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Lin SM, Huang HT, Fang PJ, Chang CF, Satange R, Chang CK, Chou SH, Neidle S, Hou MH. Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation. Nucleic Acids Res 2024:gkae594. [PMID: 38989613 DOI: 10.1093/nar/gkae594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/30/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Non-CpG methylation is associated with several cellular processes, especially neuronal development and cancer, while its effect on DNA structure remains unclear. We have determined the crystal structures of DNA duplexes containing -CGCCG- regions as CCG repeat motifs that comprise a non-CpG site with or without cytosine methylation. Crystal structure analyses have revealed that the mC:G base-pair can simultaneously form two alternative conformations arising from non-CpG methylation, including a unique water-mediated cis Watson-Crick/Hoogsteen, (w)cWH, and Watson-Crick (WC) geometries, with partial occupancies of 0.1 and 0.9, respectively. NMR studies showed that an alternative conformation of methylated mC:G base-pair at non-CpG step exhibits characteristics of cWH with a syn-guanosine conformation in solution. DNA duplexes complexed with the DNA binding drug echinomycin result in increased occupancy of the (w)cWH geometry in the methylated base-pair (from 0.1 to 0.3). Our structural results demonstrated that cytosine methylation at a non-CpG step leads to an anti→syntransition of its complementary guanosine residue toward the (w)cWH geometry as a partial population of WC, in both drug-bound and naked mC:G base pairs. This particular geometry is specific to non-CpG methylated dinucleotide sites in B-form DNA. Overall, the current study provides new insights into DNA conformation during epigenetic regulation.
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Affiliation(s)
- Shan-Meng Lin
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Hsiang-Ti Huang
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Pei-Ju Fang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Roshan Satange
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Chung-Ke Chang
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Shan-Ho Chou
- Institute of Biochemistry, National Chung Hsing University, Taichung 402, Taiwan
| | - Stephen Neidle
- School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Ming-Hon Hou
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
- Doctoral Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
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2
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The promoter methylation drives down-regulation mode of HIC1 in gastric cancer, its molecular characteristics and downstream functional pathways. Gene 2022; 824:146380. [PMID: 35276239 DOI: 10.1016/j.gene.2022.146380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/10/2022] [Accepted: 02/24/2022] [Indexed: 01/09/2023]
Abstract
Gastric cancer is a common malignant tumor of the gastrointestinal tract with a high incidence and mortality rate. Previous results have suggested that the HIC1 gene might be a tumor suppressor candidate in gastric cancer. However, several critical points need to be elucidated: (1) The correlation of HIC1 promoter methylation with its specific expression level in gastric cancer; (2) The molecular characterization of HIC1 promoter methylation; (3) The possible mechanism by which HIC1 performs its inhibitory role in gastric cancer. To address these questions, we retrieved data from TCGA database to analyze HIC1 promoter methylation levels and transcript expression data, and performed targeted region bisulfite sequencing on three stable HIC1 down-regulated cell lines and normal control cell lines, and performed whole transcriptome and metabolite assays in HIC1 knockout cell lines by CRISPR-Cas9 technique. Results demonstrated that HIC1 promoter hypermethylation might be a crucial driving force leading to its down-regulation in HIC1 expression in gastric cancer. This implicated that promoter CG methylation of HIC1 might play a major role in the development of gastric carcinogenesis. Besides, HIC1 may suppress gastric cancer progression by maintaining the normal cellular metabolism, and inhibiting the mTOR signaling pathway activity.
