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Rivera-Peña B, Folawiyo O, Turaga N, Rodríguez-Benítez RJ, Felici ME, Aponte-Ortiz JA, Pirini F, Rodríguez-Torres S, Vázquez R, López R, Sidransky D, Guerrero-Preston R, Báez A. Promoter DNA methylation patterns in oral, laryngeal and oropharyngeal anatomical regions are associated with tumor differentiation, nodal involvement and survival. Oncol Lett 2024; 27:89. [PMID: 38268779 PMCID: PMC10804364 DOI: 10.3892/ol.2024.14223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 11/23/2023] [Indexed: 01/26/2024] Open
Abstract
Differentially methylated regions (DMRs) can be used as head and neck squamous cell carcinoma (HNSCC) diagnostic, prognostic and therapeutic targets in precision medicine workflows. DNA from 21 HNSCC and 10 healthy oral tissue samples was hybridized to a genome-wide tiling array to identify DMRs in a discovery cohort. Downstream analyses identified differences in promoter DNA methylation patterns in oral, laryngeal and oropharyngeal anatomical regions associated with tumor differentiation, nodal involvement and survival. Genome-wide DMR analysis showed 2,565 DMRs common to the three subsites. A total of 738 DMRs were unique to laryngeal cancer (n=7), 889 DMRs were unique to oral cavity cancer (n=10) and 363 DMRs were unique to pharyngeal cancer (n=6). Based on the genome-wide analysis and a Gene Ontology analysis, 10 candidate genes were selected to test for prognostic value and association with clinicopathological features. TIMP3 was associated with tumor differentiation in oral cavity cancer (P=0.039), DAPK1 was associated with nodal involvement in pharyngeal cancer (P=0.017) and PAX1 was associated with tumor differentiation in laryngeal cancer (P=0.040). A total of five candidate genes were selected, DAPK1, CDH1, PAX1, CALCA and TIMP3, for a prevalence study in a larger validation cohort: Oral cavity cancer samples (n=42), pharyngeal cancer tissues (n=25) and laryngeal cancer samples (n=52). PAX1 hypermethylation differed across HNSCC anatomic subsites (P=0.029), and was predominantly detected in laryngeal cancer. Kaplan-Meier survival analysis (P=0.043) and Cox regression analysis of overall survival (P=0.001) showed that DAPK1 methylation is associated with better prognosis in HNSCC. The findings of the present study showed that the HNSCC subsites oral cavity, pharynx and larynx display substantial differences in aberrant DNA methylation patterns, which may serve as prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Bianca Rivera-Peña
- Department of Biology, University of Puerto Rico, San Juan 00925, Puerto Rico
- Department of Pharmacology, University of Puerto Rico School of Medicine, San Juan 00936, Puerto Rico
- Department of Otolaryngology-Head and Neck Surgery, University of Puerto Rico School of Medicine, San Juan 00936, Puerto Rico
| | - Oluwasina Folawiyo
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Nitesh Turaga
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Rosa J. Rodríguez-Benítez
- Department of General Social Sciences, Faculty of Social Sciences, University of Puerto Rico, San Juan 00925, Puerto Rico
| | - Marcos E. Felici
- Oral Health Division, Puerto Rico Department of Health, San Juan 00927, Puerto Rico
| | - Jaime A. Aponte-Ortiz
- Department of General Surgery, University of Puerto Rico School of Medicine, San Juan 00936, Puerto Rico
| | - Francesca Pirini
- Biosciences Laboratory, IRCCS Instituto Romagnolo per lo Studio dei Tumori ‘Dino Amadori’, Meldola I-47014, Italy
| | | | - Roger Vázquez
- Department of Biology, University of Puerto Rico, San Juan 00925, Puerto Rico
| | - Ricardo López
- Department of Biology, University of Puerto Rico, San Juan 00925, Puerto Rico
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Rafael Guerrero-Preston
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Research and Development, LifeGene-Biomarks, San Juan 00909, Puerto Rico
| | - Adriana Báez
- Department of Pharmacology, University of Puerto Rico School of Medicine, San Juan 00936, Puerto Rico
- Department of Otolaryngology-Head and Neck Surgery, University of Puerto Rico School of Medicine, San Juan 00936, Puerto Rico
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Aghiorghiesei O, Irimie AI, Braicu C, Raduly L, Nutu A, Balint E, Mehterov N, Vladimirov B, Sarafian V, Lucaciu O, Campian R, Berindan-Neagoe I. Epigenetic methylation changes: implication as biomarkers in oral and maxillofacial area cancers. Med Pharm Rep 2023; 96:310-317. [PMID: 37577021 PMCID: PMC10419680 DOI: 10.15386/mpr-2570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/07/2022] [Accepted: 10/21/2022] [Indexed: 08/15/2023] Open
Abstract
