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Mantel I, Sadiq BA, Blander JM. Spotlight on TAP and its vital role in antigen presentation and cross-presentation. Mol Immunol 2022; 142:105-119. [PMID: 34973498 PMCID: PMC9241385 DOI: 10.1016/j.molimm.2021.12.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/18/2021] [Accepted: 12/16/2021] [Indexed: 02/03/2023]
Abstract
In the late 1980s and early 1990s, the hunt for a transporter molecule ostensibly responsible for the translocation of peptides across the endoplasmic reticulum (ER) membrane yielded the successful discovery of transporter associated with antigen processing (TAP) protein. TAP is a heterodimer complex comprised of TAP1 and TAP2, which utilizes ATP to transport cytosolic peptides into the ER across its membrane. In the ER, together with other components it forms the peptide loading complex (PLC), which directs loading of high affinity peptides onto nascent major histocompatibility complex class I (MHC-I) molecules that are then transported to the cell surface for presentation to CD8+ T cells. TAP also plays a crucial role in transporting peptides into phagosomes and endosomes during cross-presentation in dendritic cells (DCs). Because of the critical role that TAP plays in both classical MHC-I presentation and cross-presentation, its expression and function are often compromised by numerous types of cancers and viruses to evade recognition by cytotoxic CD8 T cells. Here we review the discovery and function of TAP with a major focus on its role in cross-presentation in DCs. We discuss a recently described emergency route of noncanonical cross-presentation that is mobilized in DCs upon TAP blockade to restore CD8 T cell cross-priming. We also discuss the various strategies employed by cancer cells and viruses to target TAP expression or function to evade immunosurveillance - along with some strategies by which the repertoire of peptides presented by cells which downregulate TAP can be targeted as a therapeutic strategy to mobilize a TAP-independent CD8 T cell response. Lastly, we discuss TAP polymorphisms and the role of TAP in inherited disorders.
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Affiliation(s)
- Ian Mantel
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, New York, NY, 10021, USA; Joan and Sanford I. Weill Department of Medicine, New York, NY, 10021, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY, 10021, USA
| | - Barzan A Sadiq
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, New York, NY, 10021, USA; Joan and Sanford I. Weill Department of Medicine, New York, NY, 10021, USA
| | - J Magarian Blander
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, New York, NY, 10021, USA; Joan and Sanford I. Weill Department of Medicine, New York, NY, 10021, USA; Department of Microbiology and Immunology, New York, NY, 10021, USA; Sandra and Edward Meyer Cancer Center, New York, NY, 10021, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY, 10021, USA.
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2
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Herreros-Pomares A, Llorens C, Soriano B, Bagan L, Moreno A, Calabuig-Fariñas S, Jantus-Lewintre E, Bagan J. Differentially methylated genes in proliferative verrucous leukoplakia reveal potential malignant biomarkers for oral squamous cell carcinoma. Oral Oncol 2021; 116:105191. [PMID: 33657465 DOI: 10.1016/j.oraloncology.2021.105191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/31/2020] [Accepted: 01/13/2021] [Indexed: 01/03/2023]
Abstract
OBJECTIVES To explore the pathophysiology of proliferative verrucous leucoplakia (PVL) through a methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) case-control study. MATERIALS AND METHODS Oral biopsies from ten PVL patients and five healthy individuals were obtained and used to compare their epigenetic patterns. Network biology methods and integrative analyses of MeDIP-seq and RNAseq data were applied to investigate functional relations among differentially methylated genes (DMGs). The value of selected genes as malignant biomarkers was evaluated in a large cohort of oral squamous cell carcinoma (OSCC) patients from TCGA. RESULTS A total of 4647 differentially methylated regions were found, with a prominent state of hypermethylation in PVL patients. At the gene level, differentially methylated regions (DMRs) covered 826 genes with distinct roles, including transcription factors and binding proteins with functions in cell adhesion, migration, proliferation, regulation of transcription, bone morphogenesis, and cell signalling. Network analysis revealed three major hubs, two of them collecting proteins related to the response of the patients to PVL and treatment and one hub collecting proteins related to PVL and cancer. The integrative analysis revealed 8 genes (ARTN, CD8A, GATA3, HOXD10, MYO7A, OSR2, PLCB1, and SPOCK2) significantly upregulated in PVL compared to control and 5 genes (ANKRD6, DLG2, GPX3, PITX2, and ZNF736) significantly downregulated. The status of de-regulation found for PVL patients was concordant with what was found for OSCC samples compared to normal adjacent tissue. CONCLUSION Our findings show the potential of methylation markers in PVL and suggest novel OSCC diagnostic biomarkers which may boost the development of novel epigenetic-based therapies.
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Affiliation(s)
- Alejandro Herreros-Pomares
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, Valencia, Spain; CIBERONC, Valencia, Spain
| | - Carlos Llorens
- Biotechvana, Parc Cientific, Universitat de València, Paterna, Valencia, Spain
| | - Beatriz Soriano
- Biotechvana, Parc Cientific, Universitat de València, Paterna, Valencia, Spain
| | - Leticia Bagan
- Medicina Oral Unit, Stomatology Department, Valencia University, Spain
| | - Andrea Moreno
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, Valencia, Spain; TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, Valencia, Spain
| | - Silvia Calabuig-Fariñas
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, Valencia, Spain; CIBERONC, Valencia, Spain; TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, Valencia, Spain; Department of Pathology, Universitat de València, Valencia, Spain
| | - Eloísa Jantus-Lewintre
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, Valencia, Spain; CIBERONC, Valencia, Spain; TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, Valencia, Spain; Department of Biotechnology, Universitat Politècnica de València, Valencia, Spain.
| | - José Bagan
- CIBERONC, Valencia, Spain; Medicina Oral Unit, Stomatology Department, Valencia University, Spain; Department of Stomatology and Maxillofacial Surgery, Hospital General Universitario de Valencia, Valencia, Spain.
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3
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Marthong L, Ghosh S, Palodhi A, Imran M, Shunyu NB, Maitra A, Ghosh S. Whole Genome DNA Methylation and Gene Expression Profiling of Oropharyngeal Cancer Patients in North-Eastern India: Identification of Epigenetically Altered Gene Expression Reveals Potential Biomarkers. Front Genet 2020; 11:986. [PMID: 33133131 PMCID: PMC7578381 DOI: 10.3389/fgene.2020.00986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/05/2020] [Indexed: 12/31/2022] Open
Abstract
Oropharyngeal cancer is a subtype of head and neck squamous cell carcinoma that is associated with unique risk exposures like consumption of smokeless tobacco and areca nut and is highly prevalent in the northeastern region of India, especially Meghalaya. However, the underlying epigenetic and transcriptomic changes in this cancer type is yet to be delineated. We have undertaken a study on genome wide somatic alterations in the DNA methylation and transcriptome in oropharyngeal cancer patients from this region using genome wide techniques in paired tumors and adjacent normal tissues. By using integrative approaches, we have identified 194 epigenetically silenced and 241 epigenetically overexpressed genes in the tumor tissue of these patients. Pathways that are significantly enriched by these genes include the pathways of immune systems, such as the interleukin signaling pathways and Toll-like receptor signaling pathway. Also, osteoclast differentiation pathway was found to be epigenetically upregulated. The pathways enriched by the epigenetically downregulated genes were found to be predominantly those involved in xenobiotic metabolism and keratinization. Two major transcription factors - SPI1 and RUNX1 were identified as epigenetically dysregulated, which further modulates 129 downstream genes. Comparison of our observations with the head and neck cancer data from TCGA revealed distinct DNA methylation and gene expression landscapes which might be specific for oropharyngeal cancer. HPV DNA sequences were not detected in any of the tumor samples in RNA-Seq data. The results obtained in this study might provide improved understanding of the disease.
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Affiliation(s)
- Lastborn Marthong
- Department of Zoology, North Eastern Hill University (NEHU), Shillong, India
| | - Sahana Ghosh
- National Institute of Biomedical Genomics (NIBMG), Kalyani, India
| | - Arindam Palodhi
- National Institute of Biomedical Genomics (NIBMG), Kalyani, India
| | - Mohamed Imran
- National Institute of Biomedical Genomics (NIBMG), Kalyani, India
| | - Neizekhotuo Brian Shunyu
- Department of Otorhinolaryngology (ENT), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences (NEIGRIHMS), Shillong, India
| | - Arindam Maitra
- National Institute of Biomedical Genomics (NIBMG), Kalyani, India
| | - Srimoyee Ghosh
- Department of Zoology, North Eastern Hill University (NEHU), Shillong, India
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Shin Y, Kim M, Won J, Kim J, Oh SB, Lee JH, Park K. Epigenetic Modification of CFTR in Head and Neck Cancer. J Clin Med 2020; 9:jcm9030734. [PMID: 32182826 PMCID: PMC7141320 DOI: 10.3390/jcm9030734] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/29/2020] [Accepted: 03/06/2020] [Indexed: 12/24/2022] Open
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR), a cyclic AMP (cAMP)-regulated chloride channel, is critical for secretion and absorption across diverse epithelia. Mutations or absence of CFTR result in pathogeneses, including cancer. While CFTR has been proposed as a tumor suppressing gene in tumors of the intestine, lung, and breast cancers, its effects in head and neck cancer (HNC) have yet to be investigated. This study aimed to define expression patterns and epigenetic modifications of CFTR in HNC. CFTR was expressed in normal but not in HNC cells and tissues. Treatment with 5-aza-2'-deoxycytidine (5-Aza-CdR) was associated with rescued expression of CFTR, whose function was confirmed by patch clamp technique. Further experiments demonstrated that CFTR CpG islands were hypermethylated in cancer cells and tissues and hypomethylated in normal cells and tissue. Our results suggest that CFTR epigenetic modifications are critical in both down-regulation and up-regulation of CFTR expression in HNC and normal cells respectively. We then investigated the impact of CFTR on expressions and functions of cancer-related genes. CFTR silencing was closely associated with changes to other cancer-related genes, suppressing apoptosis while enhancing proliferation, cell motility, and invasion in HNC. Our findings demonstrate that hypermethylation of CFTR CpG islands and CFTR deficiency is closely related to HNC.
