Perfusion Cell Culture Research Articles

A two-step procedure for the design of perfusion bioreactors

A two-step procedure for the design and optimization of mammalian cell perfusion cultures for therapeutic protein production, for a given expression system, is developed. The considered operating variables include the cell specific perfusion rate (CSPR), the perfusion rate (P) and the viable cell density (VCD). The procedure is articulated in two steps, each including a reactor operation through which different steady states are explored sequentially. In the first one, a suitable minimum value of the CSPR is found. This can be achieved through two alternative approaches. These include keeping the perfusion rate or the VCD constant, while changing the other so as to decrease the CSPR. Cellular growth and metabolite in- and output rates decrease when minimizing the CSPR resulting in a lower bleed rate and a better process performance. In the second step, steady states at constant CSPR but increasing VCD values are investigated, by properly adjusting the perfusion rate. In this case, the cellular activity remains constant, while the harvest yield and volumetric productivity further increase with higher perfusion rates. The product quality (charge variants, N-linked glycosylation) investigated during both steps of the procedure shows only minor changes among the different steady states. If product quality properties obtained at this point of the procedure are not satisfactory, they have to be fine-tuned in an additional step. As reported previously, the addition of supplements in the feed stream can be applied to induce significant changes in product quality.

Monitoring of antibody glycosylation pattern based on microarray MALDI-TOF mass spectrometry

Biologically manufactured monoclonal antibodies (mAb) can strongly vary in their efficacy and affinity. Therefore, engineering and production of the mAb is highly regulated and requires product monitoring, especially in terms of N-glycosylation patterns. In this work, we present a high-throughput matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) method based on a microarray technology to monitor N-glycopeptides of IgG1 produced in a perfusion cell culture. A bottom-up approach combined with zwitterionic-hydrophilic interaction liquid chromatography for sample purification was used to determine the day-by-day variation of the terminal galactose within two major N-glycoforms. Our results show that microarrays for mass spectrometry (MAMS) are a robust platform for the rapid determination of the carbohydrate distribution. The spectral repeatability is characterized by a low coefficient of variations (1.7% and 7.1% for the FA2 and FA2G1 structures, respectively) and allows to detect the N-glycosylation variability resulting from operating conditions during the bioreactor process. The observed trend of released N-glycans was confirmed using capillary gel electrophoresis with laser-induced fluorescence detection. Therefore, the microarray technology is a promising analytical tool for glycosylation control during the production process of recombinant proteins.

Perfusion cell culture for the production of conjugated recombinant fusion proteins reduces clipping and quality heterogeneity compared to batch-mode processes

Perfusion cell culture technologies for the production of therapeuthic recombinant proteins are currently on the rise for diverse applications with the aim of process intensification (Bielser et al., 2018; Chen et al., 2018; Fisher et al., 2018; Jordan et al., 2018). This study reports a unique comparison of low (LS) and high (HS) seeding fed-batch bioreactors, corresponding to traditional and intensified operation using perfusion at the N-1 stage, respectively, with perfusion (PF) bioreactors, using a bispecific conjugated fusion protein as a model. It is found that the gain in daily volumetric productivity compared to the traditional LS fed-batch, increases by a factor 3 with HS and 7 with PF. Critical quality attributes (CQAs) also benefited from the perfusion operation. In particular, levels of clipping, that is the fragmentation of the fusion protein, are significantly reduced compared to both fed-batch operations. In PF the clipping varied between 0.6 and 1.5% while in the LS and HS it reached up to 8.7 and 4.9%, respectively. Aggregate levels were also decreased using PF, while the charge variant distribution was more homogeneous and the glycosylation pattern was also significantly affected. The comparison of LS, HS and PF for the manufacturing of a bispecific conjugated fusion protein reported here highlight some productivity and quality benefits inherent to the nature of continuous processing.

A novel scale-down mimic of perfusion cell culture using sedimentation in an automated microbioreactor (SAM).

