CpG island methylation profile in non-invasive oral rinse samples is predictive of oral and pharyngeal carcinoma

Abstract

BackgroundThere are currently no screening tests in routine use for oral and pharyngeal cancer beyond visual inspection and palpation, which are provided on an opportunistic basis, indicating a need for development of novel methods for early detection, particularly in high-risk populations. We sought to address this need through comprehensive interrogation of CpG island methylation in oral rinse samples.MethodsWe used the Infinium HumanMethylation450 BeadArray to interrogate DNA methylation in oral rinse samples collected from 154 patients with incident oral or pharyngeal carcinoma prior to treatment and 72 cancer-free control subjects. Subjects were randomly allocated to either a training or a testing set. For each subject, average methylation was calculated for each CpG island represented on the array. We applied a semi-supervised recursively partitioned mixture model to the CpG island methylation data to identify a classifier for prediction of case status in the training set. We then applied the resultant classifier to the testing set for validation and to assess the predictive accuracy.ResultsWe identified a methylation classifier comprised of 22 CpG islands, which predicted oral and pharyngeal carcinoma with a high degree of accuracy (AUC = 0.92, 95 % CI 0.86, 0.98).ConclusionsThis novel methylation panel is a strong predictor of oral and pharyngeal carcinoma case status in oral rinse samples and may have utility in early detection and post-treatment follow-up.

CpG location and methylation level are crucial factors for the early detection of oral squamous cell carcinoma in brushing samples using bisulfite sequencing of a 13-gene panel

“…This study adopted a different approach from 450k methylation arrays to interrogate a set of genes already known to be altered in HNSCC [ 5 , 15 , 19 , 20 , 27 ]. For in-depth investigation of the true methylation level, we developed a novel accurate, sensitive, and specific assay to detect early OSCC and HGSIL from oral brushing specimens using bisulfite NGS.…”

“…In particular, ZAP70 , KIF1A , GP1BB , and MIR137HG were previously described to be differentially methylated in OSCC by our group [ 15 ] and others [ 5 , 18 , 19 ], while PAX1 , LRRTM1 , PARP15 , FLI1 , NTM , LINC00599 , EPHX3 , and ITGA4 were discovered by Guerrero-Preston et al [ 20 ]. Additionally, the remaining MIR193A , MIR296 , TERT , TERC , H19 , DNMT1A , and LINE1 were found to be epigenetically altered in OSCC by various authors [ 21 – 27 ] (see Table 2 for details).…”

13-gene DNA Methylation Analysis from Oral Brushing: A Promising Non Invasive Tool in the Follow-up of Oral Cancer Patients

“…Meanwhile, the potential use of DNA methylation analysis of one or a combination of genes has been investigated as a prognostic marker in head and neck squamous cell carcinoma based on non-invasive sampling collection [9,11,13,14,16,18,[44][45][46][47][48]; however, the majority of these studies found that an altered methylation level was related to poor prognosis and the samples were collected at the time of OSCC diagnosis (pretreatment). The prognostic value of promoter hypermethylation was identified for one gene in a pattern of genes from post-operative saliva samples.…”

Epigenetic Modifications and Head and Neck Cancer: Implications for Tumor Progression and Resistance to Therapy

“…CpG dinucleotides are highly accumulated in the 5′ promoter region of genes referred as CpG islands, which are unmethylated in transcriptionally active genes. Once CpG islands become methylated, transcriptional repression occurs [ 27 ].…”