Single-cell RNA sequencing reveals homogeneous transcriptome patterns and low variance both in suspension CHO-K1 and adherent HEK293FT cell lines

Chinese hamster ovary (CHO) cells represent one of the most important mammalian host cell systems for the industrial production of recombinant therapeutic proteins owing to their manufacturing adaptability, capacity for correct folding, and human-like-post-translational modifications. Although their characteristic genomic instability is well known, some control mechanisms that allow shifts in response to changes in the environmental conditions are still not fully understood. In order to produce adequate amounts of recombinant proteins, an appropriate growth condition is a crucial requisite for CHO cells. In this study, we used a full-length coverage single-cell RNA sequencing (scRNA-seq) approach to investigate and compare cell-to-cell variability and the impact of standardized and homogenous culture conditions on the diversity of individual cell transcriptomes in immortalized cell lines, comparing suspension CHO-K1 and adherent HEK293FT cell lines. First of all, the debate that we addressed was whether the low number of cells available was generally representative of the bulk transcriptome. Our data showed an initial critical batch effect from the sequencing of four 96-well plates of CHO-K1 single cells stored at -80oC for different periods of time and therefore, that this is a key issue to consider in experimental planning. Besides, our results indicate that in an artificial culture environment such as used in routine cell culture technology, the gene expression pattern of a given population is discreetly homogeneous. The variation observed in the samples of the CHO-K1 cell line is comparable to the one detected in the HEK293FT cells, and it is in both cases principally driven by the cell cycle.