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Meseguer S, Mudduluru G, Escamilla JM, Allgayer H, Barettino D. MicroRNAs-10a and -10b contribute to retinoic acid-induced differentiation of neuroblastoma cells and target the alternative splicing regulatory factor SFRS1 (SF2/ASF). J Biol Chem 2010; 286:4150-64. [PMID: 21118818 DOI: 10.1074/jbc.m110.167817] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
MicroRNAs (miRNAs) are an emerging class of non-coding endogenous RNAs involved in multiple cellular processes, including cell differentiation. Treatment with retinoic acid (RA) results in neural differentiation of neuroblastoma cells. We wanted to elucidate whether miRNAs contribute to the gene expression changes induced by RA in neuroblastoma cells and whether miRNA regulation is involved in the transduction of the RA signal. We show here that RA treatment of SH-SY5Y neuroblastoma cells results in profound changes in the expression pattern of miRNAs. Up to 42 different miRNA species significantly changed their expression (26 up-regulated and 16 down-regulated). Among them, the closely related miR-10a and -10b showed the most prominent expression changes. Induction of miR-10a and -10b by RA also could be detected in LA-N-1 neuroblastoma cells. Loss of function experiments demonstrated that miR-10a and -10b are essential mediators of RA-induced neuroblastoma differentiation and of the associated changes in migration, invasion, and in vivo metastasis. In addition, we found that the SR-family splicing factor SFRS1 (SF2/ASF) is a target for miR-10a -and -10b in HeLa and SH-SY5Y neuroblastoma cells. We show here that changes in miR-10a and -10b expression levels may regulate SFRS1-dependent alternative splicing and translational functions. Taken together, our results give support to the idea that miRNA regulation plays a key role in RA-induced neuroblastoma cell differentiation. The discovery of SFRS1 as direct target of miR-10a and -10b supports the emerging functional interaction between two post-transcriptional mechanisms, microRNAs and splicing, in the neuronal differentiation context.
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Affiliation(s)
- Salvador Meseguer
- Biology of Hormone Action Unit, Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia E-46010, Spain
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202
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Stallings RL, Foley NH, Bryan K, Buckley PG, Bray I. Therapeutic targeting of miRNAs in neuroblastoma. Expert Opin Ther Targets 2010; 14:951-62. [PMID: 20658962 DOI: 10.1517/14728222.2010.510136] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
IMPORTANCE OF THE FIELD Neuroblastomas arise from precursor cells of the sympathetic nervous system and are noted for highly heterogeneous clinical behavior. These tumors currently account for approximately 15% of all childhood cancer related deaths in spite of intensive multimodal chemotherapy and are a major problem in pediatric oncology. The identification of novel therapeutic targets is urgently required to reduce patient morbidity. AREAS COVERED IN THIS REVIEW The purpose of this article is to review and synthesize all of the rapidly expanding evidence for the contribution of microRNAs (miRNAs) in neuroblastoma aggressive disease pathogenesis, along with the prospect of using small RNAs as therapeutics. WHAT THE READER WILL GAIN The reader will obtain insight on the miRNAs that are dysregulated in neuroblastoma along with potential therapeutic strategies and the most promising targets. TAKE HOME MESSAGE A number of miRNAs which are associated with aggressive disease pathogenesis in neuroblastoma patients have been demonstrated to contribute in major ways to cell proliferation rates, apoptosis, differentiation, invasiveness and tumor growth in vitro and in vivo. Directly or indirectly interfering with the function of these miRNAs may prove to be an important and novel form of therapy.
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203
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Schulte JH, Schowe B, Mestdagh P, Kaderali L, Kalaghatgi P, Schlierf S, Vermeulen J, Brockmeyer B, Pajtler K, Thor T, de Preter K, Speleman F, Morik K, Eggert A, Vandesompele J, Schramm A. Accurate prediction of neuroblastoma outcome based on miRNA expression profiles. Int J Cancer 2010; 127:2374-85. [PMID: 20473924 DOI: 10.1002/ijc.25436] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
For neuroblastoma, the most common extracranial tumour of childhood, identification of new biomarkers and potential therapeutic targets is mandatory to improve risk stratification and survival rates. MicroRNAs are deregulated in most cancers, including neuroblastoma. In this study, we analysed 430 miRNAs in 69 neuroblastomas by stem-loop RT-qPCR. Prediction of event-free survival (EFS) with support vector machines (SVM) and actual survival times with Cox regression-based models (CASPAR) were highly accurate and were independently validated. SVM-accuracy for prediction of EFS was 88.7% (95% CI: 88.5-88.8%). For CASPAR-based predictions, 5y-EFS probability was 0.19% (95% CI: 0-38%) in the CASPAR-predicted short survival group compared with 0.78% (95%CI: 64-93%) in the CASPAR-predicted long survival group. Both classifiers were validated on an independent test set yielding accuracies of 94.74% (SVM) and 5y-EFS probabilities as 0.25 (95% CI: 0.0-0.55) for short versus 1 ± 0.0 for long survival (CASPAR), respectively. Amplification of the MYCN oncogene was highly correlated with deregulation of miRNA expression. In addition, 37 miRNAs correlated with TrkA expression, a marker of excellent outcome, and 6 miRNAs further analysed in vitro were regulated upon TrkA transfection, suggesting a functional relationship. Expression of the most significant TrkA-correlated miRNA, miR-542-5p, also discriminated between local and metastatic disease and was inversely correlated with MYCN amplification and event-free survival. We conclude that neuroblastoma patient outcome prediction using miRNA expression is feasible and effective. Studies testing miRNA-based predictors in comparison to and in combination with mRNA and aCGH information should be initiated. Specific miRNAs (e.g., miR-542-5p) might be important in neuroblastoma tumour biology, and qualify as potential therapeutic targets.
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Affiliation(s)
- Johannes H Schulte
- University Children's Hospital Essen, Hufelandstr 55, 45122 Essen, Germany
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204
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Ohira M, Nakagawara A. Global genomic and RNA profiles for novel risk stratification of neuroblastoma. Cancer Sci 2010; 101:2295-301. [PMID: 20731666 PMCID: PMC11159775 DOI: 10.1111/j.1349-7006.2010.01681.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Neuroblastoma is one of the most common solid tumors in children. Its clinical behavior ranges widely from spontaneous regression to life-threatening aggressive growth. The molecular etiology of neuroblastoma is still enigmatic and the overall cure rate of advanced disease is still very poor. Recent microarray-based technology provided us with important information such as comprehensive genomic alterations and gene expression profiles to help us understand the molecular characteristics of each tumor in detail. Several retrospective studies have revealed that these signatures are strongly correlated with patient prognoses and led to the construction of new risk stratification systems, some of which are considered for evaluation in upcoming clinical studies in a prospective way. Large-scale analyses using a variety of genetic tools also discovered a major familial neuroblastoma predisposition gene ALK, as well as new candidate susceptibility genes at 6q22 and 2q35 for sporadic neuroblastoma. Of note, ALK is mutated in 6-9% of sporadic cases, and is either amplified or constitutively activated through mutations mainly within the kinase domain, promoting the possibility of new therapeutic strategies using ALK inhibitors. Additional candidates for outcome predictors such as the methylation phenotype of tumor DNA and expression profiles of microRNA have also been proposed. Such variety of information will help us understand the heterogeneity of neuroblastoma biology and further, the combined use of these signatures will be beneficial in predicting prognosis with high accuracy, as well as choosing a suitable therapy for the individual patient.
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Affiliation(s)
- Miki Ohira
- Division of Biochemistry and Innovative Cancer Therapeutics Laboratory of Cancer Genomics, Chiba Cancer Center Research Institute, Chuoh-ku, Chiba, Japan
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205
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Buechner J, Henriksen JR, Haug BH, Tømte E, Flaegstad T, Einvik C. Inhibition of mir-21, which is up-regulated during MYCN knockdown-mediated differentiation, does not prevent differentiation of neuroblastoma cells. Differentiation 2010; 81:25-34. [PMID: 20980091 DOI: 10.1016/j.diff.2010.09.184] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 09/02/2010] [Accepted: 09/30/2010] [Indexed: 11/18/2022]
Abstract
BACKGROUND Neuroblastoma is a malignant childhood tumour arising from precursor cells of the sympathetic nervous system. Genomic amplification of the MYCN oncogene is associated with dismal prognosis. For this group of high-risk tumours, the induction of tumour cell differentiation is part of current treatment protocols. MicroRNAs (miRNAs) are small non-coding RNA molecules that effectively reduce the translation of target mRNAs. MiRNAs play an important role in cell proliferation, apoptosis, differentiation and cancer. In this study, we investigated the role of N-myc on miRNA expression in MYCN-amplified neuroblastoma. We performed a miRNA profiling study on SK-N-BE (2) cells, and determined differentially expressed miRNAs during differentiation initiated by MYCN knockdown, using anti-MYCN short-hairpin RNA (shRNA) technology. RESULTS Microarray analyses revealed 23 miRNAs differentially expressed during the MYCN knockdown-mediated neuronal differentiation of MNA neuroblastoma cells. The expression changes were bidirectional, with 11 and 12 miRNAs being up- and down-regulated, respectively. Among the down-regulated miRNAs, we found several members of the mir-17 family of miRNAs. Mir-21, an established oncomir in a variety of cancer types, became strongly up-regulated upon MYCN knockdown and the subsequent differentiation. Neither overexpression of mir-21 in the high-MYCN neuroblastoma cells, nor repression of increased mir-21 levels during MYCN knockdown-mediated differentiation had any significant effects on cell differentiation or proliferation. CONCLUSIONS We describe a subset of miRNAs that were altered during the N-myc deprived differentiation of MYCN-amplified neuroblastoma cells. In this context, N-myc acts as both an activator and suppressor of miRNA expression. Mir-21 was up-regulated during cell differentiation, but inhibition of mir-21 did not prevent this process. We were unable to establish a role for this miRNA during differentiation and proliferation of the two neuroblastoma cell lines used in this study.
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Affiliation(s)
- Jochen Buechner
- Department of Paediatrics, University Hospital of North-Norway, 9038 Tromsø, Norway.
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206
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Lee DY, Jeyapalan Z, Fang L, Yang J, Zhang Y, Yee AY, Li M, Du WW, Shatseva T, Yang BB. Expression of versican 3'-untranslated region modulates endogenous microRNA functions. PLoS One 2010; 5:e13599. [PMID: 21049042 PMCID: PMC2963607 DOI: 10.1371/journal.pone.0013599] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Accepted: 09/23/2010] [Indexed: 12/14/2022] Open
Abstract
Background Mature microRNAs (miRNAs) are single-stranded RNAs that regulate post-transcriptional gene expression. In our previous study, we have shown that versican 3′UTR, a fragment of non-coding transcript, has the ability to antagonize miR-199a-3p function thereby regulating expression of the matrix proteins versican and fibronectin, and thus resulting in enhanced cell-cell adhesion and organ adhesion. However, the impact of this non-coding fragment on tumorigenesis is yet to be determined. Methods and Findings Using computational prediction confirmed with in vitro and in vivo experiments, we report that the expression of versican 3′UTR not only antagonizes miR-199a-3p but can also lower its steady state expression. We found that expression of versican 3′UTR in a mouse breast carcinoma cell line, 4T1, decreased miR-199a-3p levels. The decrease in miRNA activity consequently translated into differences in tumor growth. Computational analysis indicated that both miR-199a-3p and miR-144 targeted a cell cycle regulator, Rb1. In addition, miR-144 and miR-136, which have also been shown to interact with versican 3′UTR, was found to target PTEN. Expression of Rb1 and PTEN were up-regulated synergistically in vitro and in vivo, suggesting that the 3′UTR binds and modulates miRNA activities, freeing Rb1 and PTEN mRNAs for translation. In tumor formation assays, cells transfected with the 3′UTR formed smaller tumors compared with cells transfected with a control vector. Conclusion Our results demonstrated that a 3′UTR fragment can be used to modulate miRNA functions. Our study also suggests that miRNAs in the cancer cells are more susceptible to degradation, due to its interaction with a non-coding 3′UTR. This non-coding component of mRNA may be used retrospectively to modulate miRNA activities.
