Multi-omics approach reveals dysregulated genes during hESCs neuronal differentiation exposure to paracetamol

Abstract

Background: Several epidemiological studies have found associations between long-term prenatal exposure to paracetamol and neurodevelopmental outcomes in childhood. Pharmacoepigenetic studies have identified differences in DNA methylation (DNAm) in cord blood between exposed and unexposed neonates. However, the causal implications and impact of prenatal long-term paracetamol exposure on brain development are not known. Methods: We exposed human embryonic stem cells (hESCs) undergoing in vitro neuronal differentiation to daily changes of media containing amount of paracetamol corresponding to human foetal exposure with maternal therapeutic doses. An integrated multi-omics approach was used to investigate epigenetic and transcriptomic effects of paracetamol on the early stages of human brain development. Results: Multi-omics analyses of DNAm, chromatin opening, and gene expression identified dose-dependent effects on cell proliferation and maturation. We found differentially methylated and/or expressed genes involved in signal transduction, neurotransmitter secretion and cell fate determination trajectories. Integration of single-cell RNA-seq and ATAC-seq showed that paracetamol-induced changes in chromatin opening were linked to transcription. For example, EP300 encoding a histone acetyltransferase and H3K27ac were linked to many putative cis regulatory elements and downregulated upon paracetamol exposure. Some of the genes are involved in neuronal injury, response to toxic insults and development-specific pathways, such as KCNE3, overlapped with differentially methylated genes previously identified in cord blood associated with prenatal paracetamol exposure. Conclusion: We identified dose-dependent epigenetic and transcriptional changes in hESCs undergoing neuronal differentiation after paracetamol exposure. The overlap of differentially methylated genes with our previous analysis in cord blood from children exposed to paracetamol during pregnancy could suggest a causal role in impaired neurodevelopment.

Single-cell transcriptomics of pathological pregnancies

“…The top involved functional pathways were cell-cycle transition (MKI67, PCNA, TP53, CDK1, MYBL2 and GJA1), neurite outgrowth and cortical neurogenesis (GBA2, ASPM), neuronal maturation (CDKN1C, POU2F1, POU3F1, ROBO1, STMN2 and STMN4) and transcription factors associated with brain development (NKX2.1, OTX2, FOXG1, ASCL1, ISL1, EMX2 and HOXA1). [48] Congenital heart disease During the 1st trimester of pregnancy, the placenta and fetal heart develop concurrently, and share key developmental pathways. 328 commonly expressed genes and two major HTTPS://WWW.HKSMP.COM/JOURNALS/PRM pathways (vasculature development and angiogenesis) between fetal heart and placenta endothelial cells have been identified.…”