An ultra scale‐down characterization of low shear stress primary recovery stages to enhance selectivity of fusion protein recovery from its molecular variants

Fusion proteins offer the prospect of new therapeutic products with multiple functions. The primary recovery is investigated of a fusion protein consisting of modified E2 protein from hepatitis C virus fused to human IgG1 Fc and expressed in a Chinese hamster ovary (CHO) cell line. Fusion protein products inevitably pose increased challenge in preparation and purification. Of particular concerns are: (i) the impact of shear stress on product integrity and (ii) the presence of product‐related contaminants which could prove challenging to remove during the high resolution purification steps. This paper addresses the use of microwell‐based ultra scale‐down (USD) methods to develop a bioprocess strategy focused on the integration of cell culture and cell removal operations and where the focus is on the use of operations which impart low shear stress levels even when applied at eventual manufacturing scale. An USD shear device was used to demonstrate that cells exposed to high process stresses such as those that occur in the feed zone of a continuous non‐hermetic centrifuge resulted in the reduction of the fusion protein and also the release of glycosylated intracellular variants. In addition, extended cell culture resulted in release of such variants. USD mimics of low shear stress, hydrohermetic feed zone centrifugation and of depth filtration were used to demonstrate little to no release during recovery of these variants with both results verified at pilot scale. Furthermore, the USD studies were used to predict removal of contaminants such as lipids, nucleic acids, and cell debris with, for example, depth filtration delivering greater removal than for centrifugation but a small (～10%) decrease in yield of the fusion protein. These USD observations of product recovery and carryover of contaminants were also confirmed at pilot scale as was also the capacity or throughput achievable for continuous centrifugation or for depth filtration. The advantages are discussed of operating a lower yield cell culture and a low shear stress recovery process in return for a considerably less challenging purification demand. Biotechnol. Bioeng. 2013; 110: 1973–1983. © 2013 Wiley Periodicals, Inc.     

Assessment of the manufacturability of Escherichia coli high cell density fermentations

The physical and biological conditions of the host cell obtained at the end of fermentation influences subsequent downstream processing unit operations. The ability to monitor these characteristics is central to the improvement of biopharmaceutical manufacture. In this study, we have used a combination of techniques such as adaptive focus acoustics (AFA) and ultra scale-down (USD) centrifugation that utilize milliliter quantities of sample to obtain an insight into the interaction between cells from the upstream process and initial downstream unit operations. This is achieved primarily through an assessment of cell strength and its impact on large-scale disc stack centrifugation performance, measuring critical attributes such as viscosity and particle size distribution. An Escherichia coli fed-batch fermentation expressing antibody fragments in the periplasm was used as a model system representative of current manufacturing challenges. The weakening of cell strength during cultivation time, detected through increased micronization and viscosity, resulted in a 2.6-fold increase in product release rates from the cell (as measured by AFA) and approximately fourfold decrease in clarification performance (as measured by USD centrifugation). The information obtained allows for informed harvest point decisions accounting for both product leakages during fermentation and potential losses during primary recovery. The clarification performance results were verified at pilot scale. The use of these technologies forms a route to the process understanding needed to tailor the host cell and upstream process to the product and downstream process, critical to the implementation of quality-by-design principles.     

Subcellular dynamics of multifunctional protein regulation: mechanisms of GAPDH intracellular translocation

Multidimensional proteins such as glyceraldehyde-3-phosphate dehydrogenase (GAPDH) exhibit distinct activities unrelated to their originally identified functions. Apart from glycolysis, GAPDH participates in iron metabolism, membrane trafficking, histone biosynthesis, the maintenance of DNA integrity and receptor mediated cell signaling. Further, multifunctional proteins exhibit distinct changes in their subcellular localization reflecting their new activities. As such, GAPDH is not only a cytosolic protein but is localized in the membrane, the nucleus, polysomes, the ER and the Golgi. In addition, although the initial subcellular localizations of multifunctional proteins may be of significance, dynamic changes in intracellular distribution may occur as a consequence of those new activities. As such, regulatory mechanisms may exist through which cells control multifunctional protein expression as a function of their subcellular localization. The temporal sequence through which subcellular translocation and the acquisition of new GAPDH functions is considered as well as post-translational modification as a basis for its intracellular transport.     

