1
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Muhammad N, Fasih S, Malik B, Hameed S, Loya A, Rashid MU. Predominance of MGMT promoter methylation among Pakistani glioblastoma patients. Mol Biol Rep 2024; 51:433. [PMID: 38520591 DOI: 10.1007/s11033-024-09363-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/16/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND Glioblastoma multiforme (GBM), the most prevalent subgroup of neuroepithelial tumors, is characterized by dismal overall survival (OS). Several studies have linked O6-methylguanine-DNA-methyltransferase (MGMT) promoter methylation to OS in GBM patients. However, MGMT methylation frequencies vary geographically and across ethnicities, with limited data for South Asian populations, including Pakistan. This study aimed to analyze MGMT promoter methylation in Pakistani GBM patients. METHODS Consecutive primary GBM patients diagnosed ≥ 18 years-of-age, with no prior chemotherapy or radiotherapy history, were retrospectively selected. DNA was isolated from formalin-fixed-paraffin-embedded tissues. MGMT promoter methylation was analyzed using methylation-specific PCR. Clinical, pathological, and treatment data were assessed using Fisher's exact/Chi-squared tests. OS was calculated using Kaplan-Meier analysis in SPSS 27.0.1. RESULTS The study included 48 GBM patients, comprising 38 (79.2%) males and 10 (20.8%) females. The median diagnosis age was 49.5 years (range 18-70). MGMT methylation was observed in 87.5% (42/48) of all cases. Patients with MGMT methylation undergoing radiotherapy or radiotherapy plus chemotherapy exhibited significantly improved median OS of 7.2 months (95% CI, 3.7-10.7; P < 0.001) and 16.9 months (95% CI, 15.9-17.9; P < 0.001), respectively, compared to those undergoing surgical resection only (OS: 2.2 months, 95% CI, 0.8-3.6). CONCLUSION This is the first comprehensive study highlighting a predominance of MGMT methylation in Pakistani GBM patients. Furthermore, our findings underscore the association of MGMT methylation with improved OS across diverse treatment modalities. Larger studies are imperative to validate our findings for better management of Pakistani GBM patients.
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Affiliation(s)
- Noor Muhammad
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Samir Fasih
- Department of Medical Oncology, SKMCH&RC, Lahore, Pakistan
| | - Bilal Malik
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Shahid Hameed
- Department of Radiation Oncology, SKMCH&RC, Lahore, Pakistan
| | - Asif Loya
- Department of Pathology, SKMCH&RC, Lahore, Pakistan
| | - Muhammad Usman Rashid
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan.
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2
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Harachi M, Masui K, Shimizu E, Murakami K, Onizuka H, Muragaki Y, Kawamata T, Nakayama H, Miyata M, Komori T, Cavenee WK, Mischel PS, Kurata A, Shibata N. DNA hypomethylator phenotype reprograms glutamatergic network in receptor tyrosine kinase gene-mutated glioblastoma. Acta Neuropathol Commun 2024; 12:40. [PMID: 38481314 PMCID: PMC10935831 DOI: 10.1186/s40478-024-01750-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/25/2024] [Indexed: 03/17/2024] Open
Abstract
DNA methylation is crucial for chromatin structure and gene expression and its aberrancies, including the global "hypomethylator phenotype", are associated with cancer. Here we show that an underlying mechanism for this phenotype in the large proportion of the highly lethal brain tumor glioblastoma (GBM) carrying receptor tyrosine kinase gene mutations, involves the mechanistic target of rapamycin complex 2 (mTORC2), that is critical for growth factor signaling. In this scenario, mTORC2 suppresses the expression of the de novo DNA methyltransferase (DNMT3A) thereby inducing genome-wide DNA hypomethylation. Mechanistically, mTORC2 facilitates a redistribution of EZH2 histone methyltransferase into the promoter region of DNMT3A, and epigenetically represses the expression of DNA methyltransferase. Integrated analyses in both orthotopic mouse models and clinical GBM samples indicate that the DNA hypomethylator phenotype consistently reprograms a glutamate metabolism network, eventually driving GBM cell invasion and survival. These results nominate mTORC2 as a novel regulator of DNA hypomethylation in cancer and an exploitable target against cancer-promoting epigenetics.
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Affiliation(s)
- Mio Harachi
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Kenta Masui
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan.
| | - Erika Shimizu
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Kumiko Murakami
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Hiromi Onizuka
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Yoshihiro Muragaki
- Department of Neurosurgery, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
- Center for Advanced Medical Engineering Research and Development, Kobe University, Kobe, Hyogo, 650-0047, Japan
| | - Takakazu Kawamata
- Department of Neurosurgery, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Hisako Nakayama
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Mariko Miyata
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Takashi Komori
- Department of Neuropathology, Tokyo Metropolitan Neurological Hospital, Musashinodai, Tokyo, 156-8506, Japan
| | - Webster K Cavenee
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA, 92093, USA
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Atsushi Kurata
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Noriyuki Shibata
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
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3
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Guerini C, Furlan D, Ferrario G, Grillo F, Libera L, Arpa G, Klersy C, Lenti MV, Riboni R, Solcia E, Fassan M, Mastracci L, Ardizzone S, Moens A, De Hertogh G, Ferrante M, Graham RP, Sessa F, Paulli M, Di Sabatino A, Vanoli A. IDH1-mutated Crohn's disease-associated small bowel adenocarcinomas: Distinctive pathological features and association with MGMT methylation and serrated-type dysplasia. Histopathology 2024; 84:515-524. [PMID: 37988281 DOI: 10.1111/his.15095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/04/2023] [Accepted: 10/28/2023] [Indexed: 11/23/2023]
Abstract
AIMS Patients with Crohn's disease (CrD) have an elevated risk for the development of small bowel adenocarcinomas (SBAs). Actionable isocitrate dehydrogenase 1 (IDH1) mutations have been reported to be more frequent in CrD-SBAs than in sporadic SBAs. The present study aimed to investigate the clinicopathological and immunophenotypical features, as well as methylation profiles, of IDH1-mutated CrD-SBAs. METHODS AND RESULTS An international multicentre series of surgically resected CrD-SBAs was tested for IDH1 mutation. Clinicopathological features, immunophenotypical marker expression and O6-methylguanine-DNA methyltransferase (MGMT) and long interspersed nuclear element-1 (LINE-1) methylation were compared between IDH1-mutated and IDH1 wild-type CrD-SBAs. Ten (20%) of the 49 CrD-SBAs examined harboured an IDH1 mutation and all the mutated cancers harboured the R132C variant. Compared to IDH1 wild-type cases, IDH1-mutated CrD-SBAs showed significantly lower rates of cytokeratin 7 expression (P = 0.005) and higher rates of p53 overexpression (P = 0.012) and MGMT methylation (P = 0.012). All three dysplastic growths associated with IDH1-mutated SBAs harboured the same IDH1 variant (R132C) of the corresponding invasive cancer, and all were of non-conventional subtype (two serrated dysplastic lesions and one goblet cell-deficient dysplasia). In particular, non-conventional serrated dysplasia was significantly associated with IDH1-mutated CrD-SBAs (P = 0.029). No significant cancer-specific survival difference between IDH1-mutated CrD-SBA patients and IDH1 wild-type CrD-SBA patients was found (hazard ratio = 0.55, 95% confidence interval = 0.16-1.89; P = 0.313). CONCLUSIONS IDH1-mutated CrD-SBAs, which represent approximately one-fifth of total cases, are characterised by distinctive immunophenotypical features and methylation profiles, with potential therapeutic implications. Moreover, IDH1-mutated non-conventional, serrated dysplasia is likely to represent a precursor lesion to such CrD-SBAs.
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Affiliation(s)
- Camilla Guerini
- Department of Molecular Medicine, Unit of Anatomic Pathology, University of Pavia, Pavia, Italy
- Unit of Anatomic Pathology, Fondazione IRCCS San Matteo Hospital, Pavia, Italy
| | - Daniela Furlan
- Pathology Unit, Department of Medicine and Technological Innovation, University of Insubria, Varese, Italy
| | - Giuseppina Ferrario
- Department of Molecular Medicine, Unit of Anatomic Pathology, University of Pavia, Pavia, Italy
- Unit of Anatomic Pathology, Fondazione IRCCS San Matteo Hospital, Pavia, Italy
| | - Federica Grillo
- Pathology Unit, Department of Surgical and Diagnostic Sciences, University of Genoa, Genoa, Italy
- Ospedale Policlinico San Martino University Hospital, Genoa, Italy
| | - Laura Libera
- Pathology Unit, Department of Medicine and Technological Innovation, University of Insubria, Varese, Italy
| | - Giovanni Arpa
- Department of Molecular Medicine, Unit of Anatomic Pathology, University of Pavia, Pavia, Italy
| | - Catherine Klersy
- Clinical Epidemiology and Biometry, IRCCS San Matteo Hospital Foundation, University of Pavia, Pavia, Italy
| | - Marco V Lenti
- Department of Internal Medicine and Medical Therapeutics, University of Pavia, Pavia, Italy
- First Department of Internal Medicine, IRCCS San Matteo Hospital Foundation, Pavia, Italy
| | - Roberta Riboni
- Unit of Anatomic Pathology, Fondazione IRCCS San Matteo Hospital, Pavia, Italy
| | - Enrico Solcia
- Department of Molecular Medicine, Unit of Anatomic Pathology, University of Pavia, Pavia, Italy
| | - Matteo Fassan
- Surgical Pathology and Cytopathology Unit, Department of Medicine, DIMED, University of Padua, Padua, Italy
- Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | - Luca Mastracci
- Pathology Unit, Department of Surgical and Diagnostic Sciences, University of Genoa, Genoa, Italy
- Ospedale Policlinico San Martino University Hospital, Genoa, Italy
| | - Sandro Ardizzone
- Gastroenterology Unit, Luigi Sacco University Hospital, Milan, Italy
| | - Annick Moens
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Gert De Hertogh
- Department of Pathology, KU Leuven University Hospitals, Leuven, Belgium
| | - Marc Ferrante
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Rondell P Graham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Fausto Sessa
- Pathology Unit, Department of Medicine and Technological Innovation, University of Insubria, Varese, Italy
| | - Marco Paulli
- Department of Molecular Medicine, Unit of Anatomic Pathology, University of Pavia, Pavia, Italy
- Unit of Anatomic Pathology, Fondazione IRCCS San Matteo Hospital, Pavia, Italy
| | - Antonio Di Sabatino
- Department of Internal Medicine and Medical Therapeutics, University of Pavia, Pavia, Italy
- First Department of Internal Medicine, IRCCS San Matteo Hospital Foundation, Pavia, Italy
| | - Alessandro Vanoli
- Department of Molecular Medicine, Unit of Anatomic Pathology, University of Pavia, Pavia, Italy
- Unit of Anatomic Pathology, Fondazione IRCCS San Matteo Hospital, Pavia, Italy
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4
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Demir S, Razizadeh N, Indersie E, Branchereau S, Cairo S, Kappler R. Targeting G9a/DNMT1 methyltransferase activity impedes IGF2-mediated survival in hepatoblastoma. Hepatol Commun 2024; 8:e0378. [PMID: 38285887 PMCID: PMC10830081 DOI: 10.1097/hc9.0000000000000378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/12/2023] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND As the variable clinical outcome of patients with hepatoblastoma (HB) cannot be explained by genetics alone, the identification of drugs with the potential to effectively reverse epigenetic alterations is a promising approach to overcome poor therapy response. The gene ubiquitin like with PHD and ring finger domains 1 (UHRF1) represents an encouraging epigenetic target due to its regulatory function in both DNA methylation and histone modifications and its clinical relevance in HB. METHODS Patient-derived xenograft in vitro and in vivo models were used to study drug response. The mechanistic basis of CM-272 treatment was elucidated using RNA sequencing and western blot experiments. RESULTS We validated in comprehensive data sets that UHRF1 is highly expressed in HB and associated with poor outcomes. The simultaneous pharmacological targeting of UHRF1-dependent DNA methylation and histone H3 methylation by the dual inhibitor CM-272 identified a selective impact on HB patient-derived xenograft cell viability while leaving healthy fibroblasts unaffected. RNA sequencing revealed downregulation of the IGF2-activated survival pathway as the main mode of action of CM-272 treatment, subsequently leading to loss of proliferation, hindered colony formation capability, reduced spheroid growth, decreased migration potential, and ultimately, induction of apoptosis in HB cells. Importantly, drug response depended on the level of IGF2 expression, and combination assays showed a strong synergistic effect of CM-272 with cisplatin. Preclinical testing of CM-272 in a transplanted patient-derived xenograft model proved its efficacy but also uncovered side effects presumably caused by its strong antitumor effect in IGF2-driven tumors. CONCLUSIONS The inhibition of UHRF1-associated epigenetic traces, such as IGF2-mediated survival, is an attractive approach to treat high-risk HB, especially when combined with the standard-of-care therapeutic cisplatin.
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Affiliation(s)
- Salih Demir
- Department of Pediatric Surgery, Dr. von Hauner Children’s Hospital, LMU University Hospital, LMU Munich, Germany
| | - Negin Razizadeh
- Department of Pediatric Surgery, Dr. von Hauner Children’s Hospital, LMU University Hospital, LMU Munich, Germany
| | | | - Sophie Branchereau
- Department of Pediatric Surgery, Bicêtre Hospital, AP-HP Paris Saclay University, France
| | - Stefano Cairo
- XenTech, Evry, France
- Champions Oncology, Inc., Rockville, Maryland, USA
| | - Roland Kappler
- Department of Pediatric Surgery, Dr. von Hauner Children’s Hospital, LMU University Hospital, LMU Munich, Germany
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5
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Weller M, Felsberg J, Hentschel B, Gramatzki D, Kubon N, Wolter M, Reusche M, Roth P, Krex D, Herrlinger U, Westphal M, Tonn JC, Regli L, Maurage CA, von Deimling A, Pietsch T, Le Rhun E, Reifenberger G. Improved prognostic stratification of patients with isocitrate dehydrogenase-mutant astrocytoma. Acta Neuropathol 2024; 147:11. [PMID: 38183430 PMCID: PMC10771615 DOI: 10.1007/s00401-023-02662-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 01/08/2024]
Abstract
Prognostic factors and standards of care for astrocytoma, isocitrate dehydrogenase (IDH)-mutant, CNS WHO grade 4, remain poorly defined. Here we sought to explore disease characteristics, prognostic markers, and outcome in patients with this newly defined tumor type. We determined molecular biomarkers and assembled clinical and outcome data in patients with IDH-mutant astrocytomas confirmed by central pathology review. Patients were identified in the German Glioma Network cohort study; additional cohorts of patients with CNS WHO grade 4 tumors were identified retrospectively at two sites. In total, 258 patients with IDH-mutant astrocytomas (114 CNS WHO grade 2, 73 CNS WHO grade 3, 71 CNS WHO grade 4) were studied. The median age at diagnosis was similar for all grades. Karnofsky performance status at diagnosis inversely correlated with CNS WHO grade (p < 0.001). Despite more intensive treatment upfront with higher grade, CNS WHO grade was strongly prognostic: median overall survival was not reached for grade 2 (median follow-up 10.4 years), 8.1 years (95% CI 5.4-10.8) for grade 3, and 4.7 years (95% CI 3.4-6.0) for grade 4. Among patients with CNS WHO grade 4 astrocytoma, median overall survival was 5.5 years (95% CI 4.3-6.7) without (n = 58) versus 1.8 years (95% CI 0-4.1) with (n = 12) homozygous CDKN2A deletion. Lower levels of global DNA methylation as detected by LINE-1 methylation analysis were strongly associated with CNS WHO grade 4 (p < 0.001) and poor outcome. MGMT promoter methylation status was not prognostic for overall survival. Histomolecular stratification based on CNS WHO grade, LINE-1 methylation level, and CDKN2A status revealed four subgroups of patients with significantly different outcomes. In conclusion, CNS WHO grade, global DNA methylation status, and CDKN2A homozygous deletion are prognostic in patients with IDH-mutant astrocytoma. Combination of these parameters allows for improved prediction of outcome. These data aid in designing upcoming trials using IDH inhibitors.
