Identification and characterization of a residual host cell protein hexosaminidase B associated with N-glycan degradation during the stability study of a therapeutic recombinant monoclonal antibody product

Detection of host cell microprotein impurities in antibody drug products

Chinese hamster ovary (CHO) cells are used to produce almost 90% of therapeutic monoclonal antibodies (mAbs) and antibody fusion proteins (Fc-fusion). The annotation of non-canonical translation events in these cellular factories remains incomplete, limiting our ability to study CHO cell biology and detect host cell protein (HCP) impurities in the final antibody drug product. We utilised ribosome footprint profiling (Ribo-seq) to identify novel open reading frames (ORFs) including N-terminal extensions and thousands of short ORFs (sORFs) predicted to encode microproteins. Mass spectrometry-based HCP analysis of eight commercial antibody drug products (7 mAbs and 1 Fc-fusion protein) using the extended protein sequence database revealed the presence of microprotein impurities. We present evidence that microprotein abundance varies with growth phase and can be affected by the cell culture environment. In addition, our work provides a vital resource to facilitate future studies of non-canonical translation and the regulation of protein synthesis in CHO cell lines.

Advances in analytical technologies for emerging drug modalities and their separation challenges in LC-MS systems

The last few years have seen a rise in the identification and development of bio-therapeutics through the use of cutting-edge delivery methods or bio-formulations, which has created bio-analytical difficulties. Every year, new bio-pharmaceutical product innovations come out, but the analytical development of these products is challenging. Quantifying the products and components of conjugated molecular structures is essential for preclinical and clinical research in order to guide therapeutic development, given their intrinsic complexity. Furthermore, a significant amount of information is needed for the measurement of these unique modalities by LC-MS techniques. Numerous LC-MS based methods have been developed, including AEX-HPLC-MS, RP-IP-LCMS, HILIC-MS, LCHRMS, Microflow-LC-MS, ASMS, Hybrid LBA/LC-MS, and more. However, these methods continue to face problems, prompting the development of alternative approaches. Therefore, developing bio-molecules that are this complicated and, low in concentration requires a skilled LC-MS based approach and knowledgeable personnel. This review covers general novel modalities classifications, sample preparation techniques, current status and bio-analytical strategies for analyzing various novel modalities, including gene bio-therapeutics, oligonucleotides, antibody-drug conjugates, monoclonal antibodies and PROTACs. It also covers how these strategies have been used in the past and how they are being used now to address challenges in the development of LC-MS based methods, as well as improvement strategies, current advancements and recent developed methods. We additionally covered on the benefits and drawbacks of different LC-MS based techniques for the examination of bio-pharmaceutical products and the future perspectives.

diaPASEF Enables High-Throughput Proteomic Analysis of Host Cell Proteins for Biopharmaceutical Process Development

Monitoring and quantifying host cell proteins (HCPs) in biotherapeutic production processes is crucial to ensure product quality, stability, and safety. Liquid chromatography-mass spectrometry (LC-MS) analysis has emerged as an important tool for identifying and quantifying individual HCPs. However, LC-MS-based approaches face challenges due to the wide dynamic range between HCPs and the therapeutic protein as well as laborious sample preparation and long instrument time. To address these limitations, we evaluated the application of parallel accumulation-serial fragmentation combined with data-independent acquisition (diaPASEF) to HCP analysis for biopharmaceutical process development applications. We evaluated different library generation strategies and LC methods, demonstrating the suitability of these workflows for various HCP analysis needs, such as in-depth characterization and high-throughput analysis of process intermediates. Remarkably, the diaPASEF approach enabled the quantification of hundreds of HCPs that were undetectable by a standard data-dependent acquisition mode while considerably improving sample requirement, throughput, coverage, quantitative precision, and data completeness.

Analysis of Host Cell Proteins in AAV Products with ProteoMiner Protein Enrichment Technology

Despite substantial efforts to detect host cell proteins (HCPs) in antibody drugs, information regarding HCPs in gene therapy products remains limited and has not been widely integrated into the host cell engineering or purification processes. Most methods that have successfully detected HCPs in antibody drugs are not applicable to gene therapy products, except for the ProteoMiner enrichment method. Here, we demonstrate that ProteoMiner beads effectively enrich HCPs in adeno-associated virus (AAV) products and simultaneously remove the detergent Pluronic F-68 without a loss of low-abundance HCPs. Following optimization of this technique, there was up to a 34-fold increase in the enrichment of HCPs compared to direct digestion. Moreover, the detection limit was significantly lowered with the ability to detect HCPs at levels as low as 0.1 ng/mL after ProteoMiner treatment. This approach holds promise in AAV HCP analysis and may be adaptable to other gene therapy products. The findings from this study provide valuable insights into HCPs in AAV products and may facilitate process development and host cell line optimization. The high sensitivity of this approach also facilitates detection of critical low-abundance HCPs, thereby contributing to risk assessment of their impact on the safety and quality of the AAV-based gene therapy products.

