51
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Romano G, Kwong LN. miRNAs, Melanoma and Microenvironment: An Intricate Network. Int J Mol Sci 2017; 18:ijms18112354. [PMID: 29112174 PMCID: PMC5713323 DOI: 10.3390/ijms18112354] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 11/02/2017] [Accepted: 11/05/2017] [Indexed: 12/14/2022] Open
Abstract
miRNAs are central players in cancer biology and they play a pivotal role in mediating the network communication between tumor cells and their microenvironment. In melanoma, miRNAs can impair or facilitate a wide array of processes, and here we will focus on: the epithelial to mesenchymal transition (EMT), the immune milieu, and metabolism. Multiple miRNAs can affect the EMT process, even at a distance, for example through exosome-mediated mechanisms. miRNAs also strongly act on some components of the immune system, regulating the activity of key elements such as antigen presenting cells, and can facilitate an immune evasive/suppressive phenotype. miRNAs are also involved in the regulation of metabolic processes, specifically in response to hypoxic stimuli where they can mediate the metabolic switch from an oxidative to a glycolytic metabolism. Overall, this review discusses and summarizes recent findings on miRNA regulation in the melanoma tumor microenvironment, analyzing their potential diagnostic and therapeutic applications.
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Affiliation(s)
- Gabriele Romano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Lawrence N Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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52
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RNA/DNA co-analysis from bloodstains on aged polyvinyl-alcohol gloves prepared for securing evidence from the hands of victims of fatal gunshot injuries. Int J Legal Med 2017; 132:53-66. [PMID: 28956148 DOI: 10.1007/s00414-017-1687-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 08/30/2017] [Indexed: 12/22/2022]
Abstract
In contrast to cumulative techniques (e.g., tape-lift) for qualitative gunshot residues (GSR) analysis, topographic methods are commonly applied to preserve the integrity of evidence from a shooter's or victim's hand in cases of gun-related crimes. Topographic sampling techniques employing adhesive foils, latex, or the polyvinyl alcohol (PVAL) method enable unambiguous sampling of biological and non-biological trace material while preserving its spatial distribution and relation to each other. The PVAL method in particular allows for a topographically veridic and quantitative conservation of traces of GSR and biological stains that are embedded in the PVAL glove, because it completely removes these traces from the hand. The present study investigated the success rates of STR profiling and the detection of blood and brain-specific gene expression from minimal traces of blood splatter as well as parallel to the positive detection of gunshot residues embedded in 17 PVAL gloves taken from the hands of deceased persons in the context of homicide cases in the period between 1996 and 2003. The water-soluble PVAL matrix is shown to be fully compatible with successful STR profiling and the detection of blood- and brain-specific miRNA expression, even after up to 20 years of storage, demonstrating that this sampling technique offers advantages compared to other more simplistic sampling methods like taping.
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53
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Berania I, Cardin GB, Clément I, Guertin L, Ayad T, Bissada E, Nguyen-Tan PF, Filion E, Guilmette J, Gologan O, Soulieres D, Rodier F, Wong P, Christopoulos A. Four PTEN-targeting co-expressed miRNAs and ACTN4- targeting miR-548b are independent prognostic biomarkers in human squamous cell carcinoma of the oral tongue. Int J Cancer 2017; 141:2318-2328. [PMID: 28779483 DOI: 10.1002/ijc.30915] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 05/31/2017] [Accepted: 07/10/2017] [Indexed: 02/04/2023]
Abstract
The purpose of this study was to determine the prognostic value and oncogenic pathways associated to miRNA expression in squamous cell carcinoma of the oral tongue and to link these miRNA candidates with potential gene targets. We performed a miRNA screening within our institutional cohort (n = 58 patients) and reported five prognostic targets including a cluster of four co-expressed miRNAs (miR-18a, miR-92a, miR-103, and miR-205). Multivariate analysis showed that expression of miR-548b (p = 0.007) and miR-18a (p = 0.004, representative of co-expressed miRNAs) are independent prognostic markers for squamous cell carcinoma of the oral tongue. These findings were validated in The Cancer Genome Atlas (TCGA) cohort (n = 131) for both miRNAs (miR-548b: p = 0.027; miR-18a: p = 0.001). Bioinformatics analysis identified PTEN and ACTN4 as direct targets of the four co-expressed miRNAs and miR-548b, respectively. Correlations between the five identified miRNAs and their respective targeted genes were validated in the two merged cohorts and were concordantly significant (miR-18a/PTEN: p < 0.0001; miR-92a/PTEN: p = 0.0008; miR-103/PTEN: p = 0.008; miR-203/PTEN: p = 0.019; miR-548b/ACTN4: p = 0.009).
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Affiliation(s)
- Ilyes Berania
- CRCHUM and Institut du cancer de Montréal, Montreal, QC, Canada.,Otolaryngology-Head and Neck Surgery Service, Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | | | | | - Louis Guertin
- Otolaryngology-Head and Neck Surgery Service, Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Tareck Ayad
- Otolaryngology-Head and Neck Surgery Service, Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Eric Bissada
- Otolaryngology-Head and Neck Surgery Service, Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Phuc Felix Nguyen-Tan
- Department of Radiation Oncology, Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Edith Filion
- Department of Radiation Oncology, Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Julie Guilmette
- Department of Pathology, Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada.,Department of Pathology, Massachusetts General Hospital/Massachusetts Eye and Ear Infirmary, Boston, MA
| | - Olguta Gologan
- Department of Pathology, Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Denis Soulieres
- Department of Medicine, Service of Hemato-Oncology, Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Francis Rodier
- CRCHUM and Institut du cancer de Montréal, Montreal, QC, Canada.,Département de radiologie, radio-oncologie et medicine nucléaire, Université de Montréal, Montreal, QC, Canada
| | - Philip Wong
- CRCHUM and Institut du cancer de Montréal, Montreal, QC, Canada.,Department of Radiation Oncology, Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Apostolos Christopoulos
- CRCHUM and Institut du cancer de Montréal, Montreal, QC, Canada.,Otolaryngology-Head and Neck Surgery Service, Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
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54
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Yang L, Taylor J, Eustace A, Irlam JJ, Denley H, Hoskin PJ, Alsner J, Buffa FM, Harris AL, Choudhury A, West CML. A Gene Signature for Selecting Benefit from Hypoxia Modification of Radiotherapy for High-Risk Bladder Cancer Patients. Clin Cancer Res 2017; 23:4761-4768. [PMID: 28400426 DOI: 10.1158/1078-0432.ccr-17-0038] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 02/21/2017] [Accepted: 04/05/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Hypoxia modification improves overall survival in muscle-invasive bladder cancer patients who undergo radiotherapy. There is evidence that hypoxic tumors benefit most from hypoxia modification. The study aimed to identify or derive a hypoxia gene signature that predicts benefit from hypoxia-modifying treatment in bladder cancer.Experimental Design: Published hypoxia signatures were tested and a new one derived by analyzing bladder cancer transcriptomic data from public databases. Tumor samples were available from the BCON phase III randomized trial of radiotherapy alone or with carbogen and nicotinamide (CON). Gene expression data were generated for 151 tumors using Affymetrix Human 1.0 Exon ST arrays and used for independent validation.Results: A 24-gene signature was derived, which was prognostic in four of six independent surgical cohorts (n = 679; meta HR, 2.32; 95% CI, 1.73-3.12; P < 0.0001). The signature was also prognostic in BCON patients receiving radiotherapy alone (n = 75; HR for local relapse-free survival, 2.37; 95% CI, 1.26-4.47; P = 0.0076). The signature predicted benefit from CON (n = 76; HR, 0.47; 95% CI, 0.26-0.86; P = 0.015). Prognostic significance (P = 0.017) and predictive significance (P = 0.058) remained after adjusting for clinicopathologic variables. A test for interaction between hypoxia status and treatment arms was significant (P = 0.0094).Conclusions: A 24-gene hypoxia signature has strong and independent prognostic and predictive value for muscle-invasive bladder cancer patients. The signature can aid identification of patients likely to benefit from the addition of carbogen and nicotinamide to radiotherapy. Clin Cancer Res; 23(16); 4761-8. ©2017 AACR.
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Affiliation(s)
- Lingjian Yang
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester, United Kingdom
| | - Janet Taylor
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester, United Kingdom
- Applied Computational Biology and Bioinformatics Group, CRUK-MI, Manchester, United Kingdom
- HMDS, Leeds Cancer Centre, St James University Hospital, Leeds, United Kingdom
| | - Amanda Eustace
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester, United Kingdom
| | - Joely J Irlam
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester, United Kingdom
| | - Helen Denley
- Department of Cellular Pathology, Manchester Royal Infirmary, Manchester, United Kingdom
| | - Peter J Hoskin
- Cancer Centre, Mount Vernon Hospital, Rickmansworth Road, Northwood, Middlesex, United Kingdom
| | - Jan Alsner
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Francesca M Buffa
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Adrian L Harris
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Ananya Choudhury
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester, United Kingdom
| | - Catharine M L West
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester, United Kingdom.
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55
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Keller J, Diggs LP, Hsueh EC. Prognostic molecular testing in melanoma: ready for prime time? Melanoma Manag 2017; 4:171-174. [PMID: 30190922 DOI: 10.2217/mmt-2017-0013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 06/16/2017] [Indexed: 01/02/2023] Open
Affiliation(s)
- Jennifer Keller
- Department of Surgery, Saint Louis University, St Louis, MO, USA
| | - Laurence P Diggs
- Department of Surgery, Saint Louis University, St Louis, MO, USA
| | - Eddy C Hsueh
- Department of Surgery, Saint Louis University, St Louis, MO, USA
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56
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Li Z, Bai P, Peng D, Wang H, Guo Y, Jiang Y, He W, Tian H, Yang Y, Huang Y, Long B, Liang W, Zhang L. Screening and confirmation of microRNA markers for distinguishing between menstrual and peripheral blood. Forensic Sci Int Genet 2017; 30:24-33. [PMID: 28605652 DOI: 10.1016/j.fsigen.2017.05.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 05/19/2017] [Accepted: 05/30/2017] [Indexed: 12/31/2022]
Abstract
The identification of menstrual blood (MB) and peripheral blood (PB) left at a crime scene is crucial for crime reconstruction, especially in sexual assaults. MicroRNAs (miRNAs), a class of non-protein coding molecules, have been demonstrated to be a viable tool for body fluid identification in forensic casework. Several groups have searched for miRNAs that are specific to different body fluids. Blood has been studied the most extensively. However, menstrual blood was only involved in five studies, and the results confirming the presence of specific miRNAs could not be reproduced in other studies. In this study, we attempted to screen new markers that can differentiate between menstrual blood and peripheral blood by using Exiqon's miRCURY™ LNA Array. Five miRNAs were selected based on the microarray results, namely, miR-141-3p, miR-373-3p, miR-497-5p, miR-143-5p, and miR-136-5p, whose expression levels exhibited 27.95-, 17.96-, 16.74-, 10.14-, and 9.21-fold changes, respectively, compared to the level in peripheral blood. Two classic quantitative methods, TaqMan hydrolysis probes (TaqMan for short) and SYBR Green fluorochrome (SYBR Green for short), were applied in the confirmation step to study the impact of different quantitative methods on the results. Three miRNAs (miR-141-3p, miR-497-5p, and miR-143-5p) were confirmed by TaqMan and one (miR-141-3p) by SYBR Green. Furthermore, bioinformatic methods were applied to interpret the candidate miRNAs. Our results established a multi-step procedure for body fluid identification and showed that the choice of quantitative method is important when miRNAs are used to identify the origin of blood samples.
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Affiliation(s)
- Zhilong Li
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Peng Bai
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Duo Peng
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Hui Wang
- Institute of Forensic Science, Chengdu Public Security Bureau, Chengdu 610081, Sichuan, China
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410000, Hunan, China
| | - Youjing Jiang
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Wang He
- Department of Criminal Science and Technology, Sichuan Police College, Luzhou 646000, Sichuan, China
| | - Huan Tian
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yu Yang
- Institute of Criminal Science and Technology, Shenzhen Public Security Bureau, Shenzhen518000, Shenzhen, China
| | - Yuan Huang
- Department of Biochemistry and Molecular Biology, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Bing Long
- Department of Criminal Science and Technology, Sichuan Police College, Luzhou 646000, Sichuan, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China.
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57
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Asukai K, Kawamoto K, Eguchi H, Konno M, Asai A, Iwagami Y, Yamada D, Asaoka T, Noda T, Wada H, Gotoh K, Nishida N, Satoh T, Doki Y, Mori M, Ishii H. Micro-RNA-130a-3p Regulates Gemcitabine Resistance via PPARG in Cholangiocarcinoma. Ann Surg Oncol 2017; 24:2344-2352. [PMID: 28560603 DOI: 10.1245/s10434-017-5871-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Indexed: 12/15/2022]
Abstract
BACKGROUND The prognosis of cholangiocarcinoma (CCA) is so poor that its chemoresistance needs to be reduced. In this study, we focused on the microRNAs (miRNAs) associated with gemcitabine resistance of CCA and assessed the clinical significance of miRNAs and their target genes. METHODS We performed miRNA microarray analysis for two CCA cell lines (CCLP-1 and MzChA-1) and their gemcitabine-resistant (GR) cells. An miR-130a-3p mimic was induced into CCA cells using lipofection, and we used pioglitazone as a peroxisome proliferator-activated receptor-γ (PPARγ) agonist in vitro. The expression of miR-130a-3p was studied in 27 intrahepatic CCA samples after laser capture microdissection (LCM) and by immunohistochemistry from patients who had undergone curative resection from March 2004 to November 2012 at Osaka University Hospital. RESULTS miR-130a-3p expression was upregulated in CCLP-1-GRs and MzChA-1-GRs significantly more than in their parental cells. Transfection of the miR-130a-3p mimic into CCA cells increased gemcitabine resistance, and we detected PPARG as a target gene of miR-130a-3p. Furthermore, pioglitazone had a synergistic effect with gemcitabine and alleviated gemcitabine resistance of CCA GR cells. Moreover, clinical examination revealed that for patients who underwent adjuvant gemcitabine therapy, those who were PPARγ positive had significantly longer disease-free survival than those who were PPARγ negative (n = 5 and 11, respectively; p = 0.027). CONCLUSIONS Our data suggest that miR-130a-3p was associated with gemcitabine resistance in CCA through PPARG, and there is a possibility that pioglitazone can be used for the treatment of CCA.
