1
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Screening Tumor-Related Genes of Gallbladder Cancer Based on AR-Based Tumor Expression Profile Gene Chip. CONTRAST MEDIA & MOLECULAR IMAGING 2022; 2022:8579279. [PMID: 36237581 PMCID: PMC9529521 DOI: 10.1155/2022/8579279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/13/2022] [Accepted: 07/21/2022] [Indexed: 01/26/2023]
Abstract
The rapid development of molecular biology and gene chip technology has produced a large amount of gene expression profile data. The main research in this article is to screen the tumor-related genes of gallbladder cancer based on AR-based tumor expression profile gene chip. First, convert the chip data into an expression matrix pattern that can be analyzed, and then standardize and normalize all the data. Run ReliefF, GA, and IReliefF-GA on the data set, record the size of the feature subset, and use the tenfold cross-validation method to obtain the classification accuracy, specificity, and sensitivity of each method on the classifier. The target genes used in the chip were amplified by PCR with the universal primers used in cDNA library construction, and the quality of PCR was monitored by agarose gel electrophoresis. The gene chip data of gallbladder cancer was processed with missing values, singular values, and so forth, and 22294 transcripts were obtained. After statistical testing, there were 9483 transcripts with statistically significant differences. The results show that as the number of clusters increases, the network can be better reconstructed through decomposition modeling.
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Pediatric brain tumor cell lines exhibit miRNA-depleted, Y RNA-enriched extracellular vesicles. J Neurooncol 2022; 156:269-279. [PMID: 34984645 DOI: 10.1007/s11060-021-03914-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/25/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Medulloblastoma (MB) and diffuse infiltrative pontine glioma (DIPG) are malignant pediatric tumors. Extracellular vesicles (EVs) and their bioactive cargoes have been implicated in tumorigenesis. Most studies have focused on adult tumors, therefore the role of EVs and the noncoding RNA (ncRNA) landscape in pediatric brain tumors is not fully characterized. The overall aim of this pilot study was to isolate EVs from MB and DIPG patient-derived cell lines and to explore the small ncRNA transcriptome. METHODS EVs from 3 DIPG and 4 MB patient-derived cell lines were analyzed. High-throughput next generation sequencing interrogated the short non-coding RNA (ncRNA) transcriptome. Known and novel miRNAs were quantified. Differential expression analysis, in silico target prediction, and functional gene enrichment were performed. RESULTS EV secretomes from MB and DIPG patient-derived cell lines demonstrated discrete ncRNA biotypes. Notably, miRNAs were depleted and Y RNAs were enriched in EV samples. Hierarchical cluster analysis revealed high discrimination in miRNA expression between DIPG and MB cell lines and RNA-Seq identified novel miRNAs not previously implicated in MB or DIPG pathogenesis. Known and putative target genes of dysregulated miRNAs were identified. Functional annotation analysis of the target genes for differentially expressed EV-and parental-derived miRNAs revealed significant cancer-related pathway involvement. CONCLUSIONS This hypothesis-generating study demonstrated that pediatric brain tumor-derived cell lines secrete EVs comprised of various ncRNA cargoes. Validation of these findings in patient samples may provide new insights into the pediatric brain tumor microenvironment and identification of novel therapeutic candidates.
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Role of MicroRNAs in the Development and Progression of the Four Medulloblastoma Subgroups. Cancers (Basel) 2021; 13:cancers13246323. [PMID: 34944941 PMCID: PMC8699467 DOI: 10.3390/cancers13246323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/21/2022] Open
Abstract
Medulloblastoma is the most frequent malignant brain tumour in children. Medulloblastoma originate during the embryonic stage. They are located in the cerebellum, which is the area of the central nervous system (CNS) responsible for controlling equilibrium and coordination of movements. In 2012, medulloblastoma were divided into four subgroups based on a genome-wide analysis of RNA expression. These subgroups are named Wingless, Sonic Hedgehog, Group 3 and Group 4. Each subgroup has a different cell of origin, prognosis, and response to therapies. Wingless and Sonic Hedgehog medulloblastoma are so named based on the main mutation originating these tumours. Group 3 and Group 4 have generic names because we do not know the key mutation driving these tumours. Gene expression at the post-transcriptional level is regulated by a group of small single-stranded non-coding RNAs. These microRNA (miRNAs or miRs) play a central role in several cellular functions such as cell differentiation and, therefore, any malfunction in this regulatory system leads to a variety of disorders such as cancer. The role of miRNAs in medulloblastoma is still a topic of intense clinical research; previous studies have mostly concentrated on the clinical entity of the single disease rather than in the four molecular subgroups. In this review, we summarize the latest discoveries on miRNAs in the four medulloblastoma subgroups.
