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Patnaik SK, Kannisto E, Mallick R, Sharma R, Bshara W, Yendamuri S, Dhillon SS. MiR-205 and MiR-375 microRNA assays to distinguish squamous cell carcinoma from adenocarcinoma in lung cancer biopsies. J Thorac Oncol 2015; 10:446-53. [PMID: 25695220 PMCID: PMC5819754 DOI: 10.1097/jto.0000000000000423] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Identification of adenocarcinoma (AC) and squamous cell carcinoma (SCC) histology of non-small-cell lung cancer (NSCLC) in biopsies is clinically important but can be inaccurate by routine histopathologic examination. We quantify this inaccuracy at a cancer center, and evaluate the utility of a microRNA-based method to histotype AC/SCC in biopsies. METHODS RNA was extracted from tissue sections with greater than 90% tumor content that were macro- or micro-dissected from formalin-fixed, paraffin-embedded biopsy specimens. MicroRNAs in RNA from the biopsies and from resected tumors were quantified by TaqMan reverse transcription-polymerase chain reaction assays and normalized against the RNU6B housekeeping RNA. Publicly available microRNA expression datasets were examined. RESULTS NSCLC subtyping of small biopsy specimens by routine histopathologic examination either failed or mistyped the histology of 21% of 190 cases. Using 77 resectates, an reverse transcription-polymerase chain reaction-based assay of microRNAs miR-21, miR-205, and miR-375 was developed to identify AC and SCC subtypes of NSCLC. This method identified the AC/SCC histotypes of 25 biopsies with an accuracy of 96%, and correctly histotyped all 12 cases for which the histology had been mistyped by routine histopathologic examination of the biopsy. Examination of publicly available datasets identified miR-205 and miR-375 as microRNAs with the best ability to histotype AC and SCC, and that levels of the two microRNAs in AC or SCC are unaffected by the pathologic stage of the tumor or the age or race of the patient. CONCLUSIONS Histotypic microRNA assays can aid the subtyping of NSCLC biopsies as AC or SCC by standard histopathologic methods.
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Affiliation(s)
- Santosh K. Patnaik
- Department of Thoracic Surgery, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Eric Kannisto
- Department of Thoracic Surgery, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Reema Mallick
- Department of Surgery, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Rohit Sharma
- Department of Gastrointestinal Surgery, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
- Lehigh Valley Surgical Oncology, 1240 S Cedar Crest Boulevard, Allentown, PA 18103, USA (current affiliation)
| | - Wiam Bshara
- Department of Pathology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Sai Yendamuri
- Department of Thoracic Surgery, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Samjot S. Dhillon
- Department of Medicine, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
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Bass BP, Engel KB, Greytak SR, Moore HM. A review of preanalytical factors affecting molecular, protein, and morphological analysis of formalin-fixed, paraffin-embedded (FFPE) tissue: how well do you know your FFPE specimen? Arch Pathol Lab Med 2015; 138:1520-30. [PMID: 25357115 DOI: 10.5858/arpa.2013-0691-ra] [Citation(s) in RCA: 196] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Formalin fixation and paraffin embedding is a timeless, cost-efficient, and widely adopted method of preserving human tissue biospecimens that has resulted in a substantial reservoir of formalin-fixed, paraffin-embedded blocks that represent both the pathology and preanalytical handling of the biospecimen. This reservoir of specimens is increasingly being used for DNA, RNA, and proteomic analyses. OBJECTIVE To evaluate the impact of preanalytical factors associated with the formalin fixation and paraffin embedding process on downstream morphological and molecular endpoints. DATA SOURCES We surveyed the existing literature using the National Cancer Institute's Biospecimen Research Database for published reports investigating the potential influence of preanalytical factors associated with the formalin fixation and paraffin embedding process on DNA, RNA, protein, and morphological endpoints. CONCLUSIONS Based on the literature evidence, the molecular, proteomic, and morphological endpoints can be altered in formalin-fixed, paraffin-embedded specimens by suboptimal processing conditions. While the direction and magnitude of effects associated with a given preanalytical factor were dependent on the analyte (DNA, RNA, protein, and morphology) and analytical platform, acceptable conditions are highlighted, and a summary of conditions that could preclude analysis is provided.
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Affiliation(s)
- B Paige Bass
- From the Kelly Government Solutions Program, Kelly Services, Rockville (Drs Bass and Greytak), and the Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda (Dr Moore), Maryland; and the Preferred Solutions Group, Arlington, Virginia (Dr Engel)
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Sun D, Li X, Ma M, Liu J, Xu Y, Ye L, Hou H, Wang C, Li X, Jiang Y. The predictive value and potential mechanisms of miRNA-328 and miRNA-378 for brain metastases in operable and advanced non-small-cell lung cancer. Jpn J Clin Oncol 2015; 45:464-73. [DOI: 10.1093/jjco/hyv009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 01/09/2015] [Indexed: 01/04/2023] Open
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Permuth-Wey J, Chen YA, Fisher K, McCarthy S, Qu X, Lloyd MC, Kasprzak A, Fournier M, Williams VL, Ghia KM, Yoder SJ, Hall L, Georgeades C, Olaoye F, Husain K, Springett GM, Chen DT, Yeatman T, Centeno BA, Klapman J, Coppola D, Malafa M. A genome-wide investigation of microRNA expression identifies biologically-meaningful microRNAs that distinguish between high-risk and low-risk intraductal papillary mucinous neoplasms of the pancreas. PLoS One 2015; 10:e0116869. [PMID: 25607660 PMCID: PMC4301643 DOI: 10.1371/journal.pone.0116869] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 12/15/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Intraductal papillary mucinous neoplasms (IPMNs) are pancreatic ductal adenocarcinoma (PDAC) precursors. Differentiating between high-risk IPMNs that warrant surgical resection and low-risk IPMNs that can be monitored is a significant clinical problem, and we sought to discover a panel of mi(cro)RNAs that accurately classify IPMN risk status. METHODOLOGY/PRINCIPAL FINDINGS In a discovery phase, genome-wide miRNA expression profiling was performed on 28 surgically-resected, pathologically-confirmed IPMNs (19 high-risk, 9 low-risk) using Taqman MicroRNA Arrays. A validation phase was performed in 21 independent IPMNs (13 high-risk, 8 low-risk). We also explored associations between miRNA expression level and various clinical and pathological factors and examined genes and pathways regulated by the identified miRNAs by integrating data from bioinformatic analyses and microarray analysis of miRNA gene targets. Six miRNAs (miR-100, miR-99b, miR-99a, miR-342-3p, miR-126, miR-130a) were down-regulated in high-risk versus low-risk IPMNs and distinguished between groups (P<10-3, area underneath the curve (AUC) = 87%). The same trend was observed in the validation phase (AUC = 74%). Low miR-99b expression was associated with main pancreatic duct involvement (P = 0.021), and serum albumin levels were positively correlated with miR-99a (r = 0.52, P = 0.004) and miR-100 expression (r = 0.49, P = 0.008). Literature, validated miRNA:target gene interactions, and pathway enrichment analysis supported the candidate miRNAs as tumor suppressors and regulators of PDAC development. Microarray analysis revealed that oncogenic targets of miR-130a (ATG2B, MEOX2), miR-342-3p (DNMT1), and miR-126 (IRS-1) were up-regulated in high- versus low-risk IPMNs (P<0.10). CONCLUSIONS This pilot study highlights miRNAs that may aid in preoperative risk stratification of IPMNs and provides novel insights into miRNA-mediated progression to pancreatic malignancy. The miRNAs identified here and in other recent investigations warrant evaluation in biofluids in a well-powered prospective cohort of individuals newly-diagnosed with IPMNs and other pancreatic cysts and those at increased genetic risk for these lesions.
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Affiliation(s)
- Jennifer Permuth-Wey
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Y. Ann Chen
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Kate Fisher
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Susan McCarthy
- Department of Clinical Testing Development, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Xiaotao Qu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Mark C. Lloyd
- Department of Analytic Microscopy, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Agnieszka Kasprzak
- Department of Analytic Microscopy, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Michelle Fournier
- Department of Tissue Core Administration, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Vonetta L. Williams
- Department of Information Shared Services, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Kavita M. Ghia
- Department of Information Shared Services, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Sean J. Yoder
- Department of Molecular Genomics, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Laura Hall
- Department of Molecular Genomics, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Christina Georgeades
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Funmilayo Olaoye
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Kazim Husain
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Gregory M. Springett
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Dung-Tsa Chen
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Timothy Yeatman
- Department of Surgery, Gibbs Cancer Center and Research Institute, Spartanburg, SC, United States of America
| | - Barbara Ann Centeno
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Jason Klapman
- Department of Gastroenterology, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Domenico Coppola
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
| | - Mokenge Malafa
- Department of Gastrointestinal Surgical Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, United States of America
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Fesler A, Jiang J, Zhai H, Ju J. Circulating microRNA testing for the early diagnosis and follow-up of colorectal cancer patients. Mol Diagn Ther 2015; 18:303-8. [PMID: 24566942 DOI: 10.1007/s40291-014-0089-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Early detection of colorectal cancer (CRC) is key for prevention and the ability to impact long-term survival of CRC patients. However, the compliance rate of recommended colonoscopy for the population aged from 50 to 75 years is only 50-75 % in the US. A highly sensitive and specific non-invasive test is needed to enhance CRC management. As for late-stage patients, a non-invasive prognostic biomarker is also critical for improving patient treatment protocols. The discovery that non-coding microRNAs (miRNAs) are stable in body fluids such as plasma, serum and exosomes presents the opportunity to develop novel strategies, taking advantage of circulating miRNAs as early diagnostic biomarkers of CRC. The goal of using circulating miRNA-based prognostic biomarkers for CRC patients has been pursued extensively. In this review, we will try to cover the major recent advancements at the frontier of this research area.