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Affiliation(s)
- Kei Asukai
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Koichi Kawamoto
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.,Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Masamitsu Konno
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Ayumu Asai
- Department of Cancer Profiling Discovery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Yoshifumi Iwagami
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Daisaku Yamada
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Tadafumi Asaoka
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Takehiro Noda
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hiroshi Wada
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Kunihito Gotoh
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Naohiro Nishida
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Taroh Satoh
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Masaki Mori
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
| | - Hideshi Ishii
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan. .,Department of Cancer Profiling Discovery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
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58
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Stewart JP, Richman S, Maughan T, Lawler M, Dunne PD, Salto-Tellez M. Standardising RNA profiling based biomarker application in cancer-The need for robust control of technical variables. Biochim Biophys Acta Rev Cancer 2017; 1868:258-272. [PMID: 28549623 DOI: 10.1016/j.bbcan.2017.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/21/2017] [Accepted: 05/22/2017] [Indexed: 01/10/2023]
Abstract
Histopathology-based staging of colorectal cancer (CRC) has utility in assessing the prognosis of patient subtypes, but as yet cannot accurately predict individual patient's treatment response. Transcriptomics approaches, using array based or next generation sequencing (NGS) platforms, of formalin fixed paraffin embedded tissue can be harnessed to develop multi-gene biomarkers for predicting both prognosis and treatment response, leading to stratification of treatment. While transcriptomics can shape future biomarker development, currently <1% of published biomarkers become clinically validated tests, often due to poor study design or lack of independent validation. In this review of a large number of CRC transcriptional studies, we identify recurrent sources of technical variability that encompass collection, preservation and storage of malignant tissue, nucleic acid extraction, methods to quantitate RNA transcripts and data analysis pipelines. We propose a series of defined steps for removal of these confounding issues, to ultimately aid in the development of more robust clinical biomarkers.
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Affiliation(s)
- James P Stewart
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK; Northern Ireland Molecular Pathology Laboratory, Queen's University Belfast, UK
| | - Susan Richman
- Department of Pathology and Tumour Biology, St James University Hospital, Leeds, UK
| | - Tim Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, UK
| | - Mark Lawler
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Philip D Dunne
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Manuel Salto-Tellez
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK; Northern Ireland Molecular Pathology Laboratory, Queen's University Belfast, UK.
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59
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Starkey MP, Compston-Garnett L, Malho P, Dunn K, Dubielzig R. Metastasis-associated microRNA expression in canine uveal melanoma. Vet Comp Oncol 2017; 16:81-89. [PMID: 28512868 DOI: 10.1111/vco.12315] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/01/2017] [Accepted: 03/22/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND Uveal melanoma (UM) is the most common primary intraocular tumour in dogs. There is no effective means of predicting whether a tumour will metastasize. microRNA (miRNA) metastasis signatures have been identified for several human cancers, including UM. AIMS In this study we investigated whether metastasizing and non-metastasizing canine UMs can be distinguished by miRNA expression levels. MATERIALS AND METHODS miRNA microarray profiling was used to compare miRNA expression in 8 metastasizing and 12 non-metastasizing formalin-fixed, paraffin-embedded (FFPE) primary UM biopsies. RESULTS Fourteen miRNAs exhibited statistically significant differences in expression between the metastasizing and non-metastasizing tumours. Class prediction analysis pinpointed 9 miRNAs which categorized tumours as metastasizing or non-metastasizing with an accuracy of 89%. Of the discriminating miRNAs, 8 were up-regulated in metastasizing UM, and included 3 miRNAs implicated as potential "metastasis activators" in human cutaneous melanoma. The expression of 4 of the miRNAs was subsequently measured using the quantitative reverse transcription polymerase chain reaction (RT-qPCR), and their up-regulation in metastasizing tumours validated. CONCLUSION miRNA expression profiles may potentially be used to identify UMs that will metastasize, and miRNAs that are up-regulated in metastasizing tumours may be targets for therapeutic intervention.
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Affiliation(s)
- M P Starkey
- Molecular Oncology Group, Animal Health Trust, Newmarket, UK
| | | | - P Malho
- Comparative Ophthalmology Unit, Animal Health Trust, Newmarket, UK
| | - K Dunn
- FOCUS-EyePathLab, Murarrie, Australia
| | - R Dubielzig
- Comparative Ocular Pathology Laboratory, University of Wisconsin-Madison, Madison, Wisconsin
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Expression and Localization of miR-21 and miR-126 in Mucosal Tissue from Patients with Inflammatory Bowel Disease. Inflamm Bowel Dis 2017; 23:739-752. [PMID: 28426456 DOI: 10.1097/mib.0000000000001086] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND microRNAs (miRNAs) are small noncoding RNAs that guide degradation of mRNA and regulate protein expression. miRNA based diagnostic biomarkers for ulcerative colitis (UC) and Crohn's disease (CD) are emerging but information about the cellular localization of many miRNAs is limited and more detailed histologic evaluation of miRNA expression patterns is needed to understand their immunobiological function. METHODS Formalin-fixed paraffin-embedded colon biopsies from 10 patients with UC and 8 patients with CD together with 9 controls were examined by RT-qPCR and quantitative in situ hybridization (ISH). The cellular expression of miR-21 positive cells was further characterized using immunohistochemical cellular markers. RESULTS Increased levels of miR-21 and miR-126 were found in UC compared with controls and increased levels of miR-21 were observed in UC compared with CD by both RT-qPCR and quantitative in situ hybridization. miR-126 was localized to endothelial cells and miR-21 to cells in the lamina propria. Multiplex immunohistochemical staining showed miR-21 expression in subsets of CD68 macrophages and CD3 T cells in UC, however, far the majority of the miR-21 positive cells could not be categorized among CD68, CD3, and CD19 cells. CONCLUSIONS This study shows that miR-126 levels are increased in UC and expressed in endothelial cells. miR-21 is expressed in subsets of monocytes/macrophages and T cells and may work as a potential biomarker to distinguish UC from CD. Quantitative in situ hybridization may be a powerful tool for such analysis as it combines overall expression with validation of cellular origin. Studies in larger cohorts may confirm this for clinical diagnostics.
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61
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Identification of organ tissue types and skin from forensic samples by microRNA expression analysis. Forensic Sci Int Genet 2017; 28:99-110. [DOI: 10.1016/j.fsigen.2017.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/26/2017] [Accepted: 02/03/2017] [Indexed: 01/19/2023]
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62
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Rosignolo F, Memeo L, Monzani F, Colarossi C, Pecce V, Verrienti A, Durante C, Grani G, Lamartina L, Forte S, Martinetti D, Giuffrida D, Russo D, Basolo F, Filetti S, Sponziello M. MicroRNA-based molecular classification of papillary thyroid carcinoma. Int J Oncol 2017; 50:1767-1777. [PMID: 28393181 DOI: 10.3892/ijo.2017.3960] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/28/2017] [Indexed: 11/05/2022] Open
Abstract
MicroRNA (miRNA) expression is dysregulated in many human malignancies, and a growing number of studies are focused on their potential use as tumor biomarkers. To identify a miRNA signature for papillary thyroid carcinomas (PTC), we investigated miRNA expression profiles in two independent cohorts of PTCs, which included major histological subtypes [classical-type (PTC‑CT), follicular-variant (PTC‑FV), and tall-cell variant (PTC‑TCV)] and cases with low or intermediate risk of recurrence. Using TaqMan® Array Human MicroRNA A+B Cards v3.0, we first performed microRNA profiling of normal and neoplastic thyroid tissues from 29 PTC patients. Promising candidates were then investigated in a second, independent cohort of 76 PTCs using Custom TaqMan® Array MicroRNA Cards. We identified a molecular signature of 11 miRNAs that were significantly upregulated (miR‑146b-5p, miR‑146b-3p, miR‑221-3p, miR‑222‑5p, miR‑222‑3p) or downregulated (miR‑1179, miR‑486‑5p, miR‑204-5p, miR‑7-2-3p, miR‑144-5p, miR‑140-3p) in PTC tissues vs. normal thyroid tissue. Upregulation of miR‑146b-5p and miR‑222‑3p was also significantly associated with an increased risk of recurrence. Higher than normal expression of miR‑146b-5p and miR‑146b-3p characterized PTC‑CT and PTC‑TCV but not PTC‑FV, whereas miR‑21-5p was significantly upregulated only in PTC‑TCV. When PTC‑FV were subclassified as encapsulated (PTC‑EFV) or infiltrative (PTC‑IFV), miR‑204-5p was downregulated in all histological subtypes except PTC‑EFV, which displayed expression levels similar to those of normal thyroid tissues. These findings provide new insights into the molecular classification of PTC, showing that different miRNA expression profiles are associated with different histological types of PTC and different risks of recurrence.
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Affiliation(s)
- Francesca Rosignolo
- Department of Internal Medicine and Medical Specialties, 'Sapienza' University of Rome, Rome, Italy
| | - Lorenzo Memeo
- Department of Experimental Oncology, Mediterranean Institute of Oncology, Viagrande, Italy
| | - Fabio Monzani
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Cristina Colarossi
- Department of Experimental Oncology, Mediterranean Institute of Oncology, Viagrande, Italy
| | - Valeria Pecce
- Department of Internal Medicine and Medical Specialties, 'Sapienza' University of Rome, Rome, Italy
| | - Antonella Verrienti
- Department of Internal Medicine and Medical Specialties, 'Sapienza' University of Rome, Rome, Italy
| | - Cosimo Durante
- Department of Internal Medicine and Medical Specialties, 'Sapienza' University of Rome, Rome, Italy
| | - Giorgio Grani
- Department of Internal Medicine and Medical Specialties, 'Sapienza' University of Rome, Rome, Italy
| | - Livia Lamartina
- Department of Internal Medicine and Medical Specialties, 'Sapienza' University of Rome, Rome, Italy
| | | | | | - Dario Giuffrida
- Department of Experimental Oncology, Mediterranean Institute of Oncology, Viagrande, Italy
| | - Diego Russo
- Department of Health Sciences, University of Catanzaro 'Magna Graecia', Catanzaro, Italy
| | - Fulvio Basolo
- Department of Histopathology, University of Pisa, Pisa, Italy
| | - Sebastiano Filetti
- Department of Internal Medicine and Medical Specialties, 'Sapienza' University of Rome, Rome, Italy
| | - Marialuisa Sponziello
- Department of Internal Medicine and Medical Specialties, 'Sapienza' University of Rome, Rome, Italy
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63
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Koelzer VH, Sokol L, Zahnd S, Christe L, Dawson H, Berger MD, Inderbitzin D, Zlobec I, Lugli A. Digital analysis and epigenetic regulation of the signature of rejection in colorectal cancer. Oncoimmunology 2017; 6:e1288330. [PMID: 28507795 DOI: 10.1080/2162402x.2017.1288330] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 01/23/2017] [Accepted: 01/23/2017] [Indexed: 01/13/2023] Open
Abstract
The immune system plays a pivotal role in the development and progression of colorectal cancer (CRC). Tumor immune rejection has been previously linked to the activation of the interferon-stimulated genes (ISG) STAT1, IRF-5 and IRF-1. Specific immunoregulatory microRNAs (miRNAs) may impact the expression of these ISG in the tumor microenvironment. In this translational study, we develop a digital image analysis protocol to identify the ISG-gene expression signature and investigate miRNA expression in the immediate environment of invading cancer cells. Digital immunophenotyping was performed using next generation tissue microarrays from 241 well-characterized CRC patients and analyzed with clinicopathological and molecular information. Active ISG signaling in the tumor stroma differentiated an immune-activated (n = 178) and a quiescent (n = 43) phenotype. The activated phenotype was associated with high counts of intratumoral CD8+ cytotoxic T-lymphocytes (CTL; p = 0.007) and expression of the immune effector molecules granzyme B (p < 0.001) and perforin (p = 0.020). Immune-activated tumors also showed an elevated expression of the intercellular adhesion molecule-1 (ICAM-1, p = 0.006) which may facilitate CTL infiltration. Patients with immune-activated CRC had a considerably reduced risk of developing distant metastases (p = 0.001, OR = 0.034, 95%CI = 0.006-0.183). High expression of the immunoregulatory miR-34a and miR-93 corresponded to a 2-2.5-fold decrease of STAT1 (p = 0.006) and IRF-1 (p = 0.058), a feature more commonly seen in a quiescent microenvironment. Analysis of a combined ISG marker profile by digital pathology stratifies CRC patients into diametrically opposed immune phenotypes. Targeted inhibition of miRNAs within the tumor microenvironment may form a new strategy to stimulate the anti-tumoral immune response.
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Affiliation(s)
- Viktor H Koelzer
- Translational Research Unit (TRU), Institute of Pathology, University of Bern, Bern, Switzerland.,Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Lena Sokol
- Translational Research Unit (TRU), Institute of Pathology, University of Bern, Bern, Switzerland
| | - Stefan Zahnd
- Translational Research Unit (TRU), Institute of Pathology, University of Bern, Bern, Switzerland
| | - Lucine Christe
- Translational Research Unit (TRU), Institute of Pathology, University of Bern, Bern, Switzerland
| | - Heather Dawson
- Translational Research Unit (TRU), Institute of Pathology, University of Bern, Bern, Switzerland.,Clinical Pathology Division, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Martin D Berger
- Department of Medical Oncology, Bern University Hospital, Bern, Switzerland.,Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Daniel Inderbitzin
- Departments of Visceral Surgery and Medicine, Bern University Hospital, Bern, Switzerland.,Department of Surgery, Bürgerspital Solothurn, Solothurn, Switzerland
| | - Inti Zlobec
- Translational Research Unit (TRU), Institute of Pathology, University of Bern, Bern, Switzerland
| | - Alessandro Lugli
- Translational Research Unit (TRU), Institute of Pathology, University of Bern, Bern, Switzerland.,Clinical Pathology Division, Institute of Pathology, University of Bern, Bern, Switzerland
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64
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Masè M, Grasso M, Avogaro L, D’Amato E, Tessarolo F, Graffigna A, Denti MA, Ravelli F. Selection of reference genes is critical for miRNA expression analysis in human cardiac tissue. A focus on atrial fibrillation. Sci Rep 2017; 7:41127. [PMID: 28117343 PMCID: PMC5259703 DOI: 10.1038/srep41127] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 12/15/2016] [Indexed: 12/23/2022] Open
Abstract
MicroRNAs (miRNAs) are emerging as key regulators of complex biological processes in several cardiovascular diseases, including atrial fibrillation (AF). Reverse transcription-quantitative polymerase chain reaction is a powerful technique to quantitatively assess miRNA expression profile, but reliable results depend on proper data normalization by suitable reference genes. Despite the increasing number of studies assessing miRNAs in cardiac disease, no consensus on the best reference genes has been reached. This work aims to assess reference genes stability in human cardiac tissue with a focus on AF investigation. We evaluated the stability of five reference genes (U6, SNORD48, SNORD44, miR-16, and 5S) in atrial tissue samples from eighteen cardiac-surgery patients in sinus rhythm and AF. Stability was quantified by combining BestKeeper, delta-Cq, GeNorm, and NormFinder statistical tools. All methods assessed SNORD48 as the best and U6 as the worst reference gene. Applications of different normalization strategies significantly impacted miRNA expression profiles in the study population. Our results point out the necessity of a consensus on data normalization in AF studies to avoid the emergence of divergent biological conclusions.
