The role of Raman spectroscopy in biopharmaceuticals from development to manufacturing

Monitoring cellular glycolysis pathway kinetics in the extracellular medium using label-free, Raman spectroscopy

This study explored the potential of Raman spectroscopy to holistically monitor the glycolysis pathway kinetics as a function of time through the extracellular medium. Initially, the collinearity of individual metabolites of interest- glucose and lactic acid as a function of their concentration was tested followed by the sensitivity analysis of the approach by elucidating the limits of detection (0.85 mM and 2.8 mM) and quantification (2.5 mM and 9.5 mM) for glucose and lactic acid respectively in the biological range. In the process several datamining approaches were also explored. Finally, the A549 cell culture was used for kinetic spectral acquisition of the extracellular medium mimicking the kinetic glycolysis assay as a function of time under different pathway modulations. The spectra were resolved and fitted with a kinetically constrained-model (A → B → C) using the multivariate curve resolution- alternating least squares tool for all the modulated conditions to elucidate the pathway kinetics and the rate of change. The rate of change of the resolved components for the stimulated condition (k1: 0.005 min-1, k2: 0.011 min-1) was approximately twice as that of the control (k1: 0,045 min-1; k2: 0.049 min-1) while the inhibited condition (k1: 0.025 min-1, k2: 0.017 min-1) was substantially slower. The technique is superior to the targeted current gold standard kinetic assay approach, in that it is holistic in nature and has potential applications in drug discovery, bioprocessing, disease diagnostics, etc. Furthermore, this approach overcomes the limitations of the omics/multiomics approaches, limited to a snapshot of cellular metabolism. This study serves as a guideline for future, more complex subcellular kinetic spectroscopy experiments.

Digital Butterworth filter as preprocessing method for implementing Raman spectroscopy as an analytical method in downstream processing of biopharmaceuticals

For implementing Raman spectroscopy as an analytical method in downstream processing, extracting molecular information related to biopharmaceuticals is still challenging due to spectral variations caused by spectrometer, setup and fluorescence. This study explores the potential of the Butterworth filter as a preprocessing method for baseline correction and noise reduction in Raman spectra. We first investigate the Butterworth highpass filter's working principle and its optimization by introducing disturbances to spectral baselines and assessing the cutoff frequency ωc's effect on minimizing baseline variations and enhancing the linear correlation (r2) between Raman signals and protein concentrations. The optimal ωc range (0.004 to 0.008 cm) yields an r2≥0.85, outperforming the Savitzky-Golay derivative filter's 0.68. Further, we explore a Butterworth bandpass filter, adjusting low and high cutoff frequencies, showing an 11.6-15 % improvement in r2 over the highpass design. Our results suggest the necessity of specific cutoff frequency selection when applying the bandpass design to the Raman spectra of individual protein molecules and the method for this selection is discussed. By applying the optimization outputs, we developed chemometric models linking Critical Quality Attributes to the Raman data preprocessed by the Butterworth bandpass filter, covering concentrations up to 25.6 mg/mL for a biopharmaceutical immunoglobulin G (IgG) antibody and 4.2 mg/mL for Transferrin. When validated in Cation Exchange Chromatography runs with gradient lengths of 5 and 10 column volume for in-line predictions, the models show high predictability, achieving a coefficient of determination R2 of 0.99 for IgG and 0.95 for Transferrin.

Cancer Cell Line Classification Using Raman Spectroscopy of Cancer-Derived Exosomes and Machine Learning

Liquid biopsies are an emerging, noninvasive tool for cancer diagnostics, utilizing biological fluids for molecular profiling. Nevertheless, the current methods often lack the sensitivity and specificity necessary for early detection and real-time monitoring. This work explores an advanced approach to improving liquid biopsy techniques through machine learning analysis of the Raman spectra measured to classify distinct exosome solutions by their cancer origin. This was accomplished by conducting principal component analysis (PCA) of the Raman spectra of exosomes from three cancer cell lines (COLO205, A375, and LNCaP) to extract chemically significant features. This reduced set of features was then utilized to train a linear discriminant analysis (LDA) classifier to predict the source of the exosomes. Furthermore, we investigated differences in the lipid composition in these exosomes by their spectra. This spectral similarity analysis revealed differences in lipid profiles between the different cancer cell lines as well as identified the predominant lipids across all exosomes. Our PCA-LDA framework achieved 93.3% overall accuracy and F1 scores of 98.2%, 91.1%, and 91.0% for COLO205, A375, and LNCaP, respectively. Our results from spectral similarity analysis were also shown to support previous findings of lipid dynamics due to cancer pathology and pertaining to exosome function and structure. These findings underscore the benefits of enhancing Raman spectroscopy analysis with machine learning, laying the groundwork for the development of early noninvasive cancer diagnostics and personalized treatment strategies. This work potentially establishes the foundation for refining the classification model and optimizing exosome extraction and detection from clinical samples for clinical translation.