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Affiliation(s)
- Andrew Fesler
- Translational Research Laboratory, Department of Pathology, BST, L-9, Room 185, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
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206
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Aslam MI, Hussein S, West K, Singh B, Jameson JS, Pringle JH. MicroRNAs associated with initiation and progression of colonic polyp: A feasibility study. Int J Surg 2015; 13:272-279. [DOI: 10.1016/j.ijsu.2014.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 11/05/2014] [Accepted: 12/05/2014] [Indexed: 12/18/2022]
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207
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Inada K, Okoshi Y, Cho Y, Saito H, Iijima T, Hori M, Kojima H. Availability of Circulating MicroRNAs as a Biomarker for Early Diagnosis of Diffuse Large B-Cell Lymphoma. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/ojbd.2015.54008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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208
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Dymacek J, Snyder-Talkington BN, Porter DW, Mercer RR, Wolfarth MG, Castranova V, Qian Y, Guo NL. mRNA and miRNA regulatory networks reflective of multi-walled carbon nanotube-induced lung inflammatory and fibrotic pathologies in mice. Toxicol Sci 2014; 144:51-64. [PMID: 25527334 DOI: 10.1093/toxsci/kfu262] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Multi-walled carbon nanotubes (MWCNTs) are known for their transient inflammatory and progressive fibrotic pulmonary effects; however, the mechanisms underlying these pathologies are unknown. In this study, we used time-series microarray data of global lung mRNA and miRNA expression isolated from C57BL/6J mice exposed by pharyngeal aspiration to vehicle or 10, 20, 40, or 80 µg MWCNT at 1, 7, 28, or 56 days post-exposure to determine miRNA and mRNA regulatory networks that are potentially involved in MWCNT-induced inflammatory and fibrotic lung etiology. Using a non-negative matrix factorization method, we determined mRNAs and miRNAs with expression profiles associated with pathology patterns of MWCNT-induced inflammation (based on bronchoalveolar lavage score) and fibrosis (based on Sirius Red staining measured with quantitative morphometric analysis). Potential binding targets between pathology-related mRNAs and miRNAs were identified using Ingenuity Pathway Analysis and the miRTarBase, miRecords, and TargetScan databases. Using these experimentally validated and predicted binding targets, we were able to build molecular signaling networks that are potentially reflective of and play a role in MWCNT-induced lung inflammatory and fibrotic pathology. As understanding the regulatory networks between mRNAs and miRNAs in different disease states would be beneficial for understanding the complex mechanisms of pathogenesis, these identified genes and pathways may be useful for determining biomarkers of MWCNT-induced lung inflammation and fibrosis for early detection of disease.
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Affiliation(s)
- Julian Dymacek
- *Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, West Virginia 26506-6070, Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, West Virginia 26505, Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia 26506 and Department of Occupational and Environmental Health Science, School of Public Health, Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, West Virginia 26506-9300
| | - Brandi N Snyder-Talkington
- *Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, West Virginia 26506-6070, Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, West Virginia 26505, Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia 26506 and Department of Occupational and Environmental Health Science, School of Public Health, Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, West Virginia 26506-9300
| | - Dale W Porter
- *Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, West Virginia 26506-6070, Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, West Virginia 26505, Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia 26506 and Department of Occupational and Environmental Health Science, School of Public Health, Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, West Virginia 26506-9300
| | - Robert R Mercer
- *Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, West Virginia 26506-6070, Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, West Virginia 26505, Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia 26506 and Department of Occupational and Environmental Health Science, School of Public Health, Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, West Virginia 26506-9300
| | - Michael G Wolfarth
- *Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, West Virginia 26506-6070, Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, West Virginia 26505, Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia 26506 and Department of Occupational and Environmental Health Science, School of Public Health, Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, West Virginia 26506-9300
| | - Vincent Castranova
- *Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, West Virginia 26506-6070, Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, West Virginia 26505, Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia 26506 and Department of Occupational and Environmental Health Science, School of Public Health, Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, West Virginia 26506-9300
| | - Yong Qian
- *Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, West Virginia 26506-6070, Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, West Virginia 26505, Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia 26506 and Department of Occupational and Environmental Health Science, School of Public Health, Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, West Virginia 26506-9300
| | - Nancy L Guo
- *Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, West Virginia 26506-6070, Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, West Virginia 26505, Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia 26506 and Department of Occupational and Environmental Health Science, School of Public Health, Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, West Virginia 26506-9300
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Wakabayashi K, Mori F, Kakita A, Takahashi H, Utsumi J, Sasaki H. Analysis of microRNA from archived formalin-fixed paraffin-embedded specimens of amyotrophic lateral sclerosis. Acta Neuropathol Commun 2014; 2:173. [PMID: 25497327 PMCID: PMC4279903 DOI: 10.1186/s40478-014-0173-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/01/2014] [Indexed: 12/13/2022] Open
Abstract
Background MicroRNAs (miRNAs) are noncoding small RNAs that regulate gene expression. This study investigated whether formalin-fixed paraffin-embedded (FFPE) specimens from postmortem cases of neurodegenerative disorders would be suitable for miRNA profiling. Results Ten FFPE samples from 6 cases of amyotrophic lateral sclerosis (ALS) and 4 neurologically normal controls were selected for miRNA analysis on the basis of the following criteria for RNA quality: (i) a postmortem interval of less than 6 hours, (ii) a formalin fixation time of less than 4 weeks, (iii) an RNA yield per sample of more than 500 ng, and (iv) sufficient quality of the RNA agarose gel image. An overall RNA extraction success rate was 46.2%. For ALS, a total of 364 miRNAs were identified in the motor cortex, 91 being up-regulated and 233 down-regulated. Target genes were predicted using miRNA bioinformatics software, and the data applied to ontology analysis. This indicated that one of the miRNAs up-regulated in ALS (miR-338-3p) had already been identified in leukocytes, serum, cerebrospinal fluid and frozen spinal cord from ALS patients. Conclusion Although analysis was possible for just under half of the specimens examined, we were able to show that informative miRNA data can be derived from archived FFPE samples from postmortem cases of neurodegenerative disorders. Electronic supplementary material The online version of this article (doi:10.1186/s40478-014-0173-z) contains supplementary material, which is available to authorized users.
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210
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Shalaby T, Fiaschetti G, Baumgartner M, Grotzer MA. MicroRNA signatures as biomarkers and therapeutic target for CNS embryonal tumors: the pros and the cons. Int J Mol Sci 2014; 15:21554-86. [PMID: 25421247 PMCID: PMC4264241 DOI: 10.3390/ijms151121554] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 11/07/2014] [Accepted: 11/08/2014] [Indexed: 12/19/2022] Open
Abstract
Embryonal tumors of the central nervous system represent a heterogeneous group of childhood cancers with an unknown pathogenesis; diagnosis, on the basis of histological appearance alone, is controversial and patients’ response to therapy is difficult to predict. They encompass medulloblastoma, atypical teratoid/rhabdoid tumors and a group of primitive neuroectodermal tumors. All are aggressive tumors with the tendency to disseminate throughout the central nervous system. The large amount of genomic and molecular data generated over the last 5–10 years encourages optimism that new molecular targets will soon improve outcomes. Recent neurobiological studies have uncovered the key role of microRNAs (miRNAs) in embryonal tumors biology and their potential use as biomarkers is increasingly being recognized and investigated. However the successful use of microRNAs as reliable biomarkers for the detection and management of pediatric brain tumors represents a substantial challenge. This review debates the importance of miRNAs in the biology of central nervous systemembryonal tumors focusing on medulloblastoma and atypical teratoid/rhabdoid tumors and highlights the advantages as well as the limitations of their prospective application as biomarkers and candidates for molecular therapeutic targets.
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Affiliation(s)
- Tarek Shalaby
- Department of Oncology, University Children's Hospital of Zurich, Steinwiesstrasse 75, Zurich 8032, Switzerland.
| | - Giulio Fiaschetti
- Department of Oncology, University Children's Hospital of Zurich, Steinwiesstrasse 75, Zurich 8032, Switzerland.
| | - Martin Baumgartner
- Department of Oncology, University Children's Hospital of Zurich, Steinwiesstrasse 75, Zurich 8032, Switzerland.
| | - Michael A Grotzer
- Department of Oncology, University Children's Hospital of Zurich, Steinwiesstrasse 75, Zurich 8032, Switzerland.
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211
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Mulrane L, Klinger R, McGee SF, Gallagher WM, O'Connor DP. microRNAs: a new class of breast cancer biomarkers. Expert Rev Mol Diagn 2014; 14:347-63. [PMID: 24649821 DOI: 10.1586/14737159.2014.901153] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) are regulatory molecules known to be aberrantly expressed in cancer and contribute to numerous aspects of tumor biology including the initiation, growth and spread of the tumor. With such diverse roles, it is becoming apparent that some may also provide valuable information which may be of use in a clinical setting, demonstrating the potential to act as both screening tools for the stratification of high-risk patients, while informing the treatment decision-making process. There is mounting evidence to suggest that some miRNAs may even provide assistance in the diagnosis of patients with breast cancer. In addition, miRNAs may themselves be considered therapeutic targets, with inhibition or reintroduction of a particular miRNA capable of inducing a response in vivo. This review focuses on miRNAs that have prognostic, diagnostic or predictive potential in breast cancer as well as the possible challenges in the translation of such observations to the clinic.
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Affiliation(s)
- Laoighse Mulrane
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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212
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Ricciuti B, Mecca C, Crinò L, Baglivo S, Cenci M, Metro G. Non-coding RNAs in lung cancer. Oncoscience 2014; 1:674-705. [PMID: 25593996 PMCID: PMC4278269 DOI: 10.18632/oncoscience.98] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 11/15/2014] [Indexed: 12/14/2022] Open
Abstract
The discovery that protein-coding genes represent less than 2% of all human genome, and the evidence that more than 90% of it is actively transcribed, changed the classical point of view of the central dogma of molecular biology, which was always based on the assumption that RNA functions mainly as an intermediate bridge between DNA sequences and protein synthesis machinery. Accumulating data indicates that non-coding RNAs are involved in different physiological processes, providing for the maintenance of cellular homeostasis. They are important regulators of gene expression, cellular differentiation, proliferation, migration, apoptosis, and stem cell maintenance. Alterations and disruptions of their expression or activity have increasingly been associated with pathological changes of cancer cells, this evidence and the prospect of using these molecules as diagnostic markers and therapeutic targets, make currently non-coding RNAs among the most relevant molecules in cancer research. In this paper we will provide an overview of non-coding RNA function and disruption in lung cancer biology, also focusing on their potential as diagnostic, prognostic and predictive biomarkers.
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Affiliation(s)
- Biagio Ricciuti
- Medical Oncology, Santa Maria della Misericordia Hospital, Azienda Ospedaliera di Perugia, Perugia, Italy
| | | | - Lucio Crinò
- Medical Oncology, Santa Maria della Misericordia Hospital, Azienda Ospedaliera di Perugia, Perugia, Italy
| | - Sara Baglivo
- Medical Oncology, Santa Maria della Misericordia Hospital, Azienda Ospedaliera di Perugia, Perugia, Italy
| | - Matteo Cenci
- Medical Oncology, Santa Maria della Misericordia Hospital, Azienda Ospedaliera di Perugia, Perugia, Italy
| | - Giulio Metro
- Medical Oncology, Santa Maria della Misericordia Hospital, Azienda Ospedaliera di Perugia, Perugia, Italy
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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: 3.3] [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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Akamatsu S, Hayes CN, Tsuge M, Miki D, Akiyama R, Abe H, Ochi H, Hiraga N, Imamura M, Takahashi S, Aikata H, Kawaoka T, Kawakami Y, Ohishi W, Chayama K. Differences in serum microRNA profiles in hepatitis B and C virus infection. J Infect 2014; 70:273-87. [PMID: 25452043 DOI: 10.1016/j.jinf.2014.10.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 09/18/2014] [Accepted: 10/17/2014] [Indexed: 12/22/2022]
Abstract
OBJECTIVES Patients infected with chronic hepatitis B virus (HBV) or hepatitis C virus (HCV) are at greater risk of cirrhosis and hepatocellular carcinoma. The objective of this study was to identify virus-specific serum microRNA profiles associated with liver function and disease progression. Microarray analysis of serum microRNAs was performed using the Toray 3D array system in 22 healthy subjects, 42 HBV patients, and 30 HCV patients. Selected microRNAs were then validated by qRT-PCR in 186 HBV patients, 107 HCV patients, and 22 healthy subjects. RESULTS Microarray analysis showed up-regulation of a number of microRNAs in serum of both HBV and HCV patients. In qRT-PCR analysis, miR-122, miR-99a, miR-125b, miR-720, miR-22, and miR-1275 were up-regulated both in HBV patients relative to healthy subjects, and all except miR-1275 were up-regulated in HBeAg-positive patients relative to HBeAg-negative patients. Specific microRNAs were independently associated with different aspects of HBV infection. MiR-122 was independently associated with HBV DNA level, whereas miR-125b was independently associated with levels of HBV DNA, HBsAg, and HBeAg. MiR-22 and miR-1275 were independently associated with serum γ-glutamyl transpeptidase levels. CONCLUSIONS Serum microRNA levels reflect differences in the etiology and stage of viral hepatitis.
