizing OxymiRs will help us to understand their protective roles and raises the question of whether they can be exploited to alleviate the pathogenesis of ischemic insults and boost recovery. This Review takes a comparative approach to addressing such possibilities.
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Affiliation(s)
- Hanane Hadj-Moussa
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON, Canada, K1S 5B6
| | - Kenneth B. Storey
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON, Canada, K1S 5B6
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Saquib Q, Xia P, Siddiqui MA, Zhang J, Xie Y, Faisal M, Ansari SM, Alwathnani HA, Alatar AA, Al-Khedhairy AA, Zhang X. High-throughput transcriptomics: An insight on the pathways affected in HepG2 cells exposed to nickel oxide nanoparticles. CHEMOSPHERE 2020; 244:125488. [PMID: 31812053 DOI: 10.1016/j.chemosphere.2019.125488] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/24/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
Nickel oxide nanoparticles (NiO-NPs) have been used in several consumer goods, reported to demonstrate the hepatotoxic effects in vitro and in vivo test models. Nonetheless the molecular mechanism of hepatotoxicity is still missing. Hence, a toxicogenomic approach integrating microscopic techniques and high-throughput RNA sequencing (RNA-Seq) was applied to reveal hepatotoxicity in human hepatocellular carcinoma cells (HepG2). NiO-NPs induced a concentration dependent (5-100 μg/ml) cytotoxicity, with a No observed effect level (NOEL) of 5 μg/ml. Hypoxia-inducible transcription factor-1α (HIF-1α) and miR-210 microRNA were upregulated at 25 and 100 μg/ml, while significant alteration on transcriptome at mRNA and pathway level was observed at non-toxic level of NiO-NPs treatment. The treated cells also showed activation of glycolysis, glutathione, lysosomes and autophagy pathways by a pathway-driven analysis. Flow cytometric analysis affirmed the elevation in nitric oxide (NO), Ca++ influx, esterase, and disruption of mitochondrial membrane potential (ΔΨm). Cell cycle dysregulation was affirmed by the appearance of 30.5% subG1 apoptotic peak in NiO-NPs (100 μg/ml) treated cells. The molecular responses were consistent with the microscopic observation that NiO-NPs induced subcellular alterations in HepG2 cells. We conclude that hypoxia stress played a pivotal role in NiO-NPs induced hepatoxicity in HepG2 cells. Concentration dependent effects on transcriptomics specify a powerful tool to evaluate the molecular mechanisms of nanoparticle induced cytotoxicity. Overall our study unequivocally affirmed the transcriptomic alterations in human cells, consequently the prevalent usage of NiO-NPs should be given subtle consideration owing to its effects on biological processes.
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Affiliation(s)
- Quaiser Saquib
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia; A.R. Al-Jeraisy Chair for DNA Research, Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Pu Xia
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Maqsood A Siddiqui
- A.R. Al-Jeraisy Chair for DNA Research, Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Junjiang Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Yuwei Xie
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Mohammad Faisal
- Department of Botany & Microbiology, College of Sciences, King Saud University, P.O Box 2455, Riyadh, 11451, Saudi Arabia
| | - Sabiha M Ansari
- Department of Botany & Microbiology, College of Sciences, King Saud University, P.O Box 2455, Riyadh, 11451, Saudi Arabia
| | - Hend A Alwathnani
- Department of Botany & Microbiology, College of Sciences, King Saud University, P.O Box 2455, Riyadh, 11451, Saudi Arabia
| | - Abdulrahman A Alatar
- Department of Botany & Microbiology, College of Sciences, King Saud University, P.O Box 2455, Riyadh, 11451, Saudi Arabia
| | - Abdulaziz A Al-Khedhairy
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China.
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Lauer V, Grampp S, Platt J, Lafleur V, Lombardi O, Choudhry H, Kranz F, Hartmann A, Wullich B, Yamamoto A, Coleman ML, Ratcliffe PJ, Mole DR, Schödel J. Hypoxia drives glucose transporter 3 expression through hypoxia-inducible transcription factor (HIF)-mediated induction of the long noncoding RNA NICI. J Biol Chem 2020; 295:4065-4078. [PMID: 31690629 PMCID: PMC7105321 DOI: 10.1074/jbc.ra119.009827] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/18/2019] [Indexed: 12/12/2022] Open
Abstract
Hypoxia-inducible transcription factors (HIFs) directly dictate the expression of multiple RNA species including novel and as yet uncharacterized long noncoding transcripts with unknown function. We used pan-genomic HIF-binding and transcriptomic data to identify a novel long noncoding RNA Noncoding Intergenic Co-Induced transcript (NICI) on chromosome 12p13.31 which is regulated by hypoxia via HIF-1 promoter-binding in multiple cell types. CRISPR/Cas9-mediated deletion of the hypoxia-response element revealed co-regulation of NICI and the neighboring protein-coding gene, solute carrier family 2 member 3 (SLC2A3) which encodes the high-affinity glucose transporter 3 (GLUT3). Knockdown or knockout of NICI attenuated hypoxic induction of SLC2A3, indicating a direct regulatory role of NICI in SLC2A3 expression, which was further evidenced by CRISPR/Cas9-VPR-mediated activation of NICI expression. We also demonstrate that regulation of SLC2A3 is mediated through transcriptional activation rather than posttranscriptional mechanisms because knockout of NICI leads to reduced recruitment of RNA polymerase 2 to the SLC2A3 promoter. Consistent with this we observe NICI-dependent regulation of glucose consumption and cell proliferation. Furthermore, NICI expression is regulated by the von Hippel-Lindau (VHL) tumor suppressor and is highly expressed in clear cell renal cell carcinoma (ccRCC), where SLC2A3 expression is associated with patient prognosis, implying an important role for the HIF/NICI/SLC2A3 axis in this malignancy.
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Affiliation(s)
- Victoria Lauer
- Department of Nephrology and Hypertension, Universitätsklinikum Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany
| | - Steffen Grampp
- Department of Nephrology and Hypertension, Universitätsklinikum Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany
| | - James Platt
- NDM Research Building, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, United Kingdom
| | - Veronique Lafleur
- NDM Research Building, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, United Kingdom
| | - Olivia Lombardi
- NDM Research Building, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, United Kingdom
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, Center of Innovation in Personalized Medicine, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Franziska Kranz
- Department of Nephrology and Hypertension, Universitätsklinikum Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany; Department of Computer Science 9, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 11, 91058 Erlangen, Germany
| | - Arndt Hartmann
- Institute of Pathology, Universitätsklinikum Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Krankenhausstraße 8-10, 91054 Erlangen, Germany
| | - Bernd Wullich
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Krankenhausstraße 12, 91054 Erlangen, Germany
| | - Atsushi Yamamoto
- NDM Research Building, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, United Kingdom
| | - Mathew L Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Peter J Ratcliffe
- NDM Research Building, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, United Kingdom
| | - David R Mole
- NDM Research Building, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, United Kingdom
| | - Johannes Schödel
- Department of Nephrology and Hypertension, Universitätsklinikum Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany.
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14
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Chen L, Wang Z, Xu Q, Liu Y, Chen L, Guo S, Wang H, Zeng K, Liu J, Zeng S, Yu L. The failure of DAC to induce OCT2 expression and its remission by hemoglobin-based nanocarriers under hypoxia in renal cell carcinoma. Theranostics 2020; 10:3562-3578. [PMID: 32206108 PMCID: PMC7069078 DOI: 10.7150/thno.39944] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Background: Human organic cation transporter 2 (OCT2) is the most abundant and important uptake transporter involved in the renal excretion of cationic drugs. Abnormal hypermethylation- mediated silencing of OCT2 results in oxaliplatin resistance in renal cell carcinoma (RCC). The epigenetic activation of OCT2 by decitabine (DAC) reversed this resistance in normoxic conditions. Given the hypoxic characteristic of RCC, it is still unclear whether hypoxia promotes DAC resistance and is involved in the regulation of OCT2. Methods: The mRNA and protein expression of OCT2 was determined by qRT-PCR and Western blotting. MSRE-qPCR and BSP were used to examine methylation modifications at the OCT2 promoter. The ChIP-qPCR analysis was performed to detect the abundance of histone modification and HIF-1α. The accumulation of DAC and 5-mC were detected using LC-MS, and the amount of 5-hmC was determined by dot blot analysis. To understand the role of hypoxia in the regulation of equilibrative nucleoside transporter 1 (ENT1) expression, the HIF-1α KO cell model was constructed. The re-emulsion method was used for the construction of H-NPs, an oxygen nanocarrier based on hemoglobin, to alleviate the drug resistance of DAC under hypoxia. Results: DAC was unable to upregulate OCT2 expression in hypoxic conditions because of the hypermethylation and low H3K4me3 modification in its promoter region. Hypoxia-mediated repression of human ENT1, which was markedly suppressed in RCC, resulted in a decrease in the cellular accumulation of DAC. Besides, hypoxia-induced upregulation of histone deacetylase HDAC9, which impaired the enrichment of H3K27ac modification in the OCT2 promoter, led to the transcriptional repression of OCT2. H-NPs could attenuate the hypoxia-induced loss of DAC activity and sensitize RCC cells to the sequential combination therapy of DAC and oxaliplatin. Conclusions: Hypoxia-mediated repression of ENT1 led to the inability of DAC to upregulate the expression of OCT2 under hypoxia. H-NPs could alleviate resistance to oxaliplatin and DAC in RCC cells under hypoxia and may have potential clinical applications.
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Affiliation(s)
- Lu Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zeyang Wang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qingwen Xu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuxi Liu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Le Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Suhang Guo
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hua Wang
- Department of Urology, Cancer Hospital of Zhejiang Province, Hangzhou 310022, China
| | - Kui Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Junqing Liu
- The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310022, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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15
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Tsai SH, Huang PH, Tsai HY, Hsu YJ, Chen YW, Wang JC, Chen YH, Lin SJ. Roles of the hypoximir microRNA-424/322 in acute hypoxia and hypoxia-induced pulmonary vascular leakage. FASEB J 2019; 33:12565-12575. [PMID: 31461385 DOI: 10.1096/fj.201900564rr] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Acute mountain sickness (AMS) occurs in up to 25% of unacclimatized persons who ascend to 3000 m and can result in high-altitude pulmonary edema (HAPE). MicroRNAs (miRs) can regulate gene expression at the post-transcriptional level. Hypoxia selectively disrupts endothelial tight junction complexes through a hypoxia-inducible factor-1α (HIF-1α)-dependent mechanism. Though increased HIF-1α expression is associated with adaptation and protection from AMS development in the early stage of hypoxia, a downstream effector of HIF-1α, VEGF, can induce overzealous endothelial barrier dysfunction, increase vascular permeability, and ultimately result in HAPE and high-altitude cerebral edema. We hypothesized that the fine-tuning of downstream effectors by miRs is paramount for the preservation of endothelial barrier integrity and the prevention of vascular leakage. We found that several miRs were up-regulated in healthy volunteers who were subjected to a 3100-m height. By reviewing the literature and using online bioinformatics prediction software, we specifically selected miR-424 for further investigation because it can modulate both HIF-1α and VEGF. Hypoxia-induced miR-424 overexpression is HIF-1α dependent, and miR-424 stabilized HIF-1α, decreased VEGF expression, and promoted vascular endothelial cadherin phosphorylation. In addition, hypoxia resulted in endothelial barrier dysfunction with increased permeability; miR-424 thus attenuated hypoxia-induced endothelial cell senescence and apoptosis. miR-322 knockout mice were susceptible to hypoxia-induced pulmonary vascular leakage. miR-322 mimics improved hypoxia-induced pulmonary vascular leakage in vivo. We conclude that several miRs were up-regulated in healthy adult volunteers subjected to hypobaric hypoxemia. miR-424/322 could modulate the HIF-1α-VEGF axis and prevent hypoxia-induced pulmonary vascular leakage under hypoxic conditions.-Tsai, S.-H., Huang, P.-H., Tsai, H.-Y., Hsu, Y.-J., Chen, Y.-W., Wang, J.-C., Chen, Y.-H., Lin, S.-J. Roles of the hypoximir microRNA-424/322 in acute hypoxia and hypoxia-induced pulmonary vascular leakage.
