Crude Cell Culture Research Articles

Characterization of Extracellular Chitinase from Bacillus cereus SAHA 12.13 and Its Potency as a Biocontrol of Curvularia affinis

Bacillus cereus SAHA 12.13 can produce chitinase, an enzyme that digests chitin in the main compounds of cell walls, mycelia, and spores in pathogenic fungi that cause leaf spots on oil palm plants such as Curvularia affinis. This study aims to determine the properties of the chitinase enzyme B. cereus SAHA 12.13 that can inhibit the growth of C. affinis. Chitinase enzyme production and characterization were measured using the Spindler method. Antagonism test against pathogenic fungi using dual culture method by testing cell culture and enzyme crude extract. This result showed that the isolate produced a high level of specific chitinase activity at 37 °C for 45 h of incubation with 8.45 U mg-1 proteins with a growth rate (k) of 0.25 generation/h, and the generation time was 3.96 h/generation. The optimum chitinase activity was achieved at pH 7.0 and 45 °C and was stable for 3 h with a half-life (t1/2) of 770 min. The crude enzyme and cell culture of strain can inhibit the growth of C. affinis by 36.27±0.043% and 34.25±0.041%, respectively. These characteristics indicate that B. cereus strain SAHA12.13 can be used to inhibit C. affinis, which causes leaf blight of oil palm, under varying pH and temperature conditions.

Development of an Optimized Process for Functional Recombinant SARS-CoV-2 Spike S1 Receptor-Binding Domain Protein Produced in the Baculovirus Expression Vector System.

To map the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and evaluate immune response variations against this virus, it is essential to set up efficient serological tests locally. The SARS-CoV-2 immunogenic proteins were very expensive and not affordable for lower- middle-income countries (LMICs). For this purpose, the commonly used antigen, receptor-binding domain (RBD) of spike S1 protein (S1RBD), was produced using the baculovirus expression vector system (BEVS). In the current study, the expression of S1RBD was monitored using Western blot under different culture conditions. Different parameters were studied: the multiplicity of infection (MOI), cell density at infection, and harvest time. Hence, optimal conditions for efficient S1RBD production were identified: MOI 3; cell density at infection 2-3 × 106 cells/mL; and time post-infection (tPI or harvest time) of 72 h and 72-96 h, successively, for expression in shake flasks and a 7L bioreactor. A high production yield of S1RBD varying between 4 mg and 70 mg per liter of crude cell culture supernatant was achieved, respectively, in the shake flasks and 7L bioreactor. Moreover, the produced S1RBD showed an excellent antigenicity potential against COVID-19 (Wuhan strain) patient sera evaluated by Western blot. Thus, additional serological assays, such as in-house ELISA and seroprevalence studies based on the purified S1RDB, were developed.

Integration of a perfusion reactor and continuous precipitation in an entirely membrane-based process for antibody capture.

Continuous precipitation coupled with continuous tangential flow filtration is a cost-effective alternative for the capture of recombinant antibodies from crude cell culture supernatant. The removal of surge tanks between unit operations, by the adoption of tubular reactors, maintains a continuous harvest and mass flow of product with the advantage of a narrow residence time distribution (RTD). We developed a continuous process implementing two orthogonal precipitation methods, CaCl2 precipitation for removal of host-cell DNA and polyethylene glycol (PEG) for capturing the recombinant antibody, with no influence on the glycosylation profile. Our lab-scale prototype consisting of two tubular reactors and two stages of tangential flow microfiltration was continuously operated for up to 8 days in a truly continuous fashion and without any product flow interruption, both as a stand-alone capture and as an integrated perfusion-capture. Furthermore, we explored the use of a negatively charged membrane adsorber for flow-through anion exchange as first polishing step. We obtained a product recovery of approximately 80% and constant product quality, with more than two logarithmic reduction values (LRVs) for both host-cell proteins and host-cell DNA by the combination of the precipitation-based capture and the first polishing step.