Continuous upstream processing in mammalian cell culture for recombinant protein production holds promise to increase product yield and quality. To facilitate the design and optimization of large-scale perfusion cultures, suitable scale-down mimics are needed which allow high-throughput experiments to be performed with minimal raw material requirements. Automated microbioreactors are available that mimic batch and fed-batch processes effectively but these have not yet been adapted for perfusion cell culture. This article describes how an automated microbioreactor system (ambr15) can be used to scale-down perfusion cell cultures using cell sedimentation as the method for cell retention. The approach accurately predicts the viable cell concentration, in the range of about 1 × 107 cells/mL for a human cell line, and cell viability of larger scale cultures using a hollow fiber based cell retention system. While it was found to underpredict cell line productivity, the method accurately predicts product quality attributes, including glycosylation profiles, from cultures performed in bioreactors with working volumes between 1 L and 1,000 L. The spent media exchange method using the ambr15 was found to predict the influence of different media formulations on large-scale perfusion cultures in contrast to batch and chemostat experiments performed in the microbioreactor system. The described experimental setup in the microbioreactor allowed an 80-fold reduction in cell culture media requirements, half the daily operator time, which can translate into a cost reduction of approximately 2.5-fold compared to a similar experimental setup at bench scale.

Process design and development of a mammalian cell perfusion culture in shake-tube and benchtop bioreactors.

The development of mammalian cell perfusion cultures is still laborious and complex to perform due to the limited availability of scale-down models and limited knowledge of time- and cost-effective procedures. The maximum achievable viable cell density (VCDmax ), minimum cell-specific perfusion rate (CSPRmin ), cellular growth characteristics, and resulting bleed rate at steady-state operation are key variables for the effective development of perfusion cultures. In this study, we developed a stepwise procedure to use shake tubes (ST) in combination with benchtop (BR) bioreactors for the design of a mammalian cell perfusion culture at high productivity (23 pg·cell-1 ·day-1 ) and low product loss in the bleed (around 10%) for a given expression system. In a first experiment, we investigated peak VCDs in STs by the daily discontinuous medium exchange of 1 reactor volume (RV) without additional bleeding. Based on this knowledge, we performed steady-state cultures in the ST system using a working volume of 10 ml. The evaluation of the steady-state cultures allowed performing a perfusion bioreactor run at 20 × 106 cells/ml at a perfusion rate of 1 RV/day. Constant cellular environment and metabolism resulted in stable product quality patterns. This study presents a promising strategy for the effective design and development of perfusion cultures for a given expression system and underlines the potential of the ST system as a valuable scale-down tool for perfusion cultures.

Effect of scaffold architecture on cell seeding efficiency: A discrete phase model CFD analysis

Within perfusion cell culture systems, scaffold architecture is able to control important biological parameters such as permeability and fluid flow-induced shear stress. As well, one of the main factors affecting the final fate of this process as well as optimal cell differentiation and proliferation in these systems is initial adhesion of cells to scaffolds. In this study, the effect of scaffold architecture on the adhesion of the cells was computationally investigated. For this purpose, four scaffold models including double-diamond, gyroid, FR-D, and Schwarz-primitive were designed using triply periodic minimal surface (TPMS) geometry with a constant porosity of 80%. As well, the inlet velocity of zero to simulate static cell culture and three different inlet velocities for modeling the dynamic cell culture conditions were also selected. The results showed that cell culture efficiency of scaffolds could be changed up to seven times from architecture to architecture under the same conditions. The efficiency of cell culture in scaffolds with tortuous architecture was also reported higher than those with relatively straight microchannels. In terms of culture methods, unlike dynamic cell culture model in which almost a homogeneous cell distribution was observed in static cell culture simulation, more cells adhered, but they had agglomerated in the scaffold entrance regions and had failed to reach all regions. The results of this study shed more light on the selection and design of scaffold architecture for optimal cell culture in tissue engineering.

Semi-continuous scale-down models for clone and operating parameter screening in perfusion bioreactors.