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Affiliation(s)
- Michela Masè
- Department of Physics, University of Trento, Trento, Italy
| | | | - Laura Avogaro
- Department of Physics, University of Trento, Trento, Italy
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Elvira D’Amato
- Department of Physics, University of Trento, Trento, Italy
| | - Francesco Tessarolo
- Healthcare Research and Innovation Program (IRCS-PAT), Bruno Kessler Foundation, Trento, Italy
- Department of Industrial Engineering, University of Trento, Trento, Italy
| | - Angelo Graffigna
- Division of Cardiac Surgery, Santa Chiara Hospital, Trento, Italy
| | | | - Flavia Ravelli
- Department of Physics, University of Trento, Trento, Italy
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65
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Chen Z, Yu T, Cabay RJ, Jin Y, Mahjabeen I, Luan X, Huang L, Dai Y, Zhou X. miR-486-3p, miR-139-5p, and miR-21 as Biomarkers for the Detection of Oral Tongue Squamous Cell Carcinoma. BIOMARKERS IN CANCER 2017; 9:1-8. [PMID: 28096697 PMCID: PMC5224348 DOI: 10.4137/bic.s40981] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 11/06/2016] [Accepted: 11/15/2016] [Indexed: 02/06/2023]
Abstract
Oral tongue squamous cell carcinoma (TSCC) is a complex disease with extensive genetic and epigenetic defects, including microRNA deregulation. The aims of the present study were to test the feasibility of performing the microRNA profiling analysis on archived TSCC specimens and to assess the potential diagnostic utility of the identified microRNA biomarkers for the detection of TSCC. TaqMan array-based microRNA profiling analysis was performed on 10 archived TSCC samples and their matching normal tissues. A panel of 12 differentially expressed microRNAs was identified. Eight of these differentially expressed microRNAs were validated in an independent sample set. A random forest (RF) classification model was built with miR-486-3p, miR-139-5p, and miR-21, and it was able to detect TSCC with a sensitivity of 100% and a specificity of 86.7% (overall error rate = 6.7%). As such, this study demonstrated the utility of the archived clinical specimens for microRNA biomarker discovery. The feasibility of using microRNA biomarkers (miR-486-3p, miR-139-5p, and miR-21) for the detection of TSCC was confirmed.
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Affiliation(s)
- Zujian Chen
- Center for Molecular Biology of Oral Diseases, Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Tianwei Yu
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Robert J Cabay
- Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Yi Jin
- Center for Molecular Biology of Oral Diseases, Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Ishrat Mahjabeen
- Center for Molecular Biology of Oral Diseases, Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA.; Department of Biosciences, COMSATS Institute of Information and Technology, Islamabad, Pakistan
| | - Xianghong Luan
- Department of Oral Biology, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Lei Huang
- Department of Bioengineering, College of Engineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Yang Dai
- Department of Bioengineering, College of Engineering, University of Illinois at Chicago, Chicago, IL, USA.; UIC Cancer Center, Graduate College, University of Illinois at Chicago, Chicago, IL, USA
| | - Xiaofeng Zhou
- Center for Molecular Biology of Oral Diseases, Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA.; UIC Cancer Center, Graduate College, University of Illinois at Chicago, Chicago, IL, USA
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66
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Peskoe SB, Barber JR, Zheng Q, Meeker AK, De Marzo AM, Platz EA, Lupold SE. Differential long-term stability of microRNAs and RNU6B snRNA in 12-20 year old archived formalin-fixed paraffin-embedded specimens. BMC Cancer 2017; 17:32. [PMID: 28061773 PMCID: PMC5219687 DOI: 10.1186/s12885-016-3008-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 12/15/2016] [Indexed: 11/18/2022] Open
Abstract
Background The quantitative analysis of microRNA (miRNA) gene expression in archived formalin-fixed, paraffin embedded (FFPE) tissues has been instrumental to identifying their potential roles in cancer biology, diagnosis, and prognosis. However, it remains unclear whether miRNAs remain stable in FFPE tissues stored for long periods of time. Methods Here we report Taqman real-time RT-PCR quantification of miR-21, miR-141, miR-221, and RNU6B small nuclear RNA (snRNA) levels from 92 radical prostatectomy specimens stored for 12–20 years in FFPE blocks. The relative stability of each transcript over time was assessed using general linear models. The correlation between transcript quantities, sample age, and RNA integrity number (RIN) were determined utilizing Spearman rank correlation. Results All transcript levels linearly decreased with sample age, demonstrating a clear loss of miRNA stability and RNU6B snRNA stability over time. The most rapid rates of degradation were observed for RNU6B and miR-21, while miR-141 and miR-221 were more stable. RNA quality was not correlated with sample age or with miR-21, miR-221, or RNU6B snRNA levels. Conversely, miR-141 levels increased with RNA quality. Conclusions MiRNA and snRNA levels gradually decreased over an eight year period in FFPE tissue blocks. Sample age was the most consistent feature associated with miRNA stability. The reference snRNA, RUN6B, was more rapidly degraded when compared to miR-141 and miR-221 miRNAs. Various miRNAs demonstrated differential rates of degradation. Quantitative miRNA studies from long-term archived FFPE tissues may therefore benefit from epidemiologic study design or statistical analysis methods that take into account differential storage-dependent transcript degradation. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-3008-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah B Peskoe
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - John R Barber
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Qizhi Zheng
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Alan K Meeker
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA.,The James Buchanan Brady Urologic Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Angelo M De Marzo
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA.,The James Buchanan Brady Urologic Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,The James Buchanan Brady Urologic Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Shawn E Lupold
- The James Buchanan Brady Urologic Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD, USA. .,Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA.
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67
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Samir M, Vaas LAI, Pessler F. MicroRNAs in the Host Response to Viral Infections of Veterinary Importance. Front Vet Sci 2016; 3:86. [PMID: 27800484 PMCID: PMC5065965 DOI: 10.3389/fvets.2016.00086] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022] Open
Abstract
The discovery of small regulatory non-coding RNAs has been an exciting advance in the field of genomics. MicroRNAs (miRNAs) are endogenous RNA molecules, approximately 22 nucleotides in length, that regulate gene expression, mostly at the posttranscriptional level. MiRNA profiling technologies have made it possible to identify and quantify novel miRNAs and to study their regulation and potential roles in disease pathogenesis. Although miRNAs have been extensively investigated in viral infections of humans, their implications in viral diseases affecting animals of veterinary importance are much less understood. The number of annotated miRNAs in different animal species is growing continuously, and novel roles in regulating host–pathogen interactions are being discovered, for instance, miRNA-mediated augmentation of viral transcription and replication. In this review, we present an overview of synthesis and function of miRNAs and an update on the current state of research on host-encoded miRNAs in the genesis of viral infectious diseases in their natural animal host as well as in selected in vivo and in vitro laboratory models.
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Affiliation(s)
- Mohamed Samir
- TWINCORE, Center for Experimental and Clinical Infection Research, Hannover, Germany; Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Lea A I Vaas
- TWINCORE, Center for Experimental and Clinical Infection Research , Hannover , Germany
| | - Frank Pessler
- TWINCORE, Center for Experimental and Clinical Infection Research, Hannover, Germany; Helmholtz Center for Infection Research, Braunschweig, Germany
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68
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Hayes J, Thygesen H, Gregory W, Westhead DR, French PJ, Van Den Bent MJ, Lawler SE, Short SC. A validated microRNA profile with predictive potential in glioblastoma patients treated with bevacizumab. Mol Oncol 2016; 10:1296-304. [PMID: 27396951 PMCID: PMC5423205 DOI: 10.1016/j.molonc.2016.06.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 04/20/2016] [Accepted: 06/19/2016] [Indexed: 02/07/2023] Open
Abstract
PURPOSE We investigated whether microRNA expression data from glioblastoma could be used to produce a profile that defines a bevacizumab responsive group of patients. PATIENTS AND METHODS TCGA microRNA expression data from tumors resected at first diagnosis of glioblastoma in patients treated with bevacizumab at any time during the course of their disease were randomly separated into training (n = 50) and test (n = 37) groups for model generation. MicroRNA-seq data for 51 patients whose treatment included bevacizumab in the BELOB trial were used as an independent validation cohort. RESULTS Using penalized regression we identified 8 microRNAs as potential predictors of overall survival in the training set. We dichotomized the response score based on the most prognostic minimum of a density plot of the response scores (log-rank HR = 0.16, p = 1.2e(-5)) and validated the profile in the test cohort (one-sided log-rank HR = 0.34, p = 0.026). Analysis of the profile using all samples in the TCGA glioblastoma dataset, regardless of treatment received, (n = 473) showed that the prediction of patient benefit was not significant (HR = 0.84, p = 0.083) suggesting the profile is specific to bevacizumab. Further independent validation of our microRNA profile in RNA-seq data from patients treated with bevacizumab (alone or in combination with CCNU) at glioblastoma recurrence in the BELOB trial confirmed that our microRNA profile predicted patient benefit from bevacizumab (HR = 0.59, p = 0.043). CONCLUSION We have identified and validated an 8-microRNA profile that predicts overall survival in patients with glioblastoma treated with bevacizumab. This may be useful for identifying patients who are likely to benefit from this agent.
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Affiliation(s)
- Josie Hayes
- Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds LS9 7TF, UK.
| | - Helene Thygesen
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Walter Gregory
- Clinical Trials Research Unit (CTRU), University of Leeds, 71-75 Clarendon Road, Leeds, West Yorkshire LS2 9JT, UK
| | - David R Westhead
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences and Institute of Membrane and Systems Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Pim J French
- Department of Neurology, Brain Tumor Center, Erasmus MC Cancer Institute, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Martin J Van Den Bent
- Department of Neurology, Brain Tumor Center, Erasmus MC Cancer Institute, Groene Hilledijk 301, 3075 EA Rotterdam, The Netherlands
| | - Sean E Lawler
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Susan C Short
- Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds LS9 7TF, UK
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69
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Krishnan P, Ghosh S, Wang B, Heyns M, Graham K, Mackey JR, Kovalchuk O, Damaraju S. Profiling of Small Nucleolar RNAs by Next Generation Sequencing: Potential New Players for Breast Cancer Prognosis. PLoS One 2016; 11:e0162622. [PMID: 27631501 PMCID: PMC5025248 DOI: 10.1371/journal.pone.0162622] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 08/25/2016] [Indexed: 01/09/2023] Open
Abstract
One of the most abundant, yet least explored, classes of RNA is the small nucleolar RNAs (snoRNAs), which are well known for their involvement in post-transcriptional modifications of other RNAs. Although snoRNAs were only considered to perform housekeeping functions for a long time, recent studies have highlighted their importance as regulators of gene expression and as diagnostic/prognostic markers. However, the prognostic potential of these RNAs has not been interrogated for breast cancer (BC). The objective of the current study was to identify snoRNAs as prognostic markers for BC. Small RNA sequencing (Illumina Genome Analyzer IIx) was performed for 104 BC cases and 11 normal breast tissues. Partek Genomics Suite was used for analyzing the sequencing files. Two independent and proven approaches were used to identify prognostic markers: case-control (CC) and case-only (CO). For both approaches, snoRNAs significant in the permutation test, following univariate Cox proportional hazards regression model were used for constructing risk scores. Risk scores were subsequently adjusted for potential confounders in a multivariate Cox model. For both approaches, thirteen snoRNAs were associated with overall survival and/or recurrence free survival. Patients belonging to the high-risk group were associated with poor outcomes, and the risk score was significant after adjusting for confounders. Validation of representative snoRNAs (SNORD46 and SNORD89) using qRT-PCR confirmed the observations from sequencing experiments. We also observed 64 snoRNAs harboring piwi-interacting RNAs and/or microRNAs that were predicted to target genes (mRNAs) involved in tumorigenesis. Our results demonstrate the potential of snoRNAs to serve (i) as novel prognostic markers for BC and (ii) as indirect regulators of gene expression.
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Affiliation(s)
- Preethi Krishnan
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Sunita Ghosh
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.,Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
| | - Bo Wang
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Mieke Heyns
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Kathryn Graham
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.,Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
| | - John R Mackey
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.,Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Sambasivarao Damaraju
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada.,Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
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Irlam-Jones JJ, Eustace A, Denley H, Choudhury A, Harris AL, Hoskin PJ, West CML. Expression of miR-210 in relation to other measures of hypoxia and prediction of benefit from hypoxia modification in patients with bladder cancer. Br J Cancer 2016; 115:571-8. [PMID: 27441495 PMCID: PMC4997544 DOI: 10.1038/bjc.2016.218] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/10/2016] [Accepted: 06/15/2016] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The addition of hypoxia modifiers carbogen and nicotinamide (CON) to radiotherapy (RT) improved overall survival (OS) in bladder cancer patients in the BCON phase III clinical trial. We investigate whether expression of hsa-miR-210 in BCON patient samples reflects hypoxia and predicts benefit from hypoxia modification. METHODS In all, 183 T1-T4a bladder cancer samples were available for miR-210 analysis. A total of 86 received RT+CON and 97 received RT alone. TaqMan qPCR plates were used to assess miR-210 expression. Patients were classified as low ( RESULTS Patients with high miR-210 had a trend towards improved 5-year OS with RT+CON (53.2%) compared with RT alone (37.8%; hazard ratio (HR) 1.68, 95% CI 0.95-2.95, P=0.07). No benefit was seen with low miR-210 (HR 1.02, 95% CI 0.58-1.79, P=0.97). High miR-210 was significantly associated with high HIF-1α protein (P=0.001), CA9 protein (P=0.0004), Glut-1 protein (P=0.001), 26-gene hypoxia score (P=0.007), tumour necrosis (P=0.02) and concurrent pTis (P=0.03). CONCLUSIONS High miR-210 may reflect hypoxia in bladder cancer. However, its ability to predict benefit from hypoxia modification does not improve upon other hypoxia markers. Investigation as part of a miRNA hypoxia signature may reveal the full potential of miR-210.
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Affiliation(s)
- J J Irlam-Jones
- Translational Radiobiology Group, Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Centre, Manchester M20 4BX, UK
| | - A Eustace
- Translational Radiobiology Group, Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Centre, Manchester M20 4BX, UK
| | - H Denley
- Department of Histopathology, Central Manchester University Hospitals NHS Foundation Trust, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK
| | - A Choudhury
- Christie Hospital, Wilmslow Road, Manchester M20 4BX, UK
| | - A L Harris
- Molecular Oncology Laboratories, Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford University, Oxford OX3 9DS, UK
| | - P J Hoskin
- Cancer Centre, Mount Vernon Hospital, Rickmansworth Road, Northwood, Middlesex HA6 2RN, UK
| | - C M L West
- Translational Radiobiology Group, Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Centre, Manchester M20 4BX, UK
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71
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Sauer E, Reinke AK, Courts C. Differentiation of five body fluids from forensic samples by expression analysis of four microRNAs using quantitative PCR. Forensic Sci Int Genet 2016; 22:89-99. [DOI: 10.1016/j.fsigen.2016.01.018] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/26/2016] [Indexed: 01/19/2023]
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72
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Samir M, Pessler F. Small Non-coding RNAs Associated with Viral Infectious Diseases of Veterinary Importance: Potential Clinical Applications. Front Vet Sci 2016; 3:22. [PMID: 27092305 PMCID: PMC4819147 DOI: 10.3389/fvets.2016.00022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 02/22/2016] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs) represent a class of small non-coding RNA (sncRNA) molecules that can regulate mRNAs by inducing their degradation or by blocking translation. Considering that miRNAs are ubiquitous, stable, and conserved across animal species, it seems feasible to exploit them for clinical applications. Unlike in human viral diseases, where some miRNA-based molecules have progressed to clinical application, in veterinary medicine, this concept is just starting to come into view. Clinically, miRNAs could represent powerful diagnostic tools to pinpoint animal viral diseases and/or prognostic tools to follow up disease progression or remission. Additionally, the possible consequences of miRNA dysregulation make them potential therapeutic targets and open the possibilities to use them as tools to generate viral disease-resistant livestock. This review presents an update of preclinical studies on using sncRNAs to combat viral diseases that affect pet and farm animals. Moreover, we discuss the possibilities and challenges of bringing these bench-based discoveries to the veterinary clinic.