Printed monolith adsorption as an alternative to expanded bed adsorption for purifying M13 bacteriophage

An ordered 3D printed chromatography stationary phase was used to purify M13 bacteriophage (M13) directly from crude cell culture. This new approach, which offers the same advantages as expanded bed adsorption (EBA) with regard to tolerating solids-laden feed streams but without the corresponding issues associated with fluidized bed stability that affect the latter, can be described as “printed monolith adsorption (PMA)”. PMA columns (5, 10 and 15 cm length by 1 cm diameter) were made via a wax templating method from cross-linked cellulose hydrogel and functionalized with a quaternary amine ligand. The recovery of M13 was found to be strongly linked to load flow rate, with the highest recovery 89.7% ± 6% for 1.4 × 1011 pfu/mL of resin occurring at 76 cm/h with a 10 cm column length. A recovery of 87.7% ± 5% for 1.49 × 1011 pfu/mL of media was achieved with a 15 cm column length under conditions comparable to a reported EBA process. The PMA process was completed three times faster than EBA because PMA flow rates can readily be adjusted during operation, with high flow rates and low back pressure, which is unique to the ordered monolithic media geometry used. Equilibration, wash, and cleaning steps were carried out at high flow rates (611 cm/h), minimizing process time and were limited only by the volumetric flow rate capacity of the pumps used, rather than column back pressure (<0.1 MPa at 611 cm/hr). Initial capture of M13 appears to occur on the surface of the monolith solid phase (i.e. the mobile phase channel walls) and subsequently, at a slower rate, within the internal pores of the solid phase media. The difference in binding rate between these two sites is likely caused by slow pore diffusion of the large M13 particles into the pores, with similar slow diffusion out of the pores resulting in tailing of the elution peak. The results indicate that PMA is a promising technology for the efficient purification of viruses directly from crude cell culture.

Preactivation Crosslinking—An Efficient Method for the Oriented Immobilization of Antibodies

Crosslinking of proteins for their irreversible immobilization on surfaces is a proven and popular method. However, many protocols lead to random orientation and the formation of undefined or even inactive by-products. Most concepts to obtain a more targeted conjugation or immobilization requires the recombinant modification of at least one binding partner, which is often impractical or prohibitively expensive. Here a novel method is presented, which is based on the chemical preactivation of Protein A or G with selected conventional crosslinkers. In a second step, the antibody is added, which is subsequently crosslinked in the Fc part. This leads to an oriented and covalent immobilization of the immunoglobulin with a very high yield. Protocols for Protein A and Protein G with murine and human IgG are presented. This method may be useful for the preparation of columns for affinity chromatography, immunoprecipitation, antibodies conjugated to magnetic particles, permanent and oriented immobilization of antibodies in biosensor systems, microarrays, microtitration plates or any other system, where the loss of antibodies needs to be avoided, and maximum binding capacity is desired. This method is directly applicable even to antibodies in crude cell culture supernatants, raw sera or protein-stabilized antibody preparations without any purification nor enrichment of the IgG. This new method delivered much higher signals as a traditional method and, hence, seems to be preferable in many applications.

Computer-designed active human butyrylcholinesterase double mutant with a new catalytic triad

A computer-designed mutant of human butyrylcholinesterase (BChE), N322E/E325G, with a novel catalytic triad was made. The catalytic triad of the wild-type enzyme (S198·H438·E325) was replaced by S198·H438·N322E in silico. Molecular dynamics for 1.5 μs and Markov state model analysis showed that the new catalytic triad should be operative in the mutant enzyme, suggesting functionality. QM/MM modeling performed for the reaction of wild-type BChE and double mutant with echothiophate showed high reactivity of the mutant towards the organophosphate. A truncated monomeric (L530 stop) double mutant was expressed in Expi293 cells. Non-purified transfected cell culture medium was analyzed. Polyacrylamide gel electrophoresis under native conditions followed by activity staining with BTC as the substrate provided evidence that the monomeric BChE mutant was active. Inhibition of the double mutant by echothiophate followed by polyacrylamide gel electrophoresis and activity staining showed that this enzyme slowly self-reactivated. However, because Expi293 cells secrete an endogenous BChE tetramer and several organophosphate-reacting enzymes, catalytic parameters and self-reactivation constants after phosphorylation of the new mutant were not determined in the crude cell culture medium. The study shows that the computer-designed double mutant (N322E/E325G) with a new catalytic triad (S198·H438·N322E) is a suitable template for design of novel active human BChE mutants that display an organophosphate hydrolase activity.

