Scale‐down models to optimize a filter train for the downstream purification of recombinant pharmaceutical proteins produced in tobacco leaves

The extraction of biopharmaceutical proteins from intact leaves involves the release of abundant particulate contaminants that must be removed economically from the process stream before chromatography, for example, using disposable filters that comply with good manufacturing practice. We therefore scaled down an existing 200‐kg process for the purification of two target proteins from tobacco leaves (the monoclonal antibody 2G12 and the fluorescent protein DsRed, as monitored by surface plasmon resonance spectroscopy and fluorescence imaging, respectively) and screened different materials on the 2‐kg scale to reduce the number of depth filtration steps from three to one. We assessed filter cost and capacity, filtrate turbidity, and protein recovery when the filter materials were challenged with extracts from different tobacco varieties and related species grown in soil or rockwool. PDF4 was consistently the most suitable depth filter because it was the least expensive, it did not interact significantly with the target proteins, and it had the greatest overall capacity. The filter capacity was generally reduced when plants were grown in rockwool, but this substrate has a low bioburden, thus improving process safety. Our data concerning the clarification of plant extracts will help in the design of more cost‐effective downstream processes and accelerate their development.     

Clarification of recombinant proteins from high cell density mammalian cell culture systems using new improved depth filters

Increasingly high cell density, high product titer cell cultures containing mammalian cells are being used for the production of recombinant proteins. These high productivity cultures are placing a larger burden on traditional downstream clarification and purification operations due to higher product and impurity levels. Controlled flocculation and precipitation of mammalian cell culture suspensions by acidification or using polymeric flocculants have been employed to enhance clarification throughput and downstream filtration operations. While flocculation is quite effective in agglomerating cell debris and process related impurities such as (host cell) proteins and DNA, the resulting suspension is generally not easily separable solely using conventional depth filtration techniques. As a result, centrifugation is often used for clarification of cells and cell debris before filtration, which can limit process configurations and flexibility due to the investment and fixed nature of a centrifuge. To address this challenge, novel depth filter designs were designed which results in improved primary and secondary direct depth filtration of flocculated high cell density mammalian cell cultures systems feeds, thereby providing single‐use clarification solution. A framework is presented here for optimizing the particle size distribution of the mammalian cell culture systems with the pore size distribution of the gradient depth filter using various pre‐treatment conditions resulting in increased depth filter media utilization and improved clarification capacity. Feed conditions were optimized either by acidification or by polymer flocculation which resulted in the increased average feed particle‐size and improvements in throughput with improved depth filters for several mammalian systems. Biotechnol. Bioeng. 2013; 110: 1964–1972. © 2013 Wiley Periodicals, Inc.     

Application of calcium phosphate flocculation in high-density cell culture fluid with high product titer of monoclonal antibody

The calcium phosphate [Ca₃(PO4)₂] precipitation was used for improving the clarification efficiency in harvest process of the monoclonal antibody (mAb) containing cell culture fluid (CCF) with high turbidity and product titer. The flocculation conditions (concentration, addition order of flocculants, pH, and operation time), and the effect of flocculants on the mAb physical chemical properties (such as distribution of charge variants and aggregates) and process-related impurities removal (such as DNA and CHOP) were evaluated in this study. The results showed that the turbidity of CCF supernatant was significantly reduced at pH 7, 120 min with addition of phosphate ions first, while a high mAb recovery yield was kept in the CCF supernatant after flocculation. Addition of calcium ions at 15–60 mM was sufficient for flocculation in this study. A relationship between turbidity/mAb recovery yield and the concentration of calcium ions was established. More than 85% DNA in the CCF were effectively removed by the addition of optimal concentration of flocculants. Flocculation process of Ca₃(PO4)₂ is an effective pretreatment method in purification processes of mAbs from the CCF with high turbidity and product titer.

