m6A modification profiles of the CHO cells with differential recombinant protein expression using MeRIP-seq/RNA-seq

Chinese hamster ovary (CHO) cells remain the primary host system for recombinant therapeutic protein production. Enhancing transgene expression efficiency while maintaining stable production persists as a key challenge in CHO cell engineering. While N6-methyladenosine (m6A) modification - the most abundant RNA methylation - regulates RNA stability and translational efficiency, its role in modulating recombinant protein expression remains underexplored. In this study, through m6A-specific methylated RNA immunoprecipitation sequencing (MeRIP-seq) of high- (ADM-H) and low- (ADM-L) recombinant adalimumab (ADM)-producing CHO cell lines, we identified 668 differentially methylated peaks. Notably, m6A methylation patterns showed positive correlation with heavy chain (HC)/light chain (LC) expression levels between ADM-H and ADM-L cell lines. Differential expression of factors, such as Igf2bp2, Gli2, and Met correlated with PI3K-Akt and Hippo signaling pathways, suggesting m6A-mediated regulatory functions of recombinant protein expression in CHO cells. Furthermore, pharmacological inhibition of Gli2 or Met in cell culture effectively enhanced ADM production while suppressing target gene expression. These findings elucidate m6A's functional role in recombinant protein production and provide actionable strategies for CHO cell line optimization.