Using a CFD model to understand the fluid dynamics promoting E. coli breakage in a high-pressure homogenizer

A Computational Fluid Dynamic (CFD) model of flow in a high-pressure homogenizing valve (APV Gaulin model 30CD) was developed with the Fluent software. The 2D model consists of an unstructured hexagonal mesh, dense in the regions of high gradients. The flow (single-phase) was modeled as laminar upstream of and in the channel (gap) and turbulent downstream of the channel exit. Applying a realizable kappa-epsilon turbulence model, the CFD model accurately predicted the effect of gap space on fluid dynamic conditions upstream (inlet pressure and pressure gradient) and downstream (impact pressure) of the channel for a valve with a standard (CD-0) impact distance (0.25 mm) and a 1 cP fluid. This CFD model was then used to estimate the magnitude of the fluid dynamic parameters (except cavitation effects) presumed to be responsible for cell breakage, as a function of gap space, impact distance and fluid viscosity. The CFD models predicted that for a given volumetric flowrate the upstream fluid conditions (inlet pressure gradient, maximum channel strain rate) and the maximum energy dissipation rate in the post-gap jet depend only on the gap space and the fluid viscosity and not on the impact distance. The impact pressure however depends on the gap spacing, the fluid viscosity and especially the impact distance. Experimental results indicate that higher inlet pressures are required to break cells, if the impact distance is increased. By conducting experiments to isolate individual cell breakage mechanisms for a single pass, threshold values were identified for breaking Escherichia coli cells: pressure gradient, 1.2 x 10(12) Pa/m; energy dissipation rate, 1.0 x 10(10) m(3)/s(2); and impact pressure, 160 psig. By isolating the wall impact as the sole mechanism responsible for breaking the E. coli cells between 3000 and 6000 psig inlet pressure, a relationship between E. coli cell breakage rate and maximum wall impact pressure was established (eq 5).     

On the controllability of continuous fermentation processes

Simulation may be used as a powerful tool for accelerating bioprocess design. This paper demonstrates the use of simulations in exploring the nature and impact of the interactions that exist in a typical bioprocess for the recovery of an intracellular protein. The study shows that an integrated approach to design must be adopted in order to achieve acceptable process designs. Data from a fed-batch fermentation, with verified models for cell harvesting, cell disruption and cell debris removal have been integrated to demonstrate the consequence of process design and operating decisions on the resulting process performance. The trade-offs between product recovery and the extent of cell debris removal for a range of operating conditions have been represented through a series of windows of operation which show how process conditions must be altered in order for given process performance levels to be realised. The capacity to account for process performance including the impact of interactions is seen as a pre-requisite for rigorous bioprocess sequence design and optimisation.     

Post-zygotic breakage of a dicentric chromosome results in mosaicism for a telocentric 9p marker chromosome in a boy with developmental delay

Chromosomal rearrangements resulting in an inverted duplication and a terminal deletion (inv dup del) can occur due to three known mechanisms, two of them resulting in a normal copy region between the duplicated regions. These mechanisms involve the formation of a dicentric chromosome, which undergo breakage during cell division resulting in cells with either an inverted duplication and deletion or a terminal deletion. We describe a mosaic 3 year old patient with two cell lines carrying a chromosome 9p deletion where one of the cell lines contains an additional telocentric marker chromosome. Our patient is mosaic for the product of a double breakage of a dicentric chromosome including a centric fission. Mosaicism involving different rearrangements of the same chromosome is rare and suggests an early mitotic breakage event.     

