Metabolomics analysis of soy hydrolysates for the identification of productivity markers of mammalian cells for manufacturing therapeutic proteins

Soy hydrolysates are widely used as a nutrient supplement in mammalian cell culture for the production of recombinant proteins. The batch‐to‐batch variability of a soy hydrolysate often leads to productivity differences. This report describes our metabolomics platform, which includes a battery of LC‐MS/MS modes of operation, and advanced data analysis software for automated data processing. The platform was successfully used for screening productivity markers in soy hydrolysates during the production of two therapeutic antibodies in two Chinese hamster ovary cell lines. A total of 123 soy hydrolysate batches were analyzed, from which 62 batches were used in the production runs of cell line #1 and 12 batches were used in the production runs of cell line #2. For cell line #1, out of 19 amino acids, 106 other metabolites and 4,131 peptides identified in the soy hydrolysate batches being used, several nucleosides and short hydrophobic peptides showed negative correlation with antibody titer, while ornithine, citrulline and several amino acids and organic acids correlated positively with titer. For cell line #2, only ornithine and citrulline showed strong positive correlation. When ornithine was spiked into the culture media, both cell lines demonstrated accelerated cell growth, indicating ornithine as a root cause of the performance difference. It is proposed that better soy hydrolysate performance resulted from better bacterial fermentation during the hydrolysate production. A few selected markers were used to predict the performance of other soy hydrolysate batches for cell line #1. The predicted titers agreed with the experimental values with good accuracy. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:522–531, 2015     

Combined approach of NMR and chemometrics for screening peptones used in the cell culture medium for the production of a recombinant therapeutic protein

Soy peptones or soy hydrolysates are widely used as key medium additives in serum-free cell culture processes for industrial production of therapeutic recombinant proteins. The heterogeneous nature of these vegetable-derived materials can lead to substantial lot- to-lot variability in cell culture processes. In this study, we demonstrated the feasibility of nuclear magnetic resonance (NMR) spectroscopy in combination with chemometrics in rapid screening peptone lots in order to optimize efficiency and consistency of large-scale protein production. This report is the first that shows a correlation between the intrinsic NMR spectral characteristics of complex heterogeneous materials and product titer using chemometrics.     

Characterization of lipoprotein supplement and influence of its oxidized lipid content on cell culture performance and monoclonal antibody production by a SP2/0 hybridoma cell line

A challenging aspect with the use of the Sp2/0 hybridoma cell line in commercial manufacturing processes of recombinant therapeutic proteins is their exogenous lipids requirement for cell proliferation and optimal protein secretion. Lipids are commonly provided to the culture using serum or serum-derivatives, such as lipoprotein supplement. The batch-to-batch variability of these non-chemically defined raw-materials is known to impact cell culture process performance. Lipoprotein supplement variability and its impact on fed-batch production of a recombinant monoclonal antibody (mAb) expressed in Sp2/0 cells were studied using 36 batches from the same vendor. Several batches were associated with early viability drops leading to low process performance during fed-batch production. Increased caspase-3 activity (an indicator of apoptosis) was correlated to viability drops when low-performing batches were used. Addition of an antioxidant to the culture limited the increase in caspase-3 activity. Physicochemical characterization of batches confirmed that lipoproteins are mainly composed of lipids and proteins; no clear correlation between low-performing batches and lipoprotein supplement composition was observed. Controlled lipoprotein oxidation leads to lipoprotein solution browning, increasing absorbance at 276 nm and results in poor process performance. Because low-performing batches absorb more at 276 nm than other batches, oxidized lipids were suspected to be the root cause of low-performing batches. This study increased the understanding of lipoprotein supplement composition, its sensitivity to oxidation and its impact on process performance.     

