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Eschbacher KL, Tran QT, Moskalev EA, Jenkins S, Fritchie K, Stoehr R, Caron A, Link MJ, Brown PD, Guajardo A, Brat DJ, Wu A, Santagata S, Louis DN, Brastianos PK, Kaplan AB, Alexander B, Rossi S, Ferrarese F, Raleigh DR, Nguyen MP, Gross J, Velazquez Vega J, Rodriguez F, Perry A, Martinez-Lage M, Orr BA, Haller F, Giannini C. NAB2::STAT6 fusions and genome-wide DNA methylation profiling: Predictors of patient outcomes in meningeal solitary fibrous tumors. Brain Pathol 2024:e13256. [PMID: 38523251 DOI: 10.1111/bpa.13256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/01/2024] [Indexed: 03/26/2024] Open
Abstract
Meningeal solitary fibrous tumors (SFT) are rare and have a high frequency of local recurrence and distant metastasis. In a cohort of 126 patients (57 female, 69 male; mean age at surgery 53.0 years) with pathologically confirmed meningeal SFTs with extended clinical follow-up (median 9.9 years; range 15 days-43 years), we performed extensive molecular characterization including genome-wide DNA methylation profiling (n = 80) and targeted TERT promoter mutation testing (n = 98). Associations were examined with NAB2::STAT6 fusion status (n = 101 cases; 51 = ex5-7::ex16-17, 26 = ex4::ex2-3; 12 = ex2-3::exANY/other and 12 = no fusion) and placed in the context of 2021 Central Nervous System (CNS) WHO grade. NAB2::STAT6 fusion breakpoints (fusion type) were significantly associated with metastasis-free survival (MFS) (p = 0.03) and, on multivariate analysis, disease-specific survival (DSS) when adjusting for CNS WHO grade (p = 0.03). DNA methylation profiling revealed three distinct clusters: Cluster 1 (n = 38), Cluster 2 (n = 22), and Cluster 3 (n = 20). Methylation clusters were significantly associated with fusion type (p < 0.001), with Cluster 2 harboring ex4::ex2-3 fusion in 16 (of 20; 80.0%), nearly all TERT promoter mutations (7 of 8; 87.5%), and predominantly an "SFT" histologic phenotype (15 of 22; 68.2%). Clusters 1 and 3 were less distinct, both dominated by tumors having ex5-7::ex16-17 fusion (respectively, 25 of 33; 75.8%, and 12 of 18; 66.7%) and with variable histological phenotypes. Methylation clusters were significantly associated with MFS (p = 0.027), but not overall survival (OS). In summary, NAB2::STAT6 fusion type was significantly associated with MFS and DSS, suggesting that tumors with an ex5::ex16-17 fusion may have inferior patient outcomes. Methylation clusters were significantly associated with fusion type, TERT promoter mutation status, histologic phenotype, and MFS.
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Affiliation(s)
| | - Quynh T Tran
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | | | | | | | | | | | | | | | - Daniel J Brat
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Ashley Wu
- University of California, San Francisco, California, USA
| | | | - David N Louis
- Brigham and Women's Hospital, Boston, Massachusetts, USA
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | | | | | | | | | | | - Minh P Nguyen
- University of California, San Francisco, California, USA
| | | | | | - Fausto Rodriguez
- University of California Los Angeles, Los Angeles, California, USA
| | - Arie Perry
- University of California, San Francisco, California, USA
| | | | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Caterina Giannini
- Mayo Clinic, Rochester, Minnesota, USA
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
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Pan J, Li D, Fan X, Cheng J, Jin S, Chen P, Lin H, Li Y. Aberrant DNA Methylation Patterns of Deleted in Liver Cancer 1 Isoforms in Hepatocellular Carcinoma. DNA Cell Biol 2023; 42:140-150. [PMID: 36917700 DOI: 10.1089/dna.2022.0384] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Hepatocellular carcinoma (HCC), a common primary liver cancer, is the third leading cause of death worldwide. DNA methylation changes are common in HCC and have been studied to be associated with hepatocarcinogenesis. In our study, we used the MassARRAY® EpiTYPER technology to investigate the methylation differences of deleted in liver cancer 1 (DLC1) (isoform 1 and 3) promoter between HCC tissues and corresponding adjacent noncancerous tissues and the association between methylation levels and clinicopathological features. In addition, the modified CRISPR-Cas9 system and the DNA methyltransferase inhibitor (DNMTi) were utilized to explore the functional correlation of epigenetic modifications and DLC1 gene regulation. The methylation levels of the DLC1 isoforms in HCC samples were found significantly lower than those in the adjacent noncancerous tissues (all p < 0.0001). Also, we found that the expression of DLC1 could be bidirectionally regulated by the modified CRISPR-Cas9 system and the DNMTi. Moreover, the hypomethylation of DLC1 in HCC samples was connected with the presence of satellite lesions (p = 0.0305) and incomplete tumor capsule (p = 0.0204). Receiver operator characteristic curve analysis demonstrated that the methylation levels of DLC1 could be applied to discriminate HCC patients (area under the curve = 0.728, p < 0.0001). The hypomethylation status was a key regulatory mechanism of DLC1 expression and might serve as a potential biomarker for HCC.
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Affiliation(s)
- Junhai Pan
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Duguang Li
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaoxiao Fan
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- State Key Laboratory of Modern Optical Instrumentations, Centre for Optical and Electromagnetic Research, College of Optical Science and Engineering, International Research Center for Advanced Photonics, Zhejiang University, Hangzhou, China
| | - Jiaxi Cheng
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Shengxi Jin
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Peng Chen
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hui Lin
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Research Center of Cognitive Healthcare, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou,China
| | - Yirun Li
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Ozair A, Bhat V, Alisch RS, Khosla AA, Kotecha RR, Odia Y, McDermott MW, Ahluwalia MS. DNA Methylation and Histone Modification in Low-Grade Gliomas: Current Understanding and Potential Clinical Targets. Cancers (Basel) 2023; 15:cancers15041342. [PMID: 36831683 PMCID: PMC9954183 DOI: 10.3390/cancers15041342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/02/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Gliomas, the most common type of malignant primary brain tumor, were conventionally classified through WHO Grades I-IV (now 1-4), with low-grade gliomas being entities belonging to Grades 1 or 2. While the focus of the WHO Classification for Central Nervous System (CNS) tumors had historically been on histopathological attributes, the recently released fifth edition of the classification (WHO CNS5) characterizes brain tumors, including gliomas, using an integration of histological and molecular features, including their epigenetic changes such as histone methylation, DNA methylation, and histone acetylation, which are increasingly being used for the classification of low-grade gliomas. This review describes the current understanding of the role of DNA methylation, demethylation, and histone modification in pathogenesis, clinical behavior, and outcomes of brain tumors, in particular of low-grade gliomas. The review also highlights potential diagnostic and/or therapeutic targets in associated cellular biomolecules, structures, and processes. Targeting of MGMT promoter methylation, TET-hTDG-BER pathway, association of G-CIMP with key gene mutations, PARP inhibition, IDH and 2-HG-associated processes, TERT mutation and ARL9-associated pathways, DNA Methyltransferase (DNMT) inhibition, Histone Deacetylase (HDAC) inhibition, BET inhibition, CpG site DNA methylation signatures, along with others, present exciting avenues for translational research. This review also summarizes the current clinical trial landscape associated with the therapeutic utility of epigenetics in low-grade gliomas. Much of the evidence currently remains restricted to preclinical studies, warranting further investigation to demonstrate true clinical utility.
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Affiliation(s)
- Ahmad Ozair
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Faculty of Medicine, King George’s Medical University, Lucknow 226003, India
| | - Vivek Bhat
- St. John’s Medical College, Bangalore 560034, India
| | - Reid S. Alisch
- Department of Neurosurgery, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Atulya A. Khosla
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
| | - Rupesh R. Kotecha
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Yazmin Odia
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Michael W. McDermott
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
- Miami Neuroscience Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Correspondence: (M.W.M.); (M.S.A.)
| | - Manmeet S. Ahluwalia
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Miami Neuroscience Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Correspondence: (M.W.M.); (M.S.A.)
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Genome wide DNA methylation analysis identifies novel molecular subgroups and predicts survival in neuroblastoma. Br J Cancer 2022; 127:2006-2015. [PMID: 36175618 PMCID: PMC9681858 DOI: 10.1038/s41416-022-01988-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 08/22/2022] [Accepted: 09/08/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Neuroblastoma is the most common malignancy in infancy, accounting for 15% of childhood cancer deaths. Outcome for the high-risk disease remains poor. DNA-methylation patterns are significantly altered in all cancer types and can be utilised for disease stratification. METHODS Genome-wide DNA methylation (n = 223), gene expression (n = 130), genetic/clinical data (n = 213), whole-exome sequencing (n = 130) was derived from the TARGET study. Methylation data were derived from HumanMethylation450 BeadChip arrays. t-SNE was used for the segregation of molecular subgroups. A separate validation cohort of 105 cases was studied. RESULTS Five distinct neuroblastoma molecular subgroups were identified, based on genome-wide DNA-methylation patterns, with unique features in each, including three subgroups associated with known prognostic features and two novel subgroups. As expected, Cluster-4 (infant diagnosis) had significantly better 5-year progression-free survival (PFS) than the four other clusters. However, in addition, the molecular subgrouping identified multiple patient subsets with highly increased risk, most notably infant patients that do not map to Cluster-4 (PFS 50% vs 80% for Cluster-4 infants, P = 0.005), and allowed identification of subgroup-specific methylation differences that may reflect important biological differences within neuroblastoma. CONCLUSIONS Methylation-based clustering of neuroblastoma reveals novel molecular subgroups, with distinct molecular/clinical characteristics and identifies a subgroup of higher-risk infant patients.