Acoustophoresis mediated chromatography processing: Capture of proteins from cell cultures

Chromatographic purification of target biomolecules is an important downstream process step in the development of new therapeutic agents, such as antibodies. This step employs chromatographic processes, such as affinity separation utilizing Protein A, ion exchange, or mixed mode chemistries. The workflow typically involves a packed column(s) and several chromatographic steps to achieve the desired level of purity. The steps can be time-consuming and expensive. A new process will be described, employing an acoustic standing wave in a fluid chamber to partition and maintain solid phase beads in an acoustically fluidized bed format to capture, wash, and elute the target biomolecule. Purification workflow(s) will be described for the following applications: (1) capture of a monoclonal antibody by Protein A beads from a crude cell culture system, (2) capture of recombinant Green Fluorescent protein (GFP) by anion exchange from a crude cell lysate. The workflow will include wash step(s) and recovery with a specific elution conditions. This communication will clearly demonstrate that an acoustophoresis process can purify proteins without a packed chromatography column. This new approach will minimize the time and cost involved in current purification workflows.

Static and dynamic binding behavior of an IgG2 monoclonal antibody with several new mixed mode affinity adsorbents

The binding behavior of several mixed-mode chromatographic adsorbents, derived from different terpyridine-based ligands immobilized onto Sepharose FF™, has been investigated with a humanized IgG2 monoclonal antibody. Static adsorption isotherms were determined and the derived parameters used to guide the choice of ligand structure and adsorption conditions to achieve favorable IgG2 mAb binding under dynamic loading conditions. The binding and elution behavior of selected adsorbents in packed chromatographic columns were studied with the purified IgG2 mAb and crude cell culture broths containing the same IgG2 mAb. Clearance of host cell proteins was found to be strongly influenced by the structure of the ligand used to generate these mixed mode resins. One ligand candidate in particular, ES-(Cl.S.Cl)terpy, was found to possess selectivity on a par with the traditionally employed Protein A affinity adsorbents for the purification of monoclonal IgG2s with an excellent level of clearance of host cell proteins. Moreover, high binding capacities, e.g. between 34 and 70 mg IgG2 mAb/mL resin, were achieved with these new adsorbents.

A high-throughput capillary isoelectric focusing immunoassay for fingerprinting protein sialylation.

The serum half-life, biological activity, and solubility of many recombinant glycoproteins depend on their sialylation. Monitoring glycoprotein sialylation during cell culture manufacturing is, therefore, critical to ensure product efficacy and safety. Here a high-throughput method for semi-quantitative fingerprinting of glycoprotein sialylation using capillary isoelectric focusing immunoassay on NanoPro (Protein Simple) platform was developed. The method was specific, sensitive, precise, and robust. It could analyze 2 μL of crude cell culture samples without protein purification, and could automatically analyze from 8 samples in 4 h to 96 samples in 14 h without analyst supervision. Furthermore, its capability to detect various changes in sialylation fingerprints during cell culture manufacturing process was indispensable to ensure process robustness and consistency. Moreover, the changes in the sialylation fingerprints analyzed by this method showed strong correlations with intact mass analysis using liquid chromatography and mass spectrometry.

