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Du C, Tan L, Xiao X, Xin B, Xiong H, Zhang Y, Ke Z, Yin J. Detection of the DNA methylation of seven genes contribute to the early diagnosis of lung cancer. J Cancer Res Clin Oncol 2024; 150:77. [PMID: 38315228 PMCID: PMC10844440 DOI: 10.1007/s00432-023-05588-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND Low-dose Computed Tomography (CT) is used for the detection of pulmonary nodules, but the ambiguous risk evaluation causes overdiagnosis. Here, we explored the significance of the DNA methylation of 7 genes including TAC1, CDO1, HOXA9, ZFP42, SOX17, RASSF1A and SHOX2 in the blood cfDNA samples in distinguishing lung cancer from benign nodules and healthy individuals. METHOD A total of 149 lung cancer patients [72 mass and 77 ground-glass nodules (GGNs)], 5 benign and 48 healthy individuals were tested and analyzed in this study. The lasso-logistic regression model was built for distinguishing cancer and control/healthy individuals or IA lung cancer and non-IA lung cancer cases. RESULTS The positive rates of methylation of 7 genes were higher in the cancer group as compared with the healthy group. We constructed a model using age, sex and the ΔCt value of 7 gene methylation to distinguish lung cancer from benign and healthy individuals. The sensitivity, specificity and AUC (area under the curve) were 86.7%, 81.4% and 0.891, respectively. Also, we assessed the significance of 7 gene methylation together with patients' age and sex in distinguishing of GGNs type from the mass type. The sensitivity, specificity and AUC were 77.1%, 65.8% and 0.753, respectively. Furthermore, the methylation positive rates of CDO1 and SHOX2 were different between I-IV stages of lung cancer. Specifically, the positive rate of CDO1 methylation was higher in the non-IA group as compared with the IA group. CONCLUSION Collectively, this study reveals that the methylation of 7 genes has a big significance in the diagnosis of lung cancer with high sensitivity and specificity. Also, the 7 genes present with certain significance in distinguishing the GGN type lung cancer, as well as different stages.
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Affiliation(s)
- Chaoxiang Du
- Department of Thoracic Surgery, Cancer Center, Zhongshan Hospital of Fudan University, Shanghai, China
- Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
| | - Lijie Tan
- Department of Thoracic Surgery, Cancer Center, Zhongshan Hospital of Fudan University, Shanghai, China
- Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
| | - Xiao Xiao
- School of Physics, Changchun University of Science and Technology, Changchun, 130022, China
- Shanghai Rightongene Biotechnology Co. Ltd., Shanghai, 201403, China
| | - Beibei Xin
- Shanghai Rightongene Biotechnology Co. Ltd., Shanghai, 201403, China
| | - Hui Xiong
- Shanghai Rightongene Biotechnology Co. Ltd., Shanghai, 201403, China
| | - Yuying Zhang
- Shanghai Rightongene Biotechnology Co. Ltd., Shanghai, 201403, China
| | - Zhonghe Ke
- Shanghai Rightongene Biotechnology Co. Ltd., Shanghai, 201403, China.
| | - Jun Yin
- Department of Thoracic Surgery, Cancer Center, Zhongshan Hospital of Fudan University, Shanghai, China.
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Wang JZ, Nassiri F, Aldape K, von Deimling A, Sahm F. The Epigenetic Landscape of Meningiomas. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1416:175-188. [PMID: 37432627 DOI: 10.1007/978-3-031-29750-2_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Epigenetic changes have been found to be increasingly important in tumor development and progression. These alterations can be present in tumors such as meningiomas in the absence of any gene mutations and alter gene expression without affecting the sequence of the DNA itself. Some examples of these alterations that have been studied in meningiomas include DNA methylation, microRNA interaction, histone packaging, and chromatin restructuring. In this chapter we will describe in detail each of these mechanisms of epigenetic modification in meningiomas and their prognostic significance.
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Affiliation(s)
- Justin Z Wang
- Division of Neurosurgery, Department of Surgery, The University of Toronto, Toronto, ON, Canada
| | - Farshad Nassiri
- Division of Neurosurgery, Department of Surgery, The University of Toronto, Toronto, ON, Canada.
| | - Kenneth Aldape
- Laboratory of Pathology, Center Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andreas von Deimling
- CCU Neuropathology, German Cancer Research Center (DKFZ), University Heidelberg, Heidelberg, Germany
| | - Felix Sahm
- CCU Neuropathology, German Cancer Research Center (DKFZ), University Heidelberg, Heidelberg, Germany
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3
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Maier AD. Malignant meningioma. APMIS 2022; 130 Suppl 145:1-58. [DOI: 10.1111/apm.13276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Andrea Daniela Maier
- Department of Neurosurgery, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
- Department of Pathology, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
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Robert SM, Vetsa S, Nadar A, Vasandani S, Youngblood MW, Gorelick E, Jin L, Marianayagam N, Erson-Omay EZ, Günel M, Moliterno J. The integrated multiomic diagnosis of sporadic meningiomas: a review of its clinical implications. J Neurooncol 2021; 156:205-214. [PMID: 34846640 PMCID: PMC8816740 DOI: 10.1007/s11060-021-03874-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/09/2021] [Indexed: 12/28/2022]
Abstract
Introduction Meningiomas are generally considered “benign,” however, these tumors can demonstrate variability in behavior and a surprising aggressiveness with elevated rates of recurrence. The advancement of next-generation molecular technologies have led to the understanding of the genomic and epigenomic landscape of meningiomas and more recent correlations with clinical characteristics and behavior. Methods Based on a thorough review of recent peer-reviewed publications (PubMed) and edited texts, we provide a molecular overview of meningiomas with a focus on relevant clinical implications. Results The identification of specific somatic driver mutations has led to the classification of several major genomic subgroups, which account for more than 80% of sporadic meningiomas, and can be distinguished using noninvasive clinical variables to help guide management decisions. Other somatic genomic modifications, including non-coding alterations and copy number variations, have also been correlated with tumor characteristics. Furthermore, epigenomic modifications in meningiomas have recently been described, with DNA methylation being the most widely studied and potentially most clinically relevant. Based on these molecular insights, several clinical trials are currently underway in an effort to establish effective medical therapeutic options for meningioma. Conclusion As we enhance our multiomic understanding of meningiomas, our ability to care for patients with these tumors will continue to improve. Further biological insights will lead to additional progress in precision medicine for meningiomas.
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Affiliation(s)
- Stephanie M Robert
- Department of Neurosurgery, Yale School of Medicine, 15 York St, LLCI 810, New Haven, CT, 06520-8082, USA
| | - Shaurey Vetsa
- Department of Neurosurgery, Yale School of Medicine, 15 York St, LLCI 810, New Haven, CT, 06520-8082, USA
- The Chenevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, CT, USA
| | - Arushii Nadar
- Department of Neurosurgery, Yale School of Medicine, 15 York St, LLCI 810, New Haven, CT, 06520-8082, USA
- The Chenevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, CT, USA
| | - Sagar Vasandani
- Department of Neurosurgery, Yale School of Medicine, 15 York St, LLCI 810, New Haven, CT, 06520-8082, USA
- The Chenevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, CT, USA
| | - Mark W Youngblood
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - Evan Gorelick
- Department of Neurosurgery, Yale School of Medicine, 15 York St, LLCI 810, New Haven, CT, 06520-8082, USA
- The Chenevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, CT, USA
| | - Lan Jin
- Department of Neurosurgery, Yale School of Medicine, 15 York St, LLCI 810, New Haven, CT, 06520-8082, USA
| | - Neelan Marianayagam
- Department of Neurosurgery, Yale School of Medicine, 15 York St, LLCI 810, New Haven, CT, 06520-8082, USA
- The Chenevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, CT, USA
| | - E Zeynep Erson-Omay
- Department of Neurosurgery, Yale School of Medicine, 15 York St, LLCI 810, New Haven, CT, 06520-8082, USA
- The Chenevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, CT, USA
| | - Murat Günel
- Department of Neurosurgery, Yale School of Medicine, 15 York St, LLCI 810, New Haven, CT, 06520-8082, USA
- The Chenevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, CT, USA
| | - Jennifer Moliterno
- Department of Neurosurgery, Yale School of Medicine, 15 York St, LLCI 810, New Haven, CT, 06520-8082, USA.