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Affiliation(s)
- Daniel Y. Lee
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Zina Jeyapalan
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ling Fang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jennifer Yang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Yaou Zhang
- Life Science Division, Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong Province, China
| | - Albert Y. Yee
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Minhui Li
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - William W. Du
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Tatiana Shatseva
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Burton B. Yang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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207
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Das S, Foley N, Bryan K, Watters KM, Bray I, Murphy DM, Buckley PG, Stallings RL. MicroRNA mediates DNA demethylation events triggered by retinoic acid during neuroblastoma cell differentiation. Cancer Res 2010; 70:7874-81. [PMID: 20841484 PMCID: PMC2955783 DOI: 10.1158/0008-5472.can-10-1534] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Neuroblastoma is an often fatal pediatric cancer arising from precursor cells of the sympathetic nervous system. 13-Cis retinoic acid is included in the treatment regimen for patients with high-risk disease, and a similar derivative, all-trans-retinoic acid (ATRA), causes neuroblastoma cell lines to undergo differentiation. The molecular signaling pathways involved with ATRA-induced differentiation are complex, and the role that DNA methylation changes might play are unknown. The purpose of this study was to evaluate the genome-wide effects of ATRA on DNA methylation using methylated DNA immunoprecipitation applied to microarrays representing all known promoter and CpG islands. Four hundred and two gene promoters became demethylated, whereas 88 were hypermethylated post-ATRA. mRNA expression microarrays revealed that 82 of the demethylated genes were overexpressed by >2-fold, whereas 13 of the hypermethylated genes were underexpressed. Gene ontology analysis indicated that demethylated and re-expressed genes were enriched for signal transduction pathways, including NOS1, which is required for neural cell differentiation. As a potential mechanism for the DNA methylation changes, we show the downregulation of methyltransferases, DNMT1 and DNMT3B, along with the upregulation of endogenous microRNAs targeting them. Ectopic overexpression of miR-152, targeting DNMT1, also negatively affected cell invasiveness and anchorage-independent growth, contributing in part to the differentiated phenotype. We conclude that functionally important, miRNA-mediated DNA demethylation changes contribute to the process of ATRA-induced differentiation resulting in the activation of NOS1, a critical determinant of neural cell differentiation. Our findings illustrate the plasticity and dynamic nature of the epigenome during cancer cell differentiation.
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Affiliation(s)
- Sudipto Das
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
- Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
| | - Niamh Foley
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
- Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
| | - Kenneth Bryan
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
- Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
| | - Karen M Watters
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
- Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
| | - Isabella Bray
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
- Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
| | - Derek M Murphy
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
- Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
| | - Patrick G Buckley
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
- Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
| | - Raymond L Stallings
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
- Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
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208
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Liu C, Teng ZQ, Santistevan NJ, Szulwach KE, Guo W, Jin P, Zhao X. Epigenetic regulation of miR-184 by MBD1 governs neural stem cell proliferation and differentiation. Cell Stem Cell 2010; 6:433-44. [PMID: 20452318 DOI: 10.1016/j.stem.2010.02.017] [Citation(s) in RCA: 254] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 01/18/2010] [Accepted: 02/26/2010] [Indexed: 12/16/2022]
Abstract
Methyl-CpG binding protein 1 (MBD1) regulates gene expression via a DNA methylation-mediated epigenetic mechanism. We have previously demonstrated that MBD1 deficiency impairs adult neural stem/progenitor cell (aNSC) differentiation and neurogenesis, but the underlying mechanism was unclear. Here, we show that MBD1 regulates the expression of several microRNAs in aNSCs and, specifically, that miR-184 is directly repressed by MBD1. High levels of miR-184 promoted proliferation but inhibited differentiation of aNSCs, whereas inhibition of miR-184 rescued the phenotypes associated with MBD1 deficiency. We further found that miR-184 regulates the expression of Numblike (Numbl), a known regulator of brain development, by binding to the 3'-UTR of Numbl mRNA and affecting its translation. Expression of exogenous Numbl could rescue the aNSC defects that result from either miR-184 overexpression or MBD1 deficiency. Therefore, MBD1, miR-184, and Numbl form a regulatory network that helps control the balance between proliferation and differentiation of aNSCs.
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Affiliation(s)
- Changmei Liu
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
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209
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Down-regulation of miR-27a might reverse multidrug resistance of esophageal squamous cell carcinoma. Dig Dis Sci 2010; 55:2545-51. [PMID: 19960259 DOI: 10.1007/s10620-009-1051-6] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 11/10/2009] [Indexed: 12/16/2022]
Abstract
BACKGROUND So far, the miRNAs involved in multidrug resistance of esophageal cancer have not been reported. AIMS AND METHODS Here we have firstly investigated the roles of miR-27a in multidrug resistance of esophageal squamous cell carcinoma using MTT assay, flow cytometry assay, and reporter gene assay, etc. RESULTS Down-regulation of miR-27a could confer sensitivity of both P-glycoprotein-related and P-glycoprotein-non-related drugs on esophageal cancer cells, and might promote ADR-induced apoptosis, accompanied by increased accumulation and decreased releasing amount of ADR. Down-regulation of miR-27a could significantly decrease the expression of P-glycoprotein, Bcl-2, and the transcription of the multidrug resistance gene 1, but up-regulate the expression of Bax. CONCLUSIONS MiR-27a might play important roles in multidrug resistance of esophageal cancer. The further study of the biological functions of miR-27a might be helpful for developing possible strategies to treat esophageal cancer.
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210
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Lin RJ, Lin YC, Chen J, Kuo HH, Chen YY, Diccianni MB, London WB, Chang CH, Yu AL. microRNA signature and expression of Dicer and Drosha can predict prognosis and delineate risk groups in neuroblastoma. Cancer Res 2010; 70:7841-50. [PMID: 20805302 DOI: 10.1158/0008-5472.can-10-0970] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Neuroblastoma is a common childhood tumor and accounts for 15% of pediatric cancer deaths. To investigate the microRNA (miRNA) profile and role of Dicer and Drosha in neuroblastoma, we assessed the expression of 162 human miRNAs, Dicer and Drosha in 66 neuroblastoma tumors by using real-time PCR methods. We found global downregulation of miRNA expression in advanced neuroblastoma and identified 27 miRNAs that can clearly distinguish low- from high-risk patients. Furthermore, expression levels of Dicer or Drosha were low in high-risk neuroblastoma tumors, which accounted for global downregulation of miRNAs in advanced disease and correlated with poor outcome. Notably, for patients with non-MYCN-amplified tumors, low expression of Dicer can serve as a significant and independent predictor of poor outcome (hazard ratio, 9.6; P = 0.045; n = 52). Using plausible neural networks to select a combination of 15 biomarkers that consist of 12 miRNAs' signature, expression levels of Dicer and Drosha, and age at diagnosis, we were able to segregate all patients into four distinct patterns that were highly predictive of clinical outcome. In vitro studies also showed that knockdown of either Dicer or Drosha promoted the growth of neuroblastoma cell lines. Our results reveal that a combination of 15 biomarkers can delineate risk groups of neuroblastoma and serve as a powerful predictor of clinical outcome. Moreover, our findings of growth promotion by silencing Dicer/Drosha implied their potential use as therapeutic targets for neuroblastoma.
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Affiliation(s)
- Ruey-Jen Lin
- Graduate Institute of Life Science, National Defense Medical Center, and Genomics Research Center, Academia Sinica, Taipei, Taiwan
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211
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Guan Y, Mizoguchi M, Yoshimoto K, Hata N, Shono T, Suzuki SO, Araki Y, Kuga D, Nakamizo A, Amano T, Ma X, Hayashi K, Sasaki T. MiRNA-196 is upregulated in glioblastoma but not in anaplastic astrocytoma and has prognostic significance. Clin Cancer Res 2010; 16:4289-97. [PMID: 20601442 DOI: 10.1158/1078-0432.ccr-10-0207] [Citation(s) in RCA: 149] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
PURPOSE MicroRNAs (miRNA) are short noncoding RNAs that can play critical roles in diverse biological processes. They are implicated in tumorigenesis and function both as tumor suppressors and as oncogenes. The clinical significance of miRNA expression profiles in malignant gliomas remains unclear. EXPERIMENTAL DESIGN In this study, we examined the expression levels of 365 mature human miRNAs in 12 malignant gliomas, including 8 glioblastomas and 4 anaplastic astrocytomas, using TaqMan real-time quantitative PCR arrays. A validation study was done to corroborate a subset of the results, including expression levels of miR-196a, -196b, -21, and -15b, by analyzing 92 malignant gliomas by conventional real-time PCR. We modeled the relationship between the expression levels of these miRNAs and the survival rate of 39 glioblastoma patients by Kaplan-Meier method and multivariate analysis. RESULTS Expression profiles in glioblastomas and anaplastic astrocytomas suggested that 16 miRNAs were candidate markers associated with the malignant progression of gliomas. Among them, miR-196a showed the most significant difference (P = 0.0038), with miR-196b also having a high significance (P = 0.0371). Both miRNAs showed increased expression levels in glioblastomas relative to both anaplastic astrocytomas and normal brains in the validation study. Furthermore, patients with high miR-196 expression levels showed significantly poorer survival by the Kaplan-Meier method (P = 0.0073). Multivariate analysis showed that miR-196 expression levels were an independent predictor of overall survival in all 39 glioblastoma patients (P = 0.021; hazard ratio, 2.81). CONCLUSIONS Our results suggest that miR-196 may play a role in the malignant progression of gliomas and may be a prognostic predictor in glioblastomas.
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Affiliation(s)
- Yanlei Guan
- Department of Neurosurgery and Neuropathology, Kyushu University, Fukuoka, Japan
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212
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Melo SA, Esteller M. Dysregulation of microRNAs in cancer: playing with fire. FEBS Lett 2010; 585:2087-99. [PMID: 20708002 DOI: 10.1016/j.febslet.2010.08.009] [Citation(s) in RCA: 228] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 08/03/2010] [Accepted: 08/05/2010] [Indexed: 12/13/2022]
Abstract
MicroRNAs have emerged as key post-transcriptional regulators of gene expression, involved in various physiological and pathological processes. It was found that several miRNAs are directly involved in human cancers, including lung, breast, brain, liver, colon cancer and leukemia. In addition, some miRNAs may function as oncogenes or tumor suppressors in tumor development. Furthermore, a widespread down-regulation of miRNAs is commonly observed in human cancers and promotes cellular transformation and tumorigenesis. More than 50% of miRNA genes are located in cancer-associated genomic regions or in fragile sites, frequently amplified or deleted in human cancer, suggesting an important role in malignant transformation. A better understanding of the miRNA regulation and misexpression in cancer may ultimately yield further insight into the molecular mechanisms of tumorigenesis and new therapeutic strategies may arise against cancer. Here, we discuss the occurrence of the deregulated expression of miRNAs in human cancers and their importance in the tumorigenic process.
