Generic Raman‐based calibration models enabling real‐time monitoring of cell culture bioreactors

Raman‐based multivariate calibration models have been developed for real‐time in situ monitoring of multiple process parameters within cell culture bioreactors. Developed models are generic, in the sense that they are applicable to various products, media, and cell lines based on Chinese Hamster Ovarian (CHO) host cells, and are scalable to large pilot and manufacturing scales. Several batches using different CHO‐based cell lines and corresponding proprietary media and process conditions have been used to generate calibration datasets, and models have been validated using independent datasets from separate batch runs. All models have been validated to be generic and capable of predicting process parameters with acceptable accuracy. The developed models allow monitoring multiple key bioprocess metabolic variables, and hence can be utilized as an important enabling tool for Quality by Design approaches which are strongly supported by the U.S. Food and Drug Administration. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1004–1013, 2015     

Intrinsic fluorescence‐based at situ soft sensor for monitoring monoclonal antibody aggregation

Intrinsic fluorescence spectroscopy, in conjunction with partial least squares regression (PLSR), was investigated as a potential technique for online quality control and quantitative monitoring of Immunoglobulin G (IgG) aggregation that occurs following exposure to conditions that emulate those that can occur during protein downstream processing. Initially, the impact of three stress factors (temperature, pH, and protein concentration) on the degree of aggregation determined using size exclusion chromatography data, was investigated by performing a central composite designexperiment and applying a fitting response surface model. This investigation identified the influence of the factors as well as the operating regions with minimum propensity to induce protein aggregation. Spectral changes pertinent to the stressed samples were also investigated and found to corroborate the high sensitivity of the intrinsic fluorescence to conformational changes of the proteins under study. Ultimately, partial least squares regression was implemented to formulate two fluorescence‐based soft sensors for quality control—product classification—and quantitative monitoring—concentration of monomer. The resulting regression models exhibited accurate prediction ability and good potential for in situ monitoring of monoclonal antibody downstream purification processes. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1423–1432, 2015     

Fingerprint detection and process prediction by multivariate analysis of fed‐batch monoclonal antibody cell culture data

This work presents a sequential data analysis path, which was successfully applied to identify important patterns (fingerprints) in mammalian cell culture process data regarding process variables, time evolution and process response. The data set incorporates 116 fed‐batch cultivation experiments for the production of a Fc‐Fusion protein. Having precharacterized the evolutions of the investigated variables and manipulated parameters with univariate analysis, principal component analysis (PCA) and partial least squares regression (PLSR) are used for further investigation. The first major objective is to capture and understand the interaction structure and dynamic behavior of the process variables and the titer (process response) using different models. The second major objective is to evaluate those models regarding their capability to characterize and predict the titer production. Moreover, the effects of data unfolding, imputation of missing data, phase separation, and variable transformation on the performance of the models are evaluated. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1633–1644, 2015     

Quantitative modeling of viable cell density,cell size,intracellular conductivity,and membrane capacitance in batch and fed‐batch CHO processes using dielectric spectroscopy

Dielectric spectroscopy was used to analyze typical batch and fed‐batch CHO cell culture processes. Three methods of analysis (linear modeling, Cole–Cole modeling, and partial least squares regression), were used to correlate the spectroscopic data with routine biomass measurements [viable packed cell volume, viable cell concentration (VCC), cell size, and oxygen uptake rate (OUR)]. All three models predicted offline biomass measurements accurately during the growth phase of the cultures. However, during the stationary and decline phases of the cultures, the models decreased in accuracy to varying degrees. Offline cell radius measurements were unsuccessfully used to correct for the deviations from the linear model, indicating that physiological changes affecting permittivity were occurring. The β‐dispersion was analyzed using the Cole–Cole distribution parameters Δε (magnitude of the permittivity drop), f_c (critical frequency), and α (Cole–Cole parameter). Furthermore, the dielectric parameters static internal conductivity (σ_i) and membrane capacitance per area (C_m) were calculated for the cultures. Finally, the relationship between permittivity, OUR, and VCC was examined, demonstrating how the definition of viability is critical when analyzing biomass online. The results indicate that the common assumptions of constant size and dielectric properties used in dielectric analysis are not always valid during later phases of cell culture processes. The findings also demonstrate that dielectric spectroscopy, while not a substitute for VCC, is a complementary measurement of viable biomass, providing useful auxiliary information about the physiological state of a culture. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Mid‐infrared spectroscopy‐based analysis of mammalian cell culture Parameters

