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Srinath S, Jishnu PV, Varghese VK, Shukla V, Adiga D, Mallya S, Chakrabarty S, Sharan K, Pandey D, Chatterjee A, Kabekkodu SP. Regulation and tumor-suppressive function of the miR-379/miR-656 (C14MC) cluster in cervical cancer. Mol Oncol 2024; 18:1608-1630. [PMID: 38400534 PMCID: PMC11161731 DOI: 10.1002/1878-0261.13611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/05/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Cervical cancer (CC) is a key contributor to cancer-related mortality in several countries. The identification of molecular markers and the underlying mechanism may help improve CC management. We studied the regulation and biological function of the chromosome 14 microRNA cluster (C14MC; miR-379/miR-656) in CC. Most C14MC members exhibited considerably lower expression in CC tissues and cell lines in The Cancer Genome Atlas (TCGA) cervical squamous cell carcinoma and endocervical adenocarcinoma patient cohorts. Bisulfite Sanger sequencing revealed hypermethylation of the C14MC promoter in CC tissues and cell lines. 5-aza-2 deoxy cytidine treatment reactivated expression of the C14MC members. We demonstrated that C14MC is a methylation-regulated miRNA cluster via artificial methylation and luciferase reporter assays. C14MC downregulation correlated with poor overall survival and may promote metastasis. C14MC activation via the lentiviral-based CRISPRa approach inhibited growth, proliferation, migration, and invasion; enhanced G2/M arrest; and induced senescence. Post-transcriptional regulatory network analysis of C14MC transcriptomic data revealed enrichment of key cancer-related pathways, such as metabolism, the cell cycle, and phosphatidylinositol 3-kinase (PI3K)-AKT signaling. Reduced cell proliferation, growth, migration, invasion, and senescence correlated with the downregulation of active AKT, MYC, and cyclin E1 (CCNE1) and the overexpression of p16, p21, and p27. We showed that C14MC miRNA activation increases reactive oxygen species (ROS) levels, intracellular Ca2+ levels, and lipid peroxidation rates, and inhibits epithelial-mesenchymal transition (EMT). C14MC targets pyruvate dehydrogenase kinase-3 (PDK3) according to the luciferase reporter assay. PDK3 is overexpressed in CC and is inversely correlated with C14MC. Both miR-494-mimic transfection and C14MC activation inhibited PDK3 expression. Reduced glucose uptake and lactate production, and upregulation of PDK3 upon C14MC activation suggest the potential role of these proteins in metabolic reprogramming. Finally, we showed that C14MC activation may inhibit EMT signaling. Thus, C14MC is a tumor-suppressive and methylation-regulated miRNA cluster in CC. Reactivation of C14MC can be useful in the management of CC.
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Grants
- Fund for Improvement of S&T Infrastructure (FIST), Department of Science and Technology, Government of India
- Karnataka Fund for Infrastructure Strengthening in Science and Technology (K-FIST), the Government of Karnataka
- MTR/2021/000182 Department of Science and Technology, Ministry of Science and Technology, India
- EMR/2016/002314 Science and Engineering Research Board (SERB)
- Manipal Academy of Higher Education, Manipal
- IA/I/22/1/506240 DBT-Wellcome Trust India Alliance
- SPARC/2019-2020/P2297/SL SPARC
- IA/I/22/1/506240 Wellcome Trust DBT India Alliance, Government of India
- Builder Grant, Department of Biotechnology, Government of India
- Technology Information Forecasting and Assessment Council (TIFAC) Core in Pharmacogenomics at MAHE, the Manipal
- Wellcome Trust
- Science and Engineering Research Board (SERB)
- Department of Science and Technology, Ministry of Science and Technology, India
- SPARC
- Technology Information Forecasting and Assessment Council (TIFAC) Core in Pharmacogenomics at MAHE, the Manipal
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Affiliation(s)
- Sriharikrishnaa Srinath
- Department of Cell and Molecular Biology, Manipal School of Life SciencesManipal Academy of Higher EducationIndia
| | - Padacherri Vethil Jishnu
- Department of Cell and Molecular Biology, Manipal School of Life SciencesManipal Academy of Higher EducationIndia
| | - Vinay Koshy Varghese
- Department of Cell and Molecular Biology, Manipal School of Life SciencesManipal Academy of Higher EducationIndia
| | - Vaibhav Shukla
- Department of Cell and Molecular Biology, Manipal School of Life SciencesManipal Academy of Higher EducationIndia
| | - Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life SciencesManipal Academy of Higher EducationIndia
| | - Sandeep Mallya
- Department of Bioinformatics, Manipal School of Life SciencesManipal Academy of Higher EducationIndia
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life SciencesManipal Academy of Higher EducationIndia
- Center for DNA Repair and Genome Stability (CDRGS)Manipal Academy of Higher EducationIndia
| | - Krishna Sharan
- Department of Radiotherapy OncologyKasturba Medical CollegeManipalIndia
| | - Deeksha Pandey
- Department of Obstetrics & GynecologyKasturba Medical CollegeManipalIndia
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of MedicineUniversity of OtagoDunedinNew Zealand
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life SciencesManipal Academy of Higher EducationIndia
- Center for DNA Repair and Genome Stability (CDRGS)Manipal Academy of Higher EducationIndia