Single compound data supplementation to enhance transferability of fermentation specific Raman spectroscopy models

Raman spectroscopy is a valuable analytical tool for real-time analyte quantification in fermentation processes. Quantification is performed with chemometric models that translate Raman spectra into concentration values, which are typically calibrated with process data from multiple comparable fermentations. However, process-specific models underperform for minor process variation(s) or different operation modes due to the integration of cross-correlations, resulting in low target analyte specificity. Thus, model transferability is poor and labor-intensive (re-)calibration of models is required for related processes. In this work, partial least-squares models for glucose, ethanol, and biomass were calibrated with Saccharomyces cerevisiae batch fermentation data and subsequently transferred to a fed-batch operation. To enhance model transferability without additional process runs, single compound data supplementation was performed. The supplemented models increased overall target analyte specificity and demonstrated sufficient prediction accuracy for the fed-batch process (root-mean-square errors of prediction (RMSEP) of 3.06 mM, 8.65 mM, and 0.99 g/L for glucose, ethanol, and biomass), while maintaining high prediction accuracy for the batch process (RMSEP of 1.71 mM, 4.20 mM, and 0.17 g/L for glucose, ethanol, and biomass). This work showcases that process data in combination with single compound spectra is a fast and efficient strategy to apply Raman spectroscopy for real-time process monitoring across related processes.

To Acquire or Not to Acquire: Evaluating Compressive Sensing for Raman Spectroscopy in Biology

Raman spectroscopy has revolutionized the field of chemical biology by providing detailed chemical and compositional information with minimal sample preparation. Despite its advantages, the technique suffers from low throughput due to the weak Raman effect, necessitating long acquisition times and expensive equipment. This limitation is particularly acute in time-sensitive applications like bioprocess monitoring and dynamic studies. Compressive sensing offers a promising solution by reducing the burden on measurement hardware, lowering costs, and decreasing measurement times. It allows for the collection of sparse data, which can be computationally reconstructed later. This paper explores the practical application of compressive sensing in spontaneous Raman spectroscopy across various biological samples. We demonstrate its benefits in scenarios requiring portable hardware, rapid acquisition, and minimal storage, such as skin hydration prediction and cellular studies involving drug molecules. Our findings highlight the potential of compressive sensing to overcome traditional limitations of Raman spectroscopy, paving the way for broader adoption in biological research and clinical diagnostics.

Digital holographic microscopy is suitable for lipid accumulation analysis in single cells of Yarrowia lipolytica

Digital holographic microscopy (DHM) is a label-free analytical technique for the determination of the cells' volume and their cytosolic refractive index. Here, we demonstrate the suitability of DHM for the quantification of total lipid accumulation in the oleaginous yeast Yarrowia lipolytica. Presently, microbial lipids are gaining increasing attention due to their nutritional value in feed and food applications. Their microbiological synthesis in algae and yeast is subject to optimization studies, which necessitates rapid quantification of total lipids for faster progress and the possibility of process control. So far, quantification of the total intracellular long-chain fatty acid concentration in yeast cells is time-consuming though when common chromatography for a volumetric analysis or staining and flow cytometry for a single-cell based analysis are used. This study, however, demonstrates that 3D-DHM facilitates a quasi-real-time measurement that allows for a rapid quantification of total intracellular lipid accumulation on a single-cell level without cell staining. Data from wild-type and lipid overproducing Y. lipolytica strains with specific yields of long-chain fatty acids in a range between 70 and 360 mg/gCDW show a good correlation with the optical volume determined by DHM, as the total lipid accumulation in the cell is typically well correlated with the long-chain fatty acid concentration. The results further correlate with data obtained from gas chromatography and flow cytometry of Nile Red-stained cells, which proves the reliability of DHM for lipid quantification in Y. lipolytica.

Inline Raman spectroscopy as process analytical technology for SARS-CoV-2 VLP production

The present work focused on inline Raman spectroscopy monitoring of SARS-CoV-2 VLP production using two culture media by fitting chemometric models for biochemical parameters (viable cell density, cell viability, glucose, lactate, glutamine, glutamate, ammonium, and viral titer). For that purpose, linear, partial least square (PLS), and nonlinear approaches, artificial neural network (ANN), were used as correlation techniques to build the models for each variable. ANN approach resulted in better fitting for most parameters, except for viable cell density and glucose, whose PLS presented more suitable models. Both were statistically similar for ammonium. The mean absolute error of the best models, within the quantified value range for viable cell density (375,000-1,287,500 cell/mL), cell viability (29.76-100.00%), glucose (8.700-10.500 g/), lactate (0.019-0.400 g/L), glutamine (0.925-1.520 g/L), glutamate (0.552-1.610 g/L), viral titer (no virus quantified-7.505 log10 PFU/mL) and ammonium (0.0074-0.0478 g/L) were, respectively, 41,533 ± 45,273 cell/mL (PLS), 1.63 ± 1.54% (ANN), 0.058 ± 0.065 g/L (PLS), 0.007 ± 0.007 g/L (ANN), 0.007 ± 0.006 g/L (ANN), 0.006 ± 0.006 g/L (ANN), 0.211 ± 0.221 log10 PFU/mL (ANN), and 0.0026 ± 0.0026 g/L (PLS) or 0.0027 ± 0.0034 g/L (ANN). The correlation accuracy, errors, and best models obtained are in accord with studies, both online and offline approaches while using the same insect cell/baculovirus expression system or different cell host. Besides, the biochemical tracking throughout bioreactor runs using the models showed suitable profiles, even using two different culture media.

Flow cell for high throughput Raman spectroscopy of non-transparent solutions

This work introduces a high-throughput setup for Raman analysis of various flowing fluids, both transparent and non-transparent. The setup employs a microfluidic cell, used with an external optical setup, to control the sample flow's position and dimensions via 3-dimensional hydrodynamic focusing. This approach, in contrast to the prevalent use of fused silica capillaries, reduces the risk of sample photodegradation and boosts measurement efficiency, enhancing overall system throughput. The microfluidic cell has been further evolved to laminate two distinct flows from different samples in parallel. Using line excitation, both samples can be simultaneously excited without moving parts, further increasing throughput. This setup also enables real-time monitoring of phenomena like mixing or potential reactions between the two fluids. This development could significantly advance the creation of highly sensitive, high-throughput sensors for fluid composition analysis.

