Integrated genome-wide DNA methylation and transcriptomic analysis prioritizes EPHA5 as a candidate non-invasive epigenetic biomarker for oral squamous cell carcinoma
7 affiliations
- 1Department of Basic Oncology, Oncology Institute, Istanbul University , ,
- 2Department of Biostatistics and Medical Informatics, Faculty of Medicine, Acibadem Mehmet Ali Aydınlar (MAA) University , ,
- 3Institute of Graduate Studies in Health Sciences, Istanbul University , ,
- 4Department of Otorhinolaryngology and Head and Neck Surgery, Istanbul Faculty of Medicine, Istanbul University , ,
- 5Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University , ,
- 6Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Istanbul University , ,
- 7Department of Medical Pathology, Medical Faculty, Istanbul Health and Technology University , ,
Abstract
Purpose: Oral squamous cell carcinoma (OSCC) remains a major clinical challenge because of delayed diagnosis and the lack of validated non-invasive biomarkers for OSCC detection. Epigenetic alterations during oral carcinogenesis represent promising biomarker candidates. This study aimed to prioritize clinically relevant epigenetic biomarkers and validate EPHA5 using an integrated genome-wide DNA methylation and transcriptomic approach.
Experimental design: Genome-wide DNA methylation and transcriptomic profiling were performed to identify epigenetically deregulated genes in OSCC. Candidate genes were prioritized by integrating DNA methylation, transcriptomic data and biological relevance. EPHA5 was subsequently selected for validation and evaluated by quantitative methylation-specific PCR (QMSP) and quantitative real-time PCR (QRT-PCR) in tissue, saliva and serum samples from independent cohorts comprising patients with OSCC, oral premalignant lesions (OPML) and healthy controls.
Results: Genome-wide analysis identified 661 upregulated and 577 downregulated genes together with 2,431 differentially methylated regions corresponding to 1,776 genes. Integrated analysis generated a panel of 51 candidate genes, from which EPHA5 was prioritized using integrated DNA methylation, gene expression, pathway enrichment and biological relevance. EPHA5 promoter hypermethylation was detected in 66.7% of OSCC tumors, whereas concurrent promoter hypermethylation and reduced expression were observed in 28.6% of tumors. Methylation was also detected in 54.5% of OPML lesions and in the saliva of 47.6% of OSCC patients but was rarely detected in healthy controls. Tumor EPHA5 methylation significantly discriminated OSCC from healthy controls (AUC = 0.780, p = 0.004; sensitivity, 71.4%; specificity, 75%). Salivary EPHA5 methylation also significantly discriminated OSCC from healthy controls (AUC = 0.717, p = 0.025; sensitivity, 52.4%; specificity, 87.5%), whereas serum methylation showed no significant diagnostic utility (AUC = 0.571, p = 0.462). Discrimination between OSCC and OPML was limited and did not reach statistical significance (tumor AUC = 0.662, p = 0.068; salivary AUC = 0.600, p = 0.264).
Conclusions: Frequent tumor hypermethylation together with detectable salivary methylation supports further evaluation of EPHA5 as a candidate non-invasive epigenetic biomarker for OSCC. However, its moderate diagnostic performance, limited discrimination between OSCC and OPML, and lack of external validation indicate that larger prospective studies and evaluation within multimarker methylation panels are required before clinical implementation.
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BibTeX
@article{demokan2026integrated,
title = {{Integrated genome-wide DNA methylation and transcriptomic analysis prioritizes EPHA5 as a candidate non-invasive epigenetic biomarker for oral squamous cell carcinoma}},
author = {Semra Demokan and Begüm Özemek and Seval Turna and Sevde Cömert and Cömert Şen and Kağan Avcı and Ahmet Özkan and Sena Şen and Mehveş Poda and Murat Ulusan and Uğur Sezerman and Gülsüm Ak and Canan Alatlı and Nejat Dalay},
journal = {Frontiers in oncology},
year = {2026},
month = oct,
doi = {10.3389/fonc.2026.1932336},
url = {https://europepmc.org/article/PMC/PMC13671974},
note = {CC BY},
}
RIS
TY - JOUR
TI - Integrated genome-wide DNA methylation and transcriptomic analysis prioritizes EPHA5 as a candidate non-invasive epigenetic biomarker for oral squamous cell carcinoma
AU - Semra Demokan
AU - Begüm Özemek
AU - Seval Turna
AU - Sevde Cömert
AU - Cömert Şen
AU - Kağan Avcı
AU - Ahmet Özkan
AU - Sena Şen
AU - Mehveş Poda
AU - Murat Ulusan
AU - Uğur Sezerman
AU - Gülsüm Ak
AU - Canan Alatlı
AU - Nejat Dalay
PY - 2026
DA - 2026/10/02
JO - Frontiers in oncology
DO - 10.3389/fonc.2026.1932336
UR - https://europepmc.org/article/PMC/PMC13671974
AB - Purpose: Oral squamous cell carcinoma (OSCC) remains a major clinical challenge because of delayed diagnosis and the lack of validated non-invasive biomarkers for OSCC detection. Epigenetic alterations during oral carcinogenesis represent promising biomarker candidates. This study aimed to prioritize clinically relevant epigenetic biomarkers and validate EPHA5 using an integrated genome-wide DNA methylation and transcriptomic approach. Experimental design: Genome-wide DNA methylation and transcriptomic profiling were performed to identify epigenetically deregulated genes in OSCC. Candidate genes were prioritized by integrating DNA methylation, transcriptomic data and biological relevance. EPHA5 was subsequently selected for validation and evaluated by quantitative methylation-specific PCR (QMSP) and quantitative real-time PCR (QRT-PCR) in tissue, saliva and serum samples from independent cohorts comprising patients with OSCC, oral premalignant lesions (OPML) and healthy controls. Results: Genome-wide analysis identified 661 upregulated and 577 downregulated genes together with 2,431 differentially methylated regions corresponding to 1,776 genes. Integrated analysis generated a panel of 51 candidate genes, from which EPHA5 was prioritized using integrated DNA methylation, gene expression, pathway enrichment and biological relevance. EPHA5 promoter hypermethylation was detected in 66.7% of OSCC tumors, whereas concurrent promoter hypermethylation and reduced expression were observed in 28.6% of tumors. Methylation was also detected in 54.5% of OPML lesions and in the saliva of 47.6% of OSCC patients but was rarely detected in healthy controls. Tumor EPHA5 methylation significantly discriminated OSCC from healthy controls (AUC = 0.780, p = 0.004; sensitivity, 71.4%; specificity, 75%). Salivary EPHA5 methylation also significantly discriminated OSCC from healthy controls (AUC = 0.717, p = 0.025; sensitivity, 52.4%; specificity, 87.5%), whereas serum methylation showed no significant diagnostic utility (AUC = 0.571, p = 0.462). Discrimination between OSCC and OPML was limited and did not reach statistical significance (tumor AUC = 0.662, p = 0.068; salivary AUC = 0.600, p = 0.264). Conclusions: Frequent tumor hypermethylation together with detectable salivary methylation supports further evaluation of EPHA5 as a candidate non-invasive epigenetic biomarker for OSCC. However, its moderate diagnostic performance, limited discrimination between OSCC and OPML, and lack of external validation indicate that larger prospective studies and evaluation within multimarker methylation panels are required before clinical implementation.
SN - 2234-943X
ER -