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Targeted Long-Read Bisulfite Sequencing Identifies Differences in the TERT Promoter Methylation Profiles between TERT Wild-Type and TERT Mutant Cancer Cells. Cancers (Basel) 2022; 14:cancers14164018. [PMID: 36011010 PMCID: PMC9406525 DOI: 10.3390/cancers14164018] [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: 07/02/2022] [Revised: 08/06/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
Background: TERT promoter methylation, located several hundred base pairs upstream of the transcriptional start site, is cancer specific and correlates with increased TERT mRNA expression and poorer patient outcome. Promoter methylation, however, is not mutually exclusive to TERT activating genetic alterations, as predicted for functionally redundant mechanisms. To annotate the altered patterns of TERT promoter methylation and their relationship with gene expression, we applied a Pacific Biosciences-based, long-read, bisulfite-sequencing technology and compared the differences in the methylation marks between wild-type and mutant cancers in an allele-specific manner. Results: We cataloged TERT genetic alterations (i.e., promoter point mutations or structural variations), allele-specific promoter methylation patterns, and allele-specific expression levels in a cohort of 54 cancer cell lines. In heterozygous mutant cell lines, the mutant alleles were significantly less methylated than their silent, mutation-free alleles (p < 0.05). In wild-type cell lines, by contrast, both epialleles were equally methylated to high levels at the TERT distal promoter, but differentially methylated in the proximal regions. ChIP analysis showed that epialleles with the hypomethylated proximal and core promoter were enriched in the active histone mark H3K4me2/3, whereas epialleles that were methylated in those regions were enriched in the repressive histone mark H3K27me3. Decitabine therapy induced biallelic expression in the wild-type cancer cells, whereas the mutant cell lines were unaffected. Conclusions: Long-read bisulfite sequencing analysis revealed differences in the methylation profiles and responses to demethylating agents between TERT wild-type and genetically altered cancer cell lines. The causal relation between TERT promoter methylation and gene expression remains to be established.
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Gringmuth M, Walther J, Greiser S, Toussaint M, Schwalm B, Kool M, Kortmann RD, Glasow A, Patties I. Enhanced Survival of High-Risk Medulloblastoma-Bearing Mice after Multimodal Treatment with Radiotherapy, Decitabine, and Abacavir. Int J Mol Sci 2022; 23:ijms23073815. [PMID: 35409174 PMCID: PMC8998934 DOI: 10.3390/ijms23073815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/22/2022] [Accepted: 03/26/2022] [Indexed: 02/04/2023] Open
Abstract
Children with high-risk SHH/TP53-mut and Group 3 medulloblastoma (MB) have a 5-year overall survival of only 40%. Innovative approaches to enhance survival while preventing adverse effects are urgently needed. We investigated an innovative therapy approach combining irradiation (RT), decitabine (DEC), and abacavir (ABC) in a patient-derived orthotopic SHH/TP53-mut and Group 3 MB mouse model. MB-bearing mice were treated with DEC, ABC and RT. Mouse survival, tumor growth (BLI, MRT) tumor histology (H/E), proliferation (Ki-67), and endothelial (CD31) staining were analyzed. Gene expression was examined by microarray and RT-PCR (Ki-67, VEGF, CD31, CD15, CD133, nestin, CD68, IBA). The RT/DEC/ABC therapy inhibited tumor growth and enhanced mouse survival. Ki-67 decreased in SHH/TP53-mut MBs after RT, DEC, RT/ABC, and RT/DEC/ABC therapy. CD31 was higher in SHH/TP53-mut compared to Group 3 MBs and decreased after RT/DEC/ABC. Microarray analyses showed a therapy-induced downregulation of cell cycle genes. By RT-PCR, no therapy-induced effect on stem cell fraction or immune cell invasion/activation could be shown. We showed for the first time that RT/DEC/ABC therapy improves survival of orthotopic SHH/TP53-mut and Group 3 MB-bearing mice without inducing adverse effects suggesting the potential for an adjuvant application of this multimodal therapy approach in the human clinic.
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Affiliation(s)
- Marieke Gringmuth
- Department of Radiation Oncology, University of Leipzig, Stephanstraße 9a, 04103 Leipzig, Germany; (M.G.); (R.-D.K.); (A.G.)
| | - Jenny Walther
- Fraunhofer Center for Microelectronic and Optical Systems for Biomedicine, Herman-Hollerith-Straße 3, 99099 Erfurt, Germany; (J.W.); (S.G.)
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany
| | - Sebastian Greiser
- Fraunhofer Center for Microelectronic and Optical Systems for Biomedicine, Herman-Hollerith-Straße 3, 99099 Erfurt, Germany; (J.W.); (S.G.)
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany
| | - Magali Toussaint
- Department of Neuroradiopharmaceuticals, Institute of Radiopharmaceutical Cancer Research Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Research Site Leipzig, Permoserstraße 15, 04318 Leipzig, Germany;
| | - Benjamin Schwalm
- Hopp Children’s Cancer Center (KiTZ), Im Neuenheimer Feld 430, 69120 Heidelberg, Germany; (B.S.); (M.K.)
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Research Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Marcel Kool
- Hopp Children’s Cancer Center (KiTZ), Im Neuenheimer Feld 430, 69120 Heidelberg, Germany; (B.S.); (M.K.)
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Research Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands
| | - Rolf-Dieter Kortmann
- Department of Radiation Oncology, University of Leipzig, Stephanstraße 9a, 04103 Leipzig, Germany; (M.G.); (R.-D.K.); (A.G.)
| | - Annegret Glasow
- Department of Radiation Oncology, University of Leipzig, Stephanstraße 9a, 04103 Leipzig, Germany; (M.G.); (R.-D.K.); (A.G.)
| | - Ina Patties
- Department of Radiation Oncology, University of Leipzig, Stephanstraße 9a, 04103 Leipzig, Germany; (M.G.); (R.-D.K.); (A.G.)
- Correspondence:
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Genetic and Histopathological Heterogeneity of Neuroblastoma and Precision Therapeutic Approaches for Extremely Unfavorable Histology Subgroups. Biomolecules 2022; 12:biom12010079. [PMID: 35053227 PMCID: PMC8773700 DOI: 10.3390/biom12010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/16/2021] [Accepted: 12/29/2021] [Indexed: 02/04/2023] Open
Abstract
Peripheral neuroblastic tumors (neuroblastoma, ganglioneuroblastoma and ganglioneuroma) are heterogeneous and their diverse and wide range of clinical behaviors (spontaneous regression, tumor maturation and aggressive progression) are closely associated with genetic/molecular properties of the individual tumors. The International Neuroblastoma Pathology Classification, a biologically relevant and prognostically significant morphology classification distinguishing the favorable histology (FH) and unfavorable histology (UH) groups in this disease, predicts survival probabilities of the patients with the highest hazard ratio. The recent advance of neuroblastoma research with precision medicine approaches demonstrates that tumors in the UH group are also heterogeneous and four distinct subgroups—MYC, TERT, ALT and null—are identified. Among them, the first three subgroups are collectively named extremely unfavorable histology (EUH) tumors because of their highly aggressive clinical behavior. As indicated by their names, these EUH tumors are individually defined by their potential targets detected molecularly and immunohistochemically, such as MYC-family protein overexpression, TERT overexpression and ATRX (or DAXX) loss. In the latter half on this paper, the current status of therapeutic targeting of these EUH tumors is discussed for the future development of effective treatments of the patients.
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Yu M, Yu S, Zhou W, Yi B, Liu Y. HOXC6/8/10/13 predict poor prognosis and associate with immune infiltrations in glioblastoma. Int Immunopharmacol 2021; 101:108293. [PMID: 34763232 DOI: 10.1016/j.intimp.2021.108293] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/10/2021] [Accepted: 10/18/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND Glioblastoma (GBM), characterized by deregulated cell proliferation and immune cells infiltration, is a common and lethal tumor of the central nervous system. Recently, the infiltration of immune cells has attracted attention as a potential novel GBM immunotherapy option. Homeobox C cluster (HOXC) is an evolutionarily conserved family of transcriptional factors that are involved in embryogenesis and tumorigenesis. Nevertheless, the correlations of HOXCs with the prognosis and immune infiltration of GBM remain blurred. METHODS The RNA-seq data with corresponding clinical characteristics were downloaded from TCGA and GTEx databases. The correlations between HOXCs and clinical characteristics were calculated using univariable and multivariate Cox regression. R language with ggplot2, survminer, survival, GSVA, and pROC packages were employed to analyze the data and present the plots. MethSurv, UALCAN and cBioPortal were employed to evaluate the DNA methylation and mutation status of HOXCs in GBM. We also verified the expression and prognosis of HOXCs by qPCR and immunohistochemistry in a cohort of 36 patients. RESULTS We identified that HOXC6/8/10/13 were crucial biomarkers for diagnosis and prognostic judgement in GBM. Gene set variation analysis revealed that levels of expression of HOXCs were associated with the infiltration of various immune cells. The qPCR and immunohistochemistry data validated the prognostic values of HOXC6/8/10/13 in GBM. Finally, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that HOXCs might be involved in DNA-binding transcription activator activity and the apelin signaling pathway. CONCLUSION This research highlights that HOXC6/8/10/13 are involved in the immune infiltrates, also provide potential clinical utility as therapeutic targets in GBM.
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Affiliation(s)
- Mingjun Yu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, People's Republic of China; Gamma Knife Center, Shengjing Hospital of China Medical University, Shenyang, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, People's Republic of China
| | - Shijia Yu
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang 110004, People's Republic of China
| | - Wen Zhou
- Department of Pain Management, Dalian Municipal Central Hospital, Dalian 116033, People's Republic of China
| | - Bolong Yi
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, People's Republic of China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, People's Republic of China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, People's Republic of China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, People's Republic of China.
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Salimi-Jeda A, Badrzadeh F, Esghaei M, Abdoli A. The role of telomerase and viruses interaction in cancer development, and telomerase-dependent therapeutic approaches. Cancer Treat Res Commun 2021; 27:100323. [PMID: 33530025 DOI: 10.1016/j.ctarc.2021.100323] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 12/21/2022]
Abstract
Human telomerase reverse transcriptase (hTERT) is an enzyme that is critically involved in elongating and maintaining telomeres length to control cell life span and replicative potential. Telomerase activity is continuously expressed in human germ-line cells and most cancer cells, whereas it is suppressed in most somatic cells. In normal cells, by reducing telomerase activity and progressively shortening the telomeres, the cells progress to the senescence or apoptosis process. However, in cancer cells, telomere lengths remain constant due to telomerase's reactivation, and cells continue to proliferate and inhibit apoptosis, and ultimately lead to cancer development and human death due to metastasis. Studies demonstrated that several DNA and RNA oncoviruses could interact with telomerase by integrating their genome sequence within the host cell telomeres specifically. Through the activation of the hTERT promoter and lengthening the telomere, these cells contributes to cancer development. Since oncoviruses can activate telomerase and increase hTERT expression, there are several therapeutic strategies based on targeting the telomerase of cancer cells like telomerase-targeted peptide vaccines, hTERT-targeting dendritic cells (DCs), hTERT-targeting gene therapy, and hTERT-targeting CRISPR/Cas9 system that can overcome tumor-mediated toleration mechanisms and specifically apoptosis in cancer cells. This study reviews available data on the molecular structure of telomerase and the role of oncoviruses and telomerase interaction in cancer development and telomerase-dependent therapeutic approaches to conquest the cancer cells.