Different modeling approaches for inline biochemical monitoring over the VLP-making upstream stages using Raman spectroscopy

This work aimed to set inline Raman spectroscopy models to monitor biochemically (viable cell density, cell viability, glucose, lactate, glutamine, glutamate, and ammonium) all upstream stages of a virus-like particle-making process. Linear (Partial least squares, PLS; Principal components regression, PCR) and nonlinear (Artificial neural networks, ANN; supported vector machine, SVM) modeling approaches were assessed. The nonlinear models, ANN and SVM, were the more suitable models with the lowest absolute errors. The mean absolute error of the best models within the assessed parameter ranges for viable cell density (0.01-8.83 × 106 cells/mL), cell viability (1.3-100.0 %), glucose (5.22-10.93 g/L), lactate (18.6-152.7 mg/L), glutamine (158-1761 mg/L), glutamate (807.6-2159.7 mg/L), and ammonium (62.8-117.8 mg/L) were 1.55 ± 1.37 × 106 cells/mL (ANN), 5.01 ± 4.93 % (ANN), 0.27 ± 0.22 g/L (SVM), 4.7 ± 2.6 mg/L (SVM), 51 ± 49 mg/L (ANN), 57 ± 39 mg/L (SVM) and 2.0 ± 1.8 mg/L (ANN), respectively. The errors achieved, and best-fitted models were like those for the same bioprocess using offline data and others, which utilized inline spectra for mammalian cell lines as a host.

A shifted ratio spectrum strategy for effective subtraction of fluorescence interference in Raman spectra

Raman spectroscopy is an important technique for analyzing the chemical composition of samples in many fields. A severe challenge often encountered in Raman measurements is the presence of a concurrent fluorescence background, especially in biological samples. In order to obtain accurate Raman spectra, the fluorescence background must be subtracted from the original Raman spectra. We proposed a shifted ratio spectrum method to subtract the strong fluorescence background from the original Raman spectrum. First, the original Raman spectrum is divided into multiple regions according to the spectral shape of the shifted ratio spectra, and then, Gaussian fitting is performed in each region. The fitting results are stitched together in order to obtain the complete fluorescence background. Finally, this fluorescence background is subtracted from the original spectrum to obtain a pure Raman spectrum. This method can accurately subtract the fluorescence background of Rhodamine 6G (R6G)/ethanol solution and serum. This highlights the great potential of this method for applications in both biological and non-biological samples.

Non-Invasive Characterization of Different Saccharomyces Suspensions with Ultrasound

In fermentation processes, changes in yeast cell count and substrate concentration are indicators of yeast performance. Therefore, monitoring the composition of the biological suspension, particularly the dispersed solid phase (i.e., yeast cells) and the continuous liquid phase (i.e., medium), is a prerequisite to ensure favorable process conditions. However, the available monitoring methods are often invasive or restricted by detection limits, sampling requirements, or susceptibility to masking effects from interfering signals. In contrast, ultrasound measurements are non-invasive and provide real-time data. In this study, the suitability to characterize the dispersed and the liquid phase of yeast suspensions with ultrasound was investigated. The ultrasound signals collected from three commercially available Saccharomyces yeast were evaluated and compared. For all three yeasts, the attenuation coefficient and speed of sound increased linearly with increasing yeast concentrations (0.0-1.0 wt%) and cell counts (R2 > 0.95). Further characterization of the dispersed phase revealed that cell diameter and volume density influence the attenuation of the ultrasound signal, whereas changes in the speed of sound were partially attributed to compositional variations in the liquid phase. This demonstrates the ability of ultrasound to monitor industrial fermentations and the feasibility of developing targeted control strategies.

Expediting online liquid chromatography for real-time monitoring of product attributes to advance process analytical technology in downstream processing of biopharmaceuticals

The application of Process Analytical Technology (PAT) principles for manufacturing of biotherapeutics proffers the prospect of ensuring consistent product quality along with increased productivity as well as substantial cost and time savings. Although this paradigm shift from a traditional, rather rigid manufacturing model to a more scientific, risk-based approach has been advocated by health authorities for almost two decades, the practical implementation of PAT in the biopharmaceutical industry is still limited by the lack of fit-for-purpose analytical methods. In this regard, most of the proposed spectroscopic techniques are sufficiently fast but exhibit deficiencies in terms of selectivity and sensitivity, while well-established offline methods, such as (ultra-)high-performance liquid chromatography, are generally considered as too slow for this task. To address these reservations, we introduce here a novel online Liquid Chromatography (LC) setup that was specifically designed to enable real-time monitoring of critical product quality attributes during time-sensitive purification operations in downstream processing. Using this online LC solution in combination with fast, purpose-built analytical methods, sampling cycle times between 1.30 and 2.35 min were achieved, without compromising on the ability to resolve and quantify the product variants of interest. The capabilities of our approach are ultimately assessed in three case studies, involving various biotherapeutic modalities, downstream processes and analytical chromatographic separation modes. Altogether, our results highlight the expansive opportunities of online LC based applications to serve as a PAT tool for biopharmaceutical manufacturing.