- The Chenevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, CT, USA.
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Damen PJJ, Bulthuis VJ, Hanssens PEJ, Lie ST, Fleischeuer R, Melotte V, Wouters KA, Ruland A, Beckervordersandforth J, Speel EJM. WHO grade I meningiomas that show regrowth after gamma knife radiosurgery often show 1p36 loss. Sci Rep 2021; 11:16432. [PMID: 34385566 PMCID: PMC8361078 DOI: 10.1038/s41598-021-95956-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 07/21/2021] [Indexed: 12/12/2022] Open
Abstract
WHO grade I meningiomas occasionally show regrowth after radiosurgical treatment, which cannot be predicted by clinical features. There is increasing evidence that certain biomarkers are associated with regrowth of meningiomas. The aim of this retrospective study was to asses if these biomarkers could be of value to predict regrowth of WHO grade I meningiomas after additive radiosurgery. Forty-four patients with WHO grade I meningiomas who underwent additive radiosurgical treatment between 2002 and 2015 after Simpson IV resection were included in this study, of which 8 showed regrowth. Median follow-up time was 64 months (range 24–137 months). Tumors were analyzed for the proliferation marker Ki-67 by immunohistochemistry and for deletion of 1p36 by fluorescence in situ hybridization (FISH). Furthermore, genomic DNA was analyzed for promoter hypermethylation of the genes NDRG1–4, SFRP1, HOXA9 and MGMT. Comparison of meningiomas with and without regrowth after radiosurgery revealed that loss of 1p36 (p = 0.001) and hypermethylation of NDRG1 (p = 0.046) were correlated with regrowth free survival. Loss of 1p36 was the only parameter that was significantly associated with meningioma regrowth after multivariate analysis (p = 0.01). Assessment of 1p36 loss in tumor tissue prior to radiosurgery might be considered an indicator of prognosis/regrowth. However, this finding has to be validated in an independent larger set of tumors.
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Affiliation(s)
- Pim J J Damen
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, P. Debyelaan 25, Postbox 5800, 6202 AZ, Maastricht, The Netherlands
| | - Vincent J Bulthuis
- Department of Neurosurgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | | | - Suan Te Lie
- Gamma Knife Center Tilburg, ETZ-Elisabeth Hospital, Tilburg, The Netherlands
| | - Ruth Fleischeuer
- Department of Pathology, ETZ-Elisabeth Hospital, Tilburg, The Netherlands
| | - Veerle Melotte
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, P. Debyelaan 25, Postbox 5800, 6202 AZ, Maastricht, The Netherlands
| | - Kim A Wouters
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, P. Debyelaan 25, Postbox 5800, 6202 AZ, Maastricht, The Netherlands
| | - Andrea Ruland
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, P. Debyelaan 25, Postbox 5800, 6202 AZ, Maastricht, The Netherlands
| | - Jan Beckervordersandforth
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, P. Debyelaan 25, Postbox 5800, 6202 AZ, Maastricht, The Netherlands
| | - Ernst Jan M Speel
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, P. Debyelaan 25, Postbox 5800, 6202 AZ, Maastricht, The Netherlands.
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Abstract
Comprehensive genomic studies of meningioma have offered important insights about the molecular mechanisms underlying this common brain tumor. The use of next-generation sequencing techniques has identified driver mutations in approximately 80% of benign sporadic lesions, as well as epigenetic, regulatory, and copy number events that are associated with formation and disease progression. The events described to date fall into five mutually exclusive molecular subgroups that correlate with tumor location and embryological origin. Importantly, these subgroups also carry implications for clinical management, as they are predictive of histologic subtype and the likelihood of progression. Further work is necessary to understand the molecular mechanisms by which identified mutations drive tumorigenesis as well as the genomic pathways that transform benign lesions into malignancies. Progress made during the past decade has opened the door to potential molecular therapies as well as integration of meningioma genotyping data into clinical management decisions. Several pharmacologic trials are currently underway that leverage recent genomic findings to target established oncogenic pathways in refractory tumors. With the combined efforts of physicians and basic science investigators, the clinical management of meningioma will continue to make important strides in the coming years.
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Shen L, Lin D, Cheng L, Tu S, Wu H, Xu W, Pan Y, Wang X, Zhang J, Shao A. Is DNA Methylation a Ray of Sunshine in Predicting Meningioma Prognosis? Front Oncol 2020; 10:1323. [PMID: 33014773 PMCID: PMC7498674 DOI: 10.3389/fonc.2020.01323] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Meningioma is the most common intracranial tumor, and recent studies have drawn attention to the importance of further research on malignant meningioma. According to the World Health Organization (WHO) grading, meningioma is classified into 15 subtypes with three grades of malignancy. However, due to a lack of descriptions of molecular subtypes, genetic mutations, or other features, there were deficiencies in the WHO classification. The DNA methylation-based meningioma classification published in 2017 used DNA copy number analysis, mutation profiling, and RNA sequencing to distinguish six clinically relevant methylation classes, which contributed to a better prediction of tumor recurrence and prognosis. Further studies indicated that gene variation and gene mutations, such as those in neurofibromin 2 (NF2) and BRCA1, were related to the high WHO grade, malignant invasion, and recurrence. Among the mutant genes described above, some have been associated with differential DNA methylation. Herein, we searched for articles published in PubMed and Web of Science from January 2000 to May 2020 by entering the keywords “meningioma,” “methylation,” and “gene mutation,” and found a number of published studies that analyzed DNA methylation in meningiomas. In this review, we summarize the key findings of recent studies on methylation status and genetic mutations of meningioma and discuss the current deficits of the WHO grading. We also propose that a methylation-based meningioma classification could provide clues in the assessment of individual risk of meningioma recurrence, which is associated with clinical benefits for patients.
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Affiliation(s)
- Lu Shen
- Department of Surgical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Danfeng Lin
- Department of Surgical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lu Cheng
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Sheng Tu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Haijian Wu
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Weilin Xu
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuanbo Pan
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaochen Wang
- Department of Surgical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Department of Breast Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Jianmin Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Brain Research Institute, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Brain Science, Zhejiang University, Hangzhou, China
| | - Anwen Shao
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Identification of a Transcription Factor-microRNA-Gene Coregulation Network in Meningioma through a Bioinformatic Analysis. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6353814. [PMID: 32832554 PMCID: PMC7428944 DOI: 10.1155/2020/6353814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/04/2020] [Accepted: 07/18/2020] [Indexed: 12/20/2022]
Abstract
Background Meningioma is a prevalent type of brain tumor. However, the initiation and progression mechanisms involved in the meningioma are mostly unknown. This study aimed at exploring the potential transcription factors/micro(mi)RNAs/genes and biological pathways associated with meningioma. Methods mRNA expressions from GSE88720, GSE43290, and GSE54934 datasets, containing data from 83 meningioma samples and eight control samples, along with miRNA expression dataset GSE88721, which had 14 meningioma samples and one control sample, were integrated analyzed. The bioinformatics approaches were used for identifying differentially expressed genes and miRNAs, as well as predicting transcription factor targets related to the differentially expressed genes. The approaches were also used for gene ontology term analysis and biological pathway enrichment analysis, construction, and analysis of protein-protein interaction network, and transcription factor-miRNA-gene coregulation network construction. Results Fifty-six upregulated and 179 downregulated genes were identified. Thirty transcription factors able to target the differentially expressed genes were predicted and selected based on public databases. One hundred seventeen overlapping genes were identified from the differentially expressed genes and the miRNAs predicted by miRWalk. Furthermore, NF-κB/IL6, PTGS2, MYC/hsa-miR-574-5p, hsa-miR-26b-5p, hsa-miR-335-5p, and hsa-miR-98-5p, which are involved in the transcription factor-miRNA-mRNA coregulation network, were found to be associated with meningioma. Conclusion The bioinformatics analysis identified several potential molecules and relevant pathways that may represent critical mechanisms involved in the progression and development of meningioma. This work provides new insights into meningioma pathogenesis and treatments.
