Alan K. Hunter

Host cell proteins in biologics development: Identification, quantitation and risk assessment

Host cell proteins (HCPs) are those produced or encoded by the organisms and unrelated to the intended recombinant product. Some are necessary for growth, survival, and normal cellular processing whereas others may be non‐essential, simply carried along as baggage. Like the recombinant product, HCPs may also be modified by the host with a number of post‐translational modifications. Regardless of the utility, or lack thereof, HCPs are undesirable in the final drug substance. Though commonly present in small quantities (parts per million expressed as nanograms per milligrams of the intended recombinant protein) much effort and cost is expended by industry to remove them. The purpose of this review is to summarize what is of relevance in regards to the biology, the impact of genomics and proteomics on HCP evaluation, the regulatory expectations, analytical approaches, and various methodologies to remove HCPs with bioprocessing. Historical data, bioinformatics approaches and industrial case study examples are provided. Finally, a proposal for a risk assessment tool is provided which brings these facets together and proposes a means for manufacturers to classify and organize a control strategy leading to meaningful product specifications. Biotechnol. Bioeng. 2009;103: 446–458.

Protein adsorption on novel acrylamido-based polymeric ion exchangers: II. Adsorption rates and column behavior

Uptake kinetics and breakthrough behavior were determined for bovine serum albumin (BSA) and alpha-chymotrypsinogen (alphaCHY) in new polymeric ion-exchange media based on acrylamido monomers. Two anion exchangers and a cation exchanger were investigated. As shown in Part I of this work, the two anion exchangers have different morphologies. The first one, BRX-Q, comprises a low-density gel with a matrix of denser polymeric aggregates. While this material has a very low size-exclusion limit for neutral probes, it exhibits an extremely high binding capacity for BSA. The second anion exchanger, BRX-QP, comprises large open pores but has a very low binding capacity. The cation exchanger, BRX-S, also comprises large open pores but exhibits an intermediate capacity; likely as a result of the presence of smaller pores. Dynamic protein uptake experiments showed that the highest mass transfer rates are obtained with BRX-Q. The apparent diffusivity is also highest for this material and increases substantially as the protein concentration is reduced. For these particles, the external film resistance is dominant at very low protein concentrations. Much lower rates and apparent diffusivities are obtained for BRX-QP. Finally intermediate rates and apparent diffusivities are found with BRX-S. The concentration dependence of the apparent pore diffusivity is much less pronounced in this case. The apparently paradoxical result that mass transfer rates are highest for the material with the smallest neutral-probe size-exclusion limit can be explained in terms of a general conceptual model where parallel pore and adsorbed-phase diffusion paths exist in these particles. In the first case, adsorbed phase diffusion in gel pores is dominant, while in the second transport is dominated by diffusion in a macroporous network. In the third case, both contributions are important. The conceptual model provides an accurate prediction of the breakthrough behavior of columns packed with these media using independently determined rate parameters. Dynamic binding capacities of 80-140 mg/ml were observed for BSA on BRX-Q in ca. 1.5 cm columns operated at 300-900 cm/h in agreement with theoretical predictions.

Protein adsorption on novel acrylamido-based polymeric ion-exchangers. IV. Effects of protein size on adsorption capacity and rate.

The effects of protein size on the adsorption capacity and rate is determined for an acrylamido-based polymeric anion-exchanger. The proteins lactalbumin, myoglobin, ovalbumin, BSA, conalbumin, IgG, and ferritin with molecular masses ranging from 15,000 to 450,000 were investigated. At high salt concentration (50 mM Tris-HCl containing 500 mM NaCl), only the smaller proteins lactalbumin and myoglobin gained access to a significant portion of the particle volume. The larger proteins were nearly completely excluded, in agreement with the results obtained for neutral macromolecules. By contrast, at low salt concentration (50 mM Tris-HCl), the adsorption capacity was very large (280-400 mg/ml of particle volume) for all the proteins studied except for ferritin, for which the capacity was much lower. This suggests that, provided the solute is not too large, the favorable electrostatic interaction overcomes the size exclusion effect. Adsorption rate measurements showed that mass transfer rates are also quite fast at low salt concentration. Effective diffusivities were determined by matching model and experimental results and were found to decrease substantially as the protein size increased. As previously observed, the homogeneous diffusion model was found to predict the experimentally observed trends with respect to protein concentration and boundary layer mass transfer effects.

Effects of bovine serum albumin heterogeneity on frontal analysis with anion-exchange media

The presence of dimers in commercial bovine serum albumin (BSA) samples of nominal high purity is investigated along with their effects on the frontal analysis behavior of preparative anion-exchange media. Size-exclusion and analytical anion-exchange chromatography are used to determine the relative amounts of monomer and dimer for two samples of BSA. While the amount of dimer was generally low, its impact on adsorptive behavior is significant. Equilibrium experiments demonstrate that the anion-exchange media binds the dimer more strongly, leading to an unequal distribution of the monomer and dimer between the two phases. Analysis of the breakthrough behavior of BSA reveals that the monomer breaks through prior to the dimer. This leads to the characteristic tailing breakthrough curve often seen with BSA. Breakthrough experiments carried out using dimer-free BSA confirm that the extreme tailing observed with the commercial samples is curtailed by removing the dimer.

Protein adsorption on novel acrylamido-based polymeric ion-exchangers. III. Salt concentration effects and elution behavior.