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Affiliation(s)
- Mohamed Samir
- TWINCORE Center for Experimental and Clinical Infection Research, Hannover, Germany; Zoonoses Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Frank Pessler
- TWINCORE Center for Experimental and Clinical Infection Research, Hannover, Germany; Helmholtz Center for Infection Research, Braunschweig, Germany
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Rudnicki M, Beckers A, Neuwirt H, Vandesompele J. RNA expression signatures and posttranscriptional regulation in diabetic nephropathy. Nephrol Dial Transplant 2016. [PMID: 26209736 DOI: 10.1093/ndt/gfv079] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In the last decade, the integration of molecular approaches including transcriptome and miRNome analyses uncovered pathological mechanisms involved in the progression of diabetic nephropathy (DN). Using these techniques, molecular marker candidates [both messenger RNA (mRNA) and miRNA] have also been identified which may enable the characterization of patients at high risk for progression to end-stage renal disease. The results of such studies are urgently needed for a molecular definition of DN and for targeted treatment to improve patient care. The heterogeneity of kidney tissue and the minute amounts of RNA isolated from renal biopsies remain a challenge for omics-studies. Nevertheless, several studies have succeeded in the identification of RNA expression signatures in patients with diabetes and kidney disease. These studies show a reduced expression of growth factors such as VEGF and EGF, and an increased expression of matrix components and matrix-modulating enzymes, an activation of specific NF-κB modules, inflammatory pathways and the complement system. microRNAs are involved in the fine-tuning of mRNA abundance by binding to the 3' untranslated region of a target mRNA, which leads in most cases to translational repression or mRNA cleavage and a decrease in protein output. Here, we review the platforms used for miRNA expression profiling and ways to predict miRNA targets and functions. Several miRNAs have been shown to be involved in the pathogenesis of DN (e.g. miR-21, miR-192, miR-215, miR-216a, miR-29, let-7, miR-25, miR-93, etc.). Functional studies provide evidence that miRNAs are not only diagnostic tools but also represent potential therapeutic targets in DN.
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Affiliation(s)
- Michael Rudnicki
- Department of Internal Medicine IV - Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
| | | | - Hannes Neuwirt
- Department of Internal Medicine IV - Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
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Mustafa DAM, Sieuwerts AM, Smid M, de Weerd V, van der Weiden M, Meijer - van Gelder ME, Martens JWM, Foekens JA, Kros JM. A Method to Correlate mRNA Expression Datasets Obtained from Fresh Frozen and Formalin-Fixed, Paraffin-Embedded Tissue Samples: A Matter of Thresholds. PLoS One 2015; 10:e0144097. [PMID: 26716838 PMCID: PMC4696787 DOI: 10.1371/journal.pone.0144097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/12/2015] [Indexed: 11/19/2022] Open
Abstract
Background Gene expression profiling of tumors is a successful tool for the discovery of new cancer biomarkers and potential targets for the development of new therapeutic strategies. Reliable profiling is preferably performed on fresh frozen (FF) tissues in which the quality of nucleic acids is better preserved than in formalin-fixed paraffin-embedded (FFPE) material. However, since snap-freezing of biopsy materials is often not part of daily routine in pathology laboratories, one may have to rely on archival FFPE material. Procedures to retrieve the RNAs from FFPE materials have been developed and therefore, datasets obtained from FFPE and FF materials need to be made compatible to ensure reliable comparisons are possible. Aim To develop an efficient method to compare gene expression profiles obtained from FFPE and FF samples using the same platform. Methods Twenty-six FFPE-FF sample pairs of the same tumors representing various cancer types, and two FFPE-FF sample pairs of breast cancer cell lines, were included. Total RNA was extracted and gene expression profiling was carried out using Illumina’s Whole-Genome cDNA-mediated Annealing, Selection, extension and Ligation (WG-DASL) V3 arrays, enabling the simultaneous detection of 24,526 mRNA transcripts. A sample exclusion criterion was created based on the expression of 11 stably expressed reference genes. Pearson correlation at the probe level was calculated for paired FFPE-FF, and three cut-off values were chosen. Spearman correlation coefficients between the matched FFPE and FF samples were calculated for three probe lists with varying levels of significance and compared to the correlation based on all measured probes. Unsupervised hierarchical cluster analysis was performed to verify performance of the included probe lists to compare matched FPPE-FF samples. Results Twenty-seven FFPE-FF pairs passed the sample exclusion criterion. From the profiles of 27 FFPE and FF matched samples, the best correlating probes were identified for various levels of significance (Pearson P<0.01, n = 1,432; P<0.05, n = 2,530; and P<0.10, n = 3,351 probes). Unsupervised hierarchical clustering of the 27 pairs using the resulting probes yielded 25, 21, and 19 correctly clustered pairs, respectively, compared to 1 pair when all probes were used. Conclusion The proposed method enables comparison of gene expression profiles of FFPE and/or FF origin measured on the same platform.
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Affiliation(s)
- Dana A. M. Mustafa
- Dept. of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- * E-mail:
| | - Anieta M. Sieuwerts
- Dept. of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel Smid
- Dept. of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Vania de Weerd
- Dept. of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | | | - John W. M. Martens
- Dept. of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John A. Foekens
- Dept. of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Johan M. Kros
- Dept. of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
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Boisen MK, Dehlendorff C, Linnemann D, Schultz NA, Jensen BV, Høgdall EVS, Johansen JS. MicroRNA Expression in Formalin-fixed Paraffin-embedded Cancer Tissue: Identifying Reference MicroRNAs and Variability. BMC Cancer 2015; 15:1024. [PMID: 26714641 PMCID: PMC4696166 DOI: 10.1186/s12885-015-2030-2] [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: 07/20/2015] [Accepted: 12/17/2015] [Indexed: 01/06/2023] Open
Abstract
Background Archival formalin-fixed paraffin-embedded (FFPE) cancer tissue samples are a readily available resource for microRNA (miRNA) biomarker identification. No established standard for reference miRNAs in FFPE tissue exists. We sought to identify stable reference miRNAs for normalization of miRNA expression in FFPE tissue samples from patients with colorectal (CRC) and pancreatic (PC) cancer and to quantify the variability associated with sample age and fixation. Methods High-throughput miRNA profiling results from 203 CRC and 256 PC FFPE samples as well as from 37 paired frozen/FFPE samples from nine other CRC tumors (methodological samples) were used. Candidate reference miRNAs were identified by their correlation with global mean expression. The stability of reference genes was analyzed according to published methods. The association between sample age and global mean miRNA expression was tested using linear regression. Variability was described using correlation coefficients and linear mixed effects models. Normalization effects were determined by changes in standard deviation and by hierarchical clustering. Results We created lists of 20 miRNAs with the best correlation to global mean expression in each cancer type. Nine of these miRNAs were present in both lists, and miR-103a-3p was the most stable reference miRNA for both CRC and PC FFPE tissue. The optimal number of reference miRNAs was 4 in CRC and 10 in PC. Sample age had a significant effect on global miRNA expression in PC (50 % reduction over 20 years) but not in CRC. Formalin fixation for 2–6 days decreased miRNA expression 30–65 %. Normalization using global mean expression reduced variability for technical and biological replicates while normalization using the expression of the identified reference miRNAs reduced variability only for biological replicates. Normalization only had a minor impact on clustering results. Conclusions We identified suitable reference miRNAs for future miRNA expression experiments using CRC- and PC FFPE tissue samples. Formalin fixation decreased miRNA expression considerably, while the effect of increasing sample age was estimated to be negligible in a clinical setting. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-2030-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mogens Karsbøl Boisen
- Department of Oncology, Herlev and Gentofte Hospital, Herlev Ringvej 75, DK-2730, Herlev, Denmark.
| | - Christian Dehlendorff
- Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Copenhagen, Denmark.
| | - Dorte Linnemann
- Department of Pathology, Herlev and Gentofte Hospital, Herlev, Denmark.
| | | | - Benny Vittrup Jensen
- Department of Oncology, Herlev and Gentofte Hospital, Herlev Ringvej 75, DK-2730, Herlev, Denmark.
| | | | - Julia Sidenius Johansen
- Department of Oncology, Herlev and Gentofte Hospital, Herlev Ringvej 75, DK-2730, Herlev, Denmark. .,Department of Medicine, Herlev and Gentofte Hospital, Herlev, Denmark. .,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Warford A. In situ hybridisation: Technologies and their application to understanding disease. ACTA ACUST UNITED AC 2015; 50:37-48. [PMID: 26797255 DOI: 10.1016/j.proghi.2015.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 12/23/2022]
Abstract
In situ hybridisation (ISH) is unique amongst molecular analysis methods in providing for the precise microscopic localisation of genes, mRNA and microRNA in metaphase spreads, cell and tissue preparations. The method is well established as a tool to guide appropriate therapeutic intervention in breast, gastric and lung cancer. With the description of ultrasensitive ISH technologies for low copy mRNA demonstration and the relative ease by which microRNA can be visualised, the applications for research and diagnostic purposes is set to increase dramatically. In this review ISH is considered with emphasis on recent technological developments and surveyed for present and future applications in the context of the demonstration of genes, mRNA and microRNA in health and disease.
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Affiliation(s)
- Anthony Warford
- University of Westminster, 115 New Cavendish Street, London W1W 6UW, United Kingdom.
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Sim J, Ahn H, Abdul R, Kim H, Yi KJ, Chung YM, Chung MS, Paik SS, Song YS, Jang K. High MicroRNA-370 Expression Correlates with Tumor Progression and Poor Prognosis in Breast Cancer. J Breast Cancer 2015; 18:323-8. [PMID: 26770238 PMCID: PMC4705083 DOI: 10.4048/jbc.2015.18.4.323] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 09/18/2015] [Indexed: 12/12/2022] Open
Abstract
Purpose Deregulation of microRNA-370 (miR-370) has been reported in various cancers, in which it can act as either an oncogene or a tumor suppressor gene. However, the clinicopathologic significance of miR-370 expression in breast cancer has not been studied. Methods The expression of miR-370 was determined with quantitative real-time polymerase chain reaction in 60 formalin-fixed, paraffin-embedded primary breast cancer tissues. Additionally, the protein expression levels of previously known targets of miR-370, such as FOXM1, FOXO1, and FOXO3a, were detected using immunohistochemistry. Finally, we analyzed its correlation with target protein expression, clinicopathologic features, and clinical outcome. Results High levels of miR-370 expression correlated with lymph node metastasis (p=0.009), advanced stage (p=0.002), and frequent perineural invasion (p=0.042). Moreover, patients with high miR-370 expression had poor disease-free survival compared with the low-expression group. However, no correlation was observed between miR-370 and its target protein expression. Conclusion Our results indicate that upregulation of miR-370 in breast cancer is correlated with breast cancer progression and that it might be a potential biomarker for predicting clinical outcomes.
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Affiliation(s)
- Jongmin Sim
- Department of Pathology, Hanyang University College of Medicine, Seoul, Korea
| | - Hyein Ahn
- Department of Pathology, Hanyang University College of Medicine, Seoul, Korea
| | - Rehman Abdul
- Department of Pathology, Hanyang University College of Medicine, Seoul, Korea
| | - Hyunsung Kim
- Department of Pathology, Hanyang University College of Medicine, Seoul, Korea
| | - Ki-Jong Yi
- Department of Pathology, Hanyang University College of Medicine, Seoul, Korea
| | - Yu-Min Chung
- Department of Pathology, Hanyang University College of Medicine, Seoul, Korea
| | - Min Sung Chung
- Department of Surgery, Hanyang University College of Medicine, Seoul, Korea
| | - Seung Sam Paik
- Department of Pathology, Hanyang University College of Medicine, Seoul, Korea
| | - Young Soo Song
- Department of Pathology, Hanyang University College of Medicine, Seoul, Korea
| | - Kiseok Jang
- Department of Pathology, Hanyang University College of Medicine, Seoul, Korea
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Weiss S, Hanniford D, Hernando E, Osman I. Revisiting determinants of prognosis in cutaneous melanoma. Cancer 2015; 121:4108-23. [PMID: 26308244 PMCID: PMC4666819 DOI: 10.1002/cncr.29634] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/09/2015] [Accepted: 07/13/2015] [Indexed: 11/10/2022]
Abstract
The American Joint Committee on Cancer staging system for cutaneous melanoma is based on primary tumor thickness and the presence of ulceration, mitoses, lymph node spread, and distant metastases as determinants of prognosis. Although this cutaneous melanoma staging system has evolved over time to more accurately reflect patient prognosis, improvements are still needed, because current understanding of the particular factors (genetic mutation, expression alteration, host response, etc) that are critical for predicting patient outcomes is incomplete. Given the clinical and biologic heterogeneity of primary melanomas, new prognostic tools are needed to more precisely identify patients who are most likely to develop advanced disease. Such tools would affect clinical surveillance strategies and aid in patient selection for adjuvant therapy. The authors reviewed the literature on prognostic molecular and immunologic markers in primary cutaneous melanoma, their associations with clinicopathologic and survival outcomes, and their potential for incorporation into current staging models. Overall, the studies considered in this review did not define prognostic markers that could be readily incorporated into the current staging system. Therefore, efforts should be continued in these and other directions to maximize the likelihood of identifying clinically useful prognostic biomarkers for cutaneous melanoma.
