Hitto Kaufmann

Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing

The arrival of next-generation sequencing (NGS) technologies has led to novel opportunities for expression profiling and genome analysis by utilizing vast amounts of short read sequence data. Here, we demonstrate that expression profiling in organisms lacking any genome or transcriptome sequence information is feasible by combining Illumina’s mRNA-seq technology with a novel bioinformatics pipeline that integrates assembled and annotated Chinese hamster ovary (CHO) sequences with information derived from related organisms. We applied this pipeline to the analysis of CHO cells which were chosen as a model system owing to its relevance in the production of therapeutic proteins. Specifically, we analysed CHO cells undergoing butyrate treatment which is known to affect cell cycle regulation and to increase the specific productivity of recombinant proteins. By this means, we identified sequences for >13 000 CHO genes which added sequence information of ∼5000 novel genes to the CHO model. More than 6000 transcript sequences are predicted to be complete, as they covered >95% of the corresponding mouse orthologs. Detailed analysis of selected biological functions such as DNA replication and cell cycle control, demonstrated the potential of NGS expression profiling in organisms without extended genome sequence to improve both data quantity and quality.

An XBP-1 dependent bottle-neck in production of IgG subtype antibodies in chemically defined serum-free Chinese hamster ovary (CHO) fed-batch processes

The optimization of production processes for therapeutic antibodies is a continuing challenge in pharmaceutical biotechnology. Although it could be demonstrated that vector design and host cell engineering can improve transcriptional and translational efficiency and thereby result in generation of high producer cell lines, it is not clear whether introduction of transgenes that regulate protein transport or affect post-translational modifications could further improve such industrial processes. Here, we show that heterologous expression of the transcription factor X-box binding protein-1 (XBP-1) can lead to an increase in endoplasmic reticulum (ER) content and specific therapeutic antibody productivity of Chinese hamster ovary (CHO)-DG44 cells in inoculum suspension cultures. This effect translates into 40% increased overall antibody titers in a fed-batch format where cells are grown in chemically defined serum-free media. Protein-A purified antibody products from mock-transfected cells and XBP-1 transfected cells were found to be of comparable quality with regard to glycosylation pattern and physicochemical characteristics. The data demonstrate the potential of XBP-1 engineering to improve mammalian cell culture production processes to yield high amounts of a therapeutic protein product of desired quality.

Heterologous expression of the lipid transfer protein CERT increases therapeutic protein productivity of mammalian cells.

Recent studies have demonstrated that the introduction of transgenes regulating protein transport or affecting post-translational modifications can further improve industrial processes for the production of therapeutic proteins in mammalian cells. Our study on improving therapeutic protein production in CHO cells by heterologous expression of the ceramide transfer protein (CERT) was initiated by the recent discovery that CERT is involved in protein kinase D (PKD)-dependent protein transport from the Golgi to the plasma membrane. We generated a set of CHO DG44 cell lines by stable integration of constructs expressing either CERT wild-type or CERT S132A, a mutant conferring increased lipid transfer activity, or a mock plasmid. CHO cells expressing heterologous CERT demonstrated significantly higher specific productivities of the therapeutic protein HSA when grown in inoculum suspension cultures. This effect translated into significantly increased overall HSA titers in a fed-batch format where cells are grown in chemically defined serum-free media. Furthermore, we could show that CERT also enhanced monoclonal antibody secretion in two IgG production cell lines with different basal productivities. The data demonstrate the potential of CERT engineering to improve mammalian cell culture production processes to yield high amounts of a therapeutic protein product of desired quality. To our knowledge, this is the first study showing a bottle neck in recombinant protein secretion at the Golgi complex in mammalian cells.