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Affiliation(s)
- Sonia A Melo
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
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213
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Potenza N, Papa U, Scaruffi P, Mosca N, Tonini GP, Russo A. A novel splice variant of the human dicer gene is expressed in neuroblastoma cells. FEBS Lett 2010; 584:3452-7. [PMID: 20615407 DOI: 10.1016/j.febslet.2010.06.045] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Revised: 06/23/2010] [Accepted: 06/25/2010] [Indexed: 12/12/2022]
Abstract
Dicer is a ribonuclease playing a key role in the biogenesis of microRNAs and small interfering RNAs. Here we report the identification of a novel splice variant of human dicer gene, the first one bearing a modified coding sequence. It encodes a truncated protein, t-Dicer that lacks the dsRNA-binding domain and is defective in one of the two RNase III catalytic centers. The splice variant was found in neuroblastoma cells and in cells induced to neuronal differentiation, whereas it was not detectable in other cell lines or in normal tissues. Interestingly, it occurred in primary neuroblastic tumors, mainly in stroma poor neuroblastomas.
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Affiliation(s)
- Nicoletta Potenza
- Department of Life Sciences, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
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214
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Ragusa M, Majorana A, Banelli B, Barbagallo D, Statello L, Casciano I, Guglielmino MR, Duro LR, Scalia M, Magro G, Di Pietro C, Romani M, Purrello M. MIR152, MIR200B, and MIR338, human positional and functional neuroblastoma candidates, are involved in neuroblast differentiation and apoptosis. J Mol Med (Berl) 2010; 88:1041-53. [PMID: 20574809 DOI: 10.1007/s00109-010-0643-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 05/10/2010] [Accepted: 06/03/2010] [Indexed: 11/26/2022]
Abstract
MicroRNAs (MIRs) perform critical regulatory functions within cell networks, both in physiology as well as in pathology. Through the positional gene candidate approach, we have identified three MIRs (MIR152, MIR200B, and MIR338) that are located in regions frequently altered in neuroblastoma (NB) and target mRNAs encoding proteins involved in cell proliferation, neuroblast differentiation, neuroblast migration, and apoptosis. Expression analysis in NB biopsies and NB cell lines showed that these MIRs are dysregulated. We have characterized a CpG island, close to the gene encoding MIR200B and hypermethylated in NB samples, that explains its negative regulation. Expression of MIR152, MIR200B, and MIR338 is specifically modulated in NB cell lines during differentiation and apoptosis. Functional genomic experiments through enforced expression of MIR200B and knockdown of MIR152 resulted in a significant decrease of the invasion activity of SH-SY5Y cells. Reconstruction of a NB network comprising MIR152, MIR200B, and MIR338 allowed us to confirm their role in the control of NB cell stemness and apoptosis: This suggests that altered regulation of these MIRs could have a role in NB pathogenesis by interfering with the molecular mechanisms, which physiologically control differentiation and death of neuroblasts. Accordingly, they could be considered as new NB biomarkers and potential targets of antagomirs or epigenetic therapies.
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Affiliation(s)
- Marco Ragusa
- Unità di BioMedicina Molecolare Genomica e dei Sistemi Complessi, Genetica, Biologia Computazionale G Sichel, Dipartimento di Scienze BioMediche, Sezione di Biologia Generale, Biologia Cellulare, Genetica Molecolare, Università degli Studi di Catania, 95123, Catania, Italy
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215
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Slezak-Prochazka I, Durmus S, Kroesen BJ, van den Berg A. MicroRNAs, macrocontrol: regulation of miRNA processing. RNA (NEW YORK, N.Y.) 2010; 16:1087-95. [PMID: 20423980 PMCID: PMC2874160 DOI: 10.1261/rna.1804410] [Citation(s) in RCA: 203] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
MicroRNAs (miRNAs) are a set of small, non-protein-coding RNAs that regulate gene expression at the post-transcriptional level. Maturation of miRNAs comprises several regulated steps resulting in approximately 22-nucleotide single-stranded mature miRNAs. Regulation of miRNA expression can occur both at the transcriptional level and at the post-transcriptional level during miRNA processing. Recent studies have elucidated specific aspects of the well-regulated nature of miRNA processing involving various regulatory proteins, editing of miRNA transcripts, and cellular location. In addition, single nucleotide polymorphisms in miRNA genes can also affect the processing efficiency of primary miRNA transcripts. In this review we present an overview of the currently known regulatory pathways of miRNA processing and provide a basis to understand how aberrant miRNA processing may arise and may be involved in pathophysiological conditions such as cancer.
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Affiliation(s)
- Izabella Slezak-Prochazka
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB, Groningen, The Netherlands
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216
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Schulte JH, Marschall T, Martin M, Rosenstiel P, Mestdagh P, Schlierf S, Thor T, Vandesompele J, Eggert A, Schreiber S, Rahmann S, Schramm A. Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma. Nucleic Acids Res 2010; 38:5919-28. [PMID: 20466808 PMCID: PMC2943620 DOI: 10.1093/nar/gkq342] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Small non-coding RNAs, in particular microRNAs(miRNAs), regulate fine-tuning of gene expression and can act as oncogenes or tumor suppressor genes. Differential miRNA expression has been reported to be of functional relevance for tumor biology. Using next-generation sequencing, the unbiased and absolute quantification of the small RNA transcriptome is now feasible. Neuroblastoma(NB) is an embryonal tumor with highly variable clinical course. We analyzed the small RNA transcriptomes of five favorable and five unfavorable NBs using SOLiD next-generation sequencing, generating a total of >188 000 000 reads. MiRNA expression profiles obtained by deep sequencing correlated well with real-time PCR data. Cluster analysis differentiated between favorable and unfavorable NBs, and the miRNA transcriptomes of these two groups were significantly different. Oncogenic miRNAs of the miR17-92 cluster and the miR-181 family were overexpressed in unfavorable NBs. In contrast, the putative tumor suppressive microRNAs, miR-542-5p and miR-628, were expressed in favorable NBs and virtually absent in unfavorable NBs. In-depth sequence analysis revealed extensive post-transcriptional miRNA editing. Of 13 identified novel miRNAs, three were further analyzed, and expression could be confirmed in a cohort of 70 NBs.
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Affiliation(s)
- Johannes H Schulte
- University Children's Hospital Essen, Hufelandstr. 55, 45122 Essen, Germany.
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217
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Letzen BS, Liu C, Thakor NV, Gearhart JD, All AH, Kerr CL. MicroRNA expression profiling of oligodendrocyte differentiation from human embryonic stem cells. PLoS One 2010; 5:e10480. [PMID: 20463920 PMCID: PMC2864763 DOI: 10.1371/journal.pone.0010480] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 04/13/2010] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Cells of the oligodendrocyte (OL) lineage play a vital role in the production and maintenance of myelin, a multilamellar membrane which allows for saltatory conduction along axons. These cells may provide immense therapeutic potential for lost sensory and motor function in demyelinating conditions, such as spinal cord injury, multiple sclerosis, and transverse myelitis. However, the molecular mechanisms controlling OL differentiation are largely unknown. MicroRNAs (miRNAs) are considered the "micromanagers" of gene expression with suggestive roles in cellular differentiation and maintenance. Although unique patterns of miRNA expression in various cell lineages have been characterized, this is the first report documenting their expression during oligodendrocyte maturation from human embryonic stem (hES) cells. Here, we performed a global miRNA analysis to reveal and identify characteristic patterns in the multiple stages leading to OL maturation from hES cells including those targeting factors involved in myelin production. METHODOLOGY/PRINCIPAL FINDINGS We isolated cells from 8 stages of OL differentiation. Total RNA was subjected to miRNA profiling and validations preformed using real-time qRT-PCR. A comparison of miRNAs from our cultured OLs and OL progenitors showed significant similarities with published results from equivalent cells found in the rat and mouse central nervous system. Principal component analysis revealed four main clusters of miRNA expression corresponding to early, mid, and late progenitors, and mature OLs. These results were supported by correlation analyses between adjacent stages. Interestingly, the highest differentially-expressed miRNAs demonstrated a similar pattern of expression throughout all stages of differentiation, suggesting that they potentially regulate a common target or set of targets in this process. The predicted targets of these miRNAs include those with known or suspected roles in oligodendrocyte development and myelination including C11Orf9, CLDN11, MYTL1, MBOP, MPZL2, and DDR1. CONCLUSIONS/SIGNIFICANCE We demonstrate miRNA profiles during distinct stages in oligodendroglial differentiation that may provide key markers of OL maturation. Our results reveal pronounced trends in miRNA expression and their potential mRNA target interactions that could provide valuable insight into the molecular mechanisms of differentiation.
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Affiliation(s)
- Brian S. Letzen
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Cyndi Liu
- Stem Cell Program, Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Nitish V. Thakor
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - John D. Gearhart
- Department of Cell and Developmental Biology, Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Animal Biology, Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Angelo H. All
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Candace L. Kerr
- Department of Gynecology and Obstetrics, Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Stem Cell Program, Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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218
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Malzkorn B, Wolter M, Liesenberg F, Grzendowski M, Stühler K, Meyer HE, Reifenberger G. Identification and functional characterization of microRNAs involved in the malignant progression of gliomas. Brain Pathol 2010; 20:539-50. [PMID: 19775293 PMCID: PMC8094849 DOI: 10.1111/j.1750-3639.2009.00328.x] [Citation(s) in RCA: 262] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 08/10/2009] [Indexed: 12/31/2022] Open
Abstract
Diffuse astrocytoma of World Health Organization (WHO) grade II has an inherent tendency to spontaneously progress to anaplastic astrocytoma WHO grade III or secondary glioblastoma WHO grade IV. We explored the role of microRNAs (miRNAs) in glioma progression by investigating the expression profiles of 157 miRNAs in four patients with primary WHO grade II gliomas that spontaneously progressed to WHO grade IV secondary glioblastomas. Thereby, we identified 12 miRNAs (miR-9, miR-15a, miR-16, miR-17, miR-19a, miR-20a, miR-21, miR-25, miR-28, miR-130b, miR-140 and miR-210) showing increased expression, and two miRNAs (miR-184 and miR-328) showing reduced expression upon progression. Validation experiments on independent series of primary low-grade and secondary high-grade astrocytomas confirmed miR-17 and miR-184 as promising candidates, which were selected for functional analyses. These studies revealed miRNA-specific influences on the viability, proliferation, apoptosis and invasive growth properties of A172 and T98G glioma cells in vitro. Using mRNA and protein expression profiling, we identified distinct sets of transcripts and proteins that were differentially expressed after inhibition of miR-17 or overexpression of miR-184 in glioma cells. Taken together, our results support an important role of altered miRNA expression in gliomas, and suggest miR-17 and miR-184 as interesting candidates contributing to glioma progression.