Bioactivity and Bioavailability of Carotenoids Applied in Human Health: Technological Advances and Innovation

This article presents a groundbreaking perspective on carotenoids, focusing on their innovative applications and transformative potential in human health and medicine. Research jointly delves deeper into the bioactivity and bioavailability of carotenoids, revealing therapeutic uses and technological advances that have the potential to revolutionize medical treatments. We explore pioneering therapeutic applications in which carotenoids are used to treat chronic diseases such as cancer, cardiovascular disease, and age-related macular degeneration, offering novel protective mechanisms and innovative therapeutic benefits. Our study also shows cutting-edge technological innovations in carotenoid extraction and bioavailability, including the development of supramolecular carriers and advanced nanotechnology, which dramatically improve the absorption and efficacy of these compounds. These technological advances not only ensure consistent quality but also tailor carotenoid therapies to each patient's health needs, paving the way for personalized medicine. By integrating the latest scientific discoveries and innovative techniques, this research provides a prospective perspective on the clinical applications of carotenoids, establishing a new benchmark for future studies in this field. Our findings underscore the importance of optimizing carotenoid extraction, administration, bioactivity, and bioavailability methods to develop more effective, targeted, and personalized treatments, thus offering visionary insight into their potential in modern medical practices.

Development of generic metabolic Raman calibration models using solution titration in aqueous phase and data augmentation for in-line cell culture analysis

This study presents a novel approach for developing generic metabolic Raman calibration models for in-line cell culture analysis using glucose and lactate stock solution titration in an aqueous phase and data augmentation techniques. First, a successful set-up of the titration method was achieved by adding glucose or lactate solution at several different constant rates into the aqueous phase of a bench-top bioreactor. Subsequently, the in-line glucose and lactate concentration were calculated and interpolated based on the rate of glucose and lactate addition, enabling data augmentation and enhancing the robustness of the metabolic calibration model. Nine different combinations of spectra pretreatment, wavenumber range selection, and number of latent variables were evaluated and optimized using aqueous titration data as training set and a historical cell culture data set as validation and prediction set. Finally, Raman spectroscopy data collected from 11 historical cell culture batches (spanning four culture modes and scales ranging from 3 to 200 L) were utilized to predict the corresponding glucose and lactate values. The results demonstrated a high prediction accuracy, with an average root mean square errors of prediction of 0.65 g/L for glucose, and 0.48 g/L for lactate. This innovative method establishes a generic metabolic calibration model, and its applicability can be extended to other metabolites, reducing the cost of deploying real-time cell culture monitoring using Raman spectroscopy in bioprocesses.

Bioprocess in-line monitoring and control using Raman spectroscopy and Indirect Hard Modeling (IHM)

Process in-line monitoring and control are crucial to optimize the productivity of bioprocesses. A frequently applied Process Analytical Technology (PAT) tool for bioprocess in-line monitoring is Raman spectroscopy. However, evaluating bioprocess Raman spectra is complex and calibrating state-of-the-art statistical evaluation models is effortful. To overcome this challenge, we developed an Indirect Hard Modeling (IHM) prediction model in a previous study. The combination of Raman spectroscopy and the IHM prediction model enables non-invasive in-line monitoring of glucose and ethanol mass fractions during yeast fermentations with significantly less calibration effort than comparable approaches based on statistical models. In this study, we advance this IHM-based approach and successfully demonstrate that the combination of Raman spectroscopy and IHM is capable of not only bioprocess monitoring but also bioprocess control. For this purpose, we used this combination's in-line information as input of a simple on-off glucose controller to control the glucose mass fraction in Saccharomyces cerevisiae fermentations. When we performed two of these fermentations with different predefined glucose set points, we achieved similar process control quality as approaches using statistical models, despite considerably smaller calibration effort. Therefore, this study reaffirms that the combination of Raman spectroscopy and IHM is a powerful PAT tool for bioprocesses.

Raman and Surface-Enhanced Raman Scattering Detection in Flowing Solutions for Complex Mixture Analysis

Raman scattering provides a chemical-specific and label-free method for identifying and quantifying molecules in flowing solutions. This review provides a comprehensive examination of the application of Raman spectroscopy and surface-enhanced Raman scattering (SERS) to flowing liquid samples. We summarize developments in online and at-line detection using Raman and SERS analysis, including the design of microfluidic devices, the development of unique SERS substrates, novel sampling interfaces, and coupling these approaches to fluid-based chemical separations (e.g., chromatography and electrophoresis). The article highlights the challenges and limitations associated with these techniques and provides examples of their applications in a variety of fields, including chemistry, biology, and environmental science. Overall, this review demonstrates the utility of Raman and SERS for analysis of complex mixtures and highlights the potential for further development and optimization of these techniques.

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.

Spectroscopic insights into multi-phase protein crystallization in complex lysate using Raman spectroscopy and a particle-free bypass