CHO gene expression profiling in biopharmaceutical process analysis and design

Increase in both productivity and product yields in biopharmaceutical process development with recombinant protein producing mammalian cells can be mainly attributed to the advancements in cell line development, media, and process optimization. Only recently, genome-scale technologies enable a system-level analysis to elucidate the complex biomolecular basis of protein production in mammalian cells promising an increased process understanding and the deduction of knowledge-based approaches for further process optimization. Here, the use of gene expression profiling for the analysis of a low titer (LT) and high titer (HT) fed batch process using the same IgG producing CHO cell line was investigated. We found that gene expression (i) significantly differed in HT versus LT process conditions due to differences in applied chemically defined, serum-free media, (ii) changed over the time course of the fed batch processes, and that (iii) both metabolic pathways and 14 biological functions such as cellular growth or cell death were affected. Furthermore, detailed analysis of metabolism in a standard process format revealed the potential use of transcriptomics for rational media design as is shown for the case of lipid metabolism where the product titer could be increased by about 20% based on a lipid modified basal medium. The results demonstrate that gene expression profiling can be an important tool for mammalian biopharmaceutical process analysis and optimization.

Stable microRNA expression enhances therapeutic antibody productivity of Chinese hamster ovary cells

MicroRNAs (miRNAs) are short non-coding RNAs that post-transcriptionally regulate the expression of different target genes and, thus, enable engineered gene networks to achieve complex phenotypic changes in mammalian cells. We hypothesized that exploiting this feature of miRNAs could improve therapeutic protein production processes by increasing viable cell densities and/or productivity of the mammalian cells used for manufacturing. To identify miRNAs that increase the productivity of producer cells, we performed a genome wide functional miRNA screen by transient transfection of Chinese hamster ovary (CHO) cells stably expressing an IgG1 antibody (CHO-IgG1). Using this approach, we identified nine human miRNAs that improved the productivities not only of the CHO-IgG1 cells but also of CHO cells expressing recombinant human serum albumin (HSA), demonstrating that the miRNAs act in a product-independent manner. We selected two miRNAs (miR-557 and miR-1287) positively impacting the viable cell density and the specific productivity, respectively, and then stably co-expressed them in IgG1 expressing CHO cells. In these cells, higher IgG1 titers were observed in fed-batch cultures whilst product quality was conserved, demonstrating that miRNA-based cell line engineering provides an attractive approach toward the genetic optimization of CHO producer cells for industrial applications.

Evaluation of a combinatorial cell engineering approach to overcome apoptotic effects in XBP-1(s) expressing cells

Genetic engineering of producer cell lines for production of therapeutic antibodies in order to increase the yield of production processes remains a continuing challenge. Recently it was shown that heterologous expression of the active, spliced form of human X-box binding protein 1 (XBP-1(s)) can increase the amount of secreted protein products in mammalian cell culture processes. However, a prerequisite for the industrial application of any cell engineering approach is the ability to generate monoclonal cell lines that stably express the engineering gene to maintain the desired phenotype. Here, we show a decrease in heterologous human XBP-1(s) expression in CHO production cells producing a therapeutic antibody product monitored over a prolonged period in serial culture. Colony formation assays (CFA) in CHO-K1 cells reveal a general survival disadvantage conferred by XBP-1(s) in this cell type. We aimed to rescue this phenotype by expressing the caspase-inhibitor XIAP (x-linked inhibitor of apoptosis). Using a set of bicistronic expression vectors we engineered an antibody producing CHO cell line with XBP-1(s) and XIAP alone and in combination. Interestingly, co-expression of both genes resulted in the highest specific productivities (Qp) and final titers in a serum-free fed-batch process in chemically defined media. Thus, the combination of secretion and anti-apoptotic engineering provides an interesting approach for future applications in industrial mammalian cell culture.

Supplementation of serum free media with HT is not sufficient to restore growth properties of DHFR-/- cells in fed-batch processes - Implications for designing novel CHO-based expression platforms.

DHFR-deficient CHO cells are the most commonly used host cells in the biopharmaceutical industry and over the years, individual substrains have evolved, some have been engineered with improved properties and platform technologies have been designed around them. Unexpectedly, we have observed that different DHFR-deficient CHO cells show only poor growth in fed-batch cultures even in HT supplemented medium, whereas antibody producer cells derived from these hosts achieved least 2-3 fold higher peak cell densities. Using a set of different expression vectors, we were able to show that this impaired growth performance was not due to the selection procedure possibly favouring fast growing clones, but a direct consequence of DHFR deficiency. Re-introduction of the DHFR gene reproducibly restored the growth phenotype to the level of wild-type CHO cells or even beyond which seemed to be dose-dependent. The requirement for a functional DHFR gene to achieve optimal growth under production conditions has direct implications for cell line generation since it suggests that changing to a selection system other than DHFR would require another CHO host which - especially for transgenic CHO strains and tailor-suited process platforms - this could mean significant investments and potential changes in product quality. In these cases, DHFR engineering of the current CHO-DG44 or DuxB11-based host could be an attractive alternative.

