Basic Charge Variants Research Articles

Explainable AI for CHO cell culture media optimization and prediction of critical quality attribute

Cell culture media play a critical role in cell growth and propagation by providing a substrate; media components can also modulate the critical quality attributes (CQAs). However, the inherent complexity of the cell culture media makes unraveling the impact of the various media components on cell growth and CQAs non-trivial. In this study, we demonstrate an end-to-end machine learning framework for media component selection and prediction of CQAs. The preliminary dataset for feature selection was generated by performing CHO-GS (-/-) cell culture in media formulations with varying metal ion concentrations. Acidic and basic charge variant composition of the innovator product (24.97 ± 0.54% acidic and 11.41 ± 1.44% basic) was chosen as the target variable to evaluate the media formulations. Pearson’s correlation coefficient and random forest-based techniques were used for feature ranking and feature selection for the prediction of acidic and basic charge variants. Furthermore, a global interpretation analysis using SHapley Additive exPlanations was utilized to select optimal features by evaluating the contributions of each feature in the extracted vectors. Finally, the medium combinations were predicted by employing fifteen different regression models and utilizing a grid search and random search cross-validation for hyperparameter optimization. Experimental results demonstrate that Fe and Zn significantly impact the charge variant profile. This study aims to offer insights that are pertinent to both innovators seeking to establish a complete pipeline for media development and optimization and biosimilar-based manufacturers who strive to demonstrate the analytical and functional biosimilarity of their products to the innovator.Key points• Developed a framework for optimizing media components and prediction of CQA.• SHAP enhances global interpretability, aiding informed decision-making.• Fifteen regression models were employed to predict medium combinations.

Long term culturing of CHO cells: phenotypic drift and quality attributes of the expressed monoclonal antibody

Establishing cell lines with enhanced protein production requires a deep understanding of the cellular dynamics and cell line stability. The aim of the study is to investigate the impact of long term culturing (LTC) on cell morphology and altered cellular functions possibly leading to phenotypic drift, impacting product yield and quality. Study highlights the orthogonal cellular and analytical assay toolbox to define cell line stability for optimal culture performance and product quality. We investigated recombinant monoclonal antibody (mAb) expressing CHO cells for 60 passages or 180 generations and assessed the cell growth characteristics and morphology by confocal and scanning electron microscopy. Quality attributes of expressed mAb is accessed by performing charge variants, glycan, and host cell protein analysis. We observed a 1.65-fold increase in viable cell population and 1.3-fold increase in cell specific growth rate. A 2.5-fold decrease in antibody titer and abatement of actin filament indicate cellular phenotypic drift. Mitochondrial membrane potential (∆ΨM) signified cell health and metabolic activity during LTC. Host cell protein production is reduced by 1.8-fold. Charge heterogeneity was perturbed with 12.5% and 43% reduction in abundance of acidic and basic charge variants respectively. Glycan profile indicated a decline in fucosylation with 17% increase in galactosylated species as compared with early passaged cells. LTC impinges on cellular phenotype as well as the quality of the expressed antibody, suggesting a defined subculturing limit to retain stable protein expression and cell morphology to achieve consistent product quality. Study signifies the changes in cellular and metabolic markers, suggesting cellular and analytical toolbox which could play a significant role in defining cell characteristics and ensured product quality.

Physicochemical stability of durvalumab (Imfinzi®) concentrate for solution in original vials after first opening

Abstract Objectives Durvalumab (Imfinzi®), a PD-L1 monoclonal antibody (mAb) medication is available as concentrate (50 mg/mL) for solution for infusion. The summary of product characteristics provides information about the physicochemical stability of ready-to-administer durvalumab preparations (vehicle solution 0.9 % NaCl, G5%), but not about the concentrate after first opening. The objective of this study was to determine the physicochemical stability of durvalumab concentrate for solution after first opening over a period of 28 days. Methods Imfinzi® vials were punctured and stored refrigerated (2–8 °C) or at room temperature (20–25 °C) light protected. At predefined time points (day 0, 7, 14, 21, 28) the physicochemical stability of the concentrated solution was determined by ion-exchange/size-exclusion high-performance liquid chromatography (IE-/SE-HPLC) with photodiode array detection and pH measurement. Vials were inspected with regard to changes of color, clarity, and visible particles at any time point. Results Regardless of the storage temperature, durvalumab 50 mg/mL solutions remained physiochemically stable for 28 days in punctured vials. The concentrations of durvalumab monomer remained unchanged and no secondary peaks (fragments, aggregates) were observed in any of the SE-HPLC chromatograms. The IE-HPLC test results showed no substantial changes of the peak areas of the main peak and of the acidic and basic charge variants during the whole storage period. Appearance and pH of the test solutions remained unchanged until the end of the study. Conclusions Regardless of storage conditions none of the analytical methods indicated physicochemical instability of the intact durvalumab monomer over the 28 days of the study. To avoid microbiological instability storage under refrigeration is recommended.