Protein crystallization as opposed to well-established chromatography processes has the benefits to reduce production costs while reaching a comparable high purity. However, monitoring crystallization processes remains a challenge as the produced crystals may interfere with analytical measurements. Especially for capturing proteins from complex feedstock containing various impurities, establishing reliable process analytical technology (PAT) to monitor protein crystallization processes can be complicated. In heterogeneous mixtures, important product characteristics can be found by multivariate analysis and chemometrics, thus contributing to the development of a thorough process understanding. In this project, an analytical set-up is established combining offline analytics, on-line ultraviolet visible light (UV/Vis) spectroscopy, and in-line Raman spectroscopy to monitor a stirred-batch crystallization process with multiple phases and species being present. As an example process, the enzyme Lactobacillus kefir alcohol dehydrogenase (LkADH) was crystallized from clarified Escherichia coli (E. coli) lysate on a 300 mL scale in five distinct experiments, with the experimental conditions changing in terms of the initial lysate solution preparation method and precipitant concentration. Since UV/Vis spectroscopy is sensitive to particles, a cross-flow filtration (cross-flow filtration)-based bypass enabled the on-line analysis of the liquid phase providing information on the lysate composition regarding the nucleic acid to protein ratio. A principal component analysis (PCA) of in situ Raman spectra supported the identification of spectra and wavenumber ranges associated with productspecific information and revealed that the experiments followed a comparable, spectral trend when crystals were present. Based on preprocessed Raman spectra, a partial least squares (PLS) regression model was optimized to monitor the target molecule concentration in real-time. The off-line sample analysis provided information on the crystal number and crystal geometry by automated image analysis as well as the concentration of LkADH and host cell proteins (HCPs) In spite of a complex lysate suspension containing scattering crystals and various impurities, it was possible to monitor the target molecule concentration in a heterogeneous, multi-phase process using spectroscopic methods. With the presented analytical set-up of off-line, particle-sensitive on-line, and in-line analyzers, a crystallization capture process can be characterized better in terms of the geometry, yield, and purity of the crystals.

Robust platform for inline Raman monitoring and control of perfusion cell culture

Perfusion cell culture has been gaining increasing popularity for biologics manufacturing due to benefits such as smaller footprint, increased productivity, consistent product quality and manufacturing flexibility, cost savings, and so forth. Process Analytics Technologies tools are highly desirable for effective monitoring and control of long-running perfusion processes. Raman has been widely investigated for monitoring and control of traditional fed batch cell culture process. However, implementation of Raman for perfusion cell culture has been very limited mainly due to challenges with high-cell density and long running times during perfusion which cause extremely high fluorescence interference to Raman spectra and consequently it is exceedingly difficult to develop robust chemometrics models. In this work, a platform based on Raman measurement of permeate has been proposed for effective analysis of perfusion process. It has been demonstrated that this platform can effectively circumvent the fluorescence interference issue while providing rich and timely information about perfusion dynamics to enable efficient process monitoring and robust bioreactor feed control. With the highly consistent spectral data from cell-free sample matrix, development of chemometrics models can be greatly facilitated. Based on this platform, Raman models have been developed for good measurement of several analytes including glucose, lactate, glutamine, glutamate, and permeate titer. Performance of Raman models developed this way has been systematically evaluated and the models have shown good robustness against changes in perfusion scale and variations in permeate flowrate; thus models developed from small lab scale can be directly transferred for implementation in much larger scale of perfusion. With demonstrated robustness, this platform provides a reliable approach for automated glucose feed control in perfusion bioreactors. Glucose model developed from small lab scale has been successfully implemented for automated continuous glucose feed control of perfusion cell culture at much larger scale.

Genetic algorithm-based semisupervised convolutional neural network for real-time monitoring of Escherichia coli fermentation of recombinant protein production using a Raman sensor

As a non-destructive sensing technique, Raman spectroscopy is often combined with regression models for real-time detection of key components in microbial cultivation processes. However, achieving accurate model predictions often requires a large amount of offline measurement data for training, which is both time-consuming and labor-intensive. In order to overcome the limitations of traditional models that rely on large datasets and complex spectral preprocessing, in addition to the difficulty of training models with limited samples, we have explored a genetic algorithm-based semi-supervised convolutional neural network (GA-SCNN). GA-SCNN integrates unsupervised process spectral labeling, feature extraction, regression prediction, and transfer learning. Using only an extremely small number of offline samples of the target protein, this framework can accurately predict protein concentration, which represents a significant challenge for other models. The effectiveness of the framework has been validated in a system of Escherichia coli expressing recombinant ProA5M protein. By utilizing the labeling technique of this framework, the available dataset for glucose, lactate, ammonium ions, and optical density at 600 nm (OD600) has been expanded from 52 samples to 1302 samples. Furthermore, by introducing a small component of offline detection data for recombinant proteins into the OD600 model through transfer learning, a model for target protein detection has been retrained, providing a new direction for the development of associated models. Comparative analysis with traditional algorithms demonstrates that the GA-SCNN framework exhibits good adaptability when there is no complex spectral preprocessing. Cross-validation results confirm the robustness and high accuracy of the framework, with the predicted values of the model highly consistent with the offline measurement results.

Simultaneous prediction of 16 quality attributes during protein A chromatography using machine learning based Raman spectroscopy models

Several key technologies for advancing biopharmaceutical manufacturing depend on the successful implementation of process analytical technologies that can monitor multiple product quality attributes in a continuous in-line setting. Raman spectroscopy is an emerging technology in the biopharma industry that promises to fit this strategic need, yet its application is not widespread due to limited success for predicting a meaningful number of quality attributes. In this study, we addressed this very problem by demonstrating new capabilities for preprocessing Raman spectra using a series of Butterworth filters. The resulting increase in the number of spectral features is paired with a machine learning algorithm and laboratory automation hardware to drive the automated collection and training of a calibration model that allows for the prediction of 16 different product quality attributes in an in-line mode. The demonstrated ability to generate these Raman-based models for in-process product quality monitoring is the breakthrough to increase process understanding by delivering product quality data in a continuous manner. The implementation of this multiattribute in-line technology will create new workflows within process development, characterization, validation, and control.