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Affiliation(s)
- Ali Salimi-Jeda
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Fariba Badrzadeh
- Faculti of Medicine, Golestan University of Medical sciences, Golestan, Iran.
| | - Maryam Esghaei
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Asghar Abdoli
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran.
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Srirangam Nadhamuni V, Korbonits M. Novel Insights into Pituitary Tumorigenesis: Genetic and Epigenetic Mechanisms. Endocr Rev 2020; 41:bnaa006. [PMID: 32201880 PMCID: PMC7441741 DOI: 10.1210/endrev/bnaa006] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/19/2020] [Indexed: 02/08/2023]
Abstract
Substantial advances have been made recently in the pathobiology of pituitary tumors. Similar to many other endocrine tumors, over the last few years we have recognized the role of germline and somatic mutations in a number of syndromic or nonsyndromic conditions with pituitary tumor predisposition. These include the identification of novel germline variants in patients with familial or simplex pituitary tumors and establishment of novel somatic variants identified through next generation sequencing. Advanced techniques have allowed the exploration of epigenetic mechanisms mediated through DNA methylation, histone modifications and noncoding RNAs, such as microRNA, long noncoding RNAs and circular RNAs. These mechanisms can influence tumor formation, growth, and invasion. While genetic and epigenetic mechanisms often disrupt similar pathways, such as cell cycle regulation, in pituitary tumors there is little overlap between genes altered by germline, somatic, and epigenetic mechanisms. The interplay between these complex mechanisms driving tumorigenesis are best studied in the emerging multiomics studies. Here, we summarize insights from the recent developments in the regulation of pituitary tumorigenesis.
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Affiliation(s)
- Vinaya Srirangam Nadhamuni
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, UK
| | - Márta Korbonits
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, UK
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Wong GCH, Li KKW, Wang WW, Liu APY, Huang QJ, Chan AKY, Poon MFM, Chung NYF, Wong QHW, Chen H, Chan DTM, Liu XZ, Mao Y, Zhang ZY, Shi ZF, Ng HK. Clinical and mutational profiles of adult medulloblastoma groups. Acta Neuropathol Commun 2020; 8:191. [PMID: 33172502 PMCID: PMC7656770 DOI: 10.1186/s40478-020-01066-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022] Open
Abstract
Adult medulloblastomas are clinically and molecularly understudied due to their rarity. We performed molecular grouping, targeted sequencing, and TERT promoter Sanger sequencing on a cohort of 99 adult medulloblastomas. SHH made up 50% of the cohort, whereas Group 3 (13%) was present in comparable proportion to WNT (19%) and Group 4 (18%). In contrast to paediatric medulloblastomas, molecular groups had no prognostic impact in our adult cohort (p = 0.877). Most frequently mutated genes were TERT (including promoter mutations, mutated in 36% cases), chromatin modifiers KMT2D (31%) and KMT2C (30%), TCF4 (31%), PTCH1 (27%) and DDX3X (24%). Adult WNT patients showed enrichment of TP53 mutations (6/15 WNT cases), and 3/6 TP53-mutant WNT tumours were of large cell/anaplastic histology. Adult SHH medulloblastomas had frequent upstream pathway alterations (PTCH1 and SMO mutations) and few downstream alterations (SUFU mutations, MYCN amplifications). TERT promoter mutations were found in 72% of adult SHH patients, and were restricted to this group. Adult Group 3 tumours lacked hallmark MYC amplifications, but had recurrent mutations in KBTBD4 and NOTCH1. Adult Group 4 tumours harboured recurrent mutations in TCF4 and chromatin modifier genes. Overall, amplifications of MYC and MYCN were rare (3%). Since molecular groups were not prognostic, alternative prognostic markers are needed for adult medulloblastoma. KMT2C mutations were frequently found across molecular groups and were associated with poor survival (p = 0.002). Multivariate analysis identified histological type (p = 0.026), metastasis (p = 0.031) and KMT2C mutational status (p = 0.046) as independent prognosticators in our cohort. In summary, we identified distinct clinical and mutational characteristics of adult medulloblastomas that will inform their risk stratification and treatment.
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Shimada H, Sano H, Hazard FK. Pathology of Peripheral Neuroblastic Tumors. CLINICAL PEDIATRIC HEMATOLOGY-ONCOLOGY 2020. [DOI: 10.15264/cpho.2020.27.2.73] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Hiroyuki Shimada
- Department of Pathology and Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Hideki Sano
- Department of Pathology Oncology, Fukushima Medical University Hospital, Fukushima, Japan
| | - Florette K. Hazard
- Department of Pathology and Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
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13
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Hill RM, Richardson S, Schwalbe EC, Hicks D, Lindsey JC, Crosier S, Rafiee G, Grabovska Y, Wharton SB, Jacques TS, Michalski A, Joshi A, Pizer B, Williamson D, Bailey S, Clifford SC. Time, pattern, and outcome of medulloblastoma relapse and their association with tumour biology at diagnosis and therapy: a multicentre cohort study. THE LANCET CHILD & ADOLESCENT HEALTH 2020; 4:865-874. [PMID: 33222802 PMCID: PMC7671998 DOI: 10.1016/s2352-4642(20)30246-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 01/08/2023]
Abstract
Background Disease relapse occurs in around 30% of children with medulloblastoma, and is almost universally fatal. We aimed to establish whether the clinical and molecular characteristics of the disease at diagnosis are associated with the nature of relapse and subsequent disease course, and whether these associations could inform clinical management. Methods In this multicentre cohort study we comprehensively surveyed the clinical features of medulloblastoma relapse (time to relapse, pattern of relapse, time from relapse to death, and overall outcome) in centrally reviewed patients who relapsed following standard upfront therapies, from 16 UK Children's Cancer and Leukaemia Group institutions and four collaborating centres. We compared these relapse-associated features with clinical and molecular features at diagnosis, including established and recently described molecular features, prognostic factors, and treatment at diagnosis and relapse. Findings 247 patients (175 [71%] boys and 72 [29%] girls) with medulloblastoma relapse (median year of diagnosis 2000 [IQR 1995–2006]) were included in this study. 17 patients were later excluded from further analyses because they did not meet the age and treatment criteria for inclusion. Patients who received upfront craniospinal irradiation (irradiated group; 178 [72%] patients) had a more prolonged time to relapse compared with patients who did not receive upfront craniospinal irradiation (non-irradiated group; 52 [21%] patients; p<0·0001). In the non-irradiated group, craniospinal irradiation at relapse (hazard ratio [HR] 0·27, 95% CI 0·11–0·68) and desmoplastic/nodular histology (0·23, 0·07–0·77) were associated with prolonged time to death after relapse, MYC amplification was associated with a reduced overall survival (23·52, 4·85–114·05), and re-resection at relapse was associated with longer overall survival (0·17, 0·05–0·57). In the irradiated group, patients with MBGroup3 tumours relapsed significantly more quickly than did patients with MBGroup4 tumours (median 1·34 [0·99–1·89] years vs 2·04 [1·39–3·42 years; p=0·0043). Distant disease was prevalent in patients with MBGroup3 (23 [92%] of 25 patients) and MBGroup4 (56 [90%] of 62 patients) tumour relapses. Patients with distantly-relapsed MBGroup3 and MBGroup4 displayed both nodular and diffuse patterns of disease whereas isolated nodular relapses were rare in distantly-relapsed MBSHH (1 [8%] of 12 distantly-relapsed MBSHH were nodular alone compared with 26 [34%] of 77 distantly-relapsed MBGroup3 and MBGroup4). In MBGroup3 and MBGroup4, nodular disease was associated with a prolonged survival after relapse (HR 0·42, 0·21–0·81). Investigation of second-generation MBGroup3 and MBGroup4 molecular subtypes refined our understanding of heterogeneous relapse characteristics. Subtype VIII had prolonged time to relapse and subtype II had a rapid time from relapse to death. Subtypes II, III, and VIII developed a significantly higher incidence of distant disease at relapse whereas subtypes V and VII did not (equivalent rates to diagnosis). Interpretation This study suggests that the nature and outcome of medulloblastoma relapse are biology and therapy-dependent, providing translational opportunities for improved disease management through biology-directed disease surveillance, post-relapse prognostication, and risk-stratified selection of second-line treatment strategies. Funding Cancer Research UK, Action Medical Research, The Tom Grahame Trust, The JGW Patterson Foundation, Star for Harris, The Institute of Child Health - Newcastle University - Institute of Child Health High-Risk Childhood Brain Tumour Network (co-funded by The Brain Tumour Charity, Great Ormond Street Children's Charity, and Children with Cancer UK).
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Affiliation(s)
- Rebecca M Hill
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Stacey Richardson
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Edward C Schwalbe
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK; Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Debbie Hicks
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Janet C Lindsey
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Stephen Crosier
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Gholamreza Rafiee
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK; School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Centre for Cancer Research & Cell Biology, UK
| | - Yura Grabovska
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Stephen B Wharton
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Thomas S Jacques
- Neural Development Unit, UCL Institute of Child Health, London, UK
| | - Antony Michalski
- Neural Development Unit, UCL Institute of Child Health, London, UK
| | - Abhijit Joshi
- Department of Neuropathology, Royal Victoria Infirmary, Newcastle University Teaching Hospitals, NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Barry Pizer
- Institute of Translational Research, University of Liverpool, Liverpool, UK
| | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Simon Bailey
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Steven C Clifford
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK.
