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Proteomics reveals distinctive host cell protein expression patterns in fed batch and perfusion cell culture processes
  • +5
  • Ansuman Sahoo,
  • Taku Tsukiadate,
  • Ray Lin,
  • Erin Kotzbauer,
  • Jason Houser,
  • Misaal Patel,
  • Xuanwen LI,
  • Sri R. Madabhushi
Ansuman Sahoo
Merck Sharp & Dohme Corp
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Taku Tsukiadate
Merck Sharp & Dohme Corp
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Ray Lin
Merck Sharp & Dohme Corp
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Erin Kotzbauer
Merck Sharp & Dohme Corp
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Jason Houser
Merck Sharp & Dohme Corp
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Misaal Patel
Merck Sharp & Dohme Corp
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Xuanwen LI
Merck Sharp & Dohme Corp
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Sri R. Madabhushi
Merck Sharp & Dohme Corp

Corresponding Author:[email protected]

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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.
17 Sep 2024Submitted to Biotechnology Journal
18 Sep 2024Submission Checks Completed
18 Sep 2024Assigned to Editor
18 Sep 2024Review(s) Completed, Editorial Evaluation Pending
19 Sep 2024Reviewer(s) Assigned
09 Oct 2024Editorial Decision: Revise Major