Discovery and Control of Succinimide Formation and Accumulation at Aspartic Acid Residues in The Complementarity-Determining Region of a Therapeutic Monoclonal Antibody.

Succinimide formation and isomerization alter the chemical and physical properties of aspartic acid residues in a protein. Modification of aspartic acid residues within complementarity-determining regions (CDRs) of therapeutic monoclonal antibodies (mAbs) can be particularly detrimental to the efficacy of the molecule. The goal of this study was to characterize the site of succinimide accumulation in the CDR of a therapeutic mAb and understand its effects on potency. Furthermore, we aimed to mitigate succinimide accumulation through changes in formulation. Accumulation of succinimide was identified through intact and reduced LC-MS mass measurements. A low pH peptide mapping method was used for relative quantitation and localization of succinimide formation in the CDR. Statistical modeling was used to correlate levels of succinimide with basic variants and potency measurements. Succinimide accumulation in Formulation A was accelerated when stored at elevated temperatures. A strong correlation between succinimide accumulation in the CDR, an increase in basic charge variants, and a decrease in potency was observed. Statistical modeling suggest that a combination of ion exchange chromatography and potency measurements can be used to predict succinimide levels in a given sample. Reformulation of the mAb to Formulation B mitigates succinimide accumulation even after extended storage at elevated temperatures. Succinimide formation in the CDR of a therapeutic mAb can have a strong negative impact on potency of the molecule. We demonstrate that thorough characterization of the molecule by LC-MS, ion exchange chromatography, and potency measurements can facilitate changes in formulation that mitigate succinimide formation and the corresponding detrimental changes in potency.

Fractionation and online mass spectrometry based on imaged capillary isoelectric focusing (icIEF) for characterizing charge heterogeneity of therapeutic antibody.

Imaged capillary isoelectric focusing (icIEF) technology has been proved to be robust for the characterization of protein charge heterogeneity due to its high-resolution pI discrimination and high-throughput. Although high performance liquid chromatography (HPLC) tandem mass spectrometry (MS) and offline fraction collection technologies including isoelectric focusing (IEF), ion exchange chromatography (IEX) and free flow electrophoresis (FFE) have been widely utilized for protein charge variant characterization, there are a few applications of MS coupling with icIEF as a front-separation technique and related fractionation technologies for protein charge heterogeneity. However, the application of icIEF-MS has been much less frequent due to difficulties in MS interface, compatible ampholyte and coated capillary cartridge designation, ultimately impeding the breadth of icIEF applications in protein charge heterogeneity. In this study, a therapeutic monoclonal antibody (mAb-M-AT) was used for its charge variant characterization on an integrated icIEF platform with functions including analytical profiling, MS online coupling and fraction collection for charge heterogeneities. The main protein component and its four charge variants were identified using direct icIEF-MS coupling. Additionally, the two major acidic and basic charge variants were collected using preparative fractionation after the protein focused in the separation capillary. The identity of the fractions was confirmed by LC-MS at intact protein level and the results were consistent with those using icIEF-MS online coupling. The multiple operation modes of the icIEF platform described above can be rapidly and flexibly switched just by changing customized capillary separation cartridges without drastically altering instrument configuration. The whole workflow of icIEF-based profiling, fractionation and MS online coupling for protein heterogeneity is straightforward, reliable, and accurate, thus providing comprehensive solutions for in-depth protein heterogeneity characterization.