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Affiliation(s)
- Yonghwan Shin
- Department of Physiology, School of Dentistry, Seoul National University and Dental Research Institute, Seoul 110-749, Korea; (Y.S.); (M.K.); (J.K.)
| | - Minkyoung Kim
- Department of Physiology, School of Dentistry, Seoul National University and Dental Research Institute, Seoul 110-749, Korea; (Y.S.); (M.K.); (J.K.)
| | - Jonghwa Won
- Department of Neurobiology and Physiology, School of Dentistry, Seoul National University and Dental Research Institute, Seoul 110-749, Korea; (J.W.); (S.B.O.)
| | - Junchul Kim
- Department of Physiology, School of Dentistry, Seoul National University and Dental Research Institute, Seoul 110-749, Korea; (Y.S.); (M.K.); (J.K.)
| | - Seog Bae Oh
- Department of Neurobiology and Physiology, School of Dentistry, Seoul National University and Dental Research Institute, Seoul 110-749, Korea; (J.W.); (S.B.O.)
| | - Jong-Ho Lee
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Seoul National University, Seoul 110-749, Korea;
| | - Kyungpyo Park
- Department of Physiology, School of Dentistry, Seoul National University and Dental Research Institute, Seoul 110-749, Korea; (Y.S.); (M.K.); (J.K.)
- Correspondence: ; Tel.: +82-02-740-8658
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5
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Malousi A, Kouidou S, Tsagiopoulou M, Papakonstantinou N, Bouras E, Georgiou E, Tzimagiorgis G, Stamatopoulos K. MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment. Sci Rep 2019; 9:19148. [PMID: 31844073 PMCID: PMC6915744 DOI: 10.1038/s41598-019-55453-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/19/2019] [Indexed: 12/16/2022] Open
Abstract
DNA methylation studies have been reformed with the advent of single-base resolution arrays and bisulfite sequencing methods, enabling deeper investigation of methylation-mediated mechanisms. In addition to these advancements, numerous bioinformatics tools address important computational challenges, covering DNA methylation calling up to multi-modal interpretative analyses. However, contrary to the analytical frameworks that detect driver mutational signatures, the identification of putatively actionable epigenetic events remains an unmet need. The present work describes a novel computational framework, called MeinteR, that prioritizes critical DNA methylation events based on the following hypothesis: critical aberrations of DNA methylation more likely occur on a genomic substrate that is enriched in cis-acting regulatory elements with distinct structural characteristics, rather than in genomic “deserts”. In this context, the framework incorporates functional cis-elements, e.g. transcription factor binding sites, tentative splice sites, as well as conformational features, such as G-quadruplexes and palindromes, to identify critical epigenetic aberrations with potential implications on transcriptional regulation. The evaluation on multiple, public cancer datasets revealed significant associations between the highest-ranking loci with gene expression and known driver genes, enabling for the first time the computational identification of high impact epigenetic changes based on high-throughput DNA methylation data.
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Affiliation(s)
- Andigoni Malousi
- Lab. of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | - Sofia Kouidou
- Lab. of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria Tsagiopoulou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Nikos Papakonstantinou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Emmanouil Bouras
- Lab. of Hygiene, Social-Preventive Medicine & Medical Statistics, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Elisavet Georgiou
- Lab. of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios Tzimagiorgis
- Lab. of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
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6
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Hui L, Wang J, Zhang J, Long J. lncRNA TMEM51-AS1 and RUSC1-AS1 function as ceRNAs for induction of laryngeal squamous cell carcinoma and prediction of prognosis. PeerJ 2019; 7:e7456. [PMID: 31565549 PMCID: PMC6743450 DOI: 10.7717/peerj.7456] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/10/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) can function as competing endogenous RNAs (ceRNAs) to interact with miRNAs to regulate target genes and promote cancer initiation and progression. The expression of lncRNAs and miRNAs can be epigenetically regulated. The goal of this study was to construct an lncRNA-miRNA-mRNA ceRNA network in laryngeal squamous cell carcinoma (LSCC) and reveal their methylation patterns, which was not investigated previously. METHODS Microarray datasets available from the Gene Expression Omnibus database were used to identify differentially expressed lncRNAs (DELs), miRNAs (DEMs), and genes (DEGs) between LSCC and controls, which were then overlapped with differentially methylated regions (DMRs). The ceRNA network was established by screening the interaction relationships between miRNAs and lncRNAs/mRNAs by corresponding databases. TCGA database was used to identify prognostic biomarkers. RESULTS Five DELs (downregulated: TMEM51-AS1, SND1-IT1; upregulated: HCP5, RUSC1-AS1, LINC00324) and no DEMs were overlapped with the DMRs, but only a negative relationship occurred in the expression and methylation level of TMEM51-AS1. Five DELs could interact with 11 DEMs to regulate 242 DEGs, which was used to construct the ceRNA network, including TMEM51-AS1-miR-106b-SNX21/ TRAPPC10, LINC00324/RUSC1-AS1-miR-16-SPRY4/MICAL2/ SLC39A14, RUSC1-AS1-miR-10-SCG5 and RUSC1-AS1-miR-7-ZFP1 ceRNAs axes. Univariate Cox regression analysis showed RUSC1-AS1 and SNX21 were associated with overall survival (OS); LINC00324, miR-7 and ZFP1 correlated with recurrence-free survival (RFS); miR-16, miR-10, SCG5, SPRY4, MICAL2 and SLC39A14 were both OS and RFS-related. Furthermore, TRAPPC10 and SLC39A14 were identified as independent OS prognostic factors by multivariate Cox regression analysis. CONCLUSION DNA methylation-mediated TMEM51-AS1 and non-methylation-mediated RUSC1-AS1 may function as ceRNAs for induction of LSCC. They and their ceRNA axis genes (particularly TMEM51-AS1-miR-106b-TRAPPC10; RUSC1-AS1-miR-16-SLC39A14) may be potentially important prognostic biomarkers for LSCC.
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Affiliation(s)
- Lian Hui
- Department of Otolaryngology, the First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Jing Wang
- Department of Otolaryngology, the First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Jialiang Zhang
- Department of Otolaryngology, the First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Jin Long
- Department of General Surgery, the First Hospital of China Medical University, Shenyang, Liaoning Province, China
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7
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Németh CG, Röcken C, Siebert R, Wiltfang J, Ammerpohl O, Gassling V. Recurrent chromosomal and epigenetic alterations in oral squamous cell carcinoma and its putative premalignant condition oral lichen planus. PLoS One 2019; 14:e0215055. [PMID: 30964915 PMCID: PMC6456184 DOI: 10.1371/journal.pone.0215055] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 03/26/2019] [Indexed: 12/31/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) affects about 700.000 individuals per year worldwide with oral squamous cell carcinoma (OSCC) as a major subcategory. Despite a comprehensive treatment concept including surgery, radiation, and chemotherapy the 5-year survival rate is still only about 50 percent. Chronic inflammation is one of the hallmarks of carcinogenesis. Until now, little is known about the premalignant status of oral lichen planus (OLP) and molecular alterations in OLP are still poorly characterized. Our study aims to delineate differential DNA methylation patterns in OLP, OSCC, and normal oral mucosa. By applying a bead chip approach, we identified altered chromosomal patterns characteristic for OSCC while finding no recurrent alterations in OLP. In contrast, we identified numerous alterations in the DNA methylation pattern in OLP, as compared to normal controls, that were also present in OSCC. Our data support the hypothesis that OLP is a precursor lesion of OSCC sharing multiple epigenetic alterations with OSCC.