Perfusion cell culture, confined traditionally to the production of fragile molecules, is currently gaining broader attention in the biomanufacturing of therapeutic proteins. The development of these processes is made difficult by the limited availability of appropriate scale-down models. This is due to the continuous operation that requires complex control and cell retention capacity. For example, the determination of an optimal perfusion and bleed rate for continuous cell culture is often performed in scale-down bioreactors and requires a substantial amount of time and effort. To increase the experimental throughput and decrease the required workload, a semi-continuous procedure, referred to as the VCDmax (viable cell density) approach, has been developed on the basis of shake tubes (ST) and deepwell plates (96-DWP). Its effectiveness has been demonstrated for 12 different CHO-K1-SV cell lines expressing an IgG1. Further, its reliability has been investigated through proper comparisons with perfusion runs in lab-scale bioreactors. It was found that the volumetric productivity and the CSPRmin (cell specific perfusion rate) determined using the ST and 96-DWP models were successfully (mostly within the experimental error) confirmed in lab-scale bioreactors, which then covered a significant scale-up from the half milliliter to the liter scale. These scale-down models are very useful to design and scale-up optimal bioreactor operating conditions as well as screening for different media and cell lines.

PDMS microstencil plate-supported fabrication of ultra-thin, condensed ECM membranes for separated cell coculture on both surfaces

Thin membrane-based cell culture platforms have recently gained much attention for facilitating separated but adjacent cocultures of heterotypic cells in in vivo tissue-mimetic microenvironments. Here we propose a new approach to preparing significantly thin but highly stable membranes composed of extracellular matrix (ECM) components, mainly type I collagen, that are supported by PDMS microstencil plates. A collagen solution was introduced into the through holes of a microstencil plate and dried to form condensed membranes with a thickness of less than 1 μm. A coculture of HepG2 and Swiss-3T3 cells was performed on both membrane surfaces, and gene expression assays revealed the superiority of the presented thin membranes. Release of the membranes from the plate was possible, as was the integration of the membranes into microfluidic systems to perform perfusion cultures of cells. We were also able to prepare Matrigel membranes by the same procedure. The presented thin membrane-based cell culture platforms would provide physiologically suitable conditions for cells and thus would be widely applicable to a variety of in vitro cell culture systems.

Using a Microfluidic Device for Culture and Drug Toxicity Testing of 3D Cells.

Microfluidic devices provide convenient assays tools for testing cell cultures in three-dimensional (3D) formats. These devices have significant potential for establishing assays that are better at predicting drug toxicity and efficacy effects compared to assays in conventional two-dimensional (2D) cultures. Microfluidic cell culture devices consist of perfused cell culture chambers with inlets and outlet for seeding, culturing, sampling, and assaying the cells. This protocol describes how to prepare and seed cells in a microfluidic cell culture device for drug toxicity testing on cells in a 3D structure. The protocol exemplifies the use of a basic microfluidic device with HepG2 hepatoma cells but can be transferred and optimized for other cells and cell types, including iPSC-derived tissue and organ cells.

Long-Term Perfusion Culture of Monoclonal Embryonic Stem Cells in 3D Hydrogel Beads for Continuous Optical Analysis of Differentiation.

Developmental cell biology requires technologies in which the fate of single cells is followed over extended time periods, to monitor and understand the processes of self-renewal, differentiation, and reprogramming. A workflow is presented, in which single cells are encapsulated into droplets (Ø: 80 µm, volume: ≈270 pL) and the droplet compartment is later converted to a hydrogel bead. After on-chip de-emulsification by electrocoalescence, these 3D scaffolds are subsequently arrayed on a chip for long-term perfusion culture to facilitate continuous cell imaging over 68 h. Here, the response of murine embryonic stem cells to different growth media, 2i and N2B27, is studied, showing that the exit from pluripotency can be monitored by fluorescence time-lapse microscopy, by immunostaining and by reverse-transcription and quantitative PCR (RT-qPCR). The defined 3D environment emulates the natural context of cell growth (e.g., in tissue) and enables the study of cell development in various matrices. The large scale of cell cultivation (in 2000 beads in parallel) may reveal infrequent events that remain undetected in lower throughput or ensemble studies. This platform will help to gain qualitative and quantitative mechanistic insight into the role of external factors on cell behavior.