Effect of Host Cell Protein on Chinese Hamster Ovary Recombinant Protein Production and its Removal Strategies: A Mini Review

Chinese hamster ovary cells are the main expression system for recombinant therapeutic proteins. During the production of these proteins, certain host cell proteins are secreted, broken down, and released by host cells in the culture along with the proteins of interest. These host cell proteins are often difficult to remove during the downstream purification process, and thus affect the quality, safety, and effectiveness of recombinant protein biopharmaceutical products and increase the production cost of recombinant therapeutic proteins. Therefore, host cell protein production must be reduced as much as possible during the production process and eliminated during purification. This article reviews the harm caused by host cell proteins in the production of recombinant protein drugs using Chinese hamster ovary cell, factors affecting host cell proteins, the monitoring and identification of these proteins, and methods to reduce their type and quantity in the final product.

Identification and characterization of CHO host-cell proteins in monoclonal antibody bioprocessing

Host-cell proteins (HCPs) are the foremost class of process-related impurities to be controlled and removed in downstream processing steps in monoclonal antibody (mAb) manufacturing. However, some HCPs may evade clearance in multiple purification steps and reach the final drug product, potentially threatening drug stability and patient safety. This study extends prior work on HCP characterization and persistence in mAb process streams by using mass spectrometry (MS)-based methods to track HCPs through downstream processing steps for seven mAbs that were generated by five different cell lines. The results show considerable variability in HCP identities in the processing steps but extensive commonality in the identities and quantities of the most abundant HCPs in the harvests for different processes. Analysis of HCP abundance in the harvests shows a likely relationship between abundance and the reproducibility of quantification measurements and suggests that some groups of HCPs may hinder the characterization. Quantitative monitoring of HCPs persisting through purification steps coupled with the findings from the harvest analysis suggest that multiple factors, including HCP abundance and mAb-HCP interactions, can contribute to the persistence of individual HCPs and the identification of groups of common, persistent HCPs in mAb manufacturing.

From cell factories to patients: Stability challenges in biopharmaceuticals manufacturing and administration with mitigation strategies

Active ingredients of biopharmaceuticals consist of a wide array of biomolecular structures, including those of enzymes, monoclonal antibodies, nucleic acids, and recombinant proteins. Recently, these molecules have dominated the pharmaceutical industry owing to their safety and efficacy. However, their manufacturing is hindered by high cost, inadequate batch-to-batch equivalence, inherent instability, and other quality issues. This article is an up-to-date review of the challenges encountered during different stages of biopharmaceutical production and mitigation of problems arising during their development, formulation, manufacturing, and administration. It is a broad overview discussion of stability issues encountered during product life cycle i.e., upstream processing (aggregation, solubility, host cell proteins, color change), downstream bioprocessing (aggregation, fragmentation), formulation, manufacturing, and delivery to patients.

Recent applications of quantitative mass spectrometry in biopharmaceutical process development and manufacturing

Biopharmaceutical products have seen rapid growth over the past few decades and continue to dominate the global pharmaceutical market. Aligning with the quality by design (QbD) framework and realization, recent advances in liquid chromatography-mass spectrometry (LC-MS) instrumentation and related techniques have enhanced biopharmaceutical characterization capabilities and have supported an increased development of biopharmaceutical products. Beyond its routine qualitative characterization, the quantitative feature of LC-MS has unique applications in biopharmaceutical process development and manufacturing. This review describes the recent applications and implications of the advancement of quantitative MS methods in biopharmaceutical process development, and characterization of biopharmaceutical product, product-related variants, and process-related impurities. We also provide insights on the emerging applications of quantitative MS in the lifecycle of biopharmaceutical product development including quality control in the Good Manufacturing Practice (GMP) environment and process analytical technology (PAT) practices during process development and manufacturing. Through collaboration with instrument and software vendors and regulatory agencies, we envision broader adoption of phase-appropriate quantitative MS-based methods for the analysis of biopharmaceutical products, which in turn has the potential to enable manufacture of higher quality products for patients.