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Affiliation(s)
- Shih-Hung Tsai
- Department of Emergency Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan.,Department of Physiology and Biophysics, Graduate Institute of Physiology, National Defense Medical Center, Taipei, Taiwan
| | - Po-Hsun Huang
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Division of Cardiology, Department of Internal Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan.,Department of Critical Care Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Hsiao-Ya Tsai
- Department of Emergency Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Yu-Juei Hsu
- Division of Nephrology, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Yen-Wen Chen
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jen-Chun Wang
- Department of Emergency Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Ying-Hsin Chen
- Department of Emergency Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Shing-Jong Lin
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Division of Cardiology, Department of Internal Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan.,Healthcare and Services Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Taipei Heart Institute, Taipei Medical University, Taipei, Taiwan
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16
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Lucarelli G, Loizzo D, Franzin R, Battaglia S, Ferro M, Cantiello F, Castellano G, Bettocchi C, Ditonno P, Battaglia M. Metabolomic insights into pathophysiological mechanisms and biomarker discovery in clear cell renal cell carcinoma. Expert Rev Mol Diagn 2019; 19:397-407. [PMID: 30983433 DOI: 10.1080/14737159.2019.1607729] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Clear cell renal cell carcinoma (ccRCC) is a metabolic disease, of which the incidence rate is increasing worldwide. Renal carcinoma is characterized by mutations in target genes involved in metabolic pathways. Metabolic reprogramming covers different processes such as aerobic glycolysis, fatty acid metabolism, and the utilization of tryptophan, glutamine, and arginine. In the era of the multi-omics approach (with integrated transcriptomics, proteomics, and metabolomics), discovering biomarkers for early diagnosis is gaining renewed importance. Areas covered: In this review, we discuss the pathophysiological mechanisms underlying ccRCC metabolic reprogramming. In addition, we describe the emerging metabolomics-based biomarkers differentially expressed in ccRCC and the rationale for the recently developed drugs specifically targeting the ccRCC metabolome. Expert opinion: A number of metabolic pathways will be explored in future years, and many of these pathways are potential therapeutic targets and may serve as diagnostic and prognostic biomarkers of ccRCC.
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Affiliation(s)
- Giuseppe Lucarelli
- a Department of Emergency and Organ Transplantation - Urology, Andrology and Kidney Transplantation Unit , University of Bari , Bari , Italy
| | - Davide Loizzo
- a Department of Emergency and Organ Transplantation - Urology, Andrology and Kidney Transplantation Unit , University of Bari , Bari , Italy
| | - Rossana Franzin
- a Department of Emergency and Organ Transplantation - Urology, Andrology and Kidney Transplantation Unit , University of Bari , Bari , Italy
| | - Stefano Battaglia
- a Department of Emergency and Organ Transplantation - Urology, Andrology and Kidney Transplantation Unit , University of Bari , Bari , Italy
| | - Matteo Ferro
- b Division of Urology , European Institute of Oncology , Milan , Italy
| | - Francesco Cantiello
- c Department of Urology , Magna Graecia University of Catanzaro , Catanzaro , Italy
| | - Giuseppe Castellano
- d Department of Emergency and Organ Transplantation - Nephrology and Dialysis Unit , University of Bari , Bari , Italy
| | - Carlo Bettocchi
- a Department of Emergency and Organ Transplantation - Urology, Andrology and Kidney Transplantation Unit , University of Bari , Bari , Italy
| | - Pasquale Ditonno
- a Department of Emergency and Organ Transplantation - Urology, Andrology and Kidney Transplantation Unit , University of Bari , Bari , Italy
| | - Michele Battaglia
- a Department of Emergency and Organ Transplantation - Urology, Andrology and Kidney Transplantation Unit , University of Bari , Bari , Italy
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17
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Braga EA, Fridman MV, Loginov VI, Dmitriev AA, Morozov SG. Molecular Mechanisms in Clear Cell Renal Cell Carcinoma: Role of miRNAs and Hypermethylated miRNA Genes in Crucial Oncogenic Pathways and Processes. Front Genet 2019; 10:320. [PMID: 31110513 PMCID: PMC6499217 DOI: 10.3389/fgene.2019.00320] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/22/2019] [Indexed: 12/13/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the third most common urological cancer, and it has the highest mortality rate. The increasing drug resistance of metastatic ccRCC has resulted in the search for new biomarkers. Epigenetic regulatory mechanisms, such as genome-wide DNA methylation and inhibition of protein translation by interaction of microRNA (miRNA) with its target messenger RNA (mRNA), are deeply involved in the pathogenesis of human cancers, including ccRCC, and may be used in its diagnosis and prognosis. Here, we review oncogenic and oncosuppressive miRNAs, their putative target genes, and the crucial pathways they are involved in. The contradictory behavior of a number of miRNAs, such as suppressive and anti-metastatic miRNAs with oncogenic potential (for example, miR-99a, miR-106a, miR-125b, miR-144, miR-203, miR-378), is examined. miRNAs that contribute mostly to important pathways and processes in ccRCC, for instance, PI3K/AKT/mTOR, Wnt-β, histone modification, and chromatin remodeling, are discussed in detail. We also separately consider their participation in crucial oncogenic processes, such as hypoxia and angiogenesis, metastasis, and epithelial-mesenchymal transition (EMT). The review also considers the interactions of long non-coding RNAs (lncRNAs) and miRNAs of significance in ccRCC. Recent advances in the understanding of the role of hypermethylated miRNA genes in ccRCC and their usefulness as biomarkers are reviewed based on our own data and those available in the literature. Finally, new data and perspectives concerning the clinical applications of miRNAs in the diagnosis, prognosis, and treatment of ccRCC are discussed.
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Affiliation(s)
| | - Marina V. Fridman
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Vitaly I. Loginov
- Institute of General Pathology and Pathophysiology, Moscow, Russia
- Research Center of Medical Genetics, Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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18
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Grange C, Brossa A, Bussolati B. Extracellular Vesicles and Carried miRNAs in the Progression of Renal Cell Carcinoma. Int J Mol Sci 2019; 20:ijms20081832. [PMID: 31013896 PMCID: PMC6514717 DOI: 10.3390/ijms20081832] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 12/17/2022] Open
Abstract
The formation and maintenance of renal cell carcinomas (RCC) involve many cell types, such as cancer stem and differentiated cells, endothelial cells, fibroblasts and immune cells. These all contribute to the creation of a favorable tumor microenvironment to promote tumor growth and metastasis. Extracellular vesicles (EVs) are considered to be efficient messengers that facilitate the exchange of information within the different tumor cell types. Indeed, tumor EVs display features of their originating cells and force recipient cells towards a pro-tumorigenic phenotype. This review summarizes the recent knowledge related to the biological role of EVs, shed by renal tumor cells and renal cancer stem cells in different aspects of RCC progression, such as angiogenesis, immune escape and tumor growth. Moreover, a specific role for renal cancer stem cell derived EVs is described in the formation of the pre-metastatic niche. We also highlight the tumor EV cargo, especially the oncogenic miRNAs, which are involved in these processes. Finally, the circulating miRNAs appear to be a promising source of biomarkers in RCC.
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Affiliation(s)
- Cristina Grange
- Department of Medical Sciences, University of Turin, via Nizza 52, 10126 Turin, Italy.
- Molecular Biotechnology Centre, University of Turin, via Nizza 52, 10126 Turin, Italy.
| | - Alessia Brossa
- Molecular Biotechnology Centre, University of Turin, via Nizza 52, 10126 Turin, Italy.
- Department of Molecular Biotechnology and Health Sciences, University of Turin, via Nizza 52, 10126 Turin, Italy.
| | - Benedetta Bussolati
- Molecular Biotechnology Centre, University of Turin, via Nizza 52, 10126 Turin, Italy.
- Department of Molecular Biotechnology and Health Sciences, University of Turin, via Nizza 52, 10126 Turin, Italy.
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19
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Tian ZH, Yuan C, Yang K, Gao XL. Systematic identification of key genes and pathways in clear cell renal cell carcinoma on bioinformatics analysis. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:89. [PMID: 31019939 DOI: 10.21037/atm.2019.01.18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is the most common subtype of adult renal neoplasm and has a poor prognosis owing to a limited understanding of the disease mechanisms. The aim of this study was to explore and identify the key genes and signaling pathways in ccRCC. Methods The GSE36895 gene expression profiles were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were then screened using software packages in R. After Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, a protein-protein interaction (PPI) network of DEGs was constructed with Cytoscape software, and submodules were subsequently analyzed using the MCODE plug-in. Results Twenty-nine ccRCC samples and 23 normal samples were incorporated into this study, and a total of 468 DEGs were filtered, consisting of 180 upregulated genes and 288 downregulated genes. The upregulated DEGs were significantly enriched in the immune response, response to wounding, inflammatory response, and response to hypoxia, whereas downregulated genes were mainly enriched in ion transport, anion transport, and monovalent inorganic cation transport biological processes (BPs). According to Molecular Complex Detection analysis in PPI, C1QA, C1QB, C1QC, CCND1 and EGF had higher degrees of connectivity and could participate in the majority of important pathways, such as cytokine-cytokine receptor interactions, the chemokine signaling pathway, and the complement and coagulation cascade pathways. Conclusions Our study suggests that C1QA, C1QB, C1QC, CCND1 and EGF may play key roles in the progression of ccRCC, which will be useful for future studies on the underlying mechanisms of ccRCC.