Within the framework of process analytical technology, infrared spectroscopy (IR) has been used for characterization of biopharmaceutical production processes. Although noninvasive attenuated total reflection (ATR) spectroscopy can be regarded as gold standard within IR‐based process analytics, simpler and more cost‐effective mid‐infrared (MIR) instruments might improve acceptability of this technique for high‐level monitoring of small scale experiments as well as for academia where financial restraints impede the use of costly equipment. A simple and straightforward at‐line mid‐IR instrument was used to monitor cell viability parameters, activity of lactate dehydrogenase (LDH), amount of secreted antibody, and concentration of glutamate and lactate in a Chinese hamster ovary cell culture process, applying multivariate prediction models, including only 25–28 calibration samples per model. Glutamate amount could be predicted with high accuracy (R² 0.91 for independent test‐set) while antibody concentration achieved good prediction for concentrations >0.4 mg L^?1. Prediction of LDH activity was accurate except for the low activity regime. The model for lactate monitoring was only moderately good and requires improvements. Relative cell viability between 20 and 95% could be predicted with low error (8.82%) in comparison to reference methods. An initial model for determining the number of nonviable cells displayed only acceptable accuracy and requires further improvement. In contrast, monitoring of viable cell number showed better accuracy than previously published ATR‐based results. These results prove the principal suitability of less sophisticated MIR instruments to monitor multiple parameters in biopharmaceutical production with relatively low investments and rather fast calibration procedures. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:578–584, 2015     

Raman spectroscopy and chemometrics for on‐line control of glucose fermentation by Saccharomyces cerevisiae

This work presents the use of Raman spectroscopy and chemometrics for on‐line control of the fermentation process of glucose by Saccharomyces cerevisiae. In a first approach, an on‐line determination of glucose, ethanol, glycerol, and cells was accomplished using multivariate calibration based on partial least squares (PLS). The PLS models presented values of root mean square error of prediction (RMSEP) of 0.53, 0.25, and 0.02% for glucose, ethanol and glycerol, respectively, and RMSEP of 1.02 g L^?1 for cells. In a second approach, multivariate control charts based on multiway principal component analysis (MPCA) were developed for detection of fermentation fault‐batch. Two multivariate control charts were developed, based on the squared prediction error (Q) and Hotelling's T². The use of the Q control chart in on‐line monitoring was efficient for detection of the faults caused by temperature, type of substrate and contamination, but the T² control chart was not able to monitor these faults. On‐line monitoring by Raman spectroscopy in conjunction with chemometric procedures allows control of the fermentative process with advantages in relation to reference methods, which require pretreatment, manipulation of samples and are time consuming. Also, the use of multivariate control charts made possible the detection of faults in a simple way, based only on the spectra of the system. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012     

Cross‐scale predictive modeling of CHO cell culture growth and metabolites using Raman spectroscopy and multivariate analysis

Multi‐component, multi‐scale Raman spectroscopy modeling results from a monoclonal antibody producing CHO cell culture process including data from two development scales (3 L, 200 L) and a clinical manufacturing scale environment (2,000 L) are presented. Multivariate analysis principles are a critical component to partial least squares (PLS) modeling but can quickly turn into an overly iterative process, thus a simplified protocol is proposed for addressing necessary steps including spectral preprocessing, spectral region selection, and outlier removal to create models exclusively from cell culture process data without the inclusion of spectral data from chemically defined nutrient solutions or targeted component spiking studies. An array of single‐scale and combination‐scale modeling iterations were generated to evaluate technology capabilities and model scalability. Analysis of prediction errors across models suggests that glucose, lactate, and osmolality are well modeled. Model strength was confirmed via predictive validation and by examining performance similarity across single‐scale and combination‐scale models. Additionally, accurate predictive models were attained in most cases for viable cell density and total cell density; however, these components exhibited some scale‐dependencies that hindered model quality in cross‐scale predictions where only development data was used in calibration. Glutamate and ammonium models were also able to achieve accurate predictions in most cases. However, there are differences in the absolute concentration ranges of these components across the datasets of individual bioreactor scales. Thus, glutamate and ammonium PLS models were forced to extrapolate in cases where models were derived from small scale data only but used in cross‐scale applications predicting against manufacturing scale batches. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 31:566–577, 2015     