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Bondos SE, Geraldo Mendes G, Jons A. Context-dependent HOX transcription factor function in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:225-262. [PMID: 32828467 DOI: 10.1016/bs.pmbts.2020.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
During animal development, HOX transcription factors determine the fate of developing tissues to generate diverse organs and appendages. The power of these proteins is striking: mis-expressing a HOX protein causes homeotic transformation of one body part into another. During development, HOX proteins interpret their cellular context through protein interactions, alternative splicing, and post-translational modifications to regulate cell proliferation, cell death, cell migration, cell differentiation, and angiogenesis. Although mutation and/or mis-expression of HOX proteins during development can be lethal, changes in HOX proteins that do not pattern vital organs can result in survivable malformations. In adults, mutation and/or mis-expression of HOX proteins disrupts their gene regulatory networks, deregulating cell behaviors and leading to arthritis and cancer. On the molecular level, HOX proteins are composed of DNA binding homeodomain, and large regions of unstructured, or intrinsically disordered, protein sequence. The primary roles of HOX proteins in arthritis and cancer suggest that mutations associated with these diseases in both the structured and disordered regions of HOX proteins can have substantial functional effects. These insights lead to new questions critical for understanding and manipulating HOX function in physiological and pathological conditions.
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Affiliation(s)
- Sarah E Bondos
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX, United States.
| | - Gabriela Geraldo Mendes
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX, United States
| | - Amanda Jons
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX, United States
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Barciszewska AM. Total DNA methylation as a biomarker of DNA damage and tumor malignancy in intracranial meningiomas. BMC Cancer 2020; 20:509. [PMID: 32493231 PMCID: PMC7268775 DOI: 10.1186/s12885-020-06982-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 05/20/2020] [Indexed: 12/29/2022] Open
Abstract
Background Meningiomas are the most common primary intracranial tumors in adults. They are initially detected with neuroimaging techniques, but definite histological diagnosis requires tumor surgery to collect tumor tissue. Gross total resection is an optimal and final treatment for the majority of patients, followed by radiotherapy in malignant or refractory cases. However, there are a lot of uncertainties about i.a. the need for intervention in incidental cases, estimation of growth kinetics, risk of malignant transformation, or response to radiotherapy. Therefore a new diagnostic approach is needed. It has already been shown that epigenetics plays a crucial role in cancer biology, development, and progression. DNA methylation, the presence of 5-methylcytosine in DNA, is one of the main elements of a broad epigenetic program in a eukaryotic cell, with superior regulatory significance. Therefore, we decided to look at meningioma through changes of 5-methylcytosine. Methods We performed an analysis of the total amount of 5-methylcytosine in DNA isolated from intracranial meningioma tissues and peripheral blood samples of the same patients. The separation and identification of radioactively labeled nucleotides were performed using thin-layer chromatography. Results We found that the 5-methylcytosine level in DNA from intracranial meningiomas is inversely proportional to the malignancy grade. The higher the tumor WHO grade is, the lower the total DNA methylation. The amount of 5-methylcytosine in tumor tissue and peripheral blood is almost identical. Conclusions We conclude that the total DNA methylation can be a useful marker for brain meningioma detection, differentiation, and monitoring. It correlates with tumor WHO grade, and the 5-methylcytosine level in peripheral blood reflects that in tumor tissue. Therefore it’s applicable for liquid biopsy. Our study creates a scope for further research on epigenetic mechanisms in neurooncology and can lead to the development of new diagnostic methods in clinical practice.
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Affiliation(s)
- Anna-Maria Barciszewska
- Intraoperative Imaging Unit, Chair and Department of Neurosurgery and Neurotraumatology, Karol Marcinkowski University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznan, Poland. .,Department of Neurosurgery and Neurotraumatology, Heliodor Swiecicki Clinical Hospital, Przybyszewskiego 49, 60-355, Poznan, Poland.
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Yu M, Zhan J, Zhang H. HOX family transcription factors: Related signaling pathways and post-translational modifications in cancer. Cell Signal 2019; 66:109469. [PMID: 31733300 DOI: 10.1016/j.cellsig.2019.109469] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/09/2019] [Accepted: 11/11/2019] [Indexed: 02/06/2023]
Abstract
HOX family transcription factors belong to a highly conserved subgroup of the homeobox superfamily that determines cellular fates in embryonic morphogenesis and the maintenance of adult tissue architecture. HOX family transcription factors play key roles in numerous cellular processes including cell growth, differentiation, apoptosis, motility, and angiogenesis. As tumor promoters or suppressors HOX family members have been reported to be closely related with a variety of cancers. They closely regulate tumor initiation and growth, invasion and metastasis, angiogenesis, anti-cancer drug resistance and stem cell origin. Here, we firstly described the pivotal roles of HOX transcription factors in tumorigenesis. Then, we summarized the main signaling pathways regulated by HOX transcription factors, including Wnt/β-catenin, transforming growth factor β, mitogen-activated protein kinase, phosphoinositide 3-kinase/Akt, and nuclear factor-κB signalings. Finally, we outlined the important post-translational modifications of HOX transcription factors and their regulation in cancers. Future research directions on the HOX transcription factors are also discussed.
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Affiliation(s)
- Miao Yu
- Peking University Health Science Center, Department of Anatomy, Histology and Embryology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), State Key Laboratory of Natural and Biomimetic Drugs, Beijing 100191, China
| | - Jun Zhan
- Peking University Health Science Center, Department of Anatomy, Histology and Embryology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), State Key Laboratory of Natural and Biomimetic Drugs, Beijing 100191, China.
| | - Hongquan Zhang
- Peking University Health Science Center, Department of Anatomy, Histology and Embryology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), State Key Laboratory of Natural and Biomimetic Drugs, Beijing 100191, China.
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Paramasivam N, Hübschmann D, Toprak UH, Ishaque N, Neidert M, Schrimpf D, Stichel D, Reuss D, Sievers P, Reinhardt A, Wefers AK, Jones DTW, Gu Z, Werner J, Uhrig S, Wirsching HG, Schick M, Bewerunge-Hudler M, Beck K, Brehmer S, Urbschat S, Seiz-Rosenhagen M, Hänggi D, Herold-Mende C, Ketter R, Eils R, Ram Z, Pfister SM, Wick W, Weller M, Grossmann R, von Deimling A, Schlesner M, Sahm F. Mutational patterns and regulatory networks in epigenetic subgroups of meningioma. Acta Neuropathol 2019; 138:295-308. [PMID: 31069492 DOI: 10.1007/s00401-019-02008-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 01/05/2023]
Abstract
DNA methylation patterns delineate clinically relevant subgroups of meningioma. We previously established the six meningioma methylation classes (MC) benign 1-3, intermediate A and B, and malignant. Here, we set out to identify subgroup-specific mutational patterns and gene regulation. Whole genome sequencing was performed on 62 samples across all MCs and WHO grades from 62 patients with matched blood control, including 40 sporadic meningiomas and 22 meningiomas arising after radiation (Mrad). RNA sequencing was added for 18 of these cases and chromatin-immunoprecipitation for histone H3 lysine 27 acetylation (H3K27ac) followed by sequencing (ChIP-seq) for 16 samples. Besides the known mutations in meningioma, structural variants were found as the mechanism of NF2 inactivation in a small subset (5%) of sporadic meningiomas, similar to previous reports for Mrad. Aberrations of DMD were found to be enriched in MCs with NF2 mutations, and DMD was among the most differentially upregulated genes in NF2 mutant compared to NF2 wild-type cases. The mutational signature AC3, which has been associated with defects in homologous recombination repair (HRR), was detected in both sporadic meningioma and Mrad, but widely distributed across the genome in sporadic cases and enriched near genomic breakpoints in Mrad. Compared to the other MCs, the number of single nucleotide variants matching the AC3 pattern was significantly higher in the malignant MC, which also exhibited higher genomic instability, determined by the numbers of both large segments affected by copy number alterations and breakpoints between large segments. ChIP-seq analysis for H3K27ac revealed a specific activation of genes regulated by the transcription factor FOXM1 in the malignant MC. This analysis also revealed a super enhancer near the HOXD gene cluster in this MC, which, together with general upregulation of HOX genes in the malignant MC, indicates a role of HOX genes in meningioma aggressiveness. This data elucidates the biological mechanisms rendering different epigenetic subgroups of meningiomas, and suggests leveraging HRR as a novel therapeutic target.
