Real time monitoring of bioreactor mAb IgG3 cell culture process dynamics via Fourier transform infrared spectroscopy: Implications for enabling cell culture process analytical technology

Bioprocess monitoring applications of an innovative ATR-FTIR spectroscopy platform

Pharmaceutical manufacturing is reliant upon bioprocessing approaches to generate the range of therapeutic products that are available today. The high cost of production, susceptibility to process failure, and requirement to achieve consistent, high-quality product means that process monitoring is paramount during manufacturing. Process analytic technologies (PAT) are key to ensuring high quality product is produced at all stages of development. Spectroscopy-based technologies are well suited as PAT approaches as they are non-destructive and require minimum sample preparation. This study explored the use of a novel attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy platform, which utilises disposable internal reflection elements (IREs), as a method of upstream bioprocess monitoring. The platform was used to characterise organism health and to quantify cellular metabolites in growth media using quantification models to predict glucose and lactic acid levels both singularly and combined. Separation of the healthy and nutrient deficient cells within PC space was clearly apparent, indicating this technique could be used to characterise these classes. For the metabolite quantification, the binary models yielded R 2 values of 0.969 for glucose, 0.976 for lactic acid. When quantifying the metabolites in tandem using a multi-output partial least squares model, the corresponding R 2 value was 0.980. This initial study highlights the suitability of the platform for bioprocess monitoring and paves the way for future in-line developments.

Challenges in the Development of Soft Sensors for Bioprocesses: A Critical Review

Among the greatest challenges in soft sensor development for bioprocesses are variable process lengths, multiple process phases, and erroneous model inputs due to sensor faults. This review article describes these three challenges and critically discusses the corresponding solution approaches from a data scientist’s perspective. This main part of the article is preceded by an overview of the status quo in the development and application of soft sensors. The scope of this article is mainly the upstream part of bioprocesses, although the solution approaches are in most cases also applicable to the downstream part. Variable process lengths are accounted for by data synchronization techniques such as indicator variables, curve registration, and dynamic time warping. Multiple process phases are partitioned by trajectory or correlation-based phase detection, enabling phase-adaptive modeling. Sensor faults are detected by symptom signals, pattern recognition, or by changing contributions of the corresponding sensor to a process model. According to the current state of the literature, tolerance to sensor faults remains the greatest challenge in soft sensor development, especially in the presence of variable process lengths and multiple process phases.

Determination of Chinese hamster ovary (CHO) cell densities and antibody titers from small volumes of cell culture supernatants using multivariate analysis and partial least squares regression of UV-Vis spectra

Antibody titer and viable cell density (VCD) are two important parameters that need to be closely monitored during the process of cell line development and manufacturing of therapeutic antibodies. Typically, determination of each parameter requires 10–100 μL of supernatant sample, which is not suitable for small scale cultivation. In this study, we demonstrated that as low as 2 μL of culture supernatants were sufficient for the analysis using UV-Vis spectrum assisted with partial least squares (PLS) model. The results indicated that the optimal PLS models could be used to predict antibody titer and VCD with the linear relationship between reference values and predicted values at R² values ranging from 0.8 to > 0.9 in supernatant samples obtained from four different single clones and in polyclones that were cultured in various selection stringencies. Then, the percentage of cell viability and productivity were predicted from a set of samples of polyclones. The results indicated that while all predicted % cell viability were very similar to the actual value at RSEP value of 6.7 and R² of 0.8908, the predicted productivity from 14 of 18 samples were closed to the reference measurements at RSEP value of 22.4 and R² of 0.8522. These results indicated that UV-Vis combined with PLS has potential to be used for monitoring antibody titer, VCD, and % cell viability for both online and off-line therapeutic production process.

