Continuous downstream processing for high value biological products: A Review

Carboxylic Acid Concentration in Downstream Bioprocessing Using High-Pressure Reverse Osmosis

During the production of many bio-based chemicals from fermentation and enzymatic processes, product separations frequently represent the most expensive and energy-intensive unit operations in an integrated process, often due to the low concentrations of target bioproducts. In this study, we integrated high-pressure reverse osmosis (HPRO) to concentrate an exemplary fermentation product, butyric acid, prior to downstream extraction. Through both modeling and experimental measurements, we identified the major factors limiting the maximum achievable concentration factor (CF) of 4.0 for butyric acid concentration with an HPRO membrane compared to the 2.6-3.2 range for conventional reverse osmosis (RO) membranes. The resulting concentrated aqueous stream underwent liquid-liquid extraction with an organic solvent and distillation for butyric acid purification and solvent recycling. The integration of HPRO product concentration into an in situ product recovery (ISPR) process leads to >5-fold increase in the final butyric acid concentration in the organic phase, and a concomitant 76% reduction in organic solvent usage. These improvements lead to an estimated 53 and 46% reduction in ISPR butyric acid production cost and greenhouse gas (GHG) emissions, respectively, considerably exceeding the process performance when integrating conventional RO product concentration. Overall, the integration of an HPRO membrane for product concentration enables more economical and sustainable bioproduct recovery from dilute aqueous streams.

Implementation of machine learning tool for continued process verification of process chromatography unit operation

Recent advancements in technology, such as the emergence of artificial intelligence (AI) and machine learning (ML), have facilitated the progression of the biopharmaceutical industry toward the implementation of Industry 4.0. As per the guidelines set by the USFDA, process validation for biopharmaceutical production consists of three stages: process design, process qualification, and continuous process verification (CPV). This paper proposes a strategy for achieving CPV for a cation exchange chromatography unit operation, emphasizing the urgent need for such strategies in the biopharmaceutical industry. Statistical process control (SPC) charts were generated based on real-time measurement of the various critical process parameters (CPPs) measured via in-built sensors (pH, conductivity, UV, and delta column pressure) as well as of critical quality attributes (CQAs) like charge variant composition (Raman spectroscopy) and concentration (Near infrared spectroscopy). A Python-based program was created to read these SPC charts and respond to any deviation. The developed models for NIR coupled DNN PAT tool and Raman coupled DNN PAT tool exhibited satisfactory R2 values (> 0.90), highlighting the statistical significance of the proposed model. Further, the control strategy designed based on Raman spectroscopy for charge variant composition in CEX eluate has been demonstrated by intentional perturbations in the CEX load. The resulting CEX eluate output showed a consistent charge variant composition as that of control runs (acidic ∼20 ± 2 %, main ∼62 ± 2 % and basic ∼18 ± 2 %). It has been demonstrated how an appropriate selection of analyzers, soft sensors, and advanced data analytics can be used to execute CPV and enable the biopharmaceutical industry to implement Industry 4.0.

Computational fluid particle dynamics modeling of tangential flow filtration in perfusion cell culture

Membrane fouling is a common and complex challenge with cell culture perfusion process in biopharmaceutical manufacturing that can have detrimental effects on the process performance. In this study, we evaluated a method to calculate the hollow fiber membrane resistance at different time points for water and supernatant. In addition, the number of subvisible particles of < 200 nm. diameter suspended in the supernatant were quantified using a nano-flow cytometry method. A computational fluid dynamics (CFD) model was developed to evaluate the impact of feed flow rate and particle count on the transmembrane pressure (TMP). Then a steady-state discrete phase model was applied to incorporate particles into the model and simulate the particles deposition over the membrane wall. The results showed an increase in the number of particles and the membrane resistance along the time course of the perfusion process. The CFD model illustrated that more particle deposition was observed at lower feed stream flow rates. The fraction of deposited particle was reduced by > 50% when the feed flow rate was increased from 35 ml/min to 300 ml/min. Our findings suggest that the total number of subvisible particles has a significant impact on TMP and membrane resistance and, thus, could play a major role in the mechanism of membrane fouling. CFD modeling can be a useful tool to predict the behavior of a process in a specific membrane. CFD simulations could also be used to optimize process parameters to improve membrane cleanability, reduce particle deposition, and reduce the risk of membrane fouling.

Production and Bioseparation Applications of Polyhydroxyalkanoate Nano-Granules Functionalized with Streptavidin

Rapidly growing industrial biotechnology and bio-manufacturing require simple and cost-effective bioseparation tools. A novel strategy of bioseparation based on the streptavidin-decorated polyhydroxyalkanoate (PHA) nano-granules was developed in this study. By fusing to the N-terminus of PHA-associated phasin protein, the streptavidin was one-step immobilized on the surface of PHA nano-granules simultaneously with the accumulation of PHA in recombinant Escherichia coli. About 1.95 g/L of PHA nano-granules (54.51 wt% of cell dry weight) were produced after 48 h bacterial cultivation. The following qualitative and quantitative characterizations demonstrated that the streptavidin accounted for approximately 6.78% of the total weight of the purified PHA nano-granules and confirmed a considerable biotin affinity of 0.1 ng biotin/μg surface protein. As a proof of concept, the nano-granules were further functionalized with biotinylated oligo(dT) for mRNA isolation and about 1.26 μg of mRNA (occupied 2.59%) was purified from 48.45 μg of total RNA, achieving good integrity and high purity with few DNA and rRNA contaminations. Moreover, the nano-granules retained more than 80% of their initial mRNA recovery efficiency after ten cycles of repeated use. The PHA-SAP nano-granules were also functionalized with biotinylated magnetic beads, allowing magnetic recovery of the PHA nano-granules from cell lysates that still needs optimization. Our study provides a novel and expandable platform of PHA nano-granules that can be further functionalized with various biological groups for bioseparation applications. The functional PHA nano-granules have a great potential to serve as bioseparation resin for large-scale purification processes after suitable optimizations for "bench-to-factory" translation, contributing to scalable and sustainable bioprocessing.