Advanced mass spectrometry workflows for accurate quantification of trace-level host cell proteins in drug products: Benefits of FAIMS separation and gas-phase fractionation DIA

Therapeutic monoclonal antibodies (mAb) production relies on multiple purification steps before release as a drug product (DP). A few host cell proteins (HCPs) may co-purify with the mAb. Their monitoring is crucial due to the considerable risk they represent for mAb stability, integrity, and efficacy and their potential immunogenicity. Enzyme-linked immunosorbent assays (ELISA) commonly used for global HCP monitoring present limitations in terms of identification and quantification of individual HCPs. Therefore, liquid chromatography tandem mass spectrometry (LC-MS/MS) has emerged as a promising alternative. Challenging DP samples show an extreme dynamic range requiring high performing methods to detect and reliably quantify trace-level HCPs. Here, we investigated the benefits of adding high-field asymmetric ion mobility spectrometry (FAIMS) separation and gas phase fractionation (GPF) prior to data independent acquisition (DIA). FAIMS LC-MS/MS analysis allowed the identification of 221 HCPs among which 158 were reliably quantified for a global amount of 880 ng/mg of NIST mAb Reference Material. Our methods have also been successfully applied to two FDA/EMA approved DPs and allowed digging deeper into the HCP landscape with the identification and quantification of a few tens of HCPs with sensitivity down to the sub-ng/mg of mAb level.

Quantitation of host cell proteins in biopharmaceuticals from chinese hamster ovarian and vero cell lines using capillary electrophoresis western blots

Quantitation of host cell proteins (HCPs) is essential in the process of preparation of many biological and vaccine products. Common methods of quantitation include the widely applied enzyme-linked immunosorbent assays (ELISAs), mass spectrometry (MS) and other orthogonal assays. Prior to using these techniques, critical reagents need to be evaluated, for example, antibodies need to be assessed for HCP coverage. Percent of HCP coverage is often established by denatured 2D Western blot. However, ELISAs measure the amount of HCP only in a native state. There are limited studies linking reagents validated by 2D-Western to ensure adequate coverage in the final ELISA. ProteinSimple's newly developed capillary Western blot technology allows for separation, blotting, and detection of proteins in a semi-automated and simplified format. Capillary Westerns are similar to slab Westerns, with the added benefit of being quantitative. Here we outline the capillary Western method that links the 2D Western coverage and ultimately ELISAs for more efficient HCP quantitation. This study describes the development of the capillary Western analytical method to quantitively evaluate HCPs in Vero and Chinese Hamster Ovarian (CHO) cell lines. The amount of CHO HCPs decreases as the sample is purified as expected. Using this approach, we determined that the detected Vero HCPs amount was similar irrespective of denatured (capillary Western) versus native assay format (ELISA). This new method can also be potentially employed to quantitatively assess the anti-HCP antibody reagent coverage used in commercial HCP ELISA kits.

Ultrasensitive Quantification Method for Understanding Biologically Relevant Concentrations of Host Cell Proteins in Therapeutics

Certain host cell proteins (HCPs) in biotherapeutic drugs may be detrimental to drug product quality even when they are present at the subppm level. Therefore, an analytical method that can reliably quantify trace amounts of HCPs is desirable. This study demonstrates a novel strategy to quantify HCPs present at subppm levels with ProteoMiner enrichment coupled with limited digestion followed by targeted analysis with nano-liquid chromatography-parallel reaction monitoring. The method can achieve LLOQ values as low as 0.06 ppm, with an accuracy of 85%-111% of the theoretical value, and inter-run and intrarun precision within 12% and 25%, respectively. The approach was applied to the quantification of five high-risk HCPs in drug products. The results indicated that 2.5 ppm lysosomal acid lipase, 0.14 ppm liver carboxylesterase, 1.8 ppm palmitoyl-protein thioesterase 1, and 1 ppm cathepsin D affected the stability of drug products, whereas drug products could safely contain 1.5 ppm lipoprotein lipase, 0.1 ppm lysosomal acid lipase, or 0.3 ppm cathepsin D. In combination with lipase activity analysis, the accurate quantification of lipases/esterases in drug products enables better understanding and comparison of the enzymatic activity of polysorbate degradation from endogenous proteins.