     

Artificial neural network (ANN)‐based prediction of depth filter loading capacity for filter sizing

This article presents an application of artificial neural network (ANN) modelling towards prediction of depth filter loading capacity for clarification of a monoclonal antibody (mAb) product during commercial manufacturing. The effect of operating parameters on filter loading capacity was evaluated based on the analysis of change in the differential pressure (DP) as a function of time. The proposed ANN model uses inlet stream properties (feed turbidity, feed cell count, feed cell viability), flux, and time to predict the corresponding DP. The ANN contained a single output layer with ten neurons in hidden layer and employed a sigmoidal activation function. This network was trained with 174 training points, 37 validation points, and 37 test points. Further, a pressure cut‐off of 1.1 bar was used for sizing the filter area required under each operating condition. The modelling results showed that there was excellent agreement between the predicted and experimental data with a regression coefficient (R²) of 0.98. The developed ANN model was used for performing variable depth filter sizing for different clarification lots. Monte‐Carlo simulation was performed to estimate the cost savings by using different filter areas for different clarification lots rather than using the same filter area. A 10% saving in cost of goods was obtained for this operation. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1436–1443, 2016     

Robust depth filter sizing for centrate clarification

Cellulosic depth filters embedded with diatomaceous earth are widely used to remove colloidal cell debris from centrate as a secondary clarification step during the harvest of mammalian cell culture fluid. The high cost associated with process failure in a GMP (Good Manufacturing Practice) environment highlights the need for a robust process scale depth filter sizing that allows for (1) stochastic batch‐to‐batch variations from filter media, bioreactor feed and operation, and (2) systematic scaling differences in average performance between filter sizes and formats. Matched‐lot depth filter media tested at the same conditions with consecutive batches of the same molecule were used to assess the sources and magnitudes of process variability. Depth filter sizing safety factors of 1.2–1.6 allow a filtration process to compensate for random batch‐to‐batch process variations. Matched‐lot depth filter media in four different devices tested simultaneously at the same conditions was used with a common feed to assess scaling effects. All filter devices showed <11% capacity difference and the Pod format devices showed no statistically different capacity differences. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1542–1550, 2015     

Exploitation of the adsorptive properties of depth filters for host cell protein removal during monoclonal antibody purification

Depth filtration has been widely used during process scale clarification of cell culture supernatants for the removal of cells and cell debris. However, in addition to their filtration capabilities, depth filters also possess the ability to adsorb soluble species. This aspect of depth filtration has largely not been exploited in process scale separations and is usually ignored during cell culture harvest development. Here, we report on the ability of depth filters to adsorptively remove host cell protein contaminants from a recombinant monoclonal antibody process stream and characterize some of the underlying interactions behind the binding phenomenon. Following centrifugation, filtration through a depth filter prior to Protein A chromatographic capture was shown to significantly reduce the level of turbidity observed in the Protein A column eluate of the monoclonal antibody. The Protein A eluate turbidity was shown to be linked to host cell protein contaminant levels in the Protein A column load and not to the DNA content. Analogous to flowthrough chromatography in which residence time/bed height and column loading are key parameters, both the number of passes through the depth filter and the amount of centrifuge centrate loaded on the filter were seen to be important operational parameters governing the adsorptive removal of host cell protein contaminants. Adsorption of proteins to the depth filter was shown to be due to a combination of electrostatic and hydrophobic adsorptive interactions. These results demonstrate the ability to employ depth filtration as an integrative unit operation combining filtration for particulate removal with adsorptive binding for contaminant removal.     

Pretreatments for enhancing clarification efficiency of depth filtration during production of monoclonal antibody therapeutics

