Epigenetic Age Estimation by Detecting DNA Methylation Status in Buccal Swabs

Electrophoresis. 2024 Nov;45(21-22):2012-2018. doi: 10.1002/elps.202400075. Epub 2024 Oct 14.

Abstract

The analysis of DNA methylation (DNAm) levels at specific CpG sites represents one of the most promising molecular techniques for estimating an individual's age. To date, a considerable number of studies have reported the development of age prediction models on the basis of DNAm in body fluids, with only a few utilizing buccal swabs. The objective of this study was to identify age-dependent methylation CpG sites in three different genes (HOXC4, TRIM59, and ELOVL2) in buccal swab samples from the Chinese Han population. A total of 461 buccal swabs, with an age range of 0.4-80.8 years, were divided into a training set (n = 325) and a validation set (n = 136). Samples were analyzed by pyrosequencing in order to identify age-related genes with correlation coefficient. A random forest regression model was ultimately proposed, including eight CpGs in three genes, with a mean absolute error (MAE) of 2.119 years. The model performs independent validation set with an MAE of 4.391 years. Our findings illustrate that buccal swabs present a suitable alternative to biological traces for age prediction based on DNAm pattern using pyrosequencing and random forest regression, offering the additional advantage of being collected noninvasively.

Keywords: DNA methylation; age estimation; buccal swab samples; pyrosequencing; random forest regression.

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Aged, 80 and over
  • Aging* / genetics
  • Child
  • Child, Preschool
  • CpG Islands* / genetics
  • DNA Methylation* / genetics
  • Epigenesis, Genetic / genetics
  • Fatty Acid Elongases* / genetics
  • Female
  • Humans
  • Infant
  • Intracellular Signaling Peptides and Proteins
  • Male
  • Middle Aged
  • Mouth Mucosa* / chemistry
  • Sequence Analysis, DNA / methods
  • Tripartite Motif Proteins* / genetics
  • Young Adult

Substances

  • Tripartite Motif Proteins
  • ELOVL2 protein, human
  • Fatty Acid Elongases
  • TRIM59 protein, human
  • Intracellular Signaling Peptides and Proteins