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4
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Chen S, Deng X, Sheng H, Rong Y, Zheng Y, Zhang Y, Lin J. Noncoding RNAs in pediatric brain tumors: Molecular functions and pathological implications. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:417-431. [PMID: 34552822 PMCID: PMC8426460 DOI: 10.1016/j.omtn.2021.07.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Brain tumors are common solid pediatric malignancies and the main reason for cancer-related death in the pediatric setting. Recently, evidence has revealed that noncoding RNAs (ncRNAs), including microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs), play a critical role in brain tumor development and progression. Therefore, in this review article, we describe the functions and molecular mechanisms of ncRNAs in multiple types of cancer, including medulloblastoma, pilocytic astrocytoma, ependymoma, atypical teratoid/rhabdoid tumor, glioblastoma, diffuse intrinsic pontine glioma, and craniopharyngioma. We also mention the limitations of using ncRNAs as therapeutic targets because of the nonspecificity of ncRNA targets and the delivery methods of ncRNAs. Due to the critical role of ncRNAs in brain oncogenesis, targeting aberrantly expressed ncRNAs might be an effective strategy to improve the outcomes of pediatric patients with brain tumors.
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Affiliation(s)
- Shaohuai Chen
- Department of Neurosurgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiangyang Deng
- Department of Neurosurgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hansong Sheng
- Department of Neurosurgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuxi Rong
- Department of Neurosurgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yanhao Zheng
- Department of Neurosurgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yusong Zhang
- Department of Neurosurgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jian Lin
- Department of Neurosurgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
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5
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Zhao YN, Li K, Han XS, Pan YW. The mechanism of non-coding RNAs in medulloblastoma. Oncol Lett 2021; 22:758. [PMID: 34539862 PMCID: PMC8436364 DOI: 10.3892/ol.2021.13019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/09/2021] [Indexed: 11/11/2022] Open
Abstract
Medulloblastoma (MB) is one of the most common malignant tumors of the central nervous system in children. Although surgery, radiotherapy and chemotherapy have resulted in considerable progress in the treatment of this disease, the prognosis of patients with MB remains very poor. Therefore, highly specific molecular targeted treatment, which can improve the therapeutic efficacy and reduce the side effects of MB, has become a research hotspot. In recent years, non-coding RNAs (ncRNAs), which were initially considered to be transcriptional noise, have been shown to possess regulatory functions. A series of ncRNAs have been identified, including microRNAs and circular RNAs, which affect the expression of specific genes in a variety of tumors. These genes lead to the formation of a specific complex of proteins or they directly participate in protein synthesis in order to regulate the occurrence and development of tumors. The aim of the present review article was to summarize the recent research studies that have explored the ability of ncRNAs to regulate the occurrence and development of MB.
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Affiliation(s)
- Ying-Nan Zhao
- The Second Medical College of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Kun Li
- The Second Medical College of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Xing-Sheng Han
- The Second Medical College of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Ya-Wen Pan
- The Second Medical College of Lanzhou University, Lanzhou, Gansu 730030, P.R. China.,Department of Neurosurgery, Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China.,Key Lab of Neurology of Gansu Province, Lanzhou University, Lanzhou, Gansu 730030, P.R. China
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6
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Wang SP, Li W, Li C, Duan XY, Duan J. Effect of rs4719839 polymorphism on risk of ventilator-associated pneumonia, expression of microRNA-148 and autophagy-related 16-like 1 (ATG16L1). J Cell Mol Med 2020; 24:12599-12607. [PMID: 32940422 PMCID: PMC7686989 DOI: 10.1111/jcmm.15824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/03/2020] [Accepted: 08/13/2020] [Indexed: 12/19/2022] Open
Abstract
MiR‐148 is a negative regulator of autophagy 16‐like 1 (ATG16L1), a gene implicated in the pathogenesis of ventilator‐associated pneumonia (VAP). Therefore, the role of miR‐148 polymorphism in the pathogenesis of VAP was studied here. The expression of miR‐148, ATG16L1, Beclin‐I, LC3‐II, TNF‐α and IL‐6 in serum and peripheral blood mononuclear cells (PBMCs) of VAP patients was detected to study their relationship in the pathogenesis of VAP. Chronic obstructive pulmonary disease patients carrying the AA/AG genotypes of miR‐148 rs4719839 single nucleotide polymorphism (SNP) were more prone to VAP due to the higher expression of miR‐148, TNF‐α and IL‐6 along with suppressed expression of ATG16L1, Beclin‐I and LC3‐II in their serum and PBMCs. Transfection of miR‐148 mimics to primary PBMCs genotyped as GG and AA decreased the expression of ATG16L1, Beclin‐I and LC3‐II. Finally, cells carrying the AA genotype of rs4719839 SNP were more sensitive to the role of LPS stimulation in suppressing ATG16L1, Beclin‐I and LC3‐II expression while activating TNF‐α and IL‐6 expression. Our work presented detailed evidence, suggesting that the rs4719839 polymorphism can affect the risk of VAP.