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Starzer AM, Heller G, Tomasich E, Melchardt T, Feldmann K, Hatziioannou T, Traint S, Minichsdorfer C, Schwarz-Nemec U, Nackenhorst M, Müllauer L, Preusser M, Berghoff AS, Fuereder T. DNA methylation profiles differ in responders versus non-responders to anti-PD-1 immune checkpoint inhibitors in patients with advanced and metastatic head and neck squamous cell carcinoma. J Immunother Cancer 2022; 10:jitc-2021-003420. [PMID: 35338086 PMCID: PMC8961155 DOI: 10.1136/jitc-2021-003420] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Biomarkers for response prediction to anti-programmed cell death 1 (PD-1) immune checkpoint inhibitors (ICI) in patients with head and neck squamous cell carcinoma (HNSCC) are urgently needed for a personalized therapy approach. We investigated the predictive potential of inflammatory parameters and DNA methylation profiling in patients with HNSCC treated with anti-PD-1 ICI. METHODS We identified patients with HNSCC that were treated with anti-PD-1 ICI therapy in the recurrent or metastatic setting after progression to platinum-based chemotherapy in two independent centers. We analyzed DNA methylation profiles of >850.000 CpG sites in tumor specimens of these patients by Infinium MethylationEPIC microarrays, immune cell density in the tumor microenvironment (CD8, CD3, CD45RO, forkhead box P3 (FOXP3), CD68), PD-1 and programmed cell death ligand 1 (PD-L1) expression by immunohistochemistry, and blood inflammation markers (platelet-to-lymphocyte ratio, leucocyte-to-lymphocyte ratio, monocyte-to-lymphocyte ratio, neutrophil-to-lymphocyte ratio). DNA methylation profiles and immunological markers were bioinformatically and statistically correlated with radiological response to anti-PD-1 ICI. RESULTS 37 patients with HNSCC (median age of 62 years; range 49-83; 8 (21.6%) women, 29 (78.4%) men) were included (Center 1 N=26, 70.3%; Center 2 N=11, 29.7%). Median number of prior systemic therapies was 1 (range 1-4). Five out of 37 (13.5%) patients achieved an objective response to ICI. Median progression-free survival and median overall survival times were 3.7 months (range 0-22.9) and 9.0 months (range 0-38.8), respectively. Microarray analyses revealed a methylation signature including both hypomethylation and hypermethylation which was predictive for response to ICI and included several genes involved in cancer-related molecular pathways. Over-represented differentially methylated genes between responders and non-responders were associated with 'Axon guidance', 'Hippo signaling', 'Pathways in cancer' and 'MAPK signaling'. A statistically significant correlation of PD-L1 expression and response was present (p=0.0498). CONCLUSIONS Our findings suggest that tumor DNA methylation profiling may be useful to predict response to ICI in patients with HNSCC.
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Affiliation(s)
- Angelika Martina Starzer
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria.,Department of Medicine I, Christian Doppler Laboratory for Personalized Immunotherapy, Medical University of Vienna, Vienna, Austria
| | - Gerwin Heller
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria.,Department of Medicine I, Christian Doppler Laboratory for Personalized Immunotherapy, Medical University of Vienna, Vienna, Austria
| | - Erwin Tomasich
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria.,Department of Medicine I, Christian Doppler Laboratory for Personalized Immunotherapy, Medical University of Vienna, Vienna, Austria
| | - Thomas Melchardt
- Laboratory for Immunological and Molecular Cancer Research, Department of Internal Medicine III with Hematology, Medical Oncology, Hemostaseology, Infectious Diseases, Rheumatology, Oncologic Center, Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Katharina Feldmann
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria.,Department of Medicine I, Christian Doppler Laboratory for Personalized Immunotherapy, Medical University of Vienna, Vienna, Austria
| | - Teresa Hatziioannou
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria.,Department of Medicine I, Christian Doppler Laboratory for Personalized Immunotherapy, Medical University of Vienna, Vienna, Austria
| | - Stefan Traint
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
| | - Christoph Minichsdorfer
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
| | - Ursula Schwarz-Nemec
- Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Maja Nackenhorst
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Leonhard Müllauer
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Matthias Preusser
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria.,Department of Medicine I, Christian Doppler Laboratory for Personalized Immunotherapy, Medical University of Vienna, Vienna, Austria
| | - Anna Sophie Berghoff
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria .,Department of Medicine I, Christian Doppler Laboratory for Personalized Immunotherapy, Medical University of Vienna, Vienna, Austria
| | - Thorsten Fuereder
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
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Ramasamy D, Deva Magendhra Rao AK, Rajkumar T, Mani S. Non-CpG methylation-a key epigenetic modification in cancer. Brief Funct Genomics 2021; 20:304-311. [PMID: 34318313 DOI: 10.1093/bfgp/elab035] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/28/2021] [Accepted: 07/02/2021] [Indexed: 12/17/2022] Open
Abstract
The methylation of cytosine residues that precede adenine/thymine or other cytosine nucleotides instead of guanine in DNA is known as non-CpG methylation. It is a pronounced epigenetic modification with a central role in gene regulation similar to CpG methylation. Due to technological limitations, the locus-specific role of non-CpG methylation was scarcely understood. At present, high-throughput analyses and improved enrichment methods can elucidate the role of genome-wide non-CpG methylation distributions. Although the functional basis of non-CpG methylation in regulating gene expression control is known, its role in cancer development is yet to be ascertained. This review sheds light on the possible mechanism of non-CpG methylation in embryos and developed tissues with a special focus on cancer development and progression. In particular, the maintenance and alteration of non-CpG methylation levels and the crucial factors that determine this level of non-CpG methylation and its functional role in cancer are discussed.