Background/Aim Squamous cell carcinoma (SCC) is the most frequent cancer of the head and neck area in the oral cavity. Epigenetic alterations in oral and maxillofacial area cancers are urgently needed to be investigated, as the observed changes might have crucial diagnostic value for personalized medicine. Methods Our study aimed to identify the most frequently hypermethylated tumor suppressor gene promoters in OSCC, followed by correlation analysis with the patients' survival. We evaluated the methylation status of the promoters in a panel of 22 tumor suppressor genes in Romanian (n=9) and Bulgarian (n=12) patient groups suffering from oral and maxillofacial area cancers. The extracted DNA was further digested through EpiTect Methyl II PCR Array System containing methylation-sensitive and methylation-dependent restriction enzymes, followed by specific amplification of the products obtained by qPCR and data analysis using the online platform provided by the producer. Results Different methylation patterns were observed in the tumor suppressor genes' promoters. Among them, the methylation profile of Cccnd2, Chd1, Cdh13, Cdkn1c, Neurog1, Gstp1, and Runx3 genes further correlated with overall survival rates. Conclusions Our data emphasize that epigenetic alterations are responsible for the clinical heterogeneity of oral and maxillofacial area cancers and significantly impact on patient survival. Additional investigation on a larger patient cohort should validate these potential biomarkers.
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Affiliation(s)
- Ovidiu Aghiorghiesei
- Department of Oral Health, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Prosthetic Dentistry and Dental Materials, Division Dental Propaedeutics, Aesthetic, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alexandra Iulia Irimie
- Department of Prosthetic Dentistry and Dental Materials, Division Dental Propaedeutics, Aesthetic, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cornelia Braicu
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Lajos Raduly
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Andreea Nutu
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Emilia Balint
- Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine of Bucharest, Bucharest, Romania
| | - Nikolay Mehterov
- Department of Medical Biology, Faculty of Medicine, Medical University-Plovdiv, Plovdiv, Bulgaria
- Research Institute, Medical University-Plovdiv, Plovdiv, Bulgaria
| | - Boyan Vladimirov
- Department of Maxillofacial Surgery, Medical University-Plovdiv, Plovdiv, Bulgaria
- Clinic of Maxillofacial Surgery, University Hospital St. George, Plovdiv, Bulgaria
| | - Victoria Sarafian
- Department of Medical Biology, Faculty of Medicine, Medical University-Plovdiv, Plovdiv, Bulgaria
- Research Institute, Medical University-Plovdiv, Plovdiv, Bulgaria
| | - Ondine Lucaciu
- Department of Preventive Dental Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Radu Campian
- Department of Oral Rehabilitation, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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Ensenyat-Mendez M, Rünger D, Orozco JIJ, Le J, Baker JL, Weidhaas J, Marzese DM, DiNome ML. Epigenetic Signatures Predict Pathologic Nodal Stage in Breast Cancer Patients with Estrogen Receptor-Positive, Clinically Node-Positive Disease. Ann Surg Oncol 2022; 29:4716-4724. [DOI: 10.1245/s10434-022-11684-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/16/2022] [Indexed: 12/30/2022]
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Kutlay A, Aydin Son Y. Integrative Predictive Modeling of Metastasis in Melanoma Cancer Based on MicroRNA, mRNA, and DNA Methylation Data. Front Mol Biosci 2021; 8:637355. [PMID: 34631789 PMCID: PMC8495312 DOI: 10.3389/fmolb.2021.637355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/30/2021] [Indexed: 12/12/2022] Open
Abstract
Introduction: Despite the significant progress in understanding cancer biology, the deduction of metastasis is still a challenge in the clinic. Transcriptional regulation is one of the critical mechanisms underlying cancer development. Even though mRNA, microRNA, and DNA methylation mechanisms have a crucial impact on the metastatic outcome, there are no comprehensive data mining models that combine all transcriptional regulation aspects for metastasis prediction. This study focused on identifying the regulatory impact of genetic biomarkers for monitoring metastatic molecular signatures of melanoma by investigating the consolidated effect of miRNA, mRNA, and DNA methylation. Method: We developed multiple machine learning models to distinguish the metastasis by integrating miRNA, mRNA, and DNA methylation markers. We used the TCGA melanoma dataset to differentiate between metastatic melanoma samples by assessing a set of predictive models. For this purpose, machine learning models using a support vector machine with different kernels, artificial neural networks, random forests, AdaBoost, and Naïve Bayes are compared. An iterative combination of differentially expressed miRNA, mRNA, and methylation signatures is used as a candidate marker to reveal each new biomarker category’s impact. In each iteration, the performances of the combined models are calculated. During all comparisons, the choice of the feature selection method and under and oversampling approaches are analyzed. Selected biomarkers of the highest performing models are further analyzed for the biological interpretation of functional enrichment. Results: In the initial model, miRNA biomarkers can identify metastatic melanoma with an 81% F-score. The addition of mRNA markers upon miRNA increased the F-score to 92%. In the final integrated model, the addition of the methylation data resulted in a similar F-score of 92% but produced a stable model with low variance across multiple trials. Conclusion: Our results support the role of miRNA regulation in metastatic melanoma as miRNA markers model metastasis outcomes with high accuracy. Moreover, the integrated evaluation of miRNA with mRNA and methylation biomarkers increases the model’s power. It populates selected biomarkers on the metastasis-associated pathways of melanoma, such as the “osteoclast”, “Rap1 signaling”, and “chemokine signaling” pathways. Source Code:https://github.com/aysegul-kt/MelonomaMetastasisPrediction/