Obtaining acidic and basic charge variants using a twin-column continuous chromatography system

For recombinantly produced monoclonal antibody (mAb), charge variants including acidic and basic species are common heterogeneities. For characterization purpose, sufficient amount of acidic and basic species with high purity is needed. In this work, we developed an approach that allows for continuous separating and collecting of acidic and basic charge variants. First, with batch-mode cation exchange (CEX) chromatography, the load density and linear salt gradient elution conditions under which good separation of both charge variants can be achieved were determined. Next, a stepwise elution protocol was developed based on the linear gradient elution. Finally, acidic and basic charge variants were persistently produced under stepwise elution using a customized twin-column continuous chromatography system. This approach allows acidic and basic charge variants with high purity (i.e., >90%) to be efficiently generated in sufficient amount, which greatly facilitates the necessary characterization of these mAb variants.

Challenges and Strategies for a Thorough Characterization of Antibody Acidic Charge Variants.

Heterogeneity of therapeutic Monoclonal antibody (mAb) drugs are due to protein variants generated during the manufacturing process. These protein variants can be critical quality attributes (CQAs) depending on their potential impact on drug safety and/or efficacy. To identify CQAs and ensure the drug product qualities, a thorough characterization is required but challenging due to the complex structure of biotherapeutics. Past characterization studies for basic and acidic variants revealed that full characterizations were limited to the basic charge variants, while the quantitative measurements of acidic variants left gaps. Consequently, the characterization and quantitation of acidic variants are more challenging. A case study of a therapeutic mAb1 accounted for two-thirds of the enriched acidic variants in the initial characterization study. This led to additional investigations, closing the quantification gaps of mAb1 acidic variants. This work demonstrates that a well-designed study with the right choices of analytical methods can play a key role in characterization studies. Thus, the updated strategies for more complete antibody charge variant characterization are recommended.

Antibody charge variant modulation by in vitro enzymatic treatment in different Chinese hamster ovary cell cultures.

Charge variants represent a critical quality attribute that must be controlled during the development and manufacturing of monoclonal antibodies (mAb). Previously, we reported the development of a cost-effective enzymatic treatment capable of removing the C-terminal lysine from a mAb produced by a Chinese hamster ovary (CHO) GS cell line. This treatment resulted in a significant decrease in basic charge variants and a corresponding improvement in the main peak, enabling a longer cell culture production duration for titer improvement. Here, we describe this enzymatic treatment protocol in detail and demonstrate its applicability to two additional mAbs produced by distinct industrial cell lines. The simple addition of carboxypeptidase B (CpB) at a ratio of 1:10,000 (w/w) to whole cell cultures significantly improved the main peaks for both mAbs without affecting other critical quality attributes, including size exclusion chromatography impurities and N-glycans. Our results demonstrate that this in vitro CpB treatment protocol can be used as a platform strategy to improve main peak for mAbs that exhibit high levels of basic variants attributable to C-terminal lysines. An in vitro enzymatic treatment in general may be another good addition to existing in vivo CHO cell culture strategies for titer improvement and control of critical quality attributes.

Sample displacement chromatography of monoclonal antibody charge variants and aggregates.

The rise of biosimilar monoclonal antibodies has renewed the interest in monoclonal antibody (mAb) charge variants composition and separation. The sample displacement chromatography (SDC) has the potential to overcome the low separation efficiency and productivity associated with bind-elute separation of mAb charge variants. SDC in combination with weak cation exchanging macroporous monolithic chromatographic column was successfully implemented for a separation of charge variants and aggregates of monoclonal IgG under overloading conditions. The charge variants composition was at-line monitored by a newly developed, simple and fast analytical method, based on weak cation exchange chromatography. It was proven that basic charge variants acted as displacers of IgG molecules with lower pI, when the loading was performed 1 to 1.5pH unit below the pI of acidic charge variants. The efficiency of the SDC process is flow rate independent due to a convection-based mass transfer on the macroporous monolith. The productivity of the process at optimal conditions is 35mg of purified IgG fraction per milliliters of monolithic support with 75-80% recovery. As such, an SDC approach surpasses the standard bind-elute separation in the productivity for a factor of 3, when performed on the same column. The applicability of the SDC approach was confirmed for porous particle-based column as well, but with 1.5 lower productivity compared to the monoliths.