Real‐time monitoring of influenza virus production kinetics in HEK293 cell cultures

There is an increased interest from the vaccine industry to use mammalian cell cultures for influenza vaccine manufacturing. Therefore, it became important to study the influenza infection mechanism, the viral–host interaction, and the replication kinetics from a bioprocessing stand point to maximize the influenza viral production yield in cell culture. In the present work, influenza replication kinetics was studied in HEK293 cells. Two infection conditions were evaluated, a low (0.01) and a high multiplicity of infection (1.0). Critical time points of the viral production cycle (infection, protein synthesis, viral assembly and budding, viral release, and host‐cell death) were identified in small‐scale cell cultures. Additionally, cell growth, viability, and viral titers were monitored in the viral production process. The infection state of the cultivated cell population was assessed by influenza immunolabeling throughout the culture period. Influenza virus production kinetics were also on‐line monitored by dielectric spectroscopy and successfully correlated to real‐time capacitance measures. Overall, this work provided insights into the mechanisms associated with the infection of human HEK293 cell line by the influenza virus and demonstrated, once again, the usefulness of multifrequency scanning permittivity for in‐line monitoring and supervision of cell‐based viral production processes. Published 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2013     

Advanced online monitoring of cell culture off‐gas using proton transfer reaction mass spectrometry

Mass spectrometry has been frequently applied to monitor the O₂ and CO₂ content in the off‐gas of animal cell culture fermentations. In contrast to classical mass spectrometry the proton transfer reaction mass spectrometry (PTR‐MS) provides additional information of volatile organic compounds by application of a soft ionization technology. Hence, the spectra show less fragments and can more accurately assigned to particular compounds. In order to discriminate between compounds of non‐metabolic and metabolic origin cell free experiments and fed‐batch cultivations with a recombinant CHO cell line were conducted. As a result, in total eight volatiles showing high relevance to individual cultivation or cultivation conditions could be identified. Among the detected compounds methanethiol, with a mass‐to‐charge ratio of 49, qualifies as a key candidate in process monitoring due to its strong connectivity to lactate formation. Moreover, the versatile and complex data sets acquired by PTR MS provide a valuable resource for statistical modeling to predict non direct measurable parameters. Hence, partial least square regression was applied to the complete spectra of volatiles measured and important cell culture parameters such as viable cell density estimated (R² = 0.86). As a whole, the results of this study clearly show that PTR‐MS provides a powerful tool to improve bioprocess‐monitoring for mammalian cell culture. Thus, specific volatiles emitted by cells and measured online by the PTR‐MS and complex variables gained through statistical modeling will contribute to a deeper process understanding in the future and open promising perspectives to bioprocess control. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 30:496–504, 2014     

A completely noninvasive method of dissolved oxygen monitoring in disposable small‐scale cell culture vessels based on diffusion through permeable vessel walls

Disposable cell culture vessels are extensively used at small scales for process optimization and validation, but they lack monitoring capabilities. Optical sensors that can be easily adapted for use in small‐scale vessels are commercially available for pH, dissolved oxygen (DO), and dissolved carbon dioxide (DCO₂). However, their use has been limited due to the contamination and compatibility issues. We have developed a novel solution to these problems for DO monitoring. Oxygen diffusion through permeable vessel wall can be exploited for noninvasive monitoring. An optical oxygen sensor can be placed outside the oxygen permeable vessel wall thereby allowing oxygen diffusing through the vessel wall to be detected by the sensor. This way the sensor stays separate from the cell culture and there are no concerns about contaminants or leachants. Here we implement this method for two cell culture devices: polystyrene‐made T‐75 tissue culture flask and fluorinated ethylene propylene (FEP)‐made Vuelife^® cell culture bag. Additionally, mammalian and microbial cell cultures were performed in Vuelife^® cell culture bags, proving that a sensor placed outside can be used to track changes in cell cultures. This approach toward noninvasive monitoring will help in integrating cell culture vessels with sensors in a seamless manner. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 30:172–177, 2014     