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Starzer AM, Berghoff AS, Hamacher R, Tomasich E, Feldmann K, Hatziioannou T, Traint S, Lamm W, Noebauer-Huhmann IM, Furtner J, Müllauer L, Amann G, Bauer S, Schildhaus HU, Preusser M, Heller G, Brodowicz T. Tumor DNA methylation profiles correlate with response to anti-PD-1 immune checkpoint inhibitor monotherapy in sarcoma patients. J Immunother Cancer 2021; 9:jitc-2020-001458. [PMID: 33762319 PMCID: PMC7993298 DOI: 10.1136/jitc-2020-001458] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Some sarcomas respond to immune checkpoint inhibition, but predictive biomarkers are unknown. We analyzed tumor DNA methylation profiles in relation to immunological parameters and response to anti-programmed cell death 1 (anti-PD-1) immune checkpoint inhibitor (ICI) therapy in patients with sarcoma. PATIENTS AND METHODS We retrospectively identified adult patients who had received anti-PD-1 ICI therapy for recurrent sarcoma in two independent centers. We performed (1) blinded radiological response evaluation according to immune response evaluation criteria in solid tumors (iRECIST) ; (2) tumor DNA methylation profiling of >850,000 probes using Infinium MethylationEPIC microarrays; (3) analysis of tumor-infiltrating immune cell subsets (CD3, CD8, CD45RO, FOXP3) and intratumoral expression of immune checkpoint molecules (PD-L1, PD-1, LAG-3) using immunohistochemistry; and (4) evaluation of blood-based systemic inflammation scores (neutrophil-to-lymphocyte ratio, leucocyte-to-lymphocyte ratio, monocyte-to-lymphocyte ratio, platelet-to-lymphocyte ratio). Response to anti-PD-1 ICI therapy was bioinformatically and statistically correlated with DNA methylation profiles and immunological data. RESULTS 35 patients (median age of 50 (23-81) years; 18 females, 17 males; 27 soft tissue sarcomas; 8 osteosarcomas) were included in this study. The objective response rate to anti-PD-1 ICI therapy was 22.9% with complete responses in 3 out of 35 and partial responses in 5 out of 35 patients. Adjustment of DNA methylation data for tumor-infiltrating immune cells resulted in identification of methylation differences between responders and non-responders to anti-PD-1 ICI. 2453 differentially methylated CpG sites (DMPs; 2043 with decreased and 410 with increased methylation) were identified. Clustering of sarcoma samples based on these DMPs revealed two main clusters: methylation cluster 1 (MC1) consisted of 73% responders and methylation cluster 2 (MC2) contained only non-responders to anti-PD-1 ICI. Median progression-free survival from anti-PD-1 therapy start of MC1 and MC2 patients was 16.5 and 1.9 months, respectively (p=0.001). Median overall survival of these patients was 34.4 and 8.0 months, respectively (p=0.029). The most prominent DNA methylation differences were found in pathways implicated in Rap1 signaling, focal adhesion, adherens junction Phosphoinositide 3-kinase (PI3K)-Akt signaling and extracellular matrix (ECM)-receptor interaction. CONCLUSIONS Our data demonstrate that tumor DNA methylation profiles may serve as a predictive marker for response to anti-PD-1 ICI therapy in sarcoma.