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Affiliation(s)
- Sarah Weiss
- Department of Medical Oncology, New York University School of Medicine, New York, NY
- Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY
| | - Douglas Hanniford
- Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY
- Department of Pathology, New York University School of Medicine, New York, NY
| | - Eva Hernando
- Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY
- Department of Pathology, New York University School of Medicine, New York, NY
| | - Iman Osman
- Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY
- Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, NY
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Murphy MSQ, Casselman RC, Tayade C, Smith GN. Differential expression of plasma microRNA in preeclamptic patients at delivery and 1 year postpartum. Am J Obstet Gynecol 2015; 213:367.e1-9. [PMID: 25981845 DOI: 10.1016/j.ajog.2015.05.013] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 03/17/2015] [Accepted: 05/07/2015] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Preeclampsia (PE) is a hypertensive disorder of pregnancy characterized by widespread maternal endothelial dysfunction. Although clinical signs subside following delivery, long-term risks associated with PE include hypertension, stroke, and cardiovascular disease. MicroRNAs (miRNAs) are emerging as critical regulators of biological function, and while alterations to the miRNAome have been described in the context of pregnancy and PE, the postpartum implications of PE on miRNA expression is unknown. The goal of this study was to characterize circulating miRNA profiles at the time of delivery and at 1 year postpartum for women who did and did not develop PE. STUDY DESIGN Using a targeted reverse transcription polymerase chain reaction approach, selected miRNAs putatively involved in the pathophysiology of PE were examined in 17 normotensive control and 13 PE maternal plasma samples at the time of delivery and 1 year postpartum. Ingenuity Pathway Analysis was used to map putative messenger RNA targets of differentially expressed miRNA to global molecular networks based on gene function. RESULTS Significant increases (P < .05) in 7 miRNAs with antiangiogenic, inflammatory, and apoptotic functions (miR-98-5p, miR-222-3p, miR-210-3p, miR-155-5p, miR-296-3p, miR-181a-5p, miR-29b-3p) were evident in maternal plasma at the time of severe PE compared to time-matched controls. Plasma samples from individuals who developed mild PE exhibited no changes compared to control samples for the subset of miRNAs analyzed here. Differential expression of plasma miRNA at the time of delivery for women with PE were largely resolved at 1 year postpartum, and reduced expression of only miR-221-3p (P < .05) was evident. Network analysis of putative targets of differentially regulated miRNA identified 11 interacting networks with enrichment for proteins involved in cardiovascular disease, organ system development and function, and cell signaling and interaction. CONCLUSION The systemic effect of PE on maternal systems is evident in the circulating miRNAome with substantial alterations in miRNA expression in women who develop severe PE. In addition we provide novel evidence of disruption to miR-221 expression 1 year postpartum following a pregnancy complicated by PE compared to normotensive time-matched controls, which may allude to persistent inflammation in these women after delivery.
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Affiliation(s)
- Malia Su-Qin Murphy
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Richard Cary Casselman
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Chandrakant Tayade
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Graeme Neil Smith
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada; Department of Obstetrics and Gynecology, Kingston General Hospital, Kingston, Ontario, Canada.
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Begum S, Hayashi M, Ogawa T, Jabboure FJ, Brait M, Izumchenko E, Tabak S, Ahrendt SA, Westra WH, Koch W, Sidransky D, Hoque MO. An integrated genome-wide approach to discover deregulated microRNAs in non-small cell lung cancer: Clinical significance of miR-23b-3p deregulation. Sci Rep 2015; 5:13236. [PMID: 26314549 PMCID: PMC4551983 DOI: 10.1038/srep13236] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 05/18/2015] [Indexed: 02/06/2023] Open
Abstract
In spite of significant technical advances, genesis and progression of non-small cell lung cancer (NSCLC) remain poorly understood. We undertook an integrated genetic approach to discover novel microRNAs that were deregulated in NSCLCs. A total 119 primary NSCLCs with matched normal were analyzed for genome-wide copy number changes. We also tested a subset of matched samples by microRNA expression array, and integrated them to identify microRNAs positioned in allelic imbalance area. Our findings support that most of the identified deregulated microRNAs (miR-21, miR-23b, miR-31, miR-126, miR-150, and miR-205) were positioned in allelic imbalance areas. Among microRNAs tested in independent 114 NSCLCs, overexpression of miR-23b was revealed to be a significantly poor prognostic factor of recurrence free survival (HR = 2.40, P = 0.005, 95%CI: 1.32–4.29) and overall survival (HR = 2.35, P = 0.005, 95%CI: 1.30–4.19) in multivariable analysis. In addition, overexpression of miR-23b in H1838 cell line significantly increased cell proliferation, while inhibition of miR-23b in H1437 and H1944 cell lines significantly decreased cell doubling time. In summary, integration of genomic analysis and microRNA expression profiling could identify novel cancer-related microRNAs, and miR-23b could be a potential prognostic marker for early stage NSCLCs. Further biological studies of miR-23b are warranted for the potential development of targeted therapy.
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Affiliation(s)
- Shahnaz Begum
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, 21231 USA
| | - Masamichi Hayashi
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, Maryland, 21231 USA
| | - Takenori Ogawa
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, Maryland, 21231 USA
| | - Fayez J Jabboure
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, Maryland, 21231 USA
| | - Mariana Brait
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, Maryland, 21231 USA
| | - Evgeny Izumchenko
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, Maryland, 21231 USA
| | - Sarit Tabak
- Rosetta Genomics Ltd. 10 Plaut St., Rehovot, Israel, 76706
| | - Steven A Ahrendt
- Department of Surgery, Division of Surgical Oncology, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213 USA
| | - William H Westra
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, 21231 USA
| | - Wayne Koch
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, Maryland, 21231 USA
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, Maryland, 21231 USA
| | - Mohammad O Hoque
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, Maryland, 21231 USA.,Department of Urology, Johns Hopkins University, Baltimore, Maryland, 21231 USA.,Department of Oncology, Johns Hopkins University, Baltimore, Maryland, 21231 USA
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Hanniford D, Zhong J, Koetz L, Gaziel-Sovran A, Lackaye DJ, Shang S, Pavlick A, Shapiro R, Berman R, Darvishian F, Shao Y, Osman I, Hernando E. A miRNA-Based Signature Detected in Primary Melanoma Tissue Predicts Development of Brain Metastasis. Clin Cancer Res 2015; 21:4903-12. [PMID: 26089374 DOI: 10.1158/1078-0432.ccr-14-2566] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 06/04/2015] [Indexed: 01/07/2023]
Abstract
PURPOSE Brain metastasis is the major cause of mortality among patients with melanoma. A molecular prognostic test that can reliably stratify patients at initial melanoma diagnosis by risk of developing brain metastasis may inform the clinical management of these patients. EXPERIMENTAL DESIGN We performed a retrospective, cohort-based study analyzing genome-wide and targeted microRNA expression profiling of primary melanoma tumors of three patient cohorts (n = 92, 119, and 45) with extensive clinical follow-up. We used Cox regression analysis to establish a microRNA-based signature that improves the ability of the current clinicopathologic staging system to predict the development of brain metastasis. RESULTS Our analyses identified a 4-microRNA (miR-150-5p, miR-15b-5p, miR-16-5p, and miR-374b-3p) prognostic signature that, in combination with stage, distinguished primary melanomas that metastasized to the brain from nonrecurrent and non-brain metastatic primary tumors (training cohort: C-index = 81.4%, validation cohort: C-index = 67.4%, independent cohort: C-index = 76.9%). Corresponding Kaplan-Meier curves of high- versus low-risk patients displayed a clear separation in brain metastasis-free and overall survival (training: P < 0.001; P < 0.001, validation: P = 0.033; P = 0.007, independent: P = 0.021; P = 0.022, respectively). Finally, of the microRNA in the prognostic model, we found that the expression of a key lymphocyte miRNA, miR-150-5p, which is less abundant in primary melanomas metastatic to brain, correlated with presence of CD45(+) tumor-infiltrating lymphocytes. CONCLUSIONS A prognostic assay based on the described miRNA expression signature combined with the currently used staging criteria may improve accuracy of primary melanoma patient prognoses and aid clinical management of patients, including selection for adjuvant treatment or clinical trials of adjuvant therapies.
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Affiliation(s)
- Doug Hanniford
- Department of Pathology, NYU School of Medicine, New York, NYU School of Medicine. Interdisciplinary Melanoma Cooperative Group, NYU Perlmutter Cancer Institute, NYU School of Medicine, New York, New York
| | - Judy Zhong
- Interdisciplinary Melanoma Cooperative Group, NYU Perlmutter Cancer Institute, NYU School of Medicine, New York, New York. Department of Population Health (Biostatistics), NYU School of Medicine, New York, New York
| | - Lisa Koetz
- Department of Pathology, NYU School of Medicine, New York, NYU School of Medicine. Interdisciplinary Melanoma Cooperative Group, NYU Perlmutter Cancer Institute, NYU School of Medicine, New York, New York
| | - Avital Gaziel-Sovran
- Department of Pathology, NYU School of Medicine, New York, NYU School of Medicine. Interdisciplinary Melanoma Cooperative Group, NYU Perlmutter Cancer Institute, NYU School of Medicine, New York, New York
| | - Daniel J Lackaye
- Interdisciplinary Melanoma Cooperative Group, NYU Perlmutter Cancer Institute, NYU School of Medicine, New York, New York. Ronald O. Perelman Department of Dermatology, NYU School of Medicine, New York, New York
| | - Shulian Shang
- Interdisciplinary Melanoma Cooperative Group, NYU Perlmutter Cancer Institute, NYU School of Medicine, New York, New York. Department of Population Health (Biostatistics), NYU School of Medicine, New York, New York
| | - Anna Pavlick
- Interdisciplinary Melanoma Cooperative Group, NYU Perlmutter Cancer Institute, NYU School of Medicine, New York, New York. Ronald O. Perelman Department of Dermatology, NYU School of Medicine, New York, New York. Department of Medicine, NYU School of Medicine, New York, New York
| | - Richard Shapiro
- Interdisciplinary Melanoma Cooperative Group, NYU Perlmutter Cancer Institute, NYU School of Medicine, New York, New York. Department of Surgery, NYU School of Medicine, New York, New York
| | - Russell Berman
- Interdisciplinary Melanoma Cooperative Group, NYU Perlmutter Cancer Institute, NYU School of Medicine, New York, New York. Department of Surgery, NYU School of Medicine, New York, New York
| | - Farbod Darvishian
- Department of Pathology, NYU School of Medicine, New York, NYU School of Medicine. Interdisciplinary Melanoma Cooperative Group, NYU Perlmutter Cancer Institute, NYU School of Medicine, New York, New York
| | - Yongzhao Shao
- Interdisciplinary Melanoma Cooperative Group, NYU Perlmutter Cancer Institute, NYU School of Medicine, New York, New York. Department of Population Health (Biostatistics), NYU School of Medicine, New York, New York
| | - Iman Osman
- Interdisciplinary Melanoma Cooperative Group, NYU Perlmutter Cancer Institute, NYU School of Medicine, New York, New York. Ronald O. Perelman Department of Dermatology, NYU School of Medicine, New York, New York
| | - Eva Hernando
- Department of Pathology, NYU School of Medicine, New York, NYU School of Medicine. Interdisciplinary Melanoma Cooperative Group, NYU Perlmutter Cancer Institute, NYU School of Medicine, New York, New York.
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Vaca-Paniagua F, Alvarez-Gomez RM, Maldonado-Martínez HA, Pérez-Plasencia C, Fragoso-Ontiveros V, Lasa-Gonsebatt F, Herrera LA, Cantú D, Bargallo-Rocha E, Mohar A, Durand G, Forey N, Voegele C, Vallée M, Le Calvez-Kelm F, McKay J, Ardin M, Villar S, Zavadil J, Olivier M. Revealing the Molecular Portrait of Triple Negative Breast Tumors in an Understudied Population through Omics Analysis of Formalin-Fixed and Paraffin-Embedded Tissues. PLoS One 2015; 10:e0126762. [PMID: 25961742 PMCID: PMC4427337 DOI: 10.1371/journal.pone.0126762] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 04/07/2015] [Indexed: 12/27/2022] Open
Abstract
Triple negative breast cancer (TNBC), defined by the lack of expression of the estrogen receptor, progesterone receptor and human epidermal receptor 2, is an aggressive form of breast cancer that is more prevalent in certain populations, in particular in low- and middle-income regions. The detailed molecular features of TNBC in these regions remain unexplored as samples are mostly accessible as formalin-fixed paraffin embedded (FFPE) archived tissues, a challenging material for advanced genomic and transcriptomic studies. Using dedicated reagents and analysis pipelines, we performed whole exome sequencing and miRNA and mRNA profiling of 12 FFPE tumor tissues collected from pathological archives in Mexico. Sequencing analyses of the tumor tissues and their blood pairs identified TP53 and RB1 genes as the most frequently mutated genes, with a somatic mutation load of 1.7 mutations/exome Mb on average. Transcriptional analyses revealed an overexpression of growth-promoting signals (EGFR, PDGFR, VEGF, PIK3CA, FOXM1), a repression of cell cycle control pathways (TP53, RB1), a deregulation of DNA-repair pathways, and alterations in epigenetic modifiers through miRNA:mRNA network de-regulation. The molecular programs identified were typical of those described in basal-like tumors in other populations. This work demonstrates the feasibility of using archived clinical samples for advanced integrated genomics analyses. It thus opens up opportunities for investigating molecular features of tumors from regions where only FFPE tissues are available, allowing retrospective studies on the search for treatment strategies or on the exploration of the geographic diversity of breast cancer.
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Affiliation(s)
- Felipe Vaca-Paniagua
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, México D.F., México
- Unidad de Biomedicina, FES-Iztacala, Universidad Nacional Autónoma de México (UNAM), México D.F., México
| | - Rosa María Alvarez-Gomez
- Unidad de Genómica y Secuenciación Masiva (UGESEM), Instituto Nacional de Cancerología, México D.F., México
| | | | - Carlos Pérez-Plasencia
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, México D.F., México
- Unidad de Biomedicina, FES-Iztacala, Universidad Nacional Autónoma de México (UNAM), México D.F., México
- Unidad de Genómica y Secuenciación Masiva (UGESEM), Instituto Nacional de Cancerología, México D.F., México
| | - Veronica Fragoso-Ontiveros
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, México D.F., México
- Unidad de Genómica y Secuenciación Masiva (UGESEM), Instituto Nacional de Cancerología, México D.F., México
| | | | - Luis Alonso Herrera
- Unidad de Investigaciones Biomédicas en Cáncer, Instituto Nacional de Cancerología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), México D.F., México
| | - David Cantú
- Unidad de Investigaciones Biomédicas en Cáncer, Instituto Nacional de Cancerología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), México D.F., México
| | - Enrique Bargallo-Rocha
- Departamento de Tumores Mamarios, Instituto Nacional de Cancerología, México D.F., México
| | - Alejandro Mohar
- Departamento de Epidemiología, Instituto Nacional de Cancerología, México D.F., México
| | - Geoffroy Durand
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Nathalie Forey
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Catherine Voegele
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Maxime Vallée
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Florence Le Calvez-Kelm
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - James McKay
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Maude Ardin
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
| | - Stéphanie Villar
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
| | - Jiri Zavadil
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
| | - Magali Olivier
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
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83
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Gámez-Pozo A, Berges-Soria J, Arevalillo JM, Nanni P, López-Vacas R, Navarro H, Grossmann J, Castaneda CA, Main P, Díaz-Almirón M, Espinosa E, Ciruelos E, Fresno Vara JÁ. Combined Label-Free Quantitative Proteomics and microRNA Expression Analysis of Breast Cancer Unravel Molecular Differences with Clinical Implications. Cancer Res 2015; 75:2243-53. [PMID: 25883093 DOI: 10.1158/0008-5472.can-14-1937] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 03/12/2015] [Indexed: 11/16/2022]
Abstract
Better knowledge of the biology of breast cancer has allowed the use of new targeted therapies, leading to improved outcome. High-throughput technologies allow deepening into the molecular architecture of breast cancer, integrating different levels of information, which is important if it helps in making clinical decisions. microRNA (miRNA) and protein expression profiles were obtained from 71 estrogen receptor-positive (ER(+)) and 25 triple-negative breast cancer (TNBC) samples. RNA and proteins obtained from formalin-fixed, paraffin-embedded tumors were analyzed by RT-qPCR and LC/MS-MS, respectively. We applied probabilistic graphical models representing complex biologic systems as networks, confirming that ER(+) and TNBC subtypes are distinct biologic entities. The integration of miRNA and protein expression data unravels molecular processes that can be related to differences in the genesis and clinical evolution of these types of breast cancer. Our results confirm that TNBC has a unique metabolic profile that may be exploited for therapeutic intervention.