Screening soy hydrolysates for the production of a recombinant therapeutic protein in commercial cell line by combined approach of near-infrared spectroscopy and chemometrics

Soy hydrolysates are widely used as the major nutrient sources for cell culture processes for industrial manufacturing of therapeutic recombinant proteins. The primary goal of this study was to develop a spectroscopy based chemometric method, a partial least squares (PLS), to screen soy hydrolysates for better yield of protein production (titers) in cell culture medium. Harvest titer values of 29 soy hydrolysate lots with production yield between 490 and 1,350 mg/L were obtained from shake flask models or from manufacture engineering runs. The soy hydrolysate samples were measured by near-infrared (NIR) in reflectance mode using an infrared fiber optic probe. The fiber optic probe could easily enable in situ measurement of the soy hydrolysates for convenient raw material screening. The best PLS calibration has a determination coefficient of R ²?=?0.887 utilizing no spectral preprocessing, the two spectral ranges of 10,000–5,376 cm^?1 and 4,980–4,484 cm^?1, and a rank of 6 factors. The cross-validation of the model resulted in a determination coefficient of R ²?=?0.741 between the predicted and actual titer values with an average standard deviation of 72 mg/L. Compared with the resource demanding shake flask model, the combination of NIR and chemometric modeling provides a convenient method for soy hydrolysate screening with the advantage of fast speed, low cost and non-destructive.     

Development toward rapid and efficient screening for high performance hydrolysate lots in a recombinant monoclonal antibody manufacturing process

Plant‐derived hydrolysates are widely used in mammalian cell culture media to increase yields of recombinant proteins and monoclonal antibodies (mAbs). However, these chemically varied and undefined raw materials can have negative impact on yield and/or product quality in large‐scale cell culture processes. Traditional methods that rely on fractionation of hydrolysates yielded little success in improving hydrolysate quality. We took a holistic approach to develop an efficient and reliable method to screen intact soy hydrolysate lots for commercial recombinant mAb manufacturing. Combined high‐resolution ¹H nuclear magnetic resonance (NMR) spectroscopy and partial least squares (PLS) analysis led to a prediction model between product titer and NMR fingerprinting of soy hydrolysate with cross‐validated correlation coefficient R² of 0.87 and root‐mean‐squared‐error of cross‐validation RMSECV% of 11.2%. This approach screens for high performance hydrolysate lots, therefore ensuring process consistency and product quality in the mAb manufacturing process. Furthermore, PLS analysis was successful in discerning multiple markers (DL‐lactate, soy saccharides, citrate and succinate) among hydrolysate components that positively and negatively correlate with titer. Interestingly, these markers correlate to the metabolic characteristics of some strains of taxonomically diverse lactic acid bacteria (LAB). Thus our findings indicate that LAB strains may exist during hydrolysate manufacturing steps and their biochemical activities may attribute to the titer enhancement effect of soy hydrolysates. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 28: 1061–1068, 2012     

Chemometric analysis of soy protein hydrolysates used in animal cell culture for IgG production – An untargeted metabolomics approach

Soy protein hydrolysates are used as the most cost effective medium supplement to enhance cell growth and recombinant protein productivity in cell cultures. Such hydrolysates contain diverse classes of compounds, such as peptides, carbohydrates and phenolic compounds. To identify if specific compounds dominate the functionality of hydrolysates in cell cultures, thirty samples of hydrolysates with different cell culture performances were analyzed for chemical composition using an untargeted metabolomics approach. Out of 410 detected compounds, 157 were annotated. Most of the remaining 253 compounds were identified as peptides, but could not be annotated exactly. All compounds were quantified relatively, based on their average signal intensities. The cell growth and total immunoglobulin (IgG) production, relative to the CD medium (100%), ranged from 148 to 438% and 117 to 283%, respectively. Using bootstrapped stepwise regression (BSR), the compounds with the highest inclusion frequency were identified. The most important compound, i.e. phenyllactate and ferulate explained 29% and 30% of the variance for cell growth and total IgG production, respectively. Surprisingly, all compounds identified in the BSR showed a positive correlation with cell growth and total IgG production. This knowledge can be applied to monitor the production and accumulation of these compounds during the production process of hydrolysates. Consequently, the processing conditions can be modulated to produce soy protein hydrolysates with enhanced and consistent cell culture performance.     