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Sokolov D, Sharda N, Banerjee A, Denisenko K, Basalious EB, Shukla H, Waddell J, Hamdy NM, Banerjee A. Differential Signaling Pathways in Medulloblastoma: Nano-biomedicine Targeting Non-coding Epigenetics to Improve Current and Future Therapeutics. Curr Pharm Des 2024; 30:31-47. [PMID: 38151840 DOI: 10.2174/0113816128277350231219062154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/15/2023] [Indexed: 12/29/2023]
Abstract
BACKGROUND Medulloblastomas (MDB) are malignant, aggressive brain tumors that primarily affect children. The survival rate for children under 14 is approximately 72%, while for ages 15 to 39, it is around 78%. A growing body of evidence suggests that dysregulation of signaling mechanisms and noncoding RNA epigenetics play a pivotal role in this disease. METHODOLOGY This study conducted an electronic search of articles on websites like PubMed and Google. The current review also used an in silico databases search and bioinformatics analysis and an extensive comprehensive literature search for original research articles and review articles as well as retrieval of current and future medications in clinical trials. RESULTS This study indicates that several signaling pathways, such as sonic hedgehog, WNT/β-catenin, unfolded protein response mediated ER stress, notch, neurotrophins and TGF-β and ERK, MAPK, and ERK play a crucial role in the pathogenesis of MDB. Gene and ncRNA/protein are also involved as an axis long ncRNA to sponge micro-RNAs that affect downstream signal proteins expression and translation affection disease pathophysiology, prognosis and present potential target hit for drug repurposing. Current treatment options include surgery, radiation, and chemotherapy; unfortunately, the disease often relapses, and the survival rate is less than 5%. Therefore, there is a need to develop more effective treatments to combat recurrence and improve survival rates. CONCLUSION This review describes various MDB disease hallmarks, including the signaling mechanisms involved in pathophysiology, related-causal genes, epigenetics, downstream genes/epigenes, and possibly the causal disease genes/non-protein coding (nc)RNA/protein axis. Additionally, the challenges associated with MDB treatment are discussed, along with how they are being addressed using nano-technology and nano-biomedicine, with a listing of possible treatment options and future potential treatment modalities.
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Affiliation(s)
- Daniil Sokolov
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, MD 21201, USA
| | - Neha Sharda
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, MD 21201, USA
| | - Aindrila Banerjee
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kseniia Denisenko
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, MD 21201, USA
| | - Emad B Basalious
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Cairo University, Al Kasr Al Aini 11562, Cairo, Egypt
| | - Hem Shukla
- Division of Translational Radiation Sciences, Department of Radiation Oncology, University of Maryland, School of Medicine, Baltimore, MD 21201, USA
| | - Jaylyn Waddell
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, MD 21201, USA
| | - Nadia M Hamdy
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Abassia 11566, Cairo, Egypt
| | - Aditi Banerjee
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, MD 21201, USA
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Freire NH, Jaeger MDC, de Farias CB, Nör C, Souza BK, Gregianin L, Brunetto AT, Roesler R. Targeting the epigenome of cancer stem cells in pediatric nervous system tumors. Mol Cell Biochem 2023; 478:2241-2255. [PMID: 36637615 DOI: 10.1007/s11010-022-04655-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 12/30/2022] [Indexed: 01/14/2023]
Abstract
Medulloblastoma, neuroblastoma, and pediatric glioma account for almost 30% of all cases of pediatric cancers. Recent evidence indicates that pediatric nervous system tumors originate from stem or progenitor cells and present a subpopulation of cells with highly tumorigenic and stem cell-like features. These cancer stem cells play a role in initiation, progression, and resistance to treatment of pediatric nervous system tumors. Histone modification, DNA methylation, chromatin remodeling, and microRNA regulation display a range of regulatory activities involved in cancer origin and progression, and cellular identity, especially those associated with stem cell features, such as self-renewal and pluripotent differentiation potential. Here, we review the contribution of different epigenetic mechanisms in pediatric nervous system tumor cancer stem cells. The choice between a differentiated and undifferentiated state can be modulated by alterations in the epigenome through the regulation of stemness genes such as CD133, SOX2, and BMI1 and the activation neuronal of differentiation markers, RBFOX3, GFAP, and S100B. Additionally, we highlighted the stage of development of epigenetic drugs and the clinical benefits and efficacy of epigenetic modulators in pediatric nervous system tumors.
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Affiliation(s)
- Natália Hogetop Freire
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 (Setor IV - Campus do Vale), Porto Alegre, 91501-970, Brazil.
