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

Mari Spildrejorde; Athina Samara; Ankush Sharma; Magnus Leithaug; Martin Falck; Stefania Modafferi; Arvind Y M Sundaram; Ganesh Acharya; Hedvig Nordeng; Ragnhild Eskeland; Kristina Gervin; Robert Lyle

doi:10.1016/j.isci.2023.107755

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

iScience. 2023 Aug 28;26(10):107755. doi: 10.1016/j.isci.2023.107755. eCollection 2023 Oct 20.

Authors

Mari Spildrejorde^{1

2

3}, Athina Samara^{4

5}, Ankush Sharma^{6

7

8}, Magnus Leithaug^{1

2}, Martin Falck^{1

8}, Stefania Modafferi², Arvind Y M Sundaram², Ganesh Acharya^{9

10}, Hedvig Nordeng^{1

11}, Ragnhild Eskeland^{1

7}, Kristina Gervin^{1

11

12}, Robert Lyle^{1

2

13}

Affiliations

¹ PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.
² Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
³ Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
⁴ Division of Clinical Paediatrics, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
⁵ Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.
⁶ Department of Informatics, University of Oslo, Oslo, Norway.
⁷ Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
⁸ Department of Biosciences, University of Oslo, Oslo, Norway.
⁹ Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Alfred Nobels Allé 8, SE-14152 Stockholm, Sweden.
¹⁰ Center for Fetal Medicine, Karolinska University Hospital, SE-14186 Stockholm, Sweden.
¹¹ Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, University of Oslo, Oslo, Norway.
¹² Division of Clinical Neuroscience, Department of Research and Innovation, Oslo University Hospital, Oslo, Norway.
¹³ Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.

Abstract

Prenatal paracetamol exposure has been associated with neurodevelopmental outcomes in childhood. Pharmacoepigenetic studies show differences in cord blood DNA methylation between unexposed and paracetamol-exposed neonates, however, causality and impact of long-term prenatal paracetamol exposure on brain development remain unclear. Using a multi-omics approach, we investigated the effects of paracetamol on an in vitro model of early human neurodevelopment. We exposed human embryonic stem cells undergoing neuronal differentiation 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 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.

Keywords: Developmental neuroscience; Genomics; In vitro toxicology; Neurotoxicology; Stem cells research; Transcriptomics.