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Affiliation(s)
- Shu-Peng Wang
- Surgical Intensive Care Unit, China-Japan Friendship Hospital, Beijing, China
| | - Wen Li
- Surgical Intensive Care Unit, China-Japan Friendship Hospital, Beijing, China
| | - Chen Li
- Surgical Intensive Care Unit, China-Japan Friendship Hospital, Beijing, China
| | - Xue-Yan Duan
- Department of Internal Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Jun Duan
- Surgical Intensive Care Unit, China-Japan Friendship Hospital, Beijing, China
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7
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Ma H, Cao W, Ding M. MicroRNA-31 weakens cisplatin resistance of medulloblastoma cells via NF-κB and PI3K/AKT pathways. Biofactors 2020; 46:831-838. [PMID: 32027070 DOI: 10.1002/biof.1616] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/10/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Medulloblastoma (MB) is a malignant intracranial tumor. Cisplatin is a broad-spectrum antitumor drug. It is important to study the cisplatin resistance of MB cells for the treatment of MB. In this article, we preliminarily studied the cisplatin resistance of microRNA (miR)-31 and the possible mechanism in DAOY and UW228 cells, laying a theoretical foundation for clinical treatment of MB. METHODS Following anti-miR-31 and pre-miR-31 transfections, cell viability, BrdU, CyclinD1, and apoptosis levels of DAOY and UW228 cell were detected by CCK8, BrdU, and western blot. Meanwhile, migration, invasion, and western blot assay were respectively used to detect the functions of miR-31 migration and invasion. miR-31 levels were changed by cell transfection and detected by RT-qPCR. Furthermore, the related-proteins of pathways were also detected by western blot. RESULTS Anti-miR-31 increased DAOY and UW228 cells viability, BrdU+ numbers, and expression of CyclinD1. The migration/invasion rate and expression levels of MMP-9 and vimentin after anti-miR-31 transfection were increased. Furthermore, anti-miR-31 enhanced cells' cisplatin resistance and triggered PI3K/AKT and NF-κB pathways. Pre-miR-31 played opposite roles and promoted the apoptosis. CONCLUSION miR-31 regulated cell growth, migration, invasion and cisplatin resistance of MB cells via PI3K/AKT and NF-κB pathways.