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Affiliation(s)
- Nagarajan Paramasivam
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Hübschmann
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Stem Cells and Cancer, DKFZ, Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital, Heidelberg, Germany
| | - Umut H Toprak
- Division Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Naveed Ishaque
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center for Digital Health, Berlin Institute of Health and Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Marian Neidert
- Department of Neurosurgery, University Hospital of Zürich, Zurich, Switzerland
| | - Daniel Schrimpf
- Department of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Reuss
- Department of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Sievers
- Department of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annekathrin Reinhardt
- Department of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annika K Wefers
- Department of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Zuguang Gu
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes Werner
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Biological Oceanography, Leibniz Institute of Baltic Sea Research, Rostock, Germany
| | - Sebastian Uhrig
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hans-Georg Wirsching
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Matthias Schick
- Genomics and Proteomics Core Facility, Microarray Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Bewerunge-Hudler
- Genomics and Proteomics Core Facility, Microarray Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katja Beck
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephanie Brehmer
- Department of Neurosurgery, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany
| | - Steffi Urbschat
- Department of Neurosurgery, University Hospital Homburg Saar, Homburg, Germany
| | - Marcel Seiz-Rosenhagen
- Department of Neurosurgery, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany
| | - Daniel Hänggi
- Department of Neurosurgery, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Ralf Ketter
- Department of Neurosurgery, University Hospital Homburg Saar, Homburg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center for Digital Health, Berlin Institute of Health and Charité Universitätsmedizin Berlin, Berlin, Germany
- Health Data Science Unit, Bioquant, Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Zvi Ram
- Department of Neurosurgery, Tel Aviv Medical Center, Tel Aviv, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Stefan M Pfister
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital, Heidelberg, Germany
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Rachel Grossmann
- Department of Neurosurgery, Tel Aviv Medical Center, Tel Aviv, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany.
- Department of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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13
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Long J, Zhang L, Wan X, Lin J, Bai Y, Xu W, Xiong J, Zhao H. A four-gene-based prognostic model predicts overall survival in patients with hepatocellular carcinoma. J Cell Mol Med 2018; 22:5928-5938. [PMID: 30247807 PMCID: PMC6237588 DOI: 10.1111/jcmm.13863] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 07/26/2018] [Accepted: 07/27/2018] [Indexed: 12/15/2022] Open
Abstract
With the development of new advances in hepatocellular carcinoma (HCC) management and noninvasive radiological techniques, high‐risk patient groups such as those with hepatitis virus are closely monitored. HCC is increasingly diagnosed early, and treatment may be successful. In spite of this progress, most patients who undergo a hepatectomy will eventually relapse, and the outcomes of HCC patients remain unsatisfactory. In our study, we aimed to identify potential gene biomarkers based on RNA sequencing data to predict and improve HCC patient survival. The gene expression data and clinical information were acquired from The Cancer Genome Atlas (TCGA) database. A total of 339 differentially expressed genes (DEGs) were obtained between the HCC (n = 374) and normal tissues (n = 50). Four genes (CENPA, SPP1, MAGEB6 and HOXD9) were screened by univariate, Lasso and multivariate Cox regression analyses to develop the prognostic model. Further analysis revealed the independent prognostic capacity of the prognostic model in relation to other clinical characteristics. The receiver operating characteristic (ROC) curve analysis confirmed the good performance of the prognostic model. Then, the prognostic model and the expression levels of the four genes were validated using the Gene Expression Omnibus (GEO) dataset. A nomogram comprising the prognostic model to predict the overall survival was established, and internal validation in the TCGA cohort was performed. The predictive model and the nomogram will enable patients with HCC to be more accurately managed in trials testing new drugs and in clinical practice.
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Affiliation(s)
- Junyu Long
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Zhang
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xueshuai Wan
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianzhen Lin
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi Bai
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weiyu Xu
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianping Xiong
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haitao Zhao
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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14
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Katz LM, Hielscher T, Liechty B, Silverman J, Zagzag D, Sen R, Wu P, Golfinos JG, Reuss D, Neidert MC, Wirsching HG, Baumgarten P, Herold-Mende C, Wick W, Harter PN, Weller M, von Deimling A, Snuderl M, Sen C, Sahm F. Loss of histone H3K27me3 identifies a subset of meningiomas with increased risk of recurrence. Acta Neuropathol 2018; 135:955-963. [PMID: 29627952 DOI: 10.1007/s00401-018-1844-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/27/2018] [Accepted: 03/30/2018] [Indexed: 11/25/2022]
Abstract
Epigenetic patterns on the level of DNA methylation have already been shown to separate clinically relevant subgroups of meningiomas. We here set out to identify potential prognostic implications of epigenetic modification on the level of histones with focus on H3K27 trimethylation (H3K27me3). H3K27me3 was assessed by immunohistochemistry on 232 meningiomas from 232 patients. In 194 cases, trimethylation was detected in tumor cells. In 25 cases, staining was limited to vessels while all tumor cells were negative. Finally, 13 cases yielded equivocal staining patterns. Reduced abundance of H3K27me3 in cases with staining limited to vessels was confirmed by mass spectrometry on a subset of cases. Lack of staining for H3K27me3 in all tumor cells was significantly associated with more rapid progression (p = 0.009). In line, H3K27me3-negative cases were associated with a DNA methylation pattern of the more aggressive types among the recently introduced DNA methylation groups. Also, NF2 and SUFU mutations were enriched among cases with complete lack of H3K27me3 staining in tumor cells (p < 0.0001 and p = 0.029, respectively). H3K27me3 staining pattern added significant prognostic insight into WHO grade II cases and in the compound subset of WHO grade I and II cases (p = 0.04 and p = 0.007, respectively). However, it did not further stratify within WHO grade III cases. Collectively, these data indicate that epigenetic modifications beyond DNA methylation are involved in the aggressiveness of meningioma. It also suggests that H3K27me3 immunohistochemistry might be a useful adjunct in meningioma diagnostics, particularly for cases with WHO grade II histology or at the borderline between WHO grade I and II.
