Optimization of heavy chain and light chain signal peptides for high level expression of therapeutic antibodies in CHO cells.

Translocation of a nascent protein from the cytosol into the ER mediated by its signal peptide is a critical step in protein secretion. The aim of this work was to develop a platform technology to optimize the signal peptides for high level production of therapeutic antibodies in CHO cells. A database of signal peptides from a large number of human immunoglobulin (Ig) heavy chain (HC) and kappa light chain (LC) was generated. Most of the HC signal peptides contain 19 amino acids which can be divided into three domains and the LC signal peptides contain 22 amino acids. The signal peptides were then clustered according to sequence similarity. Based on the clustering, 8 HC and 2 LC signal peptides were analyzed for their impacts on the production of 5-top selling antibody therapeutics, namely, Herceptin, Avastin, Remicade, Rituxan, and Humira. The best HC and LC signal peptides for producing these 5 antibodies were identified. The optimized signal peptides for Rituxan is 2-fold better compared to its native signal peptides which are available in the public database. Substitution of a single amino acid in the optimized HC signal peptide for Avastin reduced its production significantly. Mass spectrometry analyses revealed that all optimized signal peptides are accurately removed in the mature antibodies. The results presented in this report are particularly important for the production of these 5 antibodies as biosimilar drugs. They also have the potential to be the best signal peptides for the production of new antibodies in CHO cells.

Rapid quantification of Escherichia coli in food and media using bacteriophage T7 amplification and liquid chromatography-multiple reaction monitoring tandem mass spectrometry.

Conventional microbiological assays have been a valuable tool for specific enumeration of indicative bacteria of relevance to food and public health, but these culture-based methods are time-consuming and require tedious biochemical and morphological identification. In this work, we exploit the ability of bacteriophage T7 to specifically infect Escherichia coli and amplify nearly a 100-fold in 1­2 h. Bacteriophage amplification is integrated with liquid chromatography-multiple reaction monitoring tandem mass spectrometry (LC-MRM­MS/MS) for quantitation of phage-specific peptides. Heavy isotopic 15N labeled T7 is introduced as the inoculum phage and internal standard. Quantification is performed by determining the ratio of phage-specific peptides over the internal standard which value is proportional to E. coli numbers. A broad dynamic range of 6-log orders ranging from 3.0 × 10(3) to 3.0 × 10(9) CFU/ml is attained in LB, while between 4.1 × 10(4)­2.7 × 10(9) CFU/ml and 1.9 × 10(3)­3.0 × 10(7) CFU/ml was enumerated respectively in coconut water and apple juice. With this method, viable E. coli are quantified in 4 h with a detection limit of 3.0 × 10(3) CFU/ml, 4.1 × 10(4) CFU/ml and 1.9 × 10(3) CFU/ml in LB, coconut water and apple juice, respectively. This method has potential as a rapid tool for detection of fecal contamination during food bioprocessing and distribution to safeguard public health.

Identification of autocrine growth factors secreted by CHO cells for applications in single-cell cloning media.

Chinese hamster ovary (CHO) cell lines are widely used for the expression of therapeutic recombinant proteins, including monoclonal antibodies and other biologics. For manufacturing, cells derived from a single-cell clone are typically used to ensure product consistency. Presently, fetal bovine serum (FBS) is commonly used to support low cell density cultures to obtain clonal cell populations because cells grow slowly, or even do not survive at low cell densities in protein-free media. However, regulatory authorities have discouraged the use of FBS to reduce the risk of contamination by adventitious agents from animal-derived components. In this study, we demonstrated how a complementary mass spectrometry-based shotgun proteomics strategy enabled the identification of autocrine growth factors in CHO cell-conditioned media, which has led to the development of a fully defined single-cell cloning media that is serum and animal component-free. Out of 290 secreted proteins that were identified, eight secreted growth factors were reported for the first time from CHO cell cultures. By supplementing a combination of these growth factors to protein-free basal media, single cell growth of CHO cells was improved with cloning efficiencies of up to 30%, a 2-fold improvement compared to unsupplemented basal media. Complementary effects of these autocrine growth factors with other paracrine growth factors were also demonstrated when the mixture improved cloning efficiency to 42%, similar to that for the conditioned medium.