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Affiliation(s)
- Ayşegül Kutlay
- Department of Health Informatics, Graduate School of Informatics, METU, Ankara, Turkey
| | - Yeşim Aydin Son
- Department of Health Informatics, Graduate School of Informatics, METU, Ankara, Turkey
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Bruine de Bruin L, Clausen MJAM, Slagter-Menkema L, de Bock GH, Langendijk JA, van der Vegt B, van der Laan BFAM, Schuuring E. High DNMT1 Is Associated With Worse Local Control in Early-Stage Laryngeal Squamous Cell Carcinoma. Laryngoscope 2021; 132:801-805. [PMID: 34427325 PMCID: PMC9290472 DOI: 10.1002/lary.29833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/08/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022]
Abstract
Objectives/Hypothesis Early‐stage laryngeal squamous cell carcinoma (LSCC) has yielded local control rates of 75% after radiotherapy. DNA methylation, in which DNA methyltransferases play an important role, has influence on tumorigenesis. In this study, we investigated the association between the expression of DNA methyltransferase 1 (DNMT1) and local control in early‐stage LSCC treated with radiotherapy. Study Design Retrospective cohort study. Methods We analyzed a well‐defined homogeneous series of 125 LSCC patients treated with radiotherapy with curative intent. The association of immunohistochemical expression of DNMT1 with local control was evaluated using Cox proportional hazard regression models. Results With a median follow‐up of 58 months, 29 local recurrences (23%) were observed. On univariate analysis, worse local control was associated with high DNMT1 expression (hazard ratio [HR] 2.57, 95% confidence interval [CI] 1.10–6.01). Also, higher T‐stage (HR 2.48, 95% CI 1.06–5.80) and positive N‐status (HR 2.62, 95% CI 1.06–6.47) were associated with worse local control. Multivariate Cox regression demonstrated that high DNMT1 (HR 2.81; 95% CI 1.20–6.58) was independently associated with worse local control. Conclusions We found an association between high DNMT1 expression and worse local control in a homogeneous well‐defined cohort of early‐stage LSCC patients treated with definitive radiotherapy. The association between DNA methylation status as determined by DNMT1 expression and local control suggests that DNMT1 acts as a potential prognostic tumor marker in treatment decision‐making in early‐stage laryngeal carcinoma. Level of evidence NA Laryngoscope, 132:801–805, 2022
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Affiliation(s)
- Leonie Bruine de Bruin
- Department of Otorhinolaryngology/Head and Neck Surgery, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Martijn J A M Clausen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lorian Slagter-Menkema
- Department of Otorhinolaryngology/Head and Neck Surgery, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gertruida H de Bock
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Johannes A Langendijk
- Department of Radiation Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Bert van der Vegt
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Bernard F A M van der Laan
- Department of Otorhinolaryngology/Head and Neck Surgery, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Aaboubout Y, van der Toom QM, de Ridder MAJ, De Herdt MJ, van der Steen B, van Lanschot CGF, Barroso EM, Nunes Soares MR, Ten Hove I, Mast H, Smits RWH, Sewnaik A, Monserez DA, Keereweer S, Caspers PJ, Baatenburg de Jong RJ, Bakker Schut TC, Puppels GJ, Hardillo JA, Koljenović S. Is the Depth of Invasion a Marker for Elective Neck Dissection in Early Oral Squamous Cell Carcinoma? Front Oncol 2021; 11:628320. [PMID: 33777774 PMCID: PMC7996205 DOI: 10.3389/fonc.2021.628320] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Objective The depth of invasion (DOI) is considered an independent risk factor for occult lymph node metastasis in oral cavity squamous cell carcinoma (OCSCC). It is used to decide whether an elective neck dissection (END) is indicated in the case of a clinically negative neck for early stage carcinoma (pT1/pT2). However, there is no consensus on the cut-off value of the DOI for performing an END. The aim of this study was to determine a cut-off value for clinical decision making on END, by assessing the association of the DOI and the risk of occult lymph node metastasis in early OCSCC. Methods A retrospective cohort study was conducted at the Erasmus MC, University Medical Centre Rotterdam, The Netherlands. Patients surgically treated for pT1/pT2 OCSCC between 2006 and 2012 were included. For all cases, the DOI was measured according to the 8th edition of the American Joint Committee on Cancer guideline. Patient characteristics, tumor characteristics (pTN, differentiation grade, perineural invasion, and lymphovascular invasion), treatment modality (END or watchful waiting), and 5-year follow-up (local recurrence, regional recurrence, and distant metastasis) were obtained from patient files. Results A total of 222 patients were included, 117 pT1 and 105 pT2. Occult lymph node metastasis was found in 39 of the 166 patients who received END. Univariate logistic regression analysis showed DOI to be a significant predictor for occult lymph node metastasis (odds ratio (OR) = 1.3 per mm DOI; 95% CI: 1.1-1.5, p = 0.001). At a DOI of 4.3 mm the risk of occult lymph node metastasis was >20% (all subsites combined). Conclusion The DOI is a significant predictor for occult lymph node metastasis in early stage oral carcinoma. A NPV of 81% was found at a DOI cut-off value of 4 mm. Therefore, an END should be performed if the DOI is >4 mm.