Longitudinal monitoring of cell metabolism in biopharmaceutical production using label-free fluorescence lifetime imaging microscopy

Chinese hamster ovary (CHO) cells are routinely used in the biopharmaceutical industry for production of therapeutic monoclonal antibodies (mAbs). Although multiple offline and time-consuming measurements of spent media composition and cell viability assays are used to monitor the status of culture in biopharmaceutical manufacturing, the day-to-day changes in the cellular microenvironment need further in-depth characterization. In this study, two-photon fluorescence lifetime imaging microscopy (2P-FLIM) was used as a tool to directly probe into the health of CHO cells from a bioreactor, exploiting the autofluorescence of intracellular nicotinamide adenine dinucleotide phosphate (NAD(P)H), an enzymatic cofactor that determines the redox state of the cells. A custom-built multimodal microscope with two-photon FLIM capability was utilized to monitor changes in NAD(P)H fluorescence for longitudinal characterization of a changing environment during cell culture processes. Three different cell lines were cultured in 0.5 L shake flasks and 3 L bioreactors. The resulting FLIM data revealed differences in the fluorescence lifetime parameters, which were an indicator of alterations in metabolic activity. In addition, a simple principal component analysis (PCA) of these optical parameters was able to identify differences in metabolic progression of two cell lines cultured in bioreactors. Improved understanding of cell health during antibody production processes can result in better streamlining of process development, thereby improving product titer and verification of scale-up. To our knowledge, this is the first study to use FLIM as a label-free measure of cellular metabolism in a biopharmaceutically relevant and clinically important CHO cell line.

ATR-FTIR spectroscopy and spectroscopic imaging to investigate the behaviour of proteins subjected to freeze-thaw cycles in droplets, wells, and under flow

Biopharmaceuticals are used to treat a range of diseases from arthritis to cancer, however, since the advent of these highly specific, effective drugs, there have been challenges involved in their production. The most common biopharmaceuticals, monoclonal antibodies (mAbs), are vulnerable to aggregation and precipitation during processing. Freeze thaw cycles (FTCs), which can be required for storage and transportation, can lead to a substantial loss of product, and contributes to the high cost of antibody production. It is therefore necessary to monitor aggregation levels at susceptible points in the production pathway, such as during purification and transportation, thus contributing to a fuller understanding of mAb aggregation and providing a basis for rational optimisation of the production process. This paper uses attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy and spectroscopic imaging to investigate the effect of these potentially detrimental FTCs on protein secondary structure in both static wells and under flowing conditions, using lysozyme as a model protein. The results revealed that the amount of protein close to the surface of the ATR crystal, and hence level of aggregates, increased with increasing FTCs. This was observed both within wells and under flow conditions, using conventional ATR-FTIR spectroscopy and ATR-FTIR spectroscopic imaging. Interestingly, we also observed changes in the Amide I band shape indicating an increase in β-sheet contribution, and therefore an increase in aggregates, with increasing number of FTCs. These results show for the first time how ATR-FTIR spectroscopy can be successfully applied to study the effect of FTC cycles on protein samples. This could have numerous broader applications, such as in biopharmaceutical production and rapid diagnostic testing.

ATR-FTIR spectroscopy and spectroscopic imaging for the analysis of biopharmaceuticals

Attenuated Total Reflection Fourier Transform Infrared (ATR-FTIR) spectroscopy is a label-free, non-destructive technique that can be applied to a vast range of biological applications, from imaging cancer tissues and live cells, to determining protein content and protein secondary structure composition. This review summarises the recent advances in applications of ATR-FTIR spectroscopy to biopharmaceuticals, the application of this technique to biosimilars, and the current uses of FTIR spectroscopy in biopharmaceutical production. We discuss the use of ATR-FTIR spectroscopic imaging to investigate biopharmaceuticals, and finally, give an outlook on the possible future developments and applications of ATR-FTIR spectroscopy and spectroscopic imaging to this field. Throughout the review comparisons will be made between FTIR spectroscopy and alternative analytical techniques, and areas will be identified where FTIR spectroscopy could perhaps offer a better alternative in future studies. This review focuses on the most recent advances in the field of using ATR-FTIR spectroscopy and spectroscopic imaging to characterise and evaluate biopharmaceuticals, both in industrial and academic research based environments.