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Affiliation(s)
- Hui Ma
- Department of Neurosurgery, Jining No. 1 People's Hospital, Jining, China
| | - Wei Cao
- Department of Neurosurgery, Jining No. 1 People's Hospital, Jining, China
| | - Meili Ding
- Department of Pediatrics, Jining No. 1 People's Hospital, Jining, China
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8
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Prieto-Fernández E, Lopez-Lopez E, Martin-Guerrero I, Bárcena L, Gonzalez-Lopez M, Aransay AM, Lozano JJ, Benito J, Falcón-Pérez JM, Garcia-Orad A. Variability in Cerebrospinal Fluid MicroRNAs Through Life. Mol Neurobiol 2020; 57:4134-4142. [PMID: 32676987 DOI: 10.1007/s12035-020-02011-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/01/2020] [Indexed: 01/02/2023]
Abstract
The development of the human brain starts in the first weeks of embryo differentiation. However, there are many relevant neurodevelopmental processes that take place after birth and during lifespan. Such a fine and changing scenario requires the coordinated expression of thousands of genes to achieve the proper specialization and inter-connectivity. In this context, microRNAs (miRNAs), which can modulate mRNA stability and translation, are gaining recognition for their involvement in both brain development and neurodevelopmental disorders. Therefore, cerebrospinal fluid (CSF) miRNAs should be perfectly differentiated in relevant age periods. In this study, we aimed to highlight the biological variability of miRNA expression in the CSF throughout life, which is also crucial for biomarker discovery in CNS pathologies, especially in children, where they are desperately needed. We analyzed the CSF microRNAome of 14 healthy children (aged 0-7.4 years) by smallRNA-Seq and compared it with previously published data in adults (N = 7) and elders (N = 11). miR-423-5p and miR-22-3p were overexpressed in the < 1 and > 3 years groups, respectively. Additionally, we detected 18 miRNAs that reached their highest peak of expression at different time-points during the lifespan and sets of miRNAs that were exclusively expressed in a specific age group. On the contrary, miR-191-5p showed stable expression in CSF from the first year of life. Our results remark the complex differential miRNA expression profile that can be observed through life, which underlines the need for including appropriate age-matched controls when the expression of CSF miRNAs is analyzed in different pathological contexts. Graphical abstract.
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Affiliation(s)
- Endika Prieto-Fernández
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of The Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain.
| | - Elixabet Lopez-Lopez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of The Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain. .,BioCruces Bizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain.
| | - Idoia Martin-Guerrero
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of The Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain. .,BioCruces Bizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain.
| | - Laura Bárcena
- Genome Analysis Platform, CIC bioGUNE, 48160, Derio, Bizkaia, Spain
| | | | - Ana María Aransay
- Genome Analysis Platform, CIC bioGUNE, 48160, Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Juan José Lozano
- Bioinformatic Platform, Hospital Clinic, CIBERehd, 08036, Barcelona, Spain
| | - Javier Benito
- Department of Pediatric Emergency, Cruces University Hospital, 48903, Barakaldo, Bizkaia, Spain.,Department of Pediatrics, University of The Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain
| | - Juan Manuel Falcón-Pérez
- Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain.,Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain.,IKERBASQUE, Basque Foundation for Science, 48015, Bilbao, Bizkaia, Spain
| | - Africa Garcia-Orad
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of The Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain.,BioCruces Bizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
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9
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Kloetgen A, Duggimpudi S, Schuschel K, Hezaveh K, Picard D, Schaal H, Remke M, Klusmann JH, Borkhardt A, McHardy AC, Hoell JI. YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA. Int J Mol Sci 2020; 21:ijms21124453. [PMID: 32585856 PMCID: PMC7352269 DOI: 10.3390/ijms21124453] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 12/18/2022] Open
Abstract
Medulloblastomas arise from undifferentiated precursor cells in the cerebellum and account for about 20% of all solid brain tumors during childhood; standard therapies include radiation and chemotherapy, which oftentimes come with severe impairment of the cognitive development of the young patients. Here, we show that the posttranscriptional regulator Y-box binding protein 1 (YBX1), a DNA- and RNA-binding protein, acts as an oncogene in medulloblastomas by regulating cellular survival and apoptosis. We observed different cellular responses upon YBX1 knockdown in several medulloblastoma cell lines, with significantly altered transcription and subsequent apoptosis rates. Mechanistically, PAR-CLIP for YBX1 and integration with RNA-Seq data uncovered direct posttranscriptional control of the heterochromatin-associated gene CBX5; upon YBX1 knockdown and subsequent CBX5 mRNA instability, heterochromatin-regulated genes involved in inflammatory response, apoptosis and death receptor signaling were de-repressed. Thus, YBX1 acts as an oncogene in medulloblastoma through indirect transcriptional regulation of inflammatory genes regulating apoptosis and represents a promising novel therapeutic target in this tumor entity.
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Affiliation(s)
- Andreas Kloetgen
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
- Correspondence:
| | - Sujitha Duggimpudi
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
| | - Konstantin Schuschel
- Department of Pediatrics 1, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (K.S.); (J.-H.K.)
| | - Kebria Hezaveh
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Daniel Picard
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany;
| | - Marc Remke
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
| | - Jan-Henning Klusmann
- Department of Pediatrics 1, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (K.S.); (J.-H.K.)
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
| | - Alice C. McHardy
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
| | - Jessica I. Hoell
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
- Department of Pediatrics 1, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (K.S.); (J.-H.K.)