Comparison of internal ribosome entry site (IRES) and Furin-2A (F2A) for monoclonal antibody expression level and quality in CHO cells.

Four versions of tricistronic vectors expressing IgG1 light chain (LC), IgG1 heavy chain (HC), and dihydrofolate reductase (DHFR) in one transcript were designed to compare internal ribosome entry site (IRES) and furin-2A (F2A) for their influence on monoclonal antibody (mAb) expression level and quality in CHO DG44 cells. LC and HC genes are arranged as either the first or the second cistron. When using mAb quantification methods based on the detection antibodies against HC Fc region, F2A-mediated tricistronic vectors appeared to express mAb at higher levels than the IRES-mediated tricistronic vectors in both transient and stable transfections. Further analysis revealed that more than 40% of products detected in stably transfected pools generated using the two F2A-mediated tricistronic vectors were aggregates. LC and HC from the F2A stably transfected pools were not properly processed, giving rise to LC+F2A+HC or HC+F2A+LC fusion proteins, LC and HC polypeptides with F2A remnants, and incorrectly cleaved signal peptides. Both IRES-mediated tricistronic vectors express mAb with correct sizes and signal peptide cleavage. Arrangement of LC as the first cistron in the IRES-mediated tricistronic vectors exhibits increased mAb expression level, better growth, and minimized product aggregation, while arrangement of HC as first cistron results in low expression, slower growth, and high aggregation. The results obtained will be beneficial for designing vectors that enhance mAb expression level and quality in mammalian cells.

Production of functional soluble Dectin-1 glycoprotein using an IRES-linked destabilized-dihydrofolate reductase expression vector.

Dectin-1 (CLEC7A) is a C-type lectin receptor that binds to ß-glucans found in fungal cell walls to act as a major pattern recognition receptor (PRR). Since ß-glucans epitope is not present in human cells, we are of the opinion that Dectin-1 can have therapeutic functions against fungal infections. We thus set out to produce a soluble extracellular domain of murine Dectin-1 (called sDectin-1) in sufficient titers to facilitate such studies in mouse models. Since sDectin-1 has previously been shown to be glycosylated, we chose to produce this protein using Chinese Hamster Ovary (CHO) cells, a mammalian host cell line suitable for the high-titer production of recombinant glycoproteins. To ensure a high titer production of sDectin-1 and minimize the effects of gene fragmentation, we constructed a mammalian expression vector with a PEST-destabilized dhfr amplifiable marker downstream of an attenuated IRES element, which was in turn downstream of the sDectin-1 gene and a CMV IE promoter. Stably transfected and MTX-amplified cell pools were generated using this vector, and maximum sDectin-1 titers of 246 mg/l and 598 mg/l were obtained in shake flask batch culture and bioreactor fed-batch culture respectively. The purified recombinant sDectin-1 was shown to be glycosylated. Protein functionality was also demonstrated by its ability to bind to zymosan particles and to the cell wall of Saccharomyces cerevisiae. We describe for the first time the use of an attenuated IRES-linked PEST-destabilized dhfr amplifiable marker for the production of recombinant proteins with stably amplified cell pools. With our process, we reached the highest reported titer for producing recombinant proteins smaller than 50 kDa in cell pools. sDectin-1 protein produced is glycosylated and functional. This vector design can thus be used efficiently for the high-titer production of functional recombinant proteins.

Metabolomics profiling of extracellular metabolites in recombinant Chinese Hamster Ovary fed-batch culture.

A metabolomics-based approach was used to time profile extracellular metabolites in duplicate fed-batch bioreactor cultures of recombinant Chinese Hamster Ovary (CHO) cells producing monoclonal IgG antibody. Culture medium was collected and analysed using a high-performance liquid chromatography (HPLC) system in tandem with an LTQ-Orbitrap mass spectrometer. An in-house software was developed to pre-process the LC/MS data in terms of filtering and peak detection. This was followed by principal component analysis (PCA) to assess variance amongst the samples, and hierarchical clustering to categorize mass peaks by their time profiles. Finally, LC/MS2 experiments using the LTQ-Orbitrap (where standard was available) and SYNAPT HDMS (where standard was unavailable) were performed to confirm the identities of the metabolites. Two groups of identified metabolites were of particular interest; the first consisted of metabolites that began to accumulate when the culture entered stationary phase. The majority of them were amino acid derivatives and they were likely to be derived from the amino acids in the feed media. Examples included acetylphenylalanine and dimethylarginine which are known to be detrimental to cell growth. The second group of metabolites showed a downward trend as the culture progressed. Two of them were medium components--tryptophan and choline, and these became depleted midway into the culture despite the addition of feed media. The findings demonstrated the potential of utilizing metabolomics to guide medium design for fed-batch culture to potentially improve cell growth and product titer.