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Affiliation(s)
- Zhao-Hui Tian
- Medical Department, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi 445000, China
| | - Cheng Yuan
- Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan 430071, China
| | - Kang Yang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430071, China
| | - Xing-Liang Gao
- Department of Lung Disease and Diabetes, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi 445000, China.,Enshi Clinical College of Wuhan University, Enshi 445000, China.,Enshi Prefecture Central Hospital Affiliated to Hubei Minzu University, Enshi 445000, China
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20
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Eminaga O, Fries J, Neiß S, Heitmann M, Wötzel F, Heidenreich A, Bruns C, Alakus H, Warnecke-Eberz U. The upregulation of hypoxia-related miRNA 210 in primary tumor of lymphogenic metastatic prostate cancer. Epigenomics 2018; 10:1347-1359. [DOI: 10.2217/epi-2017-0114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Aim: To show the association between the expression level of hsa-miR-210 (miR-210) and tumor progression in prostate cancer (PCa). Methods: Quantitative PCR was performed to measure miR-210 on 55 subjects with different tumor stages; our results were then validated using three external datasets. ANOVA and Tukey's post hoc analysis were performed for comparative analyses between different tumor stages. Using the transcriptome data from The Cancer Genome Atlas for CaP, the gene expression analyses were performed on experimentally validated target genes of miR-210 identified in Tarbase and miRWalk datasets. Results & conclusion: miR-210 was significantly higher in N1 PCa compared with nonmetastatic PCa, whereas the metastatic tumor revealed a lower expression level of miR-210 than the primary tumor.
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Affiliation(s)
- Okyaz Eminaga
- Department of Urology, University Hospital of Cologne, Kerpenerstr. 62, D-50937 Cologne, Germany
- Department of Urology, Stanford University, Stanford, CA 94305, USA
| | - Jochen Fries
- Department of Pathology, University Hospital of Cologne, Kerpenerstr. 62, D-50937 Cologne, Germany
| | - Susanne Neiß
- Laboratory for Molecular Oncology, University Hospital of Cologne, Kerpener Strasse 62, D-50937 Cologne, Germany
| | - Michaela Heitmann
- Laboratory for Molecular Oncology, University Hospital of Cologne, Kerpener Strasse 62, D-50937 Cologne, Germany
| | - Fabian Wötzel
- Department of Pathology, University Hospital of Muenster, Albert-Schweitzer-Campus 1, D- 48149 Muenster, Germany
| | - Axel Heidenreich
- Department of Urology, University Hospital of Cologne, Kerpenerstr. 62, D-50937 Cologne, Germany
| | - Christiane Bruns
- Laboratory for Molecular Oncology, University Hospital of Cologne, Kerpener Strasse 62, D-50937 Cologne, Germany
| | - Hakan Alakus
- Laboratory for Molecular Oncology, University Hospital of Cologne, Kerpener Strasse 62, D-50937 Cologne, Germany
| | - Ute Warnecke-Eberz
- Laboratory for Molecular Oncology, University Hospital of Cologne, Kerpener Strasse 62, D-50937 Cologne, Germany
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21
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Luo T, Chen X, Zeng S, Guan B, Hu B, Meng Y, Liu F, Wong T, Lu Y, Yun C, Hocher B, Yin L. Bioinformatic identification of key genes and analysis of prognostic values in clear cell renal cell carcinoma. Oncol Lett 2018; 16:1747-1757. [PMID: 30008862 PMCID: PMC6036467 DOI: 10.3892/ol.2018.8842] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 05/22/2018] [Indexed: 12/29/2022] Open
Abstract
The present study aimed to identify new key genes as potential biomarkers for the diagnosis, prognosis or targeted therapy of clear cell renal cell carcinoma (ccRCC). Three expression profiles (GSE36895, GSE46699 and GSE71963) were collected from Gene Expression Omnibus. GEO2R was used to identify differentially expressed genes (DEGs) in ccRCC tissues and normal samples. The Database for Annotation, Visualization and Integrated Discovery was utilized for functional and pathway enrichment analysis. STRING v10.5 and Molecular Complex Detection were used for protein-protein interaction (PPI) network construction and module analysis, respectively. Regulation network analyses were performed with the WebGestal tool. UALCAN web-portal was used for expression validation and survival analysis of hub genes in ccRCC patients from The Cancer Genome Atlas (TCGA). A total of 65 up- and 164 downregulated genes were identified as DEGs. DEGs were enriched with functional terms and pathways compactly related to ccRCC pathogenesis. Seventeen hub genes and one significant module were filtered out and selected from the PPI network. The differential expression of hub genes was verified in TCGA patients. Kaplan-Meier plot showed that high mRNA expression of enolase 2 (ENO2) was associated with short overall survival in ccRCC patients (P=0.023). High mRNA expression of cyclin D1 (CCND1) (P<0.001), fms related tyrosine kinase 1 (FLT1) (P=0.004), plasminogen (PLG) (P<0.001) and von Willebrand factor (VWF) (P=0.008) appeared to serve as favorable factors in survival. These findings indicate that the DEGs may be key genes in ccRCC pathogenesis and five genes, including ENO2, CCND1, PLT1, PLG and VWF, may serve as potential prognostic biomarkers in ccRCC.
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Affiliation(s)
- Ting Luo
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Xiaoyi Chen
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Shufei Zeng
- Department of Nephrology, Charité-Universitätsmedizin Berlin, Campus Mitte, D-10117 Berlin, Germany
| | - Baozhang Guan
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Bo Hu
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Yu Meng
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Fanna Liu
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Taksui Wong
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Yongpin Lu
- Department of Nephrology, Charité-Universitätsmedizin Berlin, Campus Mitte, D-10117 Berlin, Germany
| | - Chen Yun
- Department of Nephrology, Charité-Universitätsmedizin Berlin, Campus Mitte, D-10117 Berlin, Germany
| | - Berthold Hocher
- Institute of Nutritional Sciences, University of Potsdam, D-14558 Potsdam, Germany
| | - Lianghong Yin
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong 510632, P.R. China
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22
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Li Z, Chen Y, Hu S, Zhang J, Wu J, Ren W, Shao N, Ying X. Integrative analysis of protein-coding and non-coding RNAs identifies clinically relevant subtypes of clear cell renal cell carcinoma. Oncotarget 2018; 7:82671-82685. [PMID: 27705920 PMCID: PMC5347723 DOI: 10.18632/oncotarget.12340] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 09/20/2016] [Indexed: 12/25/2022] Open
Abstract
Protein-coding genes and non-coding RNAs cooperate mutually in cells. Integrative analysis of protein-coding and non-coding RNAs may facilitate characterizing tumor heterogeneity. We introduced integrated consensus clustering (ICC) method to integrate mRNA, miRNA and lncRNA expression profiles of 431 primary clear cell renal cell carcinomas (ccRCCs). We identified one RCC subgroup easily misdiagnosed as ccRCC in clinic and four robust ccRCC subtypes associated with distinct clinicopathologic and molecular features. In subtype R1, AMPK signaling pathway is significantly upregulated, which may improve the oncologic-metabolic shift and partially account for its best prognosis. Subtype R2 has more chromosomal abnormities, higher expression of cell cycle genes and less expression of genes in various metabolism pathways, which may explain its more aggressive characteristic and the worst prognosis. Moreover, much more miRNAs and lncRNAs are significantly upregulated in R2 and R4 respectively, suggesting more important roles of miRNAs in R2 and lncRNAs in R4. Triple-color co-expression network analysis identified 28 differentially expressed modules, indicating the importance of cooperative regulation of mRNAs, miRNAs and lncRNAs in ccRCC. This study establishes an integrated transcriptomic classification which may contribute to understanding the heterogeneity and implicating the treatment of ccRCC.
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Affiliation(s)
- Zongcheng Li
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China.,Translational Medicine Center of Stem Cells, 307-Ivy Translational Medicine Center, Laboratory of Oncology, Affiliated Hospital, Academy of Military Medical Sciences, Beijing 100071, China
| | - Yaowen Chen
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China.,Department of Obstetrics and Gynecology, Fuzhou General Hospital of Nanjing Military Command, Fuzhou, Fujian 350025, China
| | - Shuofeng Hu
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Jian Zhang
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Jiaqi Wu
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Wu Ren
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China.,Department of Gastrointestinal Surgery, The First Affiliated Hospital of Jilin University, Changchun 130021, China
| | - Ningsheng Shao
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Xiaomin Ying
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
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23
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Expression of VHL tumor suppressor mRNA and miR-92a in papillary thyroid carcinoma and their correlation with clinical and pathological parameters. Med Oncol 2018; 35:17. [PMID: 29340905 DOI: 10.1007/s12032-017-1066-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 11/30/2017] [Indexed: 01/20/2023]
Abstract
A growing body of evidence suggests a role of the von Hippel-Lindau (VHL) tumor suppressor gene in the progression of papillary thyroid carcinoma (PTC). Our previous study of VHL in PTCs showed that lower VHL expression was associated with aggressive tumor features, but we found no evidence for VHL downregulation through common genetic or epigenetic modifications. Several studies pointed to a role of microRNA-92a (miR-92a) in the regulation of VHL expression in different cancers. In the present study, we examined the expression levels of VHL mRNA and miR-92a in 42 pairs of PTCs and matched non-tumor thyroid tissues by means of quantitative RT-PCR. We explored the correlation between them and their association with clinicopathological parameters. The results revealed that both VHL and miR-92a were either up- or downregulated in PTCs compared to corresponding non-tumor tissues. On univariate analysis, lower VHL levels were significantly associated with extrathyroid spread (P = 0.022) and capsular invasion (P = 0.032). Multivariate analysis confirmed the association of low VHL with extrathyroid spread (OR 0.246, 95% CI 0.069-0.872, P = 0.038). Higher miR-92a among PTC tissues associated with the presence of nodal metastases (univariate analysis: P = 0.012; multivariate: OR 4.703, 95% CI 1.109-19.938, P = 0.036). A negative correlation between VHL and miR-92a was observed in a subgroup of PTCs having vascular invasion (P = 0.033, r = - 0.673). The data here reported demonstrate that the expression of both VHL and miR-92a is deregulated in PTC tissues and that in some PTCs they may have opposite roles. These roles, as well as their diagnostic and/or prognostic utility, remain to be clarified.
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24
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Nogueira I, Dias F, Teixeira AL, Medeiros R. miRNAs as potential regulators of mTOR pathway in renal cell carcinoma. Pharmacogenomics 2018; 19:249-261. [PMID: 29334302 DOI: 10.2217/pgs-2017-0160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Renal cell carcinoma (RCC) is the most commonly occurring solid cancer of the adult kidney with the majority of RCC cases being detected accidentally. The most aggressive subtype is clear cell RCC (ccRCC). miRNAs, a family of small noncoding RNAs regulating gene expression have been identified as key biological modulators. The von Hippel-Lindau pathway is one of the signaling pathways involved in the pathophysiology of ccRCC. Another oncogenic mechanism involves the activation of PI3K/AKT/mTOR signaling and serves as a central regulator of cell metabolism, proliferation and survival. Several studies have described the involvement of miRNA dysregulation in the pathogenesis and progression of ccRCC. These molecules can be considered as potential diagnostic and prognostic biomarkers, allowing response to therapy to be monitored.