LC\u2013MS based case-by-case analysis of the impact of acidic and basic charge variants of bevacizumab on stability and biological activity

The present study investigates the impact of charge variants on bevacizumab's structure, stability, and biological activity. Five basic and one acidic charge variants were separated using semi-preparative cation exchange chromatography using linear pH gradient elution with purity > 85%. Based on the commercial biosimilar product's composition, two basic variants, one acidic and the main bevacizumab product, were chosen for further investigation. Intact mass analysis and tryptic peptide mapping established the basic variants' identity as those originating from an incomplete clipping of either one or both C-terminal lysine residues in the heavy chain of bevacizumab. Based on peptide mapping data, the acidic variant formation was attributed to deamidation of asparagine residue (N84), oxidation of M258, and preservation of C-terminal lysine residue, located on the heavy chain of bevacizumab. None of the observed charge heterogeneities in bevacizumab were due to differences in glycosylation among the variants. The basic (lysine) variants exhibited similar structural, functional, and stability profiles as the bevacizumab main product. But it was also noted that both the variants did not improve bevacizumab's therapeutic utility when pooled in different proportions with the main product. The acidic variant was found to have an equivalent secondary structure with subtle differences in the tertiary structure. The conformational difference also translated into a ~ 62% decrease in biological activity. Based on these data, it can be concluded that different charge variants behave differently with respect to their structure and bioactivity. Hence, biopharmaceutical manufacturers need to incorporate this understanding into their process and product development guidelines to maintain consistency in product quality.

Isolation and characterization of charge variants of infliximab biosimilar HS626

Charge variants are the most commonly observed sources of heterogeneity in the routine manufacturing of monoclonal antibodies. To gain further insight into the structural foundation of charge heterogeneity and its influence on biological functions, an infliximab biosimilar HS626 from a biopharmaceutical facility was isolated by semipreparative cation exchange chromatography (CEX) to obtain fractions of acidic and basic charge variants and determine the main species. It was assessed again by CEX to ensure purities. Through a series of structural and physicochemical characterizations, we concluded that the acidic variants were caused by fragments, Met oxidation, Asn deamidation, higher levels of sialylation and galactosylation of N-linked glycans, and less high mannose. The basic variants resulted mainly from aggregates, fragments, and Met oxidation. Through further analysis of antigen binding affinity, cell death inhibitory activity, ADCC, and CDC, as well as FcRn, FcγRIIIa, and C1q affinity, we demonstrated that the charge heterogeneity did not affect biological functions. This research enhances the understanding of charge variants, which are usually effective components that should not be intentionally reduced unless biological functions are affected.

Multi-column displacement chromatography for separation of charge variants of monoclonal antibodies

Native forms of therapeutic monoclonal antibodies (mAbs) coexist with various acidic and basic charge variants throughout process development and into drug product formulation. During downstream purification, a product’s charge variant composition is controlled, as necessary, primarily through peak fractionation and pooling of elution fractions using cation-exchange chromatography (CEX). This can be a cumbersome process with poor resolution and it may result in a significant reduction in product yield. In the present work, separation and enrichment of the native form of a mAb and of basic and acidic variants is achieved using self-displacement chromatography in a multi-column continuous chromatography set-up. Basic mAb variants are more strongly retained in CEX owing to their higher charge, and can displace the native and the acidic variants. Similarly, the native variant can displace the acidic variants if the amount loaded exceeds the total resin capacity. To this end, we utilized a three-column continuous system to consecutively displace acidic, native and basic charge variants of a therapeutic mAb in the order of increasing binding strength during product loading. Using our optimized operating parameters, we were able to enrich the native variant from 65% to 90% while loading above the capacity of the column, with a process yield of above 90%. This method and approach will help to control and reduce in particular the charged variant heterogeneity, and, in general, aid in the separation of charged proteins at preparative scale.

Cell culture medium supplemented with taurine decreases basic charge variant levels of a monoclonal antibody.

To explore the impact of taurine on monoclonal antibody (mAb) basic charge variants in Chinese hamster ovary (CHO) cell culture. In fed-batch culture, adding taurine in the feed medium slightly increased the maximum viable cell density and mAb titers in CHO cells. What's more, taurine significantly decreased the lysine variant and oxidized variant levels, which further decreased basic variant contents from 32 to 27%. The lysine variant content in the taurine culture was approximately 4% lower than that in control condition, which was the main reason for the decrease in basic variants. Real-time PCR and cell-free assay revealed that taurine played a critical role in the upregulation of relative basic carboxypeptidase and stimulating extracellular basic carboxypeptidase activities. Taurine exhibits noticeable impact on lower basic charge variants, which are mainly due to the decrease of lysine variant and oxidized protein variants.