FTIR spectroscopy as a novel analytical approach for investigation of glucose transport and glucose transport inhibition studies in transwell in vitro barrier models

Glucose transport is key for cellular metabolism as well as physiological function and is maintained via passive facilitated and active sodium-glucose linked transport routes. Here, we present for the first time Fourier-transform infrared spectroscopy as a novel approach for quantification of apical-to-basolateral glucose transport of in vitro cell barrier models using liver, lung, intestinal and placental cancer cell lines. Results of our comparative study revealed that distinct differences could be observed upon subjection to transport inhibitors.

Monitoring yeast fermentations by nonlinear infrared technology and chemometrics-understanding process correlations and indirect predictions

Fermentation processes are still compromised by a lack of monitoring strategies providing integrated process data online, ensuring process understanding, control, and thus, optimal reactor efficiency. The crucial demand for online monitoring strategies, not only encouraged by the PAT initiative but also motivated by modern paradigms such as circular economy and sustainability, has driven research and industry to provide "next-generation process technology": in other words, technology tailored toward industrial needs. Mid-infrared (MIR) spectroscopy as such is superior to near-infrared (NIR) spectroscopy since it provides significantly enhanced selectivity. However, due to high costs and a lack of instrumental robustness, MIR spectroscopy is outcompeted by NIR when it comes to industrial application. The lack of chemometric expertise, model understanding, and practical guidance might add to the slow acceptance of industrial MIR application. This work demonstrates the use of novel MIR, so-called non-linear infrared (NLIR) technology and the importance of model understanding, exemplarily investigated on a lab-scale yeast fermentation process. The six analytes glucose, ethanol, glycerol, acetate, ammonium, and phosphate were modeled by partial least squares (PLS) based on spectral data, demonstrating the potential of the novel technology facilitating online data acquisition and the necessity of investigating indirect predictions. KEY POINTS: • NLIR spectra were acquired online during a yeast fermentation process • PLS models were constructed for six components based on uncorrelated samples • Glucose, ethanol, ammonium, and phosphates were modeled with errors of less than 15% • Acetate and glycerol were shown to rely on indirect predictions.

Insight into Heterogeneous Distribution of Protein Aggregates at the Surface Layer Using Attenuated Total Reflection-Fourier Transform Infrared Spectroscopic Imaging

Monoclonal antibodies (mAbs) have been used as therapeutics for the last few decades. It is necessary to investigate the stability of these mAbs under stress conditions and to elucidate aggregation mechanisms as a means of developing approaches which minimize the problem. Attenuated total reflection (ATR)-FTIR spectroscopic imaging allows probing of a sample at a depth of penetration of around 0.5-5 μm, which makes it suitable for the study of aggregated proteins when accumulated as a layer close to the surface of the ZnSe internal reflection element (IRE). Here, macro ATR-FTIR spectroscopic imaging, along with a variable angle of incidence accessory, have been used to differentiate between the secondary structure of proteins in bulk solution and those that have precipitated onto or near the ZnSe IRE surface. IgG spectra obtained from protein samples in individual wells have been averaged, extracted, and preprocessed, and the Amide I bands of the protein samples were compared and further analyzed to reveal protein distribution at the ZnSe IRE surface. These findings show depth profiling of IgG aggregates at the ZnSe IRE surface (0.5-5 μm) and do not follow a trend of decreasing protein presence with an increasing angle of incidence or increasing depth of penetration, suggesting an irregular distribution of aggregates in the z-direction.

Fiberoptic-Coupled Spectrofluorometer with Array Detection as a Process Analytical Chemistry Tool for Continuous Flow Monitoring of Fluoroquinolone Antibiotics

Nowadays, there is an increasing need for sensitive real-time measurements of various analytes and monitoring of industrial products and environmental processes. Herein, we describe a fluorescence spectrometer in continuous flow mode in which the sample is fed to the flow cell using a peristaltic pump. The excitation beam is introduced to the sample chamber by an optical fiber. The fluorescence emitted upon excitation is collected at the right angle using another optical fiber and then transmitted to the fluorescence spectrometer which utilizes an array detector. The array detection, as a key factor in process analytical chemistry, made the fluorescence spectrometer suited for multiwavelength detection of the fluorescence spectrum of the analytes. After optimization of the experimental parameters, the system has been successfully employed for sensitive determination of four fluoroquinolone antibiotics such as ciprofloxacin, ofloxacin, levofloxacin, and moxifloxacin. The linear dynamic ranges of four fluoroquinolones were between 0.25 and 20 μg·mL-1, and the detection limit of the method for ciprofloxacin, ofloxacin, levofloxacin, and moxifloxacin were 81, 36, 35, and 93 ng·mL-1, respectively. Finally, the proposed system is carried out for determination of fluoroquinolones in some pharmaceutical formulations.