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Affiliation(s)
- Inês Nogueira
- Molecular Oncology and Viral Pathology Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), 4200-072 Porto, Portugal.,FMUP, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Francisca Dias
- Molecular Oncology and Viral Pathology Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), 4200-072 Porto, Portugal.,ICBAS, Abel Salazar Institute for the Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal
| | - Ana Luísa Teixeira
- Molecular Oncology and Viral Pathology Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), 4200-072 Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), 4200-072 Porto, Portugal.,FMUP, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal.,Research Department, LPCC-Portuguese League, Against Cancer (NRNorte), 4200-172 Porto, Portugal.,CEBIMED, Faculty of Health Sciences, Fernando Pessoa University, 4200-150 Porto, Portugal
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25
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He YH, Chen C, Shi Z. The biological roles and clinical implications of microRNAs in clear cell renal cell carcinoma. J Cell Physiol 2017; 233:4458-4465. [PMID: 29215721 DOI: 10.1002/jcp.26347] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/02/2017] [Indexed: 12/18/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) accounts for about 3% of tumors in adults as well as 85% of all primary renal carcinoma. And it is the third most predominant urological carcinoma, but it has the maximum mortality rate. Early diagnosis and proper follow-up of ccRCC patients may improve the prognosis of the illness. Thus, it is imperative to understand the new biomarkers of ccRCC and study new method for the modern therapy of this deadly disease. Furthermore, a large number of microRNAs (miRNAs), small non-coding RNAs, have been relevant to tumor type, stage, or survival and miRNAs might be progressed as the markers of diagnosis or prognosis in ccRCC. A growing body of data also advised the rationality of regarding miRNAs as therapeutic targets for ccRCC treatment. In this review, we tried to summarize biogenesis of miRNAs and their expression profiles, biological roles, and clinical implications in ccRCC.
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Affiliation(s)
- Ying-Hua He
- Department of Pharmacy, The First Affiliated Hospital of Zhejiang Chinese Medicine University, Hangzhou, Zhejiang, China.,Department of Pharmacy, Zhejiang International Exchange Center of Clinical Traditional Chinese Medicine, Hangzhou, Zhejiang, China.,Department of Pharmacy, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang, China
| | - Chen Chen
- Department of PIVAS, Binhu Hospital of Hefei City, Hefei, Anhui Province, China
| | - Zheng Shi
- Department of Pharmacy, The First Affiliated Hospital of Zhejiang Chinese Medicine University, Hangzhou, Zhejiang, China.,Department of Pharmacy, Zhejiang International Exchange Center of Clinical Traditional Chinese Medicine, Hangzhou, Zhejiang, China.,Department of Pharmacy, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang, China
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26
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LRSSLMDA: Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction. PLoS Comput Biol 2017; 13:e1005912. [PMID: 29253885 PMCID: PMC5749861 DOI: 10.1371/journal.pcbi.1005912] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 01/02/2018] [Accepted: 12/01/2017] [Indexed: 12/17/2022] Open
Abstract
Predicting novel microRNA (miRNA)-disease associations is clinically significant due to miRNAs’ potential roles of diagnostic biomarkers and therapeutic targets for various human diseases. Previous studies have demonstrated the viability of utilizing different types of biological data to computationally infer new disease-related miRNAs. Yet researchers face the challenge of how to effectively integrate diverse datasets and make reliable predictions. In this study, we presented a computational model named Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction (LRSSLMDA), which projected miRNAs/diseases’ statistical feature profile and graph theoretical feature profile to a common subspace. It used Laplacian regularization to preserve the local structures of the training data and a L1-norm constraint to select important miRNA/disease features for prediction. The strength of dimensionality reduction enabled the model to be easily extended to much higher dimensional datasets than those exploited in this study. Experimental results showed that LRSSLMDA outperformed ten previous models: the AUC of 0.9178 in global leave-one-out cross validation (LOOCV) and the AUC of 0.8418 in local LOOCV indicated the model’s superior prediction accuracy; and the average AUC of 0.9181+/-0.0004 in 5-fold cross validation justified its accuracy and stability. In addition, three types of case studies further demonstrated its predictive power. Potential miRNAs related to Colon Neoplasms, Lymphoma, Kidney Neoplasms, Esophageal Neoplasms and Breast Neoplasms were predicted by LRSSLMDA. Respectively, 98%, 88%, 96%, 98% and 98% out of the top 50 predictions were validated by experimental evidences. Therefore, we conclude that LRSSLMDA would be a valuable computational tool for miRNA-disease association prediction. Discovering miRNA-disease associations promotes the understanding towards the molecular mechanisms of various human diseases at the miRNA level, and contributes to the development of diagnostic biomarkers and treatment tools for diseases. Computational models can make the discovery more efficient and experiments more productive. LRSSLMDA was proposed to computationally infer potential miRNA-disease associations via adopting sparse subspace learning with Laplacian regularization on the known miRNA-disease association network and the informative feature profiles extracted from the integrated miRNA/disease similarity networks. Experimental results in global and local leave-one-out cross validation and 5-fold cross validation showed a superior prediction performance of LRSSLMDA over previous models. Moreover, three types of case studies on five important human diseases were carried out to further demonstrate the model’s predictive power: respectively, 98%, 88%, 96%, 98% and 98% out of the top 50 predicted miRNAs were confirmed by experimental literatures. So, we believe that LRSSLMDA could make reliable predictions and might guide future experimental studies on miRNA-disease associations.
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27
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Schanza LM, Seles M, Stotz M, Fosselteder J, Hutterer GC, Pichler M, Stiegelbauer V. MicroRNAs Associated with Von Hippel-Lindau Pathway in Renal Cell Carcinoma: A Comprehensive Review. Int J Mol Sci 2017; 18:ijms18112495. [PMID: 29165391 PMCID: PMC5713461 DOI: 10.3390/ijms18112495] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/07/2017] [Accepted: 11/17/2017] [Indexed: 02/08/2023] Open
Abstract
Renal cell carcinoma (RCC) are the most common renal neoplasia and can be divided into three main histologic subtypes, among which clear cell RCC is by far the most common form of kidney cancer. Despite substantial advances over the last decade in the understanding of RCC biology, surgical treatments, and targeted and immuno-therapies in the metastatic setting, the prognosis for advanced RCC patients remains poor. One of the major problems with RCC treatment strategies is inherent or acquired resistance towards therapeutic agents over time. The discovery of microRNAs (miRNAs), a class of small, non-coding, single-stranded RNAs that play a crucial role in post-transcriptional regulation, has added new dimensions to the development of novel diagnostic and treatment tools. Because of an association between Von Hippel–Lindau (VHL) genes with chromosomal loss in 3p25-26 and clear cell RCC, miRNAs have attracted considerable scientific interest over the last years. The loss of VHL function leads to constitutional activation of the hypoxia inducible factor (HIF) pathway and to consequent expression of numerous angiogenic and carcinogenic factors. Since miRNAs represent key players of carcinogenesis, tumor cell invasion, angiogenesis, as well as in development of metastases in RCC, they might serve as potential therapeutic targets. Several miRNAs are already known to be dysregulated in RCC and have been linked to biological processes involved in tumor angiogenesis and response to anti-cancer therapies. This review summarizes the role of different miRNAs in RCC angiogenesis and their association with the VHL gene, highlighting their potential role as novel drug targets.
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Affiliation(s)
- Lisa-Maria Schanza
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria.
- Research Unit of Non-Coding RNA and Genome Editing in Cancer, Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria.
| | - Maximilian Seles
- Department of Urology, Medical University of Graz, 8036 Graz, Austria.
| | - Michael Stotz
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria.
| | - Johannes Fosselteder
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria.
- Research Unit of Non-Coding RNA and Genome Editing in Cancer, Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria.
| | - Georg C Hutterer
- Department of Urology, Medical University of Graz, 8036 Graz, Austria.
| | - Martin Pichler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria.
- Research Unit of Non-Coding RNA and Genome Editing in Cancer, Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria.
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
| | - Verena Stiegelbauer
- Research Unit of Non-Coding RNA and Genome Editing in Cancer, Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria.
- Department of Urology, Medical University of Graz, 8036 Graz, Austria.
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28
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Wettersten HI, Aboud OA, Lara PN, Weiss RH. Metabolic reprogramming in clear cell renal cell carcinoma. Nat Rev Nephrol 2017; 13:410-419. [PMID: 28480903 DOI: 10.1038/nrneph.2017.59] [Citation(s) in RCA: 294] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Research in many cancers has uncovered changes in metabolic pathways that control tumour energetics and biosynthesis, so-called metabolic reprogramming. Studies in clear cell renal cell carcinoma (ccRCC) have been particularly revealing, leading to the concept that ccRCC is a metabolic disease. ccRCC is generally accompanied by reprogramming of glucose and fatty acid metabolism and of the tricarboxylic acid cycle. Metabolism of tryptophan, arginine and glutamine is also reprogrammed in many ccRCCs, and these changes provide opportunities for new therapeutic strategies, biomarkers and imaging modalities. In particular, metabolic reprogramming facilitates the identification of novel and repurposed drugs that could potentially be used to treat ccRCC, which when metastatic has currently limited long-term treatment options. Further research and dissemination of these concepts to nephrologists and oncologists will lead to clinical trials of therapeutics specifically targeted to tumour metabolism, rather than generally toxic to all proliferating cells. Such novel agents are highly likely to be more effective and to have far fewer adverse effects than existing drugs.
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Affiliation(s)
- Hiromi I Wettersten
- University of California, San Diego, Sanford Consortium for Regenerative Medicine, Room 4810, 2880 Torrey Pines Scenic Drive, La Jolla, California 92037-0695, USA
| | - Omran Abu Aboud
- Division of Nephrology, University of California Davis, Genome and Biomedical Sciences Facility, Room 6311, 451 Health Sciences Drive, Davis, California 95616, USA
| | - Primo N Lara
- University of California Davis Comprehensive Cancer Center, 4501 X Street, Suite 3003, Sacramento, California 95817, USA
| | - Robert H Weiss
- Division of Nephrology, University of California Davis, Genome and Biomedical Sciences Facility, Room 6311, 451 Health Sciences Drive, Davis, California 95616, USA
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29
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Peterson LE, Kovyrshina T. Progression inference for somatic mutations in cancer. Heliyon 2017; 3:e00277. [PMID: 28492066 PMCID: PMC5415494 DOI: 10.1016/j.heliyon.2017.e00277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 03/08/2017] [Accepted: 03/23/2017] [Indexed: 01/05/2023] Open
Abstract
Computational methods were employed to determine progression inference of genomic alterations in commonly occurring cancers. Using cross-sectional TCGA data, we computed evolutionary trajectories involving selectivity relationships among pairs of gene-specific genomic alterations such as somatic mutations, deletions, amplifications, downregulation, and upregulation among the top 20 driver genes associated with each cancer. Results indicate that the majority of hierarchies involved TP53, PIK3CA, ERBB2, APC, KRAS, EGFR, IDH1, VHL, etc. Research into the order and accumulation of genomic alterations among cancer driver genes will ever-increase as the costs of nextgen sequencing subside, and personalized/precision medicine incorporates whole-genome scans into the diagnosis and treatment of cancer.