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Haltom AR, Toll SA, Cheng D, Maegawa S, Gopalakrishnan V, Khatua S. Medulloblastoma epigenetics and the path to clinical innovation. J Neurooncol 2020; 150:35-46. [PMID: 32816225 DOI: 10.1007/s11060-020-03591-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/06/2020] [Indexed: 12/30/2022]
Abstract
INTRODUCTION In the last decade, a number of genomic and pharmacological studies have demonstrated the importance of epigenetic dysregulation in medulloblastoma initiation and progression. High throughput approaches including gene expression array, next-generation sequencing (NGS), and methylation profiling have now clearly identified at least four molecular subgroups within medulloblastoma, each with distinct clinical and prognostic characteristics. These studies have clearly shown that despite the overall paucity of mutations, clinically relevant events do occur within the cellular epigenetic machinery. Thus, this review aims to provide an overview of our current understanding of the spectrum of epi-oncogenetic perturbations in medulloblastoma. METHODS Comprehensive review of epigenetic profiles of different subgroups of medulloblastoma in the context of molecular features. Epigenetic regulation is mediated mainly by DNA methylation, histone modifications and microRNAs (miRNA). Importantly, epigenetic mis-events are reversible and have immense therapeutic potential. CONCLUSION The widespread epigenetic alterations present in these tumors has generated intense interest in their use as therapeutic targets. We provide an assessment of the progress that has been made towards the development of molecular subtypes-targeted therapies and the current status of clinical trials that have leveraged these recent advances.
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Affiliation(s)
- Amanda R Haltom
- Division of Pediatrics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.,Center for Cancer Epigenetics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Stephanie A Toll
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Children's Hospital of Michigan, Detroit, USA
| | - Donghang Cheng
- Division of Pediatrics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.,Center for Cancer Epigenetics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Shinji Maegawa
- Division of Pediatrics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.,Center for Cancer Epigenetics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Vidya Gopalakrishnan
- Division of Pediatrics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA. .,Department of Molecular and Cellular Oncology, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA. .,Center for Cancer Epigenetics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA. .,Brain Tumor Center, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.
| | - Soumen Khatua
- Division of Pediatrics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA. .,Brain Tumor Center, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.
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15
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Chen X, Fan Z, Li KKW, Wu G, Yang Z, Gao X, Liu Y, Wu H, Chen H, Tang Q, Chen L, Wang Y, Mao Y, Ng HK, Shi Z, Yu J, Zhou L. Molecular subgrouping of medulloblastoma based on few-shot learning of multitasking using conventional MR images: a retrospective multicenter study. Neurooncol Adv 2020; 2:vdaa079. [PMID: 32760911 PMCID: PMC7393307 DOI: 10.1093/noajnl/vdaa079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background The determination of molecular subgroups—wingless (WNT), sonic hedgehog (SHH), Group 3, and Group 4—of medulloblastomas is very important for prognostication and risk-adaptive treatment strategies. Due to the rare disease characteristics of medulloblastoma, we designed a unique multitask framework for the few-shot scenario to achieve noninvasive molecular subgrouping with high accuracy. Methods We introduced a multitask technique based on mask regional convolutional neural network (Mask-RCNN). By effectively utilizing the comprehensive information including genotyping, tumor mask, and prognosis, multitask technique, on the one hand, realized multi-purpose modeling and simultaneously, on the other hand, promoted the accuracy of the molecular subgrouping. One hundred and thirteen medulloblastoma cases were collected from 4 hospitals during the 8-year period in the retrospective study, which were divided into 3-fold cross-validation cohorts (N = 74) from 2 hospitals and independent testing cohort (N = 39) from the other 2 hospitals. Comparative experiments of different auxiliary tasks were designed to illustrate the effect of multitasking in molecular subgrouping. Results Compared to the single-task framework, the multitask framework that combined 3 tasks increased the average accuracy of molecular subgrouping from 0.84 to 0.93 in cross-validation and from 0.79 to 0.85 in independent testing. The average area under the receiver operating characteristic curves (AUCs) of molecular subgrouping were 0.97 in cross-validation and 0.92 in independent testing. The average AUCs of prognostication also reached to 0.88 in cross-validation and 0.79 in independent testing. The tumor segmentation results achieved the Dice coefficient of 0.90 in both cohorts. Conclusions The multitask Mask-RCNN is an effective method for the molecular subgrouping and prognostication of medulloblastomas with high accuracy in few-shot learning.
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Affiliation(s)
- Xi Chen
- Department of Electronic Engineering, Fudan University, Shanghai, China
| | - Zhen Fan
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Kay Ka-Wai Li
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China SAR
| | - Guoqing Wu
- Department of Electronic Engineering, Fudan University, Shanghai, China
| | - Zhong Yang
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xin Gao
- Department of Neurosurgery, Huadong Hospital, Fudan University, Shanghai, China
| | - Yingchao Liu
- Department of Neurosurgery, Shandong Provincial Hospital, Jinan, China
| | - Haibo Wu
- Department of Pathology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Hong Chen
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Qisheng Tang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Liang Chen
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Yuanyuan Wang
- Department of Electronic Engineering, Fudan University, Shanghai, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China SAR
| | - Zhifeng Shi
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Jinhua Yu
- Department of Electronic Engineering, Fudan University, Shanghai, China
| | - Liangfu Zhou
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
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16
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Smith J, Sen S, Weeks RJ, Eccles MR, Chatterjee A. Promoter DNA Hypermethylation and Paradoxical Gene Activation. Trends Cancer 2020; 6:392-406. [PMID: 32348735 DOI: 10.1016/j.trecan.2020.02.007] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/08/2020] [Accepted: 02/11/2020] [Indexed: 12/19/2022]
Abstract
DNA methylation is a stable epigenetic modification that contributes to the spatiotemporal regulation of gene expression. The manner in which DNA methylation contributes to transcriptional control is dependent on the biological context, including physiological state and the properties of the DNA itself. Classically, dense promoter DNA methylation is associated with transcriptional repression. However, growing evidence suggests that this association may not always hold true, and promoter hypermethylation now also appears to be associated with high transcriptional activity. Furthermore, in a selection of contexts, increasing levels of promoter methylation correlate directly with increased gene expression. These findings postulate a context-dependent model whereby epigenetic contributions to transcriptional regulation occur in a more complex and dynamic manner. We present current evidence documenting promoter hypermethylation and high levels of gene expression, offer insights into the possible mechanisms by which this occurs, and discuss the potential implications for both research and clinical applications.
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Affiliation(s)
- Jim Smith
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 9016, Dunedin, New Zealand
| | - Swapnoleena Sen
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 9016, Dunedin, New Zealand
| | - Robert J Weeks
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 9016, Dunedin, New Zealand
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 9016, Dunedin, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 9016, Dunedin, New Zealand.
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17
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Abstract
As cells replicate their DNA during mitosis, telomeres are shortened due to the inherent limitations of the DNA replication process. Maintenance of telomere length is critical for cancer cells to overcome cellular senescence induced by telomere shortening. Telomerase reverse transcriptase (TERT) is the rate-limiting catalytic subunit of telomerase, an RNA-dependent DNA polymerase that lengthens telomeric DNA to maintain telomere homeostasis. TERT promoter mutations, which result in the upregulation of TERT transcription, have been identified in several central nervous system (CNS) tumors, including meningiomas, medulloblastomas, and primary glial neoplasms. Furthermore, TERT promoter hypermethylation, which also results in increased TERT transcription, has been observed in ependymomas and pediatric brain tumors. The high frequency of TERT dysregulation observed in a variety of high-grade cancers makes telomerase activity an attractive target for developing novel therapeutics. In this review, we briefly discuss normal telomere biology, as well as the structure, function, and regulation of TERT in normal human cells. We also highlight the role of TERT in cancer biology, focusing on primary CNS tumors. Finally, we summarize the clinical significance of TERT promoter mutations in cancer, the molecular mechanisms through which these mutations promote oncogenesis, and recent advances in cancer therapies targeting TERT.
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Affiliation(s)
- Bhuvic Patel
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rukayat Taiwo
- Department of Neurological Surgery, Stanford University, Stanford, California, USA
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gavin P Dunn
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri, USA.,Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, Missouri, USA
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Srinivas N, Rachakonda S, Kumar R. Telomeres and Telomere Length: A General Overview. Cancers (Basel) 2020; 12:E558. [PMID: 32121056 PMCID: PMC7139734 DOI: 10.3390/cancers12030558] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 02/06/2023] Open
Abstract
Telomeres are highly conserved tandem nucleotide repeats that include proximal double-stranded and distal single-stranded regions that in complex with shelterin proteins afford protection at chromosomal ends to maintain genomic integrity. Due to the inherent limitations of DNA replication and telomerase suppression in most somatic cells, telomeres undergo age-dependent incremental attrition. Short or dysfunctional telomeres are recognized as DNA double-stranded breaks, triggering cells to undergo replicative senescence. Telomere shortening, therefore, acts as a counting mechanism that drives replicative senescence by limiting the mitotic potential of cells. Telomere length, a complex hereditary trait, is associated with aging and age-related diseases. Epidemiological data, in general, support an association with varying magnitudes between constitutive telomere length and several disorders, including cancers. Telomere attrition is also influenced by oxidative damage and replicative stress caused by genetic, epigenetic, and environmental factors. Several single nucleotide polymorphisms at different loci, identified through genome-wide association studies, influence inter-individual variation in telomere length. In addition to genetic factors, environmental factors also influence telomere length during growth and development. Telomeres hold potential as biomarkers that reflect the genetic predisposition together with the impact of environmental conditions and as targets for anti-cancer therapies.
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Affiliation(s)
| | | | - Rajiv Kumar
- Division of Functional Genome Analysis, German Cancer Research Center, Im Neunheimer Feld 580, 69120 Heidelberg, Germany; (N.S.); (S.R.)
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19
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Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M, Brors B, Rippe K, Jones DTW, Feuerbach L. Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun 2020; 11:733. [PMID: 32024817 PMCID: PMC7002710 DOI: 10.1038/s41467-019-13824-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 11/26/2019] [Indexed: 12/14/2022] Open
Abstract
Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXXtrunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.