Quality by design for mRNA platform purification based on continuous oligo-dT chromatography

Oligo-deoxythymidine (oligo-dT) ligand-based affinity chromatography is a robust method for purifying mRNA drug substances within the manufacturing process of mRNA-based products, including vaccines and therapeutics. However, the conventional batch mode of operation for oligo-dT chromatography has certain drawbacks that reduce the productivity of this process. Here, we report a new continuous oligo-dT chromatography process for the purification of in vitro transcribed mRNA, which reduces losses, improves the efficiency of oligo-dT resin use, and intensifies the chromatography process. Furthermore, the quality by design (QbD) framework was used to establish a design space for the newly developed method. The optimization of process parameters (PPs), including salt type, salt concentration, load flow rate and mRNA load concentration both in batch and the continuous mode, achieved a greater than 90% yield (mRNA recovery) along with greater than 95% mRNA integrity and greater than 99% purity. The productivity of continuous chromatography was estimated to be 5.75-fold higher, and the operating cost was estimated 15% lower, when compared with batch chromatography. Moreover, the QbD framework was further used to map the relationship between critical quality attributes and key performance indicators as a function of critical process parameters and critical material attributes.

Hydrophobic interaction chromatography in continuous flow-through mode for product-related variant removal

Product-related impurities are challenging to remove during monoclonal antibody (mAb) purification process due to molecular similarity. Frontal chromatography on hydrophobic interaction resins has demonstrated its capability to effectively remove such impurities. However, process improvements geared towards purity level comes as a trade-off with the yield loss. In this work, we present a hydrophobic interaction chromatography process using multicolumn continuous chromatography (MCC) concept and frontal analysis to remove a high prevalence product related impurity. This design uses a two-column continuous system where the two columns are directly connected during product chase step to capture product wash loss without any in-process adjustment. This polish MCC operation resulted in a 10 % increase in yield while maintaining 99 % purity, despite the presence of 20 % product-related impurities in the feed material. One challenge associated with polish MCC design is that the accumulation of the impurities renders a non-steady state recycling. To surmount this issue and ensure a robust process, a mechanistic model was developed and validated to predict multicomponent breakthrough. This model was capable to predict multiple cycle behavior and accounts for increased impurity concentration. Assisted by the model, the optimized operation parameters and conditions can be determined to account for variation in product load quality. The simulated results demonstrate an effective doubling of productivity compared to conventional batch chromatography.

Bacterial biofilm-mediated environmental remediation: Navigating strategies to attain Sustainable Development Goals

Bacterial biofilm is a structured bacterial community enclosed within a three-dimensional polymeric matrix, governed by complex signaling pathways, including two-component systems, quorum sensing, and c-di-GMP, which regulate its development and resistance in challenging environments. The genetic configurations within biofilm empower bacteria to exhibit significant pollutant remediation abilities, offering a promising strategy to tackle diverse ecological challenges and expedite progress toward Sustainable Development Goals (SDGs). Biofilm-based technologies offer advantages such as high treatment efficiency, cost-effectiveness, and sustainability compared to conventional methods. They significantly contribute to agricultural improvement, soil fertility, nutrient cycling, and carbon sequestration, thereby supporting SDG 1 (No poverty), SDG 2 (Zero hunger), SDG 13 (Climate action), and SDG 15 (Life on land). In addition, biofilm facilitates the degradation of organic-inorganic pollutants from contaminated environments, aligning with SDG 6 (Clean water and sanitation) and SDG 14 (Life below water). Bacterial biofilm also has potential applications in industrial innovation, aligning SDG 7 (Affordable and clean energy), SDG 8 (Decent work and economic growth), and SDG 9 (Industry, innovation, and infrastructure). Besides, bacterial biofilm prevents several diseases, aligning with SDG 3 (Good health and well-being). Thus, bacterial biofilm-mediated remediation provides advanced opportunities for addressing environmental issues and progressing toward achieving the SDGs. This review explores the potential of bacterial biofilms in addressing soil pollution, wastewater, air quality improvement, and biodiversity conservation, emphasizing their critical role in promoting sustainable development.

Integrated system for temperature-controlled fast protein liquid chromatography. IV. Continuous 'one-column' 'low-salt' hydrophobic interaction chromatography

Systematic development of a temperature-controlled isocratic process for one-column low-salt hydrophobic interaction chromatography (HIC) of proteins employing a travelling cooling zone reactor (TCZR) system, is described. Batch binding and confocal scanning microscopy were employed to define process conditions for temperature-reversible binding of bovine serum albumin (BSA) which were validated in pulse-response temperature switching HIC experiments, before transferring to TCZR-HIC. A thin-walled stainless-steel column mounted with a movable assembly of copper blocks and Peltier elements (travelling cooling zone, TCZ) was used for TCZR-HIC. In pulse-response TCZR-HIC, 12 TCZ movements along the column desorbed 86.3% of the applied BSA monomers in 95.3% purity depleted >6-fold in 2-4 mers and nearly 260-fold in higher molecular weight (HMW) species. For continuous TCZR-HIC, the TCZ was moved 49-58 times during uninterrupted loading of BSA feeds at 0.25, 0.5 or 1 mg·mL-1. Each TCZ movement generated a sharp symmetrical elution peak. In the best case, (condition 1: 0.25 mg·mL-1 BSA; >17 mg BSA applied per mL of bed) the height of TCZ elution peaks approached pseudo-steady midway through the loading phase with no rise in baseline UV280 signal between peaks. Peak composition remained constant averaging 94.4% monomer, 5.6% 2-4 mers and <0.05% HMW. Monomers were recovered in quantitative yield depleted >3.1 fold in 2-4 mers and 92-fold in HMW species cf. the feed (63.6% monomers, 21.8% 2-4 mers, 14.6% HMW). However, increasing the BSA concentration to 1 mg·mL-1 (condition 2) or employing a fouled HIC column with 0.5 mg·mL-1 BSA (condition 3) compromised monomer purification performance.