BI-HEX ® -GlymaxX ® cells enable efficient production of next generation biomolecules with enhanced ADCC activity

Background Despite the succes story of therapeutic monoclonal antibodies (mAbs), a medical need remains to improve their efficacy. One possibility to achieve this is to modulate important effector functions such as the antibody dependent cellular cytotoxicity (ADCC). The advantage of highly active biotherapeutic molecules is apart from the enhanced efficacy the reduction of side effects due to lower administered doses. Furthermore, these therapeutic antibodies may enable treatment of current nonresponders, e.g. patients with low antigen bearing tumors. Enhancement of the effector functions of antibodies can be achieved either by directly mutating the antibody’s amino acid sequence or by modifying its glycosylation pattern, e.g. by using a novel host cell line able to attach a desired glycostructure to the product. The latter approach has the advantage of not impacting the antibody structure itself, thereby avoiding negative effects on the PK/PD of the molecule. During the last decade it has been shown that antibodies with a reduced level of glycan fucosylation are much more potent in mediating ADCC, a mode of action particularly relevant for cancer therapeutics. Therefore, defucosylated antibodies are of major interest for biotherapeutics developers. To produce such antibodies, Boehringer Ingelheim has inlicensed the GlymaxX system from ProBioGen, Germany. This technology utilises the bacterial protein RMD (GDP-6-deoxy-D-lyxo-4-hexulose reductase) which, when stably integrated into host cell lines, inhibits fucose de-novo biosynthesis. The enzyme deflects the fucosylation pathway by turning an intermediate (GDP-4-Keto-6-Deoxymannose) into GDP-Rhamnose, a sugar that cannot be metabolised by CHO cells. As a consequence, recombinant antibodies generated by such host cells exhibit reduced glycan fucosylation and 20100 fold higher ADCC activity. Here, we show the establishment of a new host cell line, termed BI-HEXGlymaxX which is capable of producing highly active therapeutic antibodies. We furthermore present data on the cell line properties concerning cell culture performance (e.g. titer, growth, transfection efficiency), process robustness and product quality reproducibility.

Einwegsysteme in zellkulturbasierten Herstellprozessen für Biopharmazeutika

Production of biopharmaceuticals from mammalian cells is classically performed using stainless-steel tanks and pipes for cell culture, purification and fill and finish. Recently, disposable systems have been used successfully along the entire process flow up to the 2.000 l scale. It will be crucial to characterize these systems further in particular to ensure a profound process understanding and reliable transfer between stainless-steel and fully disposable facilities.

BI HEX™ – Platform for Fast Track Generation of High Producer Cell Lines Leading to High-Titer Processes for Production of Therapeutic Proteins from Mammalian Cells

The majority of biopharmaceuticals is currently being expressed in mammalian cells, mostly Chinese hamster ovary (CHO) and mouse myeloma (NS0) cells. The two most prominent challenges for mammalian cell-based systems relate to (i) product titer in the cell culture fluid at the end of cultivation and (ii) development times from final drug candidate selection to an established process to produce clinical grade material. The newest generations of mammalian cell culture production processes evolve rapidly to overcome these limitations. Boehringer Ingelheim’s current high expression (BI HEX™) cell line generation concept combines many improvements including novel or modified genetic elements to improve transcription rate, high throughput screening concepts to obtain highly productive clones reliably, and host cell lines that grow to high densities in serum-free chemically defined media. Specific productivities above 50 pg per cell and day for monoclonal antibodies have been achieved in CHO cells and were successfully translated into product titers of up to 4 g/L in an 11-day process. Furthermore, a strategy is presented for supply of material for toxicological studies produced from CHO cells in as little as 15 months starting with cloning of product-encoding genetic sequences into BI HEX vectors. At the same time it ensures that the production cell generated during this program will have the high expression potential needed to avoid a change in production cell line at later stages in development.