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Affiliation(s)
- Leif E. Peterson
- Center for Biostatistics, Houston Methodist Research Institute, Houston, TX 77030, USA
- Dept. of Healthcare Policy and Research, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
- Dept. of Biostatistics, School of Public Health, University of Texas – Health Science Center, Houston, TX 77030, USA
- Dept. of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Dept. of Neuroscience and Experimental Therapeutics, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Tatiana Kovyrshina
- Center for Biostatistics, Houston Methodist Research Institute, Houston, TX 77030, USA
- Dept. of Mathematics and Statistics, University of Houston – Downtown, Houston, TX 77002, USA
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30
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Ke HL, Li WM, Lin HH, Hsu WC, Hsu YL, Chang LL, Huang CN, Li CC, Chang HP, Yeh HC, Li CF, Wu WJ. Hypoxia-regulated MicroRNA-210 Overexpression is Associated with Tumor Development and Progression in Upper Tract Urothelial Carcinoma. Int J Med Sci 2017; 14. [PMID: 28638274 PMCID: PMC5479127 DOI: 10.7150/ijms.15699] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Hypoxia has been shown to facilitate tumor progression. Hypoxia-regulated microRNA-210 (miR-210) may play an important role in carcinogenesis and tumor progression. In this study, we evaluated the clinical significance of miR-210 expression in upper tract urothelial carcinoma (UTUC). METHODS Eighty-three UTUC patients participated in this study. All of them provided cancer tissue samples and 50 of them provided non-cancerous urothelium samples. Clinicopathologic data were collected by reviewing medical records. The expression of miR-210 and hypoxia-inducible factor-1α (HIF-1α) was determined by quantitative real-time polymerase chain reaction. The relationship between clinicopathologic variables and the expression of miR-210 and HIF-1α was analyzed statistically. RESULTS MiR-210 is overexpressed in UTUC compared to non-cancerous urothelium (p < 0.001); it is also upregulated in high-stage and high-grade tumors (p = 0.020 and 0.049, respectively). HIF-1α is overexpressed in UTUC and correlates positively with miR-210 expression (r = 0.442, p = 0.001). CONCLUSION Both miR-210 and HIF-1α are involved in promoting UTUC carcinogenesis. MiR-210 is also correlated with tumor progression. Further studies are needed to clarify the underlying mechanism.
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Affiliation(s)
- Hung-Lung Ke
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wei-Ming Li
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, Ministry of Health and Welfare Pingtung Hospital, Pingtung, Taiwan
| | - Hui-Hui Lin
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wei-Chi Hsu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ya-Ling Hsu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Lin-Li Chang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Microbiology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chun-Nung Huang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ching-Chia Li
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan
| | - Hsin-Ping Chang
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hsin-Chih Yeh
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chien-Feng Li
- Department of Pathology, Chi Mei Medical Center, Tainan, Taiwan.,National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan.,Department of Biotechnology, Southern Taiwan University of Science and Technology, Tainan, Taiwan
| | - Wen-Jeng Wu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan
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31
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Lukamowicz-Rajska M, Mittmann C, Prummer M, Zhong Q, Bedke J, Hennenlotter J, Stenzl A, Mischo A, Bihr S, Schmidinger M, Vogl U, Blume I, Karlo C, Schraml P, Moch H. MiR-99b-5p expression and response to tyrosine kinase inhibitor treatment in clear cell renal cell carcinoma patients. Oncotarget 2016; 7:78433-78447. [PMID: 27738339 PMCID: PMC5346651 DOI: 10.18632/oncotarget.12618] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/18/2016] [Indexed: 11/25/2022] Open
Abstract
A number of treatments targeting VEGF or mTOR pathways have been approved for metastatic clear cell Renal Cell Carcinoma (ccRCC), but the majority of patients show disease progression after first line therapy with a very low rate of complete or long-term responders. It has been shown that miRs may play a role in prediction of treatment response in various cancer types. The aim of our study was to identify a miR signature predictive for RCC patients' response to antiangiogenic tyrosine kinase inhibitor (TKI) treatment in the first line therapy. Sequencing of 40 paired normal/tumor formalin fixed and paraffin embedded ccRCC tissues revealed separate clustering via unsupervised dendrograms. With supervised analysis, the strongest differential expression was obtained with miR-99b-5p, which was significantly lower in patients with short progression free survival (<8 months) and TKI non-responders (progressive disease patients according to RECIST) (p<0.0001, each). Validation using RTqPCR and a second patient cohort compiled from three different hospitals (n=65) showed higher expression of miR-99b-5p in complete responders, but this trend did not reach statistical significance. It is concluded that low miR-99b-5p expression analyzed with sequencing methodology may correlate with tumor progression in TKI-treated ccRCC patients.
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Affiliation(s)
| | - Christiane Mittmann
- Institute of Surgical Pathology, University Hospital Zürich, Zurich, Switzerland
| | - Michael Prummer
- NEXUS Personalized Health Technologies, ETH Zürich, Zürich, Switzerland
| | - Qing Zhong
- Institute of Surgical Pathology, University Hospital Zürich, Zurich, Switzerland
| | - Jens Bedke
- Department of Urology, University Tübingen, Tübingen, Germany
| | | | - Arnulf Stenzl
- Department of Urology, University Tübingen, Tübingen, Germany
| | - Axel Mischo
- Oncology Department, University Hospital Zürich, Zürich, Switzerland
| | - Svenja Bihr
- Oncology Department, University Hospital Zürich, Zürich, Switzerland
| | - Manuela Schmidinger
- Department of Internal Medicine I, Division of Oncology & Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Ursula Vogl
- Department of Internal Medicine I, Division of Oncology & Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Iris Blume
- Institute for diagnostic and interventional Radiology, University Hospital Zurich, Zürich, Switzerland
| | - Christoph Karlo
- Institute for diagnostic and interventional Radiology, University Hospital Zurich, Zürich, Switzerland
| | - Peter Schraml
- Institute of Surgical Pathology, University Hospital Zürich, Zurich, Switzerland
| | - Holger Moch
- Institute of Surgical Pathology, University Hospital Zürich, Zurich, Switzerland
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32
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Wang H, Ke C, Ma X, Zhao Q, Yang M, Zhang W, Wang J. MicroRNA-92 promotes invasion and chemoresistance by targeting GSK3β and activating Wnt signaling in bladder cancer cells. Tumour Biol 2016; 37:10.1007/s13277-016-5460-9. [PMID: 27830467 DOI: 10.1007/s13277-016-5460-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 09/23/2016] [Indexed: 12/27/2022] Open
Abstract
miR-92 has been reported to be upregulated in several human cancers. Until now, its expression pattern and biological roles in human bladder cancer still remains unexplored. The present study aims to clarify its expression, function, and potential molecular mechanisms in bladder cancer. Using real-time PCR, we found that miR-92 was upregulated in bladder cancer tissues compared with normal bladder tissues. We transfected miR-92 mimic and inhibitor in T24 and 5637 bladder cancer cells separately. We found that miR-92 mimic promoted T24 proliferation and invasion, with increased expression of cyclin D1, c-myc, and MMP7 at both mRNA and protein levels. Further investigation found that miR-92 could also promote epithelial-mesenchymal transition by downregulating E-cadherin protein and upregulating vimentin. In addition, miR-92 mimic also promoted activation of Wnt signaling. Meanwhile, miR-92 inhibitor displayed the opposite effects in 5637 cell line. By use of bioinformatic prediction software and luciferase reporter assay, we discovered that GSK3β acted as a direct target of miR-92. Additionally, GSK3β siRNA abrogated the effects of miR-92 mimic on cyclin D1 and MMP7. Moreover, we observed a negative correlation between GSK3β and miR-92 in bladder cancer tissues. In conclusion, our study demonstrated that upregulation of miR-92 is closely related with malignant progression of bladder cancer and miR-92 promotes proliferation, invasion, and Wnt/c-myc/MMP7 signaling by targeting GSK3β.
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Affiliation(s)
- Haifeng Wang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Yunnan Institute of Urology, Kunming, 650101, China
| | - Changxing Ke
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Yunnan Institute of Urology, Kunming, 650101, China
| | - Xingyong Ma
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Yunnan Institute of Urology, Kunming, 650101, China
| | - Qinghua Zhao
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Yunnan Institute of Urology, Kunming, 650101, China
| | - Mingying Yang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Yunnan Institute of Urology, Kunming, 650101, China
| | - Wei Zhang
- Department of Urology, Affiliated Hospital of Hebei University, Baoding, 071000, China.
| | - Jiansong Wang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Yunnan Institute of Urology, Kunming, 650101, China.
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Xing T, He H. Epigenomics of clear cell renal cell carcinoma: mechanisms and potential use in molecular pathology. Chin J Cancer Res 2016; 28:80-91. [PMID: 27041930 DOI: 10.3978/j.issn.1000-9604.2016.02.09] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is one frequent form of urologic malignancy with numerous genetic and epigenetic alterations. This review summarizes the recent major findings of epigenetic alterations including DNA methylation, histone modifications, microRNAs and recently identified long noncoding RNAs in the development and progression of ccRCC. These epigenetic profilings can provide a promising means of prognostication and early diagnosis for patients with ccRCCs. With the developed high-throughput technologies nowadays, the epigenetic analyses will have possible clinical applications in the molecular pathology of ccRCC.
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Affiliation(s)
- Tianying Xing
- 1 Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, 2 Department of Urology, Peking University Third Hospital, Beijing 100191, China
| | - Huiying He
- 1 Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, 2 Department of Urology, Peking University Third Hospital, Beijing 100191, China
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MiR-519d facilitates the progression and metastasis of cervical cancer through direct targeting Smad7. Cancer Cell Int 2016; 16:21. [PMID: 27006642 PMCID: PMC4802873 DOI: 10.1186/s12935-016-0298-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 03/11/2016] [Indexed: 12/19/2022] Open
Abstract
Background MicroRNAs (miRNAs) play pivotal roles in the development of various cancer types, including cervical cancer. Methods and results In this study, we showed that miR-519d, a miRNA within the chromosome 19 miRNA cluster, was significantly upregulated in cervical cancer tissues, compared with non-tumorous cervical samples. Suppression of miR-519d markedly attenuated the migration and invasion of HeLa and SiHa cervical cancer cells. Additionally, miR-519d inhibited the apoptosis of cervical cancer cells, and the proliferation of cervical cancer cells was also affected following transfection of miR-519d inhibitor. Moreover, we identified Smad7 to be a novel target of miR-519d in cervical cancer cells. MiR-519d matched the 3′-UTR of Smad7 mRNA. Transfection with miR-519d mimics led to apparent downregulation of Smad7 both at the mRNA and protein levels. Luciferase reporter analysis revealed that miR-519d reduced the luciferase activity of Smad7 mRNA 3′-UTR through matching site-dependent manner. And more notably, suppression of Smad7 remarkably restored the migration and invasion of miR-519d-depleted cervical cancer cells. Conclusion Taken together, these findings implicated that miR-519d promoted the progression and metastasis of cervical cancer through targeting Smad7.