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Affiliation(s)
- Angelo Gámez-Pozo
- Molecular Oncology and Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Julia Berges-Soria
- Molecular Oncology and Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Jorge M Arevalillo
- Department of Statistics, Operational Research and Numerical Analysis, University Nacional Educacion a Distancia (UNED), Madrid, Spain
| | - Paolo Nanni
- Functional Genomics Centre Zurich, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Rocío López-Vacas
- Molecular Oncology and Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Hilario Navarro
- Department of Statistics, Operational Research and Numerical Analysis, University Nacional Educacion a Distancia (UNED), Madrid, Spain
| | - Jonas Grossmann
- Functional Genomics Centre Zurich, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Carlos A Castaneda
- Departamento de Investigación, Instituto Nacional de Enfermedades Neoplásicas, Lima, Surquillo-Lima, Peru
| | - Paloma Main
- Department of Statistics and Operations Research, Faculty of Mathematics, Complutense University of Madrid, Madrid, Spain
| | - Mariana Díaz-Almirón
- Biostatistics Unit, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Enrique Espinosa
- Medical Oncology Service, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Eva Ciruelos
- Medical Oncology Service, Instituto de Investigación Hospital Universitario Doce de Octubre-i+12, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology and Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain.
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84
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Slaby O, Srovnal J, Radova L, Gregar J, Juracek J, Luzna P, Svoboda M, Hajduch M, Ehrmann J. Dynamic changes in microRNA expression profiles reflect progression of Barrett's esophagus to esophageal adenocarcinoma. Carcinogenesis 2015; 36:521-7. [PMID: 25784377 DOI: 10.1093/carcin/bgv023] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 03/09/2015] [Indexed: 12/22/2022] Open
Abstract
Esophageal adenocarcinoma (EAC) is highly aggressive malignancy that frequently develops from Barrett's esophagus (BE), a premalignant pathologic change occurring in the lower end of the esophagus. MicroRNAs (miRNAs) are small, non-coding RNAs that function as posttranscriptional regulators of gene expression and were repeatedly proved to play key roles in pathogenesis of BE as well as EAC. In our study, we used Affymetrix GeneChip miRNA arrays to obtain miRNA expression profiles in total of 119 tissue samples [24 normal esophageal mucosa (EM), 60 BE and 35 EAC]. We identified a number of miRNAs, that showed altered expression progressively in sequence EM, BE and EAC, including for instance miR-21, miR-25, miR-194 and miR-196a with increasing levels (P < 0.0015) and miR-203, miR-205, miR-210 and miR-378 with decreasing levels (P < 0.0001). The subsequent analysis revealed four diagnostic miRNA signatures enabling to distinguish EM and BE [12 miRNAs, area under curve (AUC) = 0.971], EM and EAC (13 miRNAs, AUC = 1.0), BE without and BE with dysplasia (21 miRNAs, AUC = 0.856) and BE without dysplastic changes and BE with dysplasia together with EAC (2 miRNAs, AUC = 0.886). We suggest that miRNA expression profiling expands current knowledge in molecular pathology of Barrett's-based carcinogenesis and enables identification of molecular biomarkers for early detection of BE dysplasia and progression to EAC.
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Affiliation(s)
- Ondrej Slaby
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Masaryk University, Faculty of Medicine, 656 53 Brno, Czech Republic, Central European Institute of Technology, Molecular Oncology II, Masaryk University, 625 00 Brno, Czech Republic,
| | - Josef Srovnal
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, 779 00 Olomouc, Czech Republic
| | - Lenka Radova
- Central European Institute of Technology, Molecular Oncology II, Masaryk University, 625 00 Brno, Czech Republic
| | - Jan Gregar
- Department of Internal Medicine II - Gastroenterology and Hepatology, University Hospital, 779 00 Olomouc, Czech Republic and
| | - Jaroslav Juracek
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Masaryk University, Faculty of Medicine, 656 53 Brno, Czech Republic, Central European Institute of Technology, Molecular Oncology II, Masaryk University, 625 00 Brno, Czech Republic
| | - Pavla Luzna
- Department of Histology and Embryology, Faculty of Medicine and Dentistry, Palacky University and University Hospital, 779 00 Olomouc, Czech Republic
| | - Marek Svoboda
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Masaryk University, Faculty of Medicine, 656 53 Brno, Czech Republic, Central European Institute of Technology, Molecular Oncology II, Masaryk University, 625 00 Brno, Czech Republic
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, 779 00 Olomouc, Czech Republic
| | - Jiri Ehrmann
- Department of Histology and Embryology, Faculty of Medicine and Dentistry, Palacky University and University Hospital, 779 00 Olomouc, Czech Republic
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85
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Korpela E, Vesprini D, Liu SK. MicroRNA in radiotherapy: miRage or miRador? Br J Cancer 2015; 112:777-82. [PMID: 25611301 PMCID: PMC4453960 DOI: 10.1038/bjc.2015.6] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 12/17/2014] [Accepted: 12/19/2014] [Indexed: 02/07/2023] Open
Abstract
At least half of all cancer patients will receive radiation therapy. Tumour radioresistance, or the failure to control certain tumours with this treatment, can result in locoregional recurrence; thus there is great interest in understanding the underlying biology and developing strategies to overcome this problem. The expanding investigation of microRNA in cancer suggests that these regulatory factors can influence the DNA damage response, the microenvironment and survival pathways, among other processes, and thereby may affect tumour radioresistance. As microRNA are readily detectable in tumours and biofluids, they hold promise as predictive biomarkers for therapy response and prognosis. This review highlights the current insights on the major ways that microRNA may contribute to tumour radiation response and whether their levels reflect treatment success. We conclude by applying the potential framework of future roles of miR in personalised radiotherapy using prostate cancer clinical management as an example.
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Affiliation(s)
- E Korpela
- Biological Sciences, Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, Ontario, Canada M4N 3M5
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - D Vesprini
- Biological Sciences, Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, Ontario, Canada M4N 3M5
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada M5T 1P5
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, 2075 Bayview Avenue, Toronto, Ontario, Canada M4N 3M5
| | - S K Liu
- Biological Sciences, Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, Ontario, Canada M4N 3M5
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada M5T 1P5
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, 2075 Bayview Avenue, Toronto, Ontario, Canada M4N 3M5
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86
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Hayes J, Thygesen H, Droop A, Hughes TA, Westhead D, Lawler SE, Wurdak H, Short SC. Prognostic microRNAs in high-grade glioma reveal a link to oligodendrocyte precursor differentiation. Oncoscience 2014; 2:252-62. [PMID: 25897422 PMCID: PMC4394131 DOI: 10.18632/oncoscience.112] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 12/22/2014] [Indexed: 12/31/2022] Open
Abstract
MicroRNA expression can be exploited to define tumor prognosis and stratification for precision medicine. It remains unclear whether prognostic microRNA signatures are exclusively tumor grade and/or molecular subtype-specific, or whether common signatures of aggressive clinical behavior can be identified. Here, we defined microRNAs that are associated with good and poor prognosis in grade III and IV gliomas using data from The Cancer Genome Atlas. Pathway analysis of microRNA targets that are differentially expressed in good and poor prognosis glioma identified a link to oligodendrocyte development. Notably, a microRNA expression profile that is characteristic of a specific oligodendrocyte precursor cell type (OP1) correlates with microRNA expression from 597 of these tumors and is consistently associated with poor patient outcome in grade III and IV gliomas. Our study reveals grade-independent and subtype-independent prognostic molecular signatures in high-grade glioma and provides a framework for investigating the mechanisms of brain tumor aggressiveness.
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Affiliation(s)
- Josie Hayes
- Leeds Institute of Cancer and Pathology, University of Leeds, St James's University Hospital, Leeds, UK
| | - Helene Thygesen
- Leeds Institute of Cancer and Pathology, University of Leeds, St James's University Hospital, Leeds, UK
| | - Alastair Droop
- Leeds Institute of Cancer and Pathology, University of Leeds, St James's University Hospital, Leeds, UK
| | - Thomas A Hughes
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, St James's University Hospital, Leeds, UK
| | - David Westhead
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences and Institute of Membrane and Systems Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Sean E Lawler
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Heiko Wurdak
- Leeds Institute of Cancer and Pathology, University of Leeds, St James's University Hospital, Leeds, UK
| | - Susan C Short
- Leeds Institute of Cancer and Pathology, University of Leeds, St James's University Hospital, Leeds, UK
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87
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Jurcevic S, Olsson B, Klinga-Levan K. MicroRNA expression in human endometrial adenocarcinoma. Cancer Cell Int 2014; 14:88. [PMID: 25419182 PMCID: PMC4240838 DOI: 10.1186/s12935-014-0088-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 08/26/2014] [Indexed: 11/21/2022] Open
Abstract
Background MicroRNAs are small non-coding RNAs that play crucial roles in the pathogenesis of different cancer types. The aim of this study was to identify miRNAs that are differentially expressed in endometrial adenocarcinoma compared to healthy endometrium. These miRNAs can potentially be used to develop a panel for classification and prognosis in order to better predict the progression of the disease and facilitate the choice of treatment strategy. Methods Formalin fixed paraffin embedded endometrial tissue samples were collected from the Örebro university hospital. QPCR was used to quantify the expression levels of 742 miRNAs in 30 malignant and 20 normal endometrium samples. After normalization of the qPCR data, miRNAs differing significantly in expression between normal and cancer samples were identified, and hierarchical clustering analysis was used to identify groups of miRNAs with coordinated expression profiles. Results In comparisons between endometrial adenocarcinoma and normal endometrium samples 138 miRNAs were found to be significantly differentially expressed (p < 0.001) among which 112 miRNAs have not been previous reported for endometrial adenocarcinoma. Conclusion Our study shows that several miRNAs are differentially expressed in endometrial adenocarcinoma. These identified miRNA hold great potential as target for classification and prognosis of this disease. Further analysis of the differentially expressed miRNA and their target genes will help to derive new biomarkers that can be used for classification and prognosis of endometrial adenocarcinoma. Electronic supplementary material The online version of this article (doi:10.1186/s12935-014-0088-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sanja Jurcevic
- Systems Biology Research Centre - Tumor Biology, Bio Science, University of Skövde, SE541 28, Skövde, Sweden
| | - Björn Olsson
- Systems Biology Research Centre - Bioinformatics, Bio Science, University of Skövde, Skövde, Sweden
| | - Karin Klinga-Levan
- Systems Biology Research Centre - Tumor Biology, Bio Science, University of Skövde, SE541 28, Skövde, Sweden
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88
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Kim TH, Song JY, Park H, Jeong JY, Kwon AY, Heo JH, Kang H, Kim G, An HJ. miR-145, targeting high-mobility group A2, is a powerful predictor of patient outcome in ovarian carcinoma. Cancer Lett 2014; 356:937-45. [PMID: 25444913 DOI: 10.1016/j.canlet.2014.11.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 11/04/2014] [Accepted: 11/05/2014] [Indexed: 11/25/2022]
Abstract
MicroRNA-145 (miR-145) expression is downregulated in several human cancers, but its clinical and functional relevance to ovarian carcinoma has not yet been elucidated. This study addressed the hypothesis that miR-145 serves as a prognostic biomarker and a tumor suppressor that regulates the expression of high-mobility group A2 (HMGA2) oncoprotein in ovarian cancer. Here, we found that low miR-145 expression and HMGA2 overexpression determined by qRT-PCR and immunohistochemistry significantly correlated with advanced stage, lymph node involvement, and distant metastasis in 74 ovarian carcinomas. Low miR-145 expression significantly correlated with tumor recurrence and worse overall survival (HR=8.62, P = 0.039). Transfection of pre-miR-145 resulted in reduced cell growth and migration, and increased apoptosis of ovarian cancer cells by TUNEL, colony forming, and cell migration assays. MiR-145 was found to directly target HMGA2 by luciferase assay and Western blotting. Our findings suggest that miR-145 functions as a tumor suppressor in ovarian cancer and directly targets HMGA2 oncoprotein. Low miR-145 and high HMGA2 expressions are potential biomarkers of poor prognosis of ovarian carcinoma and miR-145 is the more powerful predictor of patient outcome.
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Affiliation(s)
- Tae Hoen Kim
- Department of Pathology, CHA Bundang Medical Center, CHA University, 59 Yatap-rho, Bundang-gu, Seongnam-si, Gyeonggi-do 463-712, Republic of Korea; Institute for Clinical Research, CHA Bundang Medical Center, CHA University, 59 Yatap-rho, Bundang-gu, Seongnam-si, Gyeonggi-do 463-712, Republic of Korea
| | - Ji-Ye Song
- Institute for Clinical Research, CHA Bundang Medical Center, CHA University, 59 Yatap-rho, Bundang-gu, Seongnam-si, Gyeonggi-do 463-712, Republic of Korea
| | - Hyun Park
- Institute for Clinical Research, CHA Bundang Medical Center, CHA University, 59 Yatap-rho, Bundang-gu, Seongnam-si, Gyeonggi-do 463-712, Republic of Korea; Department of Gynecologic Oncology, CHA Bundang Medical Center, CHA University, 59 Yatap-rho, Bundang-gu, Seongnam-si, Gyeonggi-do 463-712, Republic of Korea
| | - Ju-Yeon Jeong
- Institute for Clinical Research, CHA Bundang Medical Center, CHA University, 59 Yatap-rho, Bundang-gu, Seongnam-si, Gyeonggi-do 463-712, Republic of Korea
| | - A-Young Kwon
- Department of Pathology, CHA Bundang Medical Center, CHA University, 59 Yatap-rho, Bundang-gu, Seongnam-si, Gyeonggi-do 463-712, Republic of Korea
| | - Jin Hyung Heo
- Department of Pathology, CHA Bundang Medical Center, CHA University, 59 Yatap-rho, Bundang-gu, Seongnam-si, Gyeonggi-do 463-712, Republic of Korea
| | - Haeyoun Kang
- Department of Pathology, CHA Bundang Medical Center, CHA University, 59 Yatap-rho, Bundang-gu, Seongnam-si, Gyeonggi-do 463-712, Republic of Korea
| | - Gwangil Kim
- Department of Pathology, CHA Bundang Medical Center, CHA University, 59 Yatap-rho, Bundang-gu, Seongnam-si, Gyeonggi-do 463-712, Republic of Korea; Institute for Clinical Research, CHA Bundang Medical Center, CHA University, 59 Yatap-rho, Bundang-gu, Seongnam-si, Gyeonggi-do 463-712, Republic of Korea
| | - Hee Jung An
- Department of Pathology, CHA Bundang Medical Center, CHA University, 59 Yatap-rho, Bundang-gu, Seongnam-si, Gyeonggi-do 463-712, Republic of Korea; Institute for Clinical Research, CHA Bundang Medical Center, CHA University, 59 Yatap-rho, Bundang-gu, Seongnam-si, Gyeonggi-do 463-712, Republic of Korea.