| | - Mariane da Cunha Jaeger
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Children's Cancer Institute, Porto Alegre, RS, Brazil
| | - Caroline Brunetto de Farias
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Children's Cancer Institute, Porto Alegre, RS, Brazil
| | - Carolina Nör
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Lauro Gregianin
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Department of Pediatrics, School of Medicine, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Pediatric Oncology Service, Clinical Hospital, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - André Tesainer Brunetto
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Children's Cancer Institute, Porto Alegre, RS, Brazil
| | - Rafael Roesler
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 (Setor IV - Campus do Vale), Porto Alegre, 91501-970, Brazil
- Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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ClustMMRA v2: A Scalable Computational Pipeline for the Identification of MicroRNA Clusters Acting Cooperatively on Tumor Molecular Subgroups. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1385:259-279. [DOI: 10.1007/978-3-031-08356-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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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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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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Braoudaki M, Koutsouris DD, Kouris I, Paidi A, Koutsouri G, George Lambrou I. Bioinformatics and Regression Analyses Manifest Tumor-Specific miRNA Expression Dynamics in Pediatric Embryonal Malignancies. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2019; 2018:5834-5837. [PMID: 30441662 DOI: 10.1109/embc.2018.8513587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Pediatric Central Nervous System (CNS) neoplasms are the second most prevalent tumors of childhood. Further on, prognosis of this type of neoplasms still remain poor and the comprehension of the etiology and pathogenesis of the disease still remains scarce. Several reports have identified microRNAs as significant molecules in the development of central nervous system tumors and propose that they might compose key molecules underlying oncogenesis. In a previous study we have identified several miRNAs, common to different subtypes of pediatric embryonal CNS malignancies as well as, we have identified miRNAs that manifest significant dynamics with respect to their expression and the neoplasmatic subtype. Overall, 19 tumor cases from children diagnosed with embryonal brain tumors were investigated. As controls, children who suffered a sudden death underwent autopsy and were not present with any brain malignancy were used (13 samples of varying localization). Our experimental approach included microarrays covering 1211 miRNAs, which appeared to manifest tumor-specific dynamics. In conclusion, it appeared that certain miRNAs are neoplasm specific and in particular, their expression manifests linear dynamics. Thus, the investigation of miRNA expression in pediatric embryonal brain tumors might contribute towards the discovery of tumor-specific miRNA signatures, which could potentially afford the identification of gene-specific biomarkers related to diagnosis, prognosis and patient targeted therapy, as well as help us understand oncogenetic dynamics.
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Abstract
While only a small part of the human genome encodes for proteins, biological functions for the so-called junk genome are increasingly being recognized through high-throughput technologies and mechanistic experimental studies. Indeed, novel mechanisms of gene regulation are being discovered that require coordinated interaction between DNA, RNA, and proteins. Therefore, interdisciplinary efforts are still needed to decipher these complex transcriptional networks. In this review, we discuss how non-coding RNAs (ncRNAs) are epigenetically regulated in cancer and metastases and consequently how ncRNAs participate in the sculpting of the epigenetic profile of a cancer cell, thus modulating the expression of other RNA molecules. In the latter case, ncRNAs not only affect the DNA methylation status of certain genomic loci but also interact with histone-modifying complexes, changing the structure of the chromatin itself. We present several examples of epigenetic changes causing aberrant expression of ncRNAs in the context of tumor progression. Interestingly, there are also important epigenetic changes and transcriptional regulatory effects derived from their aberrant expression. As ncRNAs can also be used as biomarkers for diagnosis and prognosis or explored as potential targets, we present insights into the use of ncRNAs for targeted cancer therapy.
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9
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Kumar A, Nayak S, Pathak P, Purkait S, Malgulawar PB, Sharma MC, Suri V, Mukhopadhyay A, Suri A, Sarkar C. Identification of miR-379/miR-656 (C14MC) cluster downregulation and associated epigenetic and transcription regulatory mechanism in oligodendrogliomas. J Neurooncol 2018; 139:23-31. [PMID: 29931616 PMCID: PMC6061222 DOI: 10.1007/s11060-018-2840-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/20/2018] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Although role of individual microRNAs (miRNAs) in the pathogenesis of gliomas has been well studied, their role as a clustered remains unexplored in gliomas. METHODS In this study, we performed the expression analysis of miR-379/miR-656 miRNA-cluster (C14MC) in oligodendrogliomas (ODGs) and also investigated the mechanism underlying modulation of this cluster. RESULTS We identified significant downregulation of majority of the miRNAs from this cluster in ODGs. Further data from The Cancer Genome Atlas (TCGA) also confirmed the global downregulation of C14MC. Furthermore, we observed that its regulation is maintained by transcription factor MEF2. In addition, epigenetic machinery involving DNA and histone-methylation are also involved in its regulation, which is acting independently or in synergy. The post- transcriptionally regulatory network of this cluster showed enrichment of key cancer-related biological processes such as cell adhesion and migration. Also, there was enrichment of several cancer related pathways viz PIK3 signaling pathway and glioma pathways. Survival analysis demonstrated association of C14MC (miR-487b and miR-409-3p) with poor progression free survival in ODGs. CONCLUSION Our work demonstrates tumor-suppressive role of C14MC and its role in pathogenesis of ODGs and therefore could be relevant for the development of new therapeutic strategies.
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Affiliation(s)
- Anupam Kumar
- Department of Neurosurgery, Neurosciences Centre, All India Institute of Medical Sciences - AIIMS, New Delhi, India
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Subhashree Nayak
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Pankaj Pathak
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Suvendu Purkait
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Prit Benny Malgulawar
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Mehar Chand Sharma
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Arijit Mukhopadhyay
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Room No. 331, Mathura Road (near Sukhdev Vihar), New Delhi, 110020, India.
- School of Environment and Life Sciences, University of Salford, Room 203a, Cockcroft Building, Manchester, M5 4WT, UK.
| | - Ashish Suri
- Department of Neurosurgery, Neurosciences Centre, All India Institute of Medical Sciences - AIIMS, New Delhi, India.