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Affiliation(s)
- Michael Weller
- Department of Neurology, University Hospital Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland.
- Department of Neurology, University of Zurich, Zurich, Switzerland.
| | - Jörg Felsberg
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Bettina Hentschel
- Institute for Medical Informatics, Statistics and Epidemiology, University Leipzig, Leipzig, Germany
| | - Dorothee Gramatzki
- Department of Neurology, University Hospital Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
| | - Nadezhda Kubon
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Marietta Wolter
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Matthias Reusche
- Institute for Medical Informatics, Statistics and Epidemiology, University Leipzig, Leipzig, Germany
| | - Patrick Roth
- Department of Neurology, University Hospital Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
- Department of Neurology, University of Zurich, Zurich, Switzerland
| | - Dietmar Krex
- Faculty of Medicine, Department of Neurosurgery, Technische Universität Dresden, University Hospital Carl Gustav Carus, Dresden, Germany
| | | | - Manfred Westphal
- Department of Neurosurgery, University of Hamburg, Hamburg, Germany
| | - Joerg C Tonn
- Department of Neurosurgery, Ludwig-Maximilians-University Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Luca Regli
- Department of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Department of Neurosurgery, University of Zurich, Zurich, Switzerland
| | - Claude-Alain Maurage
- Department of Pathology, Centre Biologie Pathologie, Lille University Hospital, Hopital Nord, Lille, France
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Center (DKFZ), and German Cancer Consortium (DKTK), Partner Site Heidelberg, Heidelberg, Germany
| | - Torsten Pietsch
- Department of Neuropathology, University of Bonn Medical Center, DGNN Brain Tumor Reference Center, Bonn, Germany
| | - Emilie Le Rhun
- Department of Neurology, University Hospital Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
- Department of Neurology, University of Zurich, Zurich, Switzerland
- Department of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Department of Neurosurgery, University of Zurich, Zurich, Switzerland
- Department of Neurosurgery, Lille University Hospital, Lille, France
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, and University Hospital Düsseldorf, Düsseldorf, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Düsseldorf, Germany
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Zhu L, Yuan F, Wang X, Zhu R, Guo W. Cuproptosis-related gene-located DNA methylation in lower-grade glioma: Prognosis and tumor microenvironment. Cancer Biomark 2024; 40:185-198. [PMID: 38578883 PMCID: PMC11307024 DOI: 10.3233/cbm-230341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 02/01/2024] [Indexed: 04/07/2024]
Abstract
Cuproptosis a novel copper-dependent cell death modality, plays a crucial part in the oncogenesis, progression and prognosis of tumors. However, the relationships among DNA-methylation located in cuproptosis-related genes (CRGs), overall survival (OS) and the tumor microenvironment remain undefined. In this study, we systematically assessed the prognostic value of CRG-located DNA-methylation for lower-grade glioma (LGG). Clinical and molecular data were sourced from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. We employed Cox hazard regression to examine the associations between CRG-located DNA-methylation and OS, leading to the development of a prognostic signature. Kaplan-Meier survival and time-dependent receiver operating characteristic (ROC) analyses were utilized to gauge the accuracy of the signature. Gene Set Enrichment Analysis (GSEA) was applied to uncover potential biological functions of differentially expressed genes between high- and low-risk groups. A three CRG-located DNA-methylation prognostic signature was established based on TCGA database and validated in GEO dataset. The 1-year, 3-year, and 5-year area under the curve (AUC) of ROC curves in the TCGA dataset were 0.884, 0.888, and 0.859 while those in the GEO dataset were 0.943, 0.761 and 0.725, respectively. Cox-regression-analyses revealed the risk signature as an independent risk factor for LGG patients. Immunogenomic profiling suggested that the signature was associated with immune infiltration level and immune checkpoints. Functional enrichment analysis indicated differential enrichment in cell differentiation in the hindbrain, ECM receptor interactions, glycolysis and reactive oxygen species pathway across different groups. We developed and verified a novel CRG-located DNA-methylation signature to predict the prognosis in LGG patients. Our findings emphasize the potential clinical implications of CRG-located DNA-methylation indicating that it may serve as a promising therapeutic target for LGG patients.
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Affiliation(s)
- Liucun Zhu
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Fa Yuan
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Xue Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Rui Zhu
- School of Life Sciences, Shanghai University, Shanghai, China
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai, China
| | - Wenna Guo
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
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Masui K, Mischel PS. Metabolic and epigenetic reprogramming in the pathogenesis of glioblastoma: Toward the establishment of "metabolism-based pathology". Pathol Int 2023; 73:533-541. [PMID: 37755062 DOI: 10.1111/pin.13379] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/03/2023] [Indexed: 09/28/2023]
Abstract
Molecular genetic approaches are now mandatory for cancer diagnostics, especially for brain tumors. Genotype-based diagnosis has predominated over the phenotype-based approach, with its prognostic and predictive powers. However, comprehensive genetic testing would be difficult to perform in the clinical setting, and translational research is required to histologically decipher the peculiar biology of cancer. Of interest, recent studies have demonstrated discrete links between oncogenotypes and the resultant metabolic phenotypes, revealing cancer metabolism as a promising histologic surrogate to reveal specific characteristics of each cancer type and indicate the best way to manage cancer patients. Here, we provide an overview of our research progress to work on cancer metabolism, with a particular focus on the genomically well-characterized malignant tumor glioblastoma. With the use of clinically relevant animal models and human tissue, we found that metabolic reprogramming plays a major role in the aggressive cancer biology by conferring therapeutic resistance to cancer cells and rewiring their epigenomic landscapes. We further discuss our future endeavor to establish "metabolism-based pathology" on how the basic knowledge of cancer metabolism could be leveraged to improve the management of patients by linking cancer cell genotype, epigenotype, and phenotype through metabolic reprogramming.
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Affiliation(s)
- Kenta Masui
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Paul S Mischel
- Department of Pathology, Stanford University, Stanford, California, USA
- Department of Neurosurgery, Stanford University, Stanford, California, USA
- Sarafan ChEM-H, Stanford University, Stanford, California, USA
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8
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Skouras P, Markouli M, Kalamatianos T, Stranjalis G, Korkolopoulou P, Piperi C. Advances on Liquid Biopsy Analysis for Glioma Diagnosis. Biomedicines 2023; 11:2371. [PMID: 37760812 PMCID: PMC10525418 DOI: 10.3390/biomedicines11092371] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Gliomas comprise the most frequent primary central nervous system (CNS) tumors, characterized by remarkable genetic and epigenetic heterogeneity, difficulty in monitoring, and increased relapse and mortality rates. Tissue biopsy is an established method of tumor cell collection and analysis that enables diagnosis, classification of different tumor types, and prediction of prognosis upon confirmation of tumor's location for surgical removal. However, it is an invasive and often challenging procedure that cannot be used for frequent patient screening, detection of mutations, disease monitoring, or resistance to therapy. To this end, the minimally invasive procedure of liquid biopsy has emerged, allowing effortless tumor sampling and enabling continuous monitoring. It is considered a novel preferable way to obtain faster data on potential tumor risk, personalized diagnosis, prognosis, and recurrence evaluation. The purpose of this review is to describe the advances on liquid biopsy for glioma diagnosis and management, indicating several biomarkers that can be utilized to analyze tumor characteristics, such as cell-free DNA (cfDNA), cell-free RNA (cfRNA), circulating proteins, circulating tumor cells (CTCs), and exosomes. It further addresses the benefit of combining liquid biopsy with radiogenomics to facilitate early and accurate diagnoses, enable precise prognostic assessments, and facilitate real-time disease monitoring, aiming towards more optimal treatment decisions.
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Affiliation(s)
- Panagiotis Skouras
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
- 1st Department of Neurosurgery, Evangelismos Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (T.K.); (G.S.)
| | - Mariam Markouli
- Department of Medicine, Boston Medical Center, Boston University School of Medicine, Boston, MA 02118, USA;
| | - Theodosis Kalamatianos
- 1st Department of Neurosurgery, Evangelismos Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (T.K.); (G.S.)
| | - George Stranjalis
- 1st Department of Neurosurgery, Evangelismos Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (T.K.); (G.S.)
| | - Penelope Korkolopoulou
- Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street, 11527 Athens, Greece;
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
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Suzuki MM, Iijima K, Ogami K, Shinjo K, Murofushi Y, Xie J, Wang X, Kitano Y, Mamiya A, Kibe Y, Nishimura T, Ohka F, Saito R, Sato S, Kobayashi J, Yao R, Miyata K, Kataoka K, Suzuki HI, Kondo Y. TUG1-mediated R-loop resolution at microsatellite loci as a prerequisite for cancer cell proliferation. Nat Commun 2023; 14:4521. [PMID: 37607907 PMCID: PMC10444773 DOI: 10.1038/s41467-023-40243-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/19/2023] [Indexed: 08/24/2023] Open
Abstract
Oncogene-induced DNA replication stress (RS) and consequent pathogenic R-loop formation are known to impede S phase progression. Nonetheless, cancer cells continuously proliferate under such high-stressed conditions through incompletely understood mechanisms. Here, we report taurine upregulated gene 1 (TUG1) long noncoding RNA (lncRNA), which is highly expressed in many types of cancers, as an important regulator of intrinsic R-loop in cancer cells. Under RS conditions, TUG1 is rapidly upregulated via activation of the ATR-CHK1 signaling pathway, interacts with RPA and DHX9, and engages in resolving R-loops at certain loci, particularly at the CA repeat microsatellite loci. Depletion of TUG1 leads to overabundant R-loops and enhanced RS, leading to substantial inhibition of tumor growth. Our data reveal a role of TUG1 as molecule important for resolving R-loop accumulation in cancer cells and suggest targeting TUG1 as a potent therapeutic approach for cancer treatment.
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Affiliation(s)
- Miho M Suzuki
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Kenta Iijima
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
- Laboratory Animal Facilities and Services, Preeminent Medical Photonics Education and Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Koichi Ogami
- Division of Molecular Oncology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Keiko Shinjo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Yoshiteru Murofushi
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Jingqi Xie
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Xuebing Wang
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Yotaro Kitano
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Akira Mamiya
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Yuji Kibe
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Tatsunori Nishimura
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Fumiharu Ohka
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Ryuta Saito
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Shinya Sato
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, 2-3-2 Nakao, Asahi-ku, Yokohama, Kanagawa, 241-8515, Japan
| | - Junya Kobayashi
- School of Health Sciences at Narita, International University of Health and Welfare, 4-3 Kozunomori, Narita, Chiba, 286-8686, Japan
| | - Ryoji Yao
- Department of Cell Biology, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Kanjiro Miyata
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kazunori Kataoka
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tono-machi, Kawasaki-ku, Kanagawa, 210-0821, Japan
- Institute for Future Initiatives, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroshi I Suzuki
- Division of Molecular Oncology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
- Institute for Glyco-core Research (iGCORE), Tokai National Higher Education and Research System, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Yutaka Kondo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan.
- Institute for Glyco-core Research (iGCORE), Tokai National Higher Education and Research System, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan.
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10
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Kurimoto M, Rockenbach Y, Kato A, Natsume A. Prediction of Tumor Development and Urine-Based Liquid Biopsy for Molecule-Targeted Therapy of Gliomas. Genes (Basel) 2023; 14:1201. [PMID: 37372381 DOI: 10.3390/genes14061201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/21/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
The timing of the acquisition of tumor-specific gene mutations and the systems by which these gene mutations are acquired during tumorigenesis were clarified. Advances in our understanding of tumorigenesis are being made every day, and therapies targeting fundamental genetic alterations have great potential for cancer treatment. Moreover, our research team successfully estimated tumor progression using mathematical modeling and attempted early diagnosis of brain tumors. We developed a nanodevice that enables urinary genetic diagnosis in a simple and noninvasive manner. Mainly on the basis of our research and experience, this review article presents novel therapies being developed for central nervous system cancers and six molecules, which upon mutation cause tumorigenesis and tumor progression. Further understanding of the genetic characteristics of brain tumors will lead to the development of precise drugs and improve individual treatment outcomes.
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Affiliation(s)
- Michihiro Kurimoto
- Department of Neurosurgery, Aichi Children's Health and Medical Center, Obu 464-8710, Japan
| | - Yumi Rockenbach
- Institute of Innovation for Future Society, Nagoya University, Nagoya 464-8601, Japan
| | - Akira Kato
- Institute of Innovation for Future Society, Nagoya University, Nagoya 464-8601, Japan
| | - Atsushi Natsume
- Institute of Innovation for Future Society, Nagoya University, Nagoya 464-8601, Japan
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11
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Wang H, Li W, Yang J, Wang Y, Du H, Han M, Xu L, Liu S, Yi J, Chen Y, Jiang Q, He G. Gestational exposure to perfluoroalkyl substances is associated with placental DNA methylation and birth size. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159747. [PMID: 36309289 DOI: 10.1016/j.scitotenv.2022.159747] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 10/20/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
DNA methylation is one potential mechanism for the effects of gestational exposure to perfluoroalkyl substances (PFASs) on fetal growth. We investigated 180 pregnant women who participated in a cohort study conducted in Tangshan City, Northern China, and determined the concentrations of 11 PFASs and the methylation of two genes related to fetal growth [insulin-like growth factor 2 (IGF2) and nuclear receptor subfamily 3 group C member 1 (NR3C1)] and one surrogate marker for global methylation [long interspersed nuclear element-1 (LINE-1)] in placenta tissue. Multiple linear regression analysis was performed to examine the associations of log transformed PFASs with the DNA methylation and birth size. Weighted quantile sum regression was used to determine the mixture effect of PFASs. After adjusting for potential confounders, perfluorooctane sulfonate (PFOS) was negatively associated with the overall methylation of LINE-1. PFASs mixture was negatively associated with the methylation of all CpG loci of LINE-1 and overall methylation of NR3C1. Perfluorootanoic acid (PFOA), perfluorononanoic acid (PFNA), perfluorodecanoic acid (PFDA), and the PFASs mixture showed negative associations with head circumference. After stratified by newborns' sex, PFOA, PFNA and the PFASs mixture was negatively associated with overall methylation of LINE-1 only in the male subgroup and the methylation of all CpG loci of LINE-1 was negatively associated with ponderal index only in the female subgroup. The interaction of newborns' sex with PFOS and PFOA on overall methylation of IGF2 was statistically significant and so was the interaction of sex with PFOS on overall methylation of LINE-1. These findings suggested that intrauterine exposure to PFASs affected placental DNA methylation and reduced fetal growth, which might be modified by sex.