Usability of size-excluded fractions of soy protein hydrolysates for growth and viability of Chinese hamster ovary cells in protein-free suspension culture

To investigate the effect of size-excluded fraction of non-animal protein hydrolysate on growth, viability and longevity of Chinese hamster ovary (CHO) cells, several commercially available protein hydrolysates were evaluated as a feed supplement to chemically-defined protein-free suspension culture. Soy protein hydrolysates showed better supporting capability for cell growth and viability than the other types of hydrolysates. Maximal cell growth was not affected greatly by size exclusion of some soy hydrolysates such as bacto soytone and soy hydrolysates. CHO cells supplemented with size-excluded fractions of the two hydrolysates showed viable cell density and viability almost equal to those with their crude hydrolysates, although soy hydrolysates showed a little better performance. This suggested that the size-excluded hydrolysate fractions of some soy hydrolysate might be a potential culture medium additive to achieve better downstream operation in a large-scale production as well as enhanced productivity.     

Estimation of raw material performance in mammalian cell culture using near infrared spectra combined with chemometrics approaches

Understanding variability in raw materials and their impacts on product quality is of critical importance in the biopharmaceutical manufacturing processes. For this purpose, several spectroscopic techniques have been studied for raw material characterization, providing fast and nondestructive ways to measure quality of raw materials. However, investigations of correlation between spectra of raw materials and cell culture performance have been scarce due to their complexity and uncertainty. In this study, near-infrared spectra and bioassays of multiple soy hydrolysate lots manufactured by different vendors were analyzed using chemometrics approaches in order to address variability of raw materials as well as correlation between raw material properties and corresponding cell culture performance. Principal component analysis revealed that near-infrared spectra of different soy lots contain enough physicochemical information about soy hydrolysates to allow identification of lot-to-lot variability as well as vendor-to-vendor differences. The identified compositional variability was further analyzed in order to estimate cell growth and protein production of two mammalian cell lines under the condition of varying soy dosages using partial least square regression combined with optimal variable selection. The performance of the resulting models demonstrates the potential of near-infrared spectroscopy as a robust lot selection tool for raw materials while providing a biological link between chemical composition of raw materials and cell culture performance.     

Effect of iron addition on mAb productivity and oxidative stress in Chinese hamster ovary culture

Trace metals play a critical role in the development of culture media used for the production of therapeutic proteins. Iron has been shown to enhance the productivity of monoclonal antibodies during Chinese hamster ovary (CHO) cell culture. However, the redox activity and pro-oxidant behavior of iron may also contribute toward the production of reactive oxygen species (ROS). In this work, we aim to clarify the influence of trace iron by examining the relationship between iron supplementation to culture media, mAb productivity and glycosylation, and oxidative stress interplay within the cell. Specifically, we assessed the impacts of iron supplementation on (a) mAb production and glycosylation; (b) mitochondria-generated free hydroxyl radicals (ROS); (c) the cells ability to store energy during oxidative phosphorylation; and (d) mitochondrial iron concentration. Upon the increase of iron at inoculation, CHO cells maintained a capacity to rebound from iron-induced viability lapses during exponential growth phase and improved mAb productivity and increased mAb galactosylation. Fluorescent labeling of the mitochondrial hydroxyl radical showed enhanced environments of oxidative stress upon iron supplementation. Additional labeling of active mitochondria indicated that, despite the enhanced production of ROS in the mitochondria, mitochondrial membrane potential was minimally impacted. By replicating iron treatments during seed train passaging, the CHO cells were observed to adapt to the shock of iron supplementation prior to inoculation. Results from these experiments demonstrate that CHO cells have the capacity to adapt to enhanced environments of oxidative stress and improve mAb productivity and mAb galactosylation with minimal perturbations to cell culture.     

Probing of C-terminal lysine variation in a recombinant monoclonal antibody production using Chinese hamster ovary cells with chemically defined media

C-terminal lysine (C-K) variants are commonly observed in therapeutic monoclonal antibodies and recombinant proteins. Heterogeneity of C-K residues is believed to result from varying degree of proteolysis by endogenous carboxypeptidase(s) during cell culture production. The achievement of batch-to-batch culture performance and product quality reproducibility is a key cell culture development criterion. Understanding the operational parameters affecting C-K levels provides valuable insight into the cell culture process. A CHO cell line X expressing a recombinant antibody was selected as the model cell line due to the exhibited sensitivity of its C-K level to the process conditions. A weak cation exchange chromatography (WCX) method with or without carboxypeptidase B (CpB) treatment was developed to monitor the C-K level for in-process samples. The effects of operating conditions (i.e., temperature and culture duration) and media trace elements (copper and zinc) on C-K variants were studied. The dominant effect on C-K level was identified as the trace elements concentration. Specifically, increased C-K levels were observed with increase of copper concentration and decrease of zinc concentration in chemically defined medium. Further, a hypothesis for C-K processing with intracellular and extracellular carboxypeptidase activity was proposed, based on preliminary intracellular carboxypeptidase Western blot results and the extracellular HCCF holding study.     