The effect of hyperosmolality application time on production, quality, and biopotency of monoclonal antibodies produced in CHO cell fed-batch and perfusion cultures.

Hyperosmolality has been commonly investigated due to its effects on the production and quality characteristics of monoclonal antibodies (mAbs) produced in CHO cell fed-batch cultures. However, the application of hyperosmolality at different times and its effect on biopotency have seldom been researched, especially in perfusion culture. In our study, different degrees of hyperosmolality induced by sodium chloride were investigated in anti-IgE rCHO cell fed-batch cultures and anti-CD52 rCHO cell perfusion cultures during the initial and stable phases. The results showed that the initial hyperosmolality group (IHG) in fed-batch and early phase of perfusion cultures exhibited significant suppression of the viable cell density yet an enhancement in specific productivity, whereas the stable hyperosmolality group (SHG) achieved higher mAb production in both fed-batch and perfusion cultures. Additionally, the SHG produced less aggregates and acidic charge variants than IHG in fed-batch culture, which differed from perfusion cultures. However, the contents of non-glycosylation heavy chain (NGHC) and man5 were higher in SHG than in IHG in fed-batch cultures at plus 60 and 120mOsm/kg, which was similar to perfusion cultures. Furthermore, the biopotency in the IHG was higher than in the SHG at plus 60 and 120mOsm/kg in fed-batch cultures, which is similar to complement-dependent cytotoxicity (CDC) efficacy in perfusion cultures. The biopotency of all group was acceptable, except FI3. Thus, the study shows that hyperosmolality at a certain level could be beneficial for both mAb production, quality and biopotency, which could play an important role in process development for commercial production.

Larger Pore Size Hollow Fiber Membranes as a Solution to the Product Retention Issue in Filtration-Based Perfusion Bioreactors.

Tangential flow filtration (TFF) and alternating tangential flow (ATF) filtration technologies using hollow fiber membranes are commonly utilized in perfusion cell culture for the production of monoclonal antibodies; however, product retention remains a known and common problem with these systems. To address this issue, commercially available hollow fibers ranging from several hundred kilo-Daltons (kDa) to 0.65 μm in nominal pore size are tested and are all demonstrated to undergo moderate to severe product retention. Further investigation revealed accumulation of particles in the same size range (≈20-200 nm) as the pores. Based on the assumption that these particles contribute to product retention and membrane plugging, a hollow fiber with an unconventionally larger pore size is subsequently identified and demonstrated to drastically reduce product retention with no impact to cell clarification. Furthermore, these hollow fibers demonstrate surprisingly high membrane capacities, making them an attractive solution to the problem of product retention in perfusion reactors.

The effects of alternating tangential flow (ATF) residence time, hydrodynamic stress, and filtration flux on high-density perfusion cell culture.

In this study, we investigated the effects of alternating tangential flow (ATF) cell separation on high-density perfusion cultures. We have developed methods to estimate theoretical residence times of cells in the ATF system and discovered that long residence times (above 75 s) correlate with decreased growth, metabolism, and productivity. We have calculated energy dissipation rates in the ATF transfer line and filter and empirically studied the impacts of increased exchange rates on cell culture, determining that increased hydrodynamic stress can lead to decreased cell size, lactate production, and specific productivity. Finally, we have conducted experiments to understand the relationship between filtration fluxes and ATF membrane fouling, finding that at fluxes above 60 L·m-2 ·day -1 , protein sieving coefficients see significant rates of decrease (greater than 1% per day). While most of these studies have been conducted with one cell line at one target viable cell density (40 million cells/ml), the general, directional knowledge arising from this study should be applicable to other conditions and programs, ultimately leading to more robust and well-designed perfusion processes.

Shift to high-intensity, low-volume perfusion cell culture enabling a continuous, integrated bioprocess.