The effect of salt concentration on the adsorption and desorption of BSA has been determined for a polymeric anion-exchanger based on acrylamido monomers. The material investigated possesses a high adsorption capacity at low salt concentration and the bound protein can be recovered quantitatively at high salt concentrations. The effects of salt on adsorption and desorption rates were evaluated from batch and shallow-bed experiments, and a model was developed to describe the data quantitatively. The adsorption capacity decreases as the salt concentration is increased, but both adsorption and desorption rates increase at higher salt concentrations. The predictability of the behavior of columns packed with this material was examined by comparing model predictions and experimental results obtained in laboratory columns. In general, a good agreement was obtained between predicted and experimental breakthrough and elution profiles, especially in shorter columns. Thus, the model allows a prediction of the effects of column length, mobile phase flow-rate, protein feed concentration, and salt concentration on dynamic capacity, productivity, and on the concentration of product fractions.

Comparison of agarose and dextran-grafted agarose strong ion exchangers for the separation of protein aggregates

The control of aggregate levels in recombinant protein based drugs is a primary concern during process development and manufacture. In recent years, a novel class of dextran-grafted ion exchange matrices has gained popularity for process scale protein purification due to increased mass transfer rates and higher dynamic binding capacity compared to conventional matrices. Using bovine serum albumin and a monoclonal antibody as model proteins, we studied Sepharose FF and Sepharose XL ion exchangers for the separation of protein aggregates. Experimental results comparing linear gradient elution, stepwise elution, and flow-through chromatography for aggregate separation are described. Differences in performance for the various ion exchangers are discussed and modeled. Strategies for the optimization of protein aggregate separation are provided.

Protein separations with induced pH gradients using cation-exchange chromatographic columns containing weak acid groups

The behavior of chromatographic columns packed with resins containing both weak and strong cation-exchange groups is investigated in order to obtain protein separations by means of internally generated pH gradients in response to step changes in buffer composition. A local equilibrium model is developed to predict pH transitions using non-adsorbed buffers, i.e. containing neutral and negatively charged buffering species, based exclusively on the resin titration curve. In agreement with experimental results, the model predicts practical, fairly linear gradients between pH 5 and 7, which are formed using suitable mixtures of acetate and phosphate buffers. The separation of mixtures of ovalbumin, albumin, and transferrin is used as a model system, but, unlike most previous work, we consider preparative conditions. Near baseline resolution is obtained with protein loads as high as 10mg/mL and mobile phase velocities at high as 460 cm/h using porous, 70-microm diameter particles. The peaks obtained with this approach are much sharper than could be obtained isocratically or using externally generated, unretained gradients as a result of the peak compression caused by the axial pH gradient formed along the column. Moreover, separation is obtained at very low ionic strengths (2-3 mS/cm). The effects of flow velocity, mobile phase composition, time of injection, and protein load on retention and elution pH are investigated systematically demonstrating a range of ways in which the separation can be controlled and optimized.

Binding and elution behavior of proteins on strong cation exchangers

This work provides a broad survey of binding and elution behavior of proteins on strong cation exchangers. Four proteins comprising two monoclonal antibodies, lysozyme, and cytochrome c were used as models in the investigation. Seven chromatography resins with different base matrices were compared. Dynamic binding capacity as a function of salt concentration was examined for a monoclonal antibody and lysozyme. Elution behavior as a function of gradient slope was modeled to determine the characteristic charge, essentially a measure of the number of sites involved in binding, for each protein on each resin. Trends with respect to dynamic binding capacity and elution behavior are analyzed and discussed.

Integrated solution to purification challenges in the manufacture of a soluble recombinant protein in E. coli

Apolipoprotein A 1 Milano (ApoA‐1M), the protein component of a high‐density lipoprotein (HDL) mimic with promising potential for reduction of atherosclerotic plaque, is produced at large scale by expression in E. coli. Significant difficulty with clearance of host cell proteins (HCPs) was experienced in the original manufacturing process despite a lengthy downstream purification train. Analysis of purified protein solutions and intermediate process samples led to identification of several major HCPs co‐purifying with the product and a bacterial protease potentially causing a specific truncation of ApoA‐1M found in the final product. Deletion of these genes from the original host strain succeeded in substantially reducing the levels of HCPs and the truncated species without adversely affecting the overall fermentation productivity, contributing to a much more efficient and robust new manufacturing process. Biotechnol. Bioeng. 2010; 105: 239–249.

Engineering of novel Staphylococcal Protein A ligands to enable milder elution pH and high dynamic binding capacity.

We describe novel Staphylococcal Protein A ligands that enable milder elution pH for use in affinity chromatography. The change in elution pH is the result of point mutations to the protein sequence. Two novel ligands are investigated in this study. The first, designated Z(H18S)4, represents a histidine to serine substitution single mutation. The second, designated Z(H18S, N28A)4, is a double mutant comprising histidine to serine and asparagine to alanine mutations. Both are compared against the unmutated sequence, designated Z4, which is currently utilized in a commercially available Protein A stationary phase for the purification of molecules containing Fc domains. The ligands are coupled to a chromatography support matrix and tested against a panel of antibodies and an Fc fusion protein for elution pH, dynamic binding capacity, step-wise elution, and capture from clarified culture media. Results demonstrate that the novel ligands result in milder elution pH, on average >0.5 pH units, when tested in a pH gradient. For step-wise elution at pH 4.0, the Z(H18S, N28A)4 ligand showed on average a greater than 30% increase in yield compared to Z4. Importantly, for the antibodies tested the mutations did not result in a decrease in dynamic binding capacity or other desirable attributes such as selectivity. A potential application of the novel ligands is shown with a pH sensitive molecule prone to aggregation under acidic conditions.