Characterization of mammalian cell culture raw materials by combining spectroscopy and chemometrics

Two of the primary issues with characterizing the variability of raw materials used in mammalian cell culture, such as wheat hydrolysate, is that the analyses of these materials can be time consuming, and the results of the analyses are not straightforward to interpret. To solve these issues, spectroscopy can be combined with chemometrics to provide a quick, robust and easy to understand methodology for the characterization of raw materials; which will improve cell culture performance by providing an assessment of the impact that a given raw material will have on final product quality. In this study, four spectroscopic technologies: near infrared spectroscopy, middle infrared spectroscopy, Raman spectroscopy, and fluorescence spectroscopy were used in conjunction with principal component analysis to characterize the variability of wheat hydrolysates, and to provide evidence that the classification of good and bad lots of raw material is possible. Then, the same spectroscopic platforms are combined with partial least squares regressions to quantitatively predict two cell culture critical quality attributes (CQA): integrated viable cell density and IgG titer. The results showed that near infrared (NIR) spectroscopy and fluorescence spectroscopy are capable of characterizing the wheat hydrolysate's chemical structure, with NIR performing slightly better; and that they can be used to estimate the raw materials’ impact on the CQAs. These results were justified by demonstrating that of all the components present in the wheat hydrolysates, six amino acids: arginine, glycine, phenylalanine, tyrosine, isoleucine and threonine; and five trace elements: copper, phosphorus, molybdenum, arsenic and aluminum, had a large, statistically significant effect on the CQAs, and that NIR and fluorescence spectroscopy performed the best for characterizing the important amino acids. It was also found that the trace elements of interest were not characterized well by any of the spectral technologies used; however, the trace elements were also shown to have a less significant effect on the CQAs than the amino acids. © 2017 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers, 33:1127–1138, 2017     

Influence of protein and carbohydrate contents of soy protein hydrolysates on cell density and IgG production in animal cell cultures

The variety of compounds present in chemically defined media as well as media supplements makes it difficult to use a mechanistic approach to study the effect of supplement composition on culture functionality. Typical supplements, such as soy protein hydrolysates contain peptides, amino acids, carbohydrates, isoflavones, and saponins. To study the relative contribution of these compound classes, a set of hydrolysates were produced, containing 58‐83% proteinaceous material and 5‐21% carbohydrates. While the content of the different compounds classes varied, the composition (e.g., peptide profiles, carbohydrate composition) did not vary in hydrolysates. The hydrolysates were supplemented to a chemically defined medium in cell culture, based on equal weight and on equal protein levels. The latter showed that an increase in the carbohydrate concentration significantly (P value < 0.004) increased integral viable cell density (IVCD) (R = 0.7) and decreased total IgG (R = ?0.7) and specific IgG production (R = ?0.9). The extrapolation of effects of protein concentration showed that an increase in protein concentration increased total and specific IgG production and suppressed IVCD. In addition to proteins and carbohydrates, the functionality of soy protein hydrolysates may be modulated by the presence of other minor compounds. In the current study, the large differences in the balance between total proteins and total carbohydrates in the supplemented media seem to be a main factor influencing the balance between the viable cell density, total IgG, and specific IgG production. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1396–1405, 2015     

Glycan variability on a recombinant IgG antibody transiently produced in HEK-293E cells

In this study, a recombinant monoclonal IgG antibody was produced by transient gene expression (TGE) in suspension-adapted HEK-293E cells. The objective of the study was to determine the variation in recombinant IgG yield and glycosylation in ten independent transfections. In a ten-day batch process, the variation in transient IgG yield in the ten batches was less than 30% with the specific productivity averaging 20.2 ± 2.6 pg/cell/day. We characterized the N-glycosylation profile of each batch of affinity-purified IgG by intact protein and bottom-up mass spectrometry. Four major glycans were identified at Asn(297) in the ten batches with the maximum relative deviation for a single glycoform being 2.5%. In addition, within any single transfection there was little variation in glycoforms over the ten-day culture. Our experimental data indicate that with TGE, the production of recombinant IgG with little batch-to-batch variation in volumetric yield and protein glycosylation is feasible, even in a non-instrumented cultivation system as described here.     

