Timecourse RNA Sequencing of three CHO cell lines: non-producing CHOZN®GS-/-, an IgG1 producer, and an EPO-Fc producer

We analyzed the transcriptomic response in three distinct CHO cell lines: a non-producing host cell line (CHOZN®GS-/-), an immunoglobulin G1 (IgG1) producer, and an erythropoietin Fc fusion (EPO-Fc) producer. We compared the growth and production characteristics of all three cell lines during fed-batch culture. High throughput RNA sequencing (RNASeq) and quantitative polymerase chain reaction (qPCR) were used to study differential gene expression analysis of the timecourse dataset with the host cell line CHOZN®GS-/- as the reference. The objective of this analysis was to study the common and unique responses of cell lines producing different protein products. This analysis showed enrichment and transient upregulation of mRNAs involved in ER stress, the UPR, and oxidative protein folding and processing in both protein producers. Analysis of temporal differential expression profiles led to the identification of novel engineering targets. Overall design: Comparative gene expression analysis of RNASeq data for a non-producing host CHO cell line (CHOZN®GS-/-, denoted ZN) and two protein-producing CHO cell lines (an IgG1 producer, denoted I23 and an EPO-Fc producer, denoted E33). Samples were collected in biological triplicate for each cell line from four different days of fed-batch culture (days 0, 1, 3, and 5). For example, sample "ZN_D0_1" is read as "host, day 0, replicate 1". Thirty-six samples were submitted for RNASeq. Samples of the non-producing host cell line were considered reference in this study.