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Affiliation(s)
- Hexing Wang
- School of Public Health/Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Wenyun Li
- School of Public Health/Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Jiaqi Yang
- School of Public Health/Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Yuanping Wang
- School of Public Health/Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Hongyi Du
- Healthy Lifestyle Medical Center, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Minghui Han
- Healthy Lifestyle Medical Center, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Linji Xu
- Maternal and Child Health Care Hospital, Tangshan, Hebei province, China
| | - Shuping Liu
- Maternal and Child Health Care Hospital, Tangshan, Hebei province, China
| | - Jianping Yi
- Maternal and Child Health Care Hospital, Tangshan, Hebei province, China
| | - Yue Chen
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Qingwu Jiang
- School of Public Health/Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Gengsheng He
- School of Public Health/Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China.
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12
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Casarotto M, Lupato V, Giurato G, Guerrieri R, Sulfaro S, Salvati A, D’Angelo E, Furlan C, Menegaldo A, Baboci L, Montico B, Turturici I, Dolcetti R, Romeo S, Baggio V, Corrado S, Businello G, Guido M, Weisz A, Giacomarra V, Franchin G, Steffan A, Sigalotti L, Vaccher E, Boscolo-Rizzo P, Jerry P, Fanetti G, Fratta E. LINE-1 hypomethylation is associated with poor outcomes in locoregionally advanced oropharyngeal cancer. Clin Epigenetics 2022; 14:171. [PMID: 36503584 PMCID: PMC9743592 DOI: 10.1186/s13148-022-01386-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND AND PURPOSE Currently, human papillomavirus (HPV) positivity represents a strong prognostic factor for both reduced risk of relapse and improved survival in patients with oropharyngeal squamous cell carcinoma (OPSCC). However, a subset of HPV-positive OPSCC patients still experience poor outcomes. Furthermore, HPV-negative OPSCC patients, who have an even higher risk of relapse, are still lacking suitable prognostic biomarkers for clinical outcome. Here, we evaluated the prognostic value of LINE-1 methylation level in OPSCC patients and further addressed the relationship between LINE-1 methylation status and p53 protein expression as well as genome-wide/gene-specific DNA methylation. RESULTS In this study, DNA was extracted from 163 formalin-fixed paraffin-embedded tissue samples retrospectively collected from stage III-IVB OPSCC patients managed with curative intent with up-front treatment. Quantitative methylation-specific PCR revealed that LINE-1 hypomethylation was directly associated with poor prognosis (5-year overall survival-OS: 28.1% for LINE-1 methylation < 35% vs. 69.1% for ≥ 55%; p < 0.0001). When LINE-1 methylation was dichotomized as < 55% versus ≥ 55%, interaction with HPV16 emerged: compared with hypermethylated HPV16-positive patients, subjects with hypomethylated HPV16-negative OPSCC reported an adjusted higher risk of death (HR 4.83, 95% CI 2.24-10.38) and progression (HR 4.54, 95% CI 2.18-9.48). Tumor protein p53 (TP53) gene is often mutated and overexpressed in HPV-negative OPSCC. Since p53 has been reported to repress LINE-1 promoter, we then analyzed the association between p53 protein expression and LINE-1 methylation levels. Following p53 immunohistochemistry, results indicated that among HPV16-negative patients with p53 ≥ 50%, LINE-1 methylation levels declined and remained stable at approximately 43%; any HPV16-positive patient reported p53 ≥ 50%. Finally, DNA methylation analysis demonstrated that genome-wide average methylation level at cytosine-phosphate-guanine sites was significantly lower in HPV16-negative OPSCC patients who relapsed within two years. The subsequent integrative analysis of gene expression and DNA methylation identified 20 up-regulated/hypomethylated genes in relapsed patients, and most of them contained LINE-1 elements in their promoter sequences. CONCLUSIONS Evaluation of the methylation level of LINE-1 may help in identifying the subset of OPSCC patients with bad prognosis regardless of their HPV status. Aberrant LINE-1 hypomethylation might occur along with TP53 mutations and lead to altered gene expression in OPSCC.
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Affiliation(s)
- Mariateresa Casarotto
- grid.414603.4Unit of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Valentina Lupato
- grid.415199.10000 0004 1756 8284Division of Otolaryngology, General Hospital “S. Maria Degli Angeli”, Pordenone, Italy
| | - Giorgio Giurato
- grid.11780.3f0000 0004 1937 0335Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Baronissi, SA Italy ,grid.11780.3f0000 0004 1937 0335Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi, SA Italy
| | - Roberto Guerrieri
- grid.414603.4Unit of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Sandro Sulfaro
- grid.415199.10000 0004 1756 8284Division of Pathology, General Hospital “S. Maria Degli Angeli”, Pordenone, Italy
| | - Annamaria Salvati
- grid.11780.3f0000 0004 1937 0335Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Baronissi, SA Italy ,grid.11780.3f0000 0004 1937 0335Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi, SA Italy ,grid.11780.3f0000 0004 1937 0335Medical Genomics Program, AOU ‘SS. Giovanni di Dio e Ruggi d’Aragona’, University of Salerno, Salerno, Italy
| | - Elisa D’Angelo
- grid.413363.00000 0004 1769 5275Department of Radiation Oncology, University Hospital of Modena, Modena, Italy
| | - Carlo Furlan
- grid.415199.10000 0004 1756 8284Department of Radiation Oncology, General Hospital “San Martino”, Belluno, Italy
| | - Anna Menegaldo
- Unit of Otolaryngology, AULSS 2 - Marca Trevigiana, Treviso, Italy
| | - Lorena Baboci
- grid.414603.4Unit of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Barbara Montico
- grid.414603.4Unit of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Irene Turturici
- grid.418321.d0000 0004 1757 9741Division of Radiotherapy, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, PN Italy
| | - Riccardo Dolcetti
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, VIC 3000 Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010 Australia ,grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC 3010 Australia
| | - Salvatore Romeo
- Department of Services of Diagnosis and Care, Santorso Hospital, Santorso, VI Italy
| | - Vittorio Baggio
- grid.413196.8Department of Radiation Oncology, Treviso Regional Hospital, Treviso, Italy
| | - Stefania Corrado
- grid.413363.00000 0004 1769 5275Department of Anatomy and Pathology, University Hospital of Modena, Modena, Italy
| | - Gianluca Businello
- grid.413196.8Department of Pathology, Treviso Regional Hospital, Treviso, Italy
| | - Maria Guido
- grid.413196.8Department of Pathology, Treviso Regional Hospital, Treviso, Italy ,grid.5608.b0000 0004 1757 3470Department of Medicine (DIMED), University of Padova, Padova, Italy
| | - Alessandro Weisz
- grid.11780.3f0000 0004 1937 0335Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Baronissi, SA Italy ,grid.11780.3f0000 0004 1937 0335Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi, SA Italy ,grid.11780.3f0000 0004 1937 0335Medical Genomics Program, AOU ‘SS. Giovanni di Dio e Ruggi d’Aragona’, University of Salerno, Salerno, Italy
| | - Vittorio Giacomarra
- grid.415199.10000 0004 1756 8284Division of Otolaryngology, General Hospital “S. Maria Degli Angeli”, Pordenone, Italy
| | - Giovanni Franchin
- grid.418321.d0000 0004 1757 9741Division of Radiotherapy, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, PN Italy
| | - Agostino Steffan
- grid.414603.4Unit of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Luca Sigalotti
- grid.414603.4Oncogenetics and Functional Oncogenomics Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Emanuela Vaccher
- grid.414603.4Division of Medical Oncology A, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Paolo Boscolo-Rizzo
- grid.5608.b0000 0004 1757 3470Section of Otolaryngology, Department of Neurosciences, University of Padova, Treviso, Italy
| | - Polesel Jerry
- grid.414603.4Unit of Cancer Epidemiology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Giuseppe Fanetti
- grid.418321.d0000 0004 1757 9741Division of Radiotherapy, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, PN Italy
| | - Elisabetta Fratta
- grid.414603.4Unit of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy ,grid.418321.d0000 0004 1757 9741Division of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Via Franco Gallini, 2, 33081 Aviano, PN Italy
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13
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Issah I, Arko-Mensah J, Rozek LS, Zarins KR, Dwomoh D, Agyekum TP, Basu N, Batterman S, Robins TG, Fobil JN. Association between toxic and essential metals in blood and global DNA methylation among electronic waste workers in Agbogbloshie, Ghana. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:72946-72956. [PMID: 35614359 DOI: 10.1007/s11356-022-20954-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Aberrant global DNA methylation status is a known biomarker for increased disease risk, especially cancer. There is little published data on the association between toxic and essential metal mixtures and global DNA methylation in electronic waste (e-waste) workers. We aimed to establish the association between toxic and essential metals in blood and the effect of their interactions on global DNA methylation among e-waste recyclers and a reference group in Ghana. We used ICP-MS to measure the level of five metals (Se, Zn, Mn, Cd, and Pb) in the blood of 100 e-waste workers and 51 controls. We quantified blood DNA methylation levels of LINE-1 as an indicator of global DNA methylation. Cd, Mn, and Se levels were significantly higher in the reference group than in e-waste workers. Only Pb was significantly higher in the e-waste workers compared to the controls. Our linear regression analysis results showed a significant inverse association between Zn and LINE-1 DNA methylation (βZn = - 0.912; 95% CI, - 1.512, - 0.306; p = 0.003) which corresponds to a 0.009 decrease in %LINE-1 methylation (95% CI, - 0.015, - 0.003; p = 0.003) for a 1% increase in Zn concentration. Potential interactions between Cd and Zn on global DNA methylation were observed. In summary, co-exposure to toxic and essential metals is associated with global (LINE-1) DNA methylation.
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Affiliation(s)
- Ibrahim Issah
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Accra, Ghana.
| | - John Arko-Mensah
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Accra, Ghana
| | - Laura S Rozek
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Katie R Zarins
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Duah Dwomoh
- Department of Biostatistics, School of Public Health, University of Ghana, Accra, Ghana
| | - Thomas P Agyekum
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Accra, Ghana
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Canada
| | - Stuart Batterman
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Thomas G Robins
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Julius N Fobil
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Accra, Ghana
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14
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Loh D, Reiter RJ. Melatonin: Regulation of Viral Phase Separation and Epitranscriptomics in Post-Acute Sequelae of COVID-19. Int J Mol Sci 2022; 23:8122. [PMID: 35897696 PMCID: PMC9368024 DOI: 10.3390/ijms23158122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of "viral factories" by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA;
| | - Russel J. Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
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15
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do Nascimento Gonçalves N, Caldas HC, da Silva Florim GM, Sormani GM, Arantes LMRB, Sorroche BP, Baptista MASF, Fernandes-Charpiot IMM, Nascimento-Filho CHV, de Castilho RM, Abbud-Filho M. Distinct global DNA methylation and NF-κB expression profile of preimplantation biopsies from ideal and non-ideal kidneys. J Nephrol 2022; 35:1831-1840. [PMID: 35524842 DOI: 10.1007/s40620-022-01341-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/20/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Epigenetic mechanisms may affect the ideal and non-ideal kidneys selected for transplantation and their inflammatory gene expression profile differently and may contribute to poor clinical outcomes. OBJECTIVE Study the Global DNA methylation and the expression profiles of the DNA methyltransferases (DNMTs) and nuclear factor kappa B (NF-κB) in preimplantation kidney biopsies from ideal and non-ideal kidneys (expanded criteria donor (ECD) and with KDPI > 85%). METHODS In a sample consisting of 45 consecutive pre-implantation biopsies, global DNA methylation levels were detected by LINE-1 repeated elements using bisulfite pyrosequencing. DNMT gene expression was assessed by real-time quantitative polymerase chain reaction, and NF-κB protein expression by immunofluorescence. RESULTS ECD kidneys displayed increased methylation levels in LINE-1, and DNMT1 and DNMT3B expression was upregulated when comparing ECD to standard criteria donor kidneys. Similarly, kidneys with KDPI > 85% exhibited increased LINE-1 methylation and DNMT1 upregulation when compared to a KDPI ≤ 85%. NF-κB protein expression levels were greatly increased in both types of non-ideal kidneys compared to ideal kidneys. Moreover, hypermethylation of LINE-1 was associated with cold ischemia time > 20 h and ECD kidney classification. CONCLUSIONS This study shows that global DNA hypermethylation and high expression of NF-κB occurred in both types of non-ideal kidneys and were associated with prolonged cold ischemia time. Global DNA methylation can be a useful tool to assess non-ideal kidneys and hence, could be used to expand the pool of kidneys donors.
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Affiliation(s)
- Naiane do Nascimento Gonçalves
- Department of Medicine, Faculdade de Medicina de São José do Rio Preto (FAMERP), Laboratório de Imunologia e Transplante Experimental (LITEX), Hospital de Base, Av. Brigadeiro Faria Lima, 5416, São Jose do Rio Preto, SP, 15090-000, Brazil
| | - Heloisa Cristina Caldas
- Department of Medicine, Faculdade de Medicina de São José do Rio Preto (FAMERP), Laboratório de Imunologia e Transplante Experimental (LITEX), Hospital de Base, Av. Brigadeiro Faria Lima, 5416, São Jose do Rio Preto, SP, 15090-000, Brazil
| | - Greiciane Maria da Silva Florim
- Department of Medicine, Faculdade de Medicina de São José do Rio Preto (FAMERP), Laboratório de Imunologia e Transplante Experimental (LITEX), Hospital de Base, Av. Brigadeiro Faria Lima, 5416, São Jose do Rio Preto, SP, 15090-000, Brazil
| | - Giovanna Mattiello Sormani
- Department of Medicine, Faculdade de Medicina de São José do Rio Preto (FAMERP), Laboratório de Imunologia e Transplante Experimental (LITEX), Hospital de Base, Av. Brigadeiro Faria Lima, 5416, São Jose do Rio Preto, SP, 15090-000, Brazil
| | | | | | - Maria Alice Sperto Ferreira Baptista
- Department of Medicine, Faculdade de Medicina de São José do Rio Preto (FAMERP), Laboratório de Imunologia e Transplante Experimental (LITEX), Hospital de Base, Av. Brigadeiro Faria Lima, 5416, São Jose do Rio Preto, SP, 15090-000, Brazil
| | - Ida Maria Maximina Fernandes-Charpiot
- Department of Medicine, Faculdade de Medicina de São José do Rio Preto (FAMERP), Laboratório de Imunologia e Transplante Experimental (LITEX), Hospital de Base, Av. Brigadeiro Faria Lima, 5416, São Jose do Rio Preto, SP, 15090-000, Brazil
| | | | - Rogério Moraes de Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI, USA
| | - Mario Abbud-Filho
- Department of Medicine, Faculdade de Medicina de São José do Rio Preto (FAMERP), Laboratório de Imunologia e Transplante Experimental (LITEX), Hospital de Base, Av. Brigadeiro Faria Lima, 5416, São Jose do Rio Preto, SP, 15090-000, Brazil.
