Whole-Genome Sequencing – CHO Mammalian Cells

CHO (Chinese hamster ovary) cells are the most dependable host cells for large-scale production of therapeutic proteins and have been used in the pharmaceutical industry for over 60 years. Because this cell line has been immortalized, its genome has accumulated many mutations, thus impairing certain biochemical pathways in CHO mammalian cells. As a result, there are several limitations in the range of products that can be expressed and secreted by this cell line. By using specifically designed bioinformatics to analyze data from trancriptome and genome sequencing, Selexis has been able to generate tools to engineer CHO mammalian cells and repair defined biochemical pathways that enable the expression of difficult-to-express proteins. The combination of these new tools is unprecedented in the industry and includes:

SURE CHO-Mplus Libraries

SURE CHO-Mplus Libraries are a powerful and sophisticated holistic approach that is based on data that have been generated by transcriptomics analysis. These libraries significantly de risk expression and production issues of difficult-to-express recombinant proteins in CHO mammalian cells, thus helping reduce attrition rates in biologic drug discovery and development. Because optimal expression of certain proteins can not be achieved by elevated transcription alone, this platform offers an unprecedented solution for generating manufacturing cell lines that are specifically tailored to the particular expression and secretory needs of many of difficult-to-express recombinant proteins.

Whole-Genome Sequencing + Bioinformatics

The combination of faster, more cost-effective next-generation sequencing (NGS) methods and the generation of specifically designed, unique, and proprietary bioinformatics tools has led Selexis to launch its whole-genome sequencing (WGS) initiative. The WGS platforms can analyze data from NGS sequencing (Illumina or PacBio technologies) of any RCB, MCB, or WCB genome in just a few days. Unlike other platforms, WGS is unbiased, because it analyzes data from entire genomes and not from partial regions of the genome. WGS allows:

  • Determination of clonality (and the purity) of a RCB, MCB, or WCB (by analyzing SNPs)
  • Determination of the DNA sequence of all integrated copies of the gene of interest (not only the transcribed copies through mRNA extraction)
  • Calculation of  the exact copy number of the integrated gene
  • Determination of the DNA sequences at the junctions of the integration sites (ensuring that the gene of interest is not truncated at those sites)
  • Analysis of the sequence of genes that are important for the metabolism and life of the CHO cell (e.g., detecting mutations that may impair the stability of the CHO mammalian cell)
  • Additionally, Selexis is able to identify viral genetic sequences (adventitious agents) and define a direct baseline that can be used to anticipate an infection that occur during the manufacturing process

WGS provides Selexis partners with an in-depth analysis of their recombinant cell lines and allows for these cell lines to be barcoded to facilitate tracking of clonal drift or the identification of adventitious agents that have been introduced (from filing an IND to market launch and beyond).

WGS data packages:

  • Provide NGS data that have been analyzed using SUREScan
  • Identify and validate integration sites
  • Prove clonality using SNPs
  • Provide transgene sequence, copy number, and integrity