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
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Zeng A, Yin J, Li Y, Li R, Wang Z, Zhou X, Jin X, Shen F, Yan W, You Y. miR-129-5p targets Wnt5a to block PKC/ERK/NF-κB and JNK pathways in glioblastoma. Cell Death Dis 2018. [PMID: 29531296 PMCID: PMC5847604 DOI: 10.1038/s41419-018-0343-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Therapeutic application of microRNAs (miRNAs) in Wnt-driven glioma has been valuable; however, their specific roles and mechanisms have not been completely investigated. Real-time quantitative PCR (RT-qPCR) was used to analyse the expression of microRNA-129-5p (miR-129-5p) in human glioma samples. Cell-Counting Kit 8 (CCK-8), flow cytometry, EdU, angiogenesis, Transwell invasion, wound healing, in vitro 3D migration and neurosphere formation assays were employed to assess the role of miR-129-5p in glioblastoma multiforme (GBM) cells. Moreover, we performed the luciferase reporter assay and the RNA-ChIP (chromatin immunoprecipitation) assay to confirm whether Wnt5a was a direct target of miR-129-5p. We also confirmed the correlation between the expression profile of miR-129-5p and Wnt5a in glioma patients from the Chinese Glioma Genome Atlas (CGGA) and investigated the overall survival of GBM patients using two data sets, namely, TCGA and GSE16011, according to their Wnt5a expression status. MiR-129-5p expression levels were downregulated and inversely correlated with Wnt5a expression levels in CGGA glioma patients. Restored expression of miR-129-5p blocked GBM cell proliferation, invasion, migration, angiogenesis, neurosphere formation and resistance to temozolomide. We reported that miR-129-5p directly targeted Wnt5a in glioma. Furthermore, we observed that overexpression of miR-129-5p inhibited the expression of Wnt5a, thus blocking the protein kinase C(PKC)/ERK/NF-κB and JNK pathways. Inhibiting Wnt5a rescued the effects of miR-129-5p loss and increased Wnt5a expression was associated with reduced overall survival of GBM patients. We also demonstrated the inhibitory effect of miR-129-5p on tumour growth in GBM using an in vivo model. The miR-129-5p/Wnt5a-axis-mediated PKC/ERK/NF-κB and JNK pathways have therapeutic potential in GBM treatment.
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Affiliation(s)
- Ailiang Zeng
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, 210029, Nanjing, PR China
| | - Jianxing Yin
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, 210029, Nanjing, PR China
| | - Yan Li
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, 210029, Nanjing, PR China
| | - Rui Li
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, 210029, Nanjing, PR China
| | - Zheng Wang
- Beijing Neurosurgical Institute, Capital Medical University, 100050, Beijing, PR China
| | - Xu Zhou
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, 210029, Nanjing, PR China
| | - Xin Jin
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, 210029, Nanjing, PR China
| | - Feng Shen
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, 210029, Nanjing, PR China
| | - Wei Yan
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, 210029, Nanjing, PR China.
| | - Yongping You
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, 210029, Nanjing, PR China.
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Pan X, Wang Z, Wan B, Zheng Z. MicroRNA-206 inhibits the viability and migration of medulloblastoma cells by targeting LIM and SH3 protein 1. Exp Ther Med 2017; 14:3894-3900. [PMID: 29042998 DOI: 10.3892/etm.2017.5016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 04/07/2017] [Indexed: 12/30/2022] Open
Abstract
MicroRNA (miR)-206 has been found to be deregulated in various types of human cancer, including medulloblastoma. However, the regulatory mechanism of miR-206 in medulloblastoma growth and metastasis remains largely unclear. In the present study, reverse transcription-quantitative polymerase chain reaction data indicated that miR-206 was significantly downregulated in medulloblastoma tissues compared with adjacent non-tumor tissues (P<0.01). Furthermore, low expression of miR-206 was significantly associated with seeding at presentation and anaplastic histology (P<0.01), but not with sex, age, or residual tumors. Overexpression of miR-206 significantly reduced the viability and migration of medulloblastoma D341 cells (P<0.01). LIM and SH3 protein 1 (LASP1) was further identified as a novel target of miR-206 in D341 cells. mRNA levels of LASP1 were significantly higher in medulloblastoma tissues compared to adjacent non-tumor tissues (P<0.01), with an inverse correlation to the miR-206 levels in medulloblastoma tissues. In addition, protein expression levels of LASP1 ere negatively regulated by miR-206 in D341 cells. Further investigation showed that overexpression of LASP1 significantly eliminated the inhibitory effects of miR-206 on the migration and invasion of D341 cells (P<0.01). In conclusion, our study demonstrates that miR-206 has a suppressive role in medulloblastoma cell viability and invasion, partly at least, via the targeting of LASP1. Our study highlights the importance of the miR-206/LASP1 in medulloblastoma.
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Affiliation(s)
- Xuexia Pan
- Third Department of Pediatrics, People's Hospital of Binzhou, Binzhou, Shandong 256610, P.R. China
| | - Zhimin Wang
- Department of Hematology, People's Hospital of Binzhou, Binzhou, Shandong 256610, P.R. China
| | - Bin Wan
- Department of Neonatology, Affiliated Hospital of Binzhou Medical College, Binzhou, Shandong 256603, P.R. China
| | - Zhenwen Zheng
- Third Department of Pediatrics, People's Hospital of Binzhou, Binzhou, Shandong 256610, P.R. China
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Enterina JR, Enfield KSS, Anderson C, Marshall EA, Ng KW, Lam WL. DLK1-DIO3 imprinted locus deregulation in development, respiratory disease, and cancer. Expert Rev Respir Med 2017; 11:749-761. [PMID: 28715922 DOI: 10.1080/17476348.2017.1355241] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
INTRODUCTION The imprinted DLK1-DIO3 locus at 14q32.1-32.31 holds biological significance in fetal development, whereby imprinting errors are causal to developmental disorders. Emerging evidence has implicated this locus in other diseases including cancer, highlighting the biological parallels between fetal organ and tumour development. Areas covered: Controlled regulation of gene expression from the imprinted DLK1-DIO3 locus at 14q32.1-32.31 is crucial for proper fetal development. Deregulation of locus gene expression due to imprinting errors has been mechanistically linked to the developmental disorders Kagami-Ogata Syndrome and Temple Syndrome. In adult tissues, deregulation of locus genes has been associated with multiple malignancies although the causal genetic mechanisms remain largely uncharacterised. Here, we summarize the genetic mechanisms underlying the developmental disorders that arise as a result of improper locus imprinting and the resulting developmental phenotypes, emphasizing both the coding and noncoding components of the locus. We further highlight biological parallels common to both fetal development and disease, with a specific focus on lung development, respiratory disease, and lung cancer. Expert commentary: Many commonalities between respiratory and developmental defects have emerged with respect to the 14q32 locus, emphasizing the importance of studying the effects of imprinting on gene regulation patterns at this locus in both biological settings.