In order to address the increasing demand for biologics, cell culture intensification using perfusion offers significantly higher productivities while also reducing manufacturing costs, especially when part of an integrated, continuous bioprocess. An initial study of a long-duration perfusion process using a cell-bleed to maintain a target cell density observed a 2.1-fold higher cell-specific productivity and a gradual decline in the culture growth rate when perfused at an overall lower rate. Subsequent studies sought an alternative process that largely reduced the overall volume of media needed by first perfusing at a high cell-specific perfusion rate (CSPR) to support a high cell density followed by continued perfusion at a low CSPR to promote a more productive stationary phase. This high intensity, low-volume perfusion (HILVOP) process achieved cumulative volumetric productivities of 1.5-1.6 g/L/day with two CHO cell lines. When compared to each cell line's respective commercial-ready, fed-batch process, a 3.1-3.8-fold productivity increase was demonstrated while yielding similar product quality. Furthermore, the higher productivity achieved with HILVOP used 6.6-12.3-fold less media than a similarly productive long-duration process. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:1472-1481, 2018.

A microfluidic chip with gravity-induced unidirectional flow for perfusion cell culture.

Perfusion flow is one of the essential elements and advantages of organ-on-a-chip technology. For example, microfluidics have enabled implementation of perfusion flow and recapitulation of fluidic environment for vascular endothelial cells. The most prevalent method of implementing flow in a chip is to use a pump, which requires elaborate manipulation and complex connections, and accompanies a large amount of dead volume. Previously we devised a gravity-induced flow system which does not require tubing connections, but this method results in bidirectional flow to enable recirculation, which is somewhat different from physiological blood flow. Here, we have developed a novel microfluidic chip that enables gravity-induced, unidirectional flow by using a bypass channel with geometry different from the main channel. Human umbilical vein endothelial cells were cultured inside the chip and the effect of flow direction was examined. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2701, 2019.

Glycosylation Flux Analysis of Immunoglobulin G in Chinese Hamster Ovary Perfusion Cell Culture

The terminal sugar molecules of the N-linked glycan attached to the fragment crystalizable (Fc) region is a critical quality attribute of therapeutic monoclonal antibodies (mAbs) such as immunoglobulin G (IgG). There exists naturally-occurring heterogeneity in the N-linked glycan structure of mAbs, and such heterogeneity has a significant influence on the clinical safety and efficacy of mAb drugs. We previously proposed a constraint-based modeling method called glycosylation flux analysis (GFA) to characterize the rates (fluxes) of intracellular glycosylation reactions. One contribution of this work is a significant improvement in the computational efficiency of the GFA, which is beneficial for analyzing large datasets. Another contribution of our study is the analysis of IgG glycosylation in continuous perfusion Chinese Hamster Ovary (CHO) cell cultures. The GFA of the perfusion cell culture data indicated that the dynamical changes of IgG glycan heterogeneity are mostly attributed to alterations in the galactosylation flux activity. By using a random forest regression analysis of the IgG galactosylation flux activity, we were further able to link the dynamics of galactosylation with two process parameters: cell-specific productivity of IgG and extracellular ammonia concentration. The characteristics of IgG galactosylation dynamics agree well with what we previously reported for fed-batch cultivations of the same CHO cell strain.

High-density Vero cell perfusion culture in BioBLU 5p single-use vessels

Inflammation may underlie the association between obesity, atherosclerosis and cardiovascular disease. We investigated to what extent markers of inflammation mediate associations between overall and visceral body fat and subclinical atherosclerosis.In this cross-sectional analysis of the Netherlands Epidemiology of Obesity study we estimated total body fat (TBF) by bio-impedance analysis, carotid artery intima media thickness (cIMT) by ultrasound, C-reactive protein (hs-CRP) and glycoprotein acetyls (GlycA) concentrations in fasting blood samples (n = 5627), and visceral adipose tissue (VAT) by magnetic resonance imaging (n = 2247). We examined associations between TBF and VAT, and cIMT using linear regression, adjusted for potential confounding factors, and for mediators: cardiometabolic risk factors (blood pressure, glucose and low-density lipoprotein cholesterol), and inflammation using CRP and GlycA as proxies.Mean (SD) cIMT was 615 (90) μm. Per SD of TBF (8%), cIMT was 19 μm larger (95% confidence interval, CI: 10, 28). This association was 17 μm (95% CI: 8, 27) after adjustment for cardiometabolic risk factors, and did not change after adjustment for markers of inflammation. Per SD (56 cm2) VAT, cIMT was 9 μm larger (95% CI: 2, 16) which changed to 5 μm (95% CI: −3, 12) after adjustment for cardiometabolic risk factors, and did not change after adjustment for inflammatory markers.Our results suggest that associations between measures of overall and visceral body fat and subclinical atherosclerosis are not mediated by inflammation as measured by CRP and GlycA. Obesity may exert cardiovascular risk via other markers of systemic inflammation.

