Alternative Splicing in Recombinant Protein-Producing Chinese Hamster Ovary Cell Lines

Abstract

This thesis investigates the dynamics of alternative splicing (AS) in Chinese Hamster Ovary (CHO) cells, which are the industry standard for recombinant protein production. During the transition to the stationary growth phase, these cells experience high endoplasmic reticulum (ER) stress, yet the specific splicing changes that occur during this window have remained largely unexplored. To address this, the study utilized RNA sequencing (RNA-seq) combined with a rigorous bioinformatics pipeline to identify and validate significant AS events driven by culture progression. The analysis successfully isolated 28 alternatively spliced protein-coding genes with valid structural and functional predictions. These findings reveal a coordinated cellular survival strategy where cells reprogram their post-transcriptional and epigenetic machinery to endure nutrient deprivation and stress. Ultimately, this research highlights how AS shapes the adaptive ER stress response, providing valuable new molecular targets for future cell line engineering and proactive bioreactor monitoring.