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bioRxiv · 10.1101/2024.11.08.621377

Considerations for Cell Type Heterogeneity in Pediatric Salivary DNA Methylation Analyses: Comparison of Reference Panels & Stratification by Estimated Cell TypeProportion

Chan, M. H.-M.·Meijer, M.·Merrill, S. M.·Fu, M. P. Y.·Lin, D.·MacIsaac, J. L.·Riis, J. L.·Granger, D. A.·Thomas, E. A.·Kobor, M. S.
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Abstract

Saliva is widely used in biomedical population research, including epigenetic analyses to investigate gene-environment interplay and identify biomarkers. Its minimally invasive collection procedure makes it ideal for studies in pediatric populations. Saliva is a heterogenous tissue composed of immune and buccal epithelial cells (BEC). Amongst the many epigenetic marks, DNA methylation (DNAm) is the most studied in human populations. Given DNAms integral role to cellular differentiation and maintenance, DNAm profiles are often highly cell type (CT)-specific and CT composition can drive salivary DNAm associations with environments or health as well as epigenetic age acceleration (EAA), discrepancy between chronological age and biological age derived from DNAm. To address this, reference-based CT deconvolution and statistically adjustment with estimated CT in DNAm analyses have become a common practice. However, it remains unclear how different CT reference panels--constructed from adult versus pediatric samples--affect DNAm results. Additionally, whether DNAm and EAA associations in saliva primarily originate from immune cells or BECs, or if they persist across saliva samples despite varying CT proportions, has yet to be examined. The current study used salivary DNAm samples obtained from 529 children (mean age=7.26 years, SD=0.26 years) in a community-based cohort, the Family Life Project. Our results highlighted the impact of estimated CT discrepancies across child and adult reference panels on DNAm associations. Upon stratifying the salivary DNAm samples into three subsamples--primarily BECs, primarily immune cells, and an approximately equal mix of both, we found significantly different EAAs across stratified samples when CT proportions were not accounted for. In both the context of DNAm and EAA associations, we detected stronger effects of cotinine concentrations, a tobacco smoke-exposure biomarker, in the subsample with primarily immune cells. We discussed the implications of our findings for the interpretation and replication of epigenetic research involving pediatric saliva samples.

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Chan, M. H.-M., Meijer, M., Merrill, S. M., Fu, M. P. Y., Lin, D., MacIsaac, J. L., Riis, J. L., Granger, D. A., Thomas, E. A., Kobor, M. S.. 2024-11-11. Considerations for Cell Type Heterogeneity in Pediatric Salivary DNA Methylation Analyses: Comparison of Reference Panels & Stratification by Estimated Cell TypeProportion. https://doi.org/10.1101/2024.11.08.621377

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