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Affiliation(s)
- Yassine Aaboubout
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Otorhinolaryngology and Head and Neck Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Quincy M van der Toom
- Department of Otorhinolaryngology and Head and Neck Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Maria A J de Ridder
- Department of Medical informatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Maria J De Herdt
- Department of Otorhinolaryngology and Head and Neck Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Berdine van der Steen
- Department of Otorhinolaryngology and Head and Neck Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Cornelia G F van Lanschot
- Department of Otorhinolaryngology and Head and Neck Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Elisa M Barroso
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Dermatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Maria R Nunes Soares
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Dermatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Ivo Ten Hove
- Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Hetty Mast
- Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Roeland W H Smits
- Department of Otorhinolaryngology and Head and Neck Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Aniel Sewnaik
- Department of Otorhinolaryngology and Head and Neck Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Dominiek A Monserez
- Department of Otorhinolaryngology and Head and Neck Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Stijn Keereweer
- Department of Otorhinolaryngology and Head and Neck Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Peter J Caspers
- Department of Dermatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Robert J Baatenburg de Jong
- Department of Otorhinolaryngology and Head and Neck Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Tom C Bakker Schut
- Department of Dermatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Gerwin J Puppels
- Department of Dermatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - José A Hardillo
- Department of Otorhinolaryngology and Head and Neck Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Senada Koljenović
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
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Jensen GL, Axelrud G, Fink D, Hammonds K, Walker K, Volz M, Gowan A, Rao A, Deb N, Jhavar SG. Improved local control in p16 negative oropharyngeal cancers with hypermethylated MGMT. Radiother Oncol 2021; 157:234-240. [PMID: 33577867 DOI: 10.1016/j.radonc.2021.01.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 10/22/2022]
Abstract
INTRODUCTION Patients with oropharyngeal cancers that are p16 negative (p16-) have worse outcomes than those who are p16 positive (p16+) and there is an unmet need for prognostic markers in this population. O6-Methylguanine (O6-MG)-DNA-methyltransferase (MGMT) gene methylation has been associated with response to chemoradiotherapy (CRT) in glioblastoma. We sought to find if MGMT promoter methylation was associated with outcomes of locally advanced oropharyngeal and oral cavity squamous cell carcinoma (OOSCC) in patients treated with definitive concurrent CRT. METHODS Patients were identified with primary OOSCC, known p16 status, retrievable pre-treatment biopsies, and at least 6 months of follow-up who received definitive concurrent CRT from 2004 to 2015. Biopsies were tested for MGMT hypermethylation (MGMT+) using a Qiagen pyrosequencing kit (Catalog number 970061). Outcomes were subsequently recorded and analyzed. RESULTS Fifty-eight patients were included with a median follow up of 78 (range 6-196) months. Fourteen patients (24.1%) had oral cavity cancer and 44 (75.9%) had oropharyngeal cancer. A significant difference was found for local recurrence free survival (LRFS) by combined MGMT and p16 status (p = 0.0004). Frequency of LR in MGMT+/p16+, MGMT+/p16-, MGMT-/p16+, and MGMT-p16- patients was 14.3%, 14.3%, 13.0%, and 69.2%, respectively (p = 0.0019). A significant difference was not found for distant recurrence free survival (p = 0.6165) or overall survival (p = 0.1615). LRFS remained significant on analysis restricted to oropharyngeal cancer patients (p-value = 0.0038). CONCLUSION Patients who are p16- and MGMT+ with oropharyngeal and oral cavity squamous cell carcinoma have significantly better LC with definitive CRT than those who are p16- and MGMT-. Prospective studies are needed to verify these findings.
