American Association for Cancer Research
crc-23-0009_fig2.png (600.7 kB)

FIGURE 2 from Whole-genome CpG-resolution DNA Methylation Profiling of HNSCC Reveals Distinct Mechanisms of Carcinogenesis for Fine-scale HPV+ Cancer Subtypes

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posted on 2023-08-30, 14:20 authored by Tingting Qin, Shiting Li, Leanne E. Henry, Elysia Chou, Raymond G. Cavalcante, Bailey F. Garb, Nisha J. D'Silva, Laura S. Rozek, Maureen A. Sartor

Global methylation is associated with genomic stability and tumor subtype. A, Overall methylation profiles at repetitive regions, as well as their upstream and downstream 2 kb regions in normal epithelial cell lines, IMU, KRT subtypes, and HPV(−) tumors. B, Average methylation at repetitive elements (Alu, L1, and L2) by subtype. C, Boxplots of genome-wide average methylation in normal cell types and subtypes/HPV(−) HNSCC samples of our cohort. D, Average cancer-specific methylation grouped by HPV(+) HNSCC subtypes (IMU and KRT) and HPV(−) HNSCC. Cancer-specific methylation levels derived from EPIC and MethylCIBERSORT approaches are shown separately. E, Correlation between genomic instability and cancer-specific methylation of the 36 HNSCC samples, denoted by different colors according to their subtypes. The Pearson correlation (R) and correlation test P value are shown on top right.


HHS | NIH | National Cancer Institute (NCI)



This study revealed that the previously observed hypermethylation of HPV(+) HNSCC is due solely to the IMU subtype, illustrating the importance of fine-scale subtype analysis in such a heterogeneous disease. Particularly, IMU has significantly higher methylation of transposable elements, which can be tested as a prognosis biomarker in future translational studies.