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Affiliation(s)
- Sakura Akamatsu
- Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan; Laboratory for Digestive Diseases, Center for Genomic Medicine, RIKEN, Hiroshima, Japan; Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - C Nelson Hayes
- Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan; Laboratory for Digestive Diseases, Center for Genomic Medicine, RIKEN, Hiroshima, Japan; Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Masataka Tsuge
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan; Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima, Japan
| | - Daiki Miki
- Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan; Laboratory for Digestive Diseases, Center for Genomic Medicine, RIKEN, Hiroshima, Japan; Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Rie Akiyama
- Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan; Laboratory for Digestive Diseases, Center for Genomic Medicine, RIKEN, Hiroshima, Japan; Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Hiromi Abe
- Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan; Laboratory for Digestive Diseases, Center for Genomic Medicine, RIKEN, Hiroshima, Japan; Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Hidenori Ochi
- Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan; Laboratory for Digestive Diseases, Center for Genomic Medicine, RIKEN, Hiroshima, Japan; Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Nobuhiko Hiraga
- Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan; Laboratory for Digestive Diseases, Center for Genomic Medicine, RIKEN, Hiroshima, Japan; Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Michio Imamura
- Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan; Laboratory for Digestive Diseases, Center for Genomic Medicine, RIKEN, Hiroshima, Japan; Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | | | - Hiroshi Aikata
- Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan; Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Tomokazu Kawaoka
- Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan; Laboratory for Digestive Diseases, Center for Genomic Medicine, RIKEN, Hiroshima, Japan; Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Yoshiiku Kawakami
- Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan; Laboratory for Digestive Diseases, Center for Genomic Medicine, RIKEN, Hiroshima, Japan; Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Waka Ohishi
- Department of Clinical Studies, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan; Laboratory for Digestive Diseases, Center for Genomic Medicine, RIKEN, Hiroshima, Japan; Liver Research Project Center, Hiroshima University, Hiroshima, Japan.
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Okugawa Y, Toiyama Y, Goel A. An update on microRNAs as colorectal cancer biomarkers: where are we and what's next? Expert Rev Mol Diagn 2014; 14:999-1021. [PMID: 25163355 PMCID: PMC4374444 DOI: 10.1586/14737159.2014.946907] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
miRNAs are abundant classes of small, endogenous non-coding RNAs, which inhibit the expression of target gene via post-transcriptional regulation. In addition to an important functional role miRNAs play in carcinogenesis, emerging evidence has demonstrated their feasibility as robust cancer biomarkers. In particular, the recent discovery of miRNAs in the body fluids provides an attractive opportunity for the development of non-invasive biomarkers for the diagnosis, prognosis and predictive response to cancer therapy. Colorectal cancer (CRC) is one of the most common cancers worldwide, and accumulating data provides a compelling case for the potential exploitation of miRNAs as CRC-biomarkers. This review summarizes the current state of literature in the field, focusing on the clinical relevance of miRNAs as potential biomarkers for CRC treatment and discussing the forthcoming challenges to further advance this exciting field of 'academic research' into 'bedside clinical care' of patients suffering from CRC.
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Affiliation(s)
- Yoshinaga Okugawa
- Gastrointestinal Cancer Research Laboratory, Division of Gastroenterology, Department of Internal Medicine, Charles A. Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, Texas 75246-2017, USA
| | - Yuji Toiyama
- Gastrointestinal Cancer Research Laboratory, Division of Gastroenterology, Department of Internal Medicine, Charles A. Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, Texas 75246-2017, USA
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Graduate School of Medicine, Mie University, Mie 514-8507, Japan
| | - Ajay Goel
- Gastrointestinal Cancer Research Laboratory, Division of Gastroenterology, Department of Internal Medicine, Charles A. Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, Texas 75246-2017, USA
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Lee JC, Gundara JS, Glover A, Serpell J, Sidhu SB. MicroRNA expression profiles in the management of papillary thyroid cancer. Oncologist 2014; 19:1141-7. [PMID: 25323484 DOI: 10.1634/theoncologist.2014-0135] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Papillary thyroid cancer (PTC) is the major contributor to the dramatically increasing incidence of thyroid cancer. Low-risk PTC shows the most rapid rate of increase because of changing trends in neck imaging and the use of fine needle aspiration to investigate thyroid nodules. The need for a paradigm shift in the management of these patients, to provide personalized treatment and surveillance plans, has led to the focus on molecular biomarker research. MicroRNAs (miRNAs) compose a class of molecules with promising applications for every stage of PTC management, including diagnosis, prognosis, treatment, and surveillance. Although most of the miRNA studies are currently preclinical, given the rapid progress of scientific discovery, clinical trials will not be far away. Thyroid clinicians will be expected to have good insights into the current status of PTC-related molecular translational research. This article focuses on the potential roles of miRNA in PTC management in the context of contemporary recommended clinical practice.
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Affiliation(s)
- James C Lee
- Department of Surgery, Monash University, Melbourne, Victoria, Australia; Endocrine Surgery Unit, Alfred Hospital, Melbourne, Victoria, Australia; Kolling Institute of Medical Research, Sydney, New South Wales, Australia; University of Sydney, Sydney, New South Wales, Australia; Endocrine Surgical Unit, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Justin S Gundara
- Department of Surgery, Monash University, Melbourne, Victoria, Australia; Endocrine Surgery Unit, Alfred Hospital, Melbourne, Victoria, Australia; Kolling Institute of Medical Research, Sydney, New South Wales, Australia; University of Sydney, Sydney, New South Wales, Australia; Endocrine Surgical Unit, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Anthony Glover
- Department of Surgery, Monash University, Melbourne, Victoria, Australia; Endocrine Surgery Unit, Alfred Hospital, Melbourne, Victoria, Australia; Kolling Institute of Medical Research, Sydney, New South Wales, Australia; University of Sydney, Sydney, New South Wales, Australia; Endocrine Surgical Unit, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Jonathan Serpell
- Department of Surgery, Monash University, Melbourne, Victoria, Australia; Endocrine Surgery Unit, Alfred Hospital, Melbourne, Victoria, Australia; Kolling Institute of Medical Research, Sydney, New South Wales, Australia; University of Sydney, Sydney, New South Wales, Australia; Endocrine Surgical Unit, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Stan B Sidhu
- Department of Surgery, Monash University, Melbourne, Victoria, Australia; Endocrine Surgery Unit, Alfred Hospital, Melbourne, Victoria, Australia; Kolling Institute of Medical Research, Sydney, New South Wales, Australia; University of Sydney, Sydney, New South Wales, Australia; Endocrine Surgical Unit, Royal North Shore Hospital, Sydney, New South Wales, Australia
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217
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Boisen MK, Dehlendorff C, Linnemann D, Nielsen BS, Larsen JS, Østerlind K, Nielsen SE, Tarpgaard LS, Qvortrup C, Pfeiffer P, Holländer NH, Keldsen N, Hansen TF, Jensen BB, Høgdall EVS, Jensen BV, Johansen JS. Tissue microRNAs as predictors of outcome in patients with metastatic colorectal cancer treated with first line Capecitabine and Oxaliplatin with or without Bevacizumab. PLoS One 2014; 9:e109430. [PMID: 25329796 PMCID: PMC4198118 DOI: 10.1371/journal.pone.0109430] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 08/22/2014] [Indexed: 01/01/2023] Open
Abstract
Purpose We tested the hypothesis that expression of microRNAs (miRNAs) in cancer tissue can predict effectiveness of bevacizumab added to capecitabine and oxaliplatin (CAPEOX) in patients with metastatic colorectal cancer (mCRC). Experimental Design Patients with mCRC treated with first line CAPEOX and bevacizumab (CAPEOXBEV): screening (n = 212) and validation (n = 121) cohorts, or CAPEOX alone: control cohort (n = 127), were identified retrospectively and archival primary tumor samples were collected. Expression of 754 miRNAs was analyzed in the screening cohort using polymerase chain reaction (PCR) arrays and expression levels were related to time to disease progression (TTP) and overall survival (OS). Significant miRNAs from the screening study were analyzed in all three cohorts using custom PCR arrays. In situ hybridization (ISH) was done for selected miRNAs. Results In the screening study, 26 miRNAs were significantly correlated with outcome in multivariate analyses. Twenty-two miRNAs were selected for further study. Higher miR-664-3p expression and lower miR-455-5p expression were predictive of improved outcome in the CAPEOXBEV cohorts and showed a significant interaction with bevacizumab effectiveness. The effects were strongest for OS. Both miRNAs showed high expression in stromal cells. Higher expression of miR-196b-5p and miR-592 predicted improved outcome regardless of bevacizumab treatment, with similar effect estimates in all three cohorts. Conclusions We have identified potentially predictive miRNAs for bevacizumab effectiveness and additional miRNAs that could be related to chemotherapy effectiveness or prognosis in patients with mCRC. Our findings need further validation in large cohorts, preferably from completed randomized trials.