Integrated continuous downstream process of monoclonal antibody developed by converting the batch platform process based on the process characterization

A continuous downstream process of monoclonal antibody was developed based on the process characterization. Periodic-counter current chromatography (PCCC) with two protein A columns was used for the capture step. For low pH virus inactivation (VI), a batch reactor was employed, which can work as a surge (buffer) tank. Flow-through chromatography (FTC) with two connected columns of different separation modes (anion-mixed mode and cation exchange) was designed as a polish step. After 24 h PCCC run, the collected pool was processed for VI. After adjusting pH and electric conductivity, the solution was fed to the two connected FTC columns for 24 h. Virus filter was also connected to the exit of the connected-column. PCCC and FTC were run in parallel. Six runs of different feed rates (0.5-10 L/day) and feed concentrations (1-3.2 g/L) were performed with protein A columns of 1-5 mL and FTC columns of 3-10 mL. The largest run (feed rate 10 L/day, feed concentration 2 g/L) was carried out at a GMP facility with 15 mL protein A columns and 100 mL FTC columns. Good recovery and purity values were obtained for all runs. The process was found to be flexible and stable for feed fluctuations. Only three surge or pool tanks were needed in addition to the final product pool tank.

Continuous precipitation-filtration process for initial capture of a monoclonal antibody product using a four-stage countercurrent hollow fiber membrane washing step

The significant increase in product titers, coupled with the growing focus on continuous bioprocessing, has renewed interest in using precipitation as a low-cost alternative to Protein A chromatography for the primary capture of monoclonal antibody (mAb) products. In this work, a commercially relevant mAb was purified from clarified cell culture fluid using a tubular flow precipitation reactor with dewatering and washing provided by tangential flow microfiltration. The particle morphology was evaluated using an inline high-resolution optical probe, providing quantitative data on the particle size distribution throughout the precipitation process. Data were obtained in both a lab-built 2-stage countercurrent washing system and a commercial countercurrent contacting skid that provided 4 stages of continuous washing. The processes were operated continuously for 2 h with overall mAb yield of 92 ± 3% and DNA removal of nearly 3 logs in the 4-stage system. The high DNA clearance was achieved by selective redissolution of the mAb using a low pH acetate buffer. Host cell protein clearance was 0.59 ± 0.08 logs, comparable to that based on model predictions. The process mass intensity was slightly better than typical Protein A processes and could be significantly improved by preconcentration of the antibody feed material.

Status and future developments for downstream processing of biological products: Perspectives from the Recovery XIX yield roundtable discussions

Governments and biopharmaceutical organizations aggressively leveraged expeditious communication capabilities, decision models, and global strategies to make a COVID-19 vaccine happen within a period of 12 months. This was an unusual effort and cannot be transferred to normal times. However, this focus on a single vaccine has also led to other treatments and drug developments being sidelined. Society expects the pharmaceutical industry to provide an uninterrupted supply of medicines. However, it is often overlooked how complex the manufacture of these compounds is and what logistics are required, not to mention the time needed to develop new drugs. The overarching theme, therefore, is patient access and how we can help ensure access and extend it to low- and middle-income countries. Despite unceasing efforts to make medications available to all patient populations, this must never be done at the expense of patient safety. A major fraction of the costs in biopharmaceutical manufacturing are for drug discovery, process development, and clinical studies. Infrastructure costs are very difficult to quantify because they often depend on whether a greenfield facility or an existing, depreciated facility is used or adapted for a new product. To accelerate process development concepts of platform process and prior knowledge are increasingly leveraged. While more traditional protein therapeutics continue to dominate the field, we are also experiencing the exciting emergence and evolution of other therapeutic formats (bispecifics, tetravalent mAbs, antibody-drug conjugates, enzymes, peptides, etc.) that offer unique treatment options for patients. Protein modalities are still dominant, but new modalities are being developed that can be learned from including advanced therapeutics-like cell and gene therapies. The industry must develop a model-based strategy for process development and technologies such as continuous integrated biomanufacturing must be adopted. The overall conclusion is that the pandemic pace was unsustainable, focused on vaccine delivery at the expense of other modalities/disease targets, and had implications for professional and personal life (work-life balance). Routinely reducing development time from 10 years to 1 year is nearly impossible to achieve. Environmental aspects of sustainable downstream processing are also described.

Sustainable menaquinone-7 production through continuous fermentation in biofilm bioreactors

Menaquinone-7 (MK-7), a vital vitamin with numerous health benefits, is synthesized and secreted extracellularly by the formation of biofilm, dominantly in Bacillus strains. Our team developed an innovative biofilm reactor utilizing Bacillus subtilis natto cells to foster biofilm growth on plastic composite supports to produce MK-7. Continuous fermentation in biofilm reactors offers a promising strategy for achieving sustainable and efficient production of Menaquinone-7 (MK-7). Unlike conventional batch fermentation, continuous biofilm reactors maintain a steady state of operation, which reduces resource consumption and waste generation, contributing to sustainability. By optimizing fermentation conditions, MK-7 production was significantly enhanced in this study, demonstrating the potential for sustainable industrial-scale production. To determine the optimal operational parameters, various dilution rates were tested. These rates were selected based on their potential to enhance nutrient supply and biofilm stability, thereby improving MK-7 production. By carefully considering the fermentation conditions and systematically varying the dilution rates, MK-7 production was significantly enhanced during continuous fermentation. The MK-7 productivity was found to increase from 0.12 mg/L/h to 0.33 mg/L/h with a dilution rate increment from 0.007 to 0.042 h-1). This range was chosen to explore the impact of various nutrient supply rates on MK-7 production and to identify the optimal conditions for maximizing productivity. However, a further increase in the dilution rate to 0.084 h-1 led to reduced productivity at approximately 0.16 mg/L/h, likely due to insufficient retention time for effective biofilm formation. Consequently, a dilution rate of 0.042 h-1 exhibited the highest productivity of 0.33 mg/L/h, outperforming all investigated dilution rates and demonstrating the critical balance between nutrient supply and retention time in continuous fermentation. These findings validate the feasibility of operating continuous fermentation at a 0.084 h-1 dilution rate, corresponding to a 48 h retention time, to achieve the highest MK-7 productivity compared to conventional batch fermentation. The significant advancements achieved in enhancing Menaquinone-7 (MK-7) productivity through continuous fermentation at optimal dilution rates in the present work indicate promising prospects for even greater efficiency and sustainability in MK-7 production through future developments.

