Distinct Epigenetic Profiling in Head and Neck Squamous Cell Carcinoma Stem Cells

Abstract

Objective. To identify unique epigenetic signature in cancer stem cells (CSCs) in head and neck squamous cell carcinoma (HNSCC).

Study Design. Molecular and microarray studies.

Setting. Tertiary referral center.

Subjects and Methods. Head and neck CSCs were isolated in HNSCC cells by CD44 staining and flow cytometry sorting. CSCs with highest CD44 expression (CD44^hi) and non–stem cells (non-SCs) with lowest CD44 expression (CD44^low) were then characterized for stemness gene expression and their responses to chemotherapeutic agents, followed by high-throughput epigenetic profiling using the Illumina BeadChip Array, targeting 28,544 CpG sites covering more than 14,956 genes.

Results. CD44^hi CSCs expressed higher levels of stem cell markers and were more resistant to chemotherapeutic agents as compared to CD44^low non-SCs. By DNA methylation microarray analysis, 17 hypomethylated and 9 hypermethylated genes were identified in CD44^hi CSCs as compared to non-SCs in most HNSCC cell lines. Cluster analysis using these 26 genes showed that CD44^hi CSCs were epigenetically distinct from the CD44^low non-SCs in all 5 HNSCC cell lines.

Conclusion. A unique epigenetic profile consisting of 17 hypomethylated and 9 hypermethylated genes was seen in HNSCC CSCs. These genes may be critically required in maintaining the stemness or pluripotency of CSCs and may represent novel molecular targets for anticancer therapies aimed at eradicating CSCs in HNSCC.