Elucidating the impact of cottonseed hydrolysates on CHO cell culture performance through transcriptomic analysis

Abstract: In order to evaluate the impact of plant-based hydrolysates on CHO cells, a transcriptomic study was undertaken using cottonseed hydrolysate and Illumina’s NextSeq transcriptomics profiling for 2 days of a batch cell culture. While cottonseed hydrolysate extended cell growth and increased antibody titer, significant effects were seen on transcriptomic signatures of supplemented cultures when compared to untreated cultures, evaluated using fold change, gene ontology (GO), and KEGG pathway analysis. Transcription and other factors commonly associated with cell growth such as those of the Atf family and homeobox proteins were upregulated while genes in the Hippo signaling pathway were downregulated. Genes involved in anabolic pathways such as gluconeogenesis and those involving protein folding and translation elongation were upregulated. GO analysis of biological processes for cottonseed-supplemented cultures indicated enrichments in DNA replication, protein processing, and unfolded protein response while molecular functions associated with growth such as GTPases, ATP binding, and aminoacyl t-RNA ligase activity were also enriched. Cellular components associated with structural integrity such as actin cytoskeleton, microtubules, mitochondrion, and Lewy body were enriched. Enriched KEGG pathways include growth-associated pathways such as cell cycle, pI3K-AKT-mTOR, and cancer-related pathways as well as those enhancing glycan metabolism, purine metabolism, amino acid biosynthesis, and protein processing in the endoplasmic reticulum (ER). These transcriptomic profiles provide insights into the roles that hydrolysates such as cottonseed can play in altering CHO cell growth and other physiological characteristics as well as suggesting ways in which CHO cell culture may be modified for enhancing performance in biotechnology applications. Key points: • Hydrolysate-supplemented cultures increased mammalian cell growth and productivity. • Fold-change analysis revealed upregulation in transcription and translation. • Enriched GOs and KEGG pathways including cell cycle and metabolism were observed.