Process System Engineering Methodologies Applied to Tissue Development and Regenerative Medicine

Tissue engineering and the manufacturing of regenerative medicine products demand strict control over the production process and product quality monitoring. In this chapter, the application of process systems engineering (PSE) approaches in the production of cell-based products has been discussed. Mechanistic, empirical, continuum and discrete models are compared and their use in describing cellular phenomena is reviewed. In addition, model-based optimization strategies employed in the field of tissue engineering and regenerative medicine are discussed. An introduction to process control theory is given and the main applications of classical and advanced methods in cellular production processes are described. Finally, new nondestructive and noninvasive monitoring techniques have been reviewed, focusing on large-scale manufacturing systems for cell-based constructs and therapeutic products. The application of the PSE methodologies presented here offers a promising alternative to overcome the main challenges in manufacturing engineered tissue and regeneration products.

Use of near-infrared spectroscopy (NIRs) in the biopharmaceutical industry for real-time determination of critical process parameters and integration of advanced feedback control strategies using MIDUS control

Control of biopharmaceutical processes is critical to achieve consistent product quality. The most challenging unit operation to control is cell growth in bioreactors due to the exquisitely sensitive and complex nature of the cells that are converting raw materials into new cells and products. Current monitoring capabilities are increasing, however, the main challenge is now becoming the ability to use the data generated in an effective manner. There are a number of contributors to this challenge including integration of different monitoring systems as well as the functionality to perform data analytics in real-time to generate process knowledge and understanding. In addition, there is a lack of ability to easily generate strategies and close the loop to feedback into the process for advanced process control (APC). The current research aims to demonstrate the use of advanced monitoring tools along with data analytics to generate process understanding in an Escherichia coli fermentation process. NIR spectroscopy was used to measure glucose and critical amino acids in real-time to help in determining the root cause of failures associated with different lots of yeast extract. First, scale-down of the process was required to execute a simple design of experiment, followed by scale-up to build NIR models as well as soft sensors for advanced process control. In addition, the research demonstrates the potential for a novel platform technology that enables manufacturers to consistently achieve "goldenbatch" performance through monitoring, integration, data analytics, understanding, strategy design and control (MIDUS control). MIDUS control was employed to increase batch-to-batch consistency in final product titers, decrease the coefficient of variability from 8.49 to 1.16%, predict possible exhaust filter failures and close the loop to prevent their occurrence and avoid lost batches.

Advancing pharmaceutical quality: An overview of science and research in the U.S. FDA's Office of Pharmaceutical Quality

Failures surrounding pharmaceutical quality, particularly with respect to product manufacturing issues and facility remediation, account for the majority of drug shortages and product recalls in the United States. Major scientific advancements pressure established regulatory paradigms, especially in the areas of biosimilars, precision medicine, combination products, emerging manufacturing technologies, and the use of real-world data. Pharmaceutical manufacturing is increasingly globalized, prompting the need for more efficient surveillance systems for monitoring product quality. Furthermore, increasing scrutiny and accelerated approval pathways provide a driving force to be even more efficient with limited regulatory resources. To address these regulatory challenges, the Office of Pharmaceutical Quality (OPQ) in the Center for Drug Evaluation and Research (CDER) at the U.S. Food and Drug Administration (FDA) harbors a rigorous science and research program in core areas that support drug quality review, inspection, surveillance, standards, and policy development. Science and research is the foundation of risk-based quality assessment of new drugs, generic drugs, over-the-counter drugs, and biotechnology products including biosimilars. This is an overview of the science and research activities in OPQ that support the mission of ensuring that safe, effective, and high-quality drugs are available to the American public.