2026 ECNP Congress

PS03-3069

Disentangling the epigenetic landscape of saliva: a genetically informed longitudinal twin study of DNA methylation

Alicia Schowe — J. Instinske, C.K.L. Pahnke, A.J. Forstner, M. Nöthen, C. Kandler, D. Czamara, E. Binder · Max Planck Institute of Psychiatry, Genes and Environment, Munich, Germany

2026 ECNP Congress

DNA methylation (DNAm) is a cell-type and tissue-specific epigenomic mechanism through which genetic variation and environmental exposures can jointly shape biological processes across development. While DNAm has been extensively characterized in adult blood, the sources of DNAm variation in saliva remain poorly understood. This represents a critical gap, as saliva constitutes a highly promising tissue for large-scale genetic and epigenetic research: it can be collected non-invasively, repeatedly, and without specialized personnel, and can be stored and transported under relatively low-cost conditions. These advantages make saliva particularly suitable for longitudinal and population-based studies requiring large sample sizes to detect the typically small effects observed at individual CpG sites.

In the present study, we conducted genetically informed analyses using longitudinal twin data to evaluate sources of saliva DNAm as an integrative regulatory layer reflecting genotype and environmentally responsive processes relevant to development and health. We partitioned the variances of 661,631 DNAm sites measured at two timepoints into additive genetic (A), shared environmental (C) and unique environmental (E) components. Analyses were conducted using data from the TwinLife Epigenetic Change Satellite (TECS) project, comprising 489 twin pairs (263 monozygotic, 226 dizygotic) assessed at two timepoints. The sample spans key developmental stages, including children (mean ages 9.5 and 11.8 years, 46.3% female), adolescents (15.5 and 17.8 years, 52.7% female), and young adults (20.8 and 22.8 years, 60.4% female), thereby enabling the examination of developmental differences in DNAm architecture. We further contextualized saliva-based estimates by comparing them to published heritability estimates derived from skin DNAm [1], blood DNAm [2], and adipose tissue DNAm [3], as well as cross-tissue DNAm correlations reported in prior work [4].

On average, saliva DNAm showed modest heritability (mean = 13%), exceeding estimates reported for skin (10%) but remaining lower than those observed in blood (19%) and adipose tissue (37%). Across CpG sites, heritability estimates in saliva were moderately correlated with those in blood (r = 0.64), indicating partial cross-tissue consistency in genetic regulation. Notably, shared environmental influences accounted for a greater proportion of variance in saliva compared to blood (5% vs. 2.59%), suggesting that saliva may be particularly sensitive to environmental exposures shared within families. Furthermore, CpG sites with higher heritability exhibited greater temporal stability across measurement occasions (r = 0.66) and stronger cross-tissue correspondence with blood DNAm (r = 0.73), supporting the robustness of genetically influenced loci.

In ongoing work we triangulate these twin‑based heritability estimates with measured genetic variation based on methylation Quantitative Trait Loci (mQTLs). We also explore to what extend environmentally sensitive sites are influenced by environmental stressors (e.g., COVID‑19, early adversity). In addition, we explore differences in twin-based estimates between age groups in the TECS project. Overall, our findings will elucidate the genetic and environmental sensitivity of the saliva methylome, supporting the interpretability of saliva‑based multi‑omics as a bridge between static genotypes and dynamic developmental phenotypes.

References

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  2. Shore, C. J., Villicaña, S., El-Sayed Moustafa, J. S., Roberts, A. L., Gunn, D. A., Bataille, V., Deloukas, P., Spector, T. D., Small, K. S., & Bell, J. T. (2024). Genetic effects on the skin methylome in healthy older twins. American journal of human genetics, 111(9), 1932–1952. https://doi.org/10.1016/j.ajhg.2024.07.010
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  4. Karlbauer VN, Domínguez-Baleón C, Rex-Haffner M, Namendorf T, Hoffmann F, Klawitter H, Entringer S, Buss C, Winter SM, Heim C, Binder EB, Czamara D (2025) Limited generalizability of epigenetic clocks and scores across pediatric tissues and age ranges. medRxiv