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Affiliation(s)
- Christopher G Németh
- Department of Oral and Maxillofacial Surgery, University Hospital of Schleswig-Holstein, Kiel, Germany
| | - Christoph Röcken
- Department of Pathology, University Hospital of Schleswig-Holstein, Kiel, Germany
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital of Schleswig-Holstein, Kiel, Germany.,Institute of Human Genetics, University Medical Centre, Ulm, Germany
| | - Jörg Wiltfang
- Department of Oral and Maxillofacial Surgery, University Hospital of Schleswig-Holstein, Kiel, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, University Hospital of Schleswig-Holstein, Kiel, Germany.,Institute of Human Genetics, University Medical Centre, Ulm, Germany
| | - Volker Gassling
- Department of Oral and Maxillofacial Surgery, University Hospital of Schleswig-Holstein, Kiel, Germany
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8
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Puttipanyalears C, Arayataweegool A, Chalertpet K, Rattanachayoto P, Mahattanasakul P, Tangjaturonsasme N, Kerekhanjanarong V, Mutirangura A, Kitkumthorn N. TRH site-specific methylation in oral and oropharyngeal squamous cell carcinoma. BMC Cancer 2018; 18:786. [PMID: 30081853 PMCID: PMC6080527 DOI: 10.1186/s12885-018-4706-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/30/2018] [Indexed: 11/10/2022] Open
Abstract
Background The incidence of oral squamous cell carcinoma (OSCC) continues to increase each year. Clinical examination and biopsy usually detect OSCC at an advanced stage that is difficult to treat, leading to poor prognosis. DNA methylation pattern is tissue specific and has emerged as a biomarker for the detection of cancers of tissue origin. Herein, we aimed to discover a novel site-specific methylation marker for OSCC. Methods We selected OSCC datasets analyzed using the IlluminaHumanMethylation27 BeadChip from the Gene Expression Omnibus repository of the National Center for Biotechnology Information using a bioinformatics approach. From 27,578 CG dinucleotide (CpG) sites, the CpG site with the highest difference in methylation level between healthy and cancerous cells was selected for further validation. A total of 18 mucosal tissue samples were collected from nine healthy controls and nine from OSCC subjects and subjected to microdissection for cell purification, followed by DNA extraction, bisulfite conversion, and pyrosequencing. Additionally, epithelial cells were collected from 2 cohorts including oral rinse from healthy controls, oral rinse and oral swab from OSCC subjects and oral rinse from oropharyngeal squamous cell carcinoma (SCC) were examined for their methylation status using real-time polymerase chain reaction (PCR). Results Among the 27,578 differentially methylated CpG sites, cg01009664 of the thyrotropin-releasing hormone (TRH) gene showed the greatest difference in methylation level between healthy and cancerous cells. Validation of the TRH gene using pyrosequencing revealed a methylation percentage of 7% ± 3.43% in healthy cells in contrast to 63% ± 19.81% in cancerous cells. Screening of epithelial cells using real-time PCR showed that the DNA methylation level was significantly higher in oral swab and rinse samples collected from OSCC and oropharyngeal SCC subjects than those from healthy controls (p < 0.001). In addition, when using a cutoff at 3.31 ng/μL, the TRH methylation biomarker was able to distinguish OSCC and oropharyngeal SCC subjects from healthy controls with high level of area under the curve, sensitivity and specificity. Conclusion We demonstrated cg01009664 of TRH as a potential biomarker for OSCC and oropharyngeal SCC screening using oral rinse and swab techniques. Electronic supplementary material The online version of this article (10.1186/s12885-018-4706-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- C Puttipanyalears
- Department of Anatomy, Faculty of Medicine, Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, 10330, Thailand
| | - A Arayataweegool
- Department of Anatomy, Faculty of Medicine, Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, 10330, Thailand
| | - K Chalertpet
- Department of Anatomy, Faculty of Medicine, Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, 10330, Thailand
| | - P Rattanachayoto
- Division of Medical Oncology, Department of Medicine, Chulalongkorn University and The King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand
| | - P Mahattanasakul
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, Chulalongkorn University, Pathumwa, Bangkok, 10330, Thailand.,Department of Otolaryngology, Head and Neck Surgery, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Pathumwan, Bangkok, 10330, Thailand
| | - N Tangjaturonsasme
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, Chulalongkorn University, Pathumwa, Bangkok, 10330, Thailand
| | - V Kerekhanjanarong
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, Chulalongkorn University, Pathumwa, Bangkok, 10330, Thailand
| | - A Mutirangura
- Department of Anatomy, Faculty of Medicine, Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, 10330, Thailand
| | - N Kitkumthorn
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, 6 Yothi Road, Ratchathewi, Bangkok, 10400, Thailand.
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9
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Zhang H, Song G, Song G, Li R, Gao M, Ye L, Zhang C. Identification of DNA methylation prognostic signature of acute myelocytic leukemia. PLoS One 2018; 13:e0199689. [PMID: 29933410 PMCID: PMC6014658 DOI: 10.1371/journal.pone.0199689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/12/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The aim of this study is to find the potential survival related DNA methylation signature capable of predicting survival time for acute myelocytic leukemia (AML) patients. METHODS DNA methylation data were downloaded. DNA methylation signature was identified in the training group, and subsequently validated in an independent validation group. The overall survival of DNA methylation signature was performed. Functional analysis was used to explore the function of corresponding genes of DNA methylation signature. Differentially methylated sites and CpG islands were also identified in poor-risk group. RESULTS A DNA methylation signature involving 8 DNA methylation sites and 6 genes were identified. Functional analysis showed that protein binding and cytoplasm were the only two enriched Gene Ontology terms. A total of 70 differentially methylated sites and 6 differentially methylated CpG islands were identified in poor-risk group. CONCLUSIONS The identified survival related DNA methylation signature adds to the prognostic value of AML.
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Affiliation(s)
- Haiguo Zhang
- Department of Hematology, Qilu Hospital, Shandong University, Jinan, Shandong, P.R. China
- Department of Hematology, Jining NO.1 People’s Hospital, Jining, Shandong, P.R. China
| | - Guanli Song
- Department of Preventive and Health Care, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, P.R. China
| | - Guanbo Song
- Department of Clinical Laboratory, Jining Chinese Medicine Hospital, Jining, Shandong, P.R. China
| | - Ruolei Li
- Department of Clinical Laboratory, Jining NO.1 People’s Hospital, Jining, Shandong, P.R. China
| | - Min Gao
- Department of Clinical Laboratory, Jining NO.1 People’s Hospital, Jining, Shandong, P.R. China
| | - Ling Ye
- Department of Hematology, Jining NO.1 People’s Hospital, Jining, Shandong, P.R. China
| | - Chengfang Zhang
- Department of Clinical Laboratory, Jining NO.1 People’s Hospital, Jining, Shandong, P.R. China
- * E-mail:
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10
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Sultan M, Vidovic D, Paine AS, Huynh TT, Coyle KM, Thomas ML, Cruickshank BM, Dean CA, Clements DR, Kim Y, Lee K, Gujar SA, Weaver IC, Marcato P. Epigenetic Silencing of TAP1 in Aldefluor+Breast Cancer Stem Cells Contributes to Their Enhanced Immune Evasion. Stem Cells 2018; 36:641-654. [DOI: 10.1002/stem.2780] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 12/20/2017] [Accepted: 01/10/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Mohammad Sultan
- Departments of Pathology, Dalhousie University; Halifax Nova Scotia Canada
| | - Dejan Vidovic
- Departments of Pathology, Dalhousie University; Halifax Nova Scotia Canada
| | - Arianne S. Paine
- Departments of Pathology, Dalhousie University; Halifax Nova Scotia Canada
| | - Thomas T. Huynh
- Departments of Pathology, Dalhousie University; Halifax Nova Scotia Canada
| | - Krysta M. Coyle
- Departments of Pathology, Dalhousie University; Halifax Nova Scotia Canada
| | - Margaret L. Thomas
- Departments of Pathology, Dalhousie University; Halifax Nova Scotia Canada
| | | | - Cheryl A. Dean
- Departments of Pathology, Dalhousie University; Halifax Nova Scotia Canada
| | - Derek R. Clements
- Departments of Pathology, Dalhousie University; Halifax Nova Scotia Canada
| | - Youra Kim
- Departments of Pathology, Dalhousie University; Halifax Nova Scotia Canada
| | - Kristen Lee
- Psychology and Neuroscience, Dalhousie University; Halifax Nova Scotia Canada
| | - Shashi A. Gujar
- Departments of Pathology, Dalhousie University; Halifax Nova Scotia Canada
- Microbiology and Immunology, Dalhousie University; Halifax Nova Scotia Canada
| | - Ian C.G. Weaver
- Psychology and Neuroscience, Dalhousie University; Halifax Nova Scotia Canada
- Psychiatry and Brain Repair Centre; Dalhousie University; Halifax Nova Scotia Canada
| | - Paola Marcato
- Departments of Pathology, Dalhousie University; Halifax Nova Scotia Canada
- Microbiology and Immunology, Dalhousie University; Halifax Nova Scotia Canada
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11
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Boscolo-Rizzo P, Furlan C, Lupato V, Polesel J, Fratta E. Novel insights into epigenetic drivers of oropharyngeal squamous cell carcinoma: role of HPV and lifestyle factors. Clin Epigenetics 2017; 9:124. [PMID: 29209433 PMCID: PMC5704592 DOI: 10.1186/s13148-017-0424-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/18/2017] [Indexed: 12/22/2022] Open
Abstract
In the last years, the explosion of high throughput sequencing technologies has enabled epigenome-wide analyses, allowing a more comprehensive overview of the oropharyngeal squamous cell carcinoma (OPSCC) epigenetic landscape. In this setting, the cellular pathways contributing to the neoplastic phenotype, including cell cycle regulation, cell signaling, DNA repair, and apoptosis have been demonstrated to be potential targets of epigenetic alterations in OPSCC. Of note, it has becoming increasingly clear that HPV infection and OPSCC lifestyle risk factors differently drive the epigenetic machinery in cancer cells. Epigenetic changes, including DNA methylation, histone modifications, and non-coding RNA expression, can be used as powerful and reliable tools for early diagnosis of OPSCC patients and improve prognostication. Since epigenetic changes are dynamic and reversible, epigenetic enzymes may also represent suitable targets for the development of more effective OPSCC therapeutic strategies. Thus, this review will focus on the main known epigenetic modifications that can occur in OPSCC and their exploitation as potential biomarkers and therapeutic targets. Furthermore, we will address epigenetic alterations to OPSCC risk factors, with a particular focus on HPV infection, tobacco exposure, and heavy alcohol consumption.