A T-flask based screening platform for evaluating and identifying plant hydrolysates for a fed-batch cell culture process

This paper presents a T-flask based screening platform for evaluating and identifying plant hydrolysates for cell culture processes. The development of this platform was driven by an urgent need of replacing a soy hydrolysate that was no longer available for the fed-batch process of recombinant Sp2/0 cell culture expressing a humanized antibody. Series of small-scale experiments in T-flasks and 3-l bioreactors were designed to gain an insight on how this soy hydrolysate benefits the culture. A comprehensive, function-oriented screening platform then was developed, consisting of three T-flask tests, namely the protection test, the growth promotion test, and the growth inhibition test. The cell growth in these three T-flask tests enabled a good prediction of the cell growth in the fed-batch bioreactor process. Fourteen plant hydrolysate candidates were quickly evaluated by this platform for their ability to exert strong protection, high cell growth promotion, and low cell growth inhibition to the culture. One soy hydrolysate was successfully identified to support the comparable cell growth as the discontinued soy hydrolysate. Because of the advantage of using small-scale batch culture to guide bioreactor fed-batch culture, this proposed platform approach has the potential for other applications, such as the medium and feeding optimization, and the mechanism study of plant hydrolysates, in a high throughput format.     

Batch-to-Batch Quality Consistency Evaluation of Botanical Drug Products Using Multivariate Statistical Analysis of the Chromatographic Fingerprint

Botanical drug products have batch-to-batch quality variability due to botanical raw materials and the current manufacturing process. The rational evaluation and control of product quality consistency are essential to ensure the efficacy and safety. Chromatographic fingerprinting is an important and widely used tool to characterize the chemical composition of botanical drug products. Multivariate statistical analysis has showed its efficacy and applicability in the quality evaluation of many kinds of industrial products. In this paper, the combined use of multivariate statistical analysis and chromatographic fingerprinting is presented here to evaluate batch-to-batch quality consistency of botanical drug products. A typical botanical drug product in China, Shenmai injection, was selected as the example to demonstrate the feasibility of this approach. The high-performance liquid chromatographic fingerprint data of historical batches were collected from a traditional Chinese medicine manufacturing factory. Characteristic peaks were weighted by their variability among production batches. A principal component analysis model was established after outliers were modified or removed. Multivariate (Hotelling T ² and DModX) control charts were finally successfully applied to evaluate the quality consistency. The results suggest useful applications for a combination of multivariate statistical analysis with chromatographic fingerprinting in batch-to-batch quality consistency evaluation for the manufacture of botanical drug products.     

Use of soybean protein hydrolysates for promoting proliferation of human keratinocytes in serum-free medium

Human keratinocytes are generally cultured in media containing bovine pituitary extract (BPE), an animal product that can be a source of infectious contaminants. We investigated whether a safer plant product could replace BPE in the culture medium. Medium containing both BPE and soy protein hydrolysates (Bacto Soytone and Soy Hydrolysate) produced the largest number of viable cells, followed in descending order by medium supplemented only with BPE, only with the hydrolysates, and without supplementation (basal medium only). Soybean protein is thus an excellent source of nutrients for the growth of adherent keratinocytes, although they do not fully substitute for BPE.     

Submerged monoxenic culture medium development for Heterorhabditis bacteriophora and its symbiotic bacterium Photorhabdus luminescens: protein sources

Most medium formulations for improving culture of entomopathogenic nematodes (EPN) based on protein sources have used enriched media like animal feed such as dried egg yolk, lactalbumin, and liver extract, among other ingredients. Most results, however, showed unstable yields and longer production time. Many of the results do not show the detailed parameters of fermentation. Soy flour, cotton seed flour, corn gluten meal, casein powder, soytone, peptone, casein hydrolysates, and lactalbumin hydrolysate as protein sources were tested to determine the source to support optimal symbiotic bacteria and nematode growth. The protein hydrolysates selected did not improve bacterial cell mass compared with the yeast extract control, but soy flour was the best, showing 75.1% recovery and producing more bacterial cell number (1.4×10?/ml) than all other sources. The highest yield (1.85×10? IJs/ml), yield coefficient (1.67×10? IJs/g medium), and productivity (1.32×10? IJs/l/day) were also achieved at enriched medium with soybean protein.     