High cell density, high product titer mammalian cell culture is the new paradigm for production of recombinant proteins. While the typical motivation is to get a high product titer, additional undesirable outcomes often include an increase in percentage solids in the cell culture fluid (cellular debris and sub-micron colloids), thereby offering new challenges to downstream processing. This article focuses on scouting and comparison of different approaches used for clarification of cell culture fluid. The approaches include centrifugation followed by depth filtration, direct depth filtration without centrifugation and feed pretreatment with use of specially designed density gradient filtration to improve efficiency of clarification and removal of process contaminants from feed stream. The work also evaluates impact of three different pretreatment approaches, namely pH adjustment to acidic condition, metal cation (calcium phosphate) flocculation, and polycationic polymer flocculation (using polymer-I and polymer-II). The results obtained indicate that the use of pretreatment significantly improves the clarification efficiency of depth filtration. Pretreatment options like polycationic polymer-I based flocculation resulted in a >5 fold reduction in filter area requirement as well as >6 fold reduction in HCDNA while retaining acceptable recovery of the IgG (>98%). Thus, pretreatment offers a significant reduction in the depth filtration footprint (~5–6 fold decrease in filter area requirement). However, one must take into consideration the process development time required, capital cost, consumable cost, cost of the pretreatment chemical, cost of testing to demonstrate clearance of treatment agent, ease of scale-ability, and process robustness when finalizing the optimal clarification approach.     

The impact of Pseudomonas syringae type III effectors on transient protein expression in tobacco

The production of recombinant proteins in plants is often achieved by transient expression, e.g. following the injection or vacuum infiltration of Agrobacterium tumefaciens into tobacco leaves. We investigated the associated plant defence responses, revealing that callose deposition is triggered by T–DNA transfer and that subsets of secondary metabolites accumulate in response to mechanical wounding or the presence of bacteria. We also tested the ability of five co‐expressed type III effector proteins from Pseudomonas syringae to modulate these defence responses and increase the yield of two model proteins, the fluorescent marker DsRed and monoclonal antibody 2G12. HopF2 and AvrRpt2 induced necrotic lesions 5 days post‐injection (dpi) even at low doses (OD_600 nm = 0.0078), and increased the concentration of certain secondary metabolites. HopAO1 significantly reduced the number of callose deposits at 2 dpi compared to cells expressing DsRed and 2G12 alone, whereas HopI1 reduced the concentration of several secondary metabolites at 5 dpi compared to cells expressing DsRed and 2G12 alone. Co‐expression with HopAO1, AvrPtoB or HopI1 increased the concentrations of DsRed and 2G12 increased by ~6% but this was not a significant change. In contrast, HopF2 and AvrRpt2 significantly reduced the concentrations of DsRed and 2G12 by 34% and 22%, respectively. Our results show that type III effector proteins can modulate plant defence responses and secondary metabolite profiles but that transient co‐expression is not sufficient to increase the yields of target recombinant proteins in tobacco.     

Process cost and facility considerations in the selection of primary cell culture clarification technology

The bioreactor volume delineating the selection of primary clarification technology is not always easily defined. Development of a commercial scale process for the manufacture of therapeutic proteins requires scale‐up from a few liters to thousands of liters. While the separation techniques used for protein purification are largely conserved across scales, the separation techniques for primary cell culture clarification vary with scale. Process models were developed to compare monoclonal antibody production costs using two cell culture clarification technologies. One process model was created for cell culture clarification by disc stack centrifugation with depth filtration. A second process model was created for clarification by multi‐stage depth filtration. Analyses were performed to examine the influence of bioreactor volume, product titer, depth filter capacity, and facility utilization on overall operating costs. At bioreactor volumes <1,000 L, clarification using multi‐stage depth filtration offers cost savings compared to clarification using centrifugation. For bioreactor volumes >5,000 L, clarification using centrifugation followed by depth filtration offers significant cost savings. For bioreactor volumes of ～2,000 L, clarification costs are similar between depth filtration and centrifugation. At this scale, factors including facility utilization, available capital, ease of process development, implementation timelines, and process performance characterization play an important role in clarification technology selection. In the case study presented, a multi‐product facility selected multi‐stage depth filtration for cell culture clarification at the 500 and 2,000 L scales of operation. Facility implementation timelines, process development activities, equipment commissioning and validation, scale‐up effects, and process robustness are examined. © 2013 The Authors. American Institute of Chemical Engineers Biotechnol. Prog., 29:1239–1245, 2013     