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Affiliation(s)
- Bastian Malzkorn
- Department of Neuropathology, Heinrich‐Heine‐University, Düsseldorf, and
| | - Marietta Wolter
- Department of Neuropathology, Heinrich‐Heine‐University, Düsseldorf, and
| | | | | | - Kai Stühler
- Medizinisches Proteom‐Center, Ruhr‐University, Bochum, Germany
| | - Helmut E. Meyer
- Medizinisches Proteom‐Center, Ruhr‐University, Bochum, Germany
| | - Guido Reifenberger
- Department of Neuropathology, Heinrich‐Heine‐University, Düsseldorf, and
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Foley NH, Bray IM, Tivnan A, Bryan K, Murphy DM, Buckley PG, Ryan J, O'Meara A, O'Sullivan M, Stallings RL. MicroRNA-184 inhibits neuroblastoma cell survival through targeting the serine/threonine kinase AKT2. Mol Cancer 2010; 9:83. [PMID: 20409325 PMCID: PMC2864218 DOI: 10.1186/1476-4598-9-83] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 04/21/2010] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Neuroblastoma is a paediatric cancer of the sympathetic nervous system. The single most important genetic indicator of poor clinical outcome is amplification of the MYCN transcription factor. One of many down-stream MYCN targets is miR-184, which is either directly or indirectly repressed by this transcription factor, possibly due to its pro-apoptotic effects when ectopically over-expressed in neuroblastoma cells. The purpose of this study was to elucidate the molecular mechanism by which miR-184 conveys pro-apoptotic effects. RESULTS We demonstrate that the knock-down of endogenous miR-184 has the opposite effect of ectopic up-regulation, leading to enhanced neuroblastoma cell numbers. As a mechanism of how miR-184 causes apoptosis when over-expressed, and increased cell numbers when inhibited, we demonstrate direct targeting and degradation of AKT2, a major downstream effector of the phosphatidylinositol 3-kinase (PI3K) pathway, one of the most potent pro-survival pathways in cancer. The pro-apoptotic effects of miR-184 ectopic over-expression in neuroblastoma cell lines is reproduced by siRNA inhibition of AKT2, while a positive effect on cell numbers similar to that obtained by the knock-down of endogenous miR-184 can be achieved by ectopic up-regulation of AKT2. Moreover, co-transfection of miR-184 with an AKT2 expression vector lacking the miR-184 target site in the 3'UTR rescues cells from the pro-apoptotic effects of miR-184. CONCLUSIONS MYCN contributes to tumorigenesis, in part, by repressing miR-184, leading to increased levels of AKT2, a direct target of miR-184. Thus, two important genes with positive effects on cell growth and survival, MYCN and AKT2, can be linked into a common genetic pathway through the actions of miR-184. As an inhibitor of AKT2, miR-184 could be of potential benefit in miRNA mediated therapeutics of MYCN amplified neuroblastoma and other forms of cancer.
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Affiliation(s)
- Niamh H Foley
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
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220
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Buckley PG, Alcock L, Bryan K, Bray I, Schulte JH, Schramm A, Eggert A, Mestdagh P, De Preter K, Vandesompele J, Speleman F, Stallings RL. Chromosomal and microRNA expression patterns reveal biologically distinct subgroups of 11q- neuroblastoma. Clin Cancer Res 2010; 16:2971-8. [PMID: 20406844 DOI: 10.1158/1078-0432.ccr-09-3215] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The purpose of this study was to further define the biology of the 11q- neuroblastoma tumor subgroup by the integration of array-based comparative genomic hybridization with microRNA (miRNA) expression profiling data to determine if improved patient stratification is possible. EXPERIMENTAL DESIGN A set of primary neuroblastoma (n = 160), which was broadly representative of all genetic subtypes, was analyzed by array-based comparative genomic hybridization and for the expression of 430 miRNAs. A 15-miRNA expression signature previously shown to be predictive of clinical outcome was used to analyze an independent cohort of 11q- tumors (n = 37). RESULTS Loss of 4p and gain of 7q occurred at a significantly higher frequency in the 11q- tumors, further defining the genetic characteristics of this subtype. The 11q- tumors could be split into two subgroups using a miRNA expression survival signature that differed significantly in clinical outcome and the overall frequency of large-scale genomic imbalances, with the poor survival subgroup having significantly more imbalances. miRNAs from the expression signature, which were upregulated in unfavorable tumors, were predicted to target downregulated genes from a published mRNA expression classifier of clinical outcome at a higher-than-expected frequency, indicating the miRNAs might contribute to the regulation of genes within the signature. CONCLUSION We show that two distinct biological subtypes of neuroblastoma with loss of 11q occur, which differ in their miRNA expression profiles, frequency of segmental imbalances, and clinical outcome. A miRNA expression signature, combined with an analysis of segmental imbalances, provides greater prediction of event-free survival and overall survival outcomes than 11q status by itself, improving patient stratification.
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Affiliation(s)
- Patrick G Buckley
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
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221
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Localized expression pattern of miR-184 in Drosophila. Mol Biol Rep 2010; 38:355-8. [DOI: 10.1007/s11033-010-0115-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 03/16/2010] [Indexed: 11/27/2022]
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222
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Wang HW, Wu YH, Hsieh JY, Liang ML, Chao ME, Liu DJ, Hsu MT, Wong TT. Pediatric primary central nervous system germ cell tumors of different prognosis groups show characteristic miRNome traits and chromosome copy number variations. BMC Genomics 2010; 11:132. [PMID: 20178649 PMCID: PMC2837036 DOI: 10.1186/1471-2164-11-132] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Accepted: 02/24/2010] [Indexed: 01/07/2023] Open
Abstract
Background Intracranial pediatric germ cell tumors (GCTs) are rare and heterogeneous neoplasms and vary in histological differentiation, prognosis and clinical behavior. Germinoma and mature teratoma are GCTs that have a good prognosis, while other types of GCTs, termed nongerminomatous malignant germ cell tumors (NGMGCTs), are tumors with an intermediate or poor prognosis. The second group of tumors requires more extensive drug and irradiation treatment regimens. The mechanisms underlying the differences in incidence and prognosis of the various GCT subgroups are unclear. Results We identified a distinct mRNA profile correlating with GCT histological differentiation and prognosis, and also present in this study the first miRNA profile of pediatric primary intracranial GCTs. Most of the differentially expressed miRNAs were downregulated in germinomas, but miR-142-5p and miR-146a were upregulated. Genes responsible for self-renewal (such as POU5F1 (OCT4), NANOG and KLF4) and the immune response were abundant in germinomas, while genes associated with neuron differentiation, Wnt/β-catenin pathway, invasiveness and epithelial-mesenchymal transition (including SNAI2 (SLUG) and TWIST2) were abundant in NGMGCTs. Clear transcriptome segregation based on patient survival was observed, with malignant NGMGCTs being closest to embryonic stem cells. Chromosome copy number variations (CNVs) at cytobands 4q13.3-4q28.3 and 9p11.2-9q13 correlated with GCT malignancy and clinical risk. Six genes (BANK1, CXCL9, CXCL11, DDIT4L, ELOVL6 and HERC5) within 4q13.3-4q28.3 were more abundant in germinomas. Conclusions Our results integrate molecular profiles with clinical observations and provide insights into the underlying mechanisms causing GCT malignancy. The genes, pathways and microRNAs identified have the potential to be novel therapeutic targets.
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Affiliation(s)
- Hsei-Wei Wang
- School of Life Sciences, Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
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223
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Bell E, Chen L, Liu T, Marshall GM, Lunec J, Tweddle DA. MYCN oncoprotein targets and their therapeutic potential. Cancer Lett 2010; 293:144-57. [PMID: 20153925 DOI: 10.1016/j.canlet.2010.01.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 01/11/2010] [Accepted: 01/16/2010] [Indexed: 12/16/2022]
Abstract
The MYCN oncogene encodes a transcription factor which is amplified in up to 40% of high risk neuroblastomas. MYCN amplification is a well-established poor prognostic marker in neuroblastoma, however the role of MYCN expression and the mechanisms by which it acts to promote an aggressive phenotype remain largely unknown. This review discusses the current evidence identifying the direct and indirect downstream transcriptional targets of MYCN from recent studies, with particular reference to how MYCN affects the cell cycle, DNA damage response, differentiation and apoptosis in neuroblastoma.
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Affiliation(s)
- Emma Bell
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
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Liu CJ, Tsai MM, Hung PS, Kao SY, Liu TY, Wu KJ, Chiou SH, Lin SC, Chang KW. miR-31 ablates expression of the HIF regulatory factor FIH to activate the HIF pathway in head and neck carcinoma. Cancer Res 2010; 70:1635-44. [PMID: 20145132 DOI: 10.1158/0008-5472.can-09-2291] [Citation(s) in RCA: 254] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
MicroRNAs (miRNA) are endogenously expressed noncoding RNAs with important biological and pathological functions that are yet to be fully defined. This study investigated alterations in miRNA expression in head and neck squamous cell carcinoma (HNSCC), the incidence of which is rising throughout the world. Initial screening and subsequent analysis identified a panel of aberrantly expressed miRNAs in HNSCC tissues, with miR-31 among the most markedly upregulated. Ectopic expression of miR-31 increased the oncogenic potential of HNSCC cells under normoxic conditions in cell culture or tumor xenografts. Conversely, blocking miR-31 expression reduced the growth of tumor xenografts. The in silico analysis suggested that miR-31 may target the 3' untranslated region (UTR) of factor-inhibiting hypoxia-inducible factor (FIH), a hypoxia-inducible factor (HIF) regulatory factor that inhibits the ability of HIF to act as a transcriptional regulator under normoxic conditions. In support of this likelihood, miR-31 expression repressed FIH expression and mutations within the predictive miR-31 target site in the FIH 3' UTR abrogated FIH repression. Furthermore, miR-31 expression increased HIF transactivation activity. We found that FIH suppressed oncogenic phenotypes under normoxic conditions and that this activity was abrogated by functional mutations. Lastly, increased miR-31 expression was correlated with decreased levels of FIH in tumor tissues. Our findings suggest that miR-31 contributes to the development of HNSCC by impeding FIH to activate HIF under normoxic conditions.