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Noor H, Zaman A, Teo C, Sughrue ME. PODNL1 Methylation Serves as a Prognostic Biomarker and Associates with Immune Cell Infiltration and Immune Checkpoint Blockade Response in Lower-Grade Glioma. Int J Mol Sci 2021; 22:ijms222212572. [PMID: 34830454 PMCID: PMC8625785 DOI: 10.3390/ijms222212572] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 12/27/2022] Open
Abstract
Lower-grade glioma (LGG) is a diffuse infiltrative tumor of the central nervous system, which lacks targeted therapy. We investigated the role of Podocan-like 1 (PODNL1) methylation in LGG clinical outcomes using the TCGA-LGG transcriptomics dataset. We identified four PODNL1 CpG sites, cg07425555, cg26969888, cg18547299, and cg24354933, which were associated with unfavorable overall survival (OS) and disease-free survival (DFS) in univariate and multivariate analysis after adjusting for age, gender, tumor-grade, and IDH1-mutation. In multivariate analysis, the OS and DFS hazard ratios ranged from 0.44 to 0.58 (p < 0.001) and 0.62 to 0.72 (p < 0.001), respectively, for the four PODNL1 CpGs. Enrichment analysis of differential gene and protein expression and analysis of 24 infiltrating immune cell types showed significantly increased infiltration in LGGs and its histological subtypes with low-methylation levels of the PODNL1 CpGs. High PODNL1 expression and low-methylation subgroups of the PODNL1 CpG sites were associated with significantly increased PD-L1, PD-1, and CTLA4 expressions. PODNL1 methylation may thus be a potential indicator of immune checkpoint blockade response, and serve as a biomarker for determining prognosis and immune subtypes in LGG.
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Affiliation(s)
- Humaira Noor
- Cure Brain Cancer Biomarkers and Translational Research Group, Prince of Wales Clinical School, University of New South Wales, Sydney, NSW 2031, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, Randwick, NSW 2031, Australia
- Faculty of Medicine, University of New South Wales, Randwick, NSW 2031, Australia;
- Correspondence:
| | - Ashraf Zaman
- Faculty of Medicine, University of New South Wales, Randwick, NSW 2031, Australia;
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- Centre for Minimally Invasive Neurosurgery, Prince of Wales Private Hospital, Randwick, NSW 2031, Australia; (C.T.); (M.E.S.)
| | - Charles Teo
- Centre for Minimally Invasive Neurosurgery, Prince of Wales Private Hospital, Randwick, NSW 2031, Australia; (C.T.); (M.E.S.)
| | - Michael E. Sughrue
- Centre for Minimally Invasive Neurosurgery, Prince of Wales Private Hospital, Randwick, NSW 2031, Australia; (C.T.); (M.E.S.)
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17
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Libera L, Ottini G, Sahnane N, Pettenon F, Turri-Zanoni M, Lambertoni A, Chiaravalli AM, Leone F, Battaglia P, Castelnuovo P, Uccella S, Furlan D, Facco C, Sessa F. Methylation Drivers and Prognostic Implications in Sinonasal Poorly Differentiated Carcinomas. Cancers (Basel) 2021; 13:cancers13195030. [PMID: 34638515 PMCID: PMC8507885 DOI: 10.3390/cancers13195030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/30/2021] [Accepted: 10/05/2021] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Poorly differentiated sinonasal carcinomas (PDSNCs) are rare neoplasms that include a wide spectrum of malignancies characterized by alteration in different epigenetic mechanisms (SWI/SNF complex, IDH2, NUT). The aim of our study was to verify if the identification of specific genetic and epigenetic alterations can be useful to recognize different clinico-pathological subsets of PDSNCs to guide treatment decisions. In our cohort, 14 cases showed alterations in SWI/SNF complex or IDH2 genes, which were associated with a higher global DNA methylation level and worst prognosis. The integration of genetic and epigenetic features appears to be a good strategy to improve the clinico-pathological classification of these tumors and to recognize distinct prognostic entities that deserve tailored clinical management. Abstract Background: Poorly differentiated sinonasal carcinomas (PDSNCs) are rare and aggressive malignancies, which include squamous cell carcinoma (SCC), sinonasal undifferentiated carcinoma (SNUC), and neuroendocrine carcinomas (NEC). Several epigenetic markers have been suggested to support the histopathological classification, predict prognosis, and guide therapeutic decision. Indeed, molecularly distinct subtypes of sinonasal carcinomas, including SMARCB1-INI1 or SMARCA4 deficient sinonasal carcinoma, isocitrate dehydrogenase (IDH)-mutant SNUC, ARID1A mutant PDSNCs, and NUT carcinomas, have recently been proposed as separate entities. Identification of aberrant DNA methylation levels associated with these specific epigenetic driver genes could be useful for prognostic and therapeutic purpose. Methods: Histopathological review and immunohistochemical study was performed on 53 PDSNCs. Molecular analysis included mutational profile by NGS, Sanger sequencing, and MLPA analyses, and global DNA methylation profile using LINE-1 bisulfite-PCR and pyrosequencing analysis. Results: Nine SWI/SNF complex defective cases and five IDH2 p.Arg172x cases were identified. A significant correlation between INI-1 or IDH2 defects and LINE-1 hypermethylation was observed (p = 0.002 and p = 0.032, respectively), which were associated with a worse prognosis (p = 0.007). Conclusions: Genetic and epigenetic characterization of PDSNCs should be performed to identify distinct prognostic entities, which deserved a tailored clinical treatment.
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Affiliation(s)
- Laura Libera
- Unit of Pathology, Department of Medicine and Surgery, ASST Sette-Laghi, University of Insubria, 21100 Varese, Italy; (L.L.); (G.O.); (F.P.); (A.M.C.); (S.U.); (D.F.); (C.F.); (F.S.)
| | - Giorgia Ottini
- Unit of Pathology, Department of Medicine and Surgery, ASST Sette-Laghi, University of Insubria, 21100 Varese, Italy; (L.L.); (G.O.); (F.P.); (A.M.C.); (S.U.); (D.F.); (C.F.); (F.S.)
| | - Nora Sahnane
- Unit of Pathology, Department of Medicine and Surgery, ASST Sette-Laghi, University of Insubria, 21100 Varese, Italy; (L.L.); (G.O.); (F.P.); (A.M.C.); (S.U.); (D.F.); (C.F.); (F.S.)
- Correspondence:
| | - Fabiana Pettenon
- Unit of Pathology, Department of Medicine and Surgery, ASST Sette-Laghi, University of Insubria, 21100 Varese, Italy; (L.L.); (G.O.); (F.P.); (A.M.C.); (S.U.); (D.F.); (C.F.); (F.S.)
| | - Mario Turri-Zanoni
- Division of Otorhinolaryngology, Department of Biotechnology and Life Sciences, ASST Sette-Laghi, University of Insubria, 21100 Varese, Italy; (M.T.-Z.); (A.L.); (F.L.); (P.B.); (P.C.)
| | - Alessia Lambertoni
- Division of Otorhinolaryngology, Department of Biotechnology and Life Sciences, ASST Sette-Laghi, University of Insubria, 21100 Varese, Italy; (M.T.-Z.); (A.L.); (F.L.); (P.B.); (P.C.)
| | - Anna Maria Chiaravalli
- Unit of Pathology, Department of Medicine and Surgery, ASST Sette-Laghi, University of Insubria, 21100 Varese, Italy; (L.L.); (G.O.); (F.P.); (A.M.C.); (S.U.); (D.F.); (C.F.); (F.S.)
| | - Federico Leone
- Division of Otorhinolaryngology, Department of Biotechnology and Life Sciences, ASST Sette-Laghi, University of Insubria, 21100 Varese, Italy; (M.T.-Z.); (A.L.); (F.L.); (P.B.); (P.C.)
| | - Paolo Battaglia
- Division of Otorhinolaryngology, Department of Biotechnology and Life Sciences, ASST Sette-Laghi, University of Insubria, 21100 Varese, Italy; (M.T.-Z.); (A.L.); (F.L.); (P.B.); (P.C.)
| | - Paolo Castelnuovo
- Division of Otorhinolaryngology, Department of Biotechnology and Life Sciences, ASST Sette-Laghi, University of Insubria, 21100 Varese, Italy; (M.T.-Z.); (A.L.); (F.L.); (P.B.); (P.C.)
| | - Silvia Uccella
- Unit of Pathology, Department of Medicine and Surgery, ASST Sette-Laghi, University of Insubria, 21100 Varese, Italy; (L.L.); (G.O.); (F.P.); (A.M.C.); (S.U.); (D.F.); (C.F.); (F.S.)
| | - Daniela Furlan
- Unit of Pathology, Department of Medicine and Surgery, ASST Sette-Laghi, University of Insubria, 21100 Varese, Italy; (L.L.); (G.O.); (F.P.); (A.M.C.); (S.U.); (D.F.); (C.F.); (F.S.)
| | - Carla Facco
- Unit of Pathology, Department of Medicine and Surgery, ASST Sette-Laghi, University of Insubria, 21100 Varese, Italy; (L.L.); (G.O.); (F.P.); (A.M.C.); (S.U.); (D.F.); (C.F.); (F.S.)
| | - Fausto Sessa
- Unit of Pathology, Department of Medicine and Surgery, ASST Sette-Laghi, University of Insubria, 21100 Varese, Italy; (L.L.); (G.O.); (F.P.); (A.M.C.); (S.U.); (D.F.); (C.F.); (F.S.)
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18
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Driver Genetic Mutations in Spinal Cord Gliomas Direct the Degree of Functional Impairment in Tumor-Associated Spinal Cord Injury. Cells 2021; 10:cells10102525. [PMID: 34685506 PMCID: PMC8533877 DOI: 10.3390/cells10102525] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/12/2021] [Accepted: 09/19/2021] [Indexed: 11/16/2022] Open
Abstract
Genetic analysis in glioma has been developed recently. Spinal cord glioma is less common than intracranial glioma. Thus, the clinical significance of genetic mutations in spinal cord gliomas remains unclear. Furthermore, because the spinal cord is an important communication channel between the brain and the rest of the body, increased attention should be paid to its functional prognosis. In this study, we investigated the functional prognosis and driver genetic mutations in eight patients with spinal cord gliomas (World Health Organization grade I, three cases; grade II, two cases; grade III/IV, three cases). IDH mutations were detected in all grade II cases and H3F3A mutations were detected in all grade III/IV cases. The functional status of grade I and II gliomas remained unchanged or improved 1 year after surgery, whereas grade III/IV gliomas remained unchanged or deteriorated. Spinal glioma progenitor cells with H3F3A mutations were associated with accelerated tumor-associated spinal cord injury, which led to functional impairment. Conversely, the presence of IDH mutations, which are rarely reported in spinal gliomas, indicated a relatively favorable functional prognosis.
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19
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Dejima H, Hu X, Chen R, Zhang J, Fujimoto J, Parra ER, Haymaker C, Hubert SM, Duose D, Solis LM, Su D, Fukuoka J, Tabata K, Pham HHN, Mcgranahan N, Zhang B, Ye J, Ying L, Little L, Gumbs C, Chow CW, Estecio MR, Godoy MCB, Antonoff MB, Sepesi B, Pass HI, Behrens C, Zhang J, Vaporciyan AA, Heymach JV, Scheet P, Lee JJ, Wu J, Futreal PA, Reuben A, Kadara H, Wistuba II, Zhang J. Immune evolution from preneoplasia to invasive lung adenocarcinomas and underlying molecular features. Nat Commun 2021; 12:2722. [PMID: 33976164 PMCID: PMC8113327 DOI: 10.1038/s41467-021-22890-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 03/31/2021] [Indexed: 12/13/2022] Open
Abstract
The mechanism by which anti-cancer immunity shapes early carcinogenesis of lung adenocarcinoma (ADC) is unknown. In this study, we characterize the immune contexture of invasive lung ADC and its precursors by transcriptomic immune profiling, T cell receptor (TCR) sequencing and multiplex immunofluorescence (mIF). Our results demonstrate that anti-tumor immunity evolved as a continuum from lung preneoplasia, to preinvasive ADC, minimally-invasive ADC and frankly invasive lung ADC with a gradually less effective and more intensively regulated immune response including down-regulation of immune-activation pathways, up-regulation of immunosuppressive pathways, lower infiltration of cytotoxic T cells (CTLs) and anti-tumor helper T cells (Th), higher infiltration of regulatory T cells (Tregs), decreased T cell clonality, and lower frequencies of top T cell clones in later-stages. Driver mutations, chromosomal copy number aberrations (CNAs) and aberrant DNA methylation may collectively impinge host immune responses and facilitate immune evasion, promoting the outgrowth of fit subclones in preneoplasia into dominant clones in invasive ADC.
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Affiliation(s)
- Hitoshi Dejima
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xin Hu
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Runzhe Chen
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jiexin Zhang
- Department of Bioinformatics & Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edwin R Parra
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cara Haymaker
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shawna M Hubert
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dzifa Duose
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luisa M Solis
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dan Su
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China.,Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
| | - Junya Fukuoka
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kazuhiro Tabata
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hoa H N Pham
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Nicholas Mcgranahan
- Cancer Research United Kingdom-University College London Lung Cancer Centre of Excellence, London, UK
| | - Baili Zhang
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jie Ye
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lisha Ying
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China.,Zhejiang Cancer Research Institute, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
| | - Latasha Little
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Curtis Gumbs
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chi-Wan Chow
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marcos Roberto Estecio
- Department of Epigenetics and Molecular Carcinogenesis, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center of Cancer Epigenetics, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Myrna C B Godoy
- Department of Thoracic Imaging, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mara B Antonoff
- Department of Thoracic and Cardiovascular Surgery, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, NY, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ara A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul Scheet
- Department of Epidemiology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Jack Lee
- Department of Biostatistics, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jia Wu
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Humam Kadara
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Jianjun Zhang
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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20
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McAleenan A, Kelly C, Spiga F, Kernohan A, Cheng HY, Dawson S, Schmidt L, Robinson T, Brandner S, Faulkner CL, Wragg C, Jefferies S, Howell A, Vale L, Higgins JPT, Kurian KM. Prognostic value of test(s) for O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation for predicting overall survival in people with glioblastoma treated with temozolomide. Cochrane Database Syst Rev 2021; 3:CD013316. [PMID: 33710615 PMCID: PMC8078495 DOI: 10.1002/14651858.cd013316.pub2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Glioblastoma is an aggressive form of brain cancer. Approximately five in 100 people with glioblastoma survive for five years past diagnosis. Glioblastomas that have a particular modification to their DNA (called methylation) in a particular region (the O6-methylguanine-DNA methyltransferase (MGMT) promoter) respond better to treatment with chemotherapy using a drug called temozolomide. OBJECTIVES To determine which method for assessing MGMT methylation status best predicts overall survival in people diagnosed with glioblastoma who are treated with temozolomide. SEARCH METHODS We searched MEDLINE, Embase, BIOSIS, Web of Science Conference Proceedings Citation Index to December 2018, and examined reference lists. For economic evaluation studies, we additionally searched NHS Economic Evaluation Database (EED) up to December 2014. SELECTION CRITERIA Eligible studies were longitudinal (cohort) studies of adults with diagnosed glioblastoma treated with temozolomide with/without radiotherapy/surgery. Studies had to have related MGMT status in tumour tissue (assessed by one or more method) with overall survival and presented results as hazard ratios or with sufficient information (e.g. Kaplan-Meier curves) for us to estimate hazard ratios. We focused mainly on studies comparing two or more methods, and listed brief details of articles that examined a single method of measuring MGMT promoter methylation. We also sought economic evaluations conducted alongside trials, modelling studies and cost analysis. DATA COLLECTION AND ANALYSIS Two review authors independently undertook all steps of the identification and data extraction process for multiple-method studies. We assessed risk of bias and applicability using our own modified and extended version of the QUality In Prognosis Studies (QUIPS) tool. We compared different techniques, exact promoter regions (5'-cytosine-phosphate-guanine-3' (CpG) sites) and thresholds for interpretation within studies by examining hazard ratios. We performed meta-analyses for comparisons of the three most commonly examined methods (immunohistochemistry (IHC), methylation-specific polymerase chain reaction (MSP) and pyrosequencing (PSQ)), with ratios of hazard ratios (RHR), using an imputed value of the correlation between results based on the same individuals. MAIN RESULTS We included 32 independent cohorts involving 3474 people that compared two or more methods. We found evidence that MSP (CpG sites 76 to 80 and 84 to 87) is more prognostic than IHC for MGMT protein at varying thresholds (RHR 1.31, 95% confidence interval (CI) 1.01 to 1.71). We also found evidence that PSQ is more prognostic than IHC for MGMT protein at various thresholds (RHR 1.36, 95% CI 1.01 to 1.84). The data suggest that PSQ (mainly at CpG sites 74 to 78, using various thresholds) is slightly more prognostic than MSP at sites 76 to 80 and 84 to 87 (RHR 1.14, 95% CI 0.87 to 1.48). Many variants of PSQ have been compared, although we did not see any strong and consistent messages from the results. Targeting multiple CpG sites is likely to be more prognostic than targeting just one. In addition, we identified and summarised 190 articles describing a single method for measuring MGMT promoter methylation status. AUTHORS' CONCLUSIONS PSQ and MSP appear more prognostic for overall survival than IHC. Strong evidence is not available to draw conclusions with confidence about the best CpG sites or thresholds for quantitative methods. MSP has been studied mainly for CpG sites 76 to 80 and 84 to 87 and PSQ at CpG sites ranging from 72 to 95. A threshold of 9% for CpG sites 74 to 78 performed better than higher thresholds of 28% or 29% in two of three good-quality studies making such comparisons.