The effect of antiapoptosis genes on clarification performance

Optimal bioreactor harvest time is typically determined based on maximizing product titer without compromising product quality. We suggest that ease of downstream purification should also be considered during harvest. In this view, we studied the effect of antiapoptosis genes on downstream performance. Our hypothesis was that more robust cells would exhibit less cell lysis and thus generate lower levels of cell debris and host‐cell contaminants. We focused on the clarification unit operation, measuring postclarification turbidity and host‐cell protein (HCP) concentration as a function of bioreactor harvest time/cell viability. In order to mimic primary clarification using disk‐stack centrifugation, a scale‐down model consisting of a rotating disk (to simulate shear in the inlet feed zone of the centrifuge) and a swinging‐bucket lab centrifuge was used. Our data suggest that in the absence of shear during primary clarification (typical of depth filters), a 20–50% reduction in HCP levels and 50–65% lower postcentrifugation turbidity was observed for cells with antiapoptosis genes compared to control cells. However, on exposing the cells to shear levels typical in a disk‐stack centrifuge, the reduction in HCP was 10–15% while no difference in postcentrifugation turbidity was observed. The maximum benefit of antiapoptosis genes is, therefore, realized using clarification options that involve low shear, <1 × 10⁶ W/m³ and minimal damage to the cells. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 30:100–107, 2014     

Evaluation of Dewatering Performance and Fractal Characteristics of Alum Sludge

The dewatering performance and fractal characteristics of alum sludge from a drinking-water treatment plant were investigated in this study. Variations in residual turbidity of supernatant, dry solid content (DS), specific resistance to filtration (SRF), floc size, fractal dimension, and zeta potential were analyzed. Sludge dewatering efficiency was evaluated by measuring both DS and SRF. Results showed that the optimum sludge dewatering efficiency was achieved at 16 mg∙L^-1 flocculant dosage and pH 7. Under these conditions, the maximum DS was 54.6%, and the minimum SRF was 0.61 × 10¹⁰ m∙kg^-1. Floc-size measurements demonstrated that high flocculant dosage significantly improved floc size. Correlation analysis further revealed a strong correlation between fractal dimension and floc size after flocculation. A strong correlation also existed between floc size and zeta potential, and flocculants with a higher cationic degree had a larger correlation coefficient between floc size and zeta potential. In the flocculation process, the main flocculation mechanisms involved adsorption bridging under an acidic condition, and a combination between charge neutralization and adsorption-bridging interaction under neutral and alkaline conditions.     

黄孢原毛平革菌产絮凝剂营养条件优化

微生物絮凝剂与传统化学絮凝剂相比,安全无毒、无二次污染,具有开发潜力.黄孢原毛平革菌(Phanerochaete chrysosporium)能产生微生物絮凝剂,但目前缺少对其产絮凝剂营养条件的优化.使用高岭土并利用单因素法研究碳源、氮源、碳氮比、接种量对Phanerochaete chrysosporium产絮凝剂的...     

Virus filtration of high‐concentration monoclonal antibody solutions

The ability to process high‐concentration monoclonal antibody solutions (> 10 g/L) through small‐pore membranes typically used for virus removal can improve current antibody purification processes by eliminating the need for feed stream dilution, and by reducing filter area, cycle‐time, and costs. In this work, we present the screening of virus filters of varying configurations and materials of construction using MAb solutions with a concentration range of 4–20 g/L. For our MAbs of interest—two different humanized IgG1s—flux decay was not observed up to a filter loading of 200 L/m² with a regenerated cellulose hollow fiber virus removal filter. In contrast, PVDF and PES flat sheet disc membranes were plugged by solutions of these same MAbs with concentrations >4 g/L well before 50 L/m². These results were obtained with purified feed streams containing <2% aggregates, as measured by size exclusion chromatography, where the majority of the aggregate likely was composed of dimers. Differences in filtration flux performance between the two MAbs under similar operating conditions indicate the sensitivity of the system to small differences in protein structure, presumably due to the impact of these differences on nonspecific interactions between the protein and the membrane; these differences cannot be anticipated based on protein pI alone. Virus clearance data with two model viruses (XMuLV and MMV) confirm the ability of hollow fiber membranes with 19 ± 2 nm pore size to achieve at least 3–4 LRV, independent of MAb concentration, over the range examined. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Leveraging mathematical models for optimizing filter utility at manufacturing scale