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89
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Sana J, Radova L, Lakomy R, Kren L, Fadrus P, Smrcka M, Besse A, Nekvindova J, Hermanova M, Jancalek R, Svoboda M, Hajduch M, Slampa P, Vyzula R, Slaby O. Risk Score based on microRNA expression signature is independent prognostic classifier of glioblastoma patients. Carcinogenesis 2014; 35:2756-62. [PMID: 25322872 DOI: 10.1093/carcin/bgu212] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most malignant primary brain tumor. The prognosis of GBM patients varies considerably and the histopathological examination is not sufficient for individual risk estimation. MicroRNAs (miRNAs) are small, non-coding RNAs that function as post-transcriptional regulators of gene expression and were repeatedly proved to play important roles in pathogenesis of GBM. In our study, we performed global miRNA expression profiling of 58 glioblastoma tissue samples obtained during surgical resections and 10 non-tumor brain tissues. The subsequent analysis revealed 28 significantly deregulated miRNAs in GBM tissue, which were able to precisely classify all examined samples. Correlation with clinical data led to identification of six-miRNA signature significantly associated with progression free survival [hazard ratio (HR) 1.98, 95% confidence interval (CI) 1.33-2.94, P < 0.001] and overa+ll survival (HR 2.86, 95% CI 1.91-4.29, P < 0.001). O(6)-methylguanine-DNA methyltransferase methylation status was evaluated as reference method and Risk Score based on six-miRNA signature indicated significant superiority in prediction of clinical outcome in GBM patients. Multivariate Cox analysis indicated that the Risk Score based on six-miRNA signature is an independent prognostic classifier of GBM patients. We suggest that the Risk Score presents promising prognostic algorithm with potential for individualized treatment decisions in clinical management of GBM patients.
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Affiliation(s)
- Jiri Sana
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno 65653, Czech Republic, Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic, Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
| | - Lenka Radova
- Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
| | - Radek Lakomy
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno 65653, Czech Republic, Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic
| | - Leos Kren
- Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic, Department of Pathology, University Hospital Brno, Brno 62500, Czech Republic
| | - Pavel Fadrus
- Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic, Department of Neurosurgery, University Hospital Brno, Brno 62500, Czech Republic
| | - Martin Smrcka
- Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic, Department of Neurosurgery, University Hospital Brno, Brno 62500, Czech Republic
| | - Andrej Besse
- Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
| | - Jana Nekvindova
- Institute of Clinical Biochemistry and Diagnostics, Faculty of Medicine and Faculty Hospital in Hradec Kralove, Charles University, Hradec Kralove 50005, Czech Republic
| | - Marketa Hermanova
- Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic, First Department of Pathological Anatomy, St. Anne's University Hospital, Brno 65691, Czech Republic
| | - Radim Jancalek
- Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic, Department of Neurosurgery, St. Anne's University Hospital, Brno 65691, Czech Republic
| | - Marek Svoboda
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno 65653, Czech Republic, Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc 77900, Czech Republic and
| | - Pavel Slampa
- Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic, Department of Radiation Oncology, Masaryk Memorial Cancer Institute, Brno 65653, Czech Republic
| | - Rostislav Vyzula
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno 65653, Czech Republic, Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic
| | - Ondrej Slaby
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno 65653, Czech Republic, Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic, Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic,
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90
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Marino ALF, Evangelista AF, Vieira RAC, Macedo T, Kerr LM, Abrahão-Machado LF, Longatto-Filho A, Silveira HCS, Marques MMC. MicroRNA expression as risk biomarker of breast cancer metastasis: a pilot retrospective case-cohort study. BMC Cancer 2014; 14:739. [PMID: 25277099 PMCID: PMC4195914 DOI: 10.1186/1471-2407-14-739] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 09/26/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small, non-coding RNA molecules involved in post-transcriptional gene regulation and have recently been shown to play a role in cancer metastasis. In solid tumors, especially breast cancer, alterations in miRNA expression contribute to cancer pathogenesis, including metastasis. Considering the emerging role of miRNAs in metastasis, the identification of predictive markers is necessary to further the understanding of stage-specific breast cancer development. This is a retrospective analysis that aimed to identify molecular biomarkers related to distant breast cancer metastasis development. METHODS A retrospective case cohort study was performed in 64 breast cancer patients treated during the period from 1998-2001. The case group (n = 29) consisted of patients with a poor prognosis who presented with breast cancer recurrence or metastasis during follow up. The control group (n = 35) consisted of patients with a good prognosis who did not develop breast cancer recurrence or metastasis. These patient groups were stratified according to TNM clinical stage (CS) I, II and III, and the main clinical features of the patients were homogeneous. MicroRNA profiling was performed and biomarkers related to metastatic were identified independent of clinical stage. Finally, a hazard risk analysis of these biomarkers was performed to evaluate their relation to metastatic potential. RESULTS MiRNA expression profiling identified several miRNAs that were both specific and shared across all clinical stages (p ≤ 0.05). Among these, we identified miRNAs previously associated with cell motility (let-7 family) and distant metastasis (hsa-miR-21). In addition, hsa-miR-494 and hsa-miR-21 were deregulated in metastatic cases of CSI and CSII. Furthermore, metastatic miRNAs shared across all clinical stages did not present high sensitivity and specificity when compared to specific-CS miRNAs. Between them, hsa-miR-183 was the most significative of CSII, which miRNAs combination for CSII (hsa-miR-494, hsa-miR-183 and hsa-miR-21) was significant and were a more effective risk marker compared to the single miRNAs. CONCLUSIONS Women with metastatic breast cancer, especially CSII, presented up-regulated levels of miR-183, miR-494 and miR-21, which were associated with a poor prognosis. These miRNAs therefore represent new risk biomarkers of breast cancer metastasis and may be useful for future targeted therapies.
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Affiliation(s)
- Augusto LF Marino
- />Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, 14784-400 Brazil
| | - Adriane F Evangelista
- />Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, 14784-400 Brazil
| | - René AC Vieira
- />Department of Mastology and Breast Reconstruction, Barretos Cancer Hospital, Barretos, 14784-400 SP Brazil
| | - Taciane Macedo
- />Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, 14784-400 Brazil
| | - Ligia M Kerr
- />Department of Pathology, Barretos Cancer Hospital, CEP: 14784-400 Barretos, SP Brazil
| | | | - Adhemar Longatto-Filho
- />Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, 14784-400 Brazil
- />Laboratory of Medical Investigation (LIM) 14, Department of Pathology, University of São Paulo School of Medicine, São Paulo, SP 1246903 Brazil
- />Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4704-553 Braga, Portugal
- />ICVS/3B’s-PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Henrique CS Silveira
- />Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, 14784-400 Brazil
| | - Marcia MC Marques
- />Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, 14784-400 Brazil
- />Barretos School of Health Sciences - FACISB, Barretos, São Paulo Brazil
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91
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Park H, Lee MJ, Jeong JY, Choi MC, Jung SG, Joo WD, Lee C, An HJ. Dysregulated microRNA expression in adenocarcinoma of the uterine cervix: clinical impact of miR-363-3p. Gynecol Oncol 2014; 135:565-72. [PMID: 25230213 DOI: 10.1016/j.ygyno.2014.09.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/03/2014] [Accepted: 09/09/2014] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Adenocarcinoma (ACA) of the uterine cervix is increasing in incidence and currently accounts for approximately 20% of all cervical malignancies. MicroRNAs (miRNAs) have been investigated as potential biomarkers of cervical cancer; however, their role in ACA remains unknown. Here, we characterized miRNA expression profiles and investigated miRNAs as diagnostic and prognostic factors in ACA. METHODS Evaluation of genome-wide miRNA expression profiles in ACA by microarray led to the identification of ten candidate miRNAs, whose expression patterns were validated by qRT-PCR in 45 ACA, 10 normal control, and 15 squamous cell carcinoma samples. The association between miRNA expression and prognosis was analyzed in patients with ACA. RESULTS Microarray analysis identified 86 miRNAs that were dysregulated more than 2.0-fold (p<0.05) in ACA relative to normal tissues of the uterine cervix. Five most over- and underexpressed miRNAs were selected respectively and their expression patterns were confirmed in the validation set. MiR-135b, miR-192, and miR194 were overexpressed in ACA, and miR-363-3p, miR-195 and miR-199b were significantly associated with conventional prognostic factors. Overexpression of miR-363-3p by more than 2.5-fold relative to the normal control was a strong predictor of favorable prognosis (hazard ratio, 0.1; 95% confidence interval, 0.009-0.779) after adjusting for confounders. CONCLUSIONS MiR-135b, miR-192, and miR-194 are altered in uterine cervical ACA, and miR-363-3p is an independent favorable prognostic factor in ACA. These miRNAs could be of value as biomarkers for the diagnosis and prognosis of ACA.
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Affiliation(s)
- Hyun Park
- Department of Gynecological Oncology, CHA University, Sungnam, Republic of Korea
| | - Mi-jung Lee
- Institute for Clinical Research, CHA University, Sungnam, Republic of Korea
| | - Ju-yeon Jeong
- Institute for Clinical Research, CHA University, Sungnam, Republic of Korea
| | - Min Chul Choi
- Department of Gynecological Oncology, CHA University, Sungnam, Republic of Korea
| | - Sang Geun Jung
- Department of Gynecological Oncology, CHA University, Sungnam, Republic of Korea
| | - Won Duk Joo
- Department of Gynecological Oncology, CHA University, Sungnam, Republic of Korea
| | - Chan Lee
- Department of Gynecological Oncology, CHA University, Sungnam, Republic of Korea
| | - Hee Jung An
- Institute for Clinical Research, CHA University, Sungnam, Republic of Korea; Department of Pathology, CHA University, Sungnam, Republic of Korea
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92
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Development and validation of a microRNA based diagnostic assay for primary tumor site classification of liver core biopsies. Mol Oncol 2014; 9:68-77. [PMID: 25131495 DOI: 10.1016/j.molonc.2014.07.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/11/2014] [Accepted: 07/21/2014] [Indexed: 11/20/2022] Open
Abstract
Identification of the primary tumor site in patients with metastatic cancer is clinically important, but remains a challenge. Hence, efforts have been made towards establishing new diagnostic tools. Molecular profiling is a promising diagnostic approach, but tissue heterogeneity and inadequacy may negatively affect the accuracy and usability of molecular classifiers. We have developed and validated a microRNA-based classifier, which predicts the primary tumor site of liver biopsies, containing a limited number of tumor cells. Concurrently we explored the influence of surrounding normal tissue on classification. MicroRNA profiling was performed using quantitative Real-Time PCR on formalin-fixed paraffin-embedded samples. 278 primary tumors and liver metastases, representing nine primary tumor classes, as well as normal liver samples were used as a training set. A statistical model was applied to adjust for normal liver tissue contamination. Performance was estimated by cross-validation, followed by independent validation on 55 liver core biopsies with a tumor content as low as 10%. A microRNA classifier developed, using the statistical contamination model, showed an overall classification accuracy of 74.5% upon independent validation. Two-thirds of the samples were classified with high-confidence, with an accuracy of 92% on high-confidence predictions. A classifier trained without adjusting for liver tissue contamination, showed a classification accuracy of 38.2%. Our results indicate that surrounding normal tissue from the biopsy site may critically influence molecular classification. A significant improvement in classification accuracy was obtained when the influence of normal tissue was limited by application of a statistical contamination model.
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93
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Yang H, Yu J, Wang L, Ding DI, Zhang L, Chu C, Chen Q, Xu Z, Zou Q, Liu X. miR-320a is an independent prognostic biomarker for invasive breast cancer. Oncol Lett 2014; 8:1043-1050. [PMID: 25120655 PMCID: PMC4114662 DOI: 10.3892/ol.2014.2298] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 06/12/2014] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is one of the most common malignancies worldwide and is the second leading cause of cancer-related mortality among females. miRNAs are a class of small noncoding RNAs that are aberrantly expressed in human cancers. Due to their small size and stability, miRNAs have the potential to be efficacious clinical targets. MicroRNA-320a (miR-320a) has been shown to be dysregulated in multiple malignancies. In the present study, the expression levels of miR-320a were investigated in 15 paraffin-embedded in situ breast carcinoma and 130 invasive breast cancer tissues, and the prognostic value for breast cancer patients was assessed. Chromogenic in situ hybridization revealed that 60/130 (46%) invasive breast cancer tissues exhibited high expression levels of miR-320a (staining index score of ≥4). Furthermore, miR-320a staining was found to significantly correlate with tumor size (P=0.046), clinical stage (P<0.001), lymph node metastasis (P<0.001) and distant metastasis (P=0.006). In addition, patients exhibiting low miR-320a expression levels had shorter overall survival times (P<0.001). Univariate and multivariate analyses revealed that miR-320a was an independent prognostic biomarker for invasive breast cancer (hazard ratio, 0.221; 95% confidence interval, 0.050–0.979; P=0.047). Receiver operator characteristic curves revealed that the prognostic value of miR-320a was enhanced when compared with the widely used prognostic biomarkers (estrogen receptor, progesterone receptor and human epidermal growth factor-2) in invasive breast cancer. The results of the present study suggest that miR-320a presents a potential biomarker for the prognosis of invasive breast cancer, and dysregulation of miR-320a may be involved in invasive breast cancer progression.