Purification of monoclonal antibodies by chemical affinity mixed mode chromatography

The application of several pyridine-based compounds as immobilised ligands has been investigated for the purification of monoclonal antibodies via mixed mode chromatography. The ligands employed were 4′-terpyridinysulfanylethylamine (4′-TerPSEA), 5-bromo-2-pyridinylsulfanylethylamine (5-Br-2-PSEA), 2-quinolinylsulfanylethylamine (2-QSEA) and 4-pyridinylsulfanylethylamine (4-PSEA). The performance attributes of adsorbents, derived from the immobilisation of these different ligands onto Sepharose 6 Fast Flow™, was evaluated from batch adsorption studies and from chromatographic experiments with humanised IgG1, IgG2 and IgG4 monoclonal antibodies produced by stable CHO cell lines cultured in chemical defined media. These results demonstrated that monoclonal antibodies of different subclasses can be efficiently purified from crude CHO cell culture supernatants using these new chemical affinity chromatographic systems. Moreover, the majority of the CHO host proteins could be eliminated during the chromatographic purification step with these resins, as monitored by a specific ELISA assay.

Application of High-Speed Counter-Current Chromatography for Isolation and Purification of Paclitaxel and Related Taxanes from Taxus chinensis Cell Culture

Six taxanes were isolated and purified from Taxus chinensis cell culture extract using high-speed counter-current chromatography. The crude cell culture extract was first treated with Al2O3 column chromatography and then divided into two parts: fraction 1 and fraction 2. 52 mg of taxuyunnanine C and 11 mg of sinenxane C were yielded from 150 mg of fraction 1. 5 mg of 9-dihydrobaccatin III, 12 mg of baccatin III, 12 mg of paclitaxel, and 17 mg baccatin VI were yielded from 150 mg of fraction 2. The purities of the six compounds were 93.51%, 98.02%, 98.61%, 97.55%, 98.93%, and 98.76%.

Preparative isolation of paclitaxel and related taxanes from cell cultures of Taxus chinensis using reversed-phase flash chromatography

In this study, paclitaxel, baccatin III, taxuyunnanine C and sinenxane C were successfully separated by reversed-phase flash chromatography on a manually packed C18 column from Taxus chinensis cell culture extract. The crude cell culture extract was first treated with Al2O3 column chromatography and then divided into two parts: fraction 1 and fraction 2. Ten milligrams of baccatin III and 19 mg of paclitaxel were obtained from 100 mg dried fraction 1. Fifty-two milligrams of taxuyunnanine C and 11 mg sinenxane C were obtained from 100 mg dried fraction 2. The purities of the four compounds were 98.02%, 98.53%, 98.93% and 98.76%, respectively. Their structures were characterised by using UV, MS and NMR. These results indicate that paclitaxel and related taxanes including baccatin III can be obtained from cell culture in a highly pure state using reversed-phase flash chromatography.

Model-based rational methodology for protein purification process synthesis

A model-based rational protein purification process synthesis methodology that addresses the challenge of selecting the most optimal process scheme from several possible alternatives is presented in this study. The main rationale behind the methodology is to keep the number of purification units in the final process to the minimum through a systematic cycle of flowsheet synthesis, optimization, evaluation and the rational elimination of the least feasible process options at each purification step, taking into account the specific needs of the purification step. Process evaluation is based on techno-economic performance obtained by model-based optimization of the integrated processes using validated column models. The methodology was illustrated by synthesizing a process for the purification of monoclonal antibody from crude hybridoma cell culture supernatant using four non-affinity chromatographic methods (AEX, CEX, SEC and HIC). The results showed that four out of thirteen evaluated process options satisfied all pre-defined product specifications, with overall yields ≥90%. In order of increasing product cost, these were CEX–AEX<AEX–CEX<AEX–HIC<HIC–AEX, taking into account the need for inter-stage conditioning. The main advantages of the methodology include savings in experimentation, computational time and effort; unbiased evaluation of purification schemes by using their ideal operating conditions; and the consideration of the specific needs of each purification step during process evaluation. Finally, the methodology is generic for cell-derived proteins, irrespective of the host organism or application.

