Multi-Omics Approach Reveals Dysregulated Genes During hESCs Neuronal Differentiation Exposure to Paracetamol

Abstract

Prenatal paracetamol exposure has been associated with neurodevelopmental outcomes in childhood. Pharmacoepigenetic studies show differences in cord blood DNA methylation between paracetamol exposed and unexposed neonates. However, causal implications and impact of long-term prenatal long-term paracetamol exposure on brain development remain unclear. Using a multi-omics approach, we investigated the effects of paracetamol on a model of early human brain development. We exposed human embryonic stem cells undergoing in vitro neuronal differentiation to daily media changes with paracetamol concentrations corresponding to maternal therapeutic doses. Single-cell RNA-seq and ATAC-seq integration identified paracetamol-induced chromatin-opening changes linked to gene expression. Differentially methylated and/or expressed genes were involved in signalling, neurotransmission, and cell fate-determination trajectories. Some genes involved in neuronal injury and development-specific pathways, such as KCNE3, overlapped with differentially methylated genes previously identified in cord blood associated with prenatal paracetamol exposure. Our data suggest that paracetamol may play a causal role in impaired neurodevelopment.

Note:
Funding Information: We acknowledge funding from Research Council of Norway 262484 (R.E.), 241117 (R.L.), and 287953 (A.S.); the Swedish Research Council 2019-01157 (A.S.) and grants from the Swedish Brain FO2019-0087 (A.S.) and the Freemasons Children's House of Stockholm (A.S.) and BiomatDB+ (Horizon Europe #101058779; AS).

Declaration of Interests: The authors declare no competing interest.

Keywords: Paracetamol, Acetaminophen, DNA methylation, multi-omics, single-cell RNA-seq, scATAC-seq, human embryonic stem cells, neuronal differentiation, telencephalic signatures, cord blood