Accelerating attribute-focused process and product development through the development and deployment of autonomous process analytical technology platform system

Enabling real-time monitoring and control of the biomanufacturing processes through product quality insights continues to be an area of focus in the biopharmaceutical industry. The goal is to manufacture products with the desired quality attributes. To realize this rigorous attribute-focused Quality by Design approach, it is critical to support the development of processes that consistently deliver high-quality products and facilitate product commercialization. Time delays associated with offline analytical testing can limit the speed of process development. Thus, developing and deploying analytical technology is necessary to accelerate process development. In this study, we have developed the micro sequential injection process analyzer and the automatic assay preparation platform system. These innovations address the unmet need for an automatic, online, real-time sample acquisition and preparation platform system for in-process monitoring, control, and release of biopharmaceuticals. These systems can also be deployed in laboratory areas as an offline analytical system and on the manufacturing floor to enable rapid testing and release of products manufactured in a good manufacturing practice environment.

Recent developments in the use of nanocrystals to improve bioavailability of APIs

Nanocrystals refer to materials with at least one dimension smaller than 100 nm, composing of atoms arranged in single crystals or polycrystals. Nanocrystals have significant research value as they offer unique advantages over conventional pharmaceutical formulations, such as high bioavailability, enhanced targeting selectivity and controlled release ability and are therefore suitable for the delivery of a wide range of drugs such as insoluble drugs, antitumor drugs and genetic drugs with broad application prospects. In recent years, research on nanocrystals has been progressively refined and new products have been launched or entered the clinical phase of studies. However, issues such as safety and stability still stand that need to be addressed for further development of nanocrystal formulations, and significant gaps do exist in research in various fields in this pharmaceutical arena. This paper presents a systematic overview of the advanced development of nanocrystals, ranging from the preparation approaches of nanocrystals with which the bioavailability of poorly water-soluble drugs is improved, critical properties of nanocrystals and associated characterization techniques, the recent development of nanocrystals with different administration routes, the advantages and associated limitations of nanocrystal formulations, the mechanisms of physical instability, and the enhanced dissolution performance, to the future perspectives, with a final view to shed more light on the future development of nanocrystals as a means of optimizing the bioavailability of drug candidates. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

Development of automated metabolite control using mid-infrared probe for bioprocesses and vaccine manufacturing

Automation of metabolite control in fermenters is fundamental to develop vaccine manufacturing processes more quickly and robustly. We created an end-to-end process analytical technology and quality by design-focused process by replacing manual control of metabolites during the development of fed-batch bioprocesses with a system that is highly adaptable and automation-enabled. Mid-infrared spectroscopy with an attenuated total reflectance probe in-line, and simple linear regression using the Beer-Lambert Law, were developed to quantitate key metabolites (glucose and glutamate) from spectral data that measured complex media during fermentation. This data was digitally connected to a process information management system, to enable continuous control of feed pumps with proportional-integral-derivative controllers that maintained nutrient levels throughout fed-batch stirred-tank fermenter processes. Continuous metabolite data from mid-infrared spectra of cultures in stirred-tank reactors enabled feedback loops and control of the feed pumps in pharmaceutical development laboratories. This improved process control of nutrient levels by 20-fold and the drug substance yield by an order of magnitude. Furthermore, the method is adaptable to other systems and enables soft sensing, such as the consumption rate of metabolites. The ability to develop quantitative metabolite templates quickly and simply for changing bioprocesses was instrumental for project acceleration and heightened process control and automation.

ONE-SENTENCE SUMMARY

Intelligent digital control systems using continuous in-line metabolite data enabled end-to-end automation of fed-batch processes in stirred-tank reactors.

Validation of the cell culture monitoring using a Raman spectroscopy calibration model developed with artificially mixed samples and investigation of model learning methods using initial batch data

The development of calibration models using Raman spectra data has long been challenged owing to the substantial time and cost required for robust data acquisition. To reduce the number of experiments involving actual incubation, a calibration model development method was investigated by measuring artificially mixed samples. In this method, calibration datasets were prepared using spectra from artificially mixed samples with adjusted concentrations based on design of experiments. The precision of these calibration models was validated using the actual cell culture sample. The results showed that when the culture conditions were unchanged, the root mean square error of prediction (RMSEP) of glucose, lactate, and antibody concentrations was 0.34, 0.33, and 0.25 g/L, respectively. Even when variables such as cell line or culture media were changed, the RMSEPs of glucose, lactate, and antibody concentrations remained within acceptable limits, demonstrating the robustness of the calibration models with artificially mixed samples. To further improve accuracy, a model training method for small datasets was also investigated. The spectral pretreatment conditions were optimized using error heat maps based on the first batch of each cell culture condition and applied these settings to the second and third batches. The RMSEPs improved for glucose, lactate, and antibody concentration, with values of 0.44, 0.19, and 0.18 g/L under constant culture conditions, 0.37, 0.12, and 0.12 g/L for different cell lines, and 0.26, 0.40, and 0.12 g/L when the culture media was changed. These results indicated the efficacy of calibration modeling with artificially mixed samples for actual incubations under various conditions.

