A rapid fluorescence based method for the quantitative analysis of cell culture media photo-degradation

Excitation-Emission Matrix Fluorescence Spectroscopy Coupled with PARAFAC Modeling for Viability Prediction of Cells

Cell-based sensors and assays have great potential in bioanalysis, drug discovery screening, and biochemical mechanisms research. The cell viability tests should be fast, safe, reliable, and time- and cost-effective. Although methods stated as "gold standards", such as MTT, XTT, and LDH assays, usually fulfill these assumptions, they also show some limitations. They can be time-consuming, labor-intensive, and prone to errors and interference. Moreover, they do not enable the observation of the cell viability changes in real-time, continuously, and nondestructively. Therefore, we propose an alternative method of viability testing: native excitation-emission matrix fluorescence spectroscopy coupled with parallel factor analysis (PARAFAC), which is especially advantageous for cell monitoring due to its noninvasiveness and nondestructiveness and because there is no need for labeling and sample preparation. We demonstrate that our approach provides accurate results with even better sensitivity than the standard MTT test. With PARAFAC, it is possible to study the mechanism of the observed cell viability changes, which can be directly linked to increasing/decreasing fluorophores in the cell culture medium. The resulting parameters of the PARAFAC model are also helpful in establishing a reliable regression model for accurate and precise determination of the viability in A375 and HaCaT-adherent cell cultures treated with oxaliplatin.

Excitation–emission matrix fluorescence spectroscopy for cell viability testing in UV-treated cell culture

Monitoring of cells viability is essential in a number of biomedical applications, including cell-based sensors, cell-based microsystems, and cell-based assays. The use of spectroscopic techniques for such purposes is especially advantageous since they are non-invasive, label-free, and non-destructive. However, such an approach must include chemometric analysis of the data to assess the information on cells viability. In the presented article we demonstrate, that excitation–emission matrix (EEM) fluorescence spectroscopy can be applied for reliable determination of cells viability due to the high correlation of EEM fluorescence data with the MTT test data. A375 cells (malignant melanoma) were exposed to UV radiation as a physical stress factor, resulting in a decrease of viability up to ca. 20%, confirmed by the standard MTT test. They were also characterized by means of EEM fluorescence spectroscopy coupled with unfolded partial least squares (UPLS) regression. Statistical evaluation revealed high accordance of the two methods of viability testing in terms of accuracy, precision, and correlation. The presented results are very promising for the development of spectroscopic soft sensors that can be applied for drug screening, biocompatibility testing, tissue engineering, and pharmacodynamic studies.

Excitation-emission matrix fluorescence spectroscopy can be applied for label-free and non-destructive determination of cells viability, which is promising methodology for drug screening, biocompatibility testing, or pharmacodynamic studies.

Development of a rapid polarized total synchronous fluorescence spectroscopy (pTSFS) method for protein quantification in a model bioreactor broth

Protein quantification during bioprocess monitoring is essential for biopharmaceutical manufacturing and is complicated by the complex chemical composition of the bioreactor broth. Here we present the early-stage development and optimization of a polarized total synchronous fluorescence spectroscopy (pTSFS) method for protein quantification in a hydrolysate-protein model (mimics clarified bioreactor broth samples) using a standard benchtop laboratory fluorometer. We used UV transmitting polarizers to provide wider range pTSFS spectra for screening of the four different TSFS spectra generated by the measurement: parallel (||), perpendicular (⊥), unpolarized (T) intensity spectra and anisotropy maps. TSFS_|| (parallel polarized) measurements were the best for protein quantification compared to standard unpolarized measurements and the Bradford assay. This was because TSFS_|| spectra had a better analyte signal to noise ratio (SNR), due to the anisotropy of protein emission. This meant that protein signals were better resolved from the background emission of small molecule fluorophores in the cell culture media. SNR of >5000 was achieved for concentrations of bovine serum albumin/yeastolate 1.2/10 g L^-1 with TSFS_|| . Optimization using genetic algorithm and interval partial least squares based variable selection enabled reduction of spectral resolution and number of excitation wavelengths required without degrading performance. This enables fast (<3.5 min) online/at-line measurements, and the method had an LOD of 0.18 g L^-1 and high accuracy with a predictive error of <9%.