In the production of biopharmaceuticals depth filters followed by sterile filters are often employed to remove residual cell debris present in the feed stream. In the back drop of a global pandemic, supply chains associated with the production of biopharmaceuticals have been constrained. These constraints have limited the available amount of depth filters for the manufacture of biologics. This has placed manufacturing facilities in a difficult position having to choose between running processes with reduced number of depth filters and risking a failed batch or the prospect of plants going into temporary shutdown until the depth filter resources are replenished. This communication describes a modeling based method that leverages manufacturing scale filtration data to predict the depth filter performance with a reduced number of filters and an increased operational flux. This method can be used to quantify the acceptable level of area reduction before which the filtration process performance is affected. This enables facilities to manage their filter inventory avoiding potential plant shutdowns and reduces the risks of negative depth filter performance.     

Single-stage chromatographic clarification of Chinese Hamster Ovary cell harvest reduces cost of protein production

A single-stage clarification was developed using a single-use chromatographic clarification device (CCD) to recover a recombinant protein from Chinese Hamster Ovary (CHO) harvest cell culture fluid (HCCF). Clarification of a CHO HCCF is a complex and costly process, involving multiple stages of centrifugation and/or depth filtration to remove cells and debris and to reduce process-related impurities such as host cell protein (HCP), nucleic acids, and lipids. When using depth filtration, the filter train consists of multiple filters of varying ratios, layers, pore sizes, and adsorptive properties. The depth filters, in combination with a 0.2-micron membrane filter, clarify the HCCF based on size-exclusion, adsorptive, and charge-based mechanisms, and provide robust bioburden control. Each stage of the clarification process requires time, labor, and utilities, with product loss at each step. Here, use of the 3M™ Harvest RC Chromatographic Clarifier, a single-stage CCD, is identified as an alternative strategy to a three-stage filtration train. The CCD results in less overall filter area, less volume for flushing, and higher yield. Using bioprocess cost modeling, the single-stage clarification process was compared to a three-stage filtration process. By compressing the CHO HCCF clarification to a single chromatographic stage, the overall cost of the clarification process was reduced by 17%–30%, depending on bioreactor scale. The main drivers for the cost reduction were reduced total filtration area, labor, time, and utilities. The benefits of the single-stage harvest process extended throughout the downstream process, resulting in a 25% relative increase in cumulative yield with comparable impurity clearance.     

Coagulation/flocculation-based removal of algal-bacterial biomass from piggery wastewater treatment

Two conventional chemical coagulants (FeCl₃ and Fe₂(SO₄)₃) and five commercial polymeric flocculants (Drewfloc 447, Flocudex CS/5000, Flocusol CM/78, Chemifloc CV/300 and Chitosan) were comparatively evaluated for their ability to remove algal-bacterial biomass from the effluent of a photosynthetically oxygenated piggery wastewater biodegradation process. Chlorella sorokiniana, Scenedesmus obliquus, Chlorococcum sp. and a wild type Chlorella, in symbiosis with a bacterial consortium, were used as model algal-bacterial consortia. While the highest biomass removals (66-98%) for the ferric salts were achieved at concentrations of 150-250 mg L⁻¹, dosages of 25-50 mg L⁻¹ were required for the polymer flocculants to support comparable removal efficiencies. Process efficiency declined when the polymer flocculant was overdosed. Biomass concentration did not show a significant impact on flocculation within the concentration range tested. The high flocculant requirements herein recorded might be due to the competition of colloidal organic for the flocculants and the stationary phase conditions of biomass.     