Effect of CO2 on uninfected Sf‐9 cell growth and metabolism

A problem in the mass production of recombinant proteins and biopesticides using insect cell culture is CO₂ accumulation. This research investigated the effect of elevated CO₂ concentration on insect cell growth and metabolism. Spodoptera frugiperda Sf‐9 insect cells were grown at 20% air saturation, 27^°C, and a pH of 6.2. The cells were exposed to a constant CO₂ concentration by purging the medium with CO₂ and the headspace with air. The population doubling time (PDT) of Sf‐9 cells increased with increasing CO₂ concentration. Specifically, the PDT for 0‐37, 73, 147, 183, and 220 mm Hg CO₂ concentrations were 23.2 ± 6.7, 32.4 ± 7.2, 38.1 ± 13.3, 42.9 ± 5.4, and 69.3 ± 35.9 h (n = 3 or 4, 95% confidence level), respectively. The viability of cells in all experiments was above 90%, i.e., while increased CO₂ concentrations inhibited cell growth, it did not affect cell viability. The osmolality for all bioreactor experiments was observed to be 300–360 mOsm/kg, a range that is known to have a negligible effect on insect cell culture. Elevated CO₂ concentration did not significantly alter the cell specific glucose consumption rate (2.5–3.2 × 10^?17 mol/cell s), but slightly increased the specific lactate production rate from ?3.0 × 10^?19 to 10.2 × 10^?19 mol/cell s. Oxidative stress did not contribute to CO₂ inhibition in uninfected Sf‐9 cells as no significant increase in the levels of lipid hydroperoxide and protein carbonyl concentrations was discovered at elevated CO₂ concentration. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:465–469, 2016     

Data reconciliation of concentration estimates from mid‐infrared and dielectric spectral measurements for improved on‐line monitoring of bioprocesses

Real‐time data reconciliation of concentration estimates of process analytes and biomass in microbial fermentations is investigated. A Fourier‐transform mid‐infrared spectrometer predicting the concentrations of process metabolites is used in parallel with a dielectric spectrometer predicting the biomass concentration during a batch fermentation of the yeast Saccharomyces cerevisiae. Calibration models developed off‐line for both spectrometers suffer from poor predictive capability due to instrumental and process drifts unseen during calibration. To address this problem, the predicted metabolite and biomass concentrations, along with off‐gas analysis and base addition measurements, are reconciled in real‐time based on the closure of mass and elemental balances. A statistical test is used to confirm the integrity of the balances, and a non‐negativity constraint is used to guide the data reconciliation algorithm toward positive concentrations. It is verified experimentally that the proposed approach reduces the standard error of prediction without the need for additional off‐line analysis. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Sustaining an efficient and effective CHO cell line development platform by incorporation of 24‐deep well plate screening and multivariate analysis

Efficient and effective cell line screening is paramount toward a successful biomanufacturing program. Here we describe the implementation of 24‐deep well plate (24‐DWP) screening of CHO lines as part of the cell line development platform at AbbVie. Incorporation of this approach accelerated the identification of the best candidate lines for process development. In an effort to quantify and predict process performance comparability, we compared cell culture performance in and in shake flasks, for a panel of Chinese Hamster Ovary cell lines expressing a monoclonal antibody. The results in 24‐DWP screening showed reduced growth profiles, but comparable viability profiles. Slow growers in 24‐DWP achieved the highest productivity improvement upon scaling‐up to shake flasks. Product quality of the protein purified from shake flasks and 24‐DWP were also compared. The 24‐DWP culture conditions were found to influence the levels of acidic species, reduce the G0 N‐glycan species, and increase the high‐mannose N‐glycan species. Nevertheless, the identification of undesirable profiles is executed consistently with the scaled‐up culture. We further employed multivariate data analysis to capture differences depending on the two scales and we could demonstrate that cell line profiles were adequately clustered, regardless of the vessel used for the development. In conclusion, the 24‐DWP platform was reasonably predictive of the parameters crucial for upstream process development activities, and has been adapted as part of the AbbVie cell line development platform. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:175–186, 2018     