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Affiliation(s)
- Chung-Ji Liu
- Institute of Oral Biology and Institute of Biochemistry, National Yang-Ming University, Taipei 112, Taiwan
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225
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Neuroblastoma-specific expression of potential therapeutics cannot be achieved using a promoter region of the NCX (TLX2) gene. Cancer Gene Ther 2010; 17:373-4. [PMID: 20094074 DOI: 10.1038/cgt.2009.90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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226
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Schaefer A, Jung M, Mollenkopf HJ, Wagner I, Stephan C, Jentzmik F, Miller K, Lein M, Kristiansen G, Jung K. Diagnostic and prognostic implications of microRNA profiling in prostate carcinoma. Int J Cancer 2010; 126:1166-76. [PMID: 19676045 DOI: 10.1002/ijc.24827] [Citation(s) in RCA: 304] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This study aimed to investigate the microRNA (miRNA) profile in prostate carcinoma tissue by microarray analysis and RT-qPCR, to clarify associations of miRNA expression with clinicopathologic data and to evaluate the potential of miRNAs as diagnostic and prognostic markers. Matched tumor and adjacent normal tissues were obtained from 76 radical prostatectomy specimens. Twenty-four tissue pairs were analyzed using human miRNA microarrays for 470 human miRNAs. Differentially expressed miRNAs were validated by TaqMan RT-qPCR using all 76 tissue pairs. The diagnostic potential of miRNAs was calculated by receiver operating characteristics analyses. The prognostic value was assessed in terms of biochemical recurrence using Kaplan-Meier and Cox regression analyses. Fifteen differentially expressed miRNAs were identified with concordant fold-changes by microarray and RT-qPCR analyses. Ten microRNAs (hsa-miR-16, hsa-miR-31, hsa-miR-125b, hsa-miR-145, hsa-miR-149, hsa-miR-181b, hsa-miR-184, hsa-miR-205, hsa-miR-221, hsa-miR-222) were downregulated and 5 miRNAs (hsa-miR-96, hsa-miR-182, hsa-miR-182, hsa-miR-183, hsa-375) were upregulated. Expression of 5 miRNAs correlated with Gleason score or pathological tumor stage. Already 2 microRNAs classified up to 84% of malignant and nonmalignant samples correctly. Expression of hsa-miR-96 was associated with cancer recurrence after radical prostatectomy and that prognostic information was confirmed by an independent tumor sample set from 79 patients. That was shown with hsa-miR-96 and the Gleason score as final variables in the Cox models build in the 2 patient sets investigated. Thus, differential miRNAs in prostate cancer are useful diagnostic and prognostic indicators. This study provides a solid basis for further functional analyses of miRNAs in prostate cancer.
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Oglesby IK, Bray IM, Chotirmall SH, Stallings RL, O’Neill SJ, McElvaney NG, Greene CM. miR-126 Is Downregulated in Cystic Fibrosis Airway Epithelial Cells and Regulates TOM1 Expression. THE JOURNAL OF IMMUNOLOGY 2010; 184:1702-9. [DOI: 10.4049/jimmunol.0902669] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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228
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Avissar M, McClean MD, Kelsey KT, Marsit CJ. MicroRNA expression in head and neck cancer associates with alcohol consumption and survival. Carcinogenesis 2010; 30:2059-63. [PMID: 19901002 DOI: 10.1093/carcin/bgp277] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The contribution of microRNAs (miRNAs) to carcinogenesis in many tumors, including head and neck squamous cell carcinomas (HNSCCs), is clear, but the etiology and clinical significance of their alteration remain important questions. Our previous work has identified four miRNAs as differentially expressed HNSCCs compared with non-diseased epithelia and showed that there is potential diagnostic utility in examining their expression. Here, we used quantitative real-time polymerase chain reaction to determine the relative expression of these miRNAs in a larger independent case series of HNSCC tumors (n = 169), examining associations of miRNA expression with exposures and clinical features associated with HNSCC. In multivariate analyses, expression of miR-375 was shown to increase with alcohol consumption (P = 0.002) and showed higher expression in tumors of pharyngeal and laryngeal origin compared with oral tumors (P < 0.05 and P < 0.01, respectively). Additionally, high miR-21 expression was associated with significantly decreased 5 year survival in patients (hazard ratio, 1.68; 95% CI: 1.04-2.77) in a model controlled for patient age, gender and tumor stage. Together, these data suggest that alterations in miRNA expression are related to exposures causal in head and neck cancer and may be useful biomarkers of patient outcome.
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Affiliation(s)
- Michele Avissar
- Department of Pathology and Laboratory Medicine, Brown University, Box G-E5, Providence, RI 02912, USA
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229
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MYCN-regulated microRNAs repress estrogen receptor-alpha (ESR1) expression and neuronal differentiation in human neuroblastoma. Proc Natl Acad Sci U S A 2010; 107:1553-8. [PMID: 20080637 DOI: 10.1073/pnas.0913517107] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
MYCN, a proto-oncogene normally expressed in the migrating neural crest, is in its amplified state a key factor in the genesis of human neuroblastoma (NB). However, the mechanisms underlying MYCN-mediated NB progression are poorly understood. Here, we present a MYCN-induced miRNA signature in human NB involving the activation and transrepression of several miRNA genes from paralogous clusters. Several family members derived from the miR-17 approximately 92 cluster, including miR-18a and miR-19a, were among the up-regulated miRNAs. Expression analysis of these miRNAs in NB tumors confirmed increased levels in MYCN-amplified samples. Specifically, we show that miR-18a and miR-19a target and repress the expression of estrogen receptor-alpha (ESR1), a ligand-inducible transcription factor implicated in neuronal differentiation. Immunohistochemical staining demonstrated ESR1 expression in human fetal sympathetic ganglia, suggesting a role for ESR1 during sympathetic nervous system development. Concordantly, lentiviral restoration of ESR1 in NB cells resulted in growth arrest and neuronal differentiation. Moreover, lentiviral-mediated inhibition of miR-18a in NB cells led to severe growth retardation, outgrowth of varicosity-containing neurites, and induction of neuronal sympathetic differentiation markers. Bioinformatic analyses of microarray data from NB tumors revealed that high ESR1 expression correlates with increased event-free survival in NB patients and favorable disease outcome. Thus, MYCN amplification may disrupt estrogen signaling sensitivity in primitive sympathetic cells through deregulation of ESR1, thereby preventing the normal induction of neuroblast differentiation. Collectively, our findings demonstrate the molecular consequences of abnormal miRNA transcription in a MYCN-driven tumor and offer unique insights into the pathology underlying MYCN-amplified NB.
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Gallagher MF, Flavin RJ, Elbaruni SA, McInerney JK, Smyth PC, Salley YM, Vencken SF, O'Toole SA, Laios A, Lee MYC, Denning K, Li J, Aherne ST, Lao KQ, Martin CM, Sheils OM, O'Leary JJ. Regulation of microRNA biosynthesis and expression in 2102Ep embryonal carcinoma stem cells is mirrored in ovarian serous adenocarcinoma patients. J Ovarian Res 2009; 2:19. [PMID: 20015364 PMCID: PMC2805659 DOI: 10.1186/1757-2215-2-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 12/16/2009] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Tumours with high proportions of differentiated cells are considered to be of a lower grade to those containing high proportions of undifferentiated cells. This property may be linked to the differentiation properties of stem cell-like populations within malignancies. We aim to identify molecular mechanism associated with the generation of tumours with differing grades from malignant stem cell populations with different differentiation potentials. In this study we assessed microRNA (miRNA) regulation in two populations of malignant Embryonal Carcinoma (EC) stem cell, which differentiate (NTera2) or remain undifferentiated (2102Ep) during tumourigenesis, and compared this to miRNA regulation in ovarian serous carcinoma (OSC) patient samples. METHODS miRNA expression was assessed in NTera2 and 2102Ep cells in the undifferentiated and differentiated states and compared to that of OSC samples using miRNA qPCR. RESULTS Our analysis reveals a substantial overlap between miRNA regulation in 2102Ep cells and OSC samples in terms of miRNA biosynthesis and expression of mature miRNAs, particularly those of the miR-17/92 family and clustering to chromosomes 14 and 19. In the undifferentiated state 2102Ep cells expressed mature miRNAs at up to 15,000 fold increased levels despite decreased expression of miRNA biosynthesis genes Drosha and Dicer. 2102Ep cells avoid differentiation, which we show is associated with consistent levels of expression of miRNA biosynthesis genes and mature miRNAs while expression of miRNAs clustering to chromosomes 14 and 19 is deemphasised. OSC patient samples displayed decreased expression of miRNA biosynthesis genes, decreased expression of mature miRNAs and prominent clustering to chromosome 14 but not 19. This indicates that miRNA biosynthesis and levels of miRNA expression, particularly from chromosome 14, are tightly regulated both in progenitor cells and in tumour samples. CONCLUSION miRNA biosynthesis and expression of mature miRNAs, particularly the miR-17/92 family and those clustering to chromosomes 14 and 19, are highly regulated in both progenitor cells and tumour samples. Strikingly, 2102Ep cells are not simply malfunctioning but respond to differentiation specifically, a mechanism that is highly relevant to OSC samples. Our identification and future manipulation of these miRNAs may facilitate generation of lower grade malignancies from these high-grade cells.
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Affiliation(s)
- Michael F Gallagher
- Department of Histopathology, University of Dublin, Trinity College, Institute of Molecular Medicine, St James's Hospital, Dublin 8, Ireland
- Department of Pathology, Coombe Women and Infants University Hospital, Dublin 8, Ireland
| | - Richard J Flavin
- The Centre for Molecular Oncologic Pathology, The Dana Faber Cancer Institute, Boston, MA02115, USA
| | - Salah A Elbaruni
- Department of Histopathology, University of Dublin, Trinity College, Institute of Molecular Medicine, St James's Hospital, Dublin 8, Ireland
- Department of Pathology, Coombe Women and Infants University Hospital, Dublin 8, Ireland
| | - Jamie K McInerney
- Department of Histopathology, University of Dublin, Trinity College, Institute of Molecular Medicine, St James's Hospital, Dublin 8, Ireland
- Department of Pathology, Coombe Women and Infants University Hospital, Dublin 8, Ireland
| | - Paul C Smyth
- Department of Histopathology, University of Dublin, Trinity College, Institute of Molecular Medicine, St James's Hospital, Dublin 8, Ireland
| | - Yvonne M Salley
- Department of Histopathology, University of Dublin, Trinity College, Institute of Molecular Medicine, St James's Hospital, Dublin 8, Ireland
- Department of Pathology, Coombe Women and Infants University Hospital, Dublin 8, Ireland
| | - Sebastian F Vencken
- Department of Histopathology, University of Dublin, Trinity College, Institute of Molecular Medicine, St James's Hospital, Dublin 8, Ireland
- Department of Pathology, Coombe Women and Infants University Hospital, Dublin 8, Ireland
| | - Sharon A O'Toole
- Department of Obstetrics and Gynaecology, University of Dublin, Trinity College, Institute of Molecular Medicine, St James's Hospital, Dublin 8, Ireland
| | - Alexandros Laios
- Department of Obstetrics and Gynaecology, University of Dublin, Trinity College, Institute of Molecular Medicine, St James's Hospital, Dublin 8, Ireland
| | - Mathia YC Lee
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore
| | - Karen Denning
- Department of Histopathology, University of Dublin, Trinity College, Institute of Molecular Medicine, St James's Hospital, Dublin 8, Ireland
| | - Jinghuan Li
- Department of Histopathology, University of Dublin, Trinity College, Institute of Molecular Medicine, St James's Hospital, Dublin 8, Ireland
| | - Sinead T Aherne
- Department of Histopathology, University of Dublin, Trinity College, Institute of Molecular Medicine, St James's Hospital, Dublin 8, Ireland
| | - Kai Q Lao
- Applied Biosystems, 850 Lincoln Centre Dr, Foster City, CA 94404, USA
| | - Cara M Martin
- Department of Histopathology, University of Dublin, Trinity College, Institute of Molecular Medicine, St James's Hospital, Dublin 8, Ireland
- Department of Pathology, Coombe Women and Infants University Hospital, Dublin 8, Ireland
| | - Orla M Sheils
- Department of Histopathology, University of Dublin, Trinity College, Institute of Molecular Medicine, St James's Hospital, Dublin 8, Ireland
| | - John J O'Leary
- Department of Histopathology, University of Dublin, Trinity College, Institute of Molecular Medicine, St James's Hospital, Dublin 8, Ireland
- Department of Pathology, Coombe Women and Infants University Hospital, Dublin 8, Ireland
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Scaruffi P, Stigliani S, Moretti S, Coco S, De Vecchi C, Valdora F, Garaventa A, Bonassi S, Tonini GP. Transcribed-Ultra Conserved Region expression is associated with outcome in high-risk neuroblastoma. BMC Cancer 2009; 9:441. [PMID: 20003513 PMCID: PMC2804711 DOI: 10.1186/1471-2407-9-441] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 12/15/2009] [Indexed: 02/08/2023] Open
Abstract
Background Neuroblastoma is the most common, pediatric, extra-cranial, malignant solid tumor. Despite multimodal therapeutic protocols, outcome for children with a high-risk clinical phenotype remains poor, with long-term survival still less than 40%. Hereby, we evaluated the potential of non-coding RNA expression to predict outcome in high-risk, stage 4 neuroblastoma. Methods We analyzed expression of 481 Ultra Conserved Regions (UCRs) by reverse transcription-quantitative real-time PCR and of 723 microRNAs by microarrays in 34 high-risk, stage 4 neuroblastoma patients. Results First, the comparison of 8 short- versus 12 long-term survivors showed that 54 UCRs were significantly (P < 0.0491) over-expressed in the former group. For 48 Ultra Conserved Region (UCRs) the expression levels above the cut-off values defined by ROC curves were strongly associated with good-outcome (OS: 0.0001 <P < 0.0185, EFS: 0.0001 <P < 0.0491). Then we tested the Transcribed-UCR (T-UCR) threshold risk-prediction model on an independent cohort of 14 patients. The expression profile of 28 T-UCRs was significantly associated to prognosis and at least 15 up-regulated T-UCRs are needed to discriminate (P < 0.0001) short- from long-survivors at the highest sensitivity and specificity (94.12%). We also identified a signature of 13 microRNAs differently expressed between long- and short-surviving patients. The comparative analysis of the two classes of non-coding RNAs disclosed that 9 T-UCRs display their expression level that are inversely correlated with expression of 5 complementary microRNAs of the signature, indicating a negative regulation of T-UCRs by direct interaction with microRNAs. Moreover, 4 microRNAs down-regulated in tumors of long-survivors target 3 genes implicated in neuronal differentiation, that are known to be over-expressed in low-risk tumors. Conclusions Our pilot study suggests that a deregulation of the microRNA/T-UCR network may play an important role in the pathogenesis of neuroblastoma. After further validation on a larger independent set of samples, such findings may be applied as the first T-UCR prognostic signature for high-risk neuroblastoma patients.
