Proteomic analysis of CHO cell lines producing high and low quantities of a recombinant antibody before and after selection with methotrexate.

High levels of recombinant protein production in Chinese hamster ovary (CHO) cells can be achieved by amplification of transgenes using the dihydrofolate reductase/methotrexate (DHFR/MTX) system. With the aim to identify predictive markers enabling the preselection of suitable high producing clones we investigated the impact of MTX-based gene amplification on two CHO cells lines producing different levels of a human monoclonal antibody by carrying out a comparative proteome analysis. The difference in antibody yield between the high and low producer was 15-fold before and 245-fold after MTX selection. Difference in-gel electrophoresis of samples from before and after MTX selection revealed 17 unique proteins that were differentially expressed between the high and low productivity lines. Of these, five proteins were differently expressed before MTX selection, representing potential markers for productivity prior to selection and for engineering processes to generate novel CHO cell line with the desirable high productivity phenotype. Fifteen proteins were differently expressed between high and low producer after MTX selection. We further found that MTX selection induced more changes in the proteome of the low producer compared to the high producer.