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Affiliation(s)
- Mogens K. Boisen
- Department of Oncology, Herlev University Hospital, Herlev, Denmark
- * E-mail:
| | - Christian Dehlendorff
- Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Dorte Linnemann
- Department of Pathology, Herlev University Hospital, Herlev, Denmark
| | | | - Jim S. Larsen
- Department of Oncology, Roskilde Hospital, Roskilde, Denmark
| | - Kell Østerlind
- Department of Oncology, Rigshospitalet, Copenhagen, Denmark
| | - Svend E. Nielsen
- Department of Oncology and Palliation, Hillerød Hospital, Hillerød, Denmark
| | | | - Camilla Qvortrup
- Department of Oncology, Odense University Hospital, Odense, Denmark
| | - Per Pfeiffer
- Department of Oncology, Odense University Hospital, Odense, Denmark
| | | | - Nina Keldsen
- Department of Oncology, Herning Hospital, Herning, Denmark
| | | | - Brita B. Jensen
- Department of Medicine, Queen Ingrid Hospital, Nuuk, Greenland
- Department of Oncology, Sydvestjysk Hospital, Esbjerg, Denmark
| | | | - Benny V. Jensen
- Department of Oncology, Herlev University Hospital, Herlev, Denmark
| | - Julia S. Johansen
- Department of Oncology, Herlev University Hospital, Herlev, Denmark
- Department of Medicine, Herlev University Hospital, Herlev, Denmark
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Vescovo VD, Grasso M, Barbareschi M, Denti MA. MicroRNAs as lung cancer biomarkers. World J Clin Oncol 2014; 5:604-620. [PMID: 25302165 PMCID: PMC4129526 DOI: 10.5306/wjco.v5.i4.604] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/28/2014] [Accepted: 05/08/2014] [Indexed: 02/06/2023] Open
Abstract
Lung cancer is the leading cause of cancer mortality worldwide. Its high mortality is due to the poor prognosis of the disease caused by a late disease presentation, tumor heterogeneities within histological subtypes, and the relatively limited understanding of tumor biology. Importantly, lung cancer histological subgroups respond differently to some chemotherapeutic substances and side effects of some therapies appear to vary between subgroups. Biomarkers able to stratify for the subtype of lung cancer, prognosticate the course of disease, or predict the response to treatment are in high demand. In the last decade, microRNAs (miRNAs), measured in resected tumor samples or in fine needle aspirate samples have emerged as biomarkers for tumor diagnosis, prognosis and prediction of response to treatment, due to the ease of their detection and in their extreme specificity. Moreover, miRNAs present in sputum, in plasma, in serum or in whole blood have increasingly been explored in the last five years as less invasive biomarkers for the early detection of cancers. In this review we cover the increasing amounts of data that have accumulated in the last ten years on the use of miRNAs as lung cancer biomarkers.
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219
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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: 3.3] [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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Distinct miRNA signatures associate with subtypes of cholangiocarcinoma from infection with the tumourigenic liver fluke Opisthorchis viverrini. J Hepatol 2014; 61:850-8. [PMID: 25017828 DOI: 10.1016/j.jhep.2014.05.035] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 05/07/2014] [Accepted: 05/21/2014] [Indexed: 12/22/2022]
Abstract
BACKGROUND & AIMS Intrahepatic cholangiocarcinoma (ICC) is a significant public health problem in East Asia, where it is strongly associated with chronic infection by the food-borne parasite Opisthorchis viverrini (OV). We report the first comprehensive miRNA expression profiling by microarray of the most common histologic grades and subtypes of ICC: well differentiated, moderately differentiated, and papillary ICC. METHODS MicroRNA expression profiles from FFPE were compared among the following: ICC tumour tissue (n = 16), non-tumour tissue distally macrodissected from the same ICC tumour block (n = 15), and normal tissue (n = 13) from individuals undergoing gastric bypass surgery. A panel of deregulated miRNAs was validated by qPCR. RESULTS Each histologic grade and subtype of ICC displayed a distinct miRNA profile, with no cohort of miRNAs emerging as commonly deregulated. Moderately differentiated ICC showed the greatest miRNA deregulation in quantity and magnitude, followed by the papillary subtype, and then well differentiated ICC. Moreover, when ICC tumour tissues were compared to adjacent non-tumour tissue, similar miRNA dysregulation profiles were observed. CONCLUSIONS We show that common histologic grades and subtypes of ICC have distinct miRNA profiles. As histological grade and subtypes are associated with ICC aggressiveness, these profiles could be used to enhance the early detection and improve the personalised treatment for ICC. These findings also suggest the involvement of specific miRNAs during ICC tumour progression and differentiation. We plan to use these insights to (a) detect these profiles in circulation and (b) conduct functional analyses to decipher the roles of miRNAs in ICC tumour differentiation.
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Orang AV, Barzegari A. MicroRNAs in Colorectal Cancer: from Diagnosis to Targeted Therapy. Asian Pac J Cancer Prev 2014; 15:6989-99. [DOI: 10.7314/apjcp.2014.15.17.6989] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Bruni R, Marcantonio C, Pulsoni A, Tataseo P, De Angelis F, Spada E, Marcucci F, Panfilio S, Bianco P, Riminucci M, Villano U, Tosti M, Ciccaglione A, Mele A. microRNA levels in paraffin-embedded indolent B-cell non-Hodgkin lymphoma tissues from patients chronically infected with hepatitis B or C virus. BMC Infect Dis 2014; 14 Suppl 5:S6. [PMID: 25236768 PMCID: PMC4160900 DOI: 10.1186/1471-2334-14-s5-s6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Epidemiological evidence links Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) to B-cell non-Hodgkin lymphoma (B-NHL). These B-NHLs, particularly those associated with HCV, may represent a distinct sub-group with peculiar molecular features, including peculiar expression of microRNAs (miRs). The aim of the present study was to search for miRs whose level in indolent B-NHL tissues could be associated with HBV or HCV infection. Methods Fourteen formalin fixed paraffin embedded (FFPE) tissues from HBV+, HCV+ and HBV-/HCV- indolent B-NHL patients were analyzed for levels of 34 selected miRs by quantitative Real-Time PCR. Reactive lymph nodes (RLNs) from HBV-/HCV- patients were included as non-tumor control. Statistical analysis of output data included Pearson and Spearman correlation and Mann-Whitney test and were carried out by the STATA software. Results MiR-92a was decreased exclusively in HBV-/HCV- B-NHLs, while miR-30b was increased in HBV+ and HCV+ samples, though only the HCV+ achieved full statistical significance. Analysis of a small subset of B-NHLs belonging to the same histological subtype (Nodal Marginal Zone Lymphoma) highlighted three miRs associated with HCV infection (miR-223, miR-29a and miR-29b) and confirmed decreased level of miR-92a in HBV-/HCV- samples also when considering this restricted B-NHL group. Conclusions Although caution is needed due to the limited number of analyzed samples, overall the results suggest that differences at the miR expression level exist between indolent B-NHLs developed in patients with or without HBV or HCV infection. The identification of three further miRs associated with HCV by analyzing histologically homogeneous samples suggests that variations of miR levels possibly associated with HBV or HCV may be obscured by the tissue-specific variability of miR level associated with the different histological subtypes of B-NHL. Thus, the identification of further miRs will require, in addition to an increased sample size, the comparison of B-NHL tissues with the same histological classification.
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Profiling miRNAs in nasopharyngeal carcinoma FFPE tissue by microarray and Next Generation Sequencing. GENOMICS DATA 2014; 2:285-9. [PMID: 26484110 PMCID: PMC4535902 DOI: 10.1016/j.gdata.2014.08.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 08/18/2014] [Accepted: 08/18/2014] [Indexed: 12/02/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a non-lymphomatous, squamous-cell carcinoma that occurs in the epithelial lining of the nasopharynx. Nasopharyngeal carcinoma has a geographically well-defined distribution worldwide, with the highest prevalence in China, Southeast Asia, and Northern Africa. Symptoms of nascent NPC may be unapparent or trivial, with diagnosis based on the histopathology of biopsied tissue following endoscopy of the nasopharynx. The tumor node metastasis (TNM) staging system is the benchmark for the prognosis of NPC and guides treatment strategy. However, there is a consensus that the TNM system is not sufficiently specific for the prognosis of NPC, as it does not reflect the biological heterogeneity of this tumor, making another biomarker for the detection of NPC a priority. We have previously reported on different approaches for microRNA (miRNA) biomarker discovery for Formalin Fixed Paraffin Embedded (FFPE) NPC tissue samples by both a targeted (microarray) and an untargeted (small RNA-Seq) discovery platform. Both miRNA discovery platforms produced similar results, narrowing the miRNA signature to 1–5% of the known mature human miRNAs, with untargeted (small RNA-Seq approach) having the advantage of indicating “unknown” miRNAs associated with NPC. Both miRNA profiles strongly associated with NPC, providing two potential discovery platforms for biomarker signatures for NPC. Herein, we provide a detailed description of the methods that we used to interrogate FFPE samples to discover biomarkers for NPC.
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Fesler A, Zhai H, Ju J. miR-129 as a novel therapeutic target and biomarker in gastrointestinal cancer. Onco Targets Ther 2014; 7:1481-5. [PMID: 25187728 PMCID: PMC4149397 DOI: 10.2147/ott.s65548] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In the last decade, cancer research efforts in the field of noncoding microRNA (miRNA) have been growing exponentially. miRNA-based therapeutics have been tested in both preclinical and clinical settings, and miRNA-based cancer diagnostics and prognostics have moved into clinics to help better manage cancer treatment. A growing body of evidence in recent literature suggests miRNA-129 plays important roles in gastrointestinal cancer, including gastric, colorectal, hepatocellular carcinoma, and esophageal cancer. In this review, we focus on accumulating evidence demonstrating the key roles that miRNA-129 plays in tumorigenesis, disease progression, chemoresistance, proliferation, and cell cycle control. Understanding the emerging roles and mechanisms of miRNA-129 in cancer will help us realize the therapeutic and diagnostic/prognostic potential.
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Affiliation(s)
- Andrew Fesler
- Department of Pathology, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Haiyan Zhai
- Department of Pathology, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Jingfang Ju
- Department of Pathology, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
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Molecular analysis of different classes of RNA molecules from formalin-fixed paraffin-embedded autoptic tissues: a pilot study. Int J Legal Med 2014; 129:11-21. [PMID: 25135750 DOI: 10.1007/s00414-014-1066-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 08/08/2014] [Indexed: 10/24/2022]
Abstract
For a long time, it has been thought that fresh and frozen tissues are the only possible source of biological material useful to extract nucleic acids suitable for downstream molecular analysis. Recently, for forensic purpose such as personal identification, also fixed tissues have been used to recover DNA molecules, whereas RNA extracted from such material is still considered too degraded for gene expression studies. In the present pilot study, we evaluated the possibility to use forensic formalin-fixed paraffin-embedded (FFPE) samples, collected at autopsy at different postmortem intervals (PMI) from four individuals, to perform advanced molecular analyses. In particular, we performed qualitative and quantitative analyses of total RNAs extracted from different FFPE tissues and put expression profiles in relation with the organ type and the duration of PMI. Different classes of RNA molecular targets were studied by real-time quantitative RT-PCR. We report molecular evidence that small RNAs are the only RNA molecules still detectable in all the FFPE autoptic tissues. In particular, microRNAs (miRNAs) represent a consistent, stable, and well-preserved molecular target detectable even from tissue sources displaying signs of ongoing putrefaction at autopsy. In this pilot study, we show that miRNAs could represent a highly sensitive and potentially useful forensic marker. Amplification of specific miRNAs using paraffin-embedded blocks could facilitate retrospective molecular analysis using specific forensic-archived tissues chosen as most suitable according to PMI, and this approach would address molecular evidence in forensic cases in which fresh or frozen material is no longer available.