Ultrasensitive method for profiling host cell proteins by coupling limited digestion to ProteoMiner technology

Host cell proteins (HCPs) are process-related impurities that remain in therapeutic protein -at trace levels. HCPs must be closely monitored because they may be detrimental to drug product quality. Liquid chromatography coupled to mass spectrometry (LC-MS) is a powerful tool for detecting individual HCPs; however, HCP-derived peptides can be four to ten orders of magnitude less abundant than therapeutic protein-derived peptides in drug products, thus posing a major challenge in LC-MS detection. We previously demonstrated that low abundant HCPs can be enriched several hundreds fold through ProteoMiner. This study further improved the degree of enrichment by coupling limited digestion to ProteoMiner technology (PMLD). HCPs with low abundance were enriched 7694-fold, thus enabling detection of HCPs at concentrations as low as 0.002 ppm. A total of 850 HCPs were detected with high confidence from a NIST monoclonal antibody preparation, a number 40% higher than previously reported.

Analysis of Host Cell Proteins in Monoclonal Antibody Therapeutics Through Size Exclusion Chromatography

PURPOSE

Host cell proteins (HCPs) are impurities derived from expression systems during the manufacturing of biotherapeutics. Even trace amounts of certain HCPs can potentially compromise product safety and quality. Therefore, comprehensive analytical characterization is necessary. In particular, understanding how each HCP co-purifies with the biotherapeutics throughout the purification process would help guide process development to avoid further contamination.

METHODS

We developed a new strategy based on size exclusion chromatography (SEC) fractionation followed by mass spectrometry (MS) analysis to study HCPs.

RESULTS

Through an optimized experimental procedure, HCPs were effectively separated from monoclonal antibody (mAb) drug substances via SEC fractionation and sensitively detected with MS. Many HCPs were enriched in the high molecular weight fraction, thus indicating the formation of HCP-mAb complexes. SEC separation under mild denaturing conditions was demonstrated to disrupt weak interactions between certain HCPs and mAbs. The binding profiles of HCPs to mAbs were further characterized through comparison of the relative abundance of HCPs in each fraction under either native or mild denaturing SEC conditions.

CONCLUSIONS

This new method not only achieves improved identification of HCPs in biotherapeutic drug substances but also offers an effective means to evaluate the binding properties between biotherapeutics and a wide range of HCPs.

Holistic Analytical Characterization and Risk Assessment of Residual Host Cell Protein Impurities in an Active Pharmaceutical Ingredient (API) Synthesized by Biocatalysts

Host cell proteins (HCPs) are a significant class of process-related impurities commonly associated with the manufacturing of biopharmaceuticals. However, due to the increased use of crude enzymes as biocatalysts for modern organic synthesis, HCPs can also be introduced as a new class of impurities in chemical drugs. In both cases, residual HCPs need to be adequately controlled to ensure product purity, quality, and patient safety. Although a lot of attentions have been focused on defining a universally acceptable limit for such impurities, the risks associated with residual HCPs on product quality, safety, and efficacy often need to be determined on a case-by-case basis taking into consideration the residual HCP profile in the product, the dose, dosage form, and administration route etc. Here we describe the unique challenges for residual HCP control presented by the biocatalytic synthesis of a Merck investigational stimulator of interferon genes protein (STING) agonist, MK-1454, which is a cyclic dinucleotide synthesized using E. coli cell lysate overexpressing cyclic GMP-AMP synthase (cGAS) as a biocatalyst. In this study, a holistic characterization of residual protein impurities using a variety of analytical tools including nano-LC-MS/MS, together with in silico immunogenicity prediction of identified proteins, facilitated risk assessment and guided process development to achieve adequate removal of residual protein impurities in MK-1454 API. This article is protected by copyright. All rights reserved.

The measurement and control of high-risk host cell proteins for polysorbate degradation in biologics formulation

Nonionic surfactant polysorbates, including PS-80 and PS-20, are commonly used in the formulation of biotherapeutic products for both preventing surface adsorption and acting as stabilizer against protein aggregation. Trace levels of residual host cell proteins (HCPs) with lipase or esterase enzymatic activity have been shown to degrade polysorbates in biologics formulation. The measurement and control of these low abundance, high-risk HCPs for polysorbate degradation are an industry-wide challenge to achieve desired shelf life of biopharmaceuticals in liquid formulation, especially for high-concentration formulation product development. Here, we reviewed the challenges, recent advances, and future opportunities of analytical method development, risk assessment, and control strategies for polysorbate degradation during formulation development with a focus on enzymatic degradation. Continued efforts to advance our understanding of polysorbate degradation in biologics formulation will help develop high-quality medicines for patients.