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Affiliation(s)
- Paola Scaruffi
- Translational Paediatric Oncology, National Cancer Research Institute (IST), Genoa, Italy.
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MYCN/c-MYC-induced microRNAs repress coding gene networks associated with poor outcome in MYCN/c-MYC-activated tumors. Oncogene 2009; 29:1394-404. [PMID: 19946337 DOI: 10.1038/onc.2009.429] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Increased activity of MYC protein-family members is a common feature in many cancers. Using neuroblastoma as a tumor model, we established a microRNA (miRNA) signature for activated MYCN/c-MYC signaling in two independent primary neuroblastoma tumor cohorts and provide evidence that c-MYC and MYCN have overlapping functions. On the basis of an integrated approach including miRNA and messenger RNA (mRNA) gene expression data we show that miRNA activation contributes to widespread mRNA repression, both in c-MYC- and MYCN-activated tumors. c-MYC/MYCN-induced miRNA activation was shown to be dependent on c-MYC/MYCN promoter binding as evidenced by chromatin immunoprecipitation. Finally, we show that pathways, repressed through c-MYC/MYCN miRNA activation, are highly correlated to tumor aggressiveness and are conserved across different tumor entities suggesting that c-MYC/MYCN activate a core set of miRNAs for cooperative repression of common transcriptional programs related to disease aggressiveness. Our results uncover a widespread correlation between miRNA activation and c-MYC/MYCN-mediated coding gene expression modulation and further substantiate the overlapping functions of c-MYC and MYCN in the process of tumorigenesis.
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233
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Bray I, Bryan K, Prenter S, Buckley PG, Foley NH, Murphy DM, Alcock L, Mestdagh P, Vandesompele J, Speleman F, London WB, McGrady PW, Higgins DG, O'Meara A, O'Sullivan M, Stallings RL. Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival. PLoS One 2009; 4:e7850. [PMID: 19924232 PMCID: PMC2773120 DOI: 10.1371/journal.pone.0007850] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Accepted: 10/22/2009] [Indexed: 12/02/2022] Open
Abstract
MiRNAs regulate gene expression at a post-transcriptional level and their dysregulation can play major roles in the pathogenesis of many different forms of cancer, including neuroblastoma, an often fatal paediatric cancer originating from precursor cells of the sympathetic nervous system. We have analyzed a set of neuroblastoma (n = 145) that is broadly representative of the genetic subtypes of this disease for miRNA expression (430 loci by stem-loop RT qPCR) and for DNA copy number alterations (array CGH) to assess miRNA involvement in disease pathogenesis. The tumors were stratified and then randomly split into a training set (n = 96) and a validation set (n = 49) for data analysis. Thirty-seven miRNAs were significantly over- or under-expressed in MYCN amplified tumors relative to MYCN single copy tumors, indicating a potential role for the MYCN transcription factor in either the direct or indirect dysregulation of these loci. In addition, we also determined that there was a highly significant correlation between miRNA expression levels and DNA copy number, indicating a role for large-scale genomic imbalances in the dysregulation of miRNA expression. In order to directly assess whether miRNA expression was predictive of clinical outcome, we used the Random Forest classifier to identify miRNAs that were most significantly associated with poor overall patient survival and developed a 15 miRNA signature that was predictive of overall survival with 72.7% sensitivity and 86.5% specificity in the validation set of tumors. We conclude that there is widespread dysregulation of miRNA expression in neuroblastoma tumors caused by both over-expression of the MYCN transcription factor and by large-scale chromosomal imbalances. MiRNA expression patterns are also predicative of clinical outcome, highlighting the potential for miRNA mediated diagnostics and therapeutics.
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Affiliation(s)
- Isabella Bray
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Kenneth Bryan
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Suzanne Prenter
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Patrick G. Buckley
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Niamh H. Foley
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Derek M. Murphy
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Leah Alcock
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Pieter Mestdagh
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Wendy B. London
- Children's Oncology Group Statistics and Data Center, University of Florida, Gainesville, Florida, United States of America
| | - Patrick W. McGrady
- Children's Oncology Group Statistics and Data Center, University of Florida, Gainesville, Florida, United States of America
| | - Desmond G. Higgins
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Anne O'Meara
- Departments of Oncology and Pathology, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Maureen O'Sullivan
- Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
- Departments of Oncology and Pathology, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Raymond L. Stallings
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
- * E-mail:
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234
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Wei J, Liu B, Cardona AF, Rosell R. Molecular biomarkers for predicting chemotherapy response in lung cancer. EXPERT OPINION ON MEDICAL DIAGNOSTICS 2009; 3:621-9. [PMID: 23496047 DOI: 10.1517/17530050903222239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Chemotherapy in non-small-cell lung cancer (NSCLC) has reached a plateau, with no evidence of substantial improvement in survival. However, recent advances in the management of lung cancer have paved the way for the optimization of treatment. Several lines of evidence indicate that multiple genetic disturbances found in human cancer cell lines and in the tumors of NSCLC patients have a role as predictive markers for response and survival with chemotherapy regimens now in use. OBJECTIVE This review highlights relevant translational research findings on potential predictive markers in lung cancer with therapeutic impact in both the near and distant future. CONCLUSION The next step is to develop clinical trials that will prospectively validate the benefits of customizing chemotherapy, which should translate into an improvement in outcome in NSCLC patients.
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Affiliation(s)
- Jia Wei
- Medical School of Nanjing University, Affiliated Drum Tower Hospital, Clinical Cancer Institute of Nanjing University, Department of Oncology, Zhongshan Road 321, Nanjing 210008, China +86 25 83317016 ; +86 25 83317016 ;
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235
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Kumar HR, Zhong X, Rescorla FJ, Hickey RJ, Malkas LH, Sandoval JA. Proteomic approaches in neuroblastoma: a complementary clinical platform for the future. Expert Rev Proteomics 2009; 6:387-94. [PMID: 19681674 DOI: 10.1586/epr.09.58] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Neuroblastoma (NB) is one of the most common solid tumors of childhood and displays a remarkable diversity in both biologic characteristics and clinical outcomes. Availability of high-throughput 'omics technologies and their subsequent application towards oncology has provided insight into the complex pathways of tumor formation and progression. Investigation of NB 'omics profiles may better define tumor behavior and provide targeted therapy with the goal of improving outcomes in patients with high-risk disease. Utilization of these technologies in NB has already led to advances in classification and risk stratification. The gradual emergence of NB-directed proteomics adds a layer of intricacy to the analysis of biologic organization but may ultimately provide a better comprehension of this complex disease. In this review, we cite specific examples of how NB-directed proteomics has provided information regarding novel biomarkers and possible therapeutic targets. We finish by examining the impact of high-throughput 'omics in the field of NB and speculate on how these emerging technologies may further be incorporated into the discipline.
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Affiliation(s)
- Hari R Kumar
- Department of Surgery, Indiana University School of Medicine, 545 Barnhill Drive, Emerson Hall 202, Indianapolis, IN 46202, USA.
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236
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Kahai S, Lee SC, Lee DY, Yang J, Li M, Wang CH, Jiang Z, Zhang Y, Peng C, Yang BB. MicroRNA miR-378 regulates nephronectin expression modulating osteoblast differentiation by targeting GalNT-7. PLoS One 2009; 4:e7535. [PMID: 19844573 PMCID: PMC2760121 DOI: 10.1371/journal.pone.0007535] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Accepted: 09/28/2009] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are small fragments of single-stranded RNA containing 18-24 nucleotides, and are generated from endogenous transcripts. MicroRNAs function in post-transcriptional gene silencing by targeting the 3'-untranslated region (UTR) of mRNAs, resulting in translational repression. We have developed a system to study the role of miRNAs in cell differentiation. We have found that one of the miRNAs tested in our system (miR-378, also called miR-378*) plays a role in modulating nephronectin-mediated differentiation in the osteoblastic cell line, MC3T3-E1. Nephronectin is an extracellular matrix protein, and we have demonstrated that its over-expression enhanced osteoblast differentiation and bone nodule formation. Furthermore, we found that the nephronectin 3'-untranslated region (3'UTR) contains a binding site for miR-378. Stable transfection of MC3T3-E1 cells with miR-378 inhibited cell differentiation. MC3T3-E1 cells stably transfected with nephronectin exhibited higher rates of differentiation and nodule formation as compared with cells transfected with nephronectin containing the 3'UTR in the early stages of development, suggesting that endogenous miR-378 is present and active. However, in the later stages of MC3T3-E1 development, the differentiation rates were opposite, with higher rates of differentiation and nodule formation in the cells over-expressing the 3'UTR of nephronectin. This appeared to be the consequence of competition between nephronectin and UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7 or GalNT7) for miR-378 binding, resulting in increased GalNT7 activity, which in turn lead to increased nephronectin glycosylation and product secretion, thereby resulting in a higher rate of osteoblast differentiation.