Multi‐dimensional fractionation and characterization of crude protein mixtures: Toward establishment of a database of protein purification process development parameters

A multi-dimensional fractionation and characterization scheme was developed for fast acquisition of the relevant molecular properties for protein separation from crude biological feedstocks by ion-exchange chromatography (IEX), hydrophobic interaction chromatography (HIC), and size-exclusion chromatography. In this approach, the linear IEX isotherm parameters were estimated from multiple linear salt-gradient IEX data, while the nonlinear IEX parameters as well as the HIC isotherm parameters were obtained by the inverse method under column overloading conditions. Collected chromatographic fractions were analyzed by gel electrophoresis for estimation of molecular mass, followed by mass spectrometry for protein identification. The usefulness of the generated molecular properties data for rational decision-making during downstream process development was equally demonstrated. Monoclonal antibody purification from crude hybridoma cell culture supernatant was used as case study. The obtained chromatographic parameters only apply to the employed stationary phases and operating conditions, hence prior high throughput screening of different chromatographic resins and mobile phase conditions is still a prerequisite. Nevertheless, it provides a quick, knowledge-based approach for rationally synthesizing purification cascades prior to more detailed process optimization and evaluation.

A high‐throughput microchip‐based glycan screening assay for antibody cell culture samples

A high-throughput screening assay was developed to quantify major glycan species in the crude mammalian cell culture samples for monoclonal antibodies (mAbs). This method utilizes high-speed microchip electrophoresis separation following a fast sample preparation procedure. Using a 96-well ultra-filtration membrane, interfering species in the cell culture media were efficiently removed as the samples were concentrated. A commercial microchip electrophoresis instrument was used for high-speed separation, allowing each sample to be analyzed in less than 1 min. This method is well suited for the purpose of high-throughput antibody glycan profiling during cell culture expression, including clone selection and cell culture process optimization. The relative levels of high mannose (HM), fucosylated and galactosylated glycan species in the Fc domain can be determined for hundreds of crude cell culture samples in a few hours.

A high throughput dimer screening assay for monoclonal antibodies using chemical cross-linking and microchip electrophoresis

A high throughput screening assay was developed to determine the total dimer level in antibody samples. This method utilizes high speed microchip electrophoresis separation following chemical cross-linking. Upon reacting with homobifunctional N-hydroxysuccinimide-esters (NHS-esters), covalent linkages can be established between the primary amines of two neighboring antibody molecules. The reaction conditions are optimized to achieve quantitative cross-linking of only physically associated monomers within an antibody dimer. The resulting cross-linked dimers, originating from either covalent or non-covalent antibody dimers, can then be separated from monomers by SDS electrophoresis. A commercial microchip electrophoresis instrument is used for high speed separation, allowing each sample to be analyzed in about 1 min. This approach was applied to crude mammalian cell culture samples. Using a 96-well gel filtration spin column format, interfering species in the cell culture media were efficiently removed from the samples. This method is well suited to the purpose of high throughput antibody dimer quantitation during cell culture expression, including clone selection and cell culture development. The total dimer content, both covalent and non-covalent, can be determined for hundreds of crude samples in a few hours. The effects of different cross-linking conditions on the determined dimer levels, as well as of different antibody p I values, are discussed.

Quantitation of soluble aggregates in recombinant monoclonal antibody cell culture by pH-gradient protein A chromatography

Monoclonal antibodies (mAbs) produced from mammalian cell culture may contain significant amounts of dimers and higher order aggregates. Quantitation of soluble aggregates in the cell culture is time-consuming and labor-intensive, usually involving a purification step to remove the impurities that interfere with the subsequent size exclusion chromatography (SEC) analysis. We have developed a novel pH-gradient protein A chromatography for rapid, non-size based separation of the aggregates in mAb cell culture samples. Our results demonstrate that this method has excellent correlation with SEC and can be applied to both human immunoglobulin gamma 1 (IgG1) and IgG2 antibodies. This approach can be useful in the quantitation of soluble aggregates in crude cell culture samples.