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MicroRNAs in the Pathogenesis of Renal Cell Carcinoma and Their Diagnostic and Prognostic Utility as Cancer Biomarkers. Int J Biol Markers 2016; 31:e26-37. [DOI: 10.5301/jbm.5000174] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2015] [Indexed: 12/18/2022]
Abstract
Purpose To provide information about the role of microRNAs in the pathogenesis of renal cell carcinoma (RCC) and their diagnostic and prognostic utility as cancer biomarkers. Methods A literature search was performed in the PubMed and Web of Science databases using the keywords “renal cancer/renal cell carcinoma/kidney cancer” and “miR*/miRNA*/microRNA*”. Articles dealing with the role of miRNAs in the pathogenesis of RCC, diagnostic miRNAs and prognostic miRNAs were separated. Results MiRNAs act both as oncogenes and tumor suppressors. They regulate apoptosis, cell growth, migration, invasion, proliferation, colony formation and angiogenesis through target proteins involved in several signaling pathways, and they are involved in key pathogenetic mechanisms such as hypoxia (HIF/VHL dependent) and epithelial-to-mesenchymal transition. Differentially expressed miRNAs can discriminate either tumor tissue from healthy renal tissue or different RCC subtypes. Circulating miRNAs are promissing as diagnostic biomarkers of RCC. Information about urinary miRNAs associated with RCC is sparse. Detection of a relapse is another implication of diagnostic miRNAs. The expression profiles of several miRNAs correlate with the prognosis of RCC patients. Comparison between primary tumor tissue and metastasis may help identify high-risk primary tumors. Finally, response to target therapy can be estimated thanks to differences in miRNA expression in tissue and serum of therapy-resistant versus therapy-sensitive patients. Conclusions Our understanding of the role of microRNAs in RCC pathogenesis has been increasing dramatically. Identification and validation of their gene targets may have direct impact on developing microRNA-based anticancer therapy. Several microRNAs can serve as diagnostic and prognostic biomarkers.
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Greenald D, Jeyakani J, Pelster B, Sealy I, Mathavan S, van Eeden FJ. Genome-wide mapping of Hif-1α binding sites in zebrafish. BMC Genomics 2015; 16:923. [PMID: 26559940 PMCID: PMC4642629 DOI: 10.1186/s12864-015-2169-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 10/31/2015] [Indexed: 02/08/2023] Open
Abstract
Background Hypoxia Inducible Factor (HIF) regulates a cascade of transcriptional events in response to decreased oxygenation, acting from the cellular to the physiological level. This response is evolutionarily conserved, allowing the use of zebrafish (Danio rerio) as a model for studying the hypoxic response. Activation of the hypoxic response can be achieved in zebrafish by homozygous null mutation of the von Hippel-Lindau (vhl) tumour suppressor gene. Previous work from our lab has focused on the phenotypic characterisation of this mutant, establishing the links between vhl mutation, the hypoxic response and cancer. To further develop fish as a model for studying hypoxic signalling, we examine the transcriptional profile of the vhl mutant with respect to Hif-1α. As our approach uses embryos consisting of many cell types, it has the potential to uncover additional HIF regulated genes that have escaped detection in analogous mammalian cell culture studies. Results We performed high-density oligonucleotide microarray analysis of the gene expression changes in von Hippel-Lindau mutant zebrafish, which identified up-regulation of well-known hypoxia response genes and down-regulation of genes primarily involved in lipid processing. To identify the dependency of these transcriptional changes on HIF, we undertook Chromatin Immunoprecipitation linked next generation sequencing (ChIP-seq) for the transcription factor Hypoxia Inducible Factor 1α (HIF-1α). We identified HIF-1α binding sites across the genome, with binding sites showing enrichment for an RCGTG motif, showing conservation with the mammalian hypoxia response element. Conclusions Transcriptome analysis of vhl mutant embryos detected activation of key hypoxia response genes seen in human cell models of hypoxia, but also suppression of many genes primarily involved in lipid processing. ChIP-seq analysis of Hif-1α binding sites unveiled an unprecedented number of loci, with a high proportion containing a canonical hypoxia response element. Whether these sites are functional remains unknown, nevertheless their frequent location near transcriptional start sites suggests functionality, and will allow for investigation into the potential hypoxic regulation of genes in their vicinity. We expect that our data will be an excellent starting point for analysis of both fish and mammalian gene regulation by HIF. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2169-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David Greenald
- Bateson Centre, Department of Biomedical Science, The University of Sheffield, Western Bank, Sheffield, UK.
| | - Justin Jeyakani
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore. .,The Genome Institute of Singapore, Biopolis, Biopolis Street, Singapore, Singapore.
| | - Bernd Pelster
- Institute of Zoology, University of Innsbruck, Technikerstr, Innsbruck, Austria.
| | - Ian Sealy
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
| | - Sinnakaruppan Mathavan
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore. .,The Genome Institute of Singapore, Biopolis, Biopolis Street, Singapore, Singapore.
| | - Fredericus J van Eeden
- Bateson Centre, Department of Biomedical Science, The University of Sheffield, Western Bank, Sheffield, UK.
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Zhao J, Fu W, Liao H, Dai L, Jiang Z, Pan Y, Huang H, Mo Y, Li S, Yang G, Yin J. The regulatory and predictive functions of miR-17 and miR-92 families on cisplatin resistance of non-small cell lung cancer. BMC Cancer 2015; 15:731. [PMID: 26482648 PMCID: PMC4617718 DOI: 10.1186/s12885-015-1713-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 10/08/2015] [Indexed: 12/20/2022] Open
Abstract
Background Chemotherapy is an important therapeutic approach for non-small cell lung cancer (NSCLC). However, a successful long-term treatment can be prevented by the occurring of chemotherapy resistance frequently, and the molecular mechanisms of chemotherapy resistance in NSCLC remain unclear. In this study, abnormal expressions of miR-17 and miR-92 families are observed in cisplatin-resistant cells, suggesting that miR-17 and miR-92 families are involved in the regulation of cisplatin resistance in NSCLC. Methods miRNA microarray shows that miR-17 and miR-92 families are all down-regulated in cisplatin-resistant A549/DDP cells compared with cisplatin-sensitive A549 cells. The aim of this study is to investigate the regulatory functions of miR-17 and miR-92 families on the formation of cisplatin resistance and the predictive functions of them as biomarkers of platinum-based chemotherapy resistance in NSCLC. Results The low expressions of miR-17 and miR-92 families can maintain cisplatin resistance through the regulation of CDKN1A and RAD21. As a result of high expressions of CDKN1A and RAD21, the inhibition of DNA synthesis and the repair of DNA damage are achieved and these may be two major contributing factors to cisplatin resistance. Moreover, we demonstrate that the expressions of miR-17 and miR-92 families in NSCLC tissues are significantly associated with platinum-based chemotherapy response. Conclusion Our study indicates that miR-17 and miR-92 families play important roles in cisplatin resistance and can be used as potential biomarkers for better predicting the clinical response to platinum-based chemotherapy in NSCLC. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1713-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jian Zhao
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Wenfan Fu
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Hongying Liao
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Lu Dai
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Zeyong Jiang
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Youguang Pan
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Haoda Huang
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Yijun Mo
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Siwen Li
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Guangping Yang
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Jun Yin
- Department of Chest Surgery, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong, China.
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MicroRNAs in clear cell renal cell carcinoma: biological functions and applications. J Kidney Cancer VHL 2015; 2:140-152. [PMID: 28326269 PMCID: PMC5345517 DOI: 10.15586/jkcvhl.2015.40] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 08/18/2015] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRs) are small noncoding RNAs that govern many biological processes. They frequently acquire a gain or a loss of function in cancer and hence play a causative role in the development and progression of neoplasms. They could be used as biomarkers to improve our knowledge on diagnosis, prognosis and drug resistance, and to attempt therapeutic approaches in several types of cancer including clear cell renal cell carcinoma (ccRCC). ccRCC is the most predominant subtype of RCC that accounts for about 90% of all renal cancers. Since ccRCC is generally asymptomatic until very late, it is difficult to diagnose early. Moreover, in the absence of preventive treatments for metastatic ccRCC after surgical resection of the primary cancer, predictive prognostic biomarkers are needed in order to achieve appropriate therapies. Herein the role of miRs in the biology of ccRCC and the potential applications of these molecules are discussed. Moreover, future applications in the diagnostic and prognostic field, as well as their impact on drug response and therapeutic targets are also explored. Their use in clinical practice as molecular biomarkers alone, or in combination with other biological markers could accelerate progress, help design personalized therapies, limit side effects, and improve quality of life of ccRCC patients.
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Hou C, Zhang Z, Zhang Z, Wu P, Zhao X, Fu M, Sheng P, Kang Y, Liao W. Presence and function of microRNA-92a in chondrogenic ATDC5 and adipose-derived mesenchymal stem cells. Mol Med Rep 2015; 12:4877-86. [PMID: 26135269 PMCID: PMC4581768 DOI: 10.3892/mmr.2015.4008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 05/28/2015] [Indexed: 12/20/2022] Open
Abstract
The aim of the present study was to investigate the presence and biological function of microRNA-92a (miR-92a) in chondrogenesis and cartilage degeneration. Human adipose-derived mesenchymal stem cells (hADSCs) in micromass and chondrocyte-like ATDC5 cells were induced to chondrogenesis, and primary human/mouse chondrocytes (PHCs/PMCs) and chondrogenic ATDC5 cells were stimulated with interleukin-1β (IL-1β). An miR-92a mimic/inhibitor was transfected into the ATDC5 cells using lipofectamine 2000. Gene expression was analyzed using reverse transcription-quantitative polymerase chain reaction. Alcian blue was used to stain the cartilage nodules and chondrogenic micromass. The potential target genes, signaling pathways and functions of miR-92a were examined using miRanda, miRDB, CLIP-Seq, TargetScan and Kyoto Encyclopedia of Genes and Genomes. The expression of miR-92a was elevated in the chondrogenic ATDC5 cells and hADSCs, and also in the IL-1β-induced ATDC5 cells, PMCs and PHCs. Forced expression of miR-92a enhanced the expression levels of col9a2 and aggrecan. A total of 279 genes were predicted as potential target genes of miR-92a. The phosphoinositide 3-kinase/PI3K)-Akt, ErbB and focal adhesion kinase pathways, extracellular matrix (ECM)-receptor interaction and the mammalian target of rapamycin (mTOR) signaling pathway were suggested to mediate the effects of miR-92a on chondrogenesis and cartilage degeneration. These results demonstrated that miR-92a was involved in chondrogenesis and the chondrocyte response induced by IL-1β. miR-92a positively contributed to the expression of col9a2 and of aggrecan.