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Affiliation(s)
- Alexandra McAleenan
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Claire Kelly
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Francesca Spiga
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ashleigh Kernohan
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Hung-Yuan Cheng
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Sarah Dawson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Applied Research Collaboration West (ARC West) , University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | - Lena Schmidt
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tomos Robinson
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Sebastian Brandner
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Claire L Faulkner
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Christopher Wragg
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Sarah Jefferies
- Department of Oncology, Addenbrooke's Hospital, Cambridge, UK
| | - Amy Howell
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Luke Vale
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Julian P T Higgins
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Applied Research Collaboration West (ARC West) , University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | - Kathreena M Kurian
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol Medical School: Brain Tumour Research Centre, Public Health Sciences, University of Bristol, Bristol, UK
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21
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Rusetska N, Kober P, Król SK, Boresowicz J, Maksymowicz M, Kunicki J, Bonicki W, Bujko M. Invasive and Noninvasive Nonfunctioning Gonadotroph Pituitary Tumors Differ in DNA Methylation Level of LINE-1 Repetitive Elements. J Clin Med 2021; 10:560. [PMID: 33546126 PMCID: PMC7913198 DOI: 10.3390/jcm10040560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Epigenetic dysregulation plays a role in pituitary tumor pathogenesis. Some differences in DNA methylation were observed between invasive and noninvasive nonfunctioning gonadotroph tumors. This study sought to determine the role of DNA methylation changes in repetitive LINE-1 elements in nonfunctioning gonadotroph pituitary tumors. METHODS We investigated LINE-1 methylation levels in 80 tumors and normal pituitary glands with bisulfite-pyrosequencing. Expression of two LINE-1 open reading frames (L1-ORF1 and L1-ORF2) was analyzed with qRT-PCR in tumor samples and mouse gonadotroph pituitary cells treated with DNA methyltransferase inhibitor. Immunohistochemical staining against L1-ORF1p was also performed in normal pituitary glands and tumors. RESULTS Hypomethylation of LINE-1 was observed in pituitary tumors. Tumors characterized by invasive growth revealed lower LINE-1 methylation level than noninvasive ones. LINE-1 methylation correlated with overall DNA methylation assessed with HM450K arrays and negatively correlated with L1-ORF1 and L1-ORF2 expression. Treatment of αT3-1 gonadotroph cells with 5-Azacytidine clearly increased the level of L1-ORF1 and L1-ORF2 mRNA; however, its effect on LβT2 cells was less pronounced. Immunoreactivity against L1-ORF1p was higher in tumors than normal tissue. No difference in L1-ORF1p expression was observed in invasive and noninvasive tumors. CONCLUSION Hypomethylation of LINE-1 is related to invasive growth and influences transcriptional activity of transposable elements.
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Affiliation(s)
- Natalia Rusetska
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (N.R.); (P.K.); (S.K.K.); (J.B.)
| | - Paulina Kober
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (N.R.); (P.K.); (S.K.K.); (J.B.)
| | - Sylwia Katarzyna Król
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (N.R.); (P.K.); (S.K.K.); (J.B.)
| | - Joanna Boresowicz
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (N.R.); (P.K.); (S.K.K.); (J.B.)
| | - Maria Maksymowicz
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland;
| | - Jacek Kunicki
- Department of Neurosurgery, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.K.); (W.B.)
| | - Wiesław Bonicki
- Department of Neurosurgery, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.K.); (W.B.)
| | - Mateusz Bujko
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (N.R.); (P.K.); (S.K.K.); (J.B.)
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22
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Farrell C, Shi W, Bodman A, Olson JJ. Congress of neurological surgeons systematic review and evidence-based guidelines update on the role of emerging developments in the management of newly diagnosed glioblastoma. J Neurooncol 2020; 150:269-359. [PMID: 33215345 DOI: 10.1007/s11060-020-03607-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/23/2020] [Indexed: 12/12/2022]
Abstract
TARGET POPULATION These recommendations apply to adult patients with newly diagnosed or suspected glioblastoma. IMAGING Question What imaging modalities are in development that may be able to provide improvements in diagnosis, and therapeutic guidance for individuals with newly diagnosed glioblastoma? RECOMMENDATION Level III: It is suggested that techniques utilizing magnetic resonance imaging for diffusion weighted imaging, and to measure cerebral blood and magnetic spectroscopic resonance imaging of N-acetyl aspartate, choline and the choline to N-acetyl aspartate index to assist in diagnosis and treatment planning in patients with newly diagnosed or suspected glioblastoma. SURGERY Question What new surgical techniques can be used to provide improved tumor definition and resectability to yield better tumor control and prognosis for individuals with newly diagnosed glioblastoma? RECOMMENDATIONS Level II: The use of 5-aminolevulinic acid is recommended to improve extent of tumor resection in patients with newly diagnosed glioblastoma. Level II: The use of 5-aminolevulinic acid is recommended to improve median survival and 2 year survival in newly diagnosed glioblastoma patients with clinical characteristics suggesting poor prognosis. Level III: It is suggested that, when available, patients be enrolled in properly designed clinical trials assessing the value of diffusion tensor imaging in improving the safety of patients with newly diagnosed glioblastoma undergoing surgery. NEUROPATHOLOGY Question What new pathology techniques and measurement of biomarkers in tumor tissue can be used to provide improved diagnostic ability, and determination of therapeutic responsiveness and prognosis for patients with newly diagnosed glioblastomas? RECOMMENDATIONS Level II: Assessment of tumor MGMT promoter methylation status is recommended as a significant predictor of a longer progression free survival and overall survival in patients with newly diagnosed with glioblastoma. Level II: Measurement of tumor expression of neuron-glia-2, neurofilament protein, glutamine synthetase and phosphorylated STAT3 is recommended as a predictor of overall survival in patients with newly diagnosed with glioblastoma. Level III: Assessment of tumor IDH1 mutation status is suggested as a predictor of longer progression free survival and overall survival in patients with newly diagnosed with glioblastoma. Level III: Evaluation of tumor expression of Phosphorylated Mitogen-Activated Protein Kinase protein, EGFR protein, and Insulin-like Growth Factor-Binding Protein-3 is suggested as a predictor of overall survival in patients with newly diagnosed with glioblastoma. RADIATION Question What radiation therapy techniques are in development that may be used to provide improved tumor control and prognosis for individuals with newly diagnosed glioblastomas? RECOMMENDATIONS Level III: It is suggested that patients with newly diagnosed glioblastoma undergo pretreatment radio-labeled amino acid tracer positron emission tomography to assess areas at risk for tumor recurrence to assist in radiation treatment planning. Level III: It is suggested that, when available, patients be with newly diagnosed glioblastomas be enrolled in properly designed clinical trials of radiation dose escalation, altered fractionation, or new radiation delivery techniques. CHEMOTHERAPY Question What emerging chemotherapeutic agents or techniques are available to provide better tumor control and prognosis for patients with newly diagnosed glioblastomas? RECOMMENDATION Level III: As no emerging chemotherapeutic agents or techniques were identified in this review that improved tumor control and prognosis it is suggested that, when available, patients with newly diagnosed glioblastomas be enrolled in properly designed clinical trials of chemotherapy. MOLECULAR AND TARGETED THERAPY Question What new targeted therapy agents are available to provide better tumor control and prognosis for individuals with newly diagnosed glioblastomas? RECOMMENDATION Level III: As no new molecular and targeted therapies have clearly provided better tumor control and prognosis it is suggested that, when available, patients with newly diagnosed glioblastomas be enrolled in properly designed clinical trials of molecular and targeted therapies IMMUNOTHERAPY: Question What emerging immunotherapeutic agents or techniques are available to provide better tumor control and prognosis for patients with newly diagnosed glioblastomas? RECOMMENDATION Level III: As no immunotherapeutic agents have clearly provided better tumor control and prognosis it is suggested that, when available, patients with newly diagnosed glioblastomas be enrolled in properly designed clinical trials of immunologically-based therapies. NOVEL THERAPIES Question What novel therapies or techniques are in development to provide better tumor control and prognosis for individuals with newly diagnosed glioblastomas? RECOMMENDATIONS Level II: The use of tumor-treating fields is recommended for patients with newly diagnosed glioblastoma who have undergone surgical debulking and completed concurrent chemoradiation without progression of disease at the time of tumor-treating field therapy initiation. Level II: It is suggested that, when available, enrollment in properly designed studies of vector containing herpes simplex thymidine kinase gene and prodrug therapies be considered in patients with newly diagnosed glioblastoma.
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Affiliation(s)
- Christopher Farrell
- Department of Neurosurgery, Thomas Jefferson University, Philadelphia, PA, USA
| | - Wenyin Shi
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Jeffrey J Olson
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA.
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23
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Cardelli M, Doorn RV, Larcher L, Donato MD, Piacenza F, Pierpaoli E, Giacconi R, Malavolta M, Rachakonda S, Gruis NA, Molven A, Andresen PA, Pjanova D, van den Oord JJ, Provinciali M, Nagore E, Kumar R. Association of HERV-K and LINE-1 hypomethylation with reduced disease-free survival in melanoma patients. Epigenomics 2020; 12:1689-1706. [PMID: 33125285 DOI: 10.2217/epi-2020-0127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To evaluate CpG methylation of long interspersed nuclear elements 1 (LINE-1) and human endogenous retrovirus K (HERV-K) retroelements as potential prognostic biomarkers in cutaneous melanoma. Materials & methods: Methylation of HERV-K and LINE-1 retroelements was assessed in resected melanoma tissues from 82 patients ranging in age from 14 to 88 years. In addition, nevi from eight patients were included for comparison with nonmalignant melanocytic lesions. Results: Methylation levels were lower in melanomas than in nevi. HERV-K and LINE-1 methylation were decreased in melanoma patients with clinical parameters associated with adverse prognosis, while they were independent of age and gender. Hypomethylation of HERV-K (but not LINE-1) was an independent predictor of reduced disease-free survival. Conclusion: HERV-K hypomethylation can be a potential independent biomarker of melanoma recurrence.
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Affiliation(s)
- Maurizio Cardelli
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, 2300RC Leiden, The Netherlands
| | - Lares Larcher
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Michela Di Donato
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Elisa Pierpaoli
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Robertina Giacconi
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Marco Malavolta
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Sivaramakrishna Rachakonda
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, 69120 Heidelberg, Germany.,Division of Functional Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Nelleke A Gruis
- Department of Dermatology, Leiden University Medical Center, 2300RC Leiden, The Netherlands
| | - Anders Molven
- Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, N-5020 Bergen, Norway.,Department of Pathology, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Per Arne Andresen
- Department of Pathology, Oslo University Hospital, Rikshospitalet, 0424 Oslo, Norway
| | - Dace Pjanova
- Latvian Biomedical Research & Study Centre, LV-1067 Riga, Latvia
| | | | - Mauro Provinciali
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncología, 46009 València, Spain
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, 69120 Heidelberg, Germany.,Division of Functional Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany
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24
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Sexually dimorphic DNA-methylation in cardiometabolic health: A systematic review. Maturitas 2020; 135:6-26. [DOI: 10.1016/j.maturitas.2020.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/03/2020] [Accepted: 02/12/2020] [Indexed: 02/06/2023]
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25
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Zhang S, William C. Educational Case: Histologic and Molecular Features of Diffuse Gliomas. Acad Pathol 2020; 7:2374289520914021. [PMID: 32284966 PMCID: PMC7133074 DOI: 10.1177/2374289520914021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 01/13/2020] [Accepted: 02/22/2020] [Indexed: 11/23/2022] Open
Abstract
The following fictional cases are intended as a learning tool within the Pathology Competencies for Medical Education (PCME), a set of national standards for teaching pathology. These are divided into three basic competencies: Disease Mechanisms and Processes, Organ System Pathology, and Diagnostic Medicine and Therapeutic Pathology. For additional information, and a full list of learning objectives for all three competencies, seehttp://journals.sagepub.com/doi/10.1177/2374289517715040.1
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Affiliation(s)
- Sarah Zhang
- NYU Langone Medical Center, New York, NY, USA
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26
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Argadal OG, Mutlu M, Ak Aksoy S, Kocaeli H, Tunca B, Civan MN, Egeli U, Cecener G, Bekar A, Taskapilioglu MO, Tekin C, Tezcan G, Tolunay S. Long noncoding RNA MALAT1 may be a prognostic biomarker in IDH1/2 wild-type primary glioblastomas. Bosn J Basic Med Sci 2020; 20:63-69. [PMID: 31479414 PMCID: PMC7029212 DOI: 10.17305/bjbms.2019.4297] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 06/28/2019] [Indexed: 01/05/2023] Open
Abstract
Primary glioblastoma (GB) is the most aggressive type of brain tumors. While mutations in isocitrate dehydrogenase (IDH) genes are frequent in secondary GBs and correlate with a better prognosis, most primary GBs are IDH wild-type. Recent studies have shown that the long noncoding RNA metastasis associated lung adenocarcinoma transcript-1 (MALAT1) is associated with aggressive tumor phenotypes in different cancers. Our aim was to clarify the prognostic significance of MALAT1 in IDH1/2 wild-type primary GB tumors. We analyzed IDH1/2 mutation status in 75 patients with primary GB by DNA sequencing. The expression of MALAT1 was detected in the 75 primary GB tissues and 5 normal brain tissues using reverse transcription quantitative PCR (RT-qPCR). The associations between MALAT1 expression, IDH1/2 mutation status, and clinicopathological variables of patients were determined. IDH1 (R132H) mutation was observed in 5/75 primary GBs. IDH2 (R172H) mutation was not detected in any of our cases. MALAT1 expression was significantly upregulated in primary GB vs. normal brain tissues (p = 0.025). Increased MALAT1 expression in IDH1/2 wild-type primary GBs correlated with patient age and tumor localization (p = 0.032 and p = 0.025, respectively). A multivariate analysis showed that high MALAT1 expression was an unfavorable prognostic factor for overall survival (p = 0.034) in IDH1/2 wild-type primary GBs. High MALAT1 expression may have a prognostic role in primary GBs independent of IDH mutations.
