Brush swab as a noninvasive surrogate for tissue biopsies in oral cancer patients to develop clinically translatable epigenetic biomarkers
Year: 2021
Type: preprint
Abstract: Background Oral squamous cell carcinoma (OSCC) has poor survival rates. There is a pressing need to develop more precise risk assessment methods to tailor clinical treatment. Epigenome-wide association studies in OSCC have not produced a viable biomarker. These studies have relied on methylation array platforms, which are limited in their ability to profile the methylome. In this study, we use MethylCap-Seq (MC-Seq), a comprehensive methylation quantification technique, and brush swab samples, to develop a noninvasive, readily translatable approach to profile the methylome in OSCC patients. Methods Three OSCC patients underwent collection of cancer and contralateral normal tissue and brush swab biopsies, totaling 4 samples for each patient. Epigenome-wide DNA methylation quantification was performed using the SureSelectXT Methyl-Seq platform. DNA quality and methylation site resolution were compared between brush swab and tissue samples. Correlation and methylation value difference were determined for brush swabs vs. tissues for each respective patient and site (i.e., cancer or normal). Correlations were calculated between cancer and normal tissues and brush swab samples for each patient to determine the robustness of DNA methylation marks using brush swabs in clinical biomarker studies. Results There were no significant differences in DNA yield between tissue and brush swab samples. Mapping efficiency exceeded 90% across all samples, with no differences between tissue and brush swabs. The average number of CpG sites with at least 10x depth of coverage was 2,716,674 for brush swabs and 2,903,261 for tissues. Matched tissue and brush swabs had excellent correlation (r = 0.913 for cancer samples and r = 0.951 for normal samples). The methylation profile of the top 1,000 CpGs was significantly different between cancer and normal samples (mean p-value = 0.00021) but not different between tissues and brush swabs (mean p-value = 0.11). Conclusions Our results demonstrate that MC-Seq is an efficient platform for epigenome profiling in cancer biomarker studies, with broader methylome coverage than array-based platforms. Brush swab biopsy provides adequate DNA yield for MC-Seq, and taken together, our findings set the stage for development of a non-invasive methylome quantification technique for oral cancer with high translational potential.
Source: Research Square
Authors: Chi Tonglien Viet, Xinyu Zhang, Ke Xu, Gary Yu, Kesava Asam, Carissa M. Thomas, Nicholas F. Callahan, Coleen Doan, Paul C. Walker, Khanh Nguyen, Stephanie C. Kidd, Steve C. Lee, Anupama Grandhi, Clint T. Allen, Simon Young, James C. Melville, Jonathan W. Shum, Dan T. Viet, Alan S. Herford, Dylan F. Roden, Manuel Lora Gonzalez, Bradley E. Aouizerat
Institutions: Rocky Vista University, Loma Linda University, Yale University, New York University, University of Alabama at Birmingham, University of Illinois Chicago, National Institute on Deafness and Other Communication Disorders, The University of Texas Health Science Center at Houston, Rutgers New Jersey Medical School
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Funder: Yale University
OpenAlex ID: W4256374433