Factors affecting the quality of therapeutic proteins in recombinant Chinese hamster ovary cell culture

Chinese hamster ovary (CHO) cells are the most widely used mammalian host cells for the commercial production of therapeutic proteins. Fed-batch culture is widely used to produce therapeutic proteins, including monoclonal antibodies, because of its operational simplicity and high product titer. Despite technical advances in the development of culture media and cell cultures, it is still challenging to maintain high productivity in fed-batch cultures while also ensuring good product quality. In this review, factors that affect the quality attributes of therapeutic proteins in recombinant CHO (rCHO) cell culture, such as glycosylation, charge variation, aggregation, and degradation, are summarized and categorized into three groups: culture environments, chemical additives, and host cell proteins accumulated in culture supernatants. Understanding the factors that influence the therapeutic protein quality in rCHO cell culture will facilitate the development of large-scale, high-yield fed-batch culture processes for the production of high-quality therapeutic proteins.

Analytics of host cell proteins (HCPs): lessons from biopharmaceutical mAb analysis for Gene therapy products

Analytics for host cell protein (HCP) analysis of therapeutic monoclonal antibody preparations have developed enormously. We consider how learnings from this can inform HCP analysis of gene therapy viral vector products. The application of mass spectrometry (MS) approaches for analysis of HCPs in viral vector preparations is being established, although such information remains limited and is yet to be widely applied into process or host cell line development to reduce HCP amounts or risk. As these MS approaches, and the data from them, are applied and become available, the process understanding created will speed process development activity. We describe technologies that have been, or can be, applied to viral vector HCP analysis to aid process development, reduce HCP amounts, identify critical HCPs and thus inform risk assessment and management based on a knowledge of specific HCPs, ultimately delivering safe and efficacious gene therapy products to the clinic.

Profiling Active Enzymes for Polysorbate Degradation in Biotherapeutics by Activity-Based Protein Profiling

Polysorbate is widely used to maintain stability of biotherapeutic proteins in pharmaceutical formulation development. Degradation of polysorbate can lead to particle formation in drug products, which is a major quality concern and potential patient risk factor. Enzymatic activity from residual host cell enzymes such as lipases and esterases plays a major role for polysorbate degradation. Their high activity, often at very low concentration, constitutes a major analytical challenge in the biopharmaceutical industry. In this study, we evaluated and optimized the activity-based protein profiling (ABPP) approach to identify active enzymes responsible for polysorbate degradation. Using an optimized chemical probe, we established the first global profile of active serine hydrolases in harvested cell culture fluid (HCCF) for monoclonal antibodies (mAbs) production from two Chinese hamster ovary (CHO) cell lines. A total of eight known lipases were identified by ABPP with enzyme activity information, while only five lipases were identified by a traditional abundance-based proteomics (TABP) approach. Interestingly, phospholipase B-like 2 (PLBL2), a well-known problematic HCP was not found to be active in process-intermediates from two different mAbs. In a proof-of-concept study with downstream samples, phospholipase A2 group VII (PLA2G7) was only identified by ABPP and confirmed to contribute to polysorbate-80 degradation for the first time. The established ABBP approach is approved to be able to identify low-abundance host cell enzymes and fills the gap between lipase abundance and activity, which enables more meaningful polysorbate degradation investigations for biotherapeutic development.

Identification and characterization of a residual host cell protein hexosaminidase B associated with N-glycan degradation during the stability study of a therapeutic recombinant monoclonal antibody product

Host cell proteins (HCPs) are process‐related impurities derived from host organisms, which need to be controlled to ensure adequate product quality and safety. In this study, product quality attributes were tracked for several monoclonal antibodies (mAbs) under the intended storage and accelerated stability conditions. One product quality attribute not expected to be stability indicating is the N‐glycan heterogeneity profile. However, significant N‐glycan degradation was observed for one mAb under accelerated and stressed stability conditions. The root cause for this instability was attributed to hexosaminidase B (HEXB), an enzyme known to remove terminal N‐acetylglucosamine (GlcNAc). HEXB was identified by liquid chromatography–mass spectrometry (LC–MS)‐based proteomics approach to be enriched in the impacted stability batches from mAb‐1. Subsequently, enzymatic and targeted multiple reaction monitoring (MRM) MS assays were developed to support process and product characterization. A potential interaction between HEXB and mAb‐1 was initially observed from the analysis of process intermediates by proteomics among several mAbs and later supported by computational modeling. An improved bioprocess was developed to significantly reduce HEXB levels in the final drug substance. A risk assessment was conducted by evaluating the in silico immunogenicity risk and the impact on product quality. To the best of our knowledge, HEXB is the first residual HCP reported to have impact on the glycan profile of a formulated drug product. The combination of different analytical tools, mass spectrometry, and computational modeling provides a general strategy on how to study residual HCP for biotherapeutics development.