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Affiliation(s)
- Garrett L Jensen
- Department of Radiation Oncology, Baylor Scott & White Health, Temple, USA.
| | - Gabriel Axelrud
- Department of Radiation Oncology, Baylor Scott & White Health, Temple, USA
| | - David Fink
- Department of Pathology, Baylor Scott & White Health, Temple, USA
| | - Kendall Hammonds
- Department of Biostatistics, Baylor Scott & White Health, Temple, USA
| | - Kimberly Walker
- Department of Pathology, Baylor Scott & White Health, Temple, USA
| | - Marcus Volz
- Department of Pathology, Baylor Scott & White Health, Temple, USA
| | - Alan Gowan
- Department of Medical Oncology, Baylor Scott & White Health, Temple, USA
| | - Arundhati Rao
- Department of Pathology, Baylor Scott & White Health, Temple, USA
| | - Niloyjyoti Deb
- Department of Radiation Oncology, Baylor Scott & White Health, Temple, USA
| | - Sameer G Jhavar
- Department of Radiation Oncology, Baylor Scott & White Health, Temple, USA.
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Dwivedi R, Pandey R, Chandra S, Mehrotra D. Apoptosis and genes involved in oral cancer - a comprehensive review. Oncol Rev 2020; 14:472. [PMID: 32685111 PMCID: PMC7365992 DOI: 10.4081/oncol.2020.472] [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: 12/24/2019] [Accepted: 03/20/2020] [Indexed: 12/24/2022] Open
Abstract
Oral cancers needs relentless research due to high mortality and morbidity associated with it. Despite of the comparable ease in accessibility to these sites, more than 2/3rd cases are diagnosed in advanced stages. Molecular/genetic studies augment clinical assessment, classification and prediction of malignant potential of oral lesions, thereby reducing its incidence and increasing the scope for early diagnosis and treatment of oral cancers. Herein we aim to review the role of apoptosis and genes associated with it in oral cancer development in order to aid in early diagnosis, prediction of malignant potential and evaluation of possible treatment targets in oral cancer. An internet-based search was done with key words apoptosis, genes, mutations, targets and analysis to extract 72 articles after considering inclusion and exclusion criteria. The knowledge of genetics and genomics of oral cancer is of utmost need in order to stop the rising prevalence of oral cancer. Translational approach and interventions at the early stage of oral cancer, targeted destruction of cancerous cells by silencing or promoting involved genes should be the ideal intervention.
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Affiliation(s)
- Ruby Dwivedi
- DHR-MRU & Department of Oral and Maxillofacial Surgery, Faculty of Dental Sciences, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Rahul Pandey
- DHR-MRU & Department of Oral and Maxillofacial Surgery, Faculty of Dental Sciences, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Shaleen Chandra
- DHR-MRU & Department of Oral and Maxillofacial Surgery, Faculty of Dental Sciences, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Divya Mehrotra
- DHR-MRU & Department of Oral and Maxillofacial Surgery, Faculty of Dental Sciences, King George's Medical University, Lucknow, Uttar Pradesh, India
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9
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Ghantous Y, Nashef A, Abu-Elnaaj I. Epigenetic Alterations Associated with the Overall Survival and Recurrence Free Survival among Oral Squamous Cell Carcinoma Patients. J Clin Med 2020; 9:E1035. [PMID: 32272578 PMCID: PMC7231254 DOI: 10.3390/jcm9041035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 03/25/2020] [Accepted: 04/03/2020] [Indexed: 12/11/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a fatal disease caused by complex interactions between environmental, genomic, and epigenetic alterations. In the current study, we aimed to identify clusters of genes whose promoter methylation status correlated with various tested clinical features. Molecular datasets of genetic and methylation analysis based on whole-genome sequencing of 159 OSCC patients were obtained from the The Cancer Genome Atlas (TCGA) data portal. Genes were clustered based on their methylation status and were tested for their association with demographic, pathological, and clinical features of the patients. Overall, seven clusters of genes were revealed that showed a significant association with the overall survival/recurrence free survival of patients. The top ranked genes within cluster 4, which showed the worst prognosis, primarily acted as paraneoplastic genes, while the genes within cluster 6 primarily acted as anti-tumor genes. A significant difference was found regarding the mean age in the different clusters. No significant correlation was found between the tumor staging and the different clusters. In conclusion, our result provided a proof-of-principle for the existence of phenotypic diversity among the epigenetic clusters of OSCC and demonstrated the utility of the use epigenetics alterations in devolving new prognostic and therapeutics tools for OSCC patients.