Soft sensor based on Raman spectroscopy for the in-line monitoring of metabolites and polymer quality in the biomanufacturing of polyhydroxyalkanoates

Polyhydroxyalkanoates (PHA) are among the most promising bio-based alternatives to conventional petroleum-based plastics. These biodegradable polyesters can in fact be produced by fermentation from bacteria like Cupriavidus necator, thus reducing the environmental footprint of the manufacturing process. However, ensuring consistent product quality attributes is a major challenge of biomanufacturing. To address this issue, the implementation of real-time monitoring tools is essential to increase process understanding, enable a prompt response to possible process deviations and realize on-line process optimization. In this work, a soft sensor based on in situ Raman spectroscopy was developed and applied to the in-line monitoring of PHA biomanufacturing. This strategy allows the collection of quantitative information directly from the culture broth, without the need for sampling, and at high frequency. In fact, through an optimized multivariate data analysis pipeline, this soft sensor allows monitoring cell dry weight, as well as carbon and nitrogen source concentrations with root mean squared errors (RMSE) equal to 3.71, 7 and 0.03 g/L, respectively. In addition, this tool allows the in-line monitoring of intracellular PHA accumulation, with an RMSE of 14 gPHA/gCells. For the first time, also the number and weight average molecular weights of the polymer produced could be monitored, with RMSE of 8.7E4 and 11.6E4 g/mol, respectively. Overall, this work demonstrates the potential of Raman spectroscopy in the in-line monitoring of biotechnology processes, leading to the simultaneous measurement of several process variables in real time without the need of sampling and labor-intensive sample preparations.

Impact of GAMP 5, data integrity and QbD on quality assurance in the pharmaceutical industry: How obvious is it?

In the pharmaceutical industry, it is essential to ensure the safety and efficacy of medicinal products. Therefore a robust quality assurance framework is needed. This manuscript examines the impact of GAMP 5 and data integrity (DI) on quality assurance, while also highlighting the role of quality by design (QbD) principles. GAMP 5 is a widely used framework for validating automated systems that establishes quality assurance practices. DI guarantees the reliability of data collected throughout various stages of drug development. The integration of QbD principles promotes a systematic approach to development that emphasizes a deep understanding of critical quality attributes, risk management, and continuous improvement. With their implementation, organizations are able to meet regulatory requirements and provide safe medications to patients worldwide.

Current and future technologies for monitoring cultured meat: A review

The high population growth rate, massive animal food consumption, fast economic progress, and limited food resources could lead to a food crisis in the future. There is a huge requirement for dietary proteins including cultured meat is being progressed to fulfill the need for meat-derived proteins in the diet. However, production of cultured meat requires monitoring numerous bioprocess parameters. This review presents a comprehensive overview of various widely adopted techniques (optical, spectroscopic, electrochemical, capacitive, FETs, resistive, microscopy, and ultrasound) for monitoring physical, chemical, and biological parameters that can improve the bioprocess control in cultured meat. The methods, operating principle, merits/demerits, and the main open challenges are reviewed with the aim to support the readers in advancing knowledge on novel sensing systems for cultured meat applications.

Automated calibration and in-line measurement of product quality during therapeutic monoclonal antibody purification using Raman spectroscopy

Current manufacturing and development processes for therapeutic monoclonal antibodies demand increasing volumes of analytical testing for both real-time process controls and high-throughput process development. The feasibility of using Raman spectroscopy as an in-line product quality measuring tool has been recently demonstrated and promises to relieve this analytical bottleneck. Here, we resolve time-consuming calibration process that requires fractionation and preparative experiments covering variations of product quality attributes (PQAs) by engineering an automation system capable of collecting Raman spectra on the order of hundreds of calibration points from two to three stock seed solutions differing in protein concentration and aggregate level using controlled mixing. We used this automated system to calibrate multi-PQA models that accurately measured product concentration and aggregation every 9.3 s using an in-line flow-cell. We demonstrate the application of a nonlinear calibration model for monitoring product quality in real-time during a biopharmaceutical purification process intended for clinical and commercial manufacturing. These results demonstrate potential feasibility to implement quality monitoring during GGMP manufacturing as well as to increase chemistry, manufacturing, and controls understanding during process development, ultimately leading to more robust and controlled manufacturing processes.

Development of Raman Calibration Model Without Culture Data for In-Line Analysis of Metabolites in Cell Culture Media

In this study, we developed a method to build Raman calibration models without culture data for cell culture monitoring. First, Raman spectra were collected and then analyzed for the signals of all the mentioned analytes: glucose, lactate, glutamine, glutamate, ammonia, antibody, viable cells, media, and feed agent. Using these spectral data, the specific peak positions and intensities for each factor were detected. Next, according to the design of the experiment method, samples were prepared by mixing the above-mentioned factors. Raman spectra of these samples were collected and were used to build calibration models. Several combinations of spectral pretreatments and wavenumber regions were compared to optimize the calibration model for cell culture monitoring without culture data. The accuracy of the developed calibration model was evaluated by performing actual cell culture and fitting the in-line measured spectra to the developed calibration model. As a result, the calibration model achieved sufficiently good accuracy for the three components, glucose, lactate, and antibody (root mean square errors of prediction, or RMSEP = 0.23, 0.29, and 0.20 g/L, respectively). This study has presented innovative results in developing a culture monitoring method without using culture data, while using a basic conventional method of investigating the Raman spectra of each component in the culture media and then utilizing a design of experiment approach.