Therapeutic proteins: developments, progress, challenges, and future perspectives

Proteins are considered magic molecules due to their enormous applications in the health sector. Over the past few decades, therapeutic proteins have emerged as a promising treatment option for various diseases, particularly cancer, cardiovascular disease, diabetes, and others. The formulation of protein-based therapies is a major area of research, however, a few factors still hinder the large-scale production of these therapeutic products, such as stability, heterogenicity, immunogenicity, high cost of production, etc. This review provides comprehensive information on various sources and production of therapeutic proteins. The review also summarizes the challenges currently faced by scientists while developing protein-based therapeutics, along with possible solutions. It can be concluded that these proteins can be used in combination with small molecular drugs to give synergistic benefits in the future.

Co-current filtrate flow in TFF perfusion processes: Decoupling transmembrane pressure from crossflow to improve product sieving

Hollow fiber-based membrane filtration has emerged as the dominant technology for cell retention in perfusion processes yet significant challenges in alleviating filter fouling remain unsolved. In this work, the benefits of co-current filtrate flow applied to a tangential flow filtration (TFF) module to reduce or even completely remove Starling recirculation caused by the axial pressure drop within the module was studied by pressure characterization experiments and perfusion cell culture runs. Additionally, a novel concept to achieve alternating Starling flow within unidirectional TFF was investigated. Pressure profiles demonstrated that precise flow control can be achieved with both lab-scale and manufacturing-scale filters. TFF systems with co-current flow showed up to 40% higher product sieving compared to standard TFF. The decoupling of transmembrane pressure from crossflow velocity and filter characteristics in co-current TFF alleviates common challenges for hollow fiber-based systems such as limited crossflow rates and relatively short filter module lengths, both of which are currently used to avoid extensive pressure drop along the filtration module. Therefore, co-current filtrate flow in unidirectional TFF systems represents an interesting and scalable alternative to standard TFF or alternating TFF operation with additional possibilities to control Starling recirculation flow.

Improved adeno-associated virus empty and full capsid separation using weak partitioning multi-column AEX chromatography

Recombinant adeno-associated virus (rAAV) empty and full capsid separation has been a topic of interest in the rAAV gene therapy community for many years and the anion exchange chromatography (AEX) step has undergone various process optimizations to improve rAAV empty capsid separation, including AEX stationary phase, mobile phase, and process parameters. Here, we present a new AEX method that employs both weak partitioning chromatography (WPC) and multi-column chromatography (MCC) to achieve improved full rAAV percentage in the AEX pool. The WPC technology allows empty rAAV to be displaced by full rAAV during loading, while the MCC technology enables parallel column processing which further increases AEX step productivity. Our results show that, compared to baseline AEX batch chromatography, the AEX-WPC-MCC method demonstrated improvements in both AEX pool full rAAV percentage (∼ 20% increase) and rAAV genome recovery (∼ 20% increase). As a result, the productivity (full capsid generated per liter of AEX column per hour of processing time) of the AEX step increased by ∼34-fold from the baseline AEX batch run to the AEX-WPC-MCC run. It is foreseeable that this AEX-WPC-MCC method could find applications in large-scale rAAV manufacturing processes to improve AEX yield and reduce the cost of goods of rAAV manufacturing.

High-performance countercurrent membrane purification for host cell protein removal from monoclonal antibody products

The transition to continuous biomanufacturing has led to renewed interest in alternative approaches for downstream processing of monoclonal antibody (mAb) products. In this study, we examined the potential of using high-performance countercurrent membrane purification (HPCMP) for the removal of host cell proteins (HCPs) derived from Chinese Hamster Ovary cells in the purification of a mAb. Initial studies used several model proteins to identify appropriate operating conditions for the hollow fiber membrane modules. HPCMP was then used for mAb purification, with mAb yield >95% and more than 100-fold reduction in HCP. Stable operation was maintained for 48 h for feeds that were first prefiltered through the 3MTM Harvest RC chromatographic clarifier to remove DNA and other foulants. In addition, the Process Mass Intensity for HPCMP can be much less than that for alternative HCP separation processes. These results highlight the potential of using HPCMP as part of a fully continuous mAb production process.

Scaling up stem cell production: harnessing the potential of microfluidic devices

Stem cells are specialised cells characterised by their unique ability to both self-renew and transform into a wide array of specialised cell types. The widespread interest in stem cells for regenerative medicine and cultivated meat has led to a significant demand for these cells in both research and practical applications. Despite the growing need for stem cell manufacturing, the industry faces significant obstacles, including high costs for equipment and maintenance, complicated operation, and low product quality and yield. Microfluidic technology presents a promising solution to the abovementioned challenges. As an innovative approach for manipulating liquids and cells within microchannels, microfluidics offers a plethora of advantages at an industrial scale. These benefits encompass low setup costs, ease of operation and multiplexing, minimal energy consumption, and the added advantage of being labour-free. This review presents a thorough examination of the prominent microfluidic technologies employed in stem cell research and explores their promising applications in the burgeoning stem cell industry. It thoroughly examines how microfluidics can enhance cell harvesting from tissue samples, facilitate mixing and cryopreservation, streamline microcarrier production, and efficiently conduct cell separation, purification, washing, and final cell formulation post-culture.

Alleviation of the necessity for supernatant prefiltering in the protein a recovery of Monoclonal antibodies from Chinese hamster ovary cell cultures

Protein A (ProA) chromatography is a mainstay in the analytical and preparative scale isolation/purification of monoclonal antibodies (mAbs). One area of interest is continuous processing or continuous chromatography, where ProA chromatography is used in the large-scale purification of mAbs. However, filtration is required prior to all ProA isolations to remove large particulates in cell culture supernatant, consisting of a mixture of cell debris, host cell contaminants, media components, etc. Currently, in-line filters are used to remove particles in the supernatant, requiring replacement over time due to fouling; regardless of the scale. Here we demonstrate the ProA isolation of unfiltered Chinese hamster ovary (CHO) cell media using capillary-channel polymer (C-CP) fiber stationary phases modified with S. aureus Protein A (rSPA). The base polymer of the analytical scale C-CP columns costs ∼$5 per 30 cm column, and when modified with ProA, the base cost is ∼$25 per 30 cm column, a cost-effective option in comparison to analytical-scale commercial columns. To directly sample unfiltered media, a 5 cm gap was created at the head of the C-CP column, where the large particulates are trapped, while molecular solutes flow through the capillary channels without sacrifice in analytical performance, mAb loading capacity, or backpressure increases. The binding capacity of the gap ProA C-CP column was ∼ 2 mg mL-1 of IgG per bed volume. The same analytical column could be operated after processing a total of ∼ 56 column bed volumes of supernatant (>25 analytical cycles) without the need for caustic clean-in-place processing.