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Affiliation(s)
- Lina Sieverling
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Chen Hong
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Sandra D Koser
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Philip Ginsbach
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Kortine Kleinheinz
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, 69120, Heidelberg, Germany
| | - Barbara Hutter
- German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Delia M Braun
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, 69120, Heidelberg, Germany
| | - Isidro Cortés-Ciriano
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Department of Chemistry, Centre for Molecular Science Informatics, University of Cambridge, Cambridge, CB2 1EW, UK
- Ludwig Center at Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Ruibin Xi
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing, 100871, China
| | - Rolf Kabbe
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Ludwig Center at Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, 69120, Heidelberg, Germany
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, 69120, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lars Feuerbach
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
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Hovestadt V, Ayrault O, Swartling FJ, Robinson GW, Pfister SM, Northcott PA. Medulloblastomics revisited: biological and clinical insights from thousands of patients. Nat Rev Cancer 2020; 20:42-56. [PMID: 31819232 PMCID: PMC9113832 DOI: 10.1038/s41568-019-0223-8] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/25/2019] [Indexed: 12/16/2022]
Abstract
Medulloblastoma, a malignant brain tumour primarily diagnosed during childhood, has recently been the focus of intensive molecular profiling efforts, profoundly advancing our understanding of biologically and clinically heterogeneous disease subgroups. Genomic, epigenomic, transcriptomic and proteomic landscapes have now been mapped for an unprecedented number of bulk samples from patients with medulloblastoma and, more recently, for single medulloblastoma cells. These efforts have provided pivotal new insights into the diverse molecular mechanisms presumed to drive tumour initiation, maintenance and recurrence across individual subgroups and subtypes. Translational opportunities stemming from this knowledge are continuing to evolve, providing a framework for improved diagnostic and therapeutic interventions. In this Review, we summarize recent advances derived from this continued molecular characterization of medulloblastoma and contextualize this progress towards the deployment of more effective, molecularly informed treatments for affected patients.
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Affiliation(s)
- Volker Hovestadt
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Olivier Ayrault
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France
- Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Fredrik J Swartling
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Giles W Robinson
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Paediatric Haematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Paul A Northcott
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA.
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Ikegaki N, Shimada H. Subgrouping of Unfavorable Histology Neuroblastomas With Immunohistochemistry Toward Precision Prognosis and Therapy Stratification. JCO Precis Oncol 2019; 3:PO.18.00312. [PMID: 31840131 PMCID: PMC6910237 DOI: 10.1200/po.18.00312] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2019] [Indexed: 12/29/2022] Open
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22
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Abstract
Medulloblastoma (MB) comprises a biologically heterogeneous group of embryonal tumours of the cerebellum. Four subgroups of MB have been described (WNT, sonic hedgehog (SHH), Group 3 and Group 4), each of which is associated with different genetic alterations, age at onset and prognosis. These subgroups have broadly been incorporated into the WHO classification of central nervous system tumours but still need to be accounted for to appropriately tailor disease risk to therapy intensity and to target therapy to disease biology. In this Primer, the epidemiology (including MB predisposition), molecular pathogenesis and integrative diagnosis taking histomorphology, molecular genetics and imaging into account are reviewed. In addition, management strategies, which encompass surgical resection of the tumour, cranio-spinal irradiation and chemotherapy, are discussed, together with the possibility of focusing more on disease biology and robust molecularly driven patient stratification in future clinical trials.
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TERT promoter methylation is significantly associated with TERT upregulation and disease progression in pituitary adenomas. J Neurooncol 2018; 141:131-138. [PMID: 30392088 DOI: 10.1007/s11060-018-03016-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/15/2018] [Indexed: 10/27/2022]
Abstract
PURPOSE Alterations in the promoter of the telomerase reverse transcriptase (TERT) gene are a major mechanism of upregulating telomerase, which plays a crucial role in tumor development. Mutations in the TERT promoter have been observed in a subset of brain tumors, including adult gliomas and high-grade meningiomas. In pituitary adenomas (PAs), however, abnormalities in TERT are not fully understood. The present study aimed to investigate not only mutational but also methylation changes in the TERT promoter in PAs and to analyze their correlations with clinical variables. METHODS We retrospectively studied 70 PAs consisting of 53 primary and 17 recurrent samples. Clinical data, including age at surgery, sex, largest tumor dimension, tumor subtype, resection rate, and progression-free survival (PFS), were obtained from medical records. We investigated TERT promoter hotspot mutations via Sanger sequencing and quantified the methylation status of the TERT promoter using methylation-sensitive high-resolution melting analysis (MS-HRM). Additionally, we investigated TERT mRNA expression using real-time quantitative PCR. RESULTS TERT promoter hotspot mutations were not observed in any PA sample, while 16% of PAs exhibited TERT promoter methylation. PAs with methylated TERT promoters were significantly more likely to show disease progression, shorter PFS, and higher TERT expression levels compared to those with unmethylated promoters. CONCLUSIONS This is the first study showing that TERT promoter methylation is associated with disease progression and shorter PFS as well as upregulated TERT expression in PAs. Our results suggest that TERT promoter methylation may be a potential biomarker for predicting tumor recurrence in PAs.
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Callegari K, Maegawa S, Bravo-Alegria J, Gopalakrishnan V. Pharmacological inhibition of LSD1 activity blocks REST-dependent medulloblastoma cell migration. Cell Commun Signal 2018; 16:60. [PMID: 30227871 PMCID: PMC6145331 DOI: 10.1186/s12964-018-0275-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/13/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Medulloblastoma (MB) is the most common malignant brain tumor in children. Current problems in the clinic include metastasis, recurrence, and treatment-related sequelae that highlight the need for targeted therapies. Epigenetic perturbations are an established hallmark of human MB and expression of Lysine Specific Demethylase 1 (LSD1) is elevated in MBs compared to normal tissue, suggesting that LSD1 inhibitors may have efficacy against human MB tumors. METHODS Expression of LSD1 was examined across a publicly-available database and correlated with patient outcomes. Sonic Hedgehog (SHH) MB samples were clustered based on expression of LSD1 and LSD1-associated RE-1 silencing transcription factor (REST) target genes as well as genes involved in metastasis. Resulting clusters were examined for patient outcomes associated with LSD1 and REST expression. Human SHH MB cell lines were transduced with a REST-transgene to create isogenic cell pairs. In vitro viability and cell migration assays were used to examine the effect of LSD1 knockdown or inhibition on these parameters. RESULTS We demonstrate that subsets of SHH MB tumors have elevated LSD1 expression coincident with increased expression of its deubiquitylase, USP7, and REST. Patients with co-elevation of USP7, REST, and LSD1 have poorer outcomes compared to those with lower expression of these genes. In SHH MB cell lines, REST elevation increased cell growth and LSD1 protein levels. Surprisingly, while genetic loss of LSD1 reduced cell viability, pharmacological targeting of its activity using LSD1 inhibitors did not affect cell viability. However, a reduction in REST-dependent cell migration was seen in wound healing, suggesting that REST-LSD1 interaction regulates cell migration. Ingenuity pathway analyses validated these findings and identified Hypoxia Inducible Factor 1 alpha (HIF1A) as a potential target. In line with this, ectopic expression of HIF1A rescued the loss of migration seen following LSD1 inhibition. CONCLUSIONS A subset of SHH patients display increased levels of LSD1 and REST, which is associated with poor outcomes. REST elevation in MB in conjunction with elevated LSD1 promotes MB cell migration. LSD1 inhibition blocks REST-dependent cell migration of MB cells in a HIF1A-dependent manner.
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Affiliation(s)
- Keri Callegari
- Department of Pediatrics, University of Texas M.D. Anderson Cancer Center, Unit 853, 1515 Holcombe Blvd, Houston, TX, 77030, USA.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Austin, USA
| | - Shinji Maegawa
- Department of Pediatrics, University of Texas M.D. Anderson Cancer Center, Unit 853, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Javiera Bravo-Alegria
- Department of Pediatrics, University of Texas M.D. Anderson Cancer Center, Unit 853, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Vidya Gopalakrishnan
- Department of Pediatrics, University of Texas M.D. Anderson Cancer Center, Unit 853, 1515 Holcombe Blvd, Houston, TX, 77030, USA. .,Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA. .,Department of Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA. .,Department of Brain Tumor Center, University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA. .,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Austin, USA.
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25
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Leal LF, Evangelista AF, de Paula FE, Caravina Almeida G, Carloni AC, Saggioro F, Stavale JN, Malheiros SMF, Mançano B, de Oliveira MA, Luu B, Neder L, Taylor MD, Reis RM. Reproducibility of the NanoString 22-gene molecular subgroup assay for improved prognostic prediction of medulloblastoma. Neuropathology 2018; 38:475-483. [PMID: 30155928 DOI: 10.1111/neup.12508] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/22/2018] [Accepted: 07/25/2018] [Indexed: 11/30/2022]
Abstract
Medulloblastoma is the most frequent malignant brain tumor in children. Four medulloblastoma molecular subgroups, MBSHH , MBWNT , MBGRP3 and MBGRP4 , have been identified by integrated high-throughput platforms. Recently, a 22-gene panel NanoString-based assay was developed for medulloblastoma molecular subgrouping, but the robustness of this assay has not been widely evaluated. Mutations in the gene for human telomerase reverse transcriptase (hTERT) have been found in medulloblastomas and are associated with distinct molecular subtypes. This study aimed to implement the 22-gene panel in a Brazilian context, and to associate the molecular profile with patients' clinical-pathological features. Formalin-fixed, paraffin-embedded (FFPE) medulloblastoma samples (n = 104) from three Brazilian centers were evaluated. Expression profiling of the 22-gene panel was performed by NanoString and a Canadian series (n = 240) was applied for training phase. hTERT mutations were analyzed by PCR followed by direct Sanger sequencing and the molecular profile was associated with patients' clinicopathological features. Overall, 65% of the patients were male, average age at diagnosis was 18 years and 7% of the patients presented metastasis at diagnosis. The molecular classification was attained in 100% of the cases, with the following frequencies: MBSHH (n = 51), MBWNT (n = 19), MBGRP4 (n = 19) and MBGRP3 (n = 15). The MBSHH and MBGRP3 subgroups were associated with older and younger patients, respectively. The MBGRP4 subgroup exhibited the lowest 5-year cancer-specific overall survival (OS), yet in the multivariate analysis, only metastasis at diagnosis and surgical resection were associated with OS. hTERT mutations were detected in 29% of the cases and were associated with older patients, increased hTERT expression and MBSHH subgroup. The 22-gene panel provides a reproducible assay for molecular subgrouping of medulloblastoma FFPE samples in a routine setting and is well-suited for future clinical trials.