High-resolution separation of monoclonal antibodies mixtures and their charge variants by an alternative and generic CZE method.

The determination of mAb critical quality attributes (CQA) is crucial for their successful application in health diseases. A generic CZE method was developed for the high-resolution separation of various mAb charge variants, which are often recognized as important CQA. A dynamic coating of the capillary was obtained with polyethylene oxide (PEO), whereas Bis-Tris allowed the analysis of mAbs under native conditions at pH 7.0. The effect of PEO and Bis-Tris concentrations, as well as the nature of the acidic counter ion on the method performance was systematically studied. The %RSD on migration times was below 5% on three different CE instruments using the optimized method. Additional charge variants (in particular acidic variants) were resolved for 10 out of 17mAbs compared to a reference CZE approach involving the use of ε-amino-caproic acid (EACA), triethylenetetramine (TETA), and hydroxypropylmethyl cellulose (HPMC). The amount of basic and acidic charge variants of 17 Food and Drug Administration (FDA) approved mAbs covering a wide range of physico-chemical properties, e.g., pI between 8.0 and 9.4 and different hydrophobicity, were mainly comprised between 5-15% and 15-30%, respectively. It is noteworthy that applications for the quality control in hospitals as well as for the combination of the immune checkpoint inhibitors nivolumab and ipilimumab were presented.

Microheterogeneity of therapeutic monoclonal antibodies is governed by changes in the surface charge of the protein.

It has previously been shown for individual antibodies, that the microheterogenity pattern can have a significant impact on various key characteristics of the product. The aim of this study to get a more generalized understanding of the importance of microheterogeneity. For that purpose, the charge variant pattern of various different commercially available therapeutic mAb products was compared using Cation-Exchange Chromatography with linear pH gradient antigen affinity, Fc-receptor affinity, antibody dependent cellular cytotoxicity (ADCC) and conformational stability. For three of the investigated antibodies, the basic charge variants showed a stronger binding affinity towards FcγRIIIa as well as an increased ADCC response. Differences in the conformational stability of antibody charge variants and the corresponding reference samples could not be detected by differential scanning calorimetry. The different biological properties of the mAb variants are therefore governed by changes in the surface charge of the protein and not by an altered structure. This can help to identify aspects of microheterogeneity that are critical for product quality and can lead to further improvements in the development and production of therapeutic antibody products.

The molecular weight and concentration of dextran sulfate affect cell growth and antibody production in CHO cell cultures.

To investigate the effect of dextran sulfate (DS), a widely used anti-aggregation agent, on cell growth and monoclonal antibody (mAb) production including the quality attributes, DS with the three different MWs (4,000 Da, 15,000 Da, and 40,000 Da) at various concentrations (up to 1 g/L) was added to suspension cultures of two different recombinant CHO (rCHO) cell lines producing mAb, SM-0.025 and CS13-1.00. For both cell lines, the addition of DS, regardless of the MW and concentration of DS used, improved cell growth and viability in the decline phase of growth. However, it increased mAb production only in the CS13-1.00 cells. Among the three different MWs, 40,000 Da DS was most effective in attenuating cell aggregation during the cultures of CS13-1.00 cells, and showed the highest maximum mAb concentration. For SM-0.025 cells, it significantly decreased specific mAb productivity, particularly at a high concentration of DS. Overall, DS addition did not negatively affect the quality attributes of mAbs (aggregation, charge variation, and glycosylation), though its efficacy on mAb quality depended on the MW and concentration of DS and cell lines. For both cell lines, the addition of DS did not affect N-glycosylation of mAbs and decreased basic charge variants in mAbs. For CS13-1.00 cells, the mAb monomer increased with the addition of 40,000 Da DS at 0.3-1.0 g/L. Taken together, to maximize the beneficial effect of DS addition on mAb production, the optimal MW and concentration of DS should be determined for each specific rCHO cell line. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1113-1122, 2016.

