There’s nothing tongue in cheek when it comes to the consideration of buccal cell heterogeneity in sample collections methods. Although buccal epithelial cells are the target given their relationship with the brain DNA methylome, immune cells come along for the ride.
As the lab of Jeffery Craig (Deakin University, Australia) has previously shown, buccal epithelial cell sample collection methods matter. Buccal swabs contain more epithelial cells than saliva and children have more epithelial cells than adults. In their latest, the cheeky team brought the showdown to the DNA methylation arena and compared the results from EPIC arrays to cytology.
Here’s the digest of what they found when comparing the cellular content of saliva and swabs from 20 adults:
- While saliva gives greater DNA yields than swabs, cytology demonstrates that swabs are 86-87% epithelial cells and saliva is 58% epithelial cells, which is a 28.5% difference
- Estimation of cellular composition via DNA methylation through the EpiDISH and robust partial correlation (RPC) algorithm gives the same conclusion as cytology but with lower estimates for epithelial cell content
- Swabs are 69.5%-75.5% epithelial cells and saliva is 25.4% epithelial cells, which is a 47.1% difference
- Despite the difference in the estimate of overall epithelial cell abundance, the DNA methylation array and cytology estimates are strongly correlated (R = 0.84, P < 0.0001)
Finally, by leveraging a number of other published and unpublished studies, they confirmed their previous finding that epithelial cell proportion decreases with age, which they hypothesize may be related to the increase in gingivitis with aging. Together, these findings show that swabs give more buccal epithelial cells than saliva. They also demonstrate that DNA methylation based deconvolution of buccal samples can be utilized for adjustment in epigenome-wide association studies (EWAS) of buccal cell collection methods.
Drool over all the details in Epigenetics, July 2021