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Affiliation(s)
- Letícia F Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Flávia E de Paula
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Adriana C Carloni
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Fabiano Saggioro
- Department of Pathology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Brazil
| | - João N Stavale
- Department of Pathology, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Bruna Mançano
- Children and Young Adult's Cancer Hospital, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Betty Luu
- Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Luciano Neder
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | - Michael D Taylor
- Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Rui M Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil.,Life and Health Sciences Research Institute (ICVS), Health Sciences School, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
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26
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Gaspar TB, Sá A, Lopes JM, Sobrinho-Simões M, Soares P, Vinagre J. Telomere Maintenance Mechanisms in Cancer. Genes (Basel) 2018; 9:E241. [PMID: 29751586 PMCID: PMC5977181 DOI: 10.3390/genes9050241] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 12/12/2022] Open
Abstract
Tumour cells can adopt telomere maintenance mechanisms (TMMs) to avoid telomere shortening, an inevitable process due to successive cell divisions. In most tumour cells, telomere length (TL) is maintained by reactivation of telomerase, while a small part acquires immortality through the telomerase-independent alternative lengthening of telomeres (ALT) mechanism. In the last years, a great amount of data was generated, and different TMMs were reported and explained in detail, benefiting from genome-scale studies of major importance. In this review, we address seven different TMMs in tumour cells: mutations of the TERT promoter (TERTp), amplification of the genes TERT and TERC, polymorphic variants of the TERT gene and of its promoter, rearrangements of the TERT gene, epigenetic changes, ALT, and non-defined TMM (NDTMM). We gathered information from over fifty thousand patients reported in 288 papers in the last years. This wide data collection enabled us to portray, by organ/system and histotypes, the prevalence of TERTp mutations, TERT and TERC amplifications, and ALT in human tumours. Based on this information, we discuss the putative future clinical impact of the aforementioned mechanisms on the malignant transformation process in different setups, and provide insights for screening, prognosis, and patient management stratification.
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Affiliation(s)
- Tiago Bordeira Gaspar
- Cancer Signaling and Metabolism Group, Institute for Research and Innovation in Health Sciences (i3S), University of Porto, 4200-135 Porto, Portugal.
- Cancer Signaling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal.
- Medical Faculty of University of Porto (FMUP), 4200-139 Porto, Portugal.
- Abel Salazar Biomedical Sciences Institute (ICBAS), University of Porto, 4050-313 Porto, Portugal.
| | - Ana Sá
- Cancer Signaling and Metabolism Group, Institute for Research and Innovation in Health Sciences (i3S), University of Porto, 4200-135 Porto, Portugal.
- Cancer Signaling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal.
- Abel Salazar Biomedical Sciences Institute (ICBAS), University of Porto, 4050-313 Porto, Portugal.
| | - José Manuel Lopes
- Cancer Signaling and Metabolism Group, Institute for Research and Innovation in Health Sciences (i3S), University of Porto, 4200-135 Porto, Portugal.
- Cancer Signaling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal.
- Medical Faculty of University of Porto (FMUP), 4200-139 Porto, Portugal.
- Department of Pathology and Oncology, Centro Hospitalar São João, 4200-139 Porto, Portugal.
| | - Manuel Sobrinho-Simões
- Cancer Signaling and Metabolism Group, Institute for Research and Innovation in Health Sciences (i3S), University of Porto, 4200-135 Porto, Portugal.
- Cancer Signaling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal.
- Medical Faculty of University of Porto (FMUP), 4200-139 Porto, Portugal.
- Department of Pathology and Oncology, Centro Hospitalar São João, 4200-139 Porto, Portugal.
| | - Paula Soares
- Cancer Signaling and Metabolism Group, Institute for Research and Innovation in Health Sciences (i3S), University of Porto, 4200-135 Porto, Portugal.
- Cancer Signaling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal.
- Abel Salazar Biomedical Sciences Institute (ICBAS), University of Porto, 4050-313 Porto, Portugal.
| | - João Vinagre
- Cancer Signaling and Metabolism Group, Institute for Research and Innovation in Health Sciences (i3S), University of Porto, 4200-135 Porto, Portugal.
- Cancer Signaling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal.
- Medical Faculty of University of Porto (FMUP), 4200-139 Porto, Portugal.
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Wang J, Garancher A, Ramaswamy V, Wechsler-Reya RJ. Medulloblastoma: From Molecular Subgroups to Molecular Targeted Therapies. Annu Rev Neurosci 2018; 41:207-232. [PMID: 29641939 DOI: 10.1146/annurev-neuro-070815-013838] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Brain tumors are the leading cause of cancer-related death in children, and medulloblastoma (MB) is the most common malignant pediatric brain tumor. Advances in surgery, radiation, and chemotherapy have improved the survival of MB patients. But despite these advances, 25-30% of patients still die from the disease, and survivors suffer severe long-term side effects from the aggressive therapies they receive. Although MB is often considered a single disease, molecular profiling has revealed a significant degree of heterogeneity, and there is a growing consensus that MB consists of multiple subgroups with distinct driver mutations, cells of origin, and prognosis. Here, we review recent progress in MB research, with a focus on the genes and pathways that drive tumorigenesis, the animal models that have been developed to study tumor biology, and the advances in conventional and targeted therapy.
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Affiliation(s)
- Jun Wang
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA;
| | - Alexandra Garancher
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA;
| | - Vijay Ramaswamy
- Division of Haematology/Oncology and Department of Paediatrics, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Robert J Wechsler-Reya
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA;
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28
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Abstract
Epigenetics is a growing field of knowledge that is changing our understanding of pathologic processes. For many cerebellar disorders, recent discoveries of epigenetic mechanisms help us to understand their pathophysiology. In this chapter, a short explanation of each epigenetic mechanism (including methylation, histone modification, and miRNA) is followed by references to those cerebellar disorders in which relevant epigenetic advances have been made. The importance of normal timing and distribution of methylation during neurodevelopment is explained. Abnormal methylation and altered gene expression in the developing cerebellum have been related to neurodevelopmental disorders such as autism, Rett syndrome, and fragile X syndrome. DNA packaging by histones is another important epigenetic mechanism in cerebellar functioning. Current knowledge of histone abnormalities in cerebellar diseases such as Friedreich ataxia and spinocerebellar ataxias is reviewed, including implications for new therapeutic approaches to these degenerative diseases. Finally, micro RNAs, the third mechanism to modulate DNA expression, and their role in normal cerebellar development and disease are described. Understanding how genetic and epigenetic mechanisms interact not only in normal cerebellar development but also in disease is a great challenge. However, such understanding will lead to promising new therapeutic possibilities as is already occurring in other areas of medicine.
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Affiliation(s)
- Mercedes Serrano
- Pediatric Neurology Department and Pediatric Institute for Genetic Medicine and Rare Diseases, Hospital Sant Joan de Déu; and Centre for Biomedical Research on Rare Diseases, Instituto de Salud Carlos III, Barcelona, Spain.
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29
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Stern JL, Paucek RD, Huang FW, Ghandi M, Nwumeh R, Costello JC, Cech TR. Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes. Cell Rep 2017; 21:3700-3707. [PMID: 29281820 PMCID: PMC5747321 DOI: 10.1016/j.celrep.2017.12.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/29/2017] [Accepted: 11/30/2017] [Indexed: 01/18/2023] Open
Abstract
A mutation in the promoter of the Telomerase Reverse Transcriptase (TERT) gene is the most frequent noncoding mutation in cancer. The mutation drives unusual monoallelic expression of TERT, allowing immortalization. Here, we find that DNA methylation of the TERT CpG island (CGI) is also allele-specific in multiple cancers. The expressed allele is hypomethylated, which is opposite to cancers without TERT promoter mutations. The continued presence of Polycomb repressive complex 2 (PRC2) on the inactive allele suggests that histone marks of repressed chromatin may be causally linked to high DNA methylation. Consistent with this hypothesis, TERT promoter DNA containing 5-methyl-CpG has much increased affinity for PRC2 in vitro. Thus, CpG methylation and histone marks appear to collaborate to maintain the two TERT alleles in different epigenetic states in TERT promoter mutant cancers. Finally, in several cancers, DNA methylation levels at the TERT CGI correlate with altered patient survival.
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Affiliation(s)
- Josh Lewis Stern
- BioFrontiers Institute, Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Richard D Paucek
- BioFrontiers Institute, Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Franklin W Huang
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Mahmoud Ghandi
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ronald Nwumeh
- BioFrontiers Institute, Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - James C Costello
- Department of Pharmacology and University of Colorado Comprehensive Cancer Center, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Thomas R Cech
- BioFrontiers Institute, Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
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30
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Yi J, Wu J. Epigenetic regulation in medulloblastoma. Mol Cell Neurosci 2017; 87:65-76. [PMID: 29269116 DOI: 10.1016/j.mcn.2017.09.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 09/08/2017] [Accepted: 09/10/2017] [Indexed: 12/14/2022] Open
Abstract
Medulloblastoma is the most common malignant childhood brain tumor. The heterogeneous tumors are classified into four subgroups based on transcription profiles. Recent developments in genome-wide sequencing techniques have rapidly advanced the understanding of these tumors. The high percentages of somatic alterations of genes encoding chromatin regulators in all subgroups suggest that epigenetic deregulation is a major driver of medulloblastoma. In this report, we review the current understanding of epigenetic regulation in medulloblastoma with a focus on the functional studies of chromatin regulators in the initiation and progression of specific subgroups of medulloblastoma. We also discuss the potential usage of epigenetic inhibitors for medulloblastoma treatment.
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Affiliation(s)
- Jiaqing Yi
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
| | - Jiang Wu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA.