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Affiliation(s)
- Leah M Katz
- Department of Radiation Oncology, NYU Langone Hospital, New York, NY, USA
| | - Thomas Hielscher
- Department of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benjamin Liechty
- Division of Neuropathology, Department of Pathology, NYU Langone Hospital, New York, NY, USA
| | - Joshua Silverman
- Department of Radiation Oncology, NYU Langone Hospital, New York, NY, USA
| | - David Zagzag
- Division of Neuropathology, Department of Pathology, NYU Langone Hospital, New York, NY, USA
| | - Rajeev Sen
- Department of Neurosurgery, NYU Langone Hospital, New York, NY, USA
| | - Peter Wu
- Department of Radiation Oncology, NYU Langone Hospital, New York, NY, USA
| | - John G Golfinos
- Department of Neurosurgery, NYU Langone Hospital, New York, NY, USA
| | - David Reuss
- Department of Neuropathology, University Hospital Heidelberg, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Hans-Georg Wirsching
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Peter Baumgarten
- Department of Neurosurgery, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Patrick N Harter
- Neurological Institute (Edinger Institute), Goethe University Frankfurt, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site, Frankfurt/Mainz, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matija Snuderl
- Division of Neuropathology, Department of Pathology, NYU Langone Hospital, New York, NY, USA
| | - Chandra Sen
- Department of Neurosurgery, NYU Langone Hospital, New York, NY, USA
| | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg, 69120, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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15
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Chen B, Liang T, Yang P, Wang H, Liu Y, Yang F, You G. Classifying lower grade glioma cases according to whole genome gene expression. Oncotarget 2018; 7:74031-74042. [PMID: 27677590 PMCID: PMC5342033 DOI: 10.18632/oncotarget.12188] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 08/13/2016] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE To identify a gene-based signature as a novel prognostic model in lower grade gliomas. RESULTS A gene signature developed from HOXA7, SLC2A4RG and MN1 could segregate patients into low and high risk score groups with different overall survival (OS), and was validated in TCGA RNA-seq and GSE16011 mRNA array datasets. Receiver operating characteristic (ROC) was performed to show that the three-gene signature was more sensitive and specific than histology, grade, age, IDH1 mutation and 1p/19q co-deletion. Gene Set Enrichment Analysis (GSEA) and GO analysis showed high-risk samples were associated with tumor associated macrophages (TAMs) and highly invasive phenotypes. Moreover, HOXA7-siRNA inhibited migration and invasion in vitro, and downregulated MMP9 at the protein level in U251 glioma cells. METHODS A cohort of 164 glioma specimens from the Chinese Glioma Genome Atlas (CGGA) array database were assessed as the training group. TCGA RNA-seq and GSE16011 mRNA array datasets were used for validation. Regression analyses and linear risk score assessment were performed for the identification of the three-gene signature comprising HOXA7, SLC2A4RG and MN1. CONCLUSIONS We established a three-gene signature for lower grade gliomas, which could independently predict overall survival (OS) of lower grade glioma patients with higher sensitivity and specificity compared with other clinical characteristics. These findings indicate that the three-gene signature is a new prognostic model that could provide improved OS prediction and accurate therapies for lower grade glioma patients.
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Affiliation(s)
- Baoshi Chen
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Tingyu Liang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Pei Yang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Cooperative Group (CGCG), China
| | - Haoyuan Wang
- Department of Neurosurgery, Guangdong Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yanwei Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Cooperative Group (CGCG), China
| | - Fan Yang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Gan You
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Cooperative Group (CGCG), China
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16
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Olar A, Wani KM, Wilson CD, Zadeh G, DeMonte F, Jones DTW, Pfister SM, Sulman EP, Aldape KD. Global epigenetic profiling identifies methylation subgroups associated with recurrence-free survival in meningioma. Acta Neuropathol 2017; 133:431-444. [PMID: 28130639 PMCID: PMC5600514 DOI: 10.1007/s00401-017-1678-x] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 12/14/2022]
Abstract
Meningioma is the most common primary brain tumor and carries a substantial risk of local recurrence. Methylation profiles of meningioma and their clinical implications are not well understood. We hypothesized that aggressive meningiomas have unique DNA methylation patterns that could be used to better stratify patient management. Samples (n = 140) were profiled using the Illumina HumanMethylation450BeadChip. Unsupervised modeling on a training set (n = 89) identified 2 molecular methylation subgroups of meningioma (MM) with significantly different recurrence-free survival (RFS) times between the groups: a prognostically unfavorable subgroup (MM-UNFAV) and a prognostically favorable subgroup (MM-FAV). This finding was validated in the remaining 51 samples and led to a baseline meningioma methylation classifier (bMMC) defined by 283 CpG loci (283-bMMC). To further optimize a recurrence predictor, probes subsumed within the baseline classifier were subject to additional modeling using a similar training/validation approach, leading to a 64-CpG loci meningioma methylation predictor (64-MMP). After adjustment for relevant clinical variables [WHO grade, mitotic index, Simpson grade, sex, location, and copy number aberrations (CNAs)] multivariable analyses for RFS showed that the baseline methylation classifier was not significant (p = 0.0793). The methylation predictor, however, was significantly associated with tumor recurrence (p < 0.0001). CNAs were extracted from the 450k intensity profiles. Tumor samples in the MM-UNFAV subgroup showed an overall higher proportion of CNAs compared to the MM-FAV subgroup tumors and the CNAs were complex in nature. CNAs in the MM-UNFAV subgroup included recurrent losses of 1p, 6q, 14q and 18q, and gain of 1q, all of which were previously identified as indicators of poor outcome. In conclusion, our analyses demonstrate robust DNA methylation signatures in meningioma that correlate with CNAs and stratify patients by recurrence risk.
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Affiliation(s)
- Adriana Olar
- Departments of Pathology and Laboratory Medicine and Neurosurgery, Medical University of South Carolina and Hollings Cancer Center, 171 Ashley Ave., MSC 908, Charleston, SC, 29425, USA.
| | - Khalida M Wani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 2130 W Holcombe Blvd., Houston, TX, 77030, USA
| | - Charmaine D Wilson
- Center for Nursing Research, The University of Texas School of Nursing, 6901 Bertner St., Houston, TX, 77030, USA
| | - Gelareh Zadeh
- Princess Margaret Cancer Centre, MacFeeters-Hamilton Brain Tumour Centre, College Street 101, Toronto, M5G 1L7, ON, Canada
| | - Franco DeMonte
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Network (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Network (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Erik P Sulman
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 2130 W Holcombe Blvd., Houston, TX, 77030, USA
- Departments of Radiation Oncology and Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Kenneth D Aldape
- Princess Margaret Cancer Centre, MacFeeters-Hamilton Brain Tumour Centre, College Street 101, Toronto, M5G 1L7, ON, Canada
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17
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Bhat S, Kabekkodu SP, Varghese VK, Chakrabarty S, Mallya SP, Rotti H, Pandey D, Kushtagi P, Satyamoorthy K. Aberrant gene-specific DNA methylation signature analysis in cervical cancer. Tumour Biol 2017; 39:1010428317694573. [PMID: 28351298 DOI: 10.1177/1010428317694573] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024] Open
Abstract
Multicomponent molecular modifications such as DNA methylation may offer sensitive and specific cervical intraepithelial neoplasia and cervical cancer biomarkers. In this study, we tested cervical tissues at various stages of tumor progression for 5-methylcytosine and 5-hydroxymethylcytosine levels and also DNA promoter methylation profile of a panel of genes for its diagnostic potential. In total, 5-methylcytosine, 5-hydroxymethylcytosine, and promoter methylation of 33 genes were evaluated by reversed-phase high-performance liquid chromatography, enzyme-linked immunosorbent assay based technique, and bisulfate-based next generation sequencing. The 5-methylcytosine and 5-hydroxymethylcytosine contents were significantly reduced in squamous cell carcinoma and receiver operating characteristic curve analysis showed a significant difference in (1) 5-methylcytosine between normal and squamous cell carcinoma tissues (area under the curve = 0.946) and (2) 5-hydroxymethylcytosine levels among normal, squamous intraepithelial lesions and squamous cell carcinoma. Analyses of our next generation sequencing results and data from five independent published studies consisting of 191 normal, 10 low-grade squamous intraepithelial lesions, 21 high-grade squamous intraepithelial lesions, and 335 malignant tissues identified a panel of nine genes ( ARHGAP6, DAPK1, HAND2, NKX2-2, NNAT, PCDH10, PROX1, PITX2, and RAB6C) which could effectively discriminate among the various groups with sensitivity and specificity of 80%-100% (p < 0.05). Furthermore, 12 gene promoters (ARHGAP6, HAND2, LHX9, HEY2, NKX2-2, PCDH10, PITX2, PROX1, TBX3, IKBKG, RAB6C, and DAPK1) were also methylated in one or more of the cervical cancer cell lines tested. The global and gene-specific methylation of the panel of genes identified in our study may serve as useful biomarkers for the early detection and clinical management of cervical cancer.