Towards robust cell culture processes - Unraveling the impact of media preparation by spectroscopic online monitoring

Biopharmaceutical manufacturing processes can be affected by variability in cell culture media, e.g. caused by raw material impurities. Although efforts have been made in industry and academia to characterize cell culture media and raw materials with advanced analytics, the process of industrial cell culture media preparation itself has not been reported so far. Within this publication, we first compare mid-infrared and two-dimensional fluorescence spectroscopy with respect to their suitability as online monitoring tools during cell culture media preparation, followed by a thorough assessment of the impact of preparation parameters on media quality. Through the application of spectroscopic methods, we can show that media variability and its corresponding root cause can be detected online during the preparation process. This methodology is a powerful tool to avoid batch failure and is a valuable technology for media troubleshooting activities. Moreover, in a design of experiments approach, including additional liquid chromatography-mass spectrometry analytics, it is shown that variable preparation parameters such as temperature, power input and preparation time can have a strong impact on the physico-chemical composition of the media. The effect on cell culture process performance and product quality in subsequent fed-batch processes was also investigated. The presented results reveal the need for online spectroscopic methods during the preparation process and show that media variability can already be introduced by variation in media preparation parameters, with a potential impact on scale-up to a commercial manufacturing process.

An excitation emission fluorescence lifetime spectrometer using a frequency doubled supercontinuum laser source

The accurate fluorescence analysis of complex, multi-fluorophore containing proteins requires the use of multi-dimensional measurement techniques. For the measurement of intrinsic fluorescence from tyrosine (Tyr) and tryptophan (Trp) one needs tuneable UV excitation and for steady-state measurements like Excitation Emission Matrix (EEM) simple pulsed Xe lamps are commonly used. Unfortunately, simultaneous multi-dimensional wavelength and time resolved measurement of intrinsic protein fluorescence in the 260 to 400 nm spectral range are challenging and typically required the use of very complex tuneable laser systems or multiple single excitation wavelength sources. Here we have assembled and validated a novel Excitation Emission Fluorescence Lifetime Spectrometer (EEFLS) using a pulsed, frequency doubled, Super-Continuum Laser (SCL) source coupled with a 16 channel multi-anode Time Correlated Single Photon Counting (TCSPC) measurement system. This EEFLS enabled the collection of near complete lifetime and intensity maps over the most important intrinsic protein fluorescence spectral range (λ _ex = 260-350/λ _em = 300-500 nm). The 4-dimensional (λ _ex/λ _em/I_(t)/τ) Excitation Emission Fluorescence Lifetime Matrix (EEFLM) data produced can be used to better characterize the complex intrinsic emission from proteins. The system was capable of measuring fluorescence emission data with high spectral (1-2 nm) resolution and had an Instrument Response Function (IRF) of ∼650 ps for accurate measurement of nanosecond lifetimes. UV power output was stable after a warm up period, with variations of <2% over 9 hours and reproducible (relative standard deviation RSD < 1.5%). This enabled the collection of accurate EEFLM data at low resolution (∼12 nm in excitation and emission) in 1-2 hours or high resolution (4 nm) in ∼17 hours. EEFLS performance in the UV was compared with a conventional commercial TCSPC system using pulsed LED excitation and validated using solutions of p-terphenyl and tryptophan.

Media photo-degradation in pharmaceutical biotechnology - impact of ambient light on media quality, cell physiology, and IgG production in CHO cultures

BACKGROUND

Many vital components in bioprocess media are prone to photo-conversion or photo-degradation upon exposure to ambient light, with severe negative consequences for biomass yield and overall productivity. However, there is only limited awareness of light irradiation as a potential risk factor when working in transparent glass bioreactors, storage vessels or disposable bag systems. The chemical complexity of most media renders a root-cause analysis difficult. This study investigated in a novel, holistic approach how light-induced changes in media composition relate to alterations in radical burden, cell physiology, morphology, and product formation in industrial Chinese hamster ovary (CHO) bioprocesses.

RESULTS

Two media formulations from proprietary and commercial sources were tested in a pre-hoc light exposure scenario prior to cultivation. Using fluorescence excitation/emission (EEM) matrix spectroscopy, a photo-sensitization of riboflavin was identified as a likely cause for drastically decreased IgG titers (up to -80%) and specific growth rates (-50% to -90%). Up to three-fold higher radical levels were observed in photo-degraded medium. On the biological side, this resulted in significant changes in cell morphology and aberrations in the normal IgG biosynthesis/secretion pathway.