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Hansen TF, Kjær-Frifeldt S, Christensen RD, Morgenthaler S, Blondal T, Lindebjerg J, Sørensen FB, Jakobsen A. Redefining high-risk patients with stage II colon cancer by risk index and microRNA-21: results from a population-based cohort. Br J Cancer 2014; 111:1285-92. [PMID: 25051407 PMCID: PMC4183843 DOI: 10.1038/bjc.2014.409] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/22/2014] [Accepted: 06/30/2014] [Indexed: 12/12/2022] Open
Abstract
Background: The aim of the present study was to analyse the prognostic value of microRNA-21 (miRNA-21) in patients with stage II colon cancer aiming at a risk index for this group of patients. Methods: A population-based cohort of 554 patients was included. MicroRNA-21 was analysed by qPCR based on tumour tissue. An index was created using the coefficients obtained from a collective multiple Cox regression. The entire procedure was cross-validated (10-fold). The performance of the index was quantified by time-dependent receiver operating characteristics curves. Results: High miRNA-21 expression was associated with an unfavourable recurrence-free cancer-specific survival (RF-CSS), hazard ratio 1.35 (95% confidence interval, 1.03–1.76) (P=0.028). The generated RF-CSS index divided the traditional high-risk patients into subgroups with 5-year RF-CSS rates of 87% and 73%, respectively (P<0.001). The overall survival (OS) index identified three different subgroups (P<0.001). Cross-validated 5-year OS rates were 88%, 68%, and 50%, respectively. Conclusions: This population-based study supports miRNA-21 as an additional prognostic biomarker in patients with stage II colon cancer. Furthermore, the introduction of a risk index may guide the use of postoperative adjuvant treatment in a more appropriate way compared with current practice.
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Affiliation(s)
- T F Hansen
- 1] Department of Oncology, Vejle Hospital, part of Lillebaelt Hospital, Kabbeltoft 25, 7100 Vejle, Denmark [2] Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - S Kjær-Frifeldt
- 1] Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark [2] Department of Clinical Pathology, Vejle Hospital, part of Lillebaelt Hospital, Vejle, Denmark
| | - R D Christensen
- Research Unit of General Practice Odense, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | | | | | - J Lindebjerg
- Department of Clinical Pathology, Vejle Hospital, part of Lillebaelt Hospital, Vejle, Denmark
| | - F B Sørensen
- 1] Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark [2] Department of Clinical Pathology, Vejle Hospital, part of Lillebaelt Hospital, Vejle, Denmark
| | - A Jakobsen
- 1] Department of Oncology, Vejle Hospital, part of Lillebaelt Hospital, Kabbeltoft 25, 7100 Vejle, Denmark [2] Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
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Zou MX, Huang W, Wang XB, Lv GH, Li J, Deng YW. Identification of miR-140-3p as a marker associated with poor prognosis in spinal chordoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2014; 7:4877-4885. [PMID: 25197358 PMCID: PMC4152048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 07/12/2014] [Indexed: 06/03/2023]
Abstract
OBJECTIVE To investigate the expression profile of miR-140-3p in formalin-fixed paraffin-embedded (FFPE) tissues of spinal chordoma, and its correlation with the prognosis of spinal chordoma patients. METHODS Dysregulated miRNAs in FFPE tissues of spinal chordoma were identified by microarray analysis. MiR-140-3p expression in surgically removed spinal chordoma tissues of 42 spinal chordoma patients (27 males and 15 females, aged 29-76 years) and corresponding nucleus pulposus tissues of 14 patients with disc herniation as the healthy control group (8 males and 6 females, aged 24-73 years) was measured by real-time quantitative RT-PCR assay. The association of miR-140-3p expression with clinicopathologic characteristics of spinal chordoma patients was analyzed. Additionally, we investigated the prognostic significance of miR-140-3p with the use of Kaplan-Meier methods and a Cox proportional hazard model. RESULTS The expression of miR-140-3p was significantly higher in chordoma tissues than nucleus pulposus tissues (t = 3.530, P = 0.001). The expression of miR-140-3p positively correlated with surrounding muscle invasion. The Kapan-Meier survival analysis showed that the patients with high miR-140-3p expression had a significantly worse recurrence-free survival than those with a low expression (χ (2) = 31.270, P = 0.000, log-rank test). In addition, univariate and multivariate analyses for recurrence-free survival showed that miR-140-3p expression was an independent prognostic factor for patients with spinal chordoma (HR = 1.361, 95% CI: 1.135-1.633, P = 0.001). CONCLUSION Over-expression of miR-140-3p is correlated with recurrence and tumor invasion, suggesting that miR-140-3p could be a new predictor for recurrence and prognosis in patients with spinal chordoma.
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Affiliation(s)
- Ming-Xiang Zou
- Department of Spine Surgery, The Second Xiangya Hospital of Central South UniversityNo. 139, Middle of Renmin Road, Changsha 410011, Hunan, China
| | - Wei Huang
- Department of Epidemiology and Health Statistics, School of Public Health, Central South UniversityChangsha 410078, Hunan, China
| | - Xiao-Bin Wang
- Department of Spine Surgery, The Second Xiangya Hospital of Central South UniversityNo. 139, Middle of Renmin Road, Changsha 410011, Hunan, China
| | - Guo-Hua Lv
- Department of Spine Surgery, The Second Xiangya Hospital of Central South UniversityNo. 139, Middle of Renmin Road, Changsha 410011, Hunan, China
| | - Jing Li
- Department of Spine Surgery, The Second Xiangya Hospital of Central South UniversityNo. 139, Middle of Renmin Road, Changsha 410011, Hunan, China
| | - You-Wen Deng
- Department of Spine Surgery, The Second Xiangya Hospital of Central South UniversityNo. 139, Middle of Renmin Road, Changsha 410011, Hunan, China
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Bai Y, Xue Y, Xie X, Yu T, Zhu Y, Ge Q, Lu Z. The RNA expression signature of the HepG2 cell line as determined by the integrated analysis of miRNA and mRNA expression profiles. Gene 2014; 548:91-100. [PMID: 25014136 DOI: 10.1016/j.gene.2014.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 06/19/2014] [Accepted: 07/07/2014] [Indexed: 12/15/2022]
Abstract
Understanding miRNAs' regulatory networks and target genes could facilitate the development of therapies for human diseases such as cancer. Although much useful gene expression profiling data for tumor cell lines is available, microarray data for miRNAs and mRNAs in the human HepG2 cell line have only been compared with that of other cell lines separately. The relationship between miRNAs and mRNAs in integrated expression profiles for HepG2 cells is still unknown. To explore the miRNA-mRNA correlations in hepatocellular carcinoma (HCC) cells, we performed miRNA and mRNA expression profiling in HepG2 cells and normal liver HL-7702 cells at the genome scale using next-generation sequencing technology. We identified 193 miRNAs that are differentially expressed in these two cell lines. Of these, 89 miRNAs were down-regulated in HepG2 cells compared with HL-7702 cells, while 104 miRNAs were up-regulated. We also observed 3035 mRNAs that are significantly dys-regulated in HepG2 cells. We then performed an integrated analysis of the expression data for differentially expressed miRNAs and mRNAs and found several miRNA-mRNA pairs that are significantly correlated in HepG2 cells. Further analysis suggested that these differentially expressed genes were enriched in four tumorigenesis-related signaling pathways, namely, ErbB, JAK-STAT, mTOR, and WNT, which until now had not been fully reported. Our results could be helpful in understanding the mechanisms of HCC occurrence and development.
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Affiliation(s)
- Yunfei Bai
- School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Ying Xue
- School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xueying Xie
- Research Center for Learning Science, Southeast University, Nanjing 210096, China
| | - Tong Yu
- Nanjing Decode Genomics Biotechnology Co., Ltd., Nanjing 210019, China
| | - Yihua Zhu
- School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, China; College of Information Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Qinyu Ge
- Research Center for Learning Science, Southeast University, Nanjing 210096, China
| | - Zuhong Lu
- School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, China; Research Center for Learning Science, Southeast University, Nanjing 210096, China.
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229
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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: 1.9] [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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230
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Shen S, Sun Q, Liang Z, Cui X, Ren X, Chen H, Zhang X, Zhou Y. A prognostic model of triple-negative breast cancer based on miR-27b-3p and node status. PLoS One 2014; 9:e100664. [PMID: 24945253 PMCID: PMC4063964 DOI: 10.1371/journal.pone.0100664] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/27/2014] [Indexed: 12/14/2022] Open
Abstract
Objective Triple-negative breast cancer (TNBC) is an aggressive but heterogeneous subtype of breast cancer. This study aimed to identify and validate a prognostic signature for TNBC patients to improve prognostic capability and to guide individualized treatment. Methods We retrospectively analyzed the prognostic performance of clinicopathological characteristics and miRNAs in a training set of 58 patients with invasive ductal TNBC diagnosed between 2002 and 2012. A prediction model was developed based on independent clinicopathological and miRNA covariates. The prognostic value of the model was further validated in a separate set of 41 TNBC patients diagnosed between 2007 and 2008. Results Only lymph node status was marginally significantly associated with poor prognosis of TNBC (P = 0.054), whereas other clinicopathological factors, including age, tumor size, histological grade, lymphovascular invasion, P53 status, Ki-67 index, and type of surgery, were not. The expression levels of miR-27b-3p, miR-107, and miR-103a-3p were significantly elevated in the metastatic group compared with the disease-free group (P value: 0.008, 0.005, and 0.050, respectively). The Cox proportional hazards regression analysis revealed that lymph node status and miR-27b-3p were independent predictors of poor prognosis (P value: 0.012 and 0.027, respectively). A logistic regression model was developed based on these two independent covariates, and the prognostic value of the model was subsequently confirmed in a separate validation set. The two different risk groups, which were stratified according to the model, showed significant differences in the rates of distant metastasis and breast cancer-related death not only in the training set (P value: 0.001 and 0.040, respectively) but also in the validation set (P value: 0.013 and 0.012, respectively). Conclusion This model based on miRNA and node status covariates may be used to stratify TNBC patients into different prognostic subgroups for potentially individualized therapy.