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Affiliation(s)
- Changhe Hou
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat‑Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Ziji Zhang
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat‑Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Zhiqi Zhang
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat‑Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Peihui Wu
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat‑Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Xiaoyi Zhao
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat‑Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Ming Fu
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat‑Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Puyi Sheng
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat‑Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Yan Kang
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat‑Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Weiming Liao
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat‑Sen University, Guangzhou, Guangdong 510080, P.R. China
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He H, Wang L, Zhou W, Zhang Z, Wang L, Xu S, Wang D, Dong J, Tang C, Tang H, Yi X, Ge J. MicroRNA Expression Profiling in Clear Cell Renal Cell Carcinoma: Identification and Functional Validation of Key miRNAs. PLoS One 2015; 10:e0125672. [PMID: 25938468 PMCID: PMC4418764 DOI: 10.1371/journal.pone.0125672] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 03/17/2015] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVE This study aims to profile dysregulated microRNA (miRNA) expression in clear cell renal cell carcinoma (ccRCC) and to identify key regulatory miRNAs in ccRCC. METHODS AND RESULTS miRNA expression profiles in nine pairs of ccRCC tumor samples at three different stages and the adjacent, non-tumorous tissues were investigated using miRNA arrays. Eleven miRNAs were identified to be commonly dysregulated, including three up-regulated (miR-487a, miR-491-3p and miR-452) and eight down-regulated (miR-125b, miR-142-3p, miR-199a-5p, miR-22, miR-299-3p, miR-29a, miR-429, and miR-532-5p) in tumor tissues as compared with adjacent normal tissues. The 11 miRNAs and their predicted target genes were analyzed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and three key miRNAs (miR-199a-5p, miR-22 and miR-429) were identified by microRNA-gene network analysis. Dysregulation of the three key miRNAs were further validated in another cohort of 15 ccRCC samples, and the human kidney carcinoma cell line 786-O, as compared with five normal kidney samples. Further investigation showed that over-expression of miR-199a-5p significantly inhibited the invasion ability of 786-O cells. Luciferase reporter assays indicated that miR-199a-5p regulated expression of TGFBR1 and JunB by directly interacting with their 3' untranslated regions. Transfection of miR-199a-5p successfully suppressed expression of TGFBR1 and JunB in the human embryonic kidney 293T cells, further confirming the direct regulation of miR-199a-5p on these two genes. CONCLUSIONS This study identified 11 commonly dysregulated miRNAs in ccRCC, three of which (miR-199a-5p, miR-22 and miR-429) may represent key miRNAs involved in the pathogenesis of ccRCC. Further studies suggested that miR-199a-5p plays an important role in inhibition of cell invasion of ccRCC cells by suppressing expression of TGFBR1 and JunB.
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Affiliation(s)
- Haowei He
- Department of Urology, Jinling Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Linhui Wang
- Department of Urology, Changzheng Hospital, Second Military Medical University, Shanghai, Shanghai, China
| | - Wenquan Zhou
- Department of Urology, Jinling Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Zhengyu Zhang
- Department of Urology, Jinling Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Longxin Wang
- Department of Urology, Jinling Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Song Xu
- Department of Urology, Jinling Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Dong Wang
- Department of Urology, Jinling Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Jie Dong
- Department of Urology, Jinling Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Chaopeng Tang
- Department of Urology, Jinling Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Hao Tang
- Department of Urology, Jinling Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Xiaoming Yi
- Department of Urology, Jinling Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Jingping Ge
- Department of Urology, Jinling Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China
- * E-mail:
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Botella LM, Albiñana V, Ojeda-Fernandez L, Recio-Poveda L, Bernabéu C. Research on potential biomarkers in hereditary hemorrhagic telangiectasia. Front Genet 2015; 6:115. [PMID: 25873934 PMCID: PMC4379940 DOI: 10.3389/fgene.2015.00115] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 03/05/2015] [Indexed: 12/21/2022] Open
Abstract
Hereditary hemorrhagic telangiectasia (HHT) is a genetically heterogeneous disorder, involving mutations in two predominant genes known as Endoglin (ENG; HHT1) and activin receptor-like kinase 1 (ACVRL1/ALK1; HHT2), as well as in some less frequent genes, such as MADH4/SMAD4 (JP-HHT) or BMP9/GDF2 (HHT5). The diagnosis of HHT patients currently remains at the clinical level, according to the “Curaçao criteria,” whereas the molecular diagnosis is used to confirm or rule out suspected HHT cases, especially when a well characterized index case is present in the family or in an isolated population. Unfortunately, many suspected patients do not present a clear HHT diagnosis or do not show pathogenic mutations in HHT genes, prompting the need to investigate additional biomarkers of the disease. Here, several HHT biomarkers and novel methodological approaches developed during the last years will be reviewed. On one hand, products detected in plasma or serum samples: soluble proteins (vascular endothelial growth factor, transforming growth factor β1, soluble endoglin, angiopoietin-2) and microRNA variants (miR-27a, miR-205, miR-210). On the other hand, differential HHT gene expression fingerprinting, next generation sequencing of a panel of genes involved in HHT, and infrared spectroscopy combined with artificial neural network patterns will also be reviewed. All these biomarkers might help to improve and refine HHT diagnosis by distinguishing from the non-HHT population.
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Affiliation(s)
- Luisa-María Botella
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas , Madrid, Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras , Madrid, Spain
| | - Virginia Albiñana
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas , Madrid, Spain
| | - Luisa Ojeda-Fernandez
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas , Madrid, Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras , Madrid, Spain
| | - Lucia Recio-Poveda
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas , Madrid, Spain
| | - Carmelo Bernabéu
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas , Madrid, Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras , Madrid, Spain
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Low VHL mRNA expression is associated with more aggressive tumor features of papillary thyroid carcinoma. PLoS One 2014; 9:e114511. [PMID: 25490036 PMCID: PMC4260854 DOI: 10.1371/journal.pone.0114511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 11/10/2014] [Indexed: 12/05/2022] Open
Abstract
Alterations of the von Hippel–Lindau (VHL) tumor suppressor gene can cause different hereditary tumors associated with VHL syndrome, but the potential role of the VHL gene in papillary thyroid carcinoma (PTC) has not been characterized. This study set out to investigate the relationship of VHL expression level with clinicopathological features of PTC in an ethnically and geographically homogenous group of 264 patients from Serbia, for the first time. Multivariate logistic regression analysis showed a strong correlation between low level of VHL expression and advanced clinical stage (OR = 5.78, 95% CI 3.17–10.53, P<0.0001), classical papillary morphology of the tumor (OR = 2.92, 95% CI 1.33–6.44, P = 0.008) and multifocality (OR = 1.96, 95% CI 1.06–3.62, P = 0.031). In disease-free survival analysis, low VHL expression had marginal significance (P = 0.0502 by the log-rank test) but did not appear to be an independent predictor of the risk for chance of faster recurrence in a proportion hazards model. No somatic mutations or evidence of VHL downregulation via promoter hypermethylation in PTC were found. The results indicate that the decrease of VHL expression associates with tumor progression but the mechanism of downregulation remains to be elucidated.
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Zhan L, Huang C, Meng XM, Song Y, Wu XQ, Yang Y, Li J. Hypoxia-inducible factor-1alpha in hepatic fibrosis: A promising therapeutic target. Biochimie 2014; 108:1-7. [PMID: 25447141 DOI: 10.1016/j.biochi.2014.10.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 10/17/2014] [Indexed: 02/08/2023]
Abstract
Hypoxia-inducible factor-1alpha (HIF-1α) is a regulated subunit of the hypoxia-inducible factor 1 (HIF1), which functions as a key transcription factor in response to hypoxic stress by regulating genes involved in maintaining oxygen homeostasis. In recent years, a growing body of studies showed that HIF-1α was significantly increased in hepatic fibrotic tissues and activated hepatic stellate cells (HSCs). Furthermore, knockdown of HIF-1α expression inhibited the proliferation and activation of HSCs. In addition, HIF-1α-dependent genes and the extensive network of signaling cascades focus on HIF-1α have been reported to associate with the development of hepatic fibrosis, suggesting that HIF-1α might play a crucial role in hepatic fibrosis. However, the mechanisms by which HIF-1α regulates hepatic fibrosis are still undefined. In this review, we concentrate on multiple signaling pathways and genes related with HIF-1α which may be involved in the development of hepatic fibrosis, further discussing its potential as a novel therapeutic target for hepatic fibrosis.
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Affiliation(s)
- Lei Zhan
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China
| | - Cheng Huang
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China
| | - Xiao-Ming Meng
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China
| | - Yang Song
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China
| | - Xiao Qin Wu
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China
| | - Yang Yang
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China
| | - Jun Li
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China.
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44
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Wang Z, Wei M, Ren Y, Liu H, Wang M, Shi K, Jiang H. miR149 rs71428439 polymorphism and risk of clear cell renal cell carcinoma: a case-control study. Tumour Biol 2014; 35:12127-30. [PMID: 25213695 DOI: 10.1007/s13277-014-2517-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 08/15/2014] [Indexed: 12/13/2022] Open
Abstract
Clear cell renal cell carcinoma (CCRCC) is the most common subtype of renal cell cancer and accounts for 70 % of renal cell cancer. CCRCC remains an enigmatic tumor type, as the molecular genetic mechanisms are still unclear. MicroRNA (miR) 149 functions as a tumor suppressor and plays an important role in the carcinogenesis of renal cells. In this study, we enrolled 1,000 CCRCC patients and 1,000 cancer-free controls to evaluate the association of miR149 rs71428439 with the risk of CCRCC by a case-control study to determine the effects on CCRCC risk. miR149 rs71428439 was significantly associated with increased CCRCC risk (odds ratio (OR) for trend = 1.53, P for trend = 4.04 × 10(-11)), with ORs (95 % confidence intervals (CIs)) of 1.42 (1.17-1.72) associated with AG genotype and 2.27 (1.76-2.94) associated with GG genotype, compared with subjects with AA genotype. The expression levels of miR149 in cancer tissues were significantly lower than those in adjacent normal tissues (P = 0.005), and per G allele has significantly lower miR149 levels in both tumor tissues and adjacent normal tissues. Our data suggest that the GG genotypes of miR149 rs71428439 predispose their carriers to CCRCC, and miR149 rs71428439 may be a new biomarker for predicting the risk of CCRCC.
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Affiliation(s)
- Zhigang Wang
- School of Medicine Dialysis Center of First Affiliated Hospital of Medicine School, Xi'an Jiaotong University, No. 277 West Yanta Street, Xi'an, Shaanxi, 710061, China
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45
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Dias F, Teixeira AL, Santos JI, Gomes M, Nogueira A, Assis J, Medeiros R. Renal cell carcinoma development and miRNAs: a possible link to the EGFR pathway. Pharmacogenomics 2014; 14:1793-803. [PMID: 24192126 DOI: 10.2217/pgs.13.184] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Renal cell carcinoma (RCC) is the most common solid cancer of the adult kidney and the majority of RCC cases are detected accidentally. This reality and the nonexistence of a standard screening test contribute to the fact that one third of patients are diagnosed with local invasive disease or metastatic disease. miRNAs are a family of small ncRNAs that regulate gene expression and have been identified as key regulators in many biological processes including cell development, differentiation, apoptosis and proliferation. The EGF receptor signaling pathway is usually deregulated in cancer and it is suggested to have an important role in RCC. Further studies are needed to characterize deregulation of this pathway during RCC development. In this review we highlight some potential miRNAs that could be involved in the modulation of the EGF receptor pathway and consequently in RCC development.
