The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line

Abstract

Therapeutic proteins and antibodies represent a $125 billion annual market. Chinese Hamster Ovary (CHO) derived cell lines are the preferred host cells for the production of therapeutic proteins. Here, we present a draft genomic sequence of the CHO-K1 ancestral cell line. The assembly comprises 2.45Gb genomic sequence with 24,383 predicted genes. We associate most scaffolds to 21 microfluidically-isolated chromosomes to identify chromosomal locations of genes. Furthermore, we investigate genes involved in glycosylation, which affects therapeutic protein quality, and viral susceptibility genes, which affect cell engineering and regulatory concerns. Specifically, homologs for most human glycosylation-associated genes are identified in the CHO-K1 genome, although 141 are not expressed under exponential growth. In addition, many important viral entry genes are present in the genome but not expressed, which may explain the unusual viral resistance property of CHO cell lines. We demonstrate how the availability of this genome sequence may facilitate genome-scale science for biopharmaceutical protein production.

A reference genome of the Chinese hamster based on a hybrid assembly strategy

“…In addition, for >30 years, they have been the host cell of choice for production of most biotherapeutics. While the aforementioned research was carried out without genomic resources, new opportunities are arising with published CHO genome sequences [Xu et al, 2011], [Brinkrolf et al, 2013], [Lewis et al, 2013], [Yusufi et al, 2017]. However, the draft nature of these genome sequences pose challenges for many applications.…”

The “less-is-more” in therapeutic antibodies: Afucosylated anti-cancer antibodies with enhanced antibody-dependent cellular cytotoxicity

“…Mass spectrometry analyses demonstrated the complete lack of core fucose on N -glycans attached to the EPO-Fc fusion protein and IgG1 antibodies produced in the CHO-gmt3 cells 80 . The CHO-K1 transcriptome data have shown that among all Golgi fucosyltransferases, only FUT8 is expressed 82 . Therefore, inactivating Fut8 or Slc35c1 should have similar effects on CHO-K1 cells.…”

Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

“…2). The final gene set consisted of 24,044 genes in the hamster genome, which is similar to that of the CHO-K1 cell line 5 . Of these predicted genes, 23,473 clustered into 21,628 gene families (Fig.…”

“…Meanwhile, efforts to engineer mouse cells have greatly benefited from numerous genomic tools and technologies, owing in large part to the availability of the Mus musculus reference genome sequence. Genomic resources are also becoming available for CHO cells, such as the CHO-K1 genome 5 , expressed sequence tag 6,7 and bacterial artificial chromosome (BAC) libraries 8 , and compendia of proteomic [9][10][11] and transcriptomic data 7,[12][13][14][15][16] . However, much like how murine cell line data are routinely studied in the context of the Mus musculus reference genome, there is a need for a standard reference for all CHO cell lines to contextualize all of these valuable genomic resources.…”