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Affiliation(s)
- Omer Gokay Argadal
- Department of Neurosurgery, Faculty of Medicine, Uludag University, Bursa, Turkey
| | - Melis Mutlu
- Department of Medical Biology, Faculty of Medicine, Uludag University, Bursa, Turkey
| | - Secil Ak Aksoy
- Department of Medical Biology, Faculty of Medicine, Uludag University, Bursa, Turkey
| | - Hasan Kocaeli
- Department of Neurosurgery, Faculty of Medicine, Uludag University, Bursa, Turkey
| | - Berrin Tunca
- Department of Medical Biology, Faculty of Medicine, Uludag University, Bursa, Turkey.
| | | | - Unal Egeli
- Department of Medical Biology, Faculty of Medicine, Uludag University, Bursa, Turkey
| | - Gulsah Cecener
- Department of Medical Biology, Faculty of Medicine, Uludag University, Bursa, Turkey
| | - Ahmet Bekar
- Department of Neurosurgery, Faculty of Medicine, Uludag University, Bursa, Turkey
| | | | - Cagla Tekin
- Department of Medical Biology, Faculty of Medicine, Uludag University, Bursa, Turkey
| | - Gulcin Tezcan
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Sahsine Tolunay
- Department of Pathology, Faculty of Medicine, Uludag University, Bursa, Turkey.
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27
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Zeng M, Zhen J, Zheng X, Qiu H, Xu X, Wu J, Lin Z, Hu J. The Role of DNA Methylation in Ischemic Stroke: A Systematic Review. Front Neurol 2020; 11:566124. [PMID: 33193003 PMCID: PMC7652818 DOI: 10.3389/fneur.2020.566124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/28/2020] [Indexed: 02/05/2023] Open
Abstract
Background: Knowledge about the classic risk and protective factors of ischemic stroke is accumulating, but the underlying pathogenesis has not yet been fully understood. As emerging evidence indicates that DNA methylation plays a role in the pathological process of cerebral ischemia, this study aims to summarize the evidence of the association between DNA methylation and ischemic stroke. Methods: MEDLINE, EMBASE, PubMed, and Cochrane Central Register of Controlled Trials were searched for eligible studies. The results reported by each study were summarized narratively. Results: A total of 20 studies with 7,014 individuals finally met the inclusion criteria. Three studies focused on global methylation, 11 studies on candidate-gene methylation, and six on epigenome-wide methylation analysis. Long-interspersed nuclear element 1 was found to be hypomethylated in stroke cases in two studies. Another 16 studies reported 37 genes that were differentially methylated between stroke cases and controls. Individuals with ischemic stroke were also reported to have higher acceleration in Hanuum 's epigenetic age compared to controls. Conclusion: DNA methylation might be associated with ischemic stroke and play a role in several pathological pathways. It is potentially a promising biomarker for stroke prevention, diagnosis and treatment, but the current evidence is limited by sample size and cross-sectional or retrospective design. Therefore, studies on large asymptomatic populations with the prospective design are needed to validate the current evidence, explore new pathways and identify novel risk/protective loci.
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Affiliation(s)
- Minyan Zeng
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Juanying Zhen
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
- Department of Clinical Medicine, Shantou University Medical College, Shantou, China
| | - Xiaodan Zheng
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
- Department of Clinical Medicine, Shantou University Medical College, Shantou, China
| | - Hongyan Qiu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Xiaonan Xu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jun Wu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Zhijian Lin
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
- *Correspondence: Zhijian Lin
| | - Jun Hu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
- Jun Hu
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28
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Abstract
Gliomas, that do not respond to alkylating agent chemotherapy, can be made more sensitive to chemotherapy through promotor mediated epigenetic silencing of the MGMT gene. MGMT is one of the important markers in glioblastomas as it not only predicts response to therapy but may also be used as an independent prognostic marker. As such, MGMT is gaining increasing traction in diagnosis, prognostication, and therapeutic decision-making for these highly malignant gliomas. Although, MGMT promotor methylation status is becoming more commonly used in neuro-oncology; this test remains imperfect. Because of its increasing use in clinical practice and research, it is integral that we are aware of its pitfalls and complications. Currently, there are many ways to detect a patient's MGMT promotor methylation status, including: quantitative PCR, methylation-specific PCR, pyrosequencing, real time PCR with high resolution melt, and the infinitum methylation EPIC beadChip. The technical aspects, shortcomings, and optimal approach to interpreting the results of each method will be discussed. Furthermore, given that none of these methods have been prospectively validated, the challenge of equivocal cases will be discussed, and technical and logistic strategies for overcoming these challenges will be proposed. Finally, the difficulty in validating these methods, establishing standardized practice, and considerations of the cost of these competing methods will be explored.
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29
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Tahara S, Tahara T, Horiguchi N, Okubo M, Terada T, Yoshida D, Funasaka K, Nakagawa Y, Shibata T, Tsukamoto T, Ohmiya N. Lower LINE-1 methylation is associated with promoter hypermethylation and distinct molecular features in gastric cancer. Epigenomics 2019; 11:1651-1659. [DOI: 10.2217/epi-2019-0091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Aim: To investigate the associations between LINE1 methylation, an indicator for genome-wide hypomethylation, molecular and clinicopathological characteristics of gastric cancer (GC) patients. Patients & methods: LINE1 methylation statuses were examined in paired cancerous, non-neoplastic mucosa from 217 GC and gastric mucosa from separate group of 224 noncancer patients. CpG island methylator phenotype, TP53 and KRAS mutation, MLH1 methylation status and promoter hypermethylation of GC related and H. pylori-related genes were examined. Results: Lower LINE1 methylation was observed in primary GC compared with non-neoplastic gastric mucosa and associated with CpG island methylator phenotype, TP53 mutation, MLH1 methylation and promoter hypermethylation of GC related and H. pylori-related genes. Conclusion: Lower LINE1 methylation correlates specific molecular subtypes and promoter hypermethylation in GC.
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Affiliation(s)
- Sayumi Tahara
- Diagnostic Pathology I, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tomomitsu Tahara
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Noriyuki Horiguchi
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Masaaki Okubo
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tsuyoshi Terada
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Dai Yoshida
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Kohei Funasaka
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Yoshihito Nakagawa
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tomoyuki Shibata
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tetsuya Tsukamoto
- Diagnostic Pathology I, Fujita Health University School of Medicine, Toyoake, Japan
| | - Naoki Ohmiya
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
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30
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Huynh TT, Sultan M, Vidovic D, Dean CA, Cruickshank BM, Lee K, Loung CY, Holloway RW, Hoskin DW, Waisman DM, Weaver ICG, Marcato P. Retinoic acid and arsenic trioxide induce lasting differentiation and demethylation of target genes in APL cells. Sci Rep 2019; 9:9414. [PMID: 31263158 PMCID: PMC6602962 DOI: 10.1038/s41598-019-45982-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 06/19/2019] [Indexed: 12/11/2022] Open
Abstract
Acute promyelocytic leukemia (APL) is characterized by arrested differentiation of promyelocytes. Patients treated with all-trans retinoic acid (ATRA) alone experience relapse, while patients treated with ATRA and arsenic trioxide (ATO) are often relapse-free. This suggests sustained changes have been elicited by the combination therapy. To understand the lasting effects of the combination therapy, we compared the effects of ATRA and ATO on NB4 and ATRA-resistant NB4-MR2 APL cells during treatment versus post treatment termination. After treatment termination, NB4 cells treated with ATRA or ATO reverted to non-differentiated cells, while combination-treated cells remained terminally differentiated. This effect was diminished in NB4-MR2 cells. This suggests combination treatment induced more permanent changes. Combination treatment induced higher expression of target genes (e.g., transglutaminase 2 and retinoic acid receptor beta), which in NB4 cells was sustained post treatment termination. To determine whether sustained epigenetic changes were responsible, we quantified the enrichment of histone modifications by chromatin immunoprecipitation, and CpG methylation by bisulfite-pyrosequencing. While ATRA and combination treatment induced similar histone acetylation enrichment, combination treatment induced greater demethylation of target genes, which was sustained. Therefore, sustained demethylation of target genes by ATRA and ATO combination treatment is associated with lasting differentiation and gene expression changes.
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Affiliation(s)
- Thomas T Huynh
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Mohammad Sultan
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Dejan Vidovic
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Cheryl A Dean
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | | | - Kristen Lee
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, NS, Canada
| | - Chao-Yu Loung
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Ryan W Holloway
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - David W Hoskin
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - David M Waisman
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Ian C G Weaver
- Department of Pathology, Dalhousie University, Halifax, NS, Canada.
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, NS, Canada.
- Department of Psychiatry, Dalhousie University, Halifax, NS, Canada.
- Brain Repair Centre, Dalhousie University, Halifax, NS, Canada.
| | - Paola Marcato
- Department of Pathology, Dalhousie University, Halifax, NS, Canada.
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada.
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31
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Sharma A, Jamil MA, Nuesgen N, Dauksa A, Gulbinas A, Schulz WA, Oldenburg J, El-Maarri O. Detailed methylation map of LINE-1 5'-promoter region reveals hypomethylated CpG hotspots associated with tumor tissue specificity. Mol Genet Genomic Med 2019; 7:e601. [PMID: 30955237 PMCID: PMC6503062 DOI: 10.1002/mgg3.601] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 12/30/2018] [Accepted: 01/09/2019] [Indexed: 11/25/2022] Open
Abstract
Background Long interspersed nuclear elements (LINE‐1) sequences constitute a substantial portion of the human genome, and their methylation often correlating with global genomic methylation. Previous studies have highlighted the feasibility of using LINE‐1 methylation to discriminate tumors from healthy tissues. However, most studies are based on only a few specific LINE‐1 CpG sites. Methods Herein, we have performed a systematic fine‐scale analysis of methylation at 14 CpGs located in the 5′‐region of consensus LINE‐1, in bladder, colon, prostate, and gastric tumor tissues using a global degenerate approach. Results Our results reveal variable methylation levels between different CpGs, as well as some tissue‐specific differences. Trends toward hypomethylation were observed in all tumors types to certain degrees, showing statistically significance in bladder and prostate tumors. Our data points toward the presence of unique LINE‐1 DNA methylation patterns for each tumor type and tissue, indicating that not the same CpGs will be informative for testing in all tumor types. Conclusion This study provides an accurate guide that will help to design further assays that could avoid artifacts and explain the variability of obtained LINE‐1 methylation values between different studies.
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Affiliation(s)
- Amit Sharma
- Institute of Experimental Hematology and Transfusion Medicine, Bonn, Germany.,Department of Neurology, University Clinic Bonn, Bonn, Germany
| | - Muhammad A Jamil
- Institute of Experimental Hematology and Transfusion Medicine, Bonn, Germany
| | - Nicole Nuesgen
- Institute of Experimental Hematology and Transfusion Medicine, Bonn, Germany
| | - Albertas Dauksa
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Antanas Gulbinas
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, Bonn, Germany
| | - Osman El-Maarri
- Institute of Experimental Hematology and Transfusion Medicine, Bonn, Germany.,Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
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32
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Gao M, Lin Y, Liu X, Li Y, Zhang C, Wang Z, Wang Z, Wang Y, Guo Z. ISG20 promotes local tumor immunity and contributes to poor survival in human glioma. Oncoimmunology 2018; 8:e1534038. [PMID: 30713788 PMCID: PMC6343791 DOI: 10.1080/2162402x.2018.1534038] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 12/20/2022] Open
Abstract
Recent evidence has confirmed that a mutation of the isocitrate dehydrogenase (IDH) gene occurs early in gliomagenesis and contributes to suppressed immunity. The present study aimed to determine the candidate genes associated with IDH mutation status that could serve as biomarkers of immune suppression for improved prognosis prediction. Clinical information and RNA-seq gene expression data were collected for 932 glioma samples from the CGGA and TCGA databases, and differentially expressed genes in both lower-grade glioma (LGG) and glioblastoma (GBM) samples were identified according to IDH mutation status. Only one gene, interferon-stimulated exonuclease gene 20 (ISG20), with reduced expression in IDH mutant tumors, demonstrated significant prognostic value. ISG20 expression level significantly increased with increasing tumor grade, and its high expression was associated with a poor clinical outcome. Moreover, increased ISG20 expression was associated with increased infiltration of monocyte-derived macrophages and neutrophils, and suppressed adaptive immune response. ISG20 expression was also positively correlated with PD-1, PD-L1, and CTLA4 expression, along with the levels of several chemokines. We conclude that ISG20 is a useful biomarker to identify IDH-mediated immune processes in glioma and may serve as a potential therapeutic target.
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Affiliation(s)
- Mengqi Gao
- Department of Neurosurgery, the First Hospital of China Medical University, Shenyang, China
| | - Yi Lin
- Department of Neurosurgery, the First Hospital of China Medical University, Shenyang, China
| | - Xing Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Yiming Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Chuanbao Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Zheng Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Zhiliang Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Yulin Wang
- Department of Neurosurgery, the First Hospital of China Medical University, Shenyang, China
| | - Zongze Guo
- Department of Neurosurgery, the First Hospital of China Medical University, Shenyang, China
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Chen Y, Zeng Q, Liu X, Fu J, Zeng Z, Zhao Z, Liu Z, Bai W, Dong Z, Liu H, Lu X, Zhu Y, Lu Y. LINE-1 ORF-1p enhances the transcription factor activity of pregnenolone X receptor and promotes sorafenib resistance in hepatocellular carcinoma cells. Cancer Manag Res 2018; 10:4421-4438. [PMID: 30349375 PMCID: PMC6188112 DOI: 10.2147/cmar.s176088] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background LINE-1 ORF-1p is encoded by the human pro-oncogene LINE-1. Our previous work showed that LINE-1 ORF-1p could enhance the resistance of hepatocellular carcinoma (HCC) cells to antitumor agents. However, the mechanisms involved in LINE-1 ORF-1p-mediated drug resistance remain largely unknown. Materials and methods The endogenous mRNA level of LINE-1 ORF-1p in clinical HCC specimens was examined using quantitative PCR (qPCR). The prognosis of HCC patients was assessed using time to progression and overall survival. The transcription factor activity of pregnenolone X receptor (PXR) was examined using luciferase gene reporter assays, qPCR, chromatin immunoprecipitation assays and cellular subfraction assays. Protein interaction between LINE-1 ORF-1p and PXR was detected by co-immunoprecipitation. The effect of LINE-1 ORF-1p on sorafenib resistance in HCC cells was studied using in vitro and in vivo models. Results A high level of LINE-1 ORF-1p in clinical specimens was related to poor prognosis in patients who received sorafenib treatment. LINE-1 ORF-1p increased the transcription factor activity of PXR by interacting with PXR and enhancing its cytoplasmic/nuclear translocation, and recruiting PXR to its downstream gene promoter, in turn enhancing the expression of the sorafenib resistance-related genes, CYP3A4 and mdr-1. LINE-1 ORF-1p enhanced the resistance to and clearance of sorafenib in HCC cells. Conclusion LINE-1 ORF-1p enhances the transcription factor activation of PXR and promotes the clearance of and resistance to sorafenib in HCC cells.