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Affiliation(s)
- Francisca Dias
- Molecular Oncology Group, Portuguese Institute of Oncology, Rua Dr António Bernardino de Almeida, 4200-072 Porto, Portugal
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46
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Wei Q, Mi QS, Dong Z. The regulation and function of microRNAs in kidney diseases. IUBMB Life 2014; 65:602-14. [PMID: 23794512 DOI: 10.1002/iub.1174] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 03/26/2013] [Accepted: 03/26/2013] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNA) are endogenous short noncoding RNAs, which regulate virtually all major cellular processes by inhibiting target gene expression. In kidneys, miRNAs have been implicated in renal development, homeostasis, and physiological functions. In addition, miRNAs play important roles in the pathogenesis of various renal diseases, including renal carcinoma, diabetic nephropathy, acute kidney injury, hypertensive nephropathy, polycystic kidney disease, and others. Furthermore, miRNAs may have great values as biomarkers in different kidney diseases.
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Affiliation(s)
- Qingqing Wei
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Georgia Regents University and Charlie Norwood Veterans Affairs Medical Center, Augusta, GA 30912, USA
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47
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Li M, Guan X, Sun Y, Mi J, Shu X, Liu F, Li C. miR-92a family and their target genes in tumorigenesis and metastasis. Exp Cell Res 2014; 323:1-6. [PMID: 24394541 DOI: 10.1016/j.yexcr.2013.12.025] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 12/18/2013] [Indexed: 01/01/2023]
Abstract
The miR-92a family, including miR-25, miR-92a-1, miR-92a-2 and miR-363, arises from three different paralog clusters miR-17-92, miR-106a-363, and miR-106b-25 that are highly conservative in the process of evolution, and it was thought as a group of microRNAs (miRNAs) correlated with endothelial cells. Aberrant expression of miR-92a family was detected in multiple cancers, and the disturbance of miR-92a family was related with tumorigenesis and tumor development. In this review, the progress on the relationship between miR-92a family and their target genes and malignant tumors will be summarized.
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Affiliation(s)
- Molin Li
- Department of Pathophysiology, Basic Medical Science of Dalian Medical University, Dalian 116044, China; Institute of Cancer Stem Cell, Dalian Medical University Cancer Center, Dalian 116044, China.
| | - Xingfang Guan
- Department of Pathophysiology, Basic Medical Science of Dalian Medical University, Dalian 116044, China
| | - Yuqiang Sun
- Department of Pathophysiology, Basic Medical Science of Dalian Medical University, Dalian 116044, China
| | - Jun Mi
- Institute of Cancer Stem Cell, Dalian Medical University Cancer Center, Dalian 116044, China
| | - Xiaohong Shu
- College of Pharmacy, Dalian Medical University Cancer Center, Dalian 116044, China
| | - Fang Liu
- Department of Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian 116027, China
| | - Chuangang Li
- Department of Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian 116027, China.
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48
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Andreasson A, Kiss NB, Caramuta S, Sulaiman L, Svahn F, Bäckdahl M, Höög A, Juhlin CC, Larsson C. The VHL gene is epigenetically inactivated in pheochromocytomas and abdominal paragangliomas. Epigenetics 2013; 8:1347-54. [PMID: 24149047 PMCID: PMC3933494 DOI: 10.4161/epi.26686] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Pheochromocytoma (PCC) and abdominal paraganglioma (PGL) are neuroendocrine tumors that present with clinical symptoms related to increased catecholamine levels. About a third of the cases are associated with constitutional mutations in pre-disposing genes, of which some may also be somatically mutated in sporadic cases. However, little is known about inactivating epigenetic events through promoter methylation in these very genes. Using bisulphite pyrosequencing we assessed the methylation density of 11 PCC/PGL disease genes in 96 tumors (83 PCCs and 13 PGLs) and 34 normal adrenal references. Gene expression levels were determined by quantitative RT-PCR. Both tumors and normal adrenal samples exhibited low methylation index (MetI) in the EGLN1 (PDH2), MAX, MEN1, NF1, SDHB, SDHC, SDHD, SDHAF2 (SDH5), and TMEM127 promoters, not exceeding 10% in any of the samples investigated. Aberrant RET promoter methylation was observed in two cases only. For the VHL gene we found increased MetI in tumors as compared with normal adrenals (57% vs. 27%; P < 0.001), in malignant vs. benign tumors (63% vs. 55%; P < 0.05), and in PGL vs. PCC (66% vs. 55%; P < 0.0005). Decreased expression of the VHL gene was observed in all tumors compared with normal adrenals (P < 0.001). VHL MetI and gene expressions were inversely correlated (R = −0.359, P < 0.0001). Our results show that the VHL gene promoter has increased methylation compared with normal adrenals (MetI > 50%) in approximately 75% of PCCs and PGLs investigated, highlighting the role of VHL in the development of these tumors.
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Affiliation(s)
- Adam Andreasson
- Department of Oncology-Pathology; Karolinska Institutet; Karolinska University Hospital; Stockholm, Sweden
| | - Nimrod B Kiss
- Department of Oncology-Pathology; Karolinska Institutet; Karolinska University Hospital; Stockholm, Sweden
| | - Stefano Caramuta
- Department of Oncology-Pathology; Karolinska Institutet; Karolinska University Hospital; Stockholm, Sweden
| | - Luqman Sulaiman
- Department of Oncology-Pathology; Karolinska Institutet; Karolinska University Hospital; Stockholm, Sweden
| | - Fredrika Svahn
- Department of Oncology-Pathology; Karolinska Institutet; Karolinska University Hospital; Stockholm, Sweden
| | - Martin Bäckdahl
- Department of Molecular Medicine and Surgery; Karolinska Institutet; Stockholm, Sweden; Department of Breast and Endocrine Surgery; Karolinska University Hospital; Stockholm, Sweden
| | - Anders Höög
- Department of Oncology-Pathology; Karolinska Institutet; Karolinska University Hospital; Stockholm, Sweden; Department of Clinical Pathology and Cytology; Karolinska University Hospital; Stockholm, Sweden
| | - C Christofer Juhlin
- Department of Oncology-Pathology; Karolinska Institutet; Karolinska University Hospital; Stockholm, Sweden; Department of Clinical Pathology and Cytology; Karolinska University Hospital; Stockholm, Sweden
| | - Catharina Larsson
- Department of Oncology-Pathology; Karolinska Institutet; Karolinska University Hospital; Stockholm, Sweden
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49
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Silva-Santos RM, Costa-Pinheiro P, Luis A, Antunes L, Lobo F, Oliveira J, Henrique R, Jerónimo C. MicroRNA profile: a promising ancillary tool for accurate renal cell tumour diagnosis. Br J Cancer 2013; 109:2646-53. [PMID: 24129247 PMCID: PMC3833202 DOI: 10.1038/bjc.2013.552] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 08/13/2013] [Accepted: 08/19/2013] [Indexed: 12/12/2022] Open
Abstract
Background: Renal cell tumours (RCTs) are clinically, morphologically and genetically heterogeneous. Accurate identification of renal cell carcinomas (RCCs) and its discrimination from normal tissue and benign tumours is mandatory. We, thus, aimed to define a panel of microRNAs that might aid in the diagnostic workup of RCTs. Methods: Fresh-frozen tissues from 120 RCTs (clear-cell RCC, papillary RCC, chromophobe RCC (chRCC) and oncocytomas: 30 cases each), 10 normal renal tissues and 60 cases of ex-vivo fine-needle aspiration biopsies from RCTs (15 of each subtype validation set) were collected. Expression levels of miR-21, miR-141, miR-155, miR-183 and miR-200b were assessed by quantitative reverse transcription–PCR. Receiver operator characteristic curves were constructed and the areas under the curve were calculated to assess diagnostic performance. Disease-specific survival curves and a Cox regression model comprising all significant variables were computed. Results: Renal cell tumours displayed significantly lower expression levels of miR-21, miR-141 and miR-200b compared with that of normal tissues, and expression levels of all miRs differed significantly between malignant and benign RCTs. Expression analysis of miR-141 or miR-200b accurately distinguished RCTs from normal renal tissues, oncocytoma from RCC and chRCC from oncocytoma. The diagnostic performance was confirmed in the validation set. Interestingly, miR-21, miR-141 and miR-155 expression levels showed prognostic significance in a univariate analysis. Conclusion: The miR-141 or miR-200b panel accurately distinguishes RCC from normal kidney and oncocytoma in tissue samples, discriminating from normal kidney and oncocytoma, whereas miR-21, miR-141 and miR-155 convey prognostic information. This approach is feasible in fine-needle aspiration biopsies and might provide an ancillary tool for routine diagnosis.
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Affiliation(s)
- R M Silva-Santos
- 1] Cancer Epigenetics Group, Research Center of the Portuguese Oncology Institute, Rua Doutor António Bernardino Almeida, 4200-072 Porto, Portugal [2] Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
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50
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Ruiz Esparza-Garrido R, Velázquez-Flores MÁ, Diegopérez-Ramírez J, López-Aguilar E, Siordia-Reyes G, Hernández-Ortiz M, Martínez-Batallar AG, Encarnación-Guevara S, Salamanca-Gómez F, Arenas-Aranda DJ. A proteomic approach of pediatric astrocytomas: MiRNAs and network insight. J Proteomics 2013; 94:162-75. [PMID: 24060999 DOI: 10.1016/j.jprot.2013.09.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/23/2013] [Accepted: 09/12/2013] [Indexed: 12/13/2022]
Abstract
UNLABELLED Pediatric astrocytomas, a leading cause of death associated with cancer, are the most common primary central nervous system tumors found in children. Most studies of these tumors focus on adults, not on children. We examined the global protein and microRNA expression pattern by 2D SDS-PAGE, mass spectrometry (MALDI-TOF), and RT(2) miRNA PCR Array System. Proteomic studies revealed 49 proteins with changes on the expression. Interactome showed that vimentin, calreticulin, and 14-3-3 epsilon protein are hub proteins in these neoplasms. MicroRNA analyses demonstrated for the first time novel microRNAs involved in the astrocytoma biology. In conclusion, our results show that novel proteins and microRNAs with expression changes on pediatric astrocytoma could serve as biomarkers of tumor progression. BIOLOGICAL SIGNIFICANCE Astrocytomas are tumors that progress rapidly and that invade surrounding tissues. Although some drugs have been developed to treat these neoplasms, the mortality of patients is still very high. In this study, we describe for the first time, to our knowledge, some proteins and miRNAs associated with the biology of astrocytic tumors that could be postulated as possible diagnostic or prognostic biomarkers. Altogether, our results indicate that large-scale analyses allow making a fairly accurate prediction of different cellular processes altered in astrocytic tumors.
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Affiliation(s)
- Ruth Ruiz Esparza-Garrido
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, 06720 México, D.F., Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Av. Universidad 3000, C.P. 04510 Coyoacán, D. F., Mexico
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