Plasma cell‐free DNA methylome profiling in pre‐ and post‐surgery oral cavity squamous cell carcinoma

Patel, Krupal; Padhya, Tapan; Huang, Jinyong; Hernández-Prera, Juan C.; Li, Tingyi; Chung, Christine H.; Wang, Liang; Wang, Xuefeng

doi:10.1002/mc.23501

Cited by 7 publications

(7 citation statements)

References 66 publications

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“…Interestingly, the top five validated differentially methylated were located in the promoter region of the genes PENK, NXPH1, ZIK1, TBXT , and CDO1 . In addition, they found that the methylation of SFRP4, SOX1, IRF4 , and PCDH17 was associated with the overall survival of HNC patients, supporting its utility as prognostic biomarkers [86] .…”

Section: Applications Of Cell-free Dna In Head and Neck Cancermentioning

confidence: 90%

“…However, the performance of these biomarkers could be affected by the different methodological design of each study as well as the different preanalytical and postanalytical factors. Thus, the size of study cohort represents one of the most frequent limitations in the investigations [80] , [84] , [86] , [87] , so a further validation in an independent cohort is required to validate the performance of methylation biomarkers. Regarding the patient clinicopathological characteristics, the TNM stage was specified in only three studies [80] , [82] , [84] whereas the HPV status was described in one research [84] .…”

Section: Applications Of Cell-free Dna In Head and Neck Cancermentioning

confidence: 99%

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Liquid biopsies based on cell-free DNA as a potential biomarker in head and neck cancer

Rapado-González,

Rodríguez-Ces,

López-López

et al. 2023

Japanese Dental Science Review

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Section: Applications Of Cell-free Dna In Head and Neck Cancermentioning

confidence: 90%

Section: Applications Of Cell-free Dna In Head and Neck Cancermentioning

confidence: 99%

Liquid biopsies based on cell-free DNA as a potential biomarker in head and neck cancer

Rapado-González,

Rodríguez-Ces,

López-López

et al. 2023

Japanese Dental Science Review

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“…Wang et al emphasized the value of saliva by measuring cfDNA in saliva in 100% and in serum in 80% of oral cavity squamous cell carcinoma (OCSCC) (33). In a small study, plasma cell free DNA methylome analysis was feasible in OCSCC and with prognostic relevance (34). Zhou et al proposed a method for early cancer detection using tumor fractions deciphered from circulation cfDNA methylation signatures achieving 86.1% sensitivity for cancer detection at a speci city of 94.7% and an average localization accuracy of 76.9% (35).…”

Section: Discussionmentioning

confidence: 99%

Cervical cancer of unknown primary: Unveiling primary tumor sites through machine learning on DNA methylation signatures

Stark,

Kasajima,

Stögbauer

et al. 2023

Preprint

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Background The unknown primary in cervical cancer of unknown primary (cCUP) results in invasive diagnostic and unspecific treatment options for patients. The most common histological subtype, squamous cell carcinoma, can stem from various tumor primary sites including the oral cavity, oropharynx, larynx, facial skin, lungs, and esophagus. DNA methylation profiles are highly tissue specific and have been successfully used to classify tissue origin. We aimed to implement a SVM based classifier with publicly available DNA methylation profiles of commonly cervically metastasizing squamous cell carcinomas (n=1103) in order to compare the tissue of origin of own squamous cell cCUP samples (n=28). Methylation analysis was performed with Infinium MethylationEPIC v1.0 BeadChip by Illumina. Results The highest overall accuracy of tested classifiers was achieved by support vector machine algorithm with 87%. Sqamous cell cCUP samples on DNA methylation level resembled squamous cell carcinomas commonly metastasizing into cervical lymph nodes. The most frequently predicted entity was oral cavity (11 39%) followed by oropharynx and larynx (both 7, 25%), skin (2, 7%) and esophagus (1, 4%). These rates did not differ from expected distribution of lymph node metastases in literature. In tSNE clustering, cCUP samples graphically distributed into three different groups corresponding to clusters of cervically metastasizing cancer entities. Conclusions On DNA Methylation level cCUP is comparable to cancer entities that commonly metastasize to cervical lymph nodes. Our SVM based classifier can accurately predict these cancers and could greatly reduce invasiveness of cCUP diagnostics and therapy after clinical validation.

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“…OSF has a very high malignant potential rate into OSCC (33). The survival rate of OSCC ve-years has not been improved since many decades (34). Therefore, there is a serious, urgent and ongoing need to identify and discover noninvasive technique such as salivary biomarkers in OSF which will help us in early identi cation of its malignant potential (35,36).…”

Section: Discussionmentioning

confidence: 99%

Analyzing the Salivary Levels of Cathepsin B in Oral Submucous Fibosis and Oral Squamous Cell Carcinoma for Early Detection

Ahmed,

Shabbir,

Shaikh

et al. 2023

Preprint

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Background: Oral squamous cell carcinoma is one of the most prevalent and common cancers of oral cavity with significant higher rates of mortality and morbidity. Many of the OSCC are known to be preceded by oral potentially malignant disorders such as Oral Submucous Fibrosis. OSF is a chronic and insidious condition with a high malignant transformation potential into OSCC. Salivary biomarker analysis has been considered as a promising approach for early detection of malignant potential of OSF. Cathepsin B is a lysosomal cysteine protease. In many malignancies increased levels of Cathepsin B were observed including OSCC. The present study was designed to analyze and determine the salivary Cathepsin B levels in OSF and OSCC. Method: 150 research participants in total were included in this study which were further divided into 3 groups, 50 in each group. Group 1 comprised 50 OSF patients, Group 2 comprised 50 OSCC patients and group 3 comprised 50 control group. Salivary Cathepsin B levels were analyzed in all 3 groups by using ELISA technique after saliva sample collection. Results: Cathepsin B salivary levels were found to be increased significantly in both OSF and OSCC patients in comparison to control group with significant higher < 0.001 p-value. Highest mean salivary Cathepsin B levels were found in OSF 9.50s ± 7.3, followed by OSCC 4.54 ± 5.9 and control group 0.45s ± 0.9 respectively. Conclusion: Cathepsin B salivary levels were observed to be increased significantly both in patients of OSF and OSCC. Therefore, Cathepsin B can be considered a useful and beneficial salivary biomarker for early detection of OSCC.

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Plasma cell‐free DNA methylome profiling in pre‐ and post‐surgery oral cavity squamous cell carcinoma

Cited by 7 publications

References 66 publications

Liquid biopsies based on cell-free DNA as a potential biomarker in head and neck cancer

Liquid biopsies based on cell-free DNA as a potential biomarker in head and neck cancer

Cervical cancer of unknown primary: Unveiling primary tumor sites through machine learning on DNA methylation signatures

Analyzing the Salivary Levels of Cathepsin B in Oral Submucous Fibosis and Oral Squamous Cell Carcinoma for Early Detection

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