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Affiliation(s)
- Angelika M Starzer
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria.,Christian Doppler Laboratory for Personalized Immunotherapy, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Anna S Berghoff
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria.,Christian Doppler Laboratory for Personalized Immunotherapy, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Rainer Hamacher
- Department of Medical Oncology, Sarcoma Center, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Duisburg, Germany
| | - Erwin Tomasich
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Katharina Feldmann
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Teresa Hatziioannou
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Stefan Traint
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Lamm
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Iris M Noebauer-Huhmann
- Department of Biomedical Imaging and Image-guided Therapy, Division of General and Paediatric Radiology, Medical University of Vienna, Vienna, Austria
| | - Julia Furtner
- Department of Biomedical Imaging and Image-guided Therapy, Division of General and Paediatric Radiology, Medical University of Vienna, Vienna, Austria
| | - Leonhard Müllauer
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Gabriele Amann
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Sebastian Bauer
- Department of Medical Oncology, Sarcoma Center, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Duisburg, Germany
| | | | - Matthias Preusser
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria.,Christian Doppler Laboratory for Personalized Immunotherapy, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Gerwin Heller
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Thomas Brodowicz
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
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Grundy EE, Diab N, Chiappinelli KB. Transposable element regulation and expression in cancer. FEBS J 2021; 289:1160-1179. [PMID: 33471418 DOI: 10.1111/febs.15722] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/08/2021] [Accepted: 01/14/2021] [Indexed: 12/11/2022]
Abstract
Approximately 45% of the human genome is composed of transposable elements (TEs). Expression of these elements is tightly regulated during normal development. TEs may be expressed at high levels in embryonic stem cells but are epigenetically silenced in terminally differentiated cells. As part of the global 'epigenetic dysregulation' that cells undergo during transformation from normal to cancer, TEs can lose epigenetic silencing and become transcribed, and, in some cases, active. Here, we summarize recent advances detailing the consequences of TE activation in cancer and describe how these understudied residents of our genome can both aid tumorigenesis and potentially be harnessed for anticancer therapies.
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Affiliation(s)
- Erin E Grundy
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA.,The GW Cancer Center, The George Washington University, Washington, DC, USA.,The Institute for Biomedical Sciences at The George Washington University, Washington, DC, USA
| | - Noor Diab
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA.,The GW Cancer Center, The George Washington University, Washington, DC, USA
| | - Katherine B Chiappinelli
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA.,The GW Cancer Center, The George Washington University, Washington, DC, USA
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7
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Xiao W, Liu X, Niu X, Li C, Guo Y, Tan J, Xiong W, Fan L, Li Y. The frequency of CpG and non-CpG methylation of Notch3 gene promoter determines its expression levels in breast cancer cells. Exp Cell Res 2020; 386:111743. [PMID: 31770532 DOI: 10.1016/j.yexcr.2019.111743] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/17/2019] [Accepted: 11/20/2019] [Indexed: 02/05/2023]
Abstract
Notch3 can act as a tumor suppressor in the breast cancer epithelial cells. Unfortunately, Notch3 expression is decreased or lost, especially in triple-negative breast cancer (TNBC) cells, and the reasons remain unclear. Here, we found Notch3 was upregulated in MDA-MB-231 cells with 5-Aza treatment. Two CpG islands were observed in notch3 promoter. Interestingly, bisulfite sequencing exhibited that large amounts of unconverted cytosines were not only followed by guanine, but also adenine, cytosine and thymine, which implied that there simultaneously existed CpG and non-CpG methylation in notch3 promoter. To better analyze the methylation frequency of non-CpG locus, we designed CpG/non-CpG methylation analysis software. The results showed that the methylation frequency of notch3 gene in different breast cancer cell lines was in order T47D, MCF-7, SKBR3, BT-549 and MDA-MB-231. Furthermore, we identified that DNMT3b, DNMT1, DNMT3L, Mecp2 and EZH2 were important regulators of non-CpG locus of notch3 gene. Immunohistochemistry staining revealed a negative correlation between EZH2 and Notch3 from 22 luminal and 26 TNBC cases. In vitro methylation combined luciferase activity assays showed that non-CpG methylation was still crucial cause leading to notch3 transcriptional repression in TNBC. Our findings provide possible explanation for the downregulation or loss of Notch3 expression in TNBC.
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Affiliation(s)
- Wenjun Xiao
- The Central Laboratory of Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515031, China; Present Address: Health Science Center of Shenzhen University Medical College, Shenzhen, 518055, China
| | - Xiong Liu
- The Central Laboratory of Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515031, China
| | - Xia Niu
- The Central Laboratory of Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515031, China
| | - Chun Li
- The Central Laboratory of Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515031, China
| | - Yuxian Guo
- The Central Laboratory of Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515031, China
| | - Junyu Tan
- The Central Laboratory of Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515031, China
| | - Wei Xiong
- The Central Laboratory of Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515031, China
| | - Liping Fan
- The Central Laboratory of Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515031, China
| | - Yaochen Li
- The Central Laboratory of Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515031, China.