Pharmaceutical metabolite profiling using quadrupole/ion mobility spectrometry/time-of-flight mass spectrometry.

The use of hybrid quadrupole ion mobility spectrometry time-of-flight mass spectrometry (Q/IMS/TOFMS) in the metabolite profiling of leflunomide (LEF) and acetaminophen (APAP) is presented. The IMS drift times (T(d)) of the drugs and their metabolites were determined in the IMS/TOFMS experiments and correlated with their exact monoisotopic masses and other in silico generated structural properties, such as connolly molecular area (CMA), connolly solvent-excluded volume (CSEV), principal moments of inertia along the X, Y and Z Cartesian coordinates (MI-X, MI-Y and MI-Z), inverse mobility and collision cross-section (CCS). The correlation of T(d) with these parameters is presented and discussed. IMS/TOF tandem mass spectrometry experiments (MS(2) and MS(3)) were successfully performed on the N-acetyl-p-benzoquinoneimine glutathione (NAPQI-GSH) adduct derived from the in vitro microsomal metabolism of APAP. As comparison, similar experiments were also performed using hybrid triple quadrupole linear ion trap mass spectrometry (QTRAPMS) and quadrupole time-of-flight mass spectrometry (QTOFMS). The abilities to resolve the product ions of the metabolite within the drift tube and fragment the ion mobility resolved product ions in the transfer travelling wave-enabled stacked ring ion guide (TWIG) demonstrated the potential applicability of the Q/IMS/TOFMS technique in pharmaceutical metabolite profiling.

Identification of stereoisomeric metabolites of meisoindigo in rat liver microsomes by achiral and chiral liquid chromatography/tandem mass spectrometry.

N-methylisoindigotin, abbreviated as meisoindigo, has been a routine therapeutic agent in the clinical treatment of chronic myelogenous leukemia in China since the 1980s. However, information relevant to in vitro metabolism of meisoindigo is limited. In this study, in vitro stereoisomeric metabolites of meisoindigo in rat liver microsomes were identified for the first time by achiral and chiral liquid chromatography/tandem mass spectrometry, together with proton NMR spectroscopy and synchrotron infrared spectroscopy. The major in vitro phase I metabolites of meisoindigo were tentatively identified as stereoselective-reduced meisoindigo, which comprised a pair of (3-R, 3'-R) and (3-S, 3'-S) enantiomers with lower abundance, as well as another pair of (3-R, 3'-S) and (3-S, 3'-R) enantiomers with higher abundance. One type of minor in vitro metabolites was tentatively identified as stereoselective N-demethyl-reduced meisoindigo including a pair of (3-R, 3'-R) and (3-S, 3'-S) enantiomers, as well as one meso compound. Another type of minor in vitro metabolites was tentatively identified as both stereoselective and regioselective monohydroxyl-reduced meisoindigo. Based on the metabolite profiling, three parallel metabolic pathways of meisoindigo in rat liver microsomes were proposed.

Identification of proteins from feeder conditioned medium that support human embryonic stem cells.

The maintenance of undifferentiated human embryonic stem cells (hESC) requires feeder cells, either in co-culture or feeder-free with conditioned medium (CM) from the feeders. In this study, we compared the CM of a supporting primary mouse embryonic feeder (MEF) and an isogenic but non-supporting MEF line (DeltaE-MEF) in order to gain an insight to the differential expression profile of secreted factors. Using two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization-time of flight (MALDI) tandem mass spectrometry, 13 protein identities were found to be downregulated in DeltaE-MEF compared to MEF, of which 4 were found to be soluble factors and 3 proteins were membrane-associated or related to the extracellular matrix. In addition, four other proteins were identified to be differentially expressed in MEF-CM using high pressure liquid chromatography (HPLC) and cytokine arrays. In functional experiments where CM was replaced with six of the factors identified, hESC were able to proliferate for five continuous passages whilst maintaining 68-82% and 74-98% expression of pluripotent markers, Oct-4 and Tra-1-60, respectively. Using proteomic tools, important proteins from CM that supports hESC culture have been identified, which when replaced with recombinant proteins, continue to support undifferentiated hESC growth in a feeder-free culture platform.

