Correlation of Smoking-Associated DNA Methylation Changes in Buccal Cells With DNA Methylation Changes in Epithelial Cancer JAMA Oncol. Published online May 14, 2015. doi:10.1001/jamaoncol.2015.1053
Andrew E. Teschendorff, PhD1,2; Zhen Yang, PhD2; Andrew Wong, PhD3; Christodoulos P. Pipinikas, PhD4; Yinming Jiao, MSc2; Allison Jones, BSc5; Shahzia Anjum, PhD5; Rebecca Hardy, PhD3; Helga B. Salvesen, MD6; Christina Thirlwell, PhD4; Samuel M. Janes, PhD7; Diana Kuh, PhD3; Martin Widschwendter, MD5
At a Glance
¶ The purpose of the research was to assess the suitability of buccal cells as an epithelial source of tissue to examine the effects of smoking on the epigenome, and to test whether these effects are also seen in smoke-related epithelial cancers.
¶ Smoking is associated with widespread changes in the DNA methylation landscape of buccal cells.
¶ Some smoking-associated DNA methylation changes are common to buccal and blood tissue, but buccal cells exhibit significantly more changes than blood cells.
¶ Smoking-associated DNA methylation changes in buccal cells correlate with DNA methylation changes in epithelial cancers and do so most strongly in smoke-related epithelial cancer.
Biological Significance
To assess biological significance, we performed GSEA separately on the 912 hypermethylated and 589 hypomethylated sites of the 1501 differentially methylated CpGs (Figure 2).
To assess biological significance, we performed GSEA separately on the 912 hypermethylated and 589 hypomethylated sites of the 1501 differentially methylated CpGs (Figure 2).
For the hypermethylated sites, the strongest enrichment was attained for genes bivalently marked in human embryonic stem cells, for binding sites of transcription factors implicated in chromatin organization and specification of stem cell identity (RAD21, CTCF, and EZH2),36- 40 and finally also for genes hypermethylated in lung cancer,41 a cancer strongly linked to tobacco smoke exposure (Figure 2 and eTables 3-5 in the Supplement).
The results of GSEA on the hypomethylated sites did not reveal a strong enrichment of bivalently marked genes but instead showed an enrichment of genes overexpressed in a poorly differentiated human papillomavirus–negative subtype of head and neck cancer,42 a cancer for which smoking is a main risk factor (Figure 2 and eTable 4 in the Supplement). Thus, the fact that the top-ranked enriched biological terms point toward smoking-related cancers strongly supports the biological relevance of our smoking DNAme–based signature.DNAme-Based Smoking Index Derived From Buccal Cells
Given the GSEA results, we reasoned that smoking-associated DNAme changes in buccal cells might be seen in epithelial cancers for which smoking is a potent risk factor. To investigate this and to further assess whether the changes are specific to smoke-related cancers, we collected DNAme data from 15 epithelial cancer types, profiled as part of the Cancer Genome Atlas, encompassing more than 5000 samples, some strongly linked to smoking (lung squamous cell carcinoma [LSCC] and lung adenocarcinoma [LUAD]), others for which smoking is a moderate risk factor (esophageal, head and neck, bladder), and others unrelated to smoking (endometrial and breast cancer).43,44
To be able to quantify the similarity of smoking-associated DNAme changes in buccal cells to those in cancer, we constructed a DNAme-based “smoking index,” computable for any given independent sample, from the 1501 smoking-associated CpGs of the discovery buccal set. To validate the smoking index, we verified that it correlated significantly (P < 10−10) with SPY in the independent replication buccal set (eFigure 7 in the Supplement).