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10
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Laneve P, Caffarelli E. The Non-coding Side of Medulloblastoma. Front Cell Dev Biol 2020; 8:275. [PMID: 32528946 PMCID: PMC7266940 DOI: 10.3389/fcell.2020.00275] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 03/31/2020] [Indexed: 12/18/2022] Open
Abstract
Medulloblastoma (MB) is the most common pediatric brain tumor and a primary cause of cancer-related death in children. Until a few years ago, only clinical and histological features were exploited for MB pathological classification and outcome prognosis. In the past decade, the advancement of high-throughput molecular analyses that integrate genetic, epigenetic, and expression data, together with the availability of increasing wealth of patient samples, revealed the existence of four molecularly distinct MB subgroups. Their further classification into 12 subtypes not only reduced the well-characterized intertumoral heterogeneity, but also provided new opportunities for the design of targets for precision oncology. Moreover, the identification of tumorigenic and self-renewing subpopulations of cancer stem cells in MB has increased our knowledge of its biology. Despite these advancements, the origin of MB is still debated, and its molecular bases are poorly characterized. A major goal in the field is to identify the key genes that drive tumor growth and the mechanisms through which they are able to promote tumorigenesis. So far, only protein-coding genes acting as oncogenic drivers have been characterized in each MB subgroup. The contribution of the non-coding side of the genome, which produces a plethora of transcripts that control fundamental biological processes, as the cell choice between proliferation and differentiation, is still unappreciated. This review wants to fill this major gap by summarizing the recent findings on the impact of non-coding RNAs in MB initiation and progression. Furthermore, their potential role as specific MB biomarkers and novel therapeutic targets is also highlighted.
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Affiliation(s)
- Pietro Laneve
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Elisa Caffarelli
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
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11
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Abstract
Even though the treatment of childhood cancer has evolved significantly in recent decades, aggressive central nervous system (CNS) tumors are still a leading cause of morbidity and mortality in this population. Consequently, the identification of molecular targets that can be incorporated into diagnostic practice, effectively predict prognosis, follow treatment response, and materialize into potential targeted therapeutic approaches are still warranted. Since the first evidence of the participation of miRNAs in cancer development and progression 20 years ago, notable progress has been made in the basic understanding of the contribution of their dysregulation as epigenetic driver of tumorigenesis. Nevertheless, among the plethora of articles in the literature, microRNA profiling of pediatric tumors are scarce. This article gives an overview of the recent advances in the diagnostic/prognostic potential of miRNAs in a selection of pediatric CNS tumors: medulloblastoma, ependymoma, pilocytic astrocytoma, glioblastoma, diffuse intrinsic pontine glioma, atypical teratoid/rhabdoid tumors, and choroid plexus tumors.
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12
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Joshi P, Katsushima K, Zhou R, Meoded A, Stapleton S, Jallo G, Raabe E, Eberhart CG, Perera RJ. The therapeutic and diagnostic potential of regulatory noncoding RNAs in medulloblastoma. Neurooncol Adv 2019; 1:vdz023. [PMID: 31763623 PMCID: PMC6859950 DOI: 10.1093/noajnl/vdz023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Medulloblastoma, a central nervous system tumor that predominantly affects children, always requires aggressive therapy. Nevertheless, it frequently recurs as resistant disease and is associated with high morbidity and mortality. While recent efforts to subclassify medulloblastoma based on molecular features have advanced our basic understanding of medulloblastoma pathogenesis, optimal targets to increase therapeutic efficacy and reduce side effects remain largely undefined. Noncoding RNAs (ncRNAs) with known regulatory roles, particularly long noncoding RNAs (lncRNAs) and microRNAs (miRNAs), are now known to participate in medulloblastoma biology, although their functional significance remains obscure in many cases. Here we review the literature on regulatory ncRNAs in medulloblastoma. In providing a comprehensive overview of ncRNA studies, we highlight how different lncRNAs and miRNAs have oncogenic or tumor suppressive roles in medulloblastoma. These ncRNAs possess subgroup specificity that can be exploited to personalize therapy by acting as theranostic targets. Several of the already identified ncRNAs appear specific to medulloblastoma stem cells, the most difficult-to-treat component of the tumor that drives metastasis and acquired resistance, thereby providing opportunities for therapy in relapsing, disseminating, and therapy-resistant disease. Delivering ncRNAs to tumors remains challenging, but this limitation is gradually being overcome through the use of advanced technologies such as nanotechnology and rational biomaterial design.