Microchip assays for screening monoclonal antibody product quality

Microchip CE-SDS was evaluated as a high-throughput alternative to conventional CE-SDS for monitoring monoclonal antibody protein quality. A commercial instrument (LabChip) 90) was used to separate dodecyl sulfate coated proteins through a sieving polymer based on the proteins' sizes. Under reducing conditions, the microchip CE-SDS separation was similar to that of conventional CE-SDS, providing reasonable resolution of the non-glycosylated and the glycosylated heavy chains. The fluorescence detection on LabChip 90 using non-covalent fluorescent labeling method was about as sensitive as the 220 nm UV detection used in a conventional CE instrument. A simple glycan typing assay was developed for the reducing microchip CE-SDS format. Antibodies, either pure or in crude cell culture media are treated with Endoglycosidase H, which specifically cleaves the hybrid and high mannose type glycans. A heavy chain migration shift on reducing CE-SDS resulting from the loss of glycan is used to measure the level of high mannose/hybrid type glycans as a percentage of the total glycans. Microchip CE-SDS, under both non-reducing and reducing conditions, can be used in a variety of antibody product screening assays. The microchip analyses provide sufficient resolution and sensitivity for this purpose but on a time scale approximately 70 times faster (41 s versus 50 min per sample) than conventional CE separation under typical operational conditions.

Immobilized metal affinity chromatography of histidine-tagged lentiviral vectors using monolithic adsorbents

Histidine-tagged lentiviral vectors were separated from crude cell culture supernatant using labscale monolithic adsorbents by immobilized metal affinity chromatography. The capture capacity, concentration factor, purification factor, and elution efficiency of a supermacroporous cryogel monolith were evaluated against the BIA Separations convective interaction media (CIM) disc, which is a commercial macroporous monolith. The morphology of the polymeric cryogel material was characterised by scanning electron microscopy. Iminodiacetic acid was used as the metal chelating ligand in both monoliths and the chelating capacity for metal ions was found to be comparable. The CIM-IDA-Ni 2+ adsorbent had the greatest capture capacity (6.7 × 10 8 IU/ml of adsorbent), concentration factor (1.3-fold), and elution efficiency (69%). Advantages of the cryogel monoliths included rapid, low pressure processing as well low levels of protein and DNA in the final purified vector preparations.

DEVELOPMENT OF IMPROVED PRODUCTION AND PURIFICATION PROTOCOLS FOR PRECLINICAL GRADE LENTIVIRAL VECTORS.

Major issues impacting the successful use of lentiviral vectors for preclinical studies in animals include low titers and the lack of standardized methods for titration. Other problems that impact the use of such vectors are poor purity and difficulties related to their large-scale production. We have implemented a number of improvements allowing more efficient lentivirus vector manufacturing. One improvement is related to the efficiency of production of second- and third-generation lentiviral vectors by transient transfection and the effects of culture additives during virus production. Another improvement concerns the relationships between p24 concentrations, transduction units, integration units, and virus RNA particle titers. A third improvement is related to contaminating host cell proteins. We used ultracentrifugation techniques involving density gradients made with iodixanol to aid in understanding the levels of virus proteins and host cell proteins in lentivirus vector preparations. Finally, we developed a scaleable protocol that can result in both viral concentration with little volume limitation and improved purification from serum proteins and cellular contaminants. We have used Mustang Q anion exchange cartridges (PALL) to concentrate and purify lentiviral vectors from crude cell culture supernatants. Mustang Q chromatography units are capable of replacing large chromatography columns due to the rate of mass transfer to the functional quarternary (Q) ammonium group. Thus, virus binding is not limited by slow diffusion into and out of the column pores because the flow is directly through convective pores. Consequently, the flow rate of Mustang Q chromatography units is very high.