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Affiliation(s)
- Samatha Bhat
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
| | - Shama Prasada Kabekkodu
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
| | - Vinay Koshy Varghese
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
| | - Sanjiban Chakrabarty
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
| | - Sandeep P Mallya
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
| | - Harish Rotti
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
| | - Deeksha Pandey
- 2 Department of Obstetrics & Gynaecology, Kasturba Medical College, Manipal University, Manipal, India
| | - Pralhad Kushtagi
- 3 Department of Obstetrics & Gynaecology, Kasturba Medical College, Manipal University, Mangalore, India
| | - Kapaettu Satyamoorthy
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
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19
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Fogh SE, Johnson DR, Barker FG, Brastianos PK, Clarke JL, Kaufmann TJ, Oberndorfer S, Preusser M, Raghunathan A, Santagata S, Theodosopoulos PV. Case-Based Review: meningioma. Neurooncol Pract 2016; 3:120-134. [PMID: 31386096 DOI: 10.1093/nop/npv063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Indexed: 12/30/2022] Open
Abstract
Meningioma is by far the most common primary intracranial tumor in adults. Treatment of meningioma is complex due to a tremendous amount of variability in tumor behavior. Many patients are incidentally found to have tumors that will remain asymptomatic throughout their lives. It is important to identify these patients so that they can be spared from potentially morbid interventions. On the other end of the spectrum, high-grade meningiomas can behave very aggressively. When treatment is necessary, surgical resection is the cornerstone of meningioma therapy. Studies spanning decades have demonstrated that extent of resection correlates with prognosis. Radiation therapy, either in the form of external beam radiation therapy or stereotactic radiosurgery, represents another important therapeutic tool that can be used in place of or as a supplement to surgery. There are no chemotherapeutic agents of proven efficacy against meningioma, and chemotherapy treatment is generally reserved for patients who have exhausted surgical and radiotherapy options. Ongoing and future studies will help to answer unresolved questions such as the optimum use of radiation in resected WHO grade II meningiomas and the efficacy of additional chemotherapy agents.
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Affiliation(s)
- Shannon E Fogh
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA (S.E.F.); Department of Radiology, Mayo Clinic, Rochester, MN, USA (D.R.J., T.J.K.); Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (F.G.B.); Division of Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (P.K.B.); Department of Neurology and Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (J.L.C.); Department of Neurology, Karl Landsteiner University Clinic, St Pölten, Austria (S.O.); Department of Internal Medicine, Medical University, Vienna, CCC, Austria (M.P.); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA (A.R.); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA (S.S.); Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (P.V.T.)
| | - Derek R Johnson
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA (S.E.F.); Department of Radiology, Mayo Clinic, Rochester, MN, USA (D.R.J., T.J.K.); Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (F.G.B.); Division of Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (P.K.B.); Department of Neurology and Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (J.L.C.); Department of Neurology, Karl Landsteiner University Clinic, St Pölten, Austria (S.O.); Department of Internal Medicine, Medical University, Vienna, CCC, Austria (M.P.); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA (A.R.); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA (S.S.); Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (P.V.T.)
| | - Fred G Barker
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA (S.E.F.); Department of Radiology, Mayo Clinic, Rochester, MN, USA (D.R.J., T.J.K.); Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (F.G.B.); Division of Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (P.K.B.); Department of Neurology and Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (J.L.C.); Department of Neurology, Karl Landsteiner University Clinic, St Pölten, Austria (S.O.); Department of Internal Medicine, Medical University, Vienna, CCC, Austria (M.P.); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA (A.R.); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA (S.S.); Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (P.V.T.)
| | - Priscilla K Brastianos
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA (S.E.F.); Department of Radiology, Mayo Clinic, Rochester, MN, USA (D.R.J., T.J.K.); Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (F.G.B.); Division of Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (P.K.B.); Department of Neurology and Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (J.L.C.); Department of Neurology, Karl Landsteiner University Clinic, St Pölten, Austria (S.O.); Department of Internal Medicine, Medical University, Vienna, CCC, Austria (M.P.); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA (A.R.); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA (S.S.); Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (P.V.T.)
| | - Jennifer L Clarke
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA (S.E.F.); Department of Radiology, Mayo Clinic, Rochester, MN, USA (D.R.J., T.J.K.); Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (F.G.B.); Division of Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (P.K.B.); Department of Neurology and Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (J.L.C.); Department of Neurology, Karl Landsteiner University Clinic, St Pölten, Austria (S.O.); Department of Internal Medicine, Medical University, Vienna, CCC, Austria (M.P.); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA (A.R.); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA (S.S.); Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (P.V.T.)
| | - Timothy J Kaufmann
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA (S.E.F.); Department of Radiology, Mayo Clinic, Rochester, MN, USA (D.R.J., T.J.K.); Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (F.G.B.); Division of Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (P.K.B.); Department of Neurology and Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (J.L.C.); Department of Neurology, Karl Landsteiner University Clinic, St Pölten, Austria (S.O.); Department of Internal Medicine, Medical University, Vienna, CCC, Austria (M.P.); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA (A.R.); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA (S.S.); Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (P.V.T.)
| | - Stephan Oberndorfer
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA (S.E.F.); Department of Radiology, Mayo Clinic, Rochester, MN, USA (D.R.J., T.J.K.); Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (F.G.B.); Division of Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (P.K.B.); Department of Neurology and Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (J.L.C.); Department of Neurology, Karl Landsteiner University Clinic, St Pölten, Austria (S.O.); Department of Internal Medicine, Medical University, Vienna, CCC, Austria (M.P.); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA (A.R.); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA (S.S.); Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (P.V.T.)
| | - Matthias Preusser
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA (S.E.F.); Department of Radiology, Mayo Clinic, Rochester, MN, USA (D.R.J., T.J.K.); Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (F.G.B.); Division of Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (P.K.B.); Department of Neurology and Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (J.L.C.); Department of Neurology, Karl Landsteiner University Clinic, St Pölten, Austria (S.O.); Department of Internal Medicine, Medical University, Vienna, CCC, Austria (M.P.); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA (A.R.); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA (S.S.); Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (P.V.T.)
| | - Aditya Raghunathan
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA (S.E.F.); Department of Radiology, Mayo Clinic, Rochester, MN, USA (D.R.J., T.J.K.); Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (F.G.B.); Division of Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (P.K.B.); Department of Neurology and Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (J.L.C.); Department of Neurology, Karl Landsteiner University Clinic, St Pölten, Austria (S.O.); Department of Internal Medicine, Medical University, Vienna, CCC, Austria (M.P.); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA (A.R.); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA (S.S.); Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (P.V.T.)
| | - Sandro Santagata
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA (S.E.F.); Department of Radiology, Mayo Clinic, Rochester, MN, USA (D.R.J., T.J.K.); Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (F.G.B.); Division of Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (P.K.B.); Department of Neurology and Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (J.L.C.); Department of Neurology, Karl Landsteiner University Clinic, St Pölten, Austria (S.O.); Department of Internal Medicine, Medical University, Vienna, CCC, Austria (M.P.); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA (A.R.); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA (S.S.); Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (P.V.T.)
| | - Philip V Theodosopoulos
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA (S.E.F.); Department of Radiology, Mayo Clinic, Rochester, MN, USA (D.R.J., T.J.K.); Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (F.G.B.); Division of Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA (P.K.B.); Department of Neurology and Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (J.L.C.); Department of Neurology, Karl Landsteiner University Clinic, St Pölten, Austria (S.O.); Department of Internal Medicine, Medical University, Vienna, CCC, Austria (M.P.); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA (A.R.); Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA (S.S.); Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA (P.V.T.)