CONCLUSION

These findings clearly illustrate the underrated impact of room light after only short periods of exposure, occurring accidentally or knowingly during bioprocess development and scale- up. The detrimental effects, which may share a common mechanistic cause at the molecular level, correlate well with changes in spectroscopic properties. This offers new perspectives for online monitoring concepts, and improved detectability of such effects in future. © 2018 The Authors. Journal of Chemical Technology & Biotechnology published by JohnWiley & Sons Ltd on behalf of Society of Chemical Industry.

Calibration, standardization, and quantitative analysis of multidimensional fluorescence (MDF) measurements on complex mixtures (IUPAC Technical Report)

This IUPAC Technical Report describes and compares the currently applied methods for the calibration and standardization of multi-dimensional fluorescence (MDF) spectroscopy data as well as recommendations on the correct use of chemometric methods for MDF data analysis. The paper starts with a brief description of the measurement principles for the most important MDF techniques and a short introduction to the most important applications. Recommendations are provided for instrument calibration, sample preparation and handling, and data collection, as well as the proper use of chemometric data analysis methods.

Untargeted LC-MS/MS Profiling of Cell Culture Media Formulations for Evaluation of High Temperature Short Time Treatment Effects

An untargeted LC-MS/MS platform was implemented for monitoring variations in CHO cell culture media upon exposure to high temperature short time (HTST) treatment, a commonly used viral clearance upstream strategy. Chemically defined (CD) and hydrolysate-supplemented media formulations were not visibly altered by the treatment. The absence of solute precipitation effects during media treatment and very modest shifts in pH values observed indicated sufficient compatibility of the formulations evaluated with the HTST-processing conditions. Unsupervised chemometric analysis of LC-MS/MS data, however, revealed clear separation of HTST-treated samples from untreated counterparts as observed from analysis of principal components and hierarchical clustering sample grouping. An increased presence of Maillard products in HTST-treated formulations contributed to the observed differences which included organic acids, observed particularly in chemically defined formulations, and furans, pyridines, pyrazines, and pyrrolidines which were determined in hydrolysate-supplemented formulations. The presence of Maillard products in media did not affect cell culture performance with similar growth and viability profiles observed for CHO-K1 and CHO-DP12 cells when cultured using both HTST-treated and untreated media formulations.

Applications of Raman Spectroscopy in Biopharmaceutical Manufacturing: A Short Review

The production of active pharmaceutical ingredients (APIs) is currently undergoing its biggest transformation in a century. The changes are based on the rapid and dramatic introduction of protein- and macromolecule-based drugs (collectively known as biopharmaceuticals) and can be traced back to the huge investment in biomedical science (in particular in genomics and proteomics) that has been ongoing since the 1970s. Biopharmaceuticals (or biologics) are manufactured using biological-expression systems (such as mammalian, bacterial, insect cells, etc.) and have spawned a large (>€35 billion sales annually in Europe) and growing biopharmaceutical industry (BioPharma). The structural and chemical complexity of biologics, combined with the intricacy of cell-based manufacturing, imposes a huge analytical burden to correctly characterize and quantify both processes (upstream) and products (downstream). In small molecule manufacturing, advances in analytical and computational methods have been extensively exploited to generate process analytical technologies (PAT) that are now used for routine process control, leading to more efficient processes and safer medicines. In the analytical domain, biologic manufacturing is considerably behind and there is both a huge scope and need to produce relevant PAT tools with which to better control processes, and better characterize product macromolecules. Raman spectroscopy, a vibrational spectroscopy with a number of useful properties (nondestructive, non-contact, robustness) has significant potential advantages in BioPharma. Key among them are intrinsically high molecular specificity, the ability to measure in water, the requirement for minimal (or no) sample pre-treatment, the flexibility of sampling configurations, and suitability for automation. Here, we review and discuss a representative selection of the more important Raman applications in BioPharma (with particular emphasis on mammalian cell culture). The review shows that the properties of Raman have been successfully exploited to deliver unique and useful analytical solutions, particularly for online process monitoring. However, it also shows that its inherent susceptibility to fluorescence interference and the weakness of the Raman effect mean that it can never be a panacea. In particular, Raman-based methods are intrinsically limited by the chemical complexity and wide analyte-concentration-profiles of cell culture media/bioprocessing broths which limit their use for quantitative analysis. Nevertheless, with appropriate foreknowledge of these limitations and good experimental design, robust analytical methods can be produced. In addition, new technological developments such as time-resolved detectors, advanced lasers, and plasmonics offer potential of new Raman-based methods to resolve existing limitations and/or provide new analytical insights.