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Affiliation(s)
- Jhon R Enterina
- a British Columbia Cancer Research Centre , Vancouver , BC , Canada
| | | | | | - Erin A Marshall
- a British Columbia Cancer Research Centre , Vancouver , BC , Canada
| | - Kevin W Ng
- a British Columbia Cancer Research Centre , Vancouver , BC , Canada
| | - Wan L Lam
- a British Columbia Cancer Research Centre , Vancouver , BC , Canada
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Integrated genomic analyses of de novo pathways underlying atypical meningiomas. Nat Commun 2017; 8:14433. [PMID: 28195122 PMCID: PMC5316884 DOI: 10.1038/ncomms14433] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/28/2016] [Indexed: 12/31/2022] Open
Abstract
Meningiomas are mostly benign brain tumours, with a potential for becoming atypical or malignant. On the basis of comprehensive genomic, transcriptomic and epigenomic analyses, we compared benign meningiomas to atypical ones. Here, we show that the majority of primary (de novo) atypical meningiomas display loss of NF2, which co-occurs either with genomic instability or recurrent SMARCB1 mutations. These tumours harbour increased H3K27me3 signal and a hypermethylated phenotype, mainly occupying the polycomb repressive complex 2 (PRC2) binding sites in human embryonic stem cells, thereby phenocopying a more primitive cellular state. Consistent with this observation, atypical meningiomas exhibit upregulation of EZH2, the catalytic subunit of the PRC2 complex, as well as the E2F2 and FOXM1 transcriptional networks. Importantly, these primary atypical meningiomas do not harbour TERT promoter mutations, which have been reported in atypical tumours that progressed from benign ones. Our results establish the genomic landscape of primary atypical meningiomas and potential therapeutic targets. Meningiomas are mostly benign brain tumours with the potential for becoming atypical or malignant. Here, the authors show that primary atypical meningiomas are epigenetically and genetically distinct from benign and progressed tumours, highlighting possible therapeutic targets such as PRC2.
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Kaur K, Kakkar A, Kumar A, Purkait S, Mallick S, Suri V, Sharma MC, Julka PK, Gupta D, Suri A, Sarkar C. Clinicopathological characteristics, molecular subgrouping, and expression of miR-379/miR-656 cluster (C14MC) in adult medulloblastomas. J Neurooncol 2016; 130:423-430. [PMID: 27576698 DOI: 10.1007/s11060-016-2250-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 08/21/2016] [Indexed: 01/26/2023]
Abstract
Medulloblastoma (MB) is a childhood tumor comprising four molecular subgroups: WNT, SHH, group 3 and group 4, with diagnostic and prognostic connotations. Very few studies are available on molecular subgrouping of adult MBs due to their rarity. Recently, loss of chromosome14q has been reported in SHH MBs, with downregulation of miR-379/miR-656 cluster (C14MC) in pediatric SHH MBs. Hence, the present study on adult MBs was undertaken to enumerate clinicopathological characteristics and molecular subgroups, and to analyze expression of C14MC and its transcriptional regulators, MEF2, JUN and ESRRG. Immunohistochemistry for β-catenin, GAB1 and YAP1 was performed to identify molecular subgroups. MYC amplification was evaluated by FISH. Expression profiling of 47 miRNAs from C14MC was performed using customized Taqman low-density array. Expression of transcriptional regulators was examined using RT-PCR. Seventy-one adult MBs were analyzed. They had male predominance and majority were located laterally (52 %). A significant proportion of cases were of Desmoplastic/nodular histology (32 %); MBEN was not seen. WNT tumors constituted 4.2 %, SHH 62 %, and non-WNT/non-SHH 33.8 %. MYC amplification was identified in 11.1 % cases. Patient outcome was worse in adults. Significant downregulation of C14MC was observed in all MB subgroups, and MEF-2 expression was downregulated. Adult MBs are distinct from childhood MBs in terms of location, histopathological subtypes, molecular subgroups, as well as prognosis. Silencing of C14MC in all MB subgroups suggests its role as a tumor suppressor locus in tumorigenesis. Deregulation of C14MC can possibly be attributed to repression of MEF2.
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Affiliation(s)
- Kavneet Kaur
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Aanchal Kakkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Anupam Kumar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Suvendu Purkait
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Supriya Mallick
- Department of Radiation Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Mehar C Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Pramod K Julka
- Department of Radiation Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Deepak Gupta
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India
| | - Ashish Suri
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, 110029, India.