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Affiliation(s)
- Piyush Joshi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland.,Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St. Petersburg, Florida
| | - Keisuke Katsushima
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland.,Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St. Petersburg, Florida
| | - Rui Zhou
- Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St. Petersburg, Florida
| | - Avner Meoded
- Pediatric Neuroradiology, Johns Hopkins All Children's Hospital, St. Petersburg, Florida
| | - Stacie Stapleton
- Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St. Petersburg, Florida
| | - George Jallo
- Institute Brain Protection Sciences, Johns Hopkins All Children's Hospital, St. Petersburg, Florida
| | - Eric Raabe
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Charles G Eberhart
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ranjan J Perera
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland.,Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St. Petersburg, Florida.,Sanford Burnham Prebys Medical Discovery Institute, NCI-Designated Cancer Center, La Jolla, California
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13
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Shaji SK, Sunilkumar D, Mahalakshmi NV, Kumar GB, Nair BG. Analysis of microarray data for identification of key microRNA signatures in glioblastoma multiforme. Oncol Lett 2019; 18:1938-1948. [PMID: 31423264 PMCID: PMC6614686 DOI: 10.3892/ol.2019.10521] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 06/06/2019] [Indexed: 02/06/2023] Open
Abstract
Glioblastoma multiforme (GBM) is one of the most malignant types of glioma known for its reduced survival rate and rapid relapse. Previous studies have shown that the expression patterns of different microRNAs (miRNA/miR) play a crucial role in the development and progression of GBM. In order to identify potential miRNA signatures of GBM for prognostic and therapeutic purposes, we downloaded and analyzed two expression data sets from Gene Expression Omnibus profiling miRNA patterns of GBM compared with normal brain tissues. Validated targets of the deregulated miRNAs were identified using MirTarBase, and were mapped to Search Tool for the Retrieval of Interacting Genes/Proteins, Database for Annotation, Visualization and Integrated Discovery and Kyoto Encyclopedia of Genes and Genomes databases in order to construct interaction networks and identify enriched pathways of target genes. A total of 6 miRNAs were found to be deregulated in both expression datasets studied. Pathway analysis demonstrated that most of the target genes were enriched in signaling cascades connected to cancer development, such as ‘Pathways in cancer’, ‘Focal adhesion’ and ‘PI3K-Akt signaling pathway’. Of the five target genes that were enriched in the glioblastoma pathway, in the WikiPathway database, both HRas proto-oncogene, GTPase and MET proto-oncogene, receptor tyrosine kinase target genes of hsa-miR-139-5p, were found to be significantly associated with patient survival. The present study may thus form the basis for further exploration of hsa-miR-139-5p, not only as a therapeutic agent, but also as a diagnostic biomarker for GBM as well as a predictive marker for patient survival.
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Affiliation(s)
- Sanu K Shaji
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala 690525, India
| | - Damu Sunilkumar
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala 690525, India
| | - N V Mahalakshmi
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala 690525, India
| | - Geetha B Kumar
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala 690525, India
| | - Bipin G Nair
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala 690525, India
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14
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The MicroRNA Expression Profiles of Human Temporal Lobe Epilepsy in HS ILAE Type 1. Cell Mol Neurobiol 2019; 39:461-470. [PMID: 30790096 DOI: 10.1007/s10571-019-00662-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/11/2019] [Indexed: 12/31/2022]
Abstract
Temporal lobe epilepsy (TLE) is associated with neurodegeneration, often leading to hippocampal sclerosis (HS). Type 1 HS, which is characterized by severe neuronal loss and gliosis predominantly in regions CA1 and CA4, is the most common subtype and is associated with the best prognosis according to the ILAE classification system. MiRNAs participate in the biological processes underlying many nervous system diseases, including epilepsy. However, the miRNA expression profile of HS ILAE type 1 is not completely understood. A total of 14 patients were identified as having the ILAE subtype, as determined by NeuN immunohistochemistry (ILAE type 1 = 7; no-HS = 7). Next-generation sequencing and reverse transcription polymerase chain reaction technology were used to validate the dysregulated miRNAs. Bioinformatics analysis of the predicted target genes was conducted using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. In total, 1643 mature miRNAs were detected in this study, along with 5 miRNAs that were upregulated and 2 miRNAs that were downregulated in the type 1 group. Bioinformatics analysis showed that 1545 target genes were predicted using the miRDB and Targetscan databases and that these predicted genes showed enrichment in pathways associated with nucleic acid binding, intracellular and cellular macromolecule metabolic processes, and the PI3K-Akt signaling pathway. This study is the first to report the miRNA expression profile of HS ILAE type 1 compared with those of no-HS. These results provide new insights into the neuronal loss pathology of type 1 HS.