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31
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Faleiro I, Apolónio JD, Price AJ, De Mello RA, Roberto VP, Tabori U, Castelo-Branco P. The TERT hypermethylated oncologic region predicts recurrence and survival in pancreatic cancer. Future Oncol 2017; 13:2045-2051. [DOI: 10.2217/fon-2017-0167] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: We explore the biomarker potential of the TERT hypermethylated oncologic region (THOR) in pancreatic cancer. Materials & methods: We assessed the methylation status of THOR using the cancer genome atlas data on the cohort of pancreatic cancer (n = 193 patients). Results: THOR was significantly hypermethylated in pancreatic tumor tissue when compared with the normal tissue used as control (p < 0.0001). Also, THOR hypermethylation could distinguish early stage I disease from normal tissue and was associated with worse prognosis. Discussion: We found that THOR is hypermethylated in pancreatic tumor tissue when compared with normal tissue and that THOR methylation correlates with TERT expression in tumor samples. Conclusion: Our preliminary findings support the diagnostic and prognostic values of THOR in pancreatic cancer.
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Affiliation(s)
- Inês Faleiro
- Department of Biomedical Sciences & Medicine, University of Algarve, Campus de Gambelas, Edifício 2, 8005–139 Faro, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, 8005–139 Faro, Portugal
- Algarve Biomedical Center, University of Algarve, Campus de Gambelas, 8005–139, Faro, Portugal
| | - Joana Dias Apolónio
- Department of Biomedical Sciences & Medicine, University of Algarve, Campus de Gambelas, Edifício 2, 8005–139 Faro, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, 8005–139 Faro, Portugal
- Algarve Biomedical Center, University of Algarve, Campus de Gambelas, 8005–139, Faro, Portugal
| | - Aryeh J Price
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ramon Andrade De Mello
- Department of Biomedical Sciences & Medicine, University of Algarve, Campus de Gambelas, Edifício 2, 8005–139 Faro, Portugal
- Algarve Biomedical Center, University of Algarve, Campus de Gambelas, 8005–139, Faro, Portugal
| | - Vânia Palma Roberto
- Department of Biomedical Sciences & Medicine, University of Algarve, Campus de Gambelas, Edifício 2, 8005–139 Faro, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, 8005–139 Faro, Portugal
- Algarve Biomedical Center, University of Algarve, Campus de Gambelas, 8005–139, Faro, Portugal
| | - Uri Tabori
- Arthur & Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Pedro Castelo-Branco
- Department of Biomedical Sciences & Medicine, University of Algarve, Campus de Gambelas, Edifício 2, 8005–139 Faro, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, 8005–139 Faro, Portugal
- Algarve Biomedical Center, University of Algarve, Campus de Gambelas, 8005–139, Faro, Portugal
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Genetic and Epigenetic Alterations of TERT Are Associated with Inferior Outcome in Adolescent and Young Adult Patients with Melanoma. Sci Rep 2017; 7:45704. [PMID: 28378855 PMCID: PMC5381111 DOI: 10.1038/srep45704] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 03/03/2017] [Indexed: 02/06/2023] Open
Abstract
Progression of melanoma to distant sites in adolescents and young adults (AYAs) is not reliably predicted by clinicopathologic criteria. TERT promoter mutations when combined with BRAF/NRAS mutations correlate with adverse outcome in adult melanoma. To determine the prognostic value of TERT alterations in AYA melanoma, we investigated the association of TERT promoter mutations, as well as promoter methylation, an epigenetic alteration also linked to TERT upregulation, with TERT mRNA expression and outcome using a well-characterized cohort of 27 patients with melanoma (ages 8–25, mean 20). TERT mRNA expression levels were significantly higher in tumors harboring TERT promoter mutation and/or hypermethylation than those without either aberration (P = 0.046). TERT promoter mutations alone did not predict adverse outcomes (P = 0.50), but the presence of TERT promoter methylation, alone or concurrent with promoter mutations, correlated with reduced recurrence-free survival (P = 0.001). These data suggest that genetic and epigenetic alterations of TERT are associated with TERT upregulation and may predict clinical outcomes in AYA melanoma. A more exhaustive understanding of the different molecular mechanisms leading to increased TERT expression may guide development of prognostic assays to stratify AYA melanoma patients according to clinical risk.
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Lee S, Borah S, Bahrami A. Detection of Aberrant TERT Promoter Methylation by Combined Bisulfite Restriction Enzyme Analysis for Cancer Diagnosis. J Mol Diagn 2017; 19:378-386. [PMID: 28284778 DOI: 10.1016/j.jmoldx.2017.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/13/2016] [Accepted: 01/05/2017] [Indexed: 12/12/2022] Open
Abstract
Aberrant CpG dinucleotide methylation in a specific region of the telomerase reverse transcriptase (TERT) promoter is associated with increased TERT mRNA levels and malignancy in several cancer types. However, routine screening of this region to aid cancer diagnosis can be challenging because i) several established methylation assays may inaccurately report on hypermethylation of this particular region, ii) interpreting the results of methylation assays can sometimes be difficult for clinical laboratories, and iii) use of high-throughput methylation assays for a few patient samples can be cost prohibitive. Herein, we describe the use of combined bisulfite restriction enzyme analysis (COBRA) as a diagnostic tool for detecting the hypermethylated TERT promoter using in vitro methylated and unmethylated genomic DNA as well as genomic DNA from four melanomas and two benign melanocytic lesions. We compare COBRA with MassARRAY, a more commonly used high-throughput approach, in screening for promoter hypermethylation in 28 formalin-fixed, paraffin-embedded neuroblastoma samples. COBRA sensitively and specifically detected samples with hypermethylated TERT promoter and was as effective as MassARRAY at differentiating high-risk from benign or low-risk tumors. This study demonstrates the utility of this low-cost, technically straightforward, and easily interpretable assay for cancer diagnosis in tumors of an ambiguous nature.
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Affiliation(s)
- Seungjae Lee
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sumit Borah
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Armita Bahrami
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
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Lee J, Solomon DA, Tihan T. The role of histone modifications and telomere alterations in the pathogenesis of diffuse gliomas in adults and children. J Neurooncol 2017; 132:1-11. [PMID: 28064387 PMCID: PMC5354997 DOI: 10.1007/s11060-016-2349-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 12/23/2016] [Indexed: 12/26/2022]
Abstract
Genetic profiling is an increasingly useful tool for sub-classification of gliomas in adults and children. Specific gene mutations, structural rearrangements, DNA methylation patterns, and gene expression profiles are now recognized to define molecular subgroups of gliomas that arise in distinct anatomic locations and patient age groups, and also provide a better prediction of clinical outcomes for glioma patients compared to histologic assessment alone. Understanding the role of these distinctive genetic alterations in gliomagenesis is also important for the development of potential targeted therapeutic interventions. Mutations including K27M and G34R/V that affect critical amino acids within the N-terminal tail of the histone H3 variants, H3.3 and H3.1 (encoded by H3F3A and HIST1H3B genes), are prime examples of mutations in diffuse gliomas with characteristic clinical associations that can help diagnostic classification and guide effective patient management. These histone H3 mutations frequently co-occur with inactivating mutations in ATRX in association with alternative lengthening of telomeres. Telomere length can also be maintained through upregulation of telomerase reverse transcriptase (TERT) expression driven by mutation within the TERT gene promoter region, an alteration most commonly found in oligodendrogliomas and primary glioblastomas arising in adults. Interestingly, the genetic alterations perturbing histone and telomere function in pediatric gliomas tend to be different from those present in adult tumors. We present a review of these mutations affecting the histone code and telomere length, highlighting their importance in prognosis and as targets for novel therapeutics in the treatment of diffuse gliomas.
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Affiliation(s)
- Julieann Lee
- Division of Neuropathology, Department of Pathology, University of California, San Francisco, 505 Parnassus Ave, Room M-551, Box 0102, San Francisco, CA, 94143, USA
| | - David A Solomon
- Division of Neuropathology, Department of Pathology, University of California, San Francisco, 505 Parnassus Ave, Room M-551, Box 0102, San Francisco, CA, 94143, USA
| | - Tarik Tihan
- Division of Neuropathology, Department of Pathology, University of California, San Francisco, 505 Parnassus Ave, Room M-551, Box 0102, San Francisco, CA, 94143, USA.
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Transcription Regulation of the Human Telomerase Reverse Transcriptase (hTERT) Gene. Genes (Basel) 2016; 7:genes7080050. [PMID: 27548225 PMCID: PMC4999838 DOI: 10.3390/genes7080050] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/23/2016] [Accepted: 08/01/2016] [Indexed: 12/11/2022] Open
Abstract
Embryonic stem cells and induced pluripotent stem cells have the ability to maintain their telomere length via expression of an enzymatic complex called telomerase. Similarly, more than 85%–90% of cancer cells are found to upregulate the expression of telomerase, conferring them with the potential to proliferate indefinitely. Telomerase Reverse Transcriptase (TERT), the catalytic subunit of telomerase holoenzyme, is the rate-limiting factor in reconstituting telomerase activity in vivo. To date, the expression and function of the human Telomerase Reverse Transcriptase (hTERT) gene are known to be regulated at various molecular levels (including genetic, mRNA, protein and subcellular localization) by a number of diverse factors. Among these means of regulation, transcription modulation is the most important, as evident in its tight regulation in cancer cell survival as well as pluripotent stem cell maintenance and differentiation. Here, we discuss how hTERT gene transcription is regulated, mainly focusing on the contribution of trans-acting factors such as transcription factors and epigenetic modifiers, as well as genetic alterations in hTERT proximal promoter.
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Telomerase: The Devil Inside. Genes (Basel) 2016; 7:genes7080043. [PMID: 27483324 PMCID: PMC4999831 DOI: 10.3390/genes7080043] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/23/2016] [Accepted: 07/25/2016] [Indexed: 01/04/2023] Open
Abstract
High telomerase activity is detected in nearly all human cancers but most human cells are devoid of telomerase activity. There is well-documented evidence that reactivation of telomerase occurs during cellular transformation. In humans, tumors can rely in reactivation of telomerase or originate in a telomerase positive stem/progenitor cell, or rely in alternative lengthening of telomeres, a telomerase-independent telomere-length maintenance mechanism. In this review, we will focus on the telomerase positive tumors. In this context, the recent findings that telomerase reverse transcriptase (TERT) promoter mutations represent the most common non-coding mutations in human cancer have flared up the long-standing discussion whether cancer originates from telomerase positive stem cells or telomerase reactivation is a final step in cellular transformation. Here, we will discuss the pros and cons of both concepts in the context of telomere length-dependent and telomere length-independent functions of telomerase. Together, these observations may provoke a re-evaluation of telomere and telomerase based therapies, both in telomerase inhibition for cancer therapy and telomerase activation for tissue regeneration and anti-ageing strategies.
