De novo sequencing of the Chinese Hamster Ovary (CHO) cell genome

The engineering paradigm of measure, model, manipulate and manufacture underpins the design of products, processes and structures with reliable, predictable performance. The design process requires a detailed knowledge of what the interacting components are, how they interact and the forces (rules) that govern those interactions. This is why it was possible to send a man to the moon in 1969 (i.e. to predict functional performance based on known physical interactions) but not to cure cancer (unpredictability deriving from complex, unknown components and interactions). Accordingly, as we enter a new age of biological engineering, the extent to which it will be possible to engineer complex biological systems for human benefit will ultimately depend upon the extent of our knowledge of those systems - the rules that govern how the complex biological system functions - or malfunctions in the case of disease. To engineer any biological system effectively we need a basic blueprint - knowledge (or design principles) that helps us to understand specifically how that organism is functionally equipped. For biological engineers this primary information is an organism's complete DNA sequence (it's genome). For simple organisms such as bacteria the genome is relatively simple - only about 6000 genes (functional genetic units) in Escherichia coli for example. In human cells there are over 30,000 genes and a large amount of 'non-coding' DNA involved in regulation of these genes. Using microbial genome sequence information, bioengineers can for the first time truly engage in the engineering design process. New ways of measuring and modelling the complexity of simple bacterial systems have emerged (this is 'systems biology') which enables us to (genetically) manipulate cells and manufacture novel products and processes using new tools (this is 'synthetic biology'). Importantly, bioengineers can now predict the functional capability of simple bacteria growing in vitro using computer models. Similar approaches are now being developed for inherently more complex mammalian cells. This project is designed to provide a much needed genomic resource for academic and industrial bioscientists and bioengineers in the UK concerned with the production of a new generation of recombinant DNA derived medicines made by made by genetically engineered cells in culture - biopharmaceuticals. Biopharmaceuticals are proving to be revolutionary treatments for many serious diseases such as rheumatoid arthritis and a range of cancers. We want to determine the genome sequence of an extremely important type of 'cell factory' that is used to make these bio-medicines; the Chinese hamster ovary (CHO) cell. Most (60-70%) biophamaceuticals are currently made by genetically engineered CHO cells in culture as well as the vast majority of those in development. However, despite the huge industrial and scientific importance of this cell type, we still do not have the CHO cell's genome sequence: The fundamental informatic resource necessary to utilise new systems and synthetic biology tools to understand and engineer the function of this cell factory. To address this problem we have formed a consortium of the UK's leading academic groups involved in research into CHO cell based manufacturing systems based at the Universities of Kent, Manchester and Sheffield, and four key industrial partners involved in biopharmaceutical manufacturing in the UK. In this project we will utilise the most advanced DNA sequencing technology available to rapidly sequence, assemble and annotate the CHO cell genome. We will establish a network to disseminate this information and to determine how we might most effectively harness this resource for future engineering strategies to improve CHO-cell based production processes. This project is necessary for, and will lead to, cutting-edge applied research underpinning new biopharmaceutical manufacturing technology.

We have formed a BRIC-based consortium of three leading academic groups and four bio-industrial companies concerned with biopharmaceutical production by mammalian cells in culture to sequence an organism of immense industrial importance, the Chinese hamster. In this project we will (i) utilise the most advanced technology available to sequence, assemble and annotate the Chinese hamster genome and (ii) create a BRIC-enabled network to discuss, disseminate and design new research that will utilise this important resource. This project will enable UK based scientists to compete globally with other groups (notably in the USA, Singapore and Europe) who are developing informatic resources for CHO cell based bioprocess development. We will outsource CHO genomic analysis to an established commercial service provider, Source Bioscience, who have considerable experience of large scale DNA sequencing contracts. For this project, Source Bioscience will provide access to the most rapid DNA sequencing platform available: the Illumina HiSeq 2000. The genome of a single Chinese hamster (approximately 3 x 109 bp) will be sequenced to a depth of 50x, sequencing with the paired-end approach at 100bp read length. Bioinformatic assembly of the CHO genome will utilise a SIMD-accelerated assembly algorithm to assemble contiguous sequences, followed by in silico annotation based on BLAST searches. Assembled data will be returned in the GenBank format. We intend to employ a postdoctoral bioinformatician for six months to (i) liaise with the contract service provider (ii) prepare CHO genomic information for dissemination within BRIC and (iii) organise networking events involving BRIC partners. This project is essential to maintain the long-term competitiveness of UK research in CHO cell based bioprocess development.

The major impacts of this research nationally and internationally, both at the academic and industrial levels, will be on the following: (1) those in the BRIC bioprocessing/scientific community with an interest in the use of Chinese hamster ovary cell expression systems and products derived using this expression system (acroos the whole process), (2) researchers generally in the field of bioprocessing (3) those using Chinese hamster cell lines as model systems (4) bioinformaticians and genome analysis researchers The research will also impact on the wider research agenda that will ultimately benefit, academics, industrialists, the patient and ultimately the UK economy via the development of new methodology to provide recombinant protein based 'bio-drugs'. To ensure that the research findings that may impact on manufacturing, human health and public knowledge are distributed effectively we will work closely with our industrial colleagues in the BRIC network. Generation of this data set will also place members of BRIC and the UK bioprocessing sector in a much stronger position to maintain its current powerful position in relation to the biopharmaceuticals industry.