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Affiliation(s)
- Shireen Kahai
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Shao-Chen Lee
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Daniel Y. Lee
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Jennifer Yang
- Department of Biology, York University, Toronto, Canada
| | - Minhui Li
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
- Department of Plant Pathology, South China Agricultural University, Guangzhou, China
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Chia-Hui Wang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Zide Jiang
- Department of Plant Pathology, South China Agricultural University, Guangzhou, China
| | - Yaou Zhang
- Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Chun Peng
- Department of Biology, York University, Toronto, Canada
| | - Burton B. Yang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
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Feinberg-Gorenshtein G, Avigad S, Jeison M, Halevy-Berco G, Mardoukh J, Luria D, Ash S, Steinberg R, Weizman A, Yaniv I. Reduced levels of miR-34a in neuroblastoma are not caused by mutations in the TP53 binding site. Genes Chromosomes Cancer 2009; 48:539-43. [PMID: 19373781 DOI: 10.1002/gcc.20662] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Neuroblastoma (NB) is the most common extracranial solid tumor in children below the age of 5 years. miR-34a, located in chromosome band 1p36, has been recently implicated as a tumor suppressor gene in NB. In addition, it has been shown that miR-34a is activated by TP53 by binding to a TP53 binding site upstream to the mature miR-34a. We studied NB tumors from 57 patients for miR-34a expression levels, 1p status, mutations in the TP53 coding region and mutations of the TP53 binding site. Reduced expression levels of miR-34a were identified in tumors harboring 1p36.3 Loss (P = 0.028). No mutations were identified in the coding region of TP53, or in the TP53 binding site. Thus, mutations in the binding site are not an additional mechanism for the inactivation of miR-34a in NB. Other regulatory mechanisms controlling miR-34a expression and its relationship to TP53 should be further explored.
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238
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MicroRNA implications across neurodevelopment and neuropathology. J Biomed Biotechnol 2009; 2009:654346. [PMID: 19841678 PMCID: PMC2762243 DOI: 10.1155/2009/654346] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Revised: 05/11/2009] [Accepted: 07/20/2009] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) have rapidly emerged as biologically important mediators of posttranscriptional and epigenetic regulation in both plants and animals. miRNAs function through a variety of mechanisms including mRNA degradation and translational repression; additionally, miRNAs may guide gene expression by serving as transcription factors. miRNAs are highly expressed in human brain. Tissue and cell type-specific enrichments of certain miRNAs within the nervous system argue for a biological significance during neurodevelopmental stages. On the other hand, a large number of studies have reported links between alterations of miRNA homeostasis and pathologic conditions such as cancer, heart diseases, and neurodegeneration. Thus, profiles of distinct or aberrant miRNA signatures have most recently surged as one of the most fascinating interests in current biology. Here, the most recent insights into the involvement of miRNAs in the biology of the nervous system and the occurrence of neuropathological disorders are reviewed and discussed.
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239
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Sun H, Li QW, Lv XY, Ai JZ, Yang QT, Duan JJ, Bian GH, Xiao Y, Wang YD, Zhang Z, Liu YH, Tan RZ, Yang Y, Wei YQ, Zhou Q. MicroRNA-17 post-transcriptionally regulates polycystic kidney disease-2 gene and promotes cell proliferation. Mol Biol Rep 2009; 37:2951-8. [DOI: 10.1007/s11033-009-9861-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2009] [Accepted: 09/28/2009] [Indexed: 12/26/2022]
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Mdm2 deficiency suppresses MYCN-Driven neuroblastoma tumorigenesis in vivo. Neoplasia 2009; 11:753-62. [PMID: 19649205 DOI: 10.1593/neo.09466] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 04/26/2009] [Accepted: 04/30/2009] [Indexed: 12/26/2022] Open
Abstract
Neuroblastoma is derived from neural crest precursor components of the peripheral sympathetic nervous system and accounts for more than 15% of all pediatric cancer deaths. A clearer understanding of the molecular basis of neuroblastoma is required for novel therapeutic approaches to improve morbidity and mortality. Neuroblastoma is uniformly p53 wild type at diagnosis and must overcome p53-mediated tumor suppression during pathogenesis. Amplification of the MYCN oncogene correlates with the most clinically aggressive form of the cancer, and MDM2, a primary inhibitor of the p53 tumor suppressor, is a direct transcriptional target of, and positively regulated by, both MYCN and MYCC. We hypothesize that MDM2 contributes to MYCN-driven tumorigenesis helping to ameliorate p53-dependent apoptotic oncogenic stress during tumor initiation and progression. To study the interaction of MYCN and MDM2, we generated an Mdm2 haploinsufficient transgenic animal model of neuroblastoma. In Mdm2(+/-)MYCN transgenics, tumor latency and animal survival are remarkably extended, whereas tumor incidence and growth are reduced. Analysis of the Mdm2/p53 pathway reveals remarkable p53 stabilization counter-balanced by epigenetic silencing of the p19(Arf) gene in the Mdm2 haploinsufficient tumors. In human neuroblastoma xenograft models, conditional small interfering RNA-mediated knockdown of MDM2 in cells expressing wild-type p53 dramatically suppresses tumor growth in a p53-dependent manner. In summary, we provided evidence for a crucial role for direct inhibition of p53 by MDM2 and suppression of the p19(ARF)/p53 axis in neuroblastoma tumorigenesis, supporting the development of therapies targeting these pathways.
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Cervigne NK, Reis PP, Machado J, Sadikovic B, Bradley G, Galloni NN, Pintilie M, Jurisica I, Perez-Ordonez B, Gilbert R, Gullane P, Irish J, Kamel-Reid S. Identification of a microRNA signature associated with progression of leukoplakia to oral carcinoma. Hum Mol Genet 2009; 18:4818-29. [PMID: 19776030 DOI: 10.1093/hmg/ddp446] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRs) are non-coding RNA molecules involved in cancer initiation and progression. Deregulated miR expression has been implicated in cancer; however, there are no studies implicating an miR signature associated with progression in oral squamous cell carcinoma (OSCC). Although OSCC may develop from oral leukoplakia, clinical and histological assessments have limited prognostic value in predicting which leukoplakic lesions will progress. Our aim was to quantify miR expression changes in leukoplakia and same-site OSCC and to identify an miR signature associated with progression. We examined miR expression changes in 43 sequential progressive samples from 12 patients and four non-progressive leukoplakias from four different patients, using TaqMan Low Density Arrays. The findings were validated using quantitative RT-PCR in an independent cohort of 52 progressive dysplasias and OSCCs, and five non-progressive dysplasias. Global miR expression profiles distinguished progressive leukoplakia/OSCC from non-progressive leukoplakias/normal tissues. One hundred and nine miRs were highly expressed exclusively in progressive leukoplakia and invasive OSCC. miR-21, miR-181b and miR-345 expressions were consistently increased and associated with increases in lesion severity during progression. Over-expression of miR-21, miR-181b and miR-345 may play an important role in malignant transformation. Our study provides the first evidence of an miR signature potentially useful for identifying leukoplakias at risk of malignant transformation.
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Affiliation(s)
- Nilva K Cervigne
- Division of Applied Molecular Oncology, Toronto General Hospital, Ontario Cancer Institute, The University Health Network, Toronto, ON, Canada
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Yang H, Gu J, Wang KK, Zhang W, Xing J, Chen Z, Ajani JA, Wu X. MicroRNA expression signatures in Barrett's esophagus and esophageal adenocarcinoma. Clin Cancer Res 2009; 15:5744-52. [PMID: 19737949 DOI: 10.1158/1078-0432.ccr-09-0385] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
PURPOSE Esophageal adenocarcinoma is a highly aggressive malignancy that frequently develops from Barrett's esophagus, a premalignant pathologic change occurring in the lower end of the esophagus. Identifying Barrett's esophagus patients at high risk of malignant transformation is essential to the prevention of esophageal adenocarcinoma. Although microRNA (miRNA) expression signatures have been associated with the etiology and prognosis of several types of cancers, their roles in the development of esophageal adenocarcinoma have not been extensively evaluated. EXPERIMENTAL DESIGN In this study, we analyzed the expression patterns of 470 human miRNAs using Agilent miRNA microarray in 32 disease/normal-paired tissues from 16 patients diagnosed with Barrett's esophagus of either low- or high-grade dysplasia, or esophageal adenocarcinoma. RESULTS Using unsupervised hierarchical clustering and class comparison analyses, we found that miRNA expression profiles in tissues of Barrett's esophagus with high-grade dysplasia were significantly different from their corresponding normal tissues. Similar findings were observed for esophageal adenocarcinoma, but not for Barrett's esophagus with low-grade dysplasia. The expression patterns of selected miRNAs were further validated using quantitative reverse transcription real-time PCR in an independent set of 75 pairs of disease/normal tissues. Finally, we identified several miRNAs that were involved in the progressions from low grade-dysplasia Barrett's esophagus to esophageal adenocarcinoma. CONCLUSIONS We showed that miRNAs were involved in the development and progression of esophageal adenocarcinoma. The identified significant miRNAs that may become potential targets for early detection, chemoprevention, and treatment of esophageal cancer.
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Affiliation(s)
- Hushan Yang
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
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Abstract
AIMS To address the possible use of RNA interference in diagnosis, prognosis and therapy of various diseases and explain the obstacles in RNA interference based therapy. METHODS Review of the literature. RESULTS AND DISCUSSION The MicroRNAs (miRNAs) were shown to play a role in various normal and pathological biological processes, i.e. the regulation of cell cycle and apoptosis, cell differentiation, wound healing process, immune system, etc. Furthermore, abnormal expression of miRNA was found in various diseases. Therefore, when the sample can be easily collected, miRNA expression profile can be used to detect diseases where early diagnosis is advantageous, such as in various malignancies or diseases that show myriads of symptoms such as autoimmune diseases. Further, different expression of miRNA in tumour subtypes can be used to predict the subtypes and hence the prognosis. For therapy, small (short) interfering RNAs (siRNAs) can be developed to 'switch off' up-regulated genes or miRNAs or the suppressors of down-regulated genes or miRNAs. These approaches in various animal models of diseases showed promising results and human trials for viral infections are underway. However, obstacles to the application in human might be encountered, such as degradation of the siRNAs before it can exert its function, target cell penetration and 'off target' toxic effects. Still, it is believed that modification of the RNA, development of carrier vehicles and mode and route of administration might solve these obstacles. CONCLUSION MicroRNAs profile differences between normal and pathological condition might be promising as biomarker in early diagnosis and prognosis, while siRNA showed promising result in the therapy of various diseases in animal models.
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Affiliation(s)
- J A Pawitan
- Department of Histology, Faculty of Medicine, University of Indonesia, Jakarta Pusat, Jakarta, Indonesia.