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Affiliation(s)
- Songjie Shen
- Department of Breast Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Qiang Sun
- Department of Breast Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaojiang Cui
- Department of Surgery, Department of Obstetrics and Gynecology, Women's Cancer Program, Samuel Oschin Comprehensive Cancer Institute, Cedars Sinai Medical Center, Los Angeles, California, United States of America
| | - Xinyu Ren
- Department of Pathology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Huan Chen
- Department of Microbiology, Zhejiang Institute of Microbiology, Hangzhou, Zhejiang, China
| | - Xiao Zhang
- Biostatistics and Bioinformatics Core, Samuel Oschin Comprehensive Cancer Institute, Cedars Sinai Medical Center, Los Angeles, California, United States of America
| | - Yidong Zhou
- Department of Breast Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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Yin JY, Deng ZQ, Liu FQ, Qian J, Lin J, Tang Q, Wen XM, Zhou JD, Zhang YY, Zhu XW. Association between mir-24 and mir-378 in formalin-fixed paraffin-embedded tissues of breast cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2014; 7:4261-4267. [PMID: 25120807 PMCID: PMC4129042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/02/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND MiR-24/378 is thought to be onco-miRNAs for their ability of enhancing tumor growth. The objective of this study was to evaluate the potential predictive value of miR-24/378 expression in formalin-fixed paraffin-embedded tissues of breast cancer patients. METHODS The expression of miR-24/378 was examined in 101 breast cancer patients and 40 controls using real-time quantitative PCR. All statistical analyses were performed using SPSS16.0. RESULTS We found that miR-24 and miR-378 were significantly up-regulated in breast cancer patients compared with controls (all P < 0.01). The expression levels of the two miRNAs were highly correlated with each other in breast cancer patients, with r = 0.778 between miR-24 and miR-378. Moreover, the two miRNAs exhibited great capability of discriminating between cancer patients and controls by ROC analysis. MiR-24 and miR-378 showed 0.79 and 0.807 AUC values respectively. CONCLUSIONS Over-expression of miR-24 and miR-378 in FFPE tissue of breast cancer patients might conduct as an ideal source for biomarker discovery and validation in breast cancer patients.
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Affiliation(s)
- Jia-Yu Yin
- Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, China
| | - Zhao-Qun Deng
- Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, China
| | - Feng-Qiong Liu
- Department of Nutrition, School of Public Health, Sun Yat-Sen UniversityChina
| | - Jun Qian
- Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, China
| | - Jiang Lin
- Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, China
| | - Qin Tang
- Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, China
| | - Xiang-Mei Wen
- Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, China
| | - Jing-Dong Zhou
- Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, China
| | - Ying-Ying Zhang
- Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, China
| | - Xiao-Wen Zhu
- Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, China
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232
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Takei Y, Ohnishi N, Kisaka M, Mihara K. Determination of abnormally expressed microRNAs in bone marrow smears from patients with follicular lymphomas. SPRINGERPLUS 2014; 3:288. [PMID: 25019040 PMCID: PMC4072855 DOI: 10.1186/2193-1801-3-288] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/29/2014] [Indexed: 01/11/2023]
Abstract
The abnormal expression of microRNAs (miRNAs) is implicated in various human diseases, including cancers. Accordingly, miRNA expressions have been examined in many cancer tissues and blood, but there have been few studies examining smear samples from bone marrow (BM) or peripheral blood. Here we successfully isolated small RNAs from BM smears using a mirVana miRNA Isolation Kit with our original modifications. The isolated small RNAs were then used to measure the levels of representative miRNAs such as miR-155, let-7a, and U6 via real-time PCR with a specific TaqMan probe, although peaks for the ribosomal RNAs (18S, and 28S) were not identified. The PCR curves of the miRNAs were indistinguishable from those from BM living cells from the same donor. Finally, our method for BM smears identified numerous abnormally altered miRNAs (significantly decreased, 39 miRNAs; significantly increased, 27 miRNAs) in follicular lymphomas (FL) compared with normal donors via TaqMan real-time PCR miRNA array. The array indicated that miR-451 showed the greatest decrease in FL (a 345-fold decrease), while miR-338-5p showed the greatest increase in FL (172-fold) relative to normal donors. The miRNAs identified by our study might serve as markers to predict the invasion of FL cells into BM without biopsy. Furthermore, our method will provide a new avenue for the analysis of miRNAs in BM smear samples from various hematologic diseases.
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Affiliation(s)
- Yoshifumi Takei
- Division of Disease Models, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550 Japan ; Department of Biochemistry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550 Japan
| | - Naomi Ohnishi
- Division of Disease Models, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550 Japan
| | - Mayumi Kisaka
- Life Technologies Japan, 4-5-4 Hatchobori, Chuo-ku Tokyo, 104-0032 Japan
| | - Keichiro Mihara
- Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku Hiroshima, 734-8551 Japan
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Li X, Yang W, Lou L, Chen Y, Wu S, Ding G. microRNA: a promising diagnostic biomarker and therapeutic target for hepatocellular carcinoma. Dig Dis Sci 2014; 59:1099-107. [PMID: 24390674 DOI: 10.1007/s10620-013-3006-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 12/17/2013] [Indexed: 02/07/2023]
Abstract
microRNAs constitute a novel class of small, non-coding RNAs that negatively regulate gene expression via translational inhibition or mRNA degradation. Aberrant miRNA expression has been implicated in the initiation, progression, and metastasis of hepatocellular carcinoma (HCC). It is well-documented that miRNAs function as either tumor suppressor genes or oncogenes in the development and progression of HCC. Additionally, substantial evidence suggests that unique miRNA signatures can serve as valuable diagnostic and prognostic biomarkers for HCC. Interestingly, certain subsets of miRNAs have also been identified as potential therapeutic targets for HCC.
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Affiliation(s)
- Xiaofei Li
- Department of Infectious Diseases, YiWu Central Hospital, Zhejiang, 322000, China,
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Ariza Márquez YV, Beltrán López ÁP, Briceño Balcázar I, Ancizar Aristizabal F. Rol biológico y aplicaciones de los miRNAs en cáncer de seno. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2014. [DOI: 10.15446/rev.colomb.biote.v16n1.44287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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235
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Hedegaard J, Thorsen K, Lund MK, Hein AMK, Hamilton-Dutoit SJ, Vang S, Nordentoft I, Birkenkamp-Demtröder K, Kruhøffer M, Hager H, Knudsen B, Andersen CL, Sørensen KD, Pedersen JS, Ørntoft TF, Dyrskjøt L. Next-generation sequencing of RNA and DNA isolated from paired fresh-frozen and formalin-fixed paraffin-embedded samples of human cancer and normal tissue. PLoS One 2014; 9:e98187. [PMID: 24878701 PMCID: PMC4039489 DOI: 10.1371/journal.pone.0098187] [Citation(s) in RCA: 269] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 04/10/2014] [Indexed: 12/31/2022] Open
Abstract
Formalin-fixed, paraffin-embedded (FFPE) tissues are an invaluable resource for clinical research. However, nucleic acids extracted from FFPE tissues are fragmented and chemically modified making them challenging to use in molecular studies. We analysed 23 fresh-frozen (FF), 35 FFPE and 38 paired FF/FFPE specimens, representing six different human tissue types (bladder, prostate and colon carcinoma; liver and colon normal tissue; reactive tonsil) in order to examine the potential use of FFPE samples in next-generation sequencing (NGS) based retrospective and prospective clinical studies. Two methods for DNA and three methods for RNA extraction from FFPE tissues were compared and were found to affect nucleic acid quantity and quality. DNA and RNA from selected FFPE and paired FF/FFPE specimens were used for exome and transcriptome analysis. Preparations of DNA Exome-Seq libraries was more challenging (29.5% success) than that of RNA-Seq libraries, presumably because of modifications to FFPE tissue-derived DNA. Libraries could still be prepared from RNA isolated from two-decade old FFPE tissues. Data were analysed using the CLC Bio Genomics Workbench and revealed systematic differences between FF and FFPE tissue-derived nucleic acid libraries. In spite of this, pairwise analysis of DNA Exome-Seq data showed concordance for 70–80% of variants in FF and FFPE samples stored for fewer than three years. RNA-Seq data showed high correlation of expression profiles in FF/FFPE pairs (Pearson Correlations of 0.90 +/- 0.05), irrespective of storage time (up to 244 months) and tissue type. A common set of 1,494 genes was identified with expression profiles that were significantly different between paired FF and FFPE samples irrespective of tissue type. Our results are promising and suggest that NGS can be used to study FFPE specimens in both prospective and retrospective archive-based studies in which FF specimens are not available.
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Affiliation(s)
- Jakob Hedegaard
- Department of Molecular Medicine (MOMA), Molecular Diagnostic Laboratory, Aarhus University Hospital, Skejby, Aarhus, Denmark
- * E-mail:
| | - Kasper Thorsen
- Department of Molecular Medicine (MOMA), Molecular Diagnostic Laboratory, Aarhus University Hospital, Skejby, Aarhus, Denmark
| | | | | | | | - Søren Vang
- Department of Molecular Medicine (MOMA), Molecular Diagnostic Laboratory, Aarhus University Hospital, Skejby, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine (MOMA), Molecular Diagnostic Laboratory, Aarhus University Hospital, Skejby, Aarhus, Denmark
| | - Karin Birkenkamp-Demtröder
- Department of Molecular Medicine (MOMA), Molecular Diagnostic Laboratory, Aarhus University Hospital, Skejby, Aarhus, Denmark
| | - Mogens Kruhøffer
- AROS Applied Biotechnology A/S, Science Park Skejby, Aarhus, Denmark
| | - Henrik Hager
- Institute of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Claus Lindbjerg Andersen
- Department of Molecular Medicine (MOMA), Molecular Diagnostic Laboratory, Aarhus University Hospital, Skejby, Aarhus, Denmark
| | - Karina Dalsgaard Sørensen
- Department of Molecular Medicine (MOMA), Molecular Diagnostic Laboratory, Aarhus University Hospital, Skejby, Aarhus, Denmark
| | - Jakob Skou Pedersen
- Department of Molecular Medicine (MOMA), Molecular Diagnostic Laboratory, Aarhus University Hospital, Skejby, Aarhus, Denmark
| | - Torben Falck Ørntoft
- Department of Molecular Medicine (MOMA), Molecular Diagnostic Laboratory, Aarhus University Hospital, Skejby, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine (MOMA), Molecular Diagnostic Laboratory, Aarhus University Hospital, Skejby, Aarhus, Denmark
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236
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Circulating miRNAs as biomarkers for neurodegenerative disorders. Molecules 2014; 19:6891-910. [PMID: 24858274 PMCID: PMC6271879 DOI: 10.3390/molecules19056891] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 05/19/2014] [Accepted: 05/21/2014] [Indexed: 12/13/2022] Open
Abstract
Neurodegenerative disorders, such as Alzheimer’s disease (AD), Parkinson’s disease (PD) and frontotemporal dementias (FTD), are considered distinct entities, however, there is increasing evidence of an overlap from the clinical, pathological and genetic points of view. All neurodegenerative diseases are characterized by neuronal loss and death in specific areas of the brain, for example, hippocampus and cortex for AD, midbrain for PD, frontal and temporal lobes for FTD. Loss of neurons is a relatively late event in the progression of neurodegenerative diseases that is typically preceded by other events such as metabolic changes, synaptic dysfunction and loss, neurite retraction, and the appearance of other abnormalities, such as axonal transport defects. The brain’s ability to compensate for these dysfunctions occurs over a long period of time and results in late clinical manifestation of symptoms, when successful pharmacological intervention is no longer feasible. Currently, diagnosis of AD, PD and different forms of dementia is based primarily on analysis of the patient’s cognitive function. It is therefore important to find non-invasive diagnostic methods useful to detect neurodegenerative diseases during early, preferably asymptomatic stages, when a pharmacological intervention is still possible. Altered expression of microRNAs (miRNAs) in many disease states, including neurodegeneration, and increasing relevance of miRNAs in biofluids in different pathologies has prompted the study of their possible application as neurodegenerative diseases biomarkers in order to identify new therapeutic targets. Here, we review what is known about the role of miRNAs in the pathogenesis of neurodegeneration and the possibilities and challenges of using these small RNA molecules as a signature for neurodegenerative conditions.