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Environmental Epigenetics: Crossroad between Public Health, Lifestyle, and Cancer Prevention. BIOMED RESEARCH INTERNATIONAL 2015; 2015:587983. [PMID: 26339624 PMCID: PMC4538403 DOI: 10.1155/2015/587983] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/01/2015] [Indexed: 12/31/2022]
Abstract
Epigenetics provides the key to transform the genetic information into phenotype and because of its reversibility it is considered an ideal target for therapeutic interventions. This paper reviews the basic mechanisms of epigenetic control: DNA methylation, histone modifications, chromatin remodeling, and ncRNA expression and their role in disease development. We describe also the influence of the environment, lifestyle, nutritional habits, and the psychological influence on epigenetic marks and how these factors are related to cancer and other diseases development. Finally we discuss the potential use of natural epigenetic modifiers in the chemoprevention of cancer to link together public health, environment, and lifestyle.
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Torres-Martín M, Kusak ME, Isla A, Burbano RR, Pinto GR, Melendez B, Castresana JS, Rey JA. Whole exome sequencing in a case of sporadic multiple meningioma reveals shared NF2, FAM109B, and TPRXL mutations, together with unique SMARCB1 alterations in a subset of tumor nodules. Cancer Genet 2015; 208:327-32. [DOI: 10.1016/j.cancergen.2015.03.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/19/2015] [Accepted: 03/30/2015] [Indexed: 12/19/2022]
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Epigenetics of Meningiomas. BIOMED RESEARCH INTERNATIONAL 2015; 2015:532451. [PMID: 26101774 PMCID: PMC4458517 DOI: 10.1155/2015/532451] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 12/14/2014] [Indexed: 12/20/2022]
Abstract
Meningiomas account for one-third of all adult central nervous system tumours and are divided into three WHO grades. In contrast to the relatively well characterized genetic alterations, our current understanding of epigenetic modifications involved in the meningioma-genesis and progression is rather incomplete. Contrary to genetic alterations, epigenetic changes do not alter the primary DNA sequence and their reversible nature serves as an excellent basis for prevention and development of novel personalised tumour therapies. Indeed, growing body of evidence suggests that disturbed epigenetic regulation plays a key role in the pathogenesis of meningiomas. Altered DNA methylation, microRNA expression, histone, and chromatin modifications are frequently noted in meningiomas bearing prognostic and therapeutic relevance. In this review we provide an overview on recently identified epigenetic alterations in meningiomas and discuss their role in tumour initiation, progression, and recurrence.
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Venza M, Visalli M, Beninati C, Catalano T, Biondo C, Teti D, Venza I. Involvement of epimutations in meningioma. Brain Tumor Pathol 2015; 32:163-8. [PMID: 25930103 DOI: 10.1007/s10014-015-0221-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 04/21/2015] [Indexed: 01/20/2023]
Abstract
Epimutations are heritable and reversible cell markers, which can influence cell function going beyond the effects of DNA mutations. They result from multiple and coordinated mechanisms able to modulate gene expression. Regarding the significance of epigenetics in meningioma, few and somehow contradictory results are available, although promising information has been obtained. Here we highlight the most recent advances about the impact of DNA methylation, histone modifications, and microRNA regulation on meningioma development as well as the interplay between genetic and epigenetic alterations. Data indicate that epigenetics can help to identify novel candidate genes for the management and treatment of meningioma.
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Affiliation(s)
- Mario Venza
- Department of Experimental Specialized Medical and Surgical and Odontostomatology Sciences, University of Messina, Messina, Italy
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Torres-Martín M, Lassaletta L, de Campos JM, Isla A, Pinto GR, Burbano RR, Melendez B, Castresana JS, Rey JA. Genome-wide methylation analysis in vestibular schwannomas shows putative mechanisms of gene expression modulation and global hypomethylation at the HOX gene cluster. Genes Chromosomes Cancer 2014; 54:197-209. [PMID: 25533176 DOI: 10.1002/gcc.22232] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 11/09/2014] [Accepted: 11/25/2014] [Indexed: 12/17/2022] Open
Abstract
Schwannomas are tumors that develop from Schwann cells in the peripheral nerves and commonly arise from the vestibular nerve. Vestibular schwannomas can present unilaterally and sporadically or bilaterally when the tumor is associated with neurofibromatosis Type 2 (NF2) syndrome. The molecular hallmark of the disease is biallelic inactivation of the NF2 gene. The epigenetic signature of schwannomas remains poorly understood and is mostly limited to DNA methylation of the NF2 gene, whose altered expression due to epigenetic factors in this tumor is controversial. In this study, we tested the genomewide DNA methylation pattern of schwannomas to shed light on this epigenetic alteration in these particular tumors. The methodology used includes Infinium Human Methylation 450K BeadChip microarrays in a series of 36 vestibular schwannomas, 4 nonvestibular schwannomas, and 5 healthy nerves. Our results show a trend toward hypomethylation in schwannomas. Furthermore, homeobox (HOX) genes, located at four clusters in the genome, displayed hypomethylation in several CpG sites in the vestibular schwannomas but not in the nonvestibular schwannomas. Several microRNA (miRNA) and protein-coding genes were also found to be hypomethylated at promoter regions and were confirmed as upregulated by expression analysis; including miRNA-21, Met Proto-Oncogene (MET), and PMEPA1. We also detected methylation patterns that might be involved in alternative transcripts of several genes such as NRXN1 or MBP, which would increase the complexity of the methylation and expression patterns. Overall, our results show specific epigenetic signatures in several coding genes and miRNAs that could potentially be used as therapeutic targets.
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Affiliation(s)
- Miguel Torres-Martín
- Molecular Neuro-oncogenetics Laboratory, Research Unit, Hospital Universitario La Paz, IdiPAZ, Madrid, Spain
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Liu Q, Su PF, Zhao S, Shyr Y. Transcriptome-wide signatures of tumor stage in kidney renal clear cell carcinoma: connecting copy number variation, methylation and transcription factor activity. Genome Med 2014; 6:117. [PMID: 25648588 PMCID: PMC4293006 DOI: 10.1186/s13073-014-0117-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 11/26/2014] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Comparative analysis of expression profiles between early and late stage cancers can help to understand cancer progression and metastasis mechanisms and to predict the clinical aggressiveness of cancer. The observed stage-dependent expression changes can be explained by genetic and epigenetic alterations as well as transcription dysregulation. Unlike genetic and epigenetic alterations, however, activity changes of transcription factors, generally occurring at the post-transcriptional or post-translational level, are hard to detect and quantify. METHODS Here we developed a statistical framework to infer the activity changes of transcription factors by simultaneously taking into account the contributions of genetic and epigenetic alterations to mRNA expression variations. RESULTS Applied to kidney renal clear cell carcinoma (KIRC), the model underscored the role of methylation as a significant contributor to stage-dependent expression alterations and identified key transcription factors as potential drivers of cancer progression. CONCLUSIONS Integrating copy number, methylation, and transcription factor activity signatures to explain stage-dependent expression alterations presented a precise and comprehensive view on the underlying mechanisms during KIRC progression.
