Single-cell RNA sequencing reveals tissue-specific transcriptomic changes induced by perfluorooctanesulfonic acid (PFOS) in larval zebrafish (Danio rerio)

Perfluorooctanesulfonic acid (PFOS) elicits adverse effects on numerous organs and developmental processes but the mechanisms underlying these effects are not well understood. Here, we use single-cell RNA-sequencing to assess tissue-specific transcriptomic changes in zebrafish (Danio rerio) larvae exposed to 16 µM PFOS or dimethylsulfoxide (0.01 %) from 3–72 h post fertilization (hpf). Data analysis was multi-pronged and included pseudo-bulk, untargeted clustering, informed pathway queries, and a cluster curated for hepatocyte biomarkers (fabp10a, and apoa2). Overall, 8.63 % (2390/27698) genes were significantly differentially expressed. Results from untargeted analysis revealed 22 distinct clusters that were manually annotated to specific tissues using a weight-of-evidence approach. The clusters with the highest number of significant differentially expressed genes (DEGs) were digestive organs, muscle, and otolith. Additionally, we assessed the distribution of pathway-specific genes known to be involved in PFOS toxicity: the PPAR pathway, β-oxidation of fatty acids, the Nfe2l2 pathway, and epigenetic modifications by DNA methylation, across clusters and identified the blood-related tissue to be the most sensitive. The curated hepatocyte cluster showed 220 significant DEGs and was enriched for the Notch signaling pathway. These findings provide insights into both established and novel sensitive target tissues and molecular mechanisms of developmental toxicity of PFOS.