Protein fouling during constant-flux virus filtration: Mechanisms and modeling

As biomanufacturers consider the transition from batch to continuous processing, it will be necessary to re-examine the design and operating conditions for many downstream processes. For example, the integration of virus removal filtration in continuous biomanufacturing will likely require operation at low and constant filtrate flux instead of the high (constant) transmembrane pressures (TMPs) currently employed in traditional batch processing. The objective of this study was to examine the effect of low operating filtrate flux (5-100 L/m2 /h) on protein fouling during normal flow filtration of human serum Immunoglobulin G (hIgG) through the Viresolve® Pro membrane, including a direct comparison of the fouling behavior during constant-flux and constant-pressure operation. The filter capacity, defined as the volumetric throughput of hIgG solution at which the TMP increased to 30 psi, showed a distinct minimum at intermediate filtrate flux (around 20-30 L/m2 /h). The fouling data were well-described using a previously-developed mechanistic model based on sequential pore blockage and cake filtration, suitably modified for operation at constant flux. Simple analytical expressions for the pressure profiles were developed in the limits of very low and high filtrate flux, enabling rapid estimation of the filter performance and capacity. The model calculations highlight the importance of both the pressure-dependent rate of pore blockage and the compressibility of the protein cake to the fouling behavior. These results provide important insights into the overall impact of constant-flux operation on the protein fouling behavior and filter capacity during virus removal filtration using the Viresolve® Pro membrane.

Environmental modulation of exopolysaccharide production in the cyanobacterium Synechocystis 6803

Microorganisms produce extracellular polymeric substances (EPS, also known as exopolysaccharides) of diverse composition and structure. The biochemical and biophysical properties of these biopolymers enable a wide range of industrial applications. EPS from cyanobacteria are particularly versatile as they incorporate a larger number and variety of building blocks and adopt more complex structures than EPS from other organisms. However, the genetic makeup and regulation of EPS biosynthetic pathways in cyanobacteria are poorly understood. Here, we measured the effect of changing culture media on titre and composition of EPS released by Synechocystis sp. PCC 6803, and we integrated this information with transcriptomic data. Across all conditions, daily EPS productivity of individual cells was highest in the early growth phase, but the total amount of EPS obtained from the cultures was highest in the later growth phases due to accumulation. Lowering the magnesium concentration in the media enhanced per-cell productivity but the produced EPS had a lower total sugar content. Levels of individual monosaccharides correlated with specific culture media components, e.g. xylose with sulfur, glucose and N-acetyl-galactosamine with NaCl. Comparison with RNA sequencing data suggests a Wzy-dependent biosynthetic pathway and a protective role for xylose-rich EPS. This multi-level analysis offers a handle to link individual genes to the dynamic modulation of a complex biopolymer. KEY POINTS: • Synechocystis exopolysaccharide amount and composition depends on culture condition • Production rate and sugar content can be modulated by Mg and S respectively • Wzy-dependent biosynthetic pathway and protective role proposed for xylose-rich EPS.

Evaluating 3D-printed bioseparation structures using multi-length scale tomography

X-ray computed tomography was applied in imaging 3D-printed gyroids used for bioseparation in order to visualize and characterize structures from the entire geometry down to individual nanopores. Methacrylate prints were fabricated with feature sizes of 500 µm, 300 µm, and 200 µm, with the material phase exhibiting a porous substructure in all cases. Two X-ray scanners achieved pixel sizes from 5 µm to 16 nm to produce digital representations of samples across multiple length scales as the basis for geometric analysis and flow simulation. At the gyroid scale, imaged samples were visually compared to the original computed-aided designs to analyze printing fidelity across all feature sizes. An individual 500 µm feature, part of the overall gyroid structure, was compared and overlaid between design and imaged volumes, identifying individual printed layers. Internal subvolumes of all feature sizes were segmented into material and void phases for permeable flow analysis. Small pieces of 3D-printed material were optimized for nanotomographic imaging at a pixel size of 63 nm, with all three gyroid samples exhibiting similar geometric characteristics when measured. An average porosity of 45% was obtained that was within the expected design range, and a tortuosity factor of 2.52 was measured. Applying a voidage network map enabled the size, location, and connectivity of pores to be identified, obtaining an average pore size of 793 nm. Using Avizo XLAB at a bulk diffusivity of 7.00 × 10-11 m2s-1 resulted in a simulated material diffusivity of 2.17 × 10-11 m2s-1 ± 0.16 × 10-11 m2s-1.

An adaptive modeling approach using spiking-augmentation method to improve chemometric model performance in bioprocess monitoring

Intensified and continuous processes require fast and robust methods and technologies to monitor product titer for faster analytical turnaround time, process monitoring, and process control. The current titer measurements are mostly offline chromatography-based methods which may take hours or even days to get the results back from the analytical labs. Thus, offline methods will not meet the requirement of real time titer measurements for continuous production and capture processes. FTIR and chemometric based multivariate modeling are promising tools for real time titer monitoring in clarified bulk (CB) harvests and perfusate lines. However, empirical models are known to be vulnerable to unseen variability, specifically a FTIR chemometric titer model trained on a given biological molecule and process conditions often fails to provide accurate predictions of titer in another molecule under different process conditions. In this study, we developed an adaptive modeling strategy: the model was initially built using a calibration set of available perfusate and CB samples and then updated by augmenting spiking samples of the new molecules to the calibration set to make the model robust against perfusate or CB harvest of the new molecule. This strategy substantially improved the model performance and significantly reduced the modeling effort for new molecules.