Fast-Training Deep Learning Algorithm for Multiplex Quantification of Mammalian Bioproduction Metabolites via Contactless Short-Wave Infrared Hyperspectral Sensing

Within the biopharmaceutical sector, there exists the need for a contactless multiplex sensor, which can accurately detect metabolite levels in real time for precise feedback control of a bioreactor environment. Reported spectral sensors in the literature only work when fully submerged in the bioreactor and are subject to probe fouling due to a cell debris buildup. The use of a short-wave infrared (SWIR) hyperspectral (HS) cam era allows for efficient, fully contactless collection of large spectral datasets for metabolite quantification. Here, we report the development of an interpretable deep learning system, a convolution metabolite regression (CMR) approach that detects glucose and lactate concentrations using label-free contactless HS images of cell-free spent media samples from Chinese hamster ovary (CHO) cell growth flasks. Using a dataset of <500 HS images, these CMR algorithms achieved a competitive test root-mean-square error (RMSE) performance of glucose quantification within 27 mg/dL and lactate quantification within 20 mg/dL. Conventional Raman spectroscopy probes report a validation performance of 26 and 18 mg/dL for glucose and lactate, respectively. The CMR system trains within 10 epochs and uses a convolution encoder with a sparse bottleneck regression layer to pick the best-performing filters learned by CMR. Each of these filters is combined with existing interpretable models to produce a metabolite sensing system that automatically removes spurious predictions. Collectively, this work will advance the safe and efficient adoption of contactless deep learning sensing systems for fine control of a variety of bioreactor environments.

On-line Raman spectroscopy combined with multivariate curve resolution-alternating least squares (MCR-ALS) to investigate the synthesis mechanism of 3,5-diamino-1,2,4-triazole (DAT)

The precise and accurate synthesis mechanism of typical energetic materials (EMs) intermediate is extremely important for the optimization of synthesis technology of EMs. In this research, on-line Raman spectroscopy technique combined with multivariate curve resolution-alternating least squares(MCR-ALS) method was proposed and used to investigate the synthesis mechanism of EMs intermediate (3,5-diamino-1,2,4-triazole, DAT). Initially, on-line Raman spectroscopy was applied to collect the Raman spectral data of DAT synthesis process. Secondly, principal component analysis (PCA), coupled with singular value decomposition (SVD) were used to determine the number of component of the reaction system and the components was 5. Thirdly, MCR-ALS was used to extract the pure Raman spectra and concentration curves of each substance of DAT synthesis process. During the MCR-ALS operation, evolving factor analysis (EFA) was choose to acquire the initial concentration estimation for MCR-ALS. Several constraints were selected to apply to ALS optimization including non-negative, closure, equality and correlation constraint. And the correlation coefficient between the Raman spectra and the actual Raman spectra of the hydrazine hydrochloride, dicyandiamide and DAT was calculated, their correlation coefficient R² were 0.9522, 0.9446, 0.9908 respectively which showed a good data fit of MCR-ALS method. Finally, according to the results of MCR-ALS analysis, the structure of the synthetic intermediates was successfully deduced and the mechanism of DAT synthesis was proposed. Hence, a precise and comprehensive method for analyzing the DAT synthesis reaction mechanism is proposed, which is helpful to provide a new idea for the analysis of the synthesis reaction mechanism of energetic materials.

Sensors and Techniques for On-Line Determination of Cell Viability in Bioprocess Monitoring

In recent years, the bioprocessing industry has experienced significant growth and is increasingly emerging as an important economic sector. Here, efficient process management and constant control of cellular growth are essential. Good product quality and yield can only be guaranteed with high cell density and high viability. Whereas the on-line measurement of physical and chemical process parameters has been common practice for many years, the on-line determination of viability remains a challenge and few commercial on-line measurement methods have been developed to date for determining viability in industrial bioprocesses. Thus, numerous studies have recently been conducted to develop sensors for on-line viability estimation, especially in the field of optical spectroscopic sensors, which will be the focus of this review. Spectroscopic sensors are versatile, on-line and mostly non-invasive. Especially in combination with bioinformatic data analysis, they offer great potential for industrial application. Known as soft sensors, they usually enable simultaneous estimation of multiple biological variables besides viability to be obtained from the same set of measurement data. However, the majority of the presented sensors are still in the research stage, and only a few are already commercially available.

Analysis of Biologics Molecular Descriptors towards Predictive Modelling for Protein Drug Development Using Time-Gated Raman Spectroscopy

Pharmaceutical proteins, compared to small molecular weight drugs, are relatively fragile molecules, thus necessitating monitoring protein unfolding and aggregation during production and post-marketing. Currently, many analytical techniques take offline measurements, which cannot directly assess protein folding during production and unfolding during processing and storage. In addition, several orthogonal techniques are needed during production and market surveillance. In this study, we introduce the use of time-gated Raman spectroscopy to identify molecular descriptors of protein unfolding. Raman spectroscopy can measure the unfolding of proteins in-line and in real-time without labels. Using K-means clustering and PCA analysis, we could correlate local unfolding events with traditional analytical methods. This is the first step toward predictive modeling of unfolding events of proteins during production and storage.

Challenges and Opportunities of Implementing Data Fusion in Process Analytical Technology-A Review

The release of the FDA's guidance on Process Analytical Technology has motivated and supported the pharmaceutical industry to deliver consistent quality medicine by acquiring a deeper understanding of the product performance and process interplay. The technical opportunities to reach this high-level control have considerably evolved since 2004 due to the development of advanced analytical sensors and chemometric tools. However, their transfer to the highly regulated pharmaceutical sector has been limited. To this respect, data fusion strategies have been extensively applied in different sectors, such as food or chemical, to provide a more robust performance of the analytical platforms. This survey evaluates the challenges and opportunities of implementing data fusion within the PAT concept by identifying transfer opportunities from other sectors. Special attention is given to the data types available from pharmaceutical manufacturing and their compatibility with data fusion strategies. Furthermore, the integration into Pharma 4.0 is discussed.