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15
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Dong Q, Yuan G, Liu M, Xie Q, Hu J, Wang M, Liu S, Ma X, Pan Y. Downregulation of microRNA-374a predicts poor prognosis in human glioma. Exp Ther Med 2019; 17:2077-2084. [PMID: 30867694 DOI: 10.3892/etm.2019.7190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 12/03/2018] [Indexed: 12/13/2022] Open
Abstract
Certain microRNAs (miRNAs/miRs) may be used as prognostic biomarkers in various types of cancer. The purpose of the present study was to identify miRNAs that were abnormally expressed in glioma of different grades, and to evaluate their clinical implications in patients with glioma. The differentially expressed miRNAs were evaluated from the expression profiles of six glioma tissues (three low-grade and three high-grade gliomas) determined using a microarray platform. Reverse transcription-quantitative polymerase chain reaction analysis was used to further verify the aberrant expression of the candidate miRNA in a set of 42 patients and 5 healthy controls. The miRNA target genes were predicted and the protein-protein interaction network was generated; furthermore, functional enrichment analysis of the target genes in Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways was performed. Kaplan-Meier curves and Log-rank analysis, as well as multivariate Cox regression analysis were performed to assess the association of the candidate miRNA with patient survival. A total of 15 differentially expressed miRNAs, including 13 downregulated and 2 upregulated miRNAs, were identified by comparison of low-grade and high-grade glioma tissues. The miR-374a expression of high-grade gliomas was significantly lower than that of low-grade gliomas (fold change, -4.43; P=0.027). The expression levels of miR-374a gradually decreased with the increase of the pathological grade of glioma. Pearson's Chi-square test was used to determine the association of miR-374a expression with several clinicopathological factors. Furthermore, low expression of miR-374a was determined to be an independent prognostic marker and that it was significantly associated with overall survival (P=0.0213). GO and KEGG pathway analysis revealed that the target genes of miR-374a may be involved in the regulation of the RNA polymerase II promoter and mTOR signaling pathway. The four hub genes (CCND1, SP1, CDK4, CDK6) were also identified by PPI network analysis. In conclusion, the present study indicated that miR-374a may be used as a promising prognostic biomarker for the screening of high-risk populations and for the assessment of the prognosis of patients with glioma.
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Affiliation(s)
- Qiang Dong
- Department of Neurosurgery, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Guoqiang Yuan
- Institute of Neurology, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Min Liu
- Department of Pharmacy, Hebei North University, Zhangjiakou, Hebei 075000, P.R. China
| | - Qiqi Xie
- Department of Orthopaedics, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Jianhong Hu
- Department of Neurosurgery, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Maolin Wang
- Department of Neurosurgery, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Shangyu Liu
- Department of Neurosurgery, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Xiaojun Ma
- Department of Neurosurgery, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Yawen Pan
- Department of Neurosurgery, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China.,Institute of Neurology, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
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16
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Lv T, Miao YF, Jin K, Han S, Xu TQ, Qiu ZL, Zhang XH. Dysregulated circular RNAs in medulloblastoma regulate proliferation and growth of tumor cells via host genes. Cancer Med 2018; 7:6147-6157. [PMID: 30402980 PMCID: PMC6308054 DOI: 10.1002/cam4.1613] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/18/2018] [Accepted: 05/10/2018] [Indexed: 12/20/2022] Open
Abstract