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Wang S, Yang MH, Wang XY, Lin J, Ding YQ. Increased expression of miRNA-182 in colorectal carcinoma: an independent and tissue-specific prognostic factor. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2014; 7:3498-3503. [PMID: 25031782 PMCID: PMC4097234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 05/24/2014] [Indexed: 06/03/2023]
Abstract
Increasing evidence has revealed that miRNAs play a pivotal role in multiple processes of carcinogenesis, and are being explored as diagnostic, prognostic and predictive biomarker. In this study, we investigated the status of miR-182 expression in colorectal carcinoma (CRC) by in situ hybridization and its underlying clinicopathologic significance for patients with CRC. We found that 79/138 (57.25%) CRCs had high-level expression of miR-182, while 17/67 (25.37%) normal mucosa tissues had high-level expression of miR-182. The expression level of miR-182 was remarkably up-regulated in CRC tissues compared with non-neoplastic normal tissues (P < 0.001). The over-expression of miR-182 in cancer parenchyma cells in CRC were strongly correlated with T-stage (P = 0.020), lymph node metastasis (P = 0.003), distant metastasis (P = 0.002), and Dukes' stage (P = 0.005) in patients with CRC. Patients with high-level expression of miR-182 had short overall survival time than those with low-level expression of miR-182 (P < 0.001). Univariate and multivariate survival analyses further showed that miR-182 expression was a potential unfavorable prognostic factor for CRC, suggesting a potential application of miR-182 in prognosis prediction and therapeutic application in CRC.
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Affiliation(s)
- Shuang Wang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University Guangzhou 510515, China
| | - Min-Hui Yang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University Guangzhou 510515, China
| | - Xiao-Yan Wang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University Guangzhou 510515, China
| | - Jie Lin
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University Guangzhou 510515, China
| | - Yan-Qing Ding
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University Guangzhou 510515, China
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238
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Chevillet JR, Lee I, Briggs HA, He Y, Wang K. Issues and prospects of microRNA-based biomarkers in blood and other body fluids. Molecules 2014; 19:6080-105. [PMID: 24830712 PMCID: PMC6271291 DOI: 10.3390/molecules19056080] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/07/2014] [Accepted: 05/12/2014] [Indexed: 12/21/2022] Open
Abstract
Cell-free circulating microRNAs (miRNAs) in the blood are good diagnostic biomarker candidates for various physiopathological conditions, including cancer, neurodegeneration, diabetes and other diseases. Since their discovery in 2008 as blood biomarkers, the field has expanded rapidly with a number of important findings. Despite the initial optimistic views of their potential for clinical application, there are currently no circulating miRNA-based diagnostics in use. In this article, we review the status of circulating miRNAs, examine different analytical approaches, and address some of the challenges and opportunities.
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Affiliation(s)
| | - Inyoul Lee
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Hilary A Briggs
- Laboratory of the Biology of Addictive Diseases, Rockefeller University, New York, NY 10065, USA
| | - Yuqing He
- Institute of Medical Systems Biology, Guangdong Medical College, Dongguan, Guangdong 523808, China.
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA 98109, USA.
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239
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Deng ZQ, Qian J, Liu FQ, Lin J, Shao R, Yin JY, Tang Q, Zhang M, He L. Expression level of miR-93 in formalin-fixed paraffin-embedded tissues of breast cancer patients. Genet Test Mol Biomarkers 2014; 18:366-370. [PMID: 24606013 DOI: 10.1089/gtmb.2013.0440] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
MiR-93 is thought to be an onco-miRNA for its capabilities of enhancing tumor growth. The objective of this study was to evaluate the potential predictive value of miR-93 expression in formalin-fixed paraffin-embedded (FFPE) tissues of breast cancer patients. The expression of miR-93 was examined in 101 breast cancer patients and 40 controls using real-time quantitative PCR. We found that miR-93 was markedly upregulated in breast cancer patients compared with controls (p<0.01). The expression level of miR-93 was significantly correlated with miR-24/378 in breast cancer patients. MiR-93 exhibited great capability of discriminating between cancer patients and cancer-free controls by receiver-operator characteristic (ROC) curve analysis. MiR-93 showed 0.866 AUC (the area under the ROC curve) values. The MiR-93 level was found significantly correlated with breast cancer by univariable logistic regression. These results suggest that overexpression of miR-93 in FFPE tissues may serve as an indispensable source for biomarker discovery and validation in breast cancer patients.
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Affiliation(s)
- Zhao-qun Deng
- 1 School of Basic Medical Science, Wuhan University , Wuhan, People's Republic of China
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240
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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: 17] [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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242
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Amrouche L, Rabant M, Anglicheau D. MicroRNAs as biomarkers of graft outcome. Transplant Rev (Orlando) 2014; 28:111-8. [PMID: 24797471 DOI: 10.1016/j.trre.2014.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 03/21/2014] [Indexed: 12/31/2022]
Abstract
Dramatic improvements in short-term graft outcomes after solid organ transplantation over the past decade have not translated into major improvements in long-term allograft acceptance and patient survival. Innovative approaches to develop individualized therapy for the graft recipient are critically needed and have stimulated active research in the field of biomarker discovery. MicroRNAs (miRNAs) are small non-coding RNAs that function as important regulators of gene and protein expression by RNA interference. They are implicated in many biological processes and diseases. Their characteristics prompted their evaluation as candidate molecular markers to evaluate the transplant patient: their expression profile is specifically altered in pathological conditions, they can be easily detected and quantified in tissues, and they are highly stable in almost all body fluids, allowing the development of non-invasive approaches. We aimed to review the existing knowledge about miRNA biogenesis and function and summarize the recent findings demonstrating their potential use as biomarkers in solid organ transplantation. Although they still need to be validated in larger patient cohorts, miRNAs are not far from being used in transplant clinical practice as usefulness biomarkers. Ongoing multi-center trials should help to further define the clinical utility of miRNA profiles as biomarkers of allograft status and outcome.
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Affiliation(s)
- Lucile Amrouche
- INSERM U1151, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; Service de Néphrologie et Transplantation Adulte, Hôpital Necker, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Marion Rabant
- INSERM U1151, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; Laboratoire d'anatomie pathologique, Hôpital Necker, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Dany Anglicheau
- INSERM U1151, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; Service de Néphrologie et Transplantation Adulte, Hôpital Necker, Assistance Publique-Hôpitaux de Paris, Paris, France; RTRS Centaure, LabEx Transplantex.
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243
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Jang K, Ahn H, Sim J, Han H, Abdul R, Paik SS, Chung MS, Jang SJ. Loss of microRNA-200a expression correlates with tumor progression in breast cancer. Transl Res 2014; 163:242-51. [PMID: 24280074 DOI: 10.1016/j.trsl.2013.11.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 11/04/2013] [Accepted: 11/04/2013] [Indexed: 01/03/2023]
Abstract
MicroRNAs (miRNAs) are 19∼22 nucleotide-long, noncoding, small RNAs, involved in post-transcriptional regulation of many target genes. The miRNA-200 family has been shown to play a crucial role in the epithelial to mesenchymal transition in human cancers. In situ hybridization (ISH) was used to investigate the expression level of miRNA-200a in breast cancers. Formalin-fixed, paraffin embedded (FFPE) tissues from normal breast, ductal carcinoma in situ (DCIS), primary cancers, and metastatic lymph nodes were achieved and constructed to tissue microarrays. MiRNA-200a expression was demonstrated in 95.2% of normal breast tissue samples and 80.4% of DCIS, whereas 178 (58.0%) of 307 breast cancers and 83.3% of metastatic lymph node samples lacked miRNA-200a expression (P < 0.001). Moreover, loss of MiRNA-200a expression correlated with high histologic grade (P = 0.017) and perinodal tumor extension (P = 0.026). However, miRNA-200a expression did not predict tumor recurrence or patient survival. In conclusion, loss of miRNA-200a is frequently observed in breast cancers, especially tumors with high grade histology. These findings suggest that miRNA-200a may play an important role in breast cancer initiation and progression. ISH can be used to detect miRNAs in FFPE sections, and should permit the validation of miRNAs as biomarkers in large clinical samples.
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Affiliation(s)
- Kiseok Jang
- Department of Pathology, College of Medicine, Hanyang University, Seoul, Republic of Korea.
| | - Hyein Ahn
- Department of Pathology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Jongmin Sim
- Department of Pathology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Hulin Han
- Department of Pathology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Rehman Abdul
- Department of Pathology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Seung Sam Paik
- Department of Pathology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Min Sung Chung
- Department of Surgery, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Se Jin Jang
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
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244
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Wang G, Li Z, Zhao Q, Zhu Y, Zhao C, Li X, Ma Z, Li X, Zhang Y. LincRNA-p21 enhances the sensitivity of radiotherapy for human colorectal cancer by targeting the Wnt/β-catenin signaling pathway. Oncol Rep 2014; 31:1839-45. [PMID: 24573322 DOI: 10.3892/or.2014.3047] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 02/11/2014] [Indexed: 01/16/2023] Open
Abstract
Recent studies show that long intergenic noncoding RNA-p21 (lincRNA-p21) is aberrantly expressed in several types of cancer, including colorectal cancer (CRC), one of the most common cancers in the world. Radiotherapy is considered as a standard preoperative treatment approach to reduce local recurrence for local advanced rectal cancer. However, a considerable number of rectal cancers are resistant to radiotherapy. In the present study, we evaluated the role of lincRNA‑p21 in radiotherapy for CRC and detected the possible molecular mechanism. By expression profile analysis, we demonstrated that lincRNA-p21 decreases in CRC cell lines and tissue samples, which contributes to the elevation of β-catenin in CRC. We further showed that lincRNA‑p21 increases following X-ray treatment, and enforced expression of the lincRNA enhances the sensitivity of radiotherapy for CRC by promoting cell apoptosis. Suppression of the β-catenin signaling pathway and elevation of the pro-apoptosis gene Noxa expression may help explain the role of lincRNA-p21 in CRC radiotherapy. The present study not only deepens our understanding of the mechanism of radiotherapy for CRC, but it also provides a potential target for CRC radiotherapy.