Development of serum-free medium supplemented with hydrolysates for the production of therapeutic antibodies in CHO cell cultures using design of experiments

An efficient method of formulating serum-free medium (SFM) for production of therapeutic antibodies by recombinant CHO (rCHO) cells was developed using two rCHO cell lines producing a therapeutic antibody. In this method, ten kinds of SFM were prepared by supplementing the basal SFM with statistically designed mixtures (total 5 g L^?1) of three non-animal-derived hydrolysates: yeastolate, soy hydrolysate, and wheat gluten hydrolysate. When the two rCHO cell lines were cultivated, the mixtures of soy hydrolysate and wheat gluten hydrolysate showed a positive effect on cell growth. On the other hand, the mixtures including a high portion of yeastolate significantly enhanced specific antibody productivity. To reconstitute the mixture ratios of the three hydrolysates for high growth and antibody production, the effect of each medium was analyzed by the statistical program Design-Expert®. The resulting medium gave a 1.9–3.3-fold increase in the maximum antibody concentration, compared to the basal SFM. Taken together, the supplementation of hydrolysates to the basal SFM with the help of statistical analysis is an efficient means of developing SFM for therapeutic antibody production by rCHO cells.     

Culture of transgenic Drosophila melanogaster Schneider 2 cells in serum-free media based on TC100 basal medium

Requirements of eliminating animal proteins from cell culture have intensified in recent years, with the pressure of regulatory agencies related to biopharmaceuticals production. In this work, the substitution of fetal bovine serum by yeastolate and a soy hydrolysate (Hy Soy) for the culture of Drosophila melanogaster Schneider 2 cells transfected for the production of rabies virus G glycoprotein was evaluated. TC100 supplemented with glucose, glutamine, lipid emulsion and Pluronic F68 was employed as basal medium. Results show that yeastolate was more efficient on cell growth stimulation than Hy Soy. Cells adapted in medium formulation supplemented with 3 g/L yeastolate, 1% lipid emulsion, 10 g/L glucose, 3.5 g/L glutamine and 0.1% Pluronic F68 attained a maximum concentration of 10.7 x 10(6) cells/mL, with the expression of 9.4 ng/mL G glycoprotein.     

Development of an animal‐component free medium for vero cells culture

This work describes the development of an animal‐component free medium (IPT‐AFM) that allows an optimal growth of Vero cells, an adherent cell line used for the production of viral vaccines. Statistical experimental design was applied to identify crucial nutrients that affect cell growth. Using Medium 199 or MEM as a basal medium, a serum‐free medium (SFM) referred as IPT‐SFM that only enclosed transferrin as a component of animal origin was developed at first. Then, the composition of IPT‐SFM was further improved to obtain an animal‐component free medium named IPT‐AFM. IPT‐AFM contains M199 as a basal medium, plant hydrolysates, epidermal growth factor, ethanolamine, ferric citrate, and vitamin C. Among various plant hydrolysates, specific combinations of soy (Hypep 1510) and wheat gluten (Hypeps 4601 and 4605) hydrolysates, were identified to promote cell growth; whereas individual Hypeps had a minor positive effect on cell growth. Nevertheless, the removal of serum did influence cell attachment. Coating tissue‐culture flasks with teleostean, a product extracted from cold water fish skin, had not only enhanced cell attachment but also improved cell growth performance in static cultures. Different non‐animal proteases were also assessed as an alternative to trypsin. TrypLE Select, a recombinant trypsin, gave the best cell growth performances. Kinetics of cell growth in IPT‐AFM were investigated in T‐flasks, cell growth was comparable with that obtained in MEM+10% fetal calf serum (FCS). A mean cell division number equal to 2.26 ± 0.18 and a specific growth rate μ 0.019 ± 0.003 h^?1 were achieved in IPT‐AFM. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009