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Huhn S, Chang M, Kumar A, Liu R, Jiang B, Betenbaugh M, Lin H, Nyberg G, Du Z. Chromosomal instability drives convergent and divergent evolution toward advantageous inherited traits in mammalian CHO bioproduction lineages. iScience 2022; 25:104074. [PMID: 35355517 PMCID: PMC8958363 DOI: 10.1016/j.isci.2022.104074] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/17/2022] [Accepted: 03/11/2022] [Indexed: 12/15/2022] Open
Abstract
Genetic instability of Chinese hamster ovary (CHO) cells is implicated in production inconsistency through poorly defined mechanisms. Using a multi-omics approach, we analyzed the variations of CHO lineages derived from CHO-K1 cells. We identify an equilibrium between random genetic variation of the CHO genome and heritable traits driven by culture conditions, selection criteria, and genetic linkage. These inherited changes are associated with the selection pressures related to serum removal, suspension culture transition, protein expression, and secretion. We observed that a haploid reduction of a Chromosome 2 region after serum-free, suspension adaptation, was consistently inherited, suggesting common adaptation mechanisms. Genetic variations also included ∼200 insertions/deletions, ∼1000 single-nucleotide polymorphisms, and ∼300-2000 copy number variations, which were exacerbated after gene editing. In addition, heterochromatic chromosomes were preferentially lost as cells continuously evolved. Together, these observations demonstrate a highly plastic signature for adapted CHO cells and paves the way towards future host cell engineering.
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Affiliation(s)
- Steve Huhn
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Meiping Chang
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Amit Kumar
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Ren Liu
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Bo Jiang
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Henry Lin
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Gregg Nyberg
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Zhimei Du
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ 07033, USA
- Corresponding author
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