Formaldehyde Exposure Induces Systemic Epigenetic Alterations in Histone Methylation and Acetylation

Formaldehyde (FA) is a pervasive environmental organic pollutant and a Group 1 human carcinogen. While FA has been implicated in various cancers, its genotoxic effects, including DNA damage and DNA–protein cross-linking, have proven insufficient to fully explain its role in carcinogenesis, suggesting the involvement of epigenetic mechanisms. Histone post-translational modifications (PTMs) on H3 and H4, which are critical for regulating gene expression, may contribute to FA-induced pathogenesis, as lysine and arginine residues serve as targets for FA–protein adduct formation. This study aimed to elucidate the epigenetic consequences of FA on histone methylation and acetylation patterns through a comprehensive peptide analysis. Human bronchial epithelial cells (BEAS-2B) were exposed to low-dose (0.1 mM) and high-dose (0.5 mM) FA for 1 h, and their histone extracts were analyzed using high-resolution liquid chromatography–tandem mass spectrometry-based proteomics followed by PTM-combined peptide analysis and single PTM site/type comparisons. We identified 40 peptides on histone H3 and 16 on histone H4 bearing epigenetic marks. Our findings revealed that FA exposure induced systemic alterations in H3 and H4 methylation and acetylation, including hypomethylation of H3K4 and H3K79; changes in H3K9, H3K14, H3K18, H3K23, H3K27, H3K36, H3K37, and H3R40; as well as modifications in H4K5, H4K8, H4K12, and H4K16. These FA-induced histone modifications exhibited strong parallels with epigenetic alterations observed in cancers, leukemia, and Alzheimer’s disease. This study provides novel evidence of FA-induced epigenetic toxicity, offering new insights into the potential mechanisms underlying FA-driven pathogenesis.