Fine‐scale spatial variability in anatoxin‐a and homoanatoxin‐a concentrations in benthic cyanobacterial mats: implication for monitoring and management

Aims: The purpose of this study was to determine the variability in anatoxin‐a (ATX) and homoanatoxin‐a (HTX) concentrations in benthic cyanobacterial mats within sampling sites and to assess the applicability of using a PCR‐based approach to determine ATX‐ and HTX‐production potential. Methods and Results: ATX and HTX variability was investigated by collecting 15 samples from 10 × 10 m grids in seven rivers. ATX and HTX concentrations were determined using liquid chromatography–mass spectrometry (LC–MS). Samples from two sites contained no ATX or HTX and at one site ATX and HTX were detected in all samples. At four sites, both toxic and nontoxic samples co‐occurred and these samples were sometimes spaced less than 1 m apart. PCR amplification of a region of a polyketide synthase (ks2, putatively involved in the biosynthetic pathway of ATX and HTX) successfully distinguished ATX‐and‐HTX‐ and non‐ATX‐and‐HTX‐producing cultured Phormidium strains. Results from environmental samples were more variable, and the results were in congruence with the LC–MS data in only 58% of samples. Conclusions: Fine‐scale spatial variability in ATX and HTX concentrations occurs among benthic cyanobacterial mats. Significance and Impact of the Study: Multiple benthic cyanobacterial mat samples must be collected at a sampling site to provide an accurate assessment of ATX and HTX concentrations at that location. The PCR‐based technique offers the potential to be a useful early warning technique.     

Characterization of cell‐banking parameters for the cryopreservation of mammalian cell lines in 100‐mL cryobags

This article describes a cell banking process for rBHK cell lines in 100‐mL cryobags. As the use of larger volume cell banks requires greater cell numbers and longer preparation time, extensive characterization of key process parameters beyond the conventional ranges was performed to support a cGMP banking process. All experiments were conducted using two recombinant BHK21 cell lines, one of them cotransfected with Hsp70. The results show that the entire cell banking process for these BHK cell lines can be performed at room temperature. A DMSO exposure time up to 5 h either directly in a bioreactor or in shaker flasks did not result in any significant negative effect after cell thaw, when the cryocontainers were frozen immediately after filling. Extensive characterization did not indicate any significant apoptotic effects after thaw. However, the Hsp70 cotransfected cell line did show a slightly better protection from potential cryopreservation‐induced apoptosis. Surprisingly, it was found that cells transferred into cryobags showed a low recovery rate after thaw if the incubation time exceeded 1.5 h before freezing. Additional experiments confirmed that the DMSO exposure time inside the cryocontainer in contrast to the DMSO exposure in a reactor or shaker flasks is much more critical. The cryobag cell banking process should therefore be performed within a 1½–2 h window; a banking process for vials should not exceed 2½ h. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

dNTP metabolism links mechanical cues and YAP/TAZ to cell growth and oncogene‐induced senescence

YAP/TAZ, downstream transducers of the Hippo pathway, are powerful regulators of cancer growth. How these factors control proliferation remains poorly defined. Here, we found that YAP/TAZ directly regulate expression of key enzymes involved in deoxynucleotide biosynthesis and maintain dNTP precursor pools in human cancer cells. Regulation of deoxynucleotide metabolism is required for YAP‐induced cell growth and underlies the resistance of YAP‐addicted cells to chemotherapeutics targeting dNTP synthesis. During RAS‐induced senescence, YAP/TAZ bypass RAS‐mediated inhibition of nucleotide metabolism and control senescence. Endogenous YAP/TAZ targets and signatures are inhibited by RAS/MEK1 during senescence, and depletion of YAP/TAZ is sufficient to cause senescence‐associated phenotypes, suggesting a role for YAP/TAZ in suppression of senescence. Finally, mechanical cues, such as ECM stiffness and cell geometry, regulate senescence in a YAP‐dependent manner. This study indicates that YAP/TAZ couples cell proliferation with a metabolism suited for DNA replication and facilitates escape from oncogene‐induced senescence. We speculate that this activity might be relevant during the initial phases of tumour progression or during experimental stem cell reprogramming induced by YAP.