Time-course characterization of whole-transcriptome dynamics of HepG2/C3A spheroid and its toxicological implications

Physiologically relevant in vitro models are a priority in predictive toxicology in order to replace and/or reduce animal experiments. The compromised toxicant metabolism of many immortalized human liver cell lines grown as monolayers as compared to in vivo metabolism limits their physiological relevance. However, recent efforts to culture liver cells in a 3D environment, such as spheroids, to better mimic the in vivo conditions, may enhance the toxicant metabolism of human liver cell lines. In this study, we characterized the dynamic changes in the transcriptome of HepG2/C3A hepatocarcinoma cell spheroids maintained in a clinostat system (CelVivo) to gain insight into the metabolic capacity of this model as a function of spheroid size and culture time. We assessed morphological changes (size, necrotic core), cell health, and proliferation rate from initial spheroid seeding to 35 days of continuous culture in conjunction with a time-course (0, 3, 7, 10, 14, 21, 28 days) of the transcriptome (TempO-Seq, BioSpyder). The phenotypic characteristics of HepG2/C3A growing in spheroids was comparable to monolayer growth until ~Day 12 (Day 10-14) when a significant decrease in cell doubling rate was noted which was concurrent with down regulation of cell proliferation and cell cycle pathways over this time period. Principal Component Analysis and hierarchal clustering of the transcriptome data suggests that the Day 3, 7, and 10 spheroids are pronouncedly different from the Day 14, 21, and 28 spheroid in support of a biological transition time point during the long-term 3D spheroid cultures. Unexpectedly, the expression of genes encoding toxicant metabolism and transport rapidly increased during the early time points of spheroids to peak at Day 7 or Day 10 as compared to monolayer cultures with gradual decrease in expression with further culture, suggesting the most metabolically responsive time window for exposure studies. Overall, here we provide baseline information on the cellular and molecular characterization, with a particular focus on toxicant metabolic capacity dynamics and cell growth of HepG2/C3A 3D spheroid cultures over the time course. To investigate whole-transcriptome dynamics (changes) during formation and maintenance of 3D spheroid using HepG2/C3A human liver cell line, 2D monolayer and 3D spheroid (Day 3, Day 7, Day 10, Day 14, Day 21, Day 28, and Day 28) samples cultured in ClinoStar system (CelVivo) were collected. Subsequently, those samples were processesd for TempO-Seq (BioSpyder), generating time-course whole-transcriptome data and subsequent downstream analyses.