Proteomics reveals distinctive host cell protein expression patterns in
fed batch and perfusion cell culture processes
Abstract
Chinese hamster ovary (CHO) cells are widely used to produce recombinant
proteins, including monoclonal antibodies (mAbs), through various
process modes. Traditionally, fed batch (FB) processes have been the
standard. However, the shift towards high-density perfusion processes is
driven by increased productivity, flexible facility footprints, and
lower costs. Ensuring the clearance of process-related impurities, such
as host cell proteins (HCPs), is crucial in biologics manufacturing.
While purification processes remove most impurities, integrated
strategies are being developed to enhance biologics purity and address
high-risk HCPs. Current understanding of HCP expression dynamics in cell
culture is limited. This study utilized data-independent acquisition
(DIA) proteomics to compare the proteomic profiles of cell culture
supernatants from 14 FB clones and 3 perfusion clones, all expressing
the same mAb from the same host cell line. Results showed that perfusion
processes enhance cell growth and productivity, exhibiting distinct
proteomic profiles compared to FB processes. Perfusion processes also
maintain a more stable HCP profile across clones, especially for 46
problematic HCPs monitored. Cluster analysis of FB proteomics revealed
distinct abundance patterns and correlations with process parameters.
Differential abundance analysis identified significant protein
differences between the two processes. Compared to FB, the perfusion
process may provide a less stressful cellular environment. This is the
first extensive study characterizing HCPs expressed by different clones
under different process modes. Further research could lead to strategies
for preventing or managing problematic HCPs in biologics manufacturing.