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Shahar T, Granit A, Zrihan D, Canello T, Charbit H, Einstein O, Rozovski U, Elgavish S, Ram Z, Siegal T, Lavon I. Expression level of miRNAs on chromosome 14q32.31 region correlates with tumor aggressiveness and survival of glioblastoma patients. J Neurooncol 2016; 130:413-422. [PMID: 27573219 DOI: 10.1007/s11060-016-2248-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 08/21/2016] [Indexed: 12/17/2022]
Abstract
The 54 microRNAs (miRNAs) within the DLK-DIO3 genomic region on chromosome 14q32.31 (cluster-14-miRNAs) are organized into sub-clusters 14A and 14B. These miRNAs are downregulated in glioblastomas and might have a tumor suppressive role. Any association between the expression levels of cluster-14-miRNAs with overall survival (OS) is undetermined. We randomly selected miR-433, belonging to sub-cluster 14A and miR-323a-3p and miR-369-3p, belonging to sub-cluster 14B, and assessed their role in glioblastomas in vitro and in vivo. We also determined the expression level of cluster-14-miRNAs in 27 patients with newly diagnosed glioblastoma, and analyzed the association between their level of expression and OS. Overexpression of miR-323a-3p and miR-369-3p, but not miR-433, in glioblastoma cells inhibited their proliferation and migration in vitro. Mice implanted with glioblastoma cells overexpressing miR323a-3p and miR369-3p, but not miR433, exhibited prolonged survival compared to controls (P = .003). Bioinformatics analysis identified 13 putative target genes of cluster-14-miRNAs, and real-time RT-PCR validated these findings. Pathway analysis of the putative target genes identified neuregulin as the most enriched pathway. The expression level of cluster-14-miRNAs correlated with patients' OS. The median OS was 8.5 months for patients with low expression levels and 52.7 months for patients with high expression levels (HR 0.34; 95 % CI 0.12-0.59, P = .003). The expression level of cluster-14-miRNAs correlates directly with OS, suggesting a role for this cluster in promoting aggressive behavior of glioblastoma, possibly through ErBb/neuregulin signaling.
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Affiliation(s)
- Tal Shahar
- Department of Neurosurgery, Tel Aviv Medical Center, Tel Aviv, Israel.,The Laboratory for Molecular Neuro-Oncology, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Avital Granit
- Leslie and Michael Gaffin Center for Neuro-Oncology, Neurology Department, The Agnes Ginges Center for Human Neurogenetics, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Daniel Zrihan
- Leslie and Michael Gaffin Center for Neuro-Oncology, Neurology Department, The Agnes Ginges Center for Human Neurogenetics, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Tamar Canello
- Leslie and Michael Gaffin Center for Neuro-Oncology, Neurology Department, The Agnes Ginges Center for Human Neurogenetics, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Hanna Charbit
- Leslie and Michael Gaffin Center for Neuro-Oncology, Neurology Department, The Agnes Ginges Center for Human Neurogenetics, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Ofira Einstein
- Leslie and Michael Gaffin Center for Neuro-Oncology, Neurology Department, The Agnes Ginges Center for Human Neurogenetics, Hadassah Hebrew University Medical Center, Jerusalem, Israel.,Physiotherapy Department, Ariel University, Ariel, Israel
| | - Uri Rozovski
- Division of Hematology, Davidoff Institute of Oncology, Rabin Medical Center, Campus Beilinson, Petach Tikva, Israel.,Tel Aviv University, Tel Aviv, Israel
| | - Sharona Elgavish
- Info-CORE, Bioinformatics Unit of the I-CORE Computation Center, Hadassah, Hebrew University medical center, Jerusalem, Israel
| | - Zvi Ram
- Department of Neurosurgery, Tel Aviv Medical Center, Tel Aviv, Israel.,The Laboratory for Molecular Neuro-Oncology, Tel Aviv Medical Center, Tel Aviv, Israel.,Tel Aviv University, Tel Aviv, Israel
| | - Tali Siegal
- Center for Neuro-Oncology, Davidoff Institute of Oncology, Rabin Medical Center, Campus Beilinson, Petach Tikva, Israel
| | - Iris Lavon
- Leslie and Michael Gaffin Center for Neuro-Oncology, Neurology Department, The Agnes Ginges Center for Human Neurogenetics, Hadassah Hebrew University Medical Center, Jerusalem, Israel.
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MicroRNA Profiling in Patients with Upper Tract Urothelial Carcinoma Associated with Balkan Endemic Nephropathy. BIOMED RESEARCH INTERNATIONAL 2016; 2016:7450461. [PMID: 27218105 PMCID: PMC4863087 DOI: 10.1155/2016/7450461] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 03/02/2016] [Accepted: 04/04/2016] [Indexed: 02/08/2023]
Abstract
Balkan endemic nephropathy (BEN) is a disease that affects people that live in the alluvial plains along the tributaries of the Danube River in the Balkan region. BEN is a chronic tubulointerstitial disease with a slow progression to terminal renal failure and has strong association with upper tract urothelial carcinoma (UTUC). There are several hypotheses about the etiology of BEN, but only the toxic effect of aristolochic acid has been confirmed as a risk factor in the occurrence of the disease. Aberrantly expressed miRNAs have been shown to be associated with many types of cancers. A number of studies have investigated the expression of microRNAs in urothelial carcinoma, mainly on urothelial bladder cancer, and only a few have included patients with UTUC. Here we present the first study of microRNA profiling in UTUC tissues from patients with BEN (BEN-UTUC) and patients with UTUC from nonendemic Balkan regions (non-BEN-UTUC) in comparison to normal kidney tissues. We found 10 miRNAs that were differentially expressed in patients with BEN-UTUC and 15 miRNAs in patients with non-BEN-UTUC. miRNA signature determined in BEN-UTUC patients differs from the non-BEN-UTUC patients; only miR-205-5p was mutual in both groups.