Computational fluid dynamic modeling of alternating tangential flow filtration for perfusion cell culture.

Alternating tangential flow (ATF) filtration has been successfully adopted as a low shear cell separation device in many perfusion‐based processes. The reverse flow per cycle is used to minimize fouling compared with tangential flow filtration. Currently, modeling of the ATF system is based on empirically derived formulas, leading to oversimplification of model parameters. In this study, an experimentally validated porous computational fluid dynamic (CFD) model was used to predict localized fluid behavior and pressure profiles in the ATF membrane for both water and supernatant solutions. The results provided numerical evidence of Starling flow phenomena that has been theorized but not previously proven for the current operating parameters. Additionally, feed cross flow velocity was shown to significantly impact the localized flux distribution; higher feed cross flow rates lead to an increased localized permeate flux as well as irreversible and reversible fouling resistance. Further, the small average permeate flux values of 2 L·m−2·h−1 traditionally used in perfusion bioreactor membranes lead to approximately 50% of the membrane length utilized for permeate flow during each pressure and exhaust phase, leading to a full membrane utilization during one ATF cycle. Our preliminary CFD results demonstrate that local flux and resistance distribution further elucidate the dynamics of ATF membrane fouling in a perfusion‐based system.

Development of a shake tube-based scale-down model for perfusion cultures.

The use of benchtop bioreactors (BRs) for the development of mammalian cell perfusion cultures is expensive and time consuming, given its complexity in equipment and operation. Scale-down models, going from liter to milliliter scale, are needed to support the rapid determination of suitable operating conditions in terms of viable cell density (VCD), perfusion rate, and medium composition. In this study, we compare the performance of steady-state perfusion cultures in orbitally shaken tube and BR systems for a given Chinese hamster ovary cell line. The developed scale-down model relied on a daily workflow designed to keep the VCD constant at specific target values. This includes: cell count, removal of excessive cells (bleeding), spin down of remaining cells, harvest of cell-free supernatant, and resuspension in fresh medium. Steady-state cultures at different VCD values, medium exchange rates and working volumes were evaluated. Shake-tube perfusion cultures allowed the prediction of cell-specific growth, glucose consumption, ammonia, and monoclonal antibody production rates for much larger BRs, but not lactate (LAC) production rates. Although charge variant profiles remained comparable, different glycosylation patterns were obtained. The differences in LAC production and glycosylation probably resulted from the discontinuous medium exchange, the poor carbon dioxide removal, and the deficient pH control. Therefore, if requested by the specific process to be developed, product quality has to be fine-tuned directly in the BR system. Altogether, the developed strategy provides a useful scale-down model for the design and optimization of perfusion cultures with strong savings in time and media consumption.

Real-time measurement of cholesterol secreted by human hepatocytes using a novel microfluidic assay.

The use of microfluidics has become widespread in recent years because of the use of lesser resources such as small size, low volume of reagents, and physiological representation of mammalian cells. One of the advantages of microfluidic-based cell culture is the ability to perfuse culture media which tends to improve cellular health and function. Although measurement of cellular function conventionally is carried out using well-plates and plate readers, these approaches are insufficient to carry out in-line analysis of perfused cell cultures because of mismatch between volumes and sensitivity. We report the development of a novel microfluidic device and assay that is carried out under perfusion, in-line to measure the cholesterol secreted from a human hepatocyte tissue-chip. The heart of the assay is the unique implementation of enzymatic chemistry that is carried out on a polystyrene bead. Using this approach, we successfully measured cholesterol secreted by the perfused human hepatocytes.