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Affiliation(s)
- Yasmen Ghantous
- Department of Oral and Maxillofacial Surgery, Baruch Padeh medical center Poriya, The lower Galilee 15208, Israel;
| | - Aysar Nashef
- Department of Oral and Maxillofacial Surgery, Baruch Padeh medical center Poriya, The lower Galilee 15208, Israel;
| | - Imad Abu-Elnaaj
- Department of Oral and Maxillofacial Surgery, Baruch Padeh medical center Poriya, The lower Galilee 15208, Israel;
- The Azrieli Faculty of Medicine, Bar Illan University, Safed 1311502, Israel;
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10
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Ong J, van den Berg A, Faiz A, Boudewijn IM, Timens W, Vermeulen CJ, Oliver BG, Kok K, Terpstra MM, van den Berge M, Brandsma CA, Kluiver J. Current Smoking is Associated with Decreased Expression of miR-335-5p in Parenchymal Lung Fibroblasts. Int J Mol Sci 2019; 20:ijms20205176. [PMID: 31635387 PMCID: PMC6829537 DOI: 10.3390/ijms20205176] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/22/2019] [Accepted: 10/16/2019] [Indexed: 02/07/2023] Open
Abstract
Cigarette smoking causes lung inflammation and tissue damage. Lung fibroblasts play a major role in tissue repair. Previous studies have reported smoking-associated changes in fibroblast responses and methylation patterns. Our aim was to identify the effect of current smoking on miRNA expression in primary lung fibroblasts. Small RNA sequencing was performed on lung fibroblasts from nine current and six ex-smokers with normal lung function. MiR-335-5p and miR-335-3p were significantly downregulated in lung fibroblasts from current compared to ex-smokers (false discovery rate (FDR) <0.05). Differential miR-335-5p expression was validated with RT-qPCR (p-value = 0.01). The results were validated in lung tissue from current and ex-smokers and in bronchial biopsies from non-diseased smokers and never-smokers (p-value <0.05). The methylation pattern of the miR-335 host gene, determined by methylation-specific qPCR, did not differ between current and ex-smokers. To obtain insights into the genes regulated by miR-335-5p in fibroblasts, we overlapped all proven miR-335-5p targets with our previously published miRNA targetome data in lung fibroblasts. This revealed Rb1, CARF, and SGK3 as likely targets of miR-335-5p in lung fibroblasts. Our study indicates that miR-335-5p downregulation due to current smoking may affect its function in lung fibroblasts by targeting Rb1, CARF and SGK3.
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Affiliation(s)
- Jennie Ong
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, 9713 GZ Groningen, The Netherlands.
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), 9713 GZ Groningen, The Netherlands.
| | - Anke van den Berg
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, 9713 GZ Groningen, The Netherlands.
| | - Alen Faiz
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), 9713 GZ Groningen, The Netherlands.
- University of Groningen, University Medical Center Groningen, Department of Pulmonary Diseases, 9713 GZ Groningen, The Netherlands.
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB) Faculty of Science, Ultimo, NSW 2007, Australia.
| | - Ilse M Boudewijn
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), 9713 GZ Groningen, The Netherlands.
- University of Groningen, University Medical Center Groningen, Department of Pulmonary Diseases, 9713 GZ Groningen, The Netherlands.
| | - Wim Timens
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, 9713 GZ Groningen, The Netherlands.
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), 9713 GZ Groningen, The Netherlands.
| | - Cornelis J Vermeulen
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), 9713 GZ Groningen, The Netherlands.
- University of Groningen, University Medical Center Groningen, Department of Pulmonary Diseases, 9713 GZ Groningen, The Netherlands.
| | - Brian G Oliver
- Woolcock Institute of Medical Research, Respiratory Cellular and Molecular Biology, The University of Sydney, New South Wales 2037, Australia.