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Tam IS, Giguère V. There and back again: The journey of the estrogen-related receptors in the cancer realm. J Steroid Biochem Mol Biol 2016; 157:13-9. [PMID: 26151739 DOI: 10.1016/j.jsbmb.2015.06.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 06/09/2015] [Accepted: 06/16/2015] [Indexed: 12/21/2022]
Abstract
The identification of two genes encoding polypeptides with structural features common with the estrogen receptor more than a quarter century ago, referred to as the estrogen-related receptors (ERRs), subsequently led to the discovery of several previously unrecognized hormone responsive systems through the application of reverse endocrinology. Paradoxically, the natural ligand(s) associated with members of the ERR subfamily remains to be identified. While initial studies on the mode of action and physiological functions of the ERRs focused on interaction with estrogen signalling in breast cancer, subsequent work showed that the ERRs are ubiquitous master regulators of cellular energy metabolism. This review aims to demonstrate that the ERRs occupy a central node at the interface of cancer and metabolism, and that modulation of their activity may represent a worthwhile strategy to induce metabolic vulnerability in tumors of various origins and thus achieve a more comprehensive response to current therapies.
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Affiliation(s)
- Ingrid S Tam
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montréal, QC H3A 1A3, Canada
| | - Vincent Giguère
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montréal, QC H3A 1A3, Canada; Departments of Biochemistry, Medicine and Oncology, McGill University, Montréal, PQ H3G 1Y6, Canada.
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Jha P, Agrawal R, Pathak P, Kumar A, Purkait S, Mallik S, Suri V, Chand Sharma M, Gupta D, Suri A, Sharma BS, Julka PK, Kulshreshtha R, Sarkar C. Genome-wide small noncoding RNA profiling of pediatric high-grade gliomas reveals deregulation of several miRNAs, identifies downregulation of snoRNA cluster HBII-52 and delineates H3F3A and TP53 mutant-specific miRNAs and snoRNAs. Int J Cancer 2015; 137:2343-53. [PMID: 25994230 DOI: 10.1002/ijc.29610] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 05/07/2015] [Indexed: 12/20/2022]
Abstract
Pediatric high-grade gliomas (HGGs) are highly malignant tumors that remain incurable and relatively understudied. The crucial role of noncoding RNAs (ncRNAs) has been reported in various cancers. However, the study on miRNAs in pediatric HGGs is scant and there is no report till date on the status of other small ncRNAs. Genome-wide microarray analysis was performed to investigate small ncRNA expression in pediatric HGG (n = 14) and compared to adult glioblastoma (GBM) signature. The validation of miRNAs and small nucleolar RNAs (snoRNAs) was done by real-time polymerase chain reaction. TP53 and H3F3A mutation-specific miRNA and snoRNA profiles were generated and analyzed. Pediatric HGGs showed upregulation of miR-17/92 and its paralog clusters (miR106b/25 and miR-106a/363), whereas majority of downregulated miRNAs belonged to miR379/656 cluster (14q32). Unsupervised hierarchical clustering identified two distinct groups. Interestingly, Group 2 with downregulated 14q32 cluster showed better overall survival. The miRNAs unique to pediatric HGG as compared to adult GBM were predicted to affect PDGFR and SMAD2/3 pathways. Similarities were seen between pediatric HGG and TP53 mutant miRNA profiles as compared to wild types. Several of H3F3A mutation-regulated genes were found to be the targets of H3F3A mutant-specific miRNAs. Remarkably, a significant downregulation of HBII-52 snoRNA cluster was found in pediatric HGGs, and was specific to H3F3A nonmutants. This is the first genome-wide profiling study on miRNAs and snoRNAs in pediatric HGGs with respect to H3F3A and TP53 mutations. The comparison of miRNA profiles of pediatric HGGs and adult GBM reiterates the overlaps and differences as also seen with their gene expression and methylation signatures.