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Yuan Y, Qi C, Maling G, Xiang W, Yanhui L, Ruofei L, Yunhe M, Jiewen L, Qing M. TERT mutation in glioma: Frequency, prognosis and risk. J Clin Neurosci 2016; 26:57-62. [DOI: 10.1016/j.jocn.2015.05.066] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/17/2015] [Accepted: 05/22/2015] [Indexed: 10/22/2022]
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Zhang H, Weng X, Ye J, He L, Zhou D, Liu Y. Promoter hypermethylation of TERT is associated with hepatocellular carcinoma in the Han Chinese population. Clin Res Hepatol Gastroenterol 2015; 39:600-9. [PMID: 25683523 DOI: 10.1016/j.clinre.2015.01.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/05/2015] [Accepted: 01/12/2015] [Indexed: 02/04/2023]
Abstract
BACKGROUND Upstream of the transcription start site (UTSS), hypermethylation of the telomerase reverse transcriptase (TERT) gene has been shown to be associated with tumour progression and a poor prognosis in paediatric brain tumours (Castelo-Branco 2013). It has been inferred that the UTSS region of TERT is a potentially accessible biomarker for various cancers. In this study, we aimed to explore the role of TERT in hepatocellular carcinoma (HCC) and to investigate whether the UTSS region of the TERT promoter shows the same methylation pattern in HCC. METHODS We analysed the results of a methylation assay for TERT, including the UTSS region, from 125 paired HCC samples using Mass Array EpiTyper (Sequenom, San Diego, CA, USA). To determine the relationship between TERT promoter methylation status and the TERT expression level, we analysed a validation group of 12 paired HCC samples and acquired the FPKM values for the TERT gene. RESULTS Our results showed aberrant methylation of the UTSS region of the TERT promoter in HCC (mean=15.1) compared with the adjacent normal tissues (mean=6.1, P<0.00001). Furthermore, a nearly 56-fold increase in TERT expression from the hypermethylated promoter was found in HCC (P<0.05), indicating a positive relationship between TERT methylation and expression. CONCLUSIONS As hypermethylation was positively correlated with high expression of TERT in HCC, TERT is likely to be involved in the aetiology of HCC. Our findings indicate that future studies on TERT might be fruitful.
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Affiliation(s)
- Hong Zhang
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, PR China
| | - Xiaoling Weng
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, PR China
| | - Junyi Ye
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, PR China
| | - Lin He
- Bio-X Centre Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Daizhan Zhou
- Bio-X Centre Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, PR China.
| | - Yun Liu
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, PR China.
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Lindner S, Bachmann HS, Odersky A, Schaefers S, Klein-Hitpass L, Hero B, Fischer M, Eggert A, Schramm A, Schulte JH. Absence of telomerase reverse transcriptase promoter mutations in neuroblastoma. Biomed Rep 2015; 3:443-446. [PMID: 26171145 DOI: 10.3892/br.2015.463] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 04/22/2015] [Indexed: 11/06/2022] Open
Abstract
Maintenance of telomere length is a critical hallmark of malignant transformation. While silenced in somatic cells, telomerase reverse transcriptase (TERT), the catalytic subunit of telomerase, is frequently overexpressed in malignant cells thereby maintaining their telomere length. Specific point mutations in the TERT promoter region have recently been identified in melanoma and other tumor entities resulting in high TERT expression. Neuroblastoma is the most common extracranial tumor of childhood, arising from neural-crest progenitor cells. TERT overexpression has been observed in the majority of neuroblastoma. Taking into consideration that TERT promoter mutations are frequently described in neural-crest-derived tumors such as melanoma, as well as a variety of other neuronal tumors, the present study analyzed the frequency of TERT promoter mutations in primary neuroblastoma and neuroblastoma cell lines. In 131 neuroblastoma primary tumors representing the whole spectrum of neuroblastoma, no TERT promoter mutations were detected. However, in 3 out of 19 neuroblastoma cell lines the previously described C228T TERT promoter mutation was present. In conclusion, the TERT promoter mutations are not a frequent mechanism of TERT overexpression in neuroblastoma.
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Affiliation(s)
- Sven Lindner
- Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, D-45122 Essen, Germany ; German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Duesseldorf, D-45122 Essen, Germany ; German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Hagen S Bachmann
- Institute of Pharmacogenetics, University Hospital Essen, D-45147 Essen, Germany
| | - Andrea Odersky
- Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, D-45122 Essen, Germany
| | - Simon Schaefers
- Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, D-45122 Essen, Germany ; German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Duesseldorf, D-45122 Essen, Germany ; German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Ludger Klein-Hitpass
- Institute of Cell Biology (Cancer Research), Faculty of Medicine, University of Duisburg-Essen, D-45122 Essen, Germany
| | - Barbara Hero
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, D-50924 Cologne, Germany
| | - Matthias Fischer
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, D-50924 Cologne, Germany ; Center for Molecular Medicine Cologne (CMMC), University of Cologne, D-50931 Cologne, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, D-10117 Berlin, Germany
| | - Alexander Schramm
- Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, D-45122 Essen, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, D-45122 Essen, Germany ; German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Duesseldorf, D-45122 Essen, Germany ; German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany ; Translational Neuro-Oncology, West German Cancer Center (WTZ), University Hospital Essen, D-45147 Essen, Germany ; Centre for Medical Biotechnology, University Duisburg-Essen, D-45147 Essen, Germany
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The molecular landscape of pediatric brain tumors in the next-generation sequencing era. Curr Neurol Neurosci Rep 2015; 14:474. [PMID: 25037717 DOI: 10.1007/s11910-014-0474-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Pediatric brain tumors are a leading cause of cancer-related death in children. In recent years, the application of next-generation sequencing and other high-throughput technologies to analysis of pediatric brain tumors has generated an abundance of molecular information. This has provided an unprecedented understanding of their biology and is refining tumor classification into clinically relevant subgroups. In this review, we provide an overview of our evolving molecular knowledge of the commonest pediatric brain tumors, pilocytic astrocytomas, ependymomas, medulloblastomas, and pediatric glioblastomas, as well as the biological and potential clinical implications of this new knowledge. Studies aimed at investigating intratumoral heterogeneity are also discussed.
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Abstract
Low-grade gliomas (LGG) constitute grades I and II tumors of astrocytic and grade II tumors of oligodendroglial lineage. Although these tumors are typically slow growing, they may be associated with significant morbidity and mortality because of recurrence and malignant progression, even in the setting of optimal resection. LGG in pediatric and adult age groups are currently classified by morphologic criteria. Recent years have heralded a molecular revolution in understanding brain tumors, including LGG. Next-generation sequencing has definitively demonstrated that pediatric and adult LGG fundamentally differ in their underlying molecular characteristics, despite being histologically similar. Pediatric LGG show alterations in FGFR1 and BRAF in pilocytic astrocytomas and FGFR1 alterations in diffuse astrocytomas, each converging on the mitogen-activated protein kinase signaling pathway. Adult LGG are characterized by IDH1/2 mutations and ATRX mutations in astrocytic tumors and IDH1/2 mutations and 1p/19q codeletions in oligodendroglial tumors. TERT promoter mutations are also noted in LGG and are mainly associated with oligodendrogliomas. These findings have considerably refined approaches to classifying these tumors. Moreover, many of the molecular alterations identified in LGG directly impact on prognosis, tumor biology, and the development of novel therapies.
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Pon JR, Marra MA. Driver and Passenger Mutations in Cancer. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2015; 10:25-50. [DOI: 10.1146/annurev-pathol-012414-040312] [Citation(s) in RCA: 216] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Julia R. Pon
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada V5Z 1L3;
| | - Marco A. Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada V5Z 1L3;
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada V6T 1Z4;
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Cross-species epigenetics identifies a critical role for VAV1 in SHH subgroup medulloblastoma maintenance. Oncogene 2014; 34:4746-57. [PMID: 25531316 PMCID: PMC4386991 DOI: 10.1038/onc.2014.405] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 10/10/2014] [Accepted: 11/03/2014] [Indexed: 01/10/2023]
Abstract
The identification of key tumorigenic events in Sonic Hedgehog subgroup medulloblastomas (MBSHH) will be essential for the development of individualized therapies and improved outcomes. However, beyond confirmation of characteristic SHH-pathway mutations, recent genome-wide sequencing studies have not revealed commonly-mutated genes with widespread relevance as potential therapeutic targets. We therefore examined any role for epigenetic DNA methylation events in MBSHH using a cross-species approach to candidate identification, prioritization and validation. MBSHH–associated DNA methylation events were first identified in 216 subgrouped human medulloblastomas (50 MBSHH, 28 WNT, 44 Group 3, 94 Group 4) and their conservation then assessed in tumors arising from four independent murine models of Shh medulloblastoma, alongside any role in tumorigenesis using functional assessments in mouse and human models. This strategy identified widespread regional CpG hypo-methylation of VAV1, leading to its elevated expression, as a conserved aberrant epigenetic event which characterizes the majority of MBSHH tumors in both species, and is associated with a poor outcome in MBSHH patients. Moreover, direct modulation of VAV1 in mouse and human models revealed a critical role in tumor maintenance, and its abrogation markedly reduced medulloblastoma growth. Further, Vav1 activity regulated granule neuron precursor (GNP) germinal zone exit and migration initiation in an ex vivo model of early post-natal cerebellar development. These findings establish VAV1 as a critical epigenetically-regulated oncogene with a key role in MBSHH maintenance, and highlight its potential as a validated therapeutic target and prognostic biomarker for the improved therapy of medulloblastoma.
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Vinagre J, Pinto V, Celestino R, Reis M, Pópulo H, Boaventura P, Melo M, Catarino T, Lima J, Lopes JM, Máximo V, Sobrinho-Simões M, Soares P. Telomerase promoter mutations in cancer: an emerging molecular biomarker? Virchows Arch 2014; 465:119-33. [DOI: 10.1007/s00428-014-1608-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/19/2014] [Accepted: 06/16/2014] [Indexed: 12/16/2022]
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