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Affiliation(s)
- Paolo Boscolo-Rizzo
- Department of Neurosciences, ENT Clinic and Regional Center for Head and Neck Cancer, Treviso Regional Hospital, University of Padova, Treviso, Italy
| | - Carlo Furlan
- Division of Radiotherapy, Centro di Riferimento Oncologico, IRCCS-National Cancer Institute, Aviano, PN Italy
| | - Valentina Lupato
- Unit of Otolaryngology, General Hospital “S. Maria degli Angeli”, Pordenone, Italy
| | - Jerry Polesel
- Unit of Cancer Epidemiology, Centro di Riferimento Oncologico, IRCCS-National Cancer Institute, Aviano, PN Italy
| | - Elisabetta Fratta
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico, IRCCS-National Cancer Institute, Aviano, PN Italy
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12
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Ling A, Löfgren-Burström A, Larsson P, Li X, Wikberg ML, Öberg Å, Stenling R, Edin S, Palmqvist R. TAP1 down-regulation elicits immune escape and poor prognosis in colorectal cancer. Oncoimmunology 2017; 6:e1356143. [PMID: 29147604 DOI: 10.1080/2162402x.2017.1356143] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/03/2017] [Accepted: 07/07/2017] [Indexed: 01/05/2023] Open
Abstract
The anti-tumor immune response has been shown to be of great prognostic importance in colorectal cancer (CRC) and so has the tumors ability for immune evasion. Our aim of this study was to investigate tumor factors that influence immunity. We used a gene expression array to search for potential mechanisms of tumor immune escape. One candidate gene identified was TAP1, involved in antigen presentation by MHC class I. TAP1 protein expression was evaluated by immunohistochemistry in 436 CRC patients of the Colorectal Cancer in Umeå Study cohort. We found a significant association between a downregulated expression of TAP1 and low infiltration of various subtypes of lymphocytes as well as macrophages. A downregulated expression of TAP1 was further found to be independent of molecular characteristics, suggesting TAP1 down-regulation to reach beyond the well described highly immunogenic MSI CRCs. A low expression of TAP1 was also significantly associated with poor prognosis in patients with CRC, a result that stayed significant in tumor front of early stage tumors (stage I-II) through multivariable analyses. Furthermore, we found that TAP1 expression was inversely correlated with methylation at sites in close proximity to the promoter region. In summary, our results show down-regulation of TAP1 to be a general mechanism of tumor immune escape in CRC and a poor prognostic factor in stage I-II CRC patients. We also suggest that methylation of the TAP1 gene may be a putative mechanism for TAP1 downregulation.
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Affiliation(s)
- Agnes Ling
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | | | - Pär Larsson
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Xingru Li
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Maria L Wikberg
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Åke Öberg
- Department of Surgical and Perioperative Sciences, Surgery, Umeå University, Umeå, Sweden
| | - Roger Stenling
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Sofia Edin
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Richard Palmqvist
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
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13
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Degli Esposti D, Sklias A, Lima SC, Beghelli-de la Forest Divonne S, Cahais V, Fernandez-Jimenez N, Cros MP, Ecsedi S, Cuenin C, Bouaoun L, Byrnes G, Accardi R, Sudaka A, Giordanengo V, Hernandez-Vargas H, Pinto LFR, Van Obberghen-Schilling E, Herceg Z. Unique DNA methylation signature in HPV-positive head and neck squamous cell carcinomas. Genome Med 2017; 9:33. [PMID: 28381277 PMCID: PMC5382363 DOI: 10.1186/s13073-017-0419-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/24/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Head and neck squamous cell carcinomas (HNSCCs) represent a heterogeneous group of cancers for which human papilloma virus (HPV) infection is an emerging risk factor. Previous studies showed promoter hypermethylation in HPV(+) oropharyngeal cancers, but only few consistent target genes have been so far described, and the evidence of a functional impact on gene expression is still limited. METHODS We performed global and stratified pooled analyses of epigenome-wide data in HNSCCs based on the Illumina HumanMethylation450 bead-array data in order to identify tissue-specific components and common viral epigenetic targets in HPV-associated tumours. RESULTS We identified novel differentially methylated CpGs and regions associated with viral infection that are independent of the anatomic site. In particular, most hypomethylated regions were characterized by a marked loss of CpG island boundaries, which showed significant correlations with expression of neighbouring genes. Moreover, a subset of only five CpGs in a few hypomethylated regions predicted HPV status with a high level of specificity in different cohorts. Finally, this signature was a better predictor of survival compared with HPV status determined by viral gene expression by RNA sequencing in The Cancer Genome Atlas cohort. CONCLUSIONS We identified a novel epigenetic signature of HPV infection in HNSCCs which is independent of the anatomic site, is functionally correlated with gene expression and may be leveraged for improved stratification of prognosis in HNSCCs.
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Affiliation(s)
- Davide Degli Esposti
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France.
| | - Athena Sklias
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Sheila C Lima
- Instituto Nacional de Cancer, Rio de Janeiro, Brazil
| | | | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Nora Fernandez-Jimenez
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Marie-Pierre Cros
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Szilvia Ecsedi
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
- MTA-DE Public Health Research Group, University of Debrecen, Debrecen, Hungary
| | - Cyrille Cuenin
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Liacine Bouaoun
- Environment Section, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Graham Byrnes
- Environment Section, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Rosita Accardi
- Infection Cancer Biology Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Anne Sudaka
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose (iBV), 06100, Nice, France
- Centre Antoine Lacassagne, Nice, 06189, France
| | - Valérie Giordanengo
- Université Côte d'Azur, Laboratoire de Virologie, CHU Nice-Archet, 06202, Nice, France
| | - Hector Hernandez-Vargas
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | | | - Ellen Van Obberghen-Schilling
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose (iBV), 06100, Nice, France.
- Centre Antoine Lacassagne, Nice, 06189, France.
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France.