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244
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Chen Y, Gelfond JAL, McManus LM, Shireman PK. Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis. BMC Genomics 2009; 10:407. [PMID: 19715577 PMCID: PMC2753550 DOI: 10.1186/1471-2164-10-407] [Citation(s) in RCA: 232] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Accepted: 08/28/2009] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) have critical functions in various biological processes. MiRNA profiling is an important tool for the identification of differentially expressed miRNAs in normal cellular and disease processes. A technical challenge remains for high-throughput miRNA expression analysis as the number of miRNAs continues to increase with in silico prediction and experimental verification. Our study critically evaluated the performance of a novel miRNA expression profiling approach, quantitative RT-PCR array (qPCR-array), compared to miRNA detection with oligonucleotide microchip (microarray). RESULTS High reproducibility with qPCR-array was demonstrated by comparing replicate results from the same RNA sample. Pre-amplification of the miRNA cDNA improved sensitivity of the qPCR-array and increased the number of detectable miRNAs. Furthermore, the relative expression levels of miRNAs were maintained after pre-amplification. When the performance of qPCR-array and microarrays were compared using different aliquots of the same RNA, a low correlation between the two methods (r=-0.443) indicated considerable variability between the two assay platforms. Higher variation between replicates was observed in miRNAs with low expression in both assays. Finally, a higher false positive rate of differential miRNA expression was observed using the microarray compared to the qPCR-array. CONCLUSION Our studies demonstrated high reproducibility of TaqMan qPCR-array. Comparison between different reverse transcription reactions and qPCR-arrays performed on different days indicated that reverse transcription reactions did not introduce significant variation in the results. The use of cDNA pre-amplification increased the sensitivity of miRNA detection. Although there was variability associated with pre-amplification in low abundance miRNAs, the latter did not involve any systemic bias in the estimation of miRNA expression. Comparison between microarray and qPCR-array indicated superior sensitivity and specificity of qPCR-array.
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Affiliation(s)
- Yongxin Chen
- Department of Surgery, University of Texas Health Science Center, San Antonio, TX 78229, USA.
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245
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Evangelisti C, Florian MC, Massimi I, Dominici C, Giannini G, Galardi S, Buè MC, Massalini S, McDowell HP, Messi E, Gulino A, Farace MG, Ciafrè SA. MiR-128 up-regulation inhibits Reelin and DCX expression and reduces neuroblastoma cell motility and invasiveness. FASEB J 2009; 23:4276-87. [PMID: 19713529 DOI: 10.1096/fj.09-134965] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
MicroRNAs are a class of sophisticated regulators of gene expression, acting as post-transcriptional inhibitors that recognize their target mRNAs through base pairing with short regions along the 3'UTRs. Several microRNAs are tissue specific, suggesting a specialized role in tissue differentiation or maintenance, and quite a few are critically involved in tumorigenesis. We studied miR-128, a brain-enriched microRNA, in retinoic acid-differentiated neuroblastoma cells, and we found that this microRNA is up-regulated in treated cells, where it down-modulates the expression of two proteins involved in the migratory potential of neural cells: Reelin and DCX. Consistently, miR-128 ectopic overexpression suppressed Reelin and DCX, whereas the LNA antisense-mediated miR-128 knockdown caused the two proteins to increase. Ectopic miR-128 overexpression reduced neuroblastoma cell motility and invasiveness, and impaired cell growth. Finally, the analysis of a small series of primary human neuroblastomas showed an association between high levels of miR-128 expression and favorable features, such as favorable Shimada category or very young age at diagnosis. Thus, we provide evidence for a role for miR-128 in the molecular events modulating neuroblastoma progression and aggressiveness.
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Affiliation(s)
- Cristina Evangelisti
- Department of Experimental Medicine and Biochemical Sciences, University of Rome "Tor Vergata," Via Montpellier 1, 00133 Roma, Italy
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246
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Wei JS, Johansson P, Chen QR, Song YK, Durinck S, Wen X, Cheuk ATC, Smith MA, Houghton P, Morton C, Khan J. microRNA profiling identifies cancer-specific and prognostic signatures in pediatric malignancies. Clin Cancer Res 2009; 15:5560-8. [PMID: 19706822 DOI: 10.1158/1078-0432.ccr-08-3287] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
PURPOSE microRNAs have been shown to be involved in different human cancers. We therefore have performed expression profiles on a panel of pediatric tumors to identify cancer-specific microRNAs. We also investigated if microRNAs are coregulated with their host gene. EXPERIMENTAL DESIGN We performed parallel microRNAs and mRNA expression profiling on 57 tumor xenografts and cell lines representing 10 different pediatric solid tumors using microarrays. For those microRNAs that map to their host mRNA, we calculated correlations between them. RESULTS We found that the majority of cancer types clustered together based on their global microRNA expression profiles by unsupervised hierarchical clustering. Fourteen microRNAs were significantly differentially expressed between rhabdomyosarcoma and neuroblastoma, and 8 of them were validated in independent patient tumor samples. Exploration of the expression of microRNAs in relationship with their host genes showed that the expression for 43 of 68 (63%) microRNAs located inside known coding genes was significantly correlated with that of their host genes. Among these 43 microRNAs, 5 of 7 microRNAs in the OncomiR-1 cluster correlated significantly with their host gene MIRHG1 (P < 0.01). In addition, high expression of MIRHG1 was significantly associated with high stage and MYCN amplification in neuroblastoma tumors, and the expression level of MIRHG1 could predict the outcome of neuroblastoma patients independently from the current neuroblastoma risk-stratification in two independent patient cohorts. CONCLUSION Pediatric cancers express cancer-specific microRNAs. The high expression of the OncomiR-1 host gene MIRHG1 correlates with poor outcome for patients with neuroblastoma, indicating important oncogenic functions of this microRNA cluster in neuroblastoma biology.
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Affiliation(s)
- Jun S Wei
- Oncogenomics Section, Pediatric Oncology Branch, Advanced Technology Center, National Cancer Institute, Gaithersburg, Maryland 20877, USA.
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Van Roy N, De Preter K, Hoebeeck J, Van Maerken T, Pattyn F, Mestdagh P, Vermeulen J, Vandesompele J, Speleman F. The emerging molecular pathogenesis of neuroblastoma: implications for improved risk assessment and targeted therapy. Genome Med 2009; 1:74. [PMID: 19638189 PMCID: PMC2717400 DOI: 10.1186/gm74] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Neuroblastoma is one of the most common solid tumors of childhood, arising from immature sympathetic nervous system cells. The clinical course of patients with neuroblastoma is highly variable, ranging from spontaneous regression to widespread metastatic disease. Although the outcome for children with cancer has improved considerably during the past decades, the prognosis of children with aggressive neuroblastoma remains dismal. The clinical heterogeneity of neuroblastoma mirrors the biological and genetic heterogeneity of these tumors. Ploidy and MYCN amplification have been used as genetic markers for risk stratification and therapeutic decision making, and, more recently, gene expression profiling and genome-wide DNA copy number analysis have come into the picture as sensitive and specific tools for assessing prognosis. The applica tion of new genetic tools also led to the discovery of an important familial neuroblastoma cancer gene, ALK, which is mutated in approximately 8% of sporadic tumors, and genome-wide association studies have unveiled loci with risk alleles for neuroblastoma development. For some of the genomic regions that are deleted in some neuroblastomas, on 1p, 3p and 11q, candidate tumor suppressor genes have been identified. In addition, evidence has emerged for the contribution of epigenetic disturbances in neuroblastoma oncogenesis. As in other cancer entities, altered microRNA expression is also being recognized as an important player in neuroblastoma. The recent successes in unraveling the genetic basis of neuroblastoma are now opening opportunities for development of targeted therapies.
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Affiliation(s)
- Nadine Van Roy
- Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
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248
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Xu H, Cheung IY, Guo HF, Cheung NKV. MicroRNA miR-29 modulates expression of immunoinhibitory molecule B7-H3: potential implications for immune based therapy of human solid tumors. Cancer Res 2009; 69:6275-81. [PMID: 19584290 DOI: 10.1158/0008-5472.can-08-4517] [Citation(s) in RCA: 216] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
B7-H3, a surface immunomodulatory glycoprotein, inhibits natural killer cells and T cells. The monoclonal antibody (mAb) 8H9 is specific for 4Ig-B7-H3, the long and principal form of B7-H3. Early results from radioimmunotherapy using 8H9 have shown promise in patients with metastatic solid tumors to the central nervous system. Whereas B7-H3 transcript was ubiquitously expressed in a wide spectrum of human solid tumors as well as human normal tissues, B7-H3 protein was preferentially expressed only in tumor tissues. By quantitative reverse transcription-PCR, all three isoforms of microRNA miR-29 (a, b, and c) were highly expressed in normal tissues. However, they were down-regulated in a broad spectrum of solid tumors, including neuroblastoma, sarcomas, brain tumors, and tumor cell lines. B7-H3 protein expression was inversely correlated with miR-29 levels in both cell lines and tumor tissues tested. Using luciferase reporter assay, miR-29a was shown to directly target B7-H3 3' untranslated region, and knock-in and knockdown of miR-29a led to down-regulation and up-regulation, respectively, of B7-H3 protein expression. The ability of miR-29 to control B7-H3 protein expression has implications in immune escape by solid tumors. Differential modulation of this key immunoinhibitory molecule in tumor versus normal tissues may advance both cell-mediated immunotherapy and antibody-based targeted strategies using the B7-H3-specific mAb 8H9.
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Affiliation(s)
- Hong Xu
- Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
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249
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Mestdagh P, Van Vlierberghe P, De Weer A, Muth D, Westermann F, Speleman F, Vandesompele J. A novel and universal method for microRNA RT-qPCR data normalization. Genome Biol 2009; 10:R64. [PMID: 19531210 PMCID: PMC2718498 DOI: 10.1186/gb-2009-10-6-r64] [Citation(s) in RCA: 792] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 04/02/2009] [Accepted: 06/16/2009] [Indexed: 01/03/2023] Open
Abstract
The mean expression value: a new method for accurate and reliable normalization of microRNA expression data from RT-qPCR experiments. Gene expression analysis of microRNA molecules is becoming increasingly important. In this study we assess the use of the mean expression value of all expressed microRNAs in a given sample as a normalization factor for microRNA real-time quantitative PCR data and compare its performance to the currently adopted approach. We demonstrate that the mean expression value outperforms the current normalization strategy in terms of better reduction of technical variation and more accurate appreciation of biological changes.
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Affiliation(s)
- Pieter Mestdagh
- Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, Ghent, Belgium.
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250
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Stallings RL. MicroRNA involvement in the pathogenesis of neuroblastoma: potential for microRNA mediated therapeutics. Curr Pharm Des 2009; 15:456-62. [PMID: 19199973 DOI: 10.2174/138161209787315837] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Neuroblastoma arises from precursor cells of the sympathetic nervous system and presently accounts for 15% of all childhood cancer deaths. These tumors display remarkable heterogeneity in clinical behavior, ranging from spontaneous regression to rapid progression and resistance to therapy. The clinical behavior of these tumors is associated with many factors, including patient age, histopathology and genetic abnormalities such as MYCN amplification. More recently, the dysregulation of some miRNAs, including the miR-17-5p-92 cluster and miR-34a, has been implicated in the pathobiology of neuroblastoma. MiR-17-5p-92 family members act in an oncogenic manner while miR-34a has tumor suppressor functions. The evidence for the contribution of miRNAs in the aggressive neuroblastoma phenotype is reviewed in this article, along with exciting possibilities for miRNA mediated therapeutics.
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Affiliation(s)
- R L Stallings
- Royal College of Surgeons and Children's Research Centre Our Lady's Children's Hospital, Dublin, Ireland.
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