- University of Technology Sydney, School of Life Sciences, Sydney, New South Wales 2007, Australia.
| | - Klaas Kok
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9713 GZ Groningen, The Netherlands.
| | - Martijn M Terpstra
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9713 GZ Groningen, The Netherlands.
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), 9713 GZ Groningen, The Netherlands.
- University of Groningen, University Medical Center Groningen, Department of Pulmonary Diseases, 9713 GZ Groningen, The Netherlands.
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, 9713 GZ Groningen, The Netherlands.
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), 9713 GZ Groningen, The Netherlands.
| | - Joost Kluiver
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, 9713 GZ Groningen, The Netherlands.
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11
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Ribeiro IP, Caramelo F, Esteves L, Oliveira C, Marques F, Barroso L, Melo JB, Carreira IM. Genomic and epigenetic signatures associated with survival rate in oral squamous cell carcinoma patients. J Cancer 2018; 9:1885-1895. [PMID: 29896272 PMCID: PMC5995936 DOI: 10.7150/jca.23239] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/17/2018] [Indexed: 11/05/2022] Open
Abstract
Purpose: Although oral squamous cell carcinoma (OSCC) presents great mortality and morbidity worldwide, the mechanisms behind its clinical behavior remain unclear. Biomarkers are needed to forecast patients' survival and, among those patients undergoing curative therapy, which are more likely to develop tumor recurrence/metastasis. Demonstrating clinical relevance of these biomarkers could be crucial both for surveillance and in helping to establish adjuvant therapy strategies. We aimed to identify genomic and epigenetic biomarkers of OSCC prognosis as well as to explore a noninvasive strategy to perform its detection. Methods: OSCC tumor and non-tumor tissue samples and cells scrapped from the tumor surface were genomic and epigenetically evaluated by Methylation-Specific Multiplex Ligation-dependent Probe Amplification technique. Results: Copy number alterations in ATM, CASR, TP73, CADM1, RARB, CDH13, PAX5, RB1 genes and GATA5, PAX6, CADM1 and CHFR promoter methylation were shown to be associated with worse OSCC patients' survival. Copy number alterations in BRCA1, CDKN2A, CHFR, GATA5, PYCARD, STK11, TP53, VHL genes and GATA5, CADM1, KLLN, MSH6, PAX5, WT1 promoter methylation were shown to be associated with development of metastasis/relapses during or after OSCC patients' treatment. We also found a good agreement in the status of CDKN2A promoter methylation evaluated noninvasively or in the tumor tissue. Conclusions: Genomic and epigenetic signatures were validated in a larger and geographically separate cohort, from TCGA database, which reinforce their clinical applicability. Noninvasive methodologies for detection of these signatures require further studies before translation in to clinical practice.
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Affiliation(s)
- Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Francisco Caramelo
- Laboratory of Biostatistics and Medical Informatics, IBILI - Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Luísa Esteves
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Camila Oliveira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Francisco Marques
- CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,Department of Dentistry, Faculty of Medicine, University of Coimbra, 3000-075 Coimbra, Portugal.,Stomatology Unit, Coimbra Hospital and University Centre, CHUC, EPE, 3000-075 Coimbra, Portugal
| | - Leonor Barroso
- Maxillofacial Surgery Department, Coimbra Hospital and University Centre, CHUC, EPE, 3000-075 Coimbra, Portugal
| | - Joana Barbosa Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
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12
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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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13
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Kumar A, Sarode SC, Sarode GS, Majumdar B, Patil S, Sharma NK. Beyond gene dictation in oral squamous cell carcinoma progression and its therapeutic implications. TRANSLATIONAL RESEARCH IN ORAL ONCOLOGY 2017. [DOI: 10.1177/2057178x17701463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Ajay Kumar
- Cancer and Translational Research Lab, Dr D.Y. Patil Biotechnology and Bioinformatics Institute, Dr D.Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Sachin C Sarode
- Department of Oral Pathology, Dr D.Y. Patil Dental College and Research, Pimpri, Pune, Maharashtra, India
| | - Gargi S Sarode
- Department of Oral Pathology, Dr D.Y. Patil Dental College and Research, Pimpri, Pune, Maharashtra, India
| | - Barnali Majumdar
- Department of Oral Pathology and Microbiology, Bhojia Dental College and Hospital, Baddi, Himachal Pradesh, India
| | - Shankargouda Patil
- Department of Maxillofacial Surgery and Diagnostic Sciences, Division of Oral Pathology, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | - Nilesh Kumar Sharma
- Cancer and Translational Research Lab, Dr D.Y. Patil Biotechnology and Bioinformatics Institute, Dr D.Y. Patil Vidyapeeth, Pune, Maharashtra, India