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Affiliation(s)
- Prerana Jha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Rahul Agrawal
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Pankaj Pathak
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Anupam Kumar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Suvendu Purkait
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Supriyo Mallik
- Department of Radiotherapy, Dr B R Ambedkar Institute-Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Mehar Chand Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Deepak Gupta
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India
| | - Ashish Suri
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India
| | - B S Sharma
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India
| | - P K Julka
- Department of Radiotherapy, Dr B R Ambedkar Institute-Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
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Panwalkar P, Moiyadi A, Goel A, Shetty P, Goel N, Sridhar E, Shirsat N. MiR-206, a Cerebellum Enriched miRNA Is Downregulated in All Medulloblastoma Subgroups and Its Overexpression Is Necessary for Growth Inhibition of Medulloblastoma Cells. J Mol Neurosci 2015; 56:673-80. [PMID: 25859932 DOI: 10.1007/s12031-015-0548-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/19/2015] [Indexed: 02/03/2023]
Abstract
Medulloblastoma is the most common and a highly malignant pediatric brain tumor located in the cerebellar region of the brain. Medulloblastomas have recently been shown to consist of four distinct molecular subgroups, viz., WNT, SHH, group 3, and group 4. MiR-206, a miRNA first identified as a myomiR due to its enriched expression in skeletal muscle was found to be expressed specifically in the cerebellum, the site of medulloblastoma occurrence. MiR-206 expression was found to be downregulated in medulloblastomas belonging to all the four molecular subgroups as well as in established medulloblastoma cell lines. Further, the expression of murine homolog of miR-206 was also found to be downregulated in SHH subgroup medulloblastomas from the Smo (+/+) transgenic mice and the Ptch1 (+/-) knockout mice. MiR-206 downregulation in all the four medulloblastoma subgroups suggests tumor-suppressive role for miR-206 in medulloblastoma pathogenesis. The effect of miR-206 expression was analyzed in three established medulloblastoma cell lines, viz., Daoy, D425, and D283 belonging to distinct molecular subgroups. Restoration of miR-206 expression to the levels comparable to those in the normal cerebellum, however, was found to be insufficient to inhibit the growth of established medulloblastoma cell lines. OTX2, an oncogenic miR-206 target, overexpressed in all non-SHH medulloblastomas, is known to inhibit myogenic differentiation of medulloblastoma cells. Overexpression of miR-206 was necessary to downregulate OTX2 expression and inhibit growth of medulloblastoma cell lines.
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Affiliation(s)
- Pooja Panwalkar
- Shirsat Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
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Analysis of chromosome 17 miRNAs and their importance in medulloblastomas. BIOMED RESEARCH INTERNATIONAL 2015; 2015:717509. [PMID: 25866804 PMCID: PMC4383152 DOI: 10.1155/2015/717509] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 11/16/2014] [Accepted: 11/16/2014] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are small sequences of nucleotides that regulate posttranscriptionally gene expression. In recent years they have been recognized as very important general regulators of proliferation, differentiation, adhesion, cell death, and others. In some cases, the characteristic presence of miRNAs reflects some of the cellular pathways that may be altered. Particularly medulloblastomas (MB) represent entities that undergo almost characteristic alterations of chromosome 17: from loss of discrete fragments and isochromosomes formation to complete loss of one of them. An analysis of the major loci on this chromosome revealed that it contains at least 19 genes encoding miRNAs which may regulate the development and differentiation of the brain and cerebellum. miRNAs are regulators of real complex networks; they can regulate from 100 to over 300 messengers of various proteins. In this review some miRNAs are considered to be important in MB studies. Some of them are miRNA-5047, miRNA-1253, miRNA-2909, and miRNA-634. Everyone can significantly affect the development, growth, and cell invasion of MB, and they have not been explored in this tumor. In this review, we propose some miRNAs that can affect some genes in MB, and hence the importance of its study.
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Braoudaki M, Lambrou GI, Giannikou K, Milionis V, Stefanaki K, Birks DK, Prodromou N, Kolialexi A, Kattamis A, Spiliopoulou CA, Tzortzatou-Stathopoulou F, Kanavakis E. Microrna expression signatures predict patient progression and disease outcome in pediatric embryonal central nervous system neoplasms. J Hematol Oncol 2014; 7:96. [PMID: 25551588 PMCID: PMC4342799 DOI: 10.1186/s13045-014-0096-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 12/12/2014] [Indexed: 02/07/2023] Open
Abstract
Background Although, substantial experimental evidence related to diagnosis and treatment of pediatric central nervous system (CNS) neoplasms have been demonstrated, the understanding of the etiology and pathogenesis of the disease remains scarce. Recent microRNA (miRNA)-based research reveals the involvement of miRNAs in various aspects of CNS development and proposes that they might compose key molecules underlying oncogenesis. The current study evaluated miRNA differential expression detected between pediatric embryonal brain tumors and normal controls to characterize candidate biomarkers related to diagnosis, prognosis and therapy. Methods Overall, 19 embryonal brain tumors; 15 Medulloblastomas (MBs) and 4 Atypical Teratoid/Rabdoid Tumors (AT/RTs) were studied. As controls, 13 samples were used; The First-Choice Human Brain Reference RNA and 12 samples from deceased children who underwent autopsy and were not present with any brain malignancy. RNA extraction was carried out using the Trizol method, whilst miRNA extraction was performed with the mirVANA miRNA isolation kit. The experimental approach included miRNA microarrays covering 1211 miRNAs. Quantitative Real-Time Polymerase Chain Reaction was performed to validate the expression profiles of miR-34a and miR-601 in all 32 samples initially screened with miRNA microarrays and in an additional independent cohort of 30 patients (21MBs and 9 AT/RTs). Moreover, meta-analyses was performed in total 27 embryonal tumor samples; 19 MBs, 8 ATRTs and 121 control samples. Twelve germinomas were also used as an independent validation cohort. All deregulated miRNAs were correlated to patients’ clinical characteristics and pathological measures. Results In several cases, there was a positive correlation between individual miRNA expression levels and laboratory or clinical characteristics. Based on that, miR-601 could serve as a putative tumor suppressor gene, whilst miR-34a as an oncogene. In general, miR-34a demonstrated oncogenic roles in all pediatric embryonal CNS neoplasms studied. Conclusions Deeper understanding of the aberrant miRNA expression in pediatric embryonal brain tumors might aid in the development of tumor-specific miRNA signatures, which could potentially afford promising biomarkers related to diagnosis, prognosis and patient targeted therapy. Electronic supplementary material The online version of this article (doi:10.1186/s13045-014-0096-y) contains supplementary material, which is available to authorized users.
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