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14
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Lim AM, Wong NC, Pidsley R, Zotenko E, Corry J, Dobrovic A, Clark SJ, Rischin D, Solomon B. Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas. Clin Epigenetics 2016; 8:74. [PMID: 27433284 PMCID: PMC4948090 DOI: 10.1186/s13148-016-0235-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 06/06/2016] [Indexed: 01/01/2023] Open
Abstract
Background DNA methylation profiling of heterogeneous head and neck squamous cell carcinoma (HNSCC) cohorts has been reported to predict patient outcome. We investigated if a prognostic DNA methylation profile could be found in tumour tissue from a single uniform subsite, the oral tongue. The methylation status of 109 comprehensively annotated oral tongue squamous cell carcinoma (OTSCC) formalin-fixed paraffin-embedded (FFPE) samples from a single institution were examined with the Illumina HumanMethylation450K (HM450K) array. Data pre-processing, quality control and analysis were performed using R packages. Probes mapping to SNPs, sex chromosomes and unreliable probes were accounted for prior to downstream analyses. The relationship between methylation and patient survival was examined using both agnostic approaches and feature selection. The cohort was enlarged by incorporation of 331 The Cancer Genome Atlas (TCGA) HNSCC samples, which included 91 TCGA OTSCC samples with HM450K and survival data available. Results Given the use of FFPE-derived DNA, we defined different cohorts for separate analyses. Overall, similar results were found between cohorts. With an unsupervised approach, no distinct hypermethylated group of samples was identified and nor was a prognostic methylation profile identified. The use of multiple downstream feature selection approaches, including a linear models for microarray data (LIMMA), centroid feature selection (CFS), and recursive feature elimination (RFE) support vector machines, similarly failed to identify a significant methylation signature informative for patient prognosis or any clinicopathological data available. Furthermore, we were unable to confirm the prognostic methylation profiles or specific prognostic loci reported within the literature for HNSCC. Conclusions With genome-scale assessment of DNA methylation using HM450K in one of the largest OTSCC cohorts to date, we were unable to identify a hypermethylated group of tumours or a prognostic methylation signature. This suggests that either DNA methylation in isolation is not likely to be of prognostic value or larger cohorts are required to identify such a biomarker for OTSCC. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0235-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Annette M Lim
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Hospital Ave, Nedlands, Western Australia 6009 Australia.,The University of Western Australia, Perth, Australia
| | - Nicholas C Wong
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria 3010 Australia
| | - Ruth Pidsley
- Epigenetics Research Laboratory, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010 Australia
| | - Elena Zotenko
- Epigenetics Research Laboratory, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010 Australia
| | - June Corry
- Department of Radiation Oncology, Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre Building, 305 Grattan St, Melbourne, Victoria 3000 Australia
| | - Alexander Dobrovic
- The University of Melbourne, Melbourne, Australia.,Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, 145 Studley Rd, Heidelberg, Victoria 3084 Australia.,Department of Cancer Biology, La Trobe University, Bundoora, Victoria 3084 Australia
| | - Susan J Clark
- Epigenetics Research Laboratory, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010 Australia
| | - Danny Rischin
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre Building, 305 Grattan St, Melbourne, Victoria 3000 Australia
| | - Benjamin Solomon
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre Building, 305 Grattan St, Melbourne, Victoria 3000 Australia
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15
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Masuda M, Wakasaki T, Toh S. Stress-triggered atavistic reprogramming (STAR) addiction: driving force behind head and neck cancer? Am J Cancer Res 2016; 6:1149-1166. [PMID: 27429838 PMCID: PMC4937727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 05/01/2016] [Indexed: 06/06/2023] Open
Abstract
Recent results of the Cancer Genome Atlas on head and neck squamous cell carcinoma (HNSCC) revealed that HNSCC lacked predominant gain-of-function mutations in oncogenes, whereas an essential role for epigenetics in oncogenesis has become apparent. In parallel, it has gained general acceptance that cancer is considered as complex adaptive system, which evolves responding environmental selective pressures. This somatic evolution appears to proceed concurrently with the acquisition of an atavistic pluripotent state (i.e., "stemness"), which is inducible by intrinsic epigenetic reprogramming program as demonstrated by induced pluripotent stem (iPS) cells. This Nobel prize-winning discovery has markedly accelerated and expanded cancer stem cell research from the point of epigenetic reprogramming. Taken together, we hypothesize that stress-triggered atavistic reprogramming (STAR) may be the major driving force of HNSCC evolution. In this perspective, we discuss the possible mechanisms of STAR in HNSCC, focusing on recent topics of epigenetic reprogramming in developmental and cancer cell biology.
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Affiliation(s)
- Muneyuki Masuda
- Department of Head & Neck Surgery, National Kyushu Cancer Center 3-1-1, Notame, Minamiku, Fukuoka 811-1395, Japan
| | - Takahiro Wakasaki
- Department of Head & Neck Surgery, National Kyushu Cancer Center 3-1-1, Notame, Minamiku, Fukuoka 811-1395, Japan
| | - Satoshi Toh
- Department of Head & Neck Surgery, National Kyushu Cancer Center 3-1-1, Notame, Minamiku, Fukuoka 811-1395, Japan
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16
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Verma M. The Role of Epigenomics in the Study of Cancer Biomarkers and in the Development of Diagnostic Tools. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 867:59-80. [PMID: 26530360 DOI: 10.1007/978-94-017-7215-0_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epigenetics plays a key role in cancer development. Genetics alone cannot explain sporadic cancer and cancer development in individuals with no family history or a weak family history of cancer. Epigenetics provides a mechanism to explain the development of cancer in such situations. Alterations in epigenetic profiling may provide important insights into the etiology and natural history of cancer. Because several epigenetic changes occur before histopathological changes, they can serve as biomarkers for cancer diagnosis and risk assessment. Many cancers may remain asymptomatic until relatively late stages; in managing the disease, efforts should be focused on early detection, accurate prediction of disease progression, and frequent monitoring. This chapter describes epigenetic biomarkers as they are expressed during cancer development and their potential use in cancer diagnosis and prognosis. Based on epigenomic information, biomarkers have been identified that may serve as diagnostic tools; some such biomarkers also may be useful in identifying individuals who will respond to therapy and survive longer. The importance of analytical and clinical validation of biomarkers is discussed, along with challenges and opportunities in this field.
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Affiliation(s)
- Mukesh Verma
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute (NCI), National Institutes of Health (NIH), Suite# 4E102. 9609 Medical Center Drive, MSC 9763, Bethesda, MD, 20892-9726, USA.
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17
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Mohankumar KM, Currle DS, White E, Boulos N, Dapper J, Eden C, Nimmervoll B, Thiruvenkatam R, Connelly M, Kranenburg TA, Neale G, Olsen S, Wang YD, Finkelstein D, Wright K, Gupta K, Ellison DW, Thomas AO, Gilbertson RJ. An in vivo screen identifies ependymoma oncogenes and tumor-suppressor genes. Nat Genet 2015; 47:878-87. [PMID: 26075792 PMCID: PMC4520751 DOI: 10.1038/ng.3323] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 05/06/2015] [Indexed: 12/14/2022]
Abstract
Cancers are characterized by non-random chromosome copy number alterations that presumably contain oncogenes and tumor-suppressor genes (TSGs). The affected loci are often large, making it difficult to pinpoint which genes are driving the cancer. Here we report a cross-species in vivo screen of 84 candidate oncogenes and 39 candidate TSGs, located within 28 recurrent chromosomal alterations in ependymoma. Through a series of mouse models, we validate eight new ependymoma oncogenes and ten new ependymoma TSGs that converge on a small number of cell functions, including vesicle trafficking, DNA modification and cholesterol biosynthesis, identifying these as potential new therapeutic targets.
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Affiliation(s)
- Kumarasamypet M Mohankumar
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - David S Currle
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Elsie White
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Nidal Boulos
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jason Dapper
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Christopher Eden
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Birgit Nimmervoll
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Radhika Thiruvenkatam
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Michele Connelly
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Tanya A Kranenburg
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Geoffrey Neale
- Hartwell Center for Biotechnology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Scott Olsen
- Hartwell Center for Biotechnology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yong-Dong Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Karen Wright
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kirti Gupta
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Arzu Onar Thomas
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Richard J Gilbertson
- 1] Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. [2] Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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18
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Marcinkiewicz KM, Gudas LJ. Altered histone mark deposition and DNA methylation at homeobox genes in human oral squamous cell carcinoma. J Cell Physiol 2014; 229:1405-16. [PMID: 24519855 DOI: 10.1002/jcp.24577] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/16/2014] [Indexed: 01/03/2023]
Abstract
We recently reported a role of polycomb repressive complex 2 (PRC2) and PRC2 trimethylation of histone 3 lysine 27 (H3K27me3) in the regulation of homeobox (HOX) (Marcinkiewicz and Gudas, 2013, Exp Cell Res) gene transcript levels in human oral keratinocytes (OKF6-TERT1R) and tongue squamous cell carcinoma (SCC) cells. Here, we assessed both the levels of various histone modifications at a subset of homeobox genes and genome wide DNA methylation patterns in OKF6-TERT1R and SCC-9 cells by using ERRBS (enhanced reduced representation bisulfite sequencing). We detected the H3K9me3 mark at HOXB7, HOXC10, HOXC13, and HOXD8 at levels higher in OKF6-TERT1R than in SCC-9 cells; at IRX1 and SIX2 the H3K9me3 levels were conversely higher in SCC-9 than in OKF6-TERT1R. The H3K79me3 mark was detectable only at IRX1 in OKF6-TERT1R and at IRX4 in SCC-9 cells. The levels of H3K4me3 and H3K36me3 marks correlate with the transcript levels of the assessed homeobox genes in both OKF6-TERT1R and SCC-9. We detected generally lower CpG methylation levels on DNA in SCC-9 cells at annotated genomic regions which were differentially methylated between OKF6-TERT1R and SCC-9 cells; however, some genomic regions, including the HOX gene clusters, showed DNA methylation at higher levels in SCC-9 than OKF6-TERT1R. Thus, both altered histone modification patterns and changes in DNA methylation are associated with dysregulation of homeobox gene expression in human oral cavity SCC cells, and this dysregulation potentially plays a role in the neoplastic phenotype of oral keratinocytes.