Analyzing and understanding the robustness of bioprocesses

The robustness of bioprocesses is becoming increasingly important. The main driving forces of this development are, in particular, increasing demands on product purities as well as economic aspects. In general, bioprocesses exhibit extremely high complexity and variability. Biological systems often have a much higher intrinsic variability compared with chemical processes, which makes the development and characterization of robust processes tedious task. To predict and control robustness, a clear understanding of interactions between input and output variables is necessary. Robust bioprocesses can be realized, for example, by using advanced control strategies for the different unit operations. In this review, we discuss the different biological, technical, and mathematical tools for the analysis and control of bioprocess robustness.

Optimization of fluid flow in membrane chromatography devices using computational fluid dynamic simulations

Flow uniformity within the device is critically important in membrane chromatography. Recent studies have shown that the design of the device has a significant impact on flow uniformity, and thereby on separation efficiency. The main premise of this work is that computational fluid dynamics (CFD) could serve as a fast and inexpensive tool for preliminary optimization of the design of a membrane chromatography device. CFD also helps in identifying factors that affect flow uniformity. In this paper, CFD is used to compare the fluidic attributes of conventional membrane chromatography devices such as the stacked disc and radial flow devices with those of more recently developed ones such as the different versions of the laterally-fed membrane chromatography (LFMC) device. These are compared based on pulse tracer solute dispersion, which is a useful metric for measuring flow uniformity, and is thereby a good predictor of chromatographic separation performance. The poor separation performance typically observed with conventional membrane chromatography devices could be attributed to the high degree of solute dispersion within these devices. CFD is then used to analyze the impact of factors such as membrane aspect ratio, and channel dimensions on the performance of z²-laterally-fed membrane chromatography (z²LFMC) devices. The results discussed in the paper demonstrate that CFD could indeed serve as a powerful optimization and performance prediction tool for membrane chromatography.

Single-Pass Tangential Flow Filtration (SPTFF) of Nanoparticles: Achieving Sustainable Operation with Dilute Colloidal Suspensions for Gene Therapy Applications

Recent approval of several viral-vector-based therapeutics has led to renewed interest in the development of more efficient bioprocessing strategies for gene therapy products. Single-Pass Tangential Flow Filtration (SPTFF) can potentially provide inline concentration and final formulation of viral vectors with enhanced product quality due. In this study, SPTFF performance was evaluated using a suspension of 100 nm nanoparticles that mimics a typical lentivirus system. Data were obtained with flat-sheet cassettes having 300 kDa nominal molecular weight cutoff, either in full recirculation or single-pass mode. Flux-stepping experiments identified two critical fluxes, one based on boundary-layer particle accumulation (J_bl) and one based on membrane fouling (J_foul). The critical fluxes were well-described using a modified concentration polarization model that captures the observed dependence on feed flow rate and feed concentration. Long-duration filtration experiments were conducted under stable SPTFF conditions, with the results suggesting that sustainable performance could potentially be achieved for as much as 6 weeks of continuous operation. These results provide important insights into the potential application of SPTFF for the concentration of viral vectors in the downstream processing of gene therapy agents.

Understanding the Residence Time Distribution in a Transient Inline Spiking System: Modeling, Experiments, and Simulations

A transient inline spiking system is a promising tool for evaluating the performance of a virus filter in continuous operation. For better implementation of the system, we performed a systematic analysis to understand the residence time distribution (RTD) of inert tracers in the system. We aimed to understand the RTD of a salt spike, not retained onto or within the membrane pore, to focus on its mixing and spreading within the processing units. A concentrated NaCl solution was spiked into a feed stream as the spiking duration (tspike) was varied from 1 to 40 min. A static mixer was employed to mix the salt spike with the feed stream, which then passed through a single-layered nylon membrane inserted in a filter holder. The RTD curve was obtained by measuring the conductivity of the collected samples. An analytical model, the PFR-2CSTR model, was employed to predict the outlet concentration from the system. The slope and peak of the RTD curves were well-aligned with the experimental findings when τPFR = 4.3 min, τCSTR1 = 4.1 min, and τCSTR2 = 1.0 min. CFD simulations were performed to describe the flow and transport of the inert tracers through the static mixer and the membrane filter. The RTD curve spanned more than 30 min, much longer than tspike, since solutes were dispersed within processing units. The flow characteristics in each processing unit correlated with the RTD curves. Our detailed analysis of the transient inline spiking system would be helpful for implementing this protocol in continuous bioprocessing.

Use of scanning electron microscopy and energy dispersive X-ray spectroscopy to identify key fouling species during alternating tangential filtration

Alternating tangential flow filtration (ATF) has become one of the primary methods for cell retention and clarification in perfusion bioreactors. However, membrane fouling can cause product sieving losses that limit the performance of these systems. This study used scanning electron microscopy and energy dispersive X-ray spectroscopy to identify the nature and location of foulants on 0.2 μm polyethersulfone hollow fiber membranes after use in industrial Chinese hamster ovary cell perfusion bioreactors for monoclonal antibody production. Membrane fouling was dominated by proteinaceous material, primarily host cell proteins along with some monoclonal antibody. Fouling occurred primarily on the lumen surface with much less protein trapped within the depth of the fiber. Protein deposition was also most pronounced near the inlet/exit of the hollow fibers, which are the regions with the greatest flux (and transmembrane pressure) during the cyclical operation of the ATF. These results provide important insights into the underlying phenomena governing the fouling behavior of ATF systems for continuous bioprocessing.

A versatile multimodal chromatography strategy to rapidly purify protein nanostructures assembled in cell lysates

BACKGROUND

Protein nanostructures produced through the self-assembly of individual subunits are attractive scaffolds to attach and position functional molecules for applications in biomaterials, metabolic engineering, tissue engineering, and a plethora of nanomaterials. However, the assembly of multicomponent protein nanomaterials is generally a laborious process that requires each protein component to be separately expressed and purified prior to assembly. Moreover, excess components not incorporated into the final assembly must be removed from the solution and thereby necessitate additional processing steps.