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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: 6] [Impact Index Per Article: 0.8] [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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Clausen MJAM, Melchers LJ, Mastik MF, Slagter-Menkema L, Groen HJM, Laan BFAMVD, van Criekinge W, de Meyer T, Denil S, van der Vegt B, Wisman GBA, Roodenburg JLN, Schuuring E. RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis. Epigenetics 2016; 11:653-663. [PMID: 27379752 PMCID: PMC5048719 DOI: 10.1080/15592294.2016.1205176] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Oral and oropharyngeal squamous cell carcinoma (OOSCC) have a low survival rate, mainly due to metastasis to the regional lymph nodes. For optimal treatment of these metastases, a neck dissection is required; however, inaccurate detection methods results in under- and over-treatment. New DNA prognostic methylation biomarkers might improve lymph node metastases detection. To identify epigenetically regulated genes associated with lymph node metastases, genome-wide methylation analysis was performed on 6 OOSCC with (pN+) and 6 OOSCC without (pN0) lymph node metastases and combined with a gene expression signature predictive for pN+ status in OOSCC. Selected genes were validated using an independent OOSCC cohort by immunohistochemistry and pyrosequencing, and on data retrieved from The Cancer Genome Atlas. A two-step statistical selection of differentially methylated sequences revealed 14 genes with increased methylation status and mRNA downregulation in pN+ OOSCC. RAB25, a known tumor suppressor gene, was the highest-ranking gene in the discovery set. In the validation sets, both RAB25 mRNA (P = 0.015) and protein levels (P = 0.012) were lower in pN+ OOSCC. RAB25 mRNA levels were negatively correlated with RAB25 methylation levels (P < 0.001) but RAB25 protein expression was not. Our data revealed that promoter methylation is a mechanism resulting in downregulation of RAB25 expression in pN+ OOSCC and decreased expression is associated with lymph node metastasis. Detection of RAB25 methylation might contribute to lymph node metastasis diagnosis and serve as a potential new therapeutic target in OOSCC.
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Affiliation(s)
- M J A M Clausen
- a Departments of Pathology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands.,b Oral and Maxillofacial Surgery, University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - L J Melchers
- a Departments of Pathology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands.,b Oral and Maxillofacial Surgery, University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - M F Mastik
- a Departments of Pathology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - L Slagter-Menkema
- a Departments of Pathology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands.,c Otorhinolaryngology/Head & Neck Surgery, University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - H J M Groen
- d Pulmonary Diseases, University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - B F A M van der Laan
- c Otorhinolaryngology/Head & Neck Surgery, University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - W van Criekinge
- e Department of Mathematical Modeling , Statistics and Bioinformatics, Ghent University , Ghent , Belgium
| | - T de Meyer
- e Department of Mathematical Modeling , Statistics and Bioinformatics, Ghent University , Ghent , Belgium
| | - S Denil
- f Gynecologic Oncology, University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - B van der Vegt
- a Departments of Pathology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - G B A Wisman
- f Gynecologic Oncology, University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - J L N Roodenburg
- b Oral and Maxillofacial Surgery, University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - E Schuuring
- a Departments of Pathology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
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16
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Lechner M, Fenton TR. The Genomics, Epigenomics, and Transcriptomics of HPV-Associated Oropharyngeal Cancer--Understanding the Basis of a Rapidly Evolving Disease. ADVANCES IN GENETICS 2016; 93:1-56. [PMID: 26915269 DOI: 10.1016/bs.adgen.2015.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human papillomavirus (HPV) has been shown to represent a major independent risk factor for head and neck squamous cell cancer, in particular for oropharyngeal carcinoma. This type of cancer is rapidly evolving in the Western world, with rising trends particularly in the young, and represents a distinct epidemiological, clinical, and molecular entity. It is the aim of this review to give a detailed description of genomic, epigenomic, transcriptomic, and posttranscriptional changes that underlie the phenotype of this deadly disease. The review will also link these changes and examine what is known about the interactions between the host genome and viral genome, and investigate changes specific for the viral genome. These data are then integrated into an updated model of HPV-induced head and neck carcinogenesis.
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Affiliation(s)
- M Lechner
- Head and Neck Centre, University College London Hospital, London, UK; UCL Cancer Institute, University College London, London, United Kingdom
| | - T R Fenton
- UCL Cancer Institute, University College London, London, United Kingdom
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