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8
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Piccirillo SGM, Spiteri I. Intratumor heterogeneity and transcriptional profiling in glioblastoma: translational opportunities. FUTURE NEUROLOGY 2015. [DOI: 10.2217/fnl.15.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The study of phenotypic and genetic intratumor heterogeneity in glioblastoma is attracting a lot of attention. Recent studies have demonstrated that transcriptional profiling analysis can help interpret the complexity of this disease. Previously proposed molecular classifiers have been recently challenged due to the unexpected degree of intratumor heterogeneity that has been described spatially and at single-cell level. Different computational methods have been employed to analyze this huge amount of data, but new experimental designs including multisampling from individual patients and single-cell experiments require new specific approaches. In light of these results, there is hope that integration of genetic, phenotypic and transcriptional data coupled with functional experiments might help define new therapeutic strategies and classify patients according to key pathways and molecular targets that can be further investigated to develop personalized and combinatorial treatment strategies.
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Affiliation(s)
- Sara GM Piccirillo
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0PY, UK
| | - Inmaculada Spiteri
- The Institute of Cancer Research, Centre for Evolution and Cancer, 15 Cotswold Road, Sutton SM2 5NG, UK
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9
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Gómez S, Castellano G, Mayol G, Suñol M, Queiros A, Bibikova M, Nazor KL, Loring JF, Lemos I, Rodríguez E, de Torres C, Mora J, Martín-Subero JI, Lavarino C. DNA methylation fingerprint of neuroblastoma reveals new biological and clinical insights. Epigenomics 2015; 7:1137-53. [PMID: 26067621 DOI: 10.2217/epi.15.49] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
AIM To define the DNA methylation landscape of neuroblastoma and its clinicopathological impact. MATERIALS & METHODS Microarray DNA methylation data were analyzed and associated with functional/regulatory genome annotation data, transcriptional profiles and clinicobiological parameters. RESULTS DNA methylation changes in neuroblastoma affect not only promoters but also intragenic and intergenic regions at cytosine-phosphate-guanine (CpG) and non-CpG sites, and target functional chromatin domains of development and cancer-related genes such as CCND1. Tumors with diverse clinical risk showed differences affecting CpG and, remarkably, non-CpG sites. Non-CpG methylation observed essentially in clinically favorable cases was associated with the differentiation status of neuroblastoma and expression of key genes such as ALK. CONCLUSION This epigenetic fingerprint of neuroblastoma provides new insights into the pathogenesis and clinical behavior of this pediatric tumor.
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Affiliation(s)
- Soledad Gómez
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Edificio Docente 4th floor, C/Santa Rosa 39-57, 08950 Esplugues de Llobregat, Barcelona, Spain
| | - Giancarlo Castellano
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, 08036, Spain
| | - Gemma Mayol
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Edificio Docente 4th floor, C/Santa Rosa 39-57, 08950 Esplugues de Llobregat, Barcelona, Spain
| | - Mariona Suñol
- Department of Pathology, Hospital Sant Joan de Déu, Barcelona, 08950, Spain
| | - Ana Queiros
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, 08036, Spain
| | | | - Kristopher L Nazor
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeanne F Loring
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Isadora Lemos
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Edificio Docente 4th floor, C/Santa Rosa 39-57, 08950 Esplugues de Llobregat, Barcelona, Spain
| | - Eva Rodríguez
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Edificio Docente 4th floor, C/Santa Rosa 39-57, 08950 Esplugues de Llobregat, Barcelona, Spain
| | - Carmen de Torres
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Edificio Docente 4th floor, C/Santa Rosa 39-57, 08950 Esplugues de Llobregat, Barcelona, Spain
| | - Jaume Mora
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Edificio Docente 4th floor, C/Santa Rosa 39-57, 08950 Esplugues de Llobregat, Barcelona, Spain
| | - José I Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, 08036, Spain.,Department of Anatomic Pathology, Pharmacology & Microbiology, University of Barcelona, Barcelona, 08036, Spain
| | - Cinzia Lavarino
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Edificio Docente 4th floor, C/Santa Rosa 39-57, 08950 Esplugues de Llobregat, Barcelona, Spain
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