Mechanistic modeling of ion-exchange process chromatography of charge variants of monoclonal antibody products

Ion-exchange chromatography (IEX) is universally accepted as the optimal method for achieving process scale separation of charge variants of a monoclonal antibody (mAb) therapeutic. These variants are closely related to the product and a baseline separation is rarely achieved. The general practice is to fractionate the eluate from the IEX column, analyze the fractions and then pool the desired fractions to obtain the targeted composition of variants. This is, however, a very cumbersome and time consuming exercise. A mechanistic model that is capable of simulating the peak profile will be a much more elegant and effective way to make a decision on the pooling strategy. This paper proposes a mechanistic model, based on the general rate model, to predict elution peak profile for separation of the main product from its variants. The proposed approach uses inverse fit of process scale chromatogram for estimation of model parameters using the initial values that are obtained from theoretical correlations. The packed bed column has been modeled along with the chromatographic system consisting of the mixer, tubing and detectors as a series of dispersed plug flow and continuous stirred tank reactors. The model uses loading ranges starting at 25% to a maximum of 70% of the loading capacity and hence is applicable to process scale separations. Langmuir model has been extended to include the effects of salt concentration and temperature on the model parameters. The extended Langmuir model that has been proposed uses one less parameter than the SMA model and this results in a significant ease of estimating the model parameters from inverse fitting. The proposed model has been validated with experimental data and has been shown to successfully predict peak profile for a range of load capacities (15–28mg/mL), gradient lengths (10–30CV), bed heights (6–20cm), and for three different resins with good accuracy (as measured by estimation of residuals). The model has been also validated for a two component mixture consisting of the main mAb product and one of its basic charge variants. The proposed model can be used for optimization and control of preparative scale chromatography for separation of charge variants.

Effect of sodium butyrate on the assembly, charge variants, and galactosylation of antibody produced in recombinant Chinese hamster ovary cells

Sodium butyrate (NaBu) is known to increase the specific productivity of recombinant Chinese hamster ovary (rCHO) cells. To understand the effects of NaBu on the product quality, rCHO cells producing monoclonal antibody (Mab) were cultivated at various concentrations of NaBu (0 to 4 mM). NaBu increased correctly assembled Mab. In the absence of NaBu, the proportions of intact Mab (2H2L) and heavy chain dimer (2H) were 81 and 15 %. At 1 mM NaBu, the proportion of 2H2L increased to 93 %, whereas the proportion of 2H decreased to 2 %. No further increase in the proportion of 2H2L was obtained at a higher NaBu concentration. NaBu also affected the charge heterogeneity of Mab, which may affect the efficacy of Mab. The basic charge variants of Mabs increased with an increase in the NaBu concentration. In addition, NaBu affected the galactosylation of Mab negatively. Overall, the data obtained here show that NaBu used in rCHO cell cultures for improved Mab production affects certain quality aspects of Mab, in this case, the charge heterogeneity and galactosylation.

Characterization of the basic charge variants of a human IgG1

We report a case study of an IgG1 with a unique basic charge variant profile caused by C-terminal proline amidation on either one or two heavy chains. The proline amidation was sensitive to copper ion concentration in the production media during cell culture: the higher the Cu2+ ion concentration, the higher the level of proline amidation detected. This conclusion was supported by the analysis of samples that revealed direct correlation between the proline amidation level observed from peptide maps and the level of basic peaks measured by imaged capillary isoelectric focusing and a pH gradient ion-exchange chromatography method. The importance of these observations to therapeutic antibody production is discussed.

Isolation and characterization of therapeutic antibody charge variants using cation exchange displacement chromatography

In this report, we have demonstrated the isolation and enrichment of charge variants of a monoclonal antibody IgG1 using cation exchange displacement chromatography. We successfully achieved the separation of acidic, main and basic charge variants with high recovery (>70%) and purity (>90%) by using a commercially available stationary phase in conjunction with a commercially available displacer. In addition, we have isolated and enriched a trace methionine-oxidized variant of the monoclonal antibody allowing a secondary means of identification of this variant while providing sufficient enrichment for further analysis, stability tests and potency determination. Further characterization of the displacement trains by SEC indicate the possibility of enrichment of high and low molecular weight species. Glycan analysis of the displacement fractions indicates minimal variation in glycan distribution patterns among a wide spectrum of charge variants. These results provide a case study demonstrating the utility of cation exchange displacement chromatography as a viable approach to isolate and enrich antibody charge variants for enhanced molecular characterization.