Transcriptome analysis for the scale-down of a CHO cell fed-batch process

Transcriptome and metabolism analysis were performed to evaluate the scale-down of a CHO cell fed-batch process from a 10 L bioreactor to an ambr 15^® (ambr) system. Two different agitation scale-down principles were applied, resulting in two different agitation rates in the ambr system: 1300 RPM based on the agitator tip speed, and 800 rpm based on the volumetric power input (P/V). Culture performance including cell growth, product titer, glycosylation, and specific consumption/production rates of metabolites was the same for both agitation rates in the ambr and was comparable to that of the 10 L system. The initial variation in gene expression between the inocula for the ambr and 10 L system was no longer present after three days of culture, indicating comparable culture conditions in both systems. Based on principal component analysis, changes in gene expression over time were similar between both scales with less than 6% variation. 2455 genes were uniquely regulated in the ambr system compared to 1604 genes in the 10 L system. Functional analysis of these genes did not reveal their relations with scale or cellular function. This study further strengthens that the ambr system gives representative culture performance for the 10 L bench-scale bioreactor.