Shear breakage of nylon membrane microcapsules in a turbine reactor

The breakage of nylon membrane microcapsules is proposed as a new method to study and quantify shear effects in biological systems. A critique of this method shows that a narrower particle size distribution may be an important improvement in the breakage study as well as breakage control in many bioreactor and biotechnological applications. In a turbine reactor, it was shown that the primary process which determines the microcapsule breakage is the shear effect. The breakage kinetics are first order with regard to the microcapsule concentration. The breakage kinetic constant was ob served to be dependent on the temperature and the particle size, and proportional to the average shear rate and the third power of the turbine angular velocity. Decrease of the breakage kinetic constant with temperature can be explained by a decrease of fluid viscosity and a change in nylon membrane properties. An increase in the breakage kinetic constant with the microcapsule diameter can be due to a lowering of internal pressure and a reduction of the membrane resistance with size. Proportionality between the breakage kinetic constant and the shear rate shows that shear is the main process which leads to microcapsule breakage. The additional intervention in the shear rate expression of the turbine angular speed in the form of the turbine and particle velocities, results in the dependence of the breakage kinetic constant on the third power of the angular velocity.     

Optimal operation of high-pressure homogenization for intracellular product recovery

An optimal control methodology for the homogenization of bacterial cells to recover intracellular products is presented. A Fluent computational fluid dynamics (CFD) model is used to quantify the hydrodynamic forces present in the homogenizer, and empirical models are used to relate these forces to experimentally obtained cell disruption and product recovery data. The optimal homogenizer operation, in terms of either constant cell breakage or maximum intracellular product recovery, is determined using these empirical models. We illustrate this methodology with an Escherichia coli bacterial system used to produce DNA plasmids. Homogenization is performed using an industrial APV–Gaulin high-pressure homogenizer. The modeling and optimization results for this E. coli–DNA plasmid system show good agreement with the experimental data.     

Resting cells of recombinant E. coli show high epoxidation yields on energy source and high sensitivity to product inhibition

Metabolically active resting (i.e., nongrowing) bacterial cells have a high potential in cofactor-dependent redox biotransformations. Where growing cells require carbon and energy for biomass production, resting cells can potentially exploit their metabolism more efficiently for redox biocatalysis allowing higher specific activities and product yields on energy source. Here, the potential of resting recombinant E. coli containing the styrene monooxygenase StyAB was investigated for enantioselective styrene epoxidation in a two-liquid phase setup. Resting cells indeed showed twofold higher specific activities as compared to growing cells in a similar setup. However, product formation rates decreased steadily resulting in lower final product concentrations. The low intrinsic stability of the reductase component StyB was found to limit overall biocatalyst stability. Such limitation by enzyme stability was overcome by increasing intracellular StyB levels. Beyond that, product inhibition was identified as a limiting factor, whereas complete toxification of the bacterial cells, as it was observed with growing cells, and deactivation of the multicomponent enzyme system did not occur. The resting cell setup allowed high product yields on glucose of more than 5 mol mol(glucose)(-1), which makes the use of resting cells a promising approach for ecologically as well as economically sustainable oxygenase-based whole-cell biocatalysis.     

Evaluation of cell disruption effects on primary recovery of antibody fragments using microscale bioprocessing techniques

Intracellular antibody Fab' fragments periplasmically expressed in Escherichia coli require the release of Fab' from the cells before initial product recovery. This work demonstrates the utility of microscale bioprocessing techniques to evaluate the influence of different cell disruption operations on subsequent solid–liquid separation and product recovery. Initially, the industrial method of Fab' release by thermochemical extraction was established experimentally at the microwell scale and was observed to yield Fab' release consistent with the larger scale process. The influence of two further cell disruption operations, homogenization and sonication, on subsequent Fab' recovery by microfiltration was also examined. The results showed that the heat‐extracted cells give better dead‐end microfiltration performance in terms of permeate flux and specific cake resistance. In contrast, the cell suspensions prepared by homogenization and sonication showed more efficient product release but with lower product purity and poorer microfiltration performance. Having established the various microscale methods the linked sequence was automated on the deck of a laboratory robotic platform and used to show how different conditions during thermochemical extraction impacted on the optimal performance of the linked unit operations. The results illustrate the power of microscale techniques to evaluate crucial unit operation interactions in a bioprocess sequence using only microliter volumes of feed. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Ultra scale‐down studies of the effect of shear on cell quality; Processing of a human cell line for cancer vaccine therapy