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Affiliation(s)
- Katarzyna M Marcinkiewicz
- Department of Pharmacology, Weill Cornell Medical College and Weill Graduate School of Biomedical Sciences of Cornell University, New York, New York
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19
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Siegel EM, Eschrich S, Winter K, Riggs B, Berglund A, Ajidahun A, Simko J, Moughan J, Ajani J, Magliocco A, Elahi A, Hoffe S, Shibata D. Epigenomic characterization of locally advanced anal cancer: a radiation therapy oncology group 98-11 specimen study. Dis Colon Rectum 2014; 57:941-57. [PMID: 25003289 PMCID: PMC4100249 DOI: 10.1097/dcr.0000000000000160] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND The Radiation Therapy Oncology Group 98-11 clinical trial demonstrated the superiority of standard 5-fluorouracil/mitomycin-C over 5-fluorouracil/cisplatin in combination with radiation in the treatment of anal squamous cell cancer. Tumor size (>5 cm) and lymph node metastases are associated with disease progression. There may be key molecular differences (eg, DNA methylation changes) in tumors at high risk for progression. OBJECTIVE The objectives of this study were to determine whether there are differences in DNA methylation at individual CpG sites and within genes among locally advanced anal cancers, with large tumor size and/or nodal involvement, compared with those that are less advanced. DESIGN This was a case-case study among 121 patients defined as high risk (tumor size >5 cm and/or nodal involvement; n = 59) or low risk (≤5 cm, node negative; n = 62) within the mitomycin-C arm of the Radiation Therapy Oncology Group 98-11 trial. DNA methylation was measured using the Illumina HumanMethylation450 Array. SETTINGS The study was conducted in a tertiary care cancer center in collaboration with a national clinical trials cooperative group. PATIENTS The patients consisted of 74 women and 47 men with a median age of 54 years (range, 25-79 years). MAIN OUTCOME MEASURES DNA methylation differences at individual CpG sites and within genes between low- and high-risk patients were compared using the Mann-Whitney test (p < 0.001). RESULTS A total of 16 CpG loci were differentially methylated (14 increased and 2 decreased) in high- versus low-risk cases. Genes harboring differentially methylated CpG sites included known tumor suppressor genes and novel targets. LIMITATIONS This study only included patients in the mitomycin-C arm with tumor tissue; however, this sample was representative of the trial. CONCLUSIONS This is the first study to apply genome-wide methylation analysis to anal cancer. Biologically relevant differences in methylated targets were found to discriminate locally advanced from early anal cancer. Epigenetic events likely play a significant role in the progression of anal cancer and may serve as potential biomarkers.
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Affiliation(s)
- Erin M Siegel
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL
| | - Steven Eschrich
- Department of Biomedical Informatics, Moffitt Cancer Center, Tampa, FL
| | - Kathryn Winter
- Department of Statistics, Radiation Therapy Oncology Group, Philadelphia, PA and San Francisco, CA
| | - Bridget Riggs
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL
| | - Anders Berglund
- Department of Biomedical Informatics, Moffitt Cancer Center, Tampa, FL
| | - Abidemi Ajidahun
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL
| | - Jeff Simko
- Department of Biospecimen Resource, Radiation Therapy Oncology Group, Philadelphia, PA and San Francisco, CA
| | - Jennifer Moughan
- Department of Statistics, Radiation Therapy Oncology Group, Philadelphia, PA and San Francisco, CA
| | - Jaffer Ajani
- Department of Medical Oncology, MD Anderson Cancer Center, Houston, TX
| | | | - Abul Elahi
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL
| | - Sarah Hoffe
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL
| | - David Shibata
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL,Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL
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20
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Ray B, Henaff M, Ma S, Efstathiadis E, Peskin ER, Picone M, Poli T, Aliferis CF, Statnikov A. Information content and analysis methods for multi-modal high-throughput biomedical data. Sci Rep 2014; 4:4411. [PMID: 24651673 PMCID: PMC3961740 DOI: 10.1038/srep04411] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 02/27/2014] [Indexed: 01/30/2023] Open
Abstract
The spectrum of modern molecular high-throughput assaying includes diverse technologies such as microarray gene expression, miRNA expression, proteomics, DNA methylation, among many others. Now that these technologies have matured and become increasingly accessible, the next frontier is to collect "multi-modal" data for the same set of subjects and conduct integrative, multi-level analyses. While multi-modal data does contain distinct biological information that can be useful for answering complex biology questions, its value for predicting clinical phenotypes and contributions of each type of input remain unknown. We obtained 47 datasets/predictive tasks that in total span over 9 data modalities and executed analytic experiments for predicting various clinical phenotypes and outcomes. First, we analyzed each modality separately using uni-modal approaches based on several state-of-the-art supervised classification and feature selection methods. Then, we applied integrative multi-modal classification techniques. We have found that gene expression is the most predictively informative modality. Other modalities such as protein expression, miRNA expression, and DNA methylation also provide highly predictive results, which are often statistically comparable but not superior to gene expression data. Integrative multi-modal analyses generally do not increase predictive signal compared to gene expression data.
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Affiliation(s)
- Bisakha Ray
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY, USA
| | - Mikael Henaff
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY, USA
- Department of Computer Science, New York University, NY, USA
| | - Sisi Ma
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY, USA
| | - Efstratios Efstathiadis
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY, USA
| | - Eric R. Peskin
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY, USA
| | - Marco Picone
- Department of Information Engineering, University of Parma, Parma, Italy
- MultiMed Srl, Cremona, Italy
| | - Tito Poli
- Maxillofacial Surgery Section of the Head and Neck Department, University Hospital of Parma, Parma, Italy
| | - Constantin F. Aliferis
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY, USA
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Alexander Statnikov
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY, USA
- Department of Medicine, New York University School of Medicine, New York, NY, USA
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Arantes LMRB, de Carvalho AC, Melendez ME, Carvalho AL, Goloni-Bertollo EM. Methylation as a biomarker for head and neck cancer. Oral Oncol 2014; 50:587-92. [PMID: 24656975 DOI: 10.1016/j.oraloncology.2014.02.015] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 02/13/2014] [Accepted: 02/20/2014] [Indexed: 02/08/2023]
Abstract
Head and neck cancer is a collective term that describes malignant tumors of the oral cavity, pharynx, and larynx characterized by high incidence and mortality rates. Although most HNSCC originate from the mucosal surface of the upper aerodigestive tract, where they can be easily detected during a routine clinical examination. Often the definitive diagnosis is delayed because of the difficulty in differentiating from other similar lesions. Activation of proto-oncogenes and inactivation of tumor suppressor genes are the major molecular alterations involved in carcinogenesis. In addition, epigenetic changes can alter the expression of critical genes important in the development of a variety of cancers. The detection of aberrant gene promoter methylation as a tool for the detection of tumors or its use as prognostic marker have been described for many different cancers including HNSCC. The search for biomarkers has as its main aim the evaluation and measurement of the status of normal and pathological biological processes as well as pharmacological responses to certain treatments. The tracking of these biomarkers is an important part for the identification of individuals in the early stages of head and neck cancer for its diagnostic and prognostic relevance reflecting in high survival rates, better quality of life and less cost to the healthcare system. Therefore, assuming that cancer results from genetic and epigenetic changes, analyzes based on gene methylation profile in combination with the pathological diagnosis would be useful in predicting the behavior of these head and neck tumors.
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Affiliation(s)
- L M R B Arantes
- Department of Molecular Biology, São José do Rio Preto Medical School (FAMERP), São José do Rio Preto - SP, Brazil; Center for Research in Molecular Oncology, Barretos Cancer Hospital - Pio XII, Barretos - SP, Brazil
| | - A C de Carvalho
- Center for Research in Molecular Oncology, Barretos Cancer Hospital - Pio XII, Barretos - SP, Brazil
| | - M E Melendez
- Center for Research in Molecular Oncology, Barretos Cancer Hospital - Pio XII, Barretos - SP, Brazil
| | - A L Carvalho
- Center for Research in Molecular Oncology, Barretos Cancer Hospital - Pio XII, Barretos - SP, Brazil
| | - E M Goloni-Bertollo
- Department of Molecular Biology, São José do Rio Preto Medical School (FAMERP), São José do Rio Preto - SP, Brazil.
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López F, Sampedro T, Llorente JL, Domínguez F, Hermsen M, Suárez C, Alvarez-Marcos C. Utility of MS-MLPA in DNA methylation profiling in primary laryngeal squamous cell carcinoma. Oral Oncol 2014; 50:291-7. [PMID: 24444674 DOI: 10.1016/j.oraloncology.2014.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 01/04/2014] [Indexed: 01/14/2023]
Abstract
OBJECTIVES Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) assay is a method that has rarely been exploited in DNA methylation profiling of laryngeal squamous cell carcinoma (LSCC). MATERIAL AND METHODS Methylation of the gene was investigated by MS-MLPA in a well-characterized series of 53 LSCC and 30 samples of healthy mucosa. Aberrant promoter hypermethylation was confirmed using bisulfite pyrosequencing, and methylation-specific. RESULTS Promoter hypermethylation was observed in 36 of the 53 patients (68%). CDKN2B (28%), APC (17%), RARβ (15%), DAPK1 (11%) and CHFR (11%) were most frequently hypermethylated. Aberrant methylation of CHFR was mainly a late-stage event. Methylation-specific polymerase chain reaction and bisulfite pyrosequencing confirmed aberrant methylation for CDKN2B, APC and DAPK1. CONCLUSION Promoter methylation profiling of LSCC using MS-MLPA identified CDKN2B, DAPK1, RARβ, APC, and CHFR as frequent epigenetic events. The clinical implications of these genes as biomarkers are highly relevant as attractive targets for cancer therapy, given the reversible nature of epigenetic gene silencing.