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Affiliation(s)
- Yan Chen
- Comprehensive Liver Cancer Center, Beijing 302 Hospital, Beijing 100039, P.R. China, .,College of Life Sciences and Bio-Engineering, Beijing Jiaotong University, Beijing 100044, P.R. China,
| | - Qinglei Zeng
- Department of Infectious Disease, The First Affiliated Hospital of Zhengzhou University, Zheng Zhou 450052, Henan Province, P.R. China
| | - Xiufang Liu
- Department of Oncology, Chinese PLA 251 Hospital, Zhangjiakou 075000, P.R. China
| | - Junliang Fu
- Comprehensive Liver Cancer Center, Beijing 302 Hospital, Beijing 100039, P.R. China,
| | - Zhen Zeng
- Comprehensive Liver Cancer Center, Beijing 302 Hospital, Beijing 100039, P.R. China,
| | - Zhiqin Zhao
- Comprehensive Liver Cancer Center, Beijing 302 Hospital, Beijing 100039, P.R. China,
| | - Ze Liu
- Comprehensive Liver Cancer Center, Beijing 302 Hospital, Beijing 100039, P.R. China,
| | - Wenlin Bai
- Comprehensive Liver Cancer Center, Beijing 302 Hospital, Beijing 100039, P.R. China,
| | - Zheng Dong
- Comprehensive Liver Cancer Center, Beijing 302 Hospital, Beijing 100039, P.R. China,
| | - Hongjin Liu
- Comprehensive Liver Cancer Center, Beijing 302 Hospital, Beijing 100039, P.R. China,
| | - Xiaoxia Lu
- Comprehensive Liver Cancer Center, Beijing 302 Hospital, Beijing 100039, P.R. China,
| | - Yunfeng Zhu
- College of Life Sciences and Bio-Engineering, Beijing Jiaotong University, Beijing 100044, P.R. China, .,Cancer Center in Division of Internal Medicine, Chinese PLA General Hospital, Beijing 100853, P.R. China,
| | - Yinying Lu
- Comprehensive Liver Cancer Center, Beijing 302 Hospital, Beijing 100039, P.R. China,
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Line-1: Implications in the etiology of cancer, clinical applications, and pharmacologic targets. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 778:51-60. [DOI: 10.1016/j.mrrev.2018.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/15/2018] [Accepted: 09/17/2018] [Indexed: 11/21/2022]
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35
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A novel high-sensitivity assay to detect a small fraction of mutant IDH1 using droplet digital PCR. Brain Tumor Pathol 2018; 35:97-105. [DOI: 10.1007/s10014-018-0310-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 02/14/2018] [Indexed: 02/05/2023]
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36
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Hamzeiy H, Savaş D, Tunca C, Şen NE, Gündoğdu Eken A, Şahbaz I, Calini D, Tiloca C, Ticozzi N, Ratti A, Silani V, Başak AN. Elevated Global DNA Methylation Is Not Exclusive to Amyotrophic Lateral Sclerosis and Is Also Observed in Spinocerebellar Ataxia Types 1 and 2. NEURODEGENER DIS 2018; 18:38-48. [PMID: 29428949 DOI: 10.1159/000486201] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 12/08/2017] [Indexed: 12/12/2022] Open
Abstract
Adult-onset neurological disorders are caused and influenced by a multitude of different factors, including epigenetic modifications. Here, using an ELISA kit selected upon careful testing, we investigated global 5-methylcytosine (5-mC) levels in sporadic and familial amyotrophic lateral sclerosis (sALS and fALS), spinocerebellar ataxia types 1 and 2 (SCA1 and SCA2), Huntington's disease, Friedreich's ataxia, and myotonic dystrophy type 1. We report a significant elevation in global 5-mC levels of about 2-7% on average for sALS (p < 0.01 [F(1, 243) = 9.159, p = 0.0027]) and various forms of fALS along with SCA1 (p < 0.01 [F(1, 83) = 11.285], p = 0.0012) and SCA2 (p < 0.001 [F(1, 122) = 29.996, p = 0.0001]) when compared to age- and sex-matched healthy controls. C9orf72 expansion carrier ALS patients exhibit the highest global 5-mC levels along with C9orf72 promoter hypermethylation. We failed to measure global 5-hydroxymethylcytosine (5-hmC) levels in blood, probably due to the very low levels of 5-hmC and the limitations of the commercially available ELISA kits. Our results point towards a role for epigenetics modification in ALS, SCA1, and SCA2, and help conclude a dispute on the global 5-mC levels in sALS blood.
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Affiliation(s)
- Hamid Hamzeiy
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Doruk Savaş
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Ceren Tunca
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Nesli Ece Şen
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Aslı Gündoğdu Eken
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Irmak Şahbaz
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Daniela Calini
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Cinzia Tiloca
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Nicola Ticozzi
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Milan, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Milan, Italy
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Milan, Italy
| | - A Nazlı Başak
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
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O'Regan CJ, Kearney H, Beausang A, Farrell MA, Brett FM, Cryan JB, Loftus TE, Buckley PG. Temporal stability of MGMT promoter methylation in glioblastoma patients undergoing STUPP protocol. J Neurooncol 2017; 137:233-240. [PMID: 29264834 DOI: 10.1007/s11060-017-2722-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/13/2017] [Indexed: 12/11/2022]
Abstract
Epigenetic silencing of O-6-methylguanine-DNA methyltransferase (MGMT) promoter via methylation in a glioblastoma (GBM), has been correlated with a more favourable response to alkylating chemotherapeutic agents such as temozolomide. The use of global methylation surrogates such as Long Interspersed Nucleotide Element 1 (LINE1) may also be valuable in order to fully understand these highly heterogeneous tumours. In this study, we analysed both original and recurrent GBMs in 22 patients (i.e. 44 tumours), for both MGMT and LINE1 methylation status. In the 22 patients: 14 (63.6%) displayed MGMT methylation stability in the recurrent GBM versus 8 (36.4%), with instability of methylation status. No significant differences in overall and progression free survival was evident between these two groups. LINE1 methylation status remained stable for 12 (54.5%) of recurrent GBM patients versus 9 (41%) of the patients with instability in LINE1 methylation status (p = 0.02), resulting in an increase in overall survival of the stable LINE1 group (p = 0.04). The results obtained demonstrated major epigenetic instability of GBMs treated with temozolomide as part of the STUPP protocol. GBMs appear to undergo selective evolution post-treatment, and have the ability to recur with a newly reprogrammed epigenetic status. Selective targeting of the altered epigenomes in recurrent GBMs may facilitate the future development of both prognostic biomarkers and enhanced therapeutic strategies.
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Affiliation(s)
- C J O'Regan
- Department of Molecular Pathology, Beaumont Hospital, Dublin, Ireland.
| | - H Kearney
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - A Beausang
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - M A Farrell
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - F M Brett
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - J B Cryan
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - T E Loftus
- Department of Molecular Pathology, Beaumont Hospital, Dublin, Ireland
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Meng W, Jiang Y, Ma J. Is the prognostic significance of O6-methylguanine- DNA methyltransferase promoter methylation equally important in glioblastomas of patients from different continents? A systematic review with meta-analysis. Cancer Manag Res 2017; 9:411-425. [PMID: 29033608 PMCID: PMC5614747 DOI: 10.2147/cmar.s140447] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND O6-methylguanine-DNA methyltransferase (MGMT) is an independent predictor of therapeutic response and potential prognosis in patients with glioblastoma multiforme (GBM). However, its significance of clinical prognosis in different continents still needs to be explored. PATIENTS AND METHODS To explore the effects of MGMT promoter methylation on both progression-free survival (PFS) and overall survival (OS) among GBM patients from different continents, a systematic review of published studies was conducted. RESULTS A total of 5103 patients from 53 studies were involved in the systematic review and the total percentage of MGMT promoter methylation was 45.53%. Of these studies, 16 studies performed univariate analyses and 17 performed multivariate analyses of MGMT promoter methylation on PFS. The pooled hazard ratio (HR) estimated for PFS was 0.55 (95% CI 0.50, 0.60) by univariate analysis and 0.43 (95% CI 0.38, 0.48) by multivariate analysis. The effect of MGMT promoter methylation on OS was explored in 30 studies by univariate analysis and in 30 studies by multivariate analysis. The combined HR was 0.48 (95% CI 0.44, 0.52) and 0.42 (95% CI 0.38, 0.45), respectively. CONCLUSION In each subgroup divided by areas, the prognostic significance still remained highly significant. The proportion of methylation in each group was in inverse proportion to the corresponding HR in the univariate and multivariate analyses of PFS. However, from the perspective of OS, compared with data from Europe and the US, higher methylation rates in Asia did not bring better returns.
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Affiliation(s)
- Wei Meng
- Department of Pediatric Neurosurgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai
| | - Yangyang Jiang
- Department of Neurosurgery, Shanghai Deji Hospital, Shanghai Neuromedical Center Affiliated to Qingdao University, Shanghai, People's Republic of China
| | - Jie Ma
- Department of Pediatric Neurosurgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai
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Jeong S, Lee K, Wen X, Kim Y, Cho NY, Jang JJ, Kang GH. Tumoral LINE-1 hypomethylation is associated with poor survival of patients with intrahepatic cholangiocarcinoma. BMC Cancer 2017; 17:588. [PMID: 28851390 PMCID: PMC5576385 DOI: 10.1186/s12885-017-3595-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 08/23/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND DNA methylation changes occurring in cancer cells are featured with both promoter CpG island hypermethylation and diffuse genomic hypomethylation. Long interspersed element-1 (LINE-1) is repeated in an interspersed manner with an estimated 500,000 copies per genome. LINE-1 has its CpG sites of the 5' untranslated region methylated heavily in normal cells and undergoes demethylation in association with cancerization. However, little information is available regarding LINE-1 hypomethylation and its prognostic implication in intrahepatic cholangiocarcinomas. METHODS A total of 172 cases of intrahepatic cholangiocarcinomas were analyzed for their methylation levels at four CpG sites of LINE-1 using bisulfite pyrosequencing. We examined the relation between tumoral LINE-1 methylation level and clinicopathological features, including survival. RESULTS Tumor differentiation, lymphatic invasion, and T stage were associated with a low average methylation level of LINE-1 at the four CpG sites; LINE-1 methylation level tended to be lower in high-grade differentiation, lymphatic emboli, and higher T stage. LINE-1 hypomethylation was significantly linked with lower cancer-specific survival in patients with intrahepatic cholangiocarcinoma and was found to be an independent prognostic parameter. CONCLUSIONS Our findings suggest that tumoral LINE-1 hypomethylation could be a molecular biomarker heralding poor prognosis of patients with intrahepatic cholangiocarcinoma. Our findings need to be validated in further study.
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Affiliation(s)
- Seorin Jeong
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Kyoungbun Lee
- Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea
| | - Xianyu Wen
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea
| | - Younghoon Kim
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea
| | - Nam-Yun Cho
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Ja-June Jang
- Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea
| | - Gyeong Hoon Kang
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea. .,Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea. .,Laboratory of Epigenetics, Cancer Research Institute, Department of Pathology, Seoul National University College of Medicine, Seoul, Korea.
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40
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Multiple endpoints to evaluate pristine and remediated titanium dioxide nanoparticles genotoxicity in lung epithelial A549 cells. Toxicol Lett 2017; 276:48-61. [DOI: 10.1016/j.toxlet.2017.05.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 05/05/2017] [Accepted: 05/15/2017] [Indexed: 12/14/2022]
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41
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Shen J, Song R, Gong Y, Zhao H. Global DNA hypomethylation in leukocytes associated with glioma risk. Oncotarget 2017; 8:63223-63231. [PMID: 28968983 PMCID: PMC5609915 DOI: 10.18632/oncotarget.18739] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 05/21/2017] [Indexed: 11/25/2022] Open
Abstract
Global DNA hypomethylation in leukocytes has been associated with increased risk for a variety of cancers. However, the role of leukocyte global DNA hypomethylation in glioma development, if any, is largely unknown. To define this role, we performed a case-control study with 390 glioma patients and 390 controls with no known cancer. Levels of 5-methylcytosine (5-mC%), a marker for global DNA methylation, were measured in leukocyte DNA. Overall, median levels of 5-mC% were significantly lower in glioma cases than in controls (3.45 vs 3.82, P=0.001). Levels of 5-mC% differed significantly by age and sex among controls and by tumor subtype and grade among glioma cases. In multivariate analysis, lower levels of 5-mC% were associated with a 1.31-fold increased risk of glioma (odds ratio = 1.31, 95% confidence interval = 1.10-1.41). A significant dose-response trend was observed in quartile analysis (P=0.001). In an analysis further stratified by clinical characteristics at baseline, the association between lower levels of 5-mC% and glioma risk was evident only among younger participants (age <52 years), women, and those with aggressive tumor characteristics, such as glioblastoma subtype, high tumor grade (grade III or IV), and absence of IDH1 mutation. Our findings indicate that global DNA hypomethylation in leukocytes may contribute to the development of glioma and that the association is affected by age, sex, and tumor aggressiveness.