Whole cell therapy is showing potential in the clinic for the treatment of many chronic diseases. The translation of laboratory‐scale methods for cell harvesting and formulation to commercial‐scale manufacturing offers major bioprocessing challenges. This is especially the case when the cell properties determine the final product effectiveness. This study is focused on developing an ultra scale‐down method for assessing the impact of the hydrodynamic environment on human cells that constitute the therapeutic product. Small volumes of a prostate cancer cell line, currently being developed in late phase II clinical trials as an allogeneic whole cell vaccine therapy for prostate cancer, were exposed to hydrodynamic shear rates similar to those present in downstream process, formulation and vial filling operations. A small scale rotating disc shear device (20 mL) was used over a range of disc speeds to expose cells to maximum shear rates ranging from 90 × 10³ to 175 × 10³ s^‐1 (equivalent maximum power dissipation rates of 14 × 10³ to 52 × 10³ W kg^‐1). These cells were subsequently analyzed for critical cell quality attributes such as the retention of membrane integrity and cell surface marker profile and density. Three cell surface markers (CD9, CD147, and HLAA‐C) were studied. The cell markers exhibited different levels of susceptibility to hydrodynamic shear but in all cases this was less than or equal to the loss of membrane integrity. It is evident that the marker, or combination or markers, which might provide the required immunogenic response, will be affected by hydrodynamic shear environment during bioprocessing, if the engineering environment is not controlled to within the limits tolerated by the cell components. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Gaulin homogenization: a mechanistic study

Free radical-based oxidation has been detected in the normal operating regime of the Gaulin homogenizer, demonstrating that cavitation occurs in this important industrial bioprocessing equipment. Free radical generation is suppressed by imposition of back pressure, proving that such cavitation occurs in the impingement section. The calculated value of the cavitation number is consistent with submerged jet cavitation, wherein a high-speed jet exiting from the valve gap accelerates fluid in the impingement region, creating the vacuum conditions for cavitation. Using polysaccharides as a model shear-sensitive compound, their breakage pattern in the homogenizer was characterized by molecular size and polydispersity and compared to those of fluid shear flows in capillary tubes and cavitating flow from a sonic horn. The results indicate that breakage occurs primarily by fluid shear, although a contribution by cavitation is also apparent when back pressure is applied. Because biological molecules can readily react with free radicals and the alterations caused thereby are subtle in nature, a thorough evaluation of the impact of free radicals in upstream homogenization is warranted.     

Differential response in downstream processing of CHO cells grown under mild hypothermic conditions

The manufacture of complex therapeutic proteins using mammalian cells is well established, with several strategies developed to improve productivity. The application of sustained mild hypothermic conditions during culture has been associated with increases in product titer and improved product quality. However, despite associated cell physiological effects, very few studies have investigated the impact on downstream processing (DSP). Characterization of cells grown under mild hypothermic conditions demonstrated that the stationary phase was prolonged by delaying the onset of apoptosis. This enabled cells to maintain viability for extended periods and increase volumetric productivity from 0.74 to 1.02 g L^?1. However, host cell proteins, measured by ELISA, increased by ～50%, attributed to the extended time course and higher peak and harvest cell densities. The individual components making up this impurity, as determined by SELDI‐TOF MS and 2D‐PAGE, were shown to be largely comparable. Under mild hypothermic conditions, cells were less shear sensitive than those maintained at 37°C, enhancing the preliminary primary recovery step. Adaptive changes in membrane fluidity were further investigated by adopting a pronounced temperature shift immediately prior to primary recovery and the improvement observed suggests that such a strategy may be implementable when shear sensitivity is of concern. Early and late apoptotic cells were particularly susceptible to shear, at either temperature, even under the lowest shear rate investigated. These findings demonstrate the importance of considering the impact of cell culture strategies and cell physiology on DSP, by implementing a range of experimental methods for process characterization. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:688–696, 2013     

Escherichia coli heat shock protein DnaK: production and consequences in terms of monitoring cooking