RESULTS

We developed an efficient approach to purify functionalized protein nanostructures directly from bacterial lysates through a type of multimodal chromatography (MMC) that combines size-exclusion, hydrophilic interaction, and ion exchange to separate recombinant protein assemblies from excess free subunits and bacterial proteins. We employed the ultrastable filamentous protein gamma-prefoldin as a material scaffold that can be functionalized with a variety of protein domains through SpyTag/SpyCatcher conjugation chemistry. The purification of recombinant gamma-prefoldin filaments from bacterial lysates using MMC was tested across a wide range of salt concentrations and pH, demonstrating that the MMC resin is robust, however the optimal choice of salt species, salt concentration, and pH is likely dependent on the protein nanostructure to be purified. In addition, we show that pre-processing of the samples with tangential flow filtration to remove nucleotides and metabolites improves resin capacity, and that post-processing with Triton X-114 phase partitioning is useful to remove lipids and any remaining lipid-associated protein. Subsequently, functionalized protein filaments were purified from bacterial lysates using MMC and shown to be free of unincorporated subunits. The assembly and purification of protein filaments with varying amounts of functionalization was confirmed using polyacrylamide gel electrophoresis, Förster resonance energy transfer, and transmission electron microscopy. Finally, we compared our MMC workflow to anion exchange chromatography with the purification of encapsulin nanocompartments containing a fluorescent protein as a cargo, demonstrating the versatility of the protocol and that the purity of the assembly is comparable to more traditional procedures.

CONCLUSIONS

We envision that the use of MMC will increase the throughput of protein nanostructure prototyping as well as enable the upscaling of the bioproduction of protein nanodevices.

Continuous manufacturing of monoclonal antibodies: Dynamic control of multiple integrated polishing chromatography steps using BioSMB

We propose a strategy for automation and control of multi-step polishing chromatography in integrated continuous manufacturing of monoclonal antibodies. The strategy is demonstrated for a multi-step polishing process consisting of cation exchange chromatography in bind-and-elute mode followed by mixed-mode chromatography in flowthrough mode. A BioSMB system with a customized Python control layer is used for automation and scheduling of both the chromatography steps. Further, the BioSMB valve manifold is leveraged for in-line conditioning between the two steps, as tight control of pH and conductivity is essential when operating with multimodal resins because even slight fluctuations in load conditions adversely affect the chromatography performance. The pH and conductivity of the load to the multimodal chromatography columns is consistent, despite the elution gradient of the preceding cation exchange chromatography step. Inputs from the BioSMB pH and conductivity sensors are used for real-time control of the 7 pumps and 240 valves to achieve in-line conditioning inside the BioSMB manifold in a fully automated manner. This is confirmed by showcasing different elution strategies in cation exchange chromatography, including linear gradient, step gradient and process deviations like tubing leakage. In all the above cases, the model was able to maintain the pH and conductivity of multimodal chromatography load within the range of 6 ± 0.1 pH and 7 ± 0.3 mS/cm conductivity. The strategy eliminates the need for using multiple BioSMB units or integrating external pumps, valves, mixers, surge tanks, or sensors between the two steps as is currently the standard approach, thus offering a simple and robust structure for integrating multiple polishing chromatography steps in continuous downstream monoclonal antibody purification trains.

Mixed-Mode Chromatography and Its Role in Monoclonal Antibody Purification

As the biopharmaceutical industry matures and embraces process intensification methodologies allied to the emergence of newer personalized medicines, a key constant is the regulatory need to purify products that satisfy the criteria of safety, quality, and efficacy in each batch of released product destined for clinical use. Downstream processing operations and in particular chromatographic separations continue to play a key role in manufacturing strategies with the industry being well served by commercially available resins that provide different options to purify a particular target molecule of interest. In recent years, mixed-mode chromatography, a technique based on multimode interactions between ligands and proteins, had attracted much attention. This short review will discuss the concept and benefit of mixed-mode chromatography in purification strategies and specifically look at its application in the purification of IgG subtype monoclonal antibodies, a key product class in today's industry.

Continuous manufacturing of monoclonal antibodies: Automated downstream control strategy for dynamic handling of titer variations

Handling long-term dynamic variability in harvest titer is a critical challenge in continuous downstream manufacturing. This challenge is becoming increasingly important with the advent of high-titer clones and modern upstream perfusion processes where the titer can vary significantly across the course of a campaign. In this paper, we present a strategy for real-time, dynamic adjustment of the entire downstream train, including capture chromatography, viral inactivation, depth filtration, polishing chromatography, and single-pass formulation, to accommodate variations in titer from 1-7 g/L. The strategy was tested in real time in a continuous downstream purification process of 36 h duration with induced titer variations. The dynamic control strategy leverages real-time NIR-based concentration sensors in the harvest material to continuously track the titer, integrated with an in-house Python-based control system that operates a BioSMB for carrying out capture and polishing chromatography, as well as a series of pumps and solenoid valves for carrying out viral inactivation and formulation. A set of 9 different methods, corresponding to the different harvest titers have been coded onto the Python controller. The methods have a varying number of chromatography columns (3-6 for Protein A and 2-10 for CEX), designed to ensure proper scheduling and optimize productivity across the entire titer variation space. The approach allows for a wide range of titers to be processed on a single integrated setup without having to change equipment or to re-design each time. The strategy also overcomes a key unexplored challenge in continuous processing, namely hand-shaking the downstream train to upstream conditions with long-term titer variability while maintaining automated operation with high productivity and robustness.

Detergent micelle conjugates containing amino acid monomers allow purification of human IgG near neutral pH

Industrial scale production of therapeutic monoclonal antibodies (mAbs) is commonly achieved with Protein A chromatography, a process that requires exposure of the antibody to strongly acidic conditions during the eluting step. Exposure to acid inactivates virus contaminants but may, in parallel, lead to antibody aggregation that must be eliminated or kept at acceptably low levels. This report seeks to provide a practical method for overcoming a long-standing problem. We show how Brij-O20 detergent micelles, conjugated by the amphiphilic [(bathophenanthroline)₃:Fe²⁺] complex in the presence of amino acid monomers: phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp), isoleucine (Ile) or valine (Val), efficiently capture polyclonal human IgG (hIgG) at neutral pH and allow its recovery by extraction either at pH 4 (85-97% yield) or at pH 6.3 (72-84% yield). Of the five amino acid monomers surveyed, Phe or Tyr produced the highest overall process yield at both pH 4 and 6.3. The monomeric state of the purified hIgG's was confirmed by dynamic light scattering (DLS). Potential advantages of the purification method are discussed.