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Affiliation(s)
- Jie Shen
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Renduo Song
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ye Gong
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hua Zhao
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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DNA methylation variations are required for epithelial-to-mesenchymal transition induced by cancer-associated fibroblasts in prostate cancer cells. Oncogene 2017; 36:5551-5566. [PMID: 28581528 DOI: 10.1038/onc.2017.159] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 04/08/2017] [Accepted: 04/14/2017] [Indexed: 12/26/2022]
Abstract
Widespread genome hypo-methylation and promoter hyper-methylation of epithelium-specific genes are hallmarks of stable epithelial-to-mesenchymal transition (EMT), which in prostate cancer (PCa) correlates with castration resistance, cancer stem cells generation, chemoresistance and worst prognosis. Exploiting our consolidated 'ex-vivo' system, we show that cancer-associated fibroblasts (CAFs) released factors have pivotal roles in inducing genome methylation changes required for EMT and stemness in EMT-prone PCa cells. By global DNA methylation analysis and RNA-Seq, we provide compelling evidence that conditioned media from CAFs explanted from two unrelated patients with advanced PCa, stimulates concurrent DNA hypo- and hyper-methylation required for EMT and stemness in PC3 and DU145, but not in LN-CaP and its derivative C4-2B, PCa cells. CpG island (CGI) hyper-methylation associates with repression of genes required for epithelial maintenance and invasion antagonism, whereas activation of EMT markers and stemness genes correlate with CGI hypo-methylation. Remarkably, methylation variations and EMT-regulated transcripts almost completely reverse qualitatively and quantitatively during MET. Unsupervised clustering analysis of the PRAD TCGA data set with the differentially expressed (DE) and methylated EMT signature, identified a gene cluster of DE genes defined by a CAF+ and AR- phenotype and worst diagnosis. This gene cluster includes the relevant factors for EMT and stemness, which display DNA methylation variations in regulatory regions inversely correlated to their expression changes, thus strongly sustaining the ex-vivo data. DNMT3A-dependent methylation is essential for silencing epithelial maintenance and EMT counteracting genes, such as CDH1 and GRHL2, that is, the direct repressor of ZEB1, the key transcriptional factor for EMT and stemness. Accordingly, DNMT3A knock-down prevents EMT entry. These results shed light on the mechanisms of establishment and maintenance of coexisting DNA hypo- and hyper-methylation patterns during cancer progression, the generation of EMT and cell stemness in advanced PCa, and may pave the way to new therapeutic implications.
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LINE-1 methylation level and prognosis in pancreas cancer: pyrosequencing technology and literature review. Surg Today 2017; 47:1450-1459. [DOI: 10.1007/s00595-017-1539-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/04/2017] [Indexed: 12/18/2022]
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Genome-wide methylation profiles in primary intracranial germ cell tumors indicate a primordial germ cell origin for germinomas. Acta Neuropathol 2017; 133:445-462. [PMID: 28078450 DOI: 10.1007/s00401-017-1673-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 12/29/2016] [Accepted: 01/07/2017] [Indexed: 01/01/2023]
Abstract
Intracranial germ cell tumors (iGCTs) are the second most common brain tumors among children under 14 in Japan. The World Health Organization classification recognizes several subtypes of iGCTs, which are conventionally subclassified into pure germinoma or non-germinomatous GCTs. Recent exhaustive genomic studies showed that mutations of the genes involved in the MAPK and/or PI3K pathways are common in iGCTs; however, the mechanisms of how different subtypes develop, often as a mixed-GCT, are unknown. To elucidate the pathogenesis of iGCTs, we investigated 61 GCTs of various subtypes by genome-wide DNA methylation profiling. We showed that pure germinomas are characterized by global low DNA methylation, a unique epigenetic feature making them distinct from all other iGCTs subtypes. The patterns of methylation strongly resemble that of primordial germ cells (PGC) at the migration phase, possibly indicating the cell of origin for these tumors. Unlike PGC, however, hypomethylation extends to long interspersed nuclear element retrotransposons. Histologically and epigenetically distinct microdissected components of mixed-GCTs shared identical somatic mutations in the MAPK or PI3K pathways, indicating that they developed from a common ancestral cell.
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45
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Wen X, Jeong S, Kim Y, Bae JM, Cho NY, Kim JH, Kang GH. Improved results of LINE-1 methylation analysis in formalin-fixed, paraffin-embedded tissues with the application of a heating step during the DNA extraction process. Clin Epigenetics 2017; 9:1. [PMID: 28149329 PMCID: PMC5270344 DOI: 10.1186/s13148-016-0308-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/26/2016] [Indexed: 12/20/2022] Open
Abstract
Background Formalin-fixed, paraffin-embedded (FFPE) tissues are important resources for profiling DNA methylation changes and for studying a variety of diseases. However, formalin fixation introduces inter-strand crosslinking, which might cause incomplete bisulfite conversion of unmethylated cytosines, which might lead to falsely elevated measurements of methylation levels in pyrosequencing assays. Long interspersed nucleotide element-1 (LINE-1) is a major constituent of repetitive transposable DNA elements, and its methylation is referred to correlates with global DNA methylation. To identify whether formalin fixation might impact the measured values of methylation in LINE-1 repetitive elements and whether prolonged heat-induced denaturation of DNA might reduce the artificial increases in measured values caused by formalin fixation, we analyzed paired fresh-frozen (FF) and FFPE xenograft tissue samples for their methylation levels in LINE-1 using a pyrosequencing assay. To further confirm the effect of a heating step in the measurement of LINE-1 or single gene methylation levels, we analyzed FFPE tissue samples of gastric cancer and colorectal cancer for their methylation status in LINE-1 and eight single genes, respectively. Results Formalin fixation led to an increase in the measured values of LINE-1 methylation regardless of the duration of fixation. Prolonged heating of the DNA at 95 °C for 30 min before bisulfite conversion was found (1) to decrease the discrepancy in the measured values between the paired FF and FFPE tissue samples, (2) to decrease the standard deviation of the measured value of LINE-1 methylation levels in FFPE tissue samples of gastric cancer, and (3) to improve the performance in the measurement of single gene methylation levels in FFPE tissue samples of colorectal cancer. Conclusions Formalin fixation leads to artificial increases in the measured values of LINE-1 methylation, and the application of prolonged heating of DNA samples decreases the discrepancy in the measured values of LINE-1 methylation between paired FF and FFPE tissue samples. The application of prolonged heating of DNA samples improves bisulfite conversion-based measurement of LINE-1 or single gene methylation levels in FFPE tissue samples. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0308-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xianyu Wen
- Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea.,Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea
| | - Seorin Jeong
- Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea
| | - Younghoon Kim
- Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea.,Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea
| | - Jeong Mo Bae
- Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea.,Department of Pathology, SMG-SNU Boramae Medical Centre, Seoul, South Korea
| | - Nam Yun Cho
- Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea
| | - Jung Ho Kim
- Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea.,Department of Pathology, SMG-SNU Boramae Medical Centre, Seoul, South Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea.,Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea
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A CpG island methylator phenotype in acute myeloid leukemia independent of IDH mutations and associated with a favorable outcome. Leukemia 2017; 31:2011-2019. [PMID: 28074068 PMCID: PMC5537054 DOI: 10.1038/leu.2017.12] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 12/12/2022]
Abstract
Genetic changes are infrequent in acute myeloid leukemia (AML) compared to other malignancies and often involve epigenetic regulators, suggesting that an altered epigenome may underlie AML biology and outcomes. In 96 AML cases including 65 pilot samples selected for cured/not-cured, we found higher CpG island (CGI) promoter methylation in cured patients. Expanded genome-wide digital restriction enzyme analysis of methylation (DREAM) data revealed a CGI methylator phenotype independent of IDH1/2 mutations we term AML-CIMP (A-CIMP+). A-CIMP was associated with longer overall survival (OS) in this dataset (median OS, years: A-CIMP+ = Not reached, A-CIMP− =1.17; P=0.08). For validation we used 194 samples from The Cancer Genome Atlas interrogated with Illumina 450k methylation arrays where we confirmed longer OS in A-CIMP (median OS, years: A-CIMP+ =2.34, A-CIMP− =1.00; P=0.01). Hypermethylation in A-CIMP favored CGIs (OR: CGI/non-CGI=5.21), and while A-CIMP was enriched in CEBPA (P=0.002) and WT1 mutations (P=0.02), 70% of cases lacked either mutation. Hypermethylated genes in A-CIMP function in pluripotency maintenance, and a gene expression signature of A-CIMP was associated with outcomes in multiple datasets. We conclude that CIMP in AML cannot be explained solely by gene mutations (e.g. IDH1/2, TET2), and that curability in A-CIMP+ AML should be validated prospectively.
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Subhash S, Andersson PO, Kosalai ST, Kanduri C, Kanduri M. Global DNA methylation profiling reveals new insights into epigenetically deregulated protein coding and long noncoding RNAs in CLL. Clin Epigenetics 2016; 8:106. [PMID: 27777635 PMCID: PMC5062931 DOI: 10.1186/s13148-016-0274-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/04/2016] [Indexed: 12/19/2022] Open
Abstract
Background Methyl-CpG-binding domain protein enriched genome-wide sequencing (MBD-Seq) is a robust and powerful method for analyzing methylated CpG-rich regions with complete genome-wide coverage. In chronic lymphocytic leukemia (CLL), the role of CpG methylated regions associated with transcribed long noncoding RNAs (lncRNA) and repetitive genomic elements are poorly understood. Based on MBD-Seq, we characterized the global methylation profile of high CpG-rich regions in different CLL prognostic subgroups based on IGHV mutational status. Results Our study identified 5800 hypermethylated and 12,570 hypomethylated CLL-specific differentially methylated genes (cllDMGs) compared to normal controls. From cllDMGs, 40 % of hypermethylated and 60 % of hypomethylated genes were mapped to noncoding RNAs. In addition, we found that the major repetitive elements such as short interspersed elements (SINE) and long interspersed elements (LINE) have a high percentage of cllDMRs (differentially methylated regions) in IGHV subgroups compared to normal controls. Finally, two novel lncRNAs (hypermethylated CRNDE and hypomethylated AC012065.7) were validated in an independent CLL sample cohort (48 samples) compared with 6 normal sorted B cell samples using quantitative pyrosequencing analysis. The methylation levels showed an inverse correlation to gene expression levels analyzed by real-time quantitative PCR. Notably, survival analysis revealed that hypermethylation of CRNDE and hypomethylation of AC012065.7 correlated with an inferior outcome. Conclusions Thus, our comprehensive methylation analysis by MBD-Seq provided novel hyper and hypomethylated long noncoding RNAs, repetitive elements, along with protein coding genes as potential epigenetic-based CLL-signature genes involved in disease pathogenesis and prognosis. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0274-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Santhilal Subhash
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Per-Ola Andersson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden ; Department of Internal Medicine, Södra Älvsborg Hospital, Borås, Sweden
| | - Subazini Thankaswamy Kosalai
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, S-413 45 Gothenburg, Sweden
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Knothe C, Shiratori H, Resch E, Ultsch A, Geisslinger G, Doehring A, Lötsch J. Disagreement between two common biomarkers of global DNA methylation. Clin Epigenetics 2016; 8:60. [PMID: 27222668 PMCID: PMC4877994 DOI: 10.1186/s13148-016-0227-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/10/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The quantification of global DNA methylation has been established in epigenetic screening. As more practicable alternatives to the HPLC-based gold standard, the methylation analysis of CpG islands in repeatable elements (LINE-1) and the luminometric methylation assay (LUMA) of overall 5-methylcytosine content in "CCGG" recognition sites are most widely used. Both methods are applied as virtually equivalent, despite the hints that their results only partly agree. This triggered the present agreement assessments. RESULTS Three different human cell types (cultured MCF7 and SHSY5Y cell lines treated with different chemical modulators of DNA methylation and whole blood drawn from pain patients and healthy volunteers) were submitted to the global DNA methylation assays employing LINE-1 or LUMA-based pyrosequencing measurements. The agreement between the two bioassays was assessed using generally accepted approaches to the statistics for laboratory method comparison studies. Although global DNA methylation levels measured by the two methods correlated, five different lines of statistical evidence consistently rejected the assumption of complete agreement. Specifically, a bias was observed between the two methods. In addition, both the magnitude and direction of bias were tissue-dependent. Interassay differences could be grouped based on Bayesian statistics, and these groups allowed in turn to re-identify the originating tissue. CONCLUSIONS Although providing partly correlated measurements of DNA methylation, interchangeability of the quantitative results obtained with LINE-1 and LUMA was jeopardized by a consistent bias between the results. Moreover, the present analyses strongly indicate a tissue specificity of the differences between the two methods.
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Affiliation(s)
- Claudia Knothe
- />Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Hiromi Shiratori
- />Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Eduard Resch
- />Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Alfred Ultsch
- />DataBionics Research Group, University of Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
| | - Gerd Geisslinger
- />Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- />Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Alexandra Doehring
- />Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Jörn Lötsch
- />Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- />Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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Abstract
Background IDH (Isocitrate dehydrogenase) mutations occur frequently in gliomas, but their prognostic impact has not been fully assessed. We performed a meta-analysis of the association between IDH mutations and survival in gliomas. Methods Pubmed and EMBASE databases were searched for studies reporting IDH mutations (IHD1/2 and IDH1) and survival in gliomas. The primary outcome was overall survival (OS); the secondary outcome was progression-free survival (PFS). Hazard ratios (HR) with 95% confidence interval (CI) were determined using the Mantel-Haenszel random-effect modeling. Funnel plot and Egger's test were conducted to examine the risk of publication bias. Results Fifty-five studies (9487 patients) were included in the analysis. Fifty-four and twenty-seven studies investigated the association between IDH1/2 mutations and OS/PFS respectively in patients with glioma. The results showed that patients possessing an IDH1/2 mutation had significant advantages in OS (HR = 0.39, 95%CI: 0.34–0.45; P < 0.001) and PFS (HR = 0.42, 95% CI: 0.35–0.51; P < 0.001). Subgroup analysis showed a consistent result with pooled analysis, and patients with glioma of WHO grade III or II-III had better outcomes. Conclusions These findings provide further indication that patients with glioma harboring IDH mutations have improved OS and PFS, especially for patients with WHO grade III and grade II-III.
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Chen JR, Yao Y, Xu HZ, Qin ZY. Isocitrate Dehydrogenase (IDH)1/2 Mutations as Prognostic Markers in Patients With Glioblastomas. Medicine (Baltimore) 2016; 95:e2583. [PMID: 26945349 PMCID: PMC4782833 DOI: 10.1097/md.0000000000002583] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The purpose of this study was to perform a meta-analysis examining the association of isocitrate dehydrogenase (IDH)1/2 mutations with overall survival (OS) and progression-free survival (PFS) in patients with glioblastomas. Medline, Cochrane, EMBASE, and Google Scholar were searched from inception to January 28, 2015, using combinations of the following keywords: IDH mutation, brain tumor, glioma, glioblastoma, oligodendroglioma, prognosis. Randomized controlled trials, and prospective and retrospective studies of patients with glioblastomas that provided IDH mutation and survival data were included. OS and PFS were used to evaluate the association of IDH1 and IDH1/2 mutations and prognosis. Hazard ratios (HRs) with corresponding 95% confidence intervals (CIs) for OS and PFS were calculated and compared between patients with and without mutations. Of 165 studies that were identified, 136 nonrelevant studies were excluded. Twenty-nine full-text articles were assessed, and of these, 5 were excluded as they did not provide a quantitative outcome. Therefore, 24 studies were included in the qualitative synthesis. The pooled HR of 0.358 (95% CI 0.264-0.487, P < 0.001) indicated that IDH mutations were associated with better OS. Similarly, the pooled HR of 0.322 (95% CI 0.24200.455, P < 0.001) indicated that IDH mutations were associated with better PFS. When patients were stratified by surgery versus no surgery or IDH1 versus IDH1/2 mutations, the results also indicated that the presence of IDH mutations was associated with better OS and PFS. The IDH mutations are associated with improved survival in patients with glioblastomas.
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Affiliation(s)
- Jun-Rui Chen
- From the Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
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