Through use of commercially available DnaK proteins and anti-DnaK monoclonal antibodies, a competitive enzyme-linked immunosorbent assay was developed to quantify this heat shock protein in Escherichia coli ATCC 25922 subjected to various heating regimens. For a given process lethality (F(70)(10) of 1, 3, and 5 min), the intracellular concentration of DnaK in E. coli varied with the heating temperature (50 or 55 degrees C). In fact, the highest DnaK concentrations were found after treatments at the lower temperature (50 degrees C) applied for a longer time. Residual DnaK after heating was found to be necessary for cell recovery, and additional DnaK was produced during the recovery process. Overall, higher intracellular concentrations of DnaK tended to enhance cell resistance to a subsequent lethal stress. Indeed, E. coli cells that had undergone a sublethal heat shock (105 min at 55 degrees C, F(70)(10) = 3 min) accompanied by a 12-h recovery (containing 76,786 +/- 25,230 molecules/cell) resisted better than exponentially growing cells (38,500 +/- 6,056 molecules/cell) when later heated to 60 degrees C for 50 min (F(70)(10) = 5 min). Results reported here suggest that using stress protein to determine cell adaptation and survival, rather than cell counts alone, may lead to more efficient heat treatment.     

Advances in primary recovery: centrifugation and membrane technology

Significant and continual improvements in upstream processing for biologics have resulted in challenges for downstream processing, both primary recovery and purification. Given the high cell densities achievable in both microbial and mammalian cell culture processes, primary recovery can be a significant bottleneck in both clinical and commercial manufacturing. The combination of increased product titer and low viability leads to significant relative increases in the levels of process impurities such as lipids, intracellular proteins and nucleic acid versus the product. In addition, cell culture media components such as soy and yeast hydrolysates have been widely applied to achieve the cell culture densities needed for higher titers. Many of the process impurities can be negatively charged at harvest pH and can form colloids during the cell culture and harvest processes. The wide size distribution of these particles and the potential for additional particles to be generated by shear forces within a centrifuge may result in insufficient clarification to prevent fouling of subsequent filters. The other residual process impurities can lead to precipitation and increased turbidity during processing and even interference with the performance of the capturing chromatographic step. Primary recovery also poses significant challenges owing to the necessity to execute in an expedient manner to minimize both product degradation and bioburden concerns. Both microfiltration and centrifugation coupled with depth filtration have been employed successfully as primary recovery processing steps. Advances in the design and application of membrane technology for microfiltration and dead-end filtration have contributed to significant improvements in process performance and integration, in some cases allowing for a combination of multiple unit operations in a given step. Although these advances have increased productivity and reliability, the net result is that optimization of primary recovery processes has become substantially more complicated. Ironically, the application of classical chemical engineering approaches to overcome issues in primary recovery and purification (e.g., turbidity and trace impurity removal) are just recently gaining attention. Some of these techniques (e.g., membrane cascades, pretreatment, precipitation, and the use of affinity tags) are now seen almost as disruptive technologies. This paper will review the current and potential future state of research on primary recovery, including relevant papers presented at the 234th American Chemical Society (ACS) National Meeting in Boston.     

Integration of host strain bioengineering and bioprocess development using ultra‐scale down studies to select the optimum combination: An antibody fragment primary recovery case study

An ultra scale‐down primary recovery sequence was established for a platform E. coli Fab production process. It was used to evaluate the process robustness of various bioengineered strains. Centrifugal discharge in the initial dewatering stage was determined to be the major cause of cell breakage. The ability of cells to resist breakage was dependant on a combination of factors including host strain, vector, and fermentation strategy. Periplasmic extraction studies were conducted in shake flasks and it was demonstrated that key performance parameters such as Fab titre and nucleic acid concentrations were mimicked. The shake flask system also captured particle aggregation effects seen in a large scale stirred vessel, reproducing the fine particle size distribution that impacts the final centrifugal clarification stage. The use of scale‐down primary recovery process sequences can be used to screen a larger number of engineered strains. This can lead to closer integration with and better feedback between strain development, fermentation development, and primary recovery studies. Biotechnol. Bioeng. 2014;111: 1971–1981. © 2014 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.     

Dynamics of neutrophil rolling over stimulated endothelium in vitro.