GlycoVis: visualizing glycan distribution in the protein N-glycosylation pathway in mammalian cells.

Glycosylation has profound effects on the quality of recombinant proteins produced in mammalian cells. The biosynthetic pathways of N-linked glycans on glycoproteins involves a relatively small number of enzymes and nucleotide sugars. Many of these glycoconjugate enzymes can utilize multiple N-glycans as substrates, thus generating a large number of glycan intermediates, and making the biosynthetic pathway resemble a network with diverging and converging paths. The N-glycans on secreted glycoprotein molecules include not only terminal glycans, but also pathway intermediates. To better assess the glycan distribution and the potential route of their synthesis, we created GlycoVis, a visualization program that displays the distribution and the potential reaction paths leading to each N-glycan on the reaction network. The substrate specificities of the enzymes involved were organized into a relationship matrix. With the input of glycan distribution data, the program outputs a reaction pathway map which labels the relative abundance levels of different glycans with different colors. The program also traces all possible reaction paths leading to each glycan and identifies each pathway on the map. Glycoform distribution of Chinese Hamster Ovary cell-derived tissue plasminogen activator (TPA), and human and mouse IgG were used as illustrations for the application of GlycoVis. In addition, the intracellular and secreted IgG from an NS0 producer cell line were isolated, and their glycoform profiles were displayed using GlycoVis for comparison. This visualization tool facilitates the analysis of potential reaction paths utilized under different physiological or culture conditions, and may provide insight on the potential targets for metabolic engineering.

Crystallization of IgG1 by mapping its liquid-liquid phase separation curves.

Monoclonal antibody therapeutics is an important and fast expanding market. While production of these molecules has been a major area of research, much less is known regarding the stabilization of these proteins for delivery as drugs. Crystallization of antibodies is one such promising route for protein stabilization at high titers, and here we took a systematic approach to initiate crystallization through nucleation in a simple PEG (polyethylene glycol), protein in water solution. A ternary mixture of globular proteins, PEG, and water will undergo a liquid-liquid phase separation (LLPS) as shown in a phase diagram or a Binodal curve. Of particular interest within the phase diagram is the position of the critical point, which is where nucleation occurs most rapidly. Detailed LLPS maps were created by increasing concentrations of PEG (from 5% to 11%) and IgG (from 1 to 20 mg/mL). By increasing the molecular weight (MW) of PEG (and hence its radius of gyration) from 1,000 to 6,000 g/mol, the temperatures of the critical point of nucleation were shown to increase. Once these curves were determined, nucleation experiments were conducted close to a chosen critical point (10.5 mg/mL IgG in 11% PEG 1000) and after 3 weeks, crystals of IgG of approximately 100 microm in size were successfully formed. This is the first example of crystallization of an antibody through systematic mapping of LLPS curves, which is a fundamental step towards the scale-up of antibody crystallization.

Determination of interferon-gamma in Chinese hamster ovary cell culture supernatant by coupled-column liquid chromatography.

A robust tandem HPLC method coupling size-exclusion (Shodex Asahipak GS-320HQ) and reversed phase (Vydac 218TP54) columns with ultraviolet detection was developed for quantitative determination of interferon-gamma (IFN-gamma) in Chinese hamster ovary cell culture supernatant. The 2D-HPLC system was linked up by a 6-port 2-position low hold-up volume switch valve. Compared to a commercial ELISA kit for IFN-gamma, the coupled column LC approach was able to detect and quantify soluble IFN-gamma, regardless of the glycoprotein's molecular/conformational variability and sample background. Each LC-LC analysis took 90 minutes inclusive of column regeneration. The relative standard deviation of measurements (n = 5) was less than 3%. The limit of detection (LOD) was determined to be 0.35 microg IFN-gamma.