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Affiliation(s)
- Haiping Yang
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Juan Yu
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Lei Wang
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - DI Ding
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Lei Zhang
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Chengyu Chu
- Department of Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Qi Chen
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Zude Xu
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Qiang Zou
- Department of Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Xiuping Liu
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R. China ; Department of Pathology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, P.R. China
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94
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Tanic M, Yanowski K, Gómez-López G, Rodriguez-Pinilla MS, Marquez-Rodas I, Osorio A, Pisano DG, Martinez-Delgado B, Benítez J. MicroRNA expression signatures for the prediction of BRCA1/2 mutation-associated hereditary breast cancer in paraffin-embedded formalin-fixed breast tumors. Int J Cancer 2014; 136:593-602. [PMID: 24917463 DOI: 10.1002/ijc.29021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 05/26/2014] [Indexed: 01/07/2023]
Abstract
Screening for germline mutations in breast cancer-associated genes BRCA1 and BRCA2 is indicated for patients with breast cancer from high-risk breast cancer families and influences both treatment options and clinical management. However, only 25% of selected patients test positive for BRCA1/2 mutation, indicating that additional diagnostic biomarkers are necessary. We analyzed 124 formalin-fixed paraffin-embedded (FFPE) tumor samples from patients with hereditary (104) and sporadic (20) invasive breast cancer, divided into two series (A and B). Microarray expression profiling of 829 human miRNAs was performed on 76 samples (Series A), and bioinformatics tool Prophet was used to develop and test a microarray classifier. Samples were stratified into a training set (n = 38) for microarray classifier generation and a test set (n = 38) for signature validation. A 35-miRNA microarray classifier was generated for the prediction of BRCA1/2 mutation status with a reported 95% (95% CI = 0.88-1.0) and 92% (95% CI: 0.84-1.0) accuracy in the training and the test set, respectively. Differential expression of 12 miRNAs between BRCA1/2 mutation carriers versus noncarriers was validated by qPCR in an independent tumor series B (n = 48). Logistic regression model based on the expression of six miRNAs (miR-142-3p, miR-505*, miR-1248, miR-181a-2*, miR-25* and miR-340*) discriminated between tumors from BRCA1/2 mutation carriers and noncarriers with 92% (95% CI: 0.84-0.99) accuracy. In conclusion, we identified miRNA expression signatures predictive of BRCA1/2 mutation status in routinely available FFPE breast tumor samples, which may be useful to complement current patient selection criteria for gene testing by identifying individuals with high likelihood of being BRCA1/2 mutation carriers.
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Affiliation(s)
- Miljana Tanic
- Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
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95
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Wang ZH, Ren LL, Zheng P, Zheng HM, Yu YN, Wang JL, Lin YW, Chen YX, Ge ZZ, Chen XY, Hong J, Fang JY. miR-194 as a predictor for adenoma recurrence in patients with advanced colorectal adenoma after polypectomy. Cancer Prev Res (Phila) 2014; 7:607-16. [PMID: 24691499 DOI: 10.1158/1940-6207.capr-13-0426] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
microRNAs (miRNA) are promising predictors in colorectal cancer (CRC). We investigated whether miRNAs could predict adenoma recurrence in patients with advanced colorectal adenoma (ACRA) after polypectomy. miRNA expression profiling was performed by miRNA microarray to identify recurrence-related miRNAs. Candidate miRNAs extracted from formalin-fixed paraffin-embedded blocks of patients with ACRA were measured using real-time PCR. Logistic regression analysis was conducted to investigate whether validated miRNA expression profiles were independent from other known adenoma recurrence risk factors. The prognostic values of six miRNAs and three independent risk factors were assessed by the area under the receiver operating characteristic (ROC) curve analysis. The expressions of six candidate miRNAs were significantly decreased from levels in normal colorectal tissue compared with ARCA with adenoma recurrence (RACRA) in this retrospective cohort. However, only miRNA (miR)-194 emerged as a practical predictor. The sensitivity and specificity of miR-194 as a predictor were 71.0% and 78.0%, respectively, at a cutoff value of 0.1311 in the retrospective cohort. Sensitivity and specificity were 76.1% and 77.2%, respectively, in the prospective cohort using the same cutoff value. Low expression levels of miR-194, adenoma size ≥2 cm, and ≥3 adenomas were independent risk factors for adenoma recurrence. Moreover, low expression of miR-194 was a better predictor of adenoma recurrence than the adenoma size and numbers according to ROC curve analysis. miR-194 may be an independent predictor for adenoma recurrence in patients with ACRA after polypectomy.
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Affiliation(s)
- Zhen-Hua Wang
- Authors' Affiliations: Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease; and Division of Gastroenterology and Hepatology, Shanghai 1st Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Lin-Lin Ren
- Authors' Affiliations: Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease; and Division of Gastroenterology and Hepatology, Shanghai 1st Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Zheng
- Authors' Affiliations: Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease; and Division of Gastroenterology and Hepatology, Shanghai 1st Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Hai-Ming Zheng
- Authors' Affiliations: Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease; and Division of Gastroenterology and Hepatology, Shanghai 1st Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ya-Nan Yu
- Authors' Affiliations: Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease; and Division of Gastroenterology and Hepatology, Shanghai 1st Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ji-Lin Wang
- Authors' Affiliations: Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease; and Division of Gastroenterology and Hepatology, Shanghai 1st Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yan-Wei Lin
- Authors' Affiliations: Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease; and Division of Gastroenterology and Hepatology, Shanghai 1st Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ying-Xuan Chen
- Authors' Affiliations: Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease; and Division of Gastroenterology and Hepatology, Shanghai 1st Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhi-Zheng Ge
- Authors' Affiliations: Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease; and Division of Gastroenterology and Hepatology, Shanghai 1st Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Yu Chen
- Authors' Affiliations: Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease; and Division of Gastroenterology and Hepatology, Shanghai 1st Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Hong
- Authors' Affiliations: Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease; and Division of Gastroenterology and Hepatology, Shanghai 1st Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jing-Yuan Fang
- Authors' Affiliations: Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease; and Division of Gastroenterology and Hepatology, Shanghai 1st Hospital, Shanghai Jiao Tong University, Shanghai, China
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Abstract
Pan-genomic analyses of genetic and epigenetic alterations and gene expression profiles are providing important new insights into the pathogenesis and molecular classification of cancers. The technologies and methods used for these studies are rapidly diversifying and improving. The use of such methodologies for the analysis of adrenocortical tumours has revealed clear transcriptomic (mRNA and microRNA expression profiles), epigenomic (DNA methylation profiles) and genomic (DNA mutations and chromosomal alterations) differences between benign and malignant tumours. Interestingly, genomic studies of adrenal cancers have also identified subtypes of malignant tumours, which demonstrate distinct patterns of molecular alterations and are associated with different clinical outcomes. These discoveries have created the opportunity for classifying adrenocortical tumours on the basis of molecular analyses. Following these genomic studies, efforts to develop new molecular tools that improve diagnosis and prognostication of patients with adrenocortical tumours have also been made. This Review describes the progress that has been made towards classification of adrenocortical tumours to date based on key genomic approaches. In addition, the potential for the development and use of various molecular tools to personalize the management of patients with adrenocortical tumours is discussed.
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Affiliation(s)
- Guillaume Assié
- 1] Department of Endocrinology, Referral Centre for Rare Adrenal Diseases, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Cochin, 27 rue du Fg-St-Jacques, 75014 Paris, France. [2] INSERM U1016, CNRS UMR 8104, Paris Descartes University, Institut Cochin, 75014 Paris, France
| | - Anne Jouinot
- INSERM U1016, CNRS UMR 8104, Paris Descartes University, Institut Cochin, 75014 Paris, France
| | - Jérôme Bertherat
- 1] Department of Endocrinology, Referral Centre for Rare Adrenal Diseases, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Cochin, 27 rue du Fg-St-Jacques, 75014 Paris, France. [2] INSERM U1016, CNRS UMR 8104, Paris Descartes University, Institut Cochin, 75014 Paris, France
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97
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Skrzypski M, Czapiewski P, Goryca K, Jassem E, Wyrwicz L, Pawłowski R, Rzyman W, Biernat W, Jassem J. Prognostic value of microRNA expression in operable non-small cell lung cancer patients. Br J Cancer 2014; 110:991-1000. [PMID: 24448358 PMCID: PMC3929871 DOI: 10.1038/bjc.2013.786] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 11/12/2013] [Accepted: 11/27/2013] [Indexed: 12/13/2022] Open
Abstract
Background: About 50% of non-small cell lung cancer (NSCLC) patients develop distant metastases following pulmonary resection. Currently, there are no reliable factors allowing for individual selection of high-risk patients for adjuvant systemic therapies. Methods: We assessed by quantitative reverse transcription PCR microRNA (miRNA) expression in 273 stage I–IIIA NSCLC samples. Expression of 677 miRNAs was evaluated in fresh-frozen tumour samples in the training cohort of 50 squamous cell carcinoma (SCC) patients who underwent curative surgery. Of those, 20 patients developed distant metastases, and 30 were free of recurrence for >4 years. In the second step, miRNAs with highest predictive value for distant relapse were re-evaluated in formalin-fixed paraffin-embedded material in an independent group of 134 stage I–IIIA SCC patients. Additionally, the same miRNAs were investigated in 89 lung adenocarcinoma (AC) patients and in normal lung parenchyma (NLP). Results: In the training cohort of SCC, six miRNAs were differently expressed in the non-recurrent vs recurrent groups and correlated with distant recurrence-free survival, however none reached the level of significance after correction for multiple testing. Of these six miRNAs, miR-662, -192 and -192* were confirmed as prognostic in the independent SCC cohort. Expression of miR-128, -10b, -502-3p and -192 differed between SCC and AC, and miR-128 and -192 – between NLP and NSCLC. Conclusions: We identified three new miRNAs predictive of distant relapse in operable SCC. Future miRNA studies should account for differences between NSCLC subtypes.
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Affiliation(s)
- M Skrzypski
- Department of Oncology and Radiotherapy Medical University of Gdansk, ul. Dębinki 7, 80-211 Gdańsk, Poland
| | - P Czapiewski
- Department of Pathology Medical University of Gdansk, ul. Smoluchowskiego 17, 80-214 Gdańsk, Poland
| | - K Goryca
- Department of Genetics Maria Sklodowska-Curie Memorial Cancer Centre, ul. Roentgena 5, 02-781, Warsaw, Poland
| | - E Jassem
- Department of Pulmonology and Allergology Medical University of Gdansk, ul. Dębinki 7, 80-211 Gdańsk, Poland
| | - L Wyrwicz
- Laboratory of Bioinformatics and Biostatistics Maria Sklodowska-Curie Memorial Cancer Center, ul. Roentgena 5, 02-781 Warsaw, Poland
| | - R Pawłowski
- Department of Forensic Medicine Medical University of Gdańsk, ul. Dębowa 23, 80-204 Gdańsk, Poland
| | - W Rzyman
- Department of Thoracic Surgery Medical University of Gdansk, ul. Smoluchowskiego 17, 80-214 Gdańsk, Poland
| | - W Biernat
- Department of Pathology Medical University of Gdansk, ul. Smoluchowskiego 17, 80-214 Gdańsk, Poland
| | - J Jassem
- Department of Oncology and Radiotherapy Medical University of Gdansk, ul. Dębinki 7, 80-211 Gdańsk, Poland
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98
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MicroRNA expression profiles in human testicular tissues of infertile men with different histopathologic patterns. Fertil Steril 2014; 101:78-86.e2. [DOI: 10.1016/j.fertnstert.2013.09.009] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 09/01/2013] [Accepted: 09/05/2013] [Indexed: 12/14/2022]
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99
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Lee TS, Jeon HW, Kim YB, Kim YA, Kim MA, Kang SB. Aberrant microRNA expression in endometrial carcinoma using formalin-fixed paraffin-embedded (FFPE) tissues. PLoS One 2013; 8:e81421. [PMID: 24363810 PMCID: PMC3867308 DOI: 10.1371/journal.pone.0081421] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 10/12/2013] [Indexed: 12/15/2022] Open
Abstract
This study aimed to identify the candidate miRNAs in the carcinogenesis of endometrial carcinoma, and to explore whether FFPE material would be suitable for miRNA profiling. We identified the differences between miRNA expression profiles using human miRNA microarray in endometrioid endometrial adenocarcinomas (EECs) and normal endometria. Of those tested, miR-200a*, miR-200b*, miR-141, miR-182, and miR-205 were greatly enriched. The expressions of these five miRNAs were validated using quantitative real-time reverse transcription-PCR (qRT-PCR). We then performed qRT-PCR miR expression profiling in 30 FFPE specimens (20 EECs, 10 normal endometria) and re-confirmed the results of differential expression between cancer and normal tissue. Following this, we tested whether the specific inhibition of overexpressed miRNAs would alter chemosensitivity. In the in vitro cell viability assay, anti-miR200b* showed a trend toward enhanced cytotoxicity slightly in cisplatin compared to the negative control (p = 0.07). This information provided the candidate miRNAs for further confirmation of the role of miRNAs in the carcinogenesis of EECs, potentially serving as a diagnostic or therapeutic tool. FFPE specimens of endometrial tissues are suitable as a source for miRNA microarray profiling.
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Affiliation(s)
- Taek Sang Lee
- Department of Obstetrics and Gynecology, SMG–SNU Boramae Medical Center, Seoul, Korea
| | - Hye Won Jeon
- Department of Obstetrics and Gynecology, SMG–SNU Boramae Medical Center, Seoul, Korea
- * E-mail:
| | - Yong Beom Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Young A. Kim
- Department of Pathology, SMG–SNU Boramae Medical Center, Seoul Korea
| | - Min A. Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Soon Beom Kang
- Department of Obstetrics and Gynecology, Konkuk University Medical Center, Seoul, Korea
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100
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Kunder R, Jalali R, Sridhar E, Moiyadi A, Goel N, Goel A, Gupta T, Krishnatry R, Kannan S, Kurkure P, Deopujari C, Shetty P, Biyani N, Korshunov A, Pfister SM, Northcott PA, Shirsat NV. Real-time PCR assay based on the differential expression of microRNAs and protein-coding genes for molecular classification of formalin-fixed paraffin embedded medulloblastomas. Neuro Oncol 2013; 15:1644-51. [PMID: 24203893 DOI: 10.1093/neuonc/not123] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Medulloblastoma has recently been found to consist of 4 molecularly and clinically distinct subgroups: WNT, Sonce hedgehog (SHH), Group 3, and Group 4. Deregulated microRNA expression is known to contribute to pathogenesis and has been shown to have diagnostic and prognostic potential in the classification of various cancers. METHODS Molecular subgrouping and microRNA expression analysis of 44 frozen and 59 formalin-fixed paraffin embedded medulloblastomas from an Indian cohort were carried out by real-time RT-PCR assay. RESULTS The differential expression of 9 microRNAs in the 4 molecular subgroups was validated in a set of 101 medulloblastomas. The tumors in the WNT subgroup showed significant (P < .0001) overexpression of miR-193a-3p, miR-224, miR-148a, miR-23b, and miR-365. Reliable classification of medulloblastomas into the 4 molecular subgroups was obtained using a set of 12 protein-coding genes and 9 microRNAs as markers in a real-time RT-PCR assay with an accuracy of 97% as judged by the Prediction Analysis of Microarrays. Age at diagnosis, histology, gender-related incidence, and the relative survival rates of the 4 molecular subgroups in the present Indian cohort were found to be similar to those reported for medulloblastomas from the American and European subcontinent. Non-WNT, non-SHH medulloblastomas underexpressing miR-592 or overexpressing miR-182 were found to have significantly inferior survival rates, indicating utility of these miRNAs as markers for risk stratification. CONCLUSIONS The microRNA based real-time PCR assay is rapid, simple, inexpensive, and useful for molecular classification and risk stratification of medulloblastomas, in particular formalin-fixed paraffin embedded tissues, wherein the expression profile of protein-coding genes is often less reliable due to RNA fragmentation.
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Affiliation(s)
- Ratika Kunder
- Corresponding Author: Dr Neelam Vishwanath Shirsat, PhD, Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210 India.
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