Research review paper Developing genomic platforms for Chinese hamster ovary cells Anne Kantardjieff a , Peter Morin Nissom b , Song Hui Chuah b , Faraaz Yusufi b , Nitya M. Jacob a , Bhanu Chandra Mulukutla a , Miranda Yap b , Wei-Shou Hu a, ⁎ a Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, MN 55455-0132 USA b Bioprocessing Technology Institute Agency for Science, Technology and Research (A⁎STAR) 20 Biopolis Way, #06-01 Centros, 138668, Singapore abstract article info Available online 24 May 2009 Keywords: Chinese hamster ovary (CHO) cells EST sequencing Transcriptome analysis Next-generation sequencing Small RNA sequencing Chinese hamster ovary (CHO) cells are widely used in recombinant protein production, yet despite their importance in bioprocessing, few genomic resources have been developed for this cell line. Over the past several years, we have made considerable progress in the development of genomic tools for CHO. Using Sanger-based sequencing technology, we have accrued a sequence repertoire of more than 68,000 expressed sequence tags (ESTs), representing more than 28,000 unique CHO transcripts. Using closely related species, we have functionally annotated this sequence set and have currently achieved significant representation in a number of functional classes, including some closely tied to recombinant protein production. This sequence repository has been used to design custom CHO Affymetrix arrays for transcriptome analysis. Illumina Solexa deep sequencing technology was also applied to study the CHO cell transcriptome and survey the identity and expression of small RNAs. These applications demonstrate the utility of genomic tools, and illustrate the applicability of emerging next-generation sequencing technologies. © 2009 Elsevier Inc. All rights reserved. Contents 1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1028 2. Building a sequence repertoire for CHO cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1029 2.1. Library construction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1029 2.2. Sequencing, assembly and annotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1030 2.3. DNA microarrays and transcriptome analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1031 3. MicroRNA analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1033 4. Concluding remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1034 Acknowledgement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1034 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1034 1. Introduction At the conclusion of the last century, the landscape of health- care underwent a major transformation through the arrival of a new generation of therapeutics based on recombinant proteins. These biologics, as they are named to differentiate them from chemically- synthesized drugs, have been widely applied to the treatment of cancers, rheumatoid arthritis and bleeding disorders, among others (Aggarwal, 2008). Except for a few cases, the majority of these bio- logics requires extensive post-translational modifications, such as glycosylation and disulfide bond formation, and is consequently produced using recombinant mammalian cells. More than 90% of these products are manufactured using Chinese hamster ovary (CHO) cells (Jayapal et al., 2007), originally derived more than 5 decades ago (Puck et al., 1958). These cells secrete little protein in their native state, yet upon receiving the product transgene and subsequently undergoing gene amplification and other manipulations, they can become high producers, secreting as much as or even more than professional secretors in our body, such as hepatocytes and antibody- producing plasma cells (Wurm, 2004). Along the route to becoming super producers, they also develop the required capacity for folding and glycosylation of the product protein. The process is likely to entail extensive reprogramming of their cellular regulation, possibly not unlike the differentiation of endoderm cells to highly secretory hepa- tocytes in developing embryos. However, in spite of the economic importance and industrial significance of generating CHO-derived recombinant cells highly productive in the desired molecules, little is known about this biological transformation event. Biotechnology Advances 27 (2009) 1028–1035 ⁎ Corresponding author. Tel.: +1 612 626 7630; fax: +1 612 626 7246. E-mail address: acre@cems.umn.edu (W.-S. Hu). 0734-9750/$ – see front matter © 2009 Elsevier Inc. All rights reserved. doi:10.1016/j.biotechadv.2009.05.023 Contents lists available at ScienceDirect Biotechnology Advances journal homepage: www.elsevier.com/locate/biotechadv