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Affiliation(s)
- Qi Liu
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232 USA ; Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232 USA
| | - Pei-Fang Su
- Department of Statistics, National Cheng Kung University, Tainan, 70101 Taiwan
| | - Shilin Zhao
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232 USA
| | - Yu Shyr
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232 USA ; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232 USA ; Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37232 USA ; School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
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He S, Pham MH, Pease M, Zada G, Giannotta SL, Wang K, Mack WJ. A review of epigenetic and gene expression alterations associated with intracranial meningiomas. Neurosurg Focus 2014; 35:E5. [PMID: 24289130 DOI: 10.3171/2013.10.focus13360] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECT A more comprehensive understanding of the epigenetic abnormalities associated with meningioma tumorigenesis, growth, and invasion may provide useful targets for molecular classification and development of targeted therapies for meningiomas. METHODS The authors performed a review of the current literature to identify the epigenetic modifications associated with the formation and/or progression of meningiomas. RESULTS Several epigenomic alterations, mainly pertaining to DNA methylation, have been associated with meningiomas. Hypermethylation of TIMP3 inactivates its tumor suppression activity while CDKN2 (p14[ARF]) and TP73 gene hypermethylation and HIST1H1c upregulation interact with the p53 regulation of cell cycle control. Other factors such as HOX, IGF, WNK2, and TGF-β epigenetic modifications allow either upregulation or downregulation of critical pathways for meningioma development, progression, and recurrence. CONCLUSIONS Genome-wide methylation profiling demonstrated that global hypomethylation correlates with tumor grades and severity. Identification of additional epigenetic changes, such as histone modification and higher-order chromosomal structure, may allow for a more thorough understanding of tumorigenesis and enable future individualized treatment strategies for meningiomas.
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Genomic and transcriptomic analyses match medulloblastoma mouse models to their human counterparts. Acta Neuropathol 2014; 128:123-36. [PMID: 24871706 DOI: 10.1007/s00401-014-1297-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/08/2014] [Accepted: 05/19/2014] [Indexed: 12/15/2022]
Abstract
Medulloblastoma is a malignant embryonal brain tumor with highly variable outcome. In order to study the biology of this tumor and to perform preclinical treatment studies, a lot of effort has been put into the generation of appropriate mouse models. The usage of these models, however, has become debatable with the advances in human medulloblastoma subgrouping. This study brings together multiple relevant mouse models and matches genetic alterations and gene expression data of 140 murine tumors with 423 human medulloblastomas in a global way. Using AGDEX analysis and k-means clustering, we show that the Blbp-cre::Ctnnb1(ex3)(Fl/+)Trp53 (Fl/Fl) mouse model fits well to human WNT medulloblastoma, and that, among various Myc- or Mycn-based mouse medulloblastomas, tumors in Glt1-tTA::TRE-MYCN/Luc mice proved to be most specific for human group 3 medulloblastoma. None of the analyzed models displayed a significant match to group 4 tumors. Intriguingly, mice with Ptch1 or Smo mutations selectively modeled SHH medulloblastomas of adulthood, although such mutations occur in all human age groups. We therefore suggest that the infantile or adult gene expression pattern of SHH MBs are not solely determined by specific mutations. This is supported by the observation that human medulloblastomas with PTCH1 mutations displayed more similarities to PTCH1 wild-type tumors of the same age group than to PTCH1-mutated tumors of the other age group. Together, we provide novel insights into previously unrecognized specificity of distinct models and suggest these findings as a solid basis to choose the appropriate model for preclinical studies on medulloblastoma.
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Li Q, Ding C, Chen C, Zhang Z, Xiao H, Xie F, Lei L, Chen Y, Mao B, Jiang M, Li J, Wang D, Wang G. miR-224 promotion of cell migration and invasion by targeting Homeobox D 10 gene in human hepatocellular carcinoma. J Gastroenterol Hepatol 2014; 29:835-42. [PMID: 24219032 DOI: 10.1111/jgh.12429] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/24/2013] [Indexed: 01/23/2023]
Abstract
BACKGROUND AND AIM MicroRNAs (miRNAs) are small noncoding RNA molecules that control target gene expression and are implicated in the regulation of diverse cellular pathways. In our previous research, we have demonstrated that miR-224 was overexpressed in liver cancer cells and tissues, which was an important factor in the regulation of cell migration and invasion. This study aimed to further explore the regulatory mechanism of miR-224 in the migration and invasion in liver cancer cells. METHODS A luciferase reporter assay was used to confirm that the HOXD10 gene was a direct target of miR-224. Quantitative reverse transcriptase-polymerase chain reaction, Western blotting, Transwell migration, and Matrigel invasion assays were performed to clarify the molecular mechanism of miR-224 in the regulation of cell migration and invasion in human hepatocellular carcinoma (HCC). RESULTS (i) The expression of miR-224 was strongly upregulated in MHHC97H and MHCC97L cells, and its expression level was significantly associated with cell invasive potential. (ii) The HOXD10 gene was confirmed to be a direct target of miR-224. Compared with normal liver tissues and cells, HOXD10 had lower expression in HCC tissues and cells and inversely regulated HCC cell invasion. (iii) miR-224 promoted expression of the tumor invasion-associated proteins p-PAK4 and MMP-9 by directly targeting HOXD10. CONCLUSION Our findings suggest a previously undescribed regulatory pathway in which the miR-224/HOXD10/p-PAK4/MMP-9 signaling pathway contributes to the regulation of cell migration and invasion and provides a new biotarget for HCC treatment.
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Affiliation(s)
- Qiong Li
- Experimental Center of Basic Medicine, College of Basic Medical Science, Third Military Medical University, Chongqing, China
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Meethal SV, Hogan KJ, Mayanil CS, Iskandar BJ. Folate and epigenetic mechanisms in neural tube development and defects. Childs Nerv Syst 2013; 29:1427-33. [PMID: 24013316 DOI: 10.1007/s00381-013-2162-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 05/13/2013] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Multiple genetic and epigenetic factors involved in central nervous system (CNS) development influence the incidence of neural tube defects (NTDs). DISCUSSION The beneficial effect of periconceptional folic acid on NTD prevention denotes a vital role for the single-carbon biochemical pathway in NTD genesis. Indeed, NTDs are associated with polymorphisms in a diversity of genes that encode folate pathway enzymes. Recent evidence suggests that CNS development and function, and consequently NTDs, are also associated with epigenetic mechanisms, many of which participate in the folate cycle and its input and output pathways. We provide an overview with select examples drawn from the authors' research.
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Affiliation(s)
- Sivan Vadakkadath Meethal
- Department of Neurological Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, WI 53792, USA
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DNA methylation in the malignant transformation of meningiomas. PLoS One 2013; 8:e54114. [PMID: 23349797 PMCID: PMC3551961 DOI: 10.1371/journal.pone.0054114] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 12/10/2012] [Indexed: 11/19/2022] Open
Abstract
Meningiomas are central nervous system tumors that originate from the meningeal coverings of the brain and spinal cord. Most meningiomas are pathologically benign or atypical, but 3-5% display malignant features. Despite previous studies on benign and atypical meningiomas, the key molecular pathways involved in malignant transformation remain to be determined, as does the extent of epigenetic alteration in malignant meningiomas. In this study, we explored the landscape of DNA methylation in ten benign, five atypical and four malignant meningiomas. Compared to the benign tumors, the atypical and malignant meningiomas demonstrate increased global DNA hypomethylation. Clustering analysis readily separates malignant from atypical and benign tumors, implicating that DNA methylation patterns may serve as diagnostic biomarkers for malignancy. Genes with hypermethylated CpG islands in malignant meningiomas (such as HOXA6 and HOXA9) tend to coincide with the binding sites of polycomb repressive complexes (PRC) in early developmental stages. Most genes with hypermethylated CpG islands at promoters are suppressed in malignant and benign meningiomas, suggesting the switching of gene silencing machinery from PRC binding to DNA methylation in malignant meningiomas. One exception is the MAL2 gene that is highly expressed in benign group and silenced in malignant group, representing de novo gene silencing induced by DNA methylation. In summary, our results suggest that malignant meningiomas have distinct DNA methylation patterns compared to their benign and atypical counterparts, and that the differentially methylated genes may serve as diagnostic biomarkers or candidate causal genes for malignant transformation.
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