A modular 3D printed microfluidic system: a potential solution for continuous cell harvesting in large-scale bioprocessing

Microfluidic devices have shown promising applications in the bioprocessing industry. However, the lack of modularity and high cost of testing and error limit their implementation in the industry. Advances in 3D printing technologies have facilitated the conversion of microfluidic devices from research output to applicable industrial systems. Here, for the first time, we presented a 3D printed modular microfluidic system consisting of two micromixers, one spiral microfluidic separator, and one microfluidic concentrator. We showed that this system can detach and separate mesenchymal stem cells (MSCs) from microcarriers (MCs) in a short time while maintaining the cell's viability and functionality. The system can be multiplexed and scaled up to process large volumes of the industry. Importantly, this system is a closed system with no human intervention and is promising for current good manufacturing practices.

New strategy for the design, production and pre-purification of chimeric peptide with immunomodulatory activity in Salmosalar

The intensive salmon farming is associated with massive outbreaks of infections. The use of antibiotics for their prevention and control is related to damage to the environment and human health. Antimicrobial peptides (AMPs) have been proposed as an alternative to the use of antibiotics for their antimicrobial and immunomodulatory activities. However, one of the main challenges for its massive clinical application is the high production cost and the complexity of chemical synthesis. Thus, recombinant DNA technology offers a more sustainable, scalable, and profitable option. In the present study, using an AMPs function prediction methodology, we designed a chimeric peptide consisting of sequences derived from cathelicidin fused with the immunomodulatory peptide derived from flagellin. The designed peptide, CATH-FLA was produced by recombinant expression using an easy pre-purification system. The chimeric peptide was able to induce IL-1β and IL-8 expression in Salmo salar head kidney leukocytes, and prevented Piscirickettsia salmonis-induced cytotoxicity in SHK-1 cells. These results suggest that pre-purification of a recombinant AMP-based chimeric peptide designed in silico allow obtaining a peptide with immunomodulatory activity in vitro. This could solve the main obstacle of AMPs for massive clinical applications.

Development of a transient inline spiking system for evaluating virus clearance in continuous bioprocessing -- Proof of concept for virus filtration

The development of continuous/connected bioprocesses requires new approaches for viral clearance validation, both for specific unit operations and for the overall process. In this study, we have developed a transient inline spiking system that can be used to evaluate virus clearance at distinct time points during prolonged operation of continuous bioprocesses. The proof of concept for this system was demonstrated by evaluating the viral clearance for a virus filtration step, both with and without a prefilter upstream of the virus filter. The residence time distribution was evaluated using a previously identified non-interacting fluorescent tracer, while viral clearance was evaluated from measurements of the virus titer in samples obtained downstream of the virus filter. The measured log reduction values (LRV) for ϕX174, Minute Virus of Mice (MVM), Xenotropic Murine Leukemia Virus (XMuLV), and a non-infectious Mock Virus Particle (MVP) were all within 0.5 logs of those obtained using a traditional batch virus challenge for both model and real-world process streams (LRV between 2.2 and 3.4 for ϕX174 using a single layer of virus filter). The results demonstrate the effectiveness of transient inline spiking to validate the virus clearance capabilities in continuous bioprocessing, an essential element for the adoption of these processes for products made using mammalian cell lines. This article is protected by copyright. All rights reserved.

Engineering a deformation-free plastic spiral inertial microfluidic system for CHO cell clarification in biomanufacturing

Inertial microfluidics has enabled many impactful high throughput applications. However, devices fabricated in soft elastomer (i.e., polydimethylsiloxane (PDMS)) suffer reliability issues due to significant deformation generated by the high pressure and flow rates in inertial microfluidics. In this paper, we demonstrated deformation-free and mass-producible plastic spiral inertial microfluidic devices for high-throughput cell separation applications. The design of deformable PDMS spiral devices was translated to their plastic version by compensating for the channel deformation in the PDMS devices, analyzed by numerical simulation and confocal imaging methods. The developed plastic spiral devices showed similar performance to their original PDMS devices for blood separation and Chinese hamster ovary (CHO) cell retention. Furthermore, using a multiplexed plastic spiral unit containing 100 spirals, we successfully demonstrated ultra-high-throughput cell clarification (at a processing rate of 1 L min^-1) with a high cell-clarification efficiency of ∼99% (at the cell density changing from ∼2 to ∼10 × 10⁶ cells mL^-1). Benefitting from the continuous and clogging-free separation with an industry-level throughput, the cell clarification device could be a critical breakthrough for the production of therapeutic biologics such as antibodies or vaccines, impacting biomanufacturing in general.

Enablers of continuous processing of biotherapeutic products

The benefits of continuous processing over batch manufacturing are widely acknowledged across the biopharmaceutical industry, primary of which are higher productivity and greater consistency in product quality. Furthermore, the reduced equipment and facility footprint lead to significantly lower capital costs. Technology enablers have a major role in this migration from batch to continuous processing. In this review, we highlight the various enablers that are facilitating adoption of continuous upstream and downstream bioprocessing. This includes new bioreactors and cell retention devices for upstream operations, and on-column and continuous flow refolding, novel continuous chromatography, and single-pass filtration systems for downstream processes. We also elucidate the significant roles of process integration and control as well as of data analytics in these processes.

Continuous purification of influenza A virus particles using pseudo-affinity membrane chromatography

Robust and flexible continuous unit operations that enable the establishment of intensified bioprocesses is one of the most relevant trends in manufacturing of biopharmaceuticals, including virus-based products. Sulfated cellulose membrane adsorbers (SCMA) are one of the most promising matrices for chromatographic purification of virus particles, like influenza viruses. Here, a three 'column' periodical counter current set-up was used to continuously purify influenza A/PR/8/34 virus particles using SCMA in bind-elute mode. It was possible to recover 67.4% of the HA-activity and to remove 67.4% and 99.8% of the total protein and DNA, respectively. The performance of the continuous process operated over a total of 10 loops, was slightly inferior to was obtained in a comparable batch process. Nevertheless, it was possible to increase the effective usage of binding capacity to 80%, resulting on a productivity of 22.8 kHAU ml_memb^-1 min^-1. As a proof-of-principle, SCMA were successfully used as matrix for purification of cell-derived influenza virus particles, in continuous mode.