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Affiliation(s)
- Fernando López
- Department of Otorhinolaryngology and Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain.
| | - Teresa Sampedro
- Department of Medical Oncology, Hospital San Agustín, Avilés, Asturias, Spain
| | - José L Llorente
- Department of Otorhinolaryngology and Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain
| | | | - Mario Hermsen
- Department of Otorhinolaryngology and Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain
| | - Carlos Suárez
- Department of Otorhinolaryngology and Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain
| | - César Alvarez-Marcos
- Department of Otorhinolaryngology and Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain
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Sánchez-Vega F, Gotea V, Petrykowska HM, Margolin G, Krivak TC, DeLoia JA, Bell DW, Elnitski L. Recurrent patterns of DNA methylation in the ZNF154, CASP8, and VHL promoters across a wide spectrum of human solid epithelial tumors and cancer cell lines. Epigenetics 2013; 8:1355-72. [PMID: 24149212 DOI: 10.4161/epi.26701] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The study of aberrant DNA methylation in cancer holds the key to the discovery of novel biological markers for diagnostics and can help to delineate important mechanisms of disease. We have identified 12 loci that are differentially methylated in serous ovarian cancers and endometrioid ovarian and endometrial cancers with respect to normal control samples. The strongest signal showed hypermethylation in tumors at a CpG island within the ZNF154 promoter. We show that hypermethylation of this locus is recurrent across solid human epithelial tumor samples for 15 of 16 distinct cancer types from TCGA. Furthermore, ZNF154 hypermethylation is strikingly present across a diverse panel of ENCODE cell lines, but only in those derived from tumor cells. By extending our analysis from the Illumina 27K Infinium platform to the 450K platform, to sequencing of PCR amplicons from bisulfite treated DNA, we demonstrate that hypermethylation extends across the breadth of the ZNF154 CpG island. We have also identified recurrent hypomethylation in two genomic regions associated with CASP8 and VHL. These three genes exhibit significant negative correlation between methylation and gene expression across many cancer types, as well as patterns of DNaseI hypersensitivity and histone marks that reflect different chromatin accessibility in cancer vs. normal cell lines. Our findings emphasize hypermethylation of ZNF154 as a biological marker of relevance for tumor identification. Epigenetic modifications affecting the promoters of ZNF154, CASP8, and VHL are shared across a vast array of tumor types and may therefore be important for understanding the genomic landscape of cancer.
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Affiliation(s)
- Francisco Sánchez-Vega
- Genome Technology Branch; National Human Genome Research Institute; National Institutes of Health; Bethesda, MD USA
| | - Valer Gotea
- Genome Technology Branch; National Human Genome Research Institute; National Institutes of Health; Bethesda, MD USA
| | - Hanna M Petrykowska
- Genome Technology Branch; National Human Genome Research Institute; National Institutes of Health; Bethesda, MD USA
| | - Gennady Margolin
- Genome Technology Branch; National Human Genome Research Institute; National Institutes of Health; Bethesda, MD USA
| | - Thomas C Krivak
- Department of Obstetrics, Gynecology and Reproductive Sciences; University of Pittsburgh Medical School; Pittsburgh, PA USA
| | - Julie A DeLoia
- School of Public Health and Health Services; The George Washington University; Washington DC, USA
| | - Daphne W Bell
- Cancer Genetics Branch; National Human Genome Research Institute; National Institutes of Health; Bethesda, MD USA
| | - Laura Elnitski
- Genome Technology Branch; National Human Genome Research Institute; National Institutes of Health; Bethesda, MD USA
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24
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Global analysis of DNA methylation changes during progression of oral cancer. Oral Oncol 2013; 49:1033-42. [PMID: 24035722 DOI: 10.1016/j.oraloncology.2013.08.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 08/15/2013] [Accepted: 08/17/2013] [Indexed: 01/14/2023]
Abstract
OBJECTIVES Earlier studies involving a priori gene selection have identified promoter regions deregulated by DNA methylation changes in oral squamous cell cancers (OSCCs) and precancers. Interrogation of global DNA methylation patterns for such specimens has not been reported, though such analyses are needed to uncover novel molecular factors driving disease. MATERIALS AND METHODS We evaluated global DNA methylation patterns for 30 biopsies obtained from 10 patients undergoing surgical removal of an OSCC or carcinoma in situ (CIS). From a disease field in each patient, we collected (i) dysplastic, (ii) CIS or OSCC, and (iii) adjacent normal biopsies. DNA isolated from each biopsy was profiled for methylation status using the Illumina HumanMethylation27K platform. RESULTS Our data demonstrate that aberrant methylation of promoter CpG islands exists across oral precancer and OSCC genomes. Non-hierarchical clustering of all methylation data revealed distinct methylation patterns between the normal and the CIS/OSCC tissues (with results for dysplastic biopsies split between groups). Multiple genes exhibiting recurrent aberrant DNA methylation were found for both dysplastic and CIS/OSCC groups, and included enrichment for genes found in the WNT and MAPK signaling pathways. CONCLUSION In identifying aberrant DNA methylation at the earliest stages of oral precancer and finding recurring epigenetic disruption of specific genes/pathways across our analyzed cohort, we see evidence that CpG methylation changes may play a role in oral cancer progression and that global DNA methylation analyses may have significant utility in wider studies that seek to derive biomarkers or potentially druggable targets to improve oral cancer outcomes.
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25
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Lleras RA, Smith RV, Adrien LR, Schlecht NF, Burk RD, Harris TM, Childs G, Prystowsky MB, Belbin TJ. Unique DNA methylation loci distinguish anatomic site and HPV status in head and neck squamous cell carcinoma. Clin Cancer Res 2013; 19:5444-55. [PMID: 23894057 DOI: 10.1158/1078-0432.ccr-12-3280] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE We have used a genome-wide approach to identify novel differentially methylated CpG dinucleotides that are seen in different anatomic sites of head and neck squamous cell carcinoma (HNSCC), as well as those that might be related to HPV status in the oropharynx. EXPERIMENTAL DESIGN We conducted genome-wide DNA methylation profiling of primary tumor samples and corresponding adjacent mucosa from 118 HNSCC patients undergoing treatment at Montefiore Medical Center, Bronx, NY, using the Illumina HumanMethylation27 beadchip. For each matched tissue set, we measured differentially methylated CpG loci using a change in methylation level (M-value). RESULTS When datasets were individually analyzed by anatomic site of the primary tumor, we identified 293 differentially methylated CpG loci in oral cavity squamous cell carcinoma (SCC), 219 differentially methylated CpG loci in laryngeal SCC, and 460 differentially methylated in oropharyngeal SCC. A subset of these differentially methylated CpG loci was common across all anatomic sites of HNSCC. Stratification by HPV status revealed a significantly higher number of differentially methylated CpG loci in HPV+ patients. CONCLUSION Novel epigenetic biomarkers derived from clinical HNSCC specimens can be used as molecular classifiers of this disease, revealing many new avenues of investigation for this disease.
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Affiliation(s)
- Roberto A Lleras
- Authors' Affiliations: Departments of Pathology; Epidemiology & Population Health; Pediatrics, Microbiology & Immunology; Obstetrics, Gynecology & Women's Health, Albert Einstein College of Medicine; and Department of Otorhinolaryngology-Head and Neck Surgery, Montefiore Medical Center, Medical Arts Pavilion, Bronx, New York
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26
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Tan M, Myers JN, Agrawal N. Oral cavity and oropharyngeal squamous cell carcinoma genomics. Otolaryngol Clin North Am 2013; 46:545-66. [PMID: 23910469 DOI: 10.1016/j.otc.2013.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recent technological advances now permit the study of the entire cancer genome, which can elucidate complex pathway interactions that are not apparent at the level of single genes. In this review, the authors describe innovations that have allowed for whole-exome/genome analysis of genetic and epigenetic alterations and of changes in gene expression. Studies using next-generation sequencing, array comparative genomic hybridization, methylation arrays, and gene expression profiling are reviewed, with a particular focus on findings from recent whole-exome sequencing projects. A discussion of the implications of these data on treatment and future goals for cancer genomics is included.