Prior to extravasation at sites of acute inflammation, neutrophils roll over activated endothelium. Neutrophil rolling is often characterized by the average rolling velocity. An additional dynamic feature of rolling that has been identified but not extensively studied is the fluctuation in the rolling velocity about the average. To analyze this characteristic further, we have measured the instantaneous velocity of bovine neutrophils interacting with lipopolysaccharide-stimulated bovine aortic endothelium at shear stresses of 1, 2, 3, and 4 dynes/cm2. The average velocities are quantitatively similar to those reported for human neutrophils rolling over reconstituted P-selectin at a surface density of 400 sites/microns 2. At all shear stresses tested, the population average variance in the instantaneous velocity is at least 2 orders of magnitude higher than the theoretical variance generated from experimental error, indicating that the neutrophils translate with a nonconstant velocity. Possible sources of the variance are discussed. These include "macroscopic" sources such as topological heterogeneity in the endothelium and microscopic sources, such as inherent stochastic formation and breakage of the receptor-ligand bonds that mediate the rolling. Regardless of the ultimate source of the variance, these results justify the use of mathematical models that incorporate stochastic processes to describe bond formation and breakage between the neutrophil and the endothelium and hence are able to generate variable velocity trajectories.     

Ultra scale-down to define and improve the relationship between flocculation and disc-stack centrifugation

The recovery of intracellular recombinant proteins produced in microbial systems typically requires physical, chemical or thermal treatment of the cells post-harvest to release the product into the broth, followed by removal of the cell debris using centrifugation or tangential flow filtration. Often a precipitation or flocculation step is introduced to facilitate the liquid-solid separation. Due to the complex nature of the cell materials and the unit operations, it is difficult to obtain data at laboratory scale that closely reflect the performance of these operations on larger scales (pilot or manufacturing). This study uses a predictive scale-down model that enables rapid optimization of the operating conditions for a flocculation followed with a centrifugation step using only small volumes (20 mL) of a high solids ( approximately 20% w/w) E. coli heat extract. Results obtained show that, with proper theoretical and experimental consideration to account for high cell density, conditions could be found that improve the beneficial interaction between flocculation and centrifugation. These experiments suggested that adding a higher level of a cationic polymer could substantially increase the strength of the flocculated particles produced, thereby enhancing overall clarification performance in a large scale centrifuge. This was subsequently validated at pilot scale.     

Hydrodynamic damage to animal cells.

Animal cells are affected by hydrodynamic forces that occur in culture vessel, transfer piping, and recovery operations such as microfiltration. Depending on the type, intensity, and duration of the force, and the specifics of the cell, the force may induce various kinds of responses in the subject cells. Both biochemical and physiological responses are observed, including apoptosis and purely mechanical destruction of the cell. This review examines the kinds of hydrodynamic forces encountered in bioprocessing equipment and the impact of those forces on cells. Methods are given for quantifying the magnitude of the specific forces, and the response thresholds are noted for the common types of cells cultured in free suspension, supported on microcarriers, and anchored to stationary surfaces.     

Increased DNA double strand breakage is responsible for sensitivity of the pso3-1 mutant of Saccharomyces cerevisiae to hydrogen peroxide

Escherichia coli endonuclease III (endo III) is the key repair enzyme essential for removal of oxidized pyrimidines and abasic sites. Although two homologues of endo III, Ntgl and Ntg2, were found in Saccharomyces cerevisiae, they do not significantly contribute to repair of oxidative DNA damage in vivo. This suggests that an additional activity(ies) or a regulatory pathway(s) involved in cellular response to oxidative DNA damage may exist in yeast. The pso3-1 mutant of S. cerevisiae was previously shown to be specifically sensitive to toxic effects of hydrogen peroxide (H2O2) and paraquat. Here, we show that increased DNA double strand breakage is very likely the basis of sensitivity of the pso3-1 mutant cells to H2O2. Our results, thus, indicate an involvement of the Pso3 protein in protection of yeast cells from oxidative stress presumably through its ability to prevent DNA double strand breakage. Furthermore, complementation of the repair defects of the pso3-1 mutant cells by E. coli endo III has been examined. It has been found that expression of the nth gene in the pso3-1 mutant cells recovers survival, decreases mutability and protects yeast genomic DNA from breakage following H2O2 treatment. This might suggest some degree of functional similarity between Pso3 and Nth.