利用污泥提取液制备微生物絮凝剂

以污水厂剩余污泥作为培养基原料,经过一系列处理,探索微生物絮凝剂产生菌的最适发酵培养基配方,结果表明,污泥预处理条件以pH 12碱解条件最优,碳氮源产出量最大,补加8 g/L葡萄糖后灭菌,微生物絮凝剂产生菌LLin6可正常产絮,絮凝率达91.55%。该结果为降低微生物絮凝剂的制备成本,并实现污泥的减量化和污泥资源化利用提供了基础。     

IMAC capture of recombinant protein from unclarified mammalian cell feed streams

Fusion‐tag affinity chromatography is a key technique in recombinant protein purification. Current methods for protein recovery from mammalian cells are hampered by the need for feed stream clarification. We have developed a method for direct capture using immobilized metal affinity chromatography (IMAC) of hexahistidine (His6) tagged proteins from unclarified mammalian cell feed streams. The process employs radial flow chromatography with 300–500 μm diameter agarose resin beads that allow free passage of cells but capture His‐tagged proteins from the feed stream; circumventing expensive and cumbersome centrifugation and/or filtration steps. The method is exemplified by Chinese Hamster Ovary (CHO) cell expression and subsequent recovery of recombinant His‐tagged carcinoembryonic antigen (CEA); a heavily glycosylated and clinically relevant protein. Despite operating at a high NaCl concentration necessary for IMAC binding, cells remained over 96% viable after passage through the column with host cell proteases and DNA detected at ～8 U/mL and 2 ng/μL in column flow‐through, respectively. Recovery of His‐tagged CEA from unclarified feed yielded 71% product recovery. This work provides a basis for direct primary capture of fully glycosylated recombinant proteins from unclarified mammalian cell feed streams. Biotechnol. Bioeng. 2016;113: 130–140. © 2015 Wiley Periodicals, Inc.     

Flocculation of microalgae in brackish and sea waters

Flocculation is an essential step in the concentration and harvesting of microalgae from aquatic media. Salinity of brackish water and sea water requires high flocculant dosages and renders flocculation less effective than in freshwater algal media. Experiments with the marine microalgae Isochrysis galbana and Chlorella stigmatophora showed that effective alum or ferric chloride flocculation was obtained only with dosages which are 5 to 10 times higher than the dosages required for the flocculation of freshwater microalgae. The flocculant dosages required for removing over 90% of the algae from suspensions were found to increase linearly with salinity as expressed in ionic strength. High salinity was found to inhibit flocculation with polyelectrolytes which are quite effective in freshwater algae flocculation. This inhibition was diminished at reduced salinity levels and effective flocculation was attained at salinity levels of 5 g/liter and below, which is typical of desert brackish water. Two methods were found to induce flocculation in sea water: (a) combining polyelectrolytes with inorganic flocculants such as ferric chloride or alum, and (b) ozone oxidation pretreatment followed by flocculation with inorganic flocculants.     

Process development and optimisation of lactic acid purification using electrodialysis

Cell free sodium lactate solutions were subjected to purification based on mono- and bi-polar electrodialysis. Lactate concentration in the product stream increased to a maximum of 15% during mono-polar electrodialysis. Stack energy consumption averaged 0.6 kW h kg(-1) lactate transported at current efficiencies in the 90% range. Under optimum feed concentration (125 g l(-1)) and process conditions (auto-current mode with conductivity setpoints of minimum 5 and maximum 40 mS cm(-1)), lactate flux reached 300 g m(-2) h(-1) and water flux were low for mono-polar electrodialysis averaging 0.3 kg H(2)O per M lactate transported. Glucose in the concentrate stream solutions was reduced to < 2 g l(-1). Acetate impurities enriched from about 0.5 g l(-1) in the feed stream to 1.5 g l(-1) in the concentrate stream solutions. After mono-polar electrodialysis, the concentrated sodium lactate solutions were further purified using bi-polar electrodialysis. Water transport during bi-polar electrodialysis reached figures of 0.070 - 0.222 kg H(2)O per M lactate. Free lactic acid concentration reached 16% with lactate flux of up to 300 g m(-2) h(-1). Stack energy consumption ranged from 0.6 to 1 kW h per kg lactate. Under optimised process conditions current efficiency during bi-polar electrodialysis was consistently around 90%. Glucose was further reduced from 2 to <1 g l(-1) in the free lactic acid solution. Acetic acid impurity remained at around 1 g l(-1). Significant reduction in colour and minerals in the product streams was observed during electrodialysis purification.