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Affiliation(s)
- Marietta Tan
- Department of Otolaryngology, Head and Neck Surgery, Johns Hopkins University School of Medicine, 601 North Caroline Street, Baltimore, MD 21287, USA
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27
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Jung AC, Job S, Ledrappier S, Macabre C, Abecassis J, de Reyniès A, Wasylyk B. A poor prognosis subtype of HNSCC is consistently observed across methylome, transcriptome, and miRNome analysis. Clin Cancer Res 2013; 19:4174-84. [PMID: 23757353 DOI: 10.1158/1078-0432.ccr-12-3690] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Distant metastasis after treatment is observed in about 20% of squamous cell carcinoma of the head and neck (HNSCC). In the absence of any validated robust biomarker, patients at higher risk for metastasis cannot be provided with tailored therapy. To identify prognostic HNSCC molecular subgroups and potential biomarkers, we have conducted genome-wide integrated analysis of four omic sets of data. EXPERIMENTAL DESIGN Using state-of-the-art technologies, a core set of 45 metastasizing and 55 nonmetastasizing human papillomavirus (HPV)-unrelated HNSCC patient samples were analyzed at four different levels: gene expression (transcriptome), DNA methylation (methylome), DNA copy number (genome), and microRNA (miRNA) expression (miRNome). Molecular subgroups were identified by a model-based clustering analysis. Their clinical relevance was evaluated by survival analysis, and functional significance by pathway enrichment analysis. RESULTS Patient subgroups selected by transcriptome, methylome, or miRNome integrated analysis are associated with shorter metastasis-free survival (MFS). A common subgroup, R1, selected by all three omic approaches, is statistically more significantly associated with MFS than any of the single omic-selected subgroups. R1 and non-R1 samples display similar DNA copy number landscapes, but more frequent chromosomal aberrations are observed in the R1 cluster (especially loss at 13q14.2-3). R1 tumors are characterized by alterations of pathways involved in cell-cell adhesion, extracellular matrix (ECM), epithelial-to-mesenchymal transition (EMT), immune response, and apoptosis. CONCLUSIONS Integration of data across several omic profiles leads to better selection of patients at higher risk, identification of relevant molecular pathways of metastasis, and potential to discover biomarkers and drug targets.
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Affiliation(s)
- Alain C Jung
- EA3430, Laboratoire de Biologie Tumorale, Centre Régional de Lutte Contre le Cancer Paul Strauss, 3 Rue de la Porte de l'Hôpital, Strasbourg, France
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28
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Kostareli E, Holzinger D, Bogatyrova O, Hielscher T, Wichmann G, Keck M, Lahrmann B, Grabe N, Flechtenmacher C, Schmidt CR, Seiwert T, Dyckhoff G, Dietz A, Höfler D, Pawlita M, Benner A, Bosch FX, Plinkert P, Plass C, Weichenhan D, Hess J. HPV-related methylation signature predicts survival in oropharyngeal squamous cell carcinomas. J Clin Invest 2013; 123:2488-501. [PMID: 23635773 DOI: 10.1172/jci67010] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 02/22/2013] [Indexed: 01/30/2023] Open
Abstract
High-risk types of human papilloma virus (HPV) are increasingly associated with oropharyngeal squamous cell carcinoma (OPSCC). Strikingly, patients with HPV-positive OPSCC are highly curable with ionizing radiation and have better survival compared with HPV-negative patients, but the underlying molecular mechanisms remain poorly understood. We applied an array-based approach to monitor global changes in CpG island hypermethylation between HPV-negative and HPV-positive OPSCCs and identified a specific pattern of differentially methylated regions that critically depends on the presence of viral transcripts. HPV-related alterations were confirmed for the majority of candidate gene promoters by mass spectrometric, quantitative methylation analysis. There was a significant inverse correlation between promoter hypermethylation of ALDH1A2, OSR2, GATA4, GRIA4, and IRX4 and transcript levels. Interestingly, Kaplan-Meier analysis revealed that a combined promoter methylation pattern of low methylation levels in ALDH1A2 and OSR2 promoters and high methylation levels in GATA4, GRIA4, and IRX4 promoters was significantly correlated with improved survival in 3 independent patient cohorts. ALDH1A2 protein levels, determined by immunohistochemistry on tissue microarrays, confirmed the association with clinical outcome. In summary, our study highlights specific alterations in global gene promoter methylation in HPV-driven OPSCCs and identifies a signature that predicts the clinical outcome in OPSCCs.
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Affiliation(s)
- Efterpi Kostareli
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany
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Li P, Demirci F, Mahalingam G, Demirci C, Nakano M, Meyers BC. An integrated workflow for DNA methylation analysis. J Genet Genomics 2013; 40:249-60. [PMID: 23706300 DOI: 10.1016/j.jgg.2013.03.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/25/2013] [Accepted: 03/25/2013] [Indexed: 10/27/2022]
Abstract
The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many eukaryotes. DNA methylation has a demonstrated role in the genome stability and protection, regulation of gene expression and many other aspects of genome function and maintenance. BS-seq is a relatively unbiased method for profiling the DNA methylation, with a resolution capable of measuring methylation at individual cytosines. Here we describe, as an example, a workflow to handle DNA methylation analysis, from BS-seq library preparation to the data visualization. We describe some applications for the analysis and interpretation of these data. Our laboratory provides public access to plant DNA methylation data via visualization tools available at our "Next-Gen Sequence" websites (http://mpss.udel.edu), along with small RNA, RNA-seq and other data types.
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Affiliation(s)
- Pingchuan Li
- Department of Plant & Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
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30
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Identification and functional validation of HPV-mediated hypermethylation in head and neck squamous cell carcinoma. Genome Med 2013; 5:15. [PMID: 23419152 PMCID: PMC3706778 DOI: 10.1186/gm419] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/18/2013] [Accepted: 02/05/2013] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Human papillomavirus-positive (HPV+) head and neck squamous cell carcinoma (HNSCC) represents a distinct clinical and epidemiological condition compared with HPV-negative (HPV-) HNSCC. To test the possible involvement of epigenetic modulation by HPV in HNSCC, we conducted a genome-wide DNA-methylation analysis. METHODS Using laser-capture microdissection of 42 formalin-fixed paraffin wax-embedded (FFPE) HNSCCs, we generated DNA-methylation profiles of 18 HPV+ and 14 HPV- samples, using Infinium 450 k BeadArray technology. Methylation data were validated in two sets of independent HPV+/HPV- HNSCC samples (fresh-frozen samples and cell lines) using two independent methods (Infinium 450 k and whole-genome methylated DNA immunoprecipitation sequencing (MeDIP-seq)). For the functional analysis, an HPV- HNSCC cell line was transduced with lentiviral constructs containing the two HPV oncogenes (E6 and E7), and effects on methylation were assayed using the Infinium 450 k technology. RESULTS AND DISCUSSION Unsupervised clustering over the methylation variable positions (MVPs) with greatest variation showed that samples segregated in accordance with HPV status, but also that HPV+ tumors are heterogeneous. MVPs were significantly enriched at transcriptional start sites, leading to the identification of a candidate CpG island methylator phenotype in a sub-group of the HPV+ tumors. Supervised analysis identified a strong preponderance (87%) of MVPs towards hypermethylation in HPV+ HNSCC. Meta-analysis of our HNSCC and publicly available methylation data in cervical and lung cancers confirmed the observed DNA-methylation signature to be HPV-specific and tissue-independent. Grouping of MVPs into functionally more significant differentially methylated regions identified 43 hypermethylated promoter DMRs, including for three cadherins of the Polycomb group target genes. Integration with independent expression data showed strong negative correlation, especially for the cadherin gene-family members. Combinatorial ectopic expression of the two HPV oncogenes (E6 and E7) in an HPV- HNSCC cell line partially phenocopied the hypermethylation signature seen in HPV+ HNSCC tumors, and established E6 as the main viral effector gene. CONCLUSIONS Our data establish that archival FFPE tissue is very suitable for this type of methylome analysis, and suggest that HPV modulates the HNSCC epigenome through hypermethylation of Polycomb repressive complex 2 target genes such as cadherins, which are implicated in tumor progression and metastasis.
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Verma M, Khoury MJ, Ioannidis JPA. Opportunities and challenges for selected emerging technologies in cancer epidemiology: mitochondrial, epigenomic, metabolomic, and telomerase profiling. Cancer Epidemiol Biomarkers Prev 2013; 22:189-200. [PMID: 23242141 PMCID: PMC3565041 DOI: 10.1158/1055-9965.epi-12-1263] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Remarkable progress has been made in the last decade in new methods for biologic measurements using sophisticated technologies that go beyond the established genome, proteome, and gene expression platforms. These methods and technologies create opportunities to enhance cancer epidemiologic studies. In this article, we describe several emerging technologies and evaluate their potential in epidemiologic studies. We review the background, assays, methods, and challenges and offer examples of the use of mitochondrial DNA and copy number assessments, epigenomic profiling (including methylation, histone modification, miRNAs, and chromatin condensation), metabolite profiling (metabolomics), and telomere measurements. We map the volume of literature referring to each one of these measurement tools and the extent to which efforts have been made at knowledge integration (e.g., systematic reviews and meta-analyses). We also clarify strengths and weaknesses of the existing platforms and the range of type of samples that can be tested with each of them. These measurement tools can be used in identifying at-risk populations and providing novel markers of survival and treatment response. Rigorous analytic and validation standards, transparent availability of massive data, and integration in large-scale evidence are essential in fulfilling the potential of these technologies.
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Affiliation(s)
- Mukesh Verma
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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Abstract
DNA methylation is an epigenetic mark that has suspected regulatory roles in a broad range of biological processes and diseases. The technology is now available for studying DNA methylation genome-wide, at a high resolution and in a large number of samples. This Review discusses relevant concepts, computational methods and software tools for analysing and interpreting DNA methylation data. It focuses not only on the bioinformatic challenges of large epigenome-mapping projects and epigenome-wide association studies but also highlights software tools that make genome-wide DNA methylation mapping more accessible for laboratories with limited bioinformatics experience.
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Affiliation(s)
- Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.
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