Enabler for process analytical technology implementation in Pichia pastoris fermentation: Fluorescence-based soft sensors for rapid quantitation of product titer

Rapid quantitation of product titer is a critical input for control of any bioprocess. This measurement, however, is marred by the myriad components that are present in the fermentation broth, often requiring extensive sample pretreatment before analysis. Spectroscopy techniques such as fluorescence spectroscopy are widely recognized as potential monitoring tools. Here, we investigate the possibility of using fluorescence of the culture supernatant as a potential at-line monitoring tool to measure the concentration of a recombinant therapeutic protein expressed in a Pichia pastoris fed-batch fermentation. We propose an integrated method wherein both the target protein and total protein concentrations are predicted using intrinsic riboflavin fluorescence and extrinsic fluorescence, respectively. The root mean square error for estimating the concentrations of the target protein (using riboflavin fluorescence) and total protein (using extrinsic fluorescence) have been estimated to be <0.1 and <0.2, respectively. The proposed approach has been validated for two different biotherapeutic products, human serum albumin and granulocyte colony stimulating factor, that were expressed using Mut⁺ and Mut^s strains of P. pastoris, respectively. The proposed approach is rapid (1 min analysis time, 10 min total with at line sampling) and thus could be a significant enabler for process analytical technology implementation in Pichia fermentation.

Anisotropy resolved multidimensional emission spectroscopy (ARMES): A new tool for protein analysis

Structural analysis of proteins using the emission of intrinsic fluorophores is complicated by spectral overlap. Anisotropy resolved multidimensional emission spectroscopy (ARMES) overcame the overlap problem by the use of anisotropy, with chemometric analysis, to better resolve emission from different fluorophores. Total synchronous fluorescence scan (TSFS) provided information about all the fluorophores that contributed to emission while anisotropy provided information about the environment of each fluorophore. Here the utility of ARMES was demonstrated via study of the chemical and thermal denaturation of human serum albumin (HSA). Multivariate curve resolution (MCR) analysis of the constituent polarized emission ARMES data resolved contributions from four emitters: fluorescence from tryptophan (Trp), solvent exposed tyrosine (Tyr), Tyr in a hydrophobic environment, and room temperature phosphorescence (RTP) from Trp. The MCR scores, anisotropy, and literature validated these assignments and showed all the expected transitions during HSA unfolding. This new methodology for comprehensive intrinsic fluorescence analysis of proteins is applicable to any protein containing multiple fluorophores.

A fluorescence anisotropy method for measuring protein concentration in complex cell culture media

The rapid, quantitative analysis of the complex cell culture media used in biopharmaceutical manufacturing is of critical importance. Requirements for cell culture media composition profiling, or changes in specific analyte concentrations (e.g. amino acids in the media or product protein in the bioprocess broth) often necessitate the use of complicated analytical methods and extensive sample handling. Rapid spectroscopic methods like multi-dimensional fluorescence (MDF) spectroscopy have been successfully applied for the routine determination of compositional changes in cell culture media and bioprocess broths. Quantifying macromolecules in cell culture media is a specific challenge as there is a need to implement measurements rapidly on the prepared media. However, the use of standard fluorescence spectroscopy is complicated by the emission overlap from many media components. Here, we demonstrate how combining anisotropy measurements with standard total synchronous fluorescence spectroscopy (TSFS) provides a rapid, accurate quantitation method for cell culture media. Anisotropy provides emission resolution between large and small fluorophores while TSFS provides a robust measurement space. Model cell culture media was prepared using yeastolate (2.5 mg mL(-1)) spiked with bovine serum albumin (0 to 5 mg mL(-1)). Using this method, protein emission is clearly discriminated from background yeastolate emission, allowing for accurate bovine serum albumin (BSA) quantification over a 0.1 to 4.0 mg mL(-1) range with a limit of detection (LOD) of 13.8 μg mL(-1).