3.1. Time Course Transcriptome Heterogeneity in Suspension
Cultures
We performed single-cell Quartz-Seq as previously reported (Sasagawa et
al., 2013) of 85 D4, 70 D8, and 78 D11 CHO cells. To compare the
transcriptomes of the cells cultured for different lengths of time
(days), we performed PCA of all the expression data (Figure 1). The
proportion of variance in principal component 1 (PC1) was 0.3102, while
that of PC2 was 0.077. Using this approach, we could quantitatively
evaluate the cellular heterogeneity, which previously was not possible.
The standard deviations in PC1 were 1634 for D4, 3024 for D8, and 5029
for D11. We rejected the null hypothesis that heterogeneity did not
increase during culture, based on the Bartlett test for the homogeneity
of variances in the PC1 between different culture times (p <
2.2e-16). Thus, the cellular heterogeneity increased during cultivation
and this increase showed no sign of attenuation. Hence, the maximum
attainable heterogeneity of the CHO cells in a long-term high cell
density culture was not predictable from these data. To assess cellular
heterogeneity in future bioengineering processes, very long-term
cultures such as perfusion continuous cultures need to be studied. We
can control it if it can be measured.