Circular RNAs (circRNAs) have been demonstrated to be involved in various biological processes. Nevertheless, the function of circRNAs in medulloblastoma (MB) is still unknown. The present study aimed to investigate the expression profiles of circRNAs and related mechanisms for regulating the proliferation and growth of tumor cells in MB. The expression profiles of circRNAs were screened from four normal cerebellum and four MB samples using a HiSeq Sequencer. Bioinformatic analysis was employed to predict the interaction between circRNAs and mRNAs in MB. Subsequently, the expression levels of eight differential circRNAs [circ-SKA3 (hsa_circ_0029696), circ-DTL (hsa_circ_0000179), circ-CRTAM, circ-MAP3K5 (hsa_circ_0006856), circ-RIMS1-1 (hsa_circ_0132250), circ-RIMS1-2 (hsa_circ_0076967), circ-FLT3-1 (hsa_circ_0100165), and circ-FLT3-2 (hsa_circ_0100168)] were validated using quantitative reverse transcription-polymerase chain reaction. Moreover, circ-SKA3 and circ-DTL were silenced using small interfering RNAs and their host genes were overexpressed to investigate their role in the pathogenesis of MB. A total of 33 circRNAs were found to be differentially expressed in MB tissues (fold change ≥ 2.0, FDR <0.05), of which three were upregulated and 30 were downregulated; six circRNAs were experimentally validated successfully. Upregulated circ-SKA3 and circ-DTL promoted the proliferation migration and invasion in vitro by regulating the expression of host genes. This novel study exploited the profiling of circRNAs in MB and demonstrated that circ-SKA3 and circ-DTL were crucial in the tumorigenesis and development of MB and might be considered as novel and potential biomarkers for the diagnosis and new targets for the intervention of MB.
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Affiliation(s)
- Tao Lv
- Department of Neurosurgery, Ren Ji Hospital, Schoolof Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yi-Feng Miao
- Department of Neurosurgery, Ren Ji Hospital, Schoolof Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ke Jin
- Department of Neurosurgery, Ren Ji Hospital, Schoolof Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuo Han
- Department of Neurosurgery, Ren Ji Hospital, Schoolof Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tian-Qi Xu
- Department of Neurosurgery, Ren Ji Hospital, Schoolof Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zi-Long Qiu
- Institute of Neuroscience, State Kay Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Xiao-Hua Zhang
- Department of Neurosurgery, Ren Ji Hospital, Schoolof Medicine, Shanghai Jiao Tong University, Shanghai, China
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17
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Tantawy M, Elzayat MG, Yehia D, Taha H. Identification of microRNA signature in different pediatric brain tumors. Genet Mol Biol 2018; 41:27-34. [PMID: 29658967 PMCID: PMC5901491 DOI: 10.1590/1678-4685-gmb-2016-0334] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 08/21/2017] [Indexed: 12/02/2022] Open
Abstract
Understanding pediatric brain tumor biology is essential to help on disease
stratification, and to find novel markers for early diagnosis. MicroRNA (miRNA)
expression has been linked to clinical outcomes and tumor biology. Here, we
aimed to detect the expression of different miRNAs in different pediatric brain
tumor subtypes to discover biomarkers for early detection and develop novel
therapies. Expression of 82 miRNAs was detected in 120 pediatric brain tumors
from fixed-formalin paraffin-embedded tissues, low-grade glioma, high-grade
glioma, ependymoma, and medulloblastoma, using quantitative real-time PCR.
Low-expression of miR-221, miR-9, and miR-181c/d and over-expression of miR-101,
miR-222, miR-139, miR-1827, and miR-34c was found in medulloblastoma; low
expression of miR-10a and over-expression of miR-10b and miR-29a in ependymoma;
low expression of miR-26a and overexpression of miR-19a/b, miR-24, miR-27a, miR-
584, and miR-527 in low-grade glioma. Cox regression showed differential miRNA
expression between responders and non-responders. The most specific were miR-10a
and miR-29a low expression in LGG non-responders, miR-135a and miR-146b
over-expression in ependymoma non-responders, and miR-135b overexpression in
medulloblastoma non-responders. MicroRNAs are differentially expressed in
subtypes of brain tumors suggesting that they may help diagnosis. A greater
understanding of aberrant miRNA in pediatric brain tumors may support
development of novel therapies.
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Affiliation(s)
- Marwa Tantawy
- Research Department, Children's Cancer Hospital Egypt, Cairo, Egypt
| | - Mariam G Elzayat
- Research Department, Children's Cancer Hospital Egypt, Cairo, Egypt
| | - Dina Yehia
- Research Department, Children's Cancer Hospital Egypt, Cairo, Egypt
| | - Hala Taha
- Pathology Department, Children's Cancer Hospital Egypt, Cairo, Egypt.,Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
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