Toxicotranscriptomics of single cell RNA-Seq and conventional RNA-Seq in TCDD-exposed testicular tissue

Spermatogenesis is a dynamic, tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is believed to be a cause of idiopathic male infertility. To understand TCDD-induced disruption of spermatogenesis at the single cell level, we profiled adult zebrafish testes with and without early-life exposure to TCDD. Secondly, to investigate the potential for technical artifacts in scRNA-seq, we compared bulk-sequenced and scRNA-seq-paired samples from control and TCDD-exposed samples, and included an intact control fish to account for dissociation-induced artifacts. We found scRNA-seq and bulk-seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA-seq, we found TCDD exposure induces mid-late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk-seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA-seq and bulk-seq, with scRNA-seq biased towards detecting longer and more abundant transcripts, but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA-seq, remained intact for bulk-seq, or were dissociated for bulk-seq.