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Affiliation(s)
- Guangyu Wang
- Department of Gastrointestinal Medical Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang 150040, P.R. China
| | - Zhiwei Li
- Department of Gastrointestinal Medical Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang 150040, P.R. China
| | - Qi Zhao
- Department of Gastrointestinal Medical Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang 150040, P.R. China
| | - Yuanyuan Zhu
- Department of Gastrointestinal Medical Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang 150040, P.R. China
| | - Ci Zhao
- Department of Gastrointestinal Medical Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang 150040, P.R. China
| | - Xin Li
- Department of Gastrointestinal Medical Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang 150040, P.R. China
| | - Zhigang Ma
- Department of Gastrointestinal Medical Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang 150040, P.R. China
| | - Xiaobo Li
- Department of Pathology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Yanqiao Zhang
- Department of Gastrointestinal Medical Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang 150040, P.R. China
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245
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Deng ZQ, Yin JY, Tang Q, Liu FQ, Qian J, Lin J, Shao R, Zhang M, He L. Over-expression of miR-98 in FFPE tissues might serve as a valuable source for biomarker discovery in breast cancer patients. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2014; 7:1166-1171. [PMID: 24696733 PMCID: PMC3971322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 01/22/2014] [Indexed: 06/03/2023]
Abstract
The miR-98 is thought to be associated with various cancers. This study was to evaluate the potential predictive value of miR-98 expression in formalin-fixed paraffin-embedded tissue of breast cancer patients. The expression levels of miR-98 were examined in 98 breast cancer patients and 40 cancer-free controls using real-time quantitative PCR. The comparison of miR-98 expression levels between patient and control was performed using the Mann-Whitney test. The miR-98 showed higher expression levels in breast cancer patients compared with cancer free controls (p<0.01). The expression levels of miR-98 were highly correlated with miR24/93/378 in breast cancer patients. The miR-98 exhibited great capability of discriminating between cancer patients and controls by the Receiver-operator characteristic (ROC) curve analysis. The miR-98 was found highly correlated with breast cancer by Univariable logistic regression analysis. These results suggest that over-expression of miR-98 in formalin-fixed paraffin-embedded tissues might serve as a valuable source for biomarker discovery in breast cancer patients.
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Affiliation(s)
- Zhao-Qun Deng
- School of Basic Medical Science, Wuhan UniversityWuhan 430071, People’s Republic of China
- Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, 212002, People’s Republic of China
| | - Jia-Yu Yin
- Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, 212002, People’s Republic of China
| | - Qin Tang
- Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, 212002, People’s Republic of China
| | - Feng-Qiong Liu
- Department of Nutrition, School of Public Health, Sun Yat-Sen UniversityPeople’s Republic of China
| | - Jun Qian
- Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, 212002, People’s Republic of China
| | - Jiang Lin
- Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, 212002, People’s Republic of China
| | - Rui Shao
- Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, 212002, People’s Republic of China
| | - Ming Zhang
- Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, 212002, People’s Republic of China
| | - Li He
- School of Basic Medical Science, Wuhan UniversityWuhan 430071, People’s Republic of China
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246
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Zhu M, Zhang N, He S, Lui Y, Lu G, Zhao L. MicroRNA-106a targets TIMP2 to regulate invasion and metastasis of gastric cancer. FEBS Lett 2014; 588:600-7. [PMID: 24440352 DOI: 10.1016/j.febslet.2013.12.028] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/02/2013] [Accepted: 12/23/2013] [Indexed: 12/26/2022]
Abstract
Emerging evidence has shown that microRNA plays an important role in tumor development and progression. Here, we report that miR-106a is frequently up-regulated in gastric cancer tissues and positively correlates with metastasis. Restrained expression of miR-106a in gastric cancer cells significantly reduces their capacity of proliferation, migration and invasion. In tissue sections, the positive signal of miR-106a localized in metastasis-associated regions confirmed this result. Moreover, we show that TIMP2 is a direct downstream target for miR-106a and knockdown of TIMP2 strengthens the beneficial effects of miR-106a. Our study adds miR-106a to the complex mechanisms of tumor metastasis.
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Affiliation(s)
- Meng Zhu
- Department of Gastroenterology, First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Rood, Xi'an, Shanxi 710061, People's Republic of China
| | - Ning Zhang
- Department of Pathology, General Hospital of Ningxia Medical University, Yinchuan, People's Republic of China
| | - Shuixiang He
- Department of Gastroenterology, First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Rood, Xi'an, Shanxi 710061, People's Republic of China.
| | - Yuanyuan Lui
- Department of Gastroenterology, The Central Hospital of Xi'an, Xi'an, People's Republic of China
| | - Guifang Lu
- Department of Gastroenterology, First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Rood, Xi'an, Shanxi 710061, People's Republic of China
| | - Lin Zhao
- Department of Gastroenterology, First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Rood, Xi'an, Shanxi 710061, People's Republic of China
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247
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Plieskatt JL, Rinaldi G, Feng Y, Levine PH, Easley S, Martinez E, Hashmi S, Sadeghi N, Brindley PJ, Bethony JM, Mulvenna JP. Methods and matrices: approaches to identifying miRNAs for nasopharyngeal carcinoma. J Transl Med 2014; 12:3. [PMID: 24393330 PMCID: PMC3895762 DOI: 10.1186/1479-5876-12-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 12/22/2013] [Indexed: 12/15/2022] Open
Abstract
Background Nasopharyngeal carcinoma (NPC) is a solid tumor of the head and neck. Multimodal therapy is highly effective when NPC is detected early. However, due to the location of the tumor and the absence of clinical signs, early detection is difficult, making a biomarker for the early detection of NPC a priority. The dysregulation of small non-coding RNAs (miRNAs) during carcinogenesis is the focus of much current biomarker research. Herein, we examine several miRNA discovery methods using two sample matrices to identify circulating miRNAs (c-miRNAs) associated with NPC. Methods We tested two miRNA discovery workflows on two sample sources for miRNAs associated with NPC. In the first workflow, we assumed that NPC tumor tissue would be enriched for miRNAs, so we compared miRNA expression in FFPE from NPC cases and controls using microarray and RNA-Seq technologies. Candidate miRNAs from both technologies were verified by qPCR in FFPE and sera from an independent NPC sample set. In a second workflow, we directly interrogated NPC case and control sera by RNA-Seq for c-miRNAs associated with NPC, with candidate c-miRNAs verified by qPCR in the sera from the same independent NPC sample set. Results Both microarray and RNA-Seq narrowed the miRNA signature to 1-5% of the known mature human miRNAs. Moreover, these two methods produced similar results when applied to the same sample type (FFPE), with RNA-Seq additionally indicating “unknown” miRNAs associated with NPC. However, we found different miRNA profiles in NPC sera compared to FFPE using RNA-Seq, with the few overlapping miRNAs found to be significantly up-regulated in FFPE significantly down-regulated in sera (and vice versa). Despite the different miRNA profiles found in FFPE and sera, both profiles strongly associated with NPC, providing two potential sources for biomarker signatures for NPC. Conclusions We determined that the direct interrogation of sera by RNA-Seq was the most informative method for identifying a c-miRNA signature associated with NPC. We also showed that there are different miRNA expression profiles associated with NPC for tumor tissue and sera. These results reflect on the methods and meaning of miRNA biomarkers for NPC in tissue and peripheral blood.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jeffrey M Bethony
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Science, George Washington University, Washington, DC, USA.
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Mu YP, Tang S, Sun WJ, Gao WM, Wang M, Su XL. Association of miR-193b down-regulation and miR-196a up-regulation with clinicopathological features and prognosis in gastric cancer. Asian Pac J Cancer Prev 2014; 15:8893-8900. [PMID: 25374225 DOI: 10.7314/apjcp.2014.15.20.8893] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Dysregulated expression of microRNAs (miRNAs) has been shown to be closely associated with tumor development, progression, and carcinogenesis. However, their clinical implications for gastric cancer remain elusive. To investigate the hypothesis that genome-wide alternations of miRNAs differentiate gastric cancer tissues from those matched adjacent non-tumor tissues (ANTTs), miRNA arrays were employed to examine miRNA expression profiles for the 5-pair discovery stage, and the quantitative real-time polymerase chain reaction (qRT- PCR) was applied to validate candidate miRNAs for 48-pair validation stage. Furthermore, the relationship between altered miRNA and clinicopathological features and prognosis of gastric cancer was explored. Among a total of 1,146 miRNAs analyzed, 16 miRNAs were found to be significantly different expressed in tissues from gastric cancer compared to ANTTs (p<0.05). qRT-PCR further confirmed the variation in expression of miR-193b and miR-196a in the validation stage. Down-expression of miR-193b was significantly correlated with Lauren type, differentiation, UICC stage, invasion, and metastasis of gastric cancer (p<0.05), while over-expression of miR-196a was significantly associated with poor differentiation (p=0.022). Moreover, binary logistic regression analysis demonstrated that the UICC stage was a significant risk factor for down-expression of miR-193b (adjusted OR=8.69; 95%CI=1.06-56.91; p=0.043). Additionally, Kaplan-Meier survival curves indicated that patients with a high fold-change of down-regulated miR-193b had a significantly shorter survival time (n=19; median survival=29 months) compared to patients with a low fold-change of down-regulated miR-193b (n=29; median survival=54 months) (p=0.001). Overall survival time of patients with a low fold-change of up-regulated miR- 196a (n=27; median survival=52 months) was significantly longer than that of patients with a high fold-change of up-regulated miR-196a (n=21; median survival=46 months) (p=0.003). Hence, miR-193b and miR-196a may be applied as novel and promising prognostic markers in gastric cancer.
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Affiliation(s)
- Yong-Ping Mu
- Department of Clinical Laboratory Center, The Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, China E-mail : ;
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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: 8.0] [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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Gyongyosi A, Docs O, Czimmerer Z, Orosz L, Horvath A, Török O, Mehes G, Nagy L, Balint BL. Measuring expression levels of small regulatory RNA molecules from body fluids and formalin-fixed, paraffin-embedded samples. Methods Mol Biol 2014; 1182:105-19. [PMID: 25055905 DOI: 10.1007/978-1-4939-1062-5_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
MicroRNAs are involved in the regulation of various pathophysiological processes such as immune regulation and cancer. Next-generation sequencing methods enable us to monitor their presence in various types of samples but we need flexible methods for validating datasets generated by high-throughput methods. Here we describe the detailed protocols to be used with our MiRNA Primer Design Tool assay design system. The presented methods allow the flexible design of the oligonucleotides needed for the RT-qPCR detection of any variant of small regulatory RNA molecules from virtually any species. This method can be used to measure miRNA levels from formalin-fixed, paraffin-embedded (FFPE) samples and various body fluids. As an example, we show the results of the hsa-miR-515-3p, hsa-miR-325, and hsa-miR-155 quantification using a specific UPL probe (Universal Probe Library) and a stem-loop RT-qPCR assay. The small nucleolar RNA RNU43 is used as endogenous control for normalization of the results. Urine from healthy pregnant women and FFPE samples from patients diagnosed with colorectal cancer and treated with antibody-based anti-EGFR monotherapy were used as samples.
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Affiliation(s)
- Adrienn Gyongyosi
- Department of Biochemistry and Molecular Biology, Center for Clinical Genomics and Personalized Medicine, University of Debrecen Medical and Health Science Center (UD MHSC), Nagyerdei krt. 98, Debrecen, Hungary
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