Automated high throughput microscale antibody purification workflows for accelerating antibody discovery

Rapid affinity optimization of an anti-TREM2 clinical lead antibody by cross-lineage immune repertoire mining

We describe a process for rapid antibody affinity optimization by repertoire mining to identify clones across B cell clonal lineages based on convergent immune responses where antigen-specific clones with the same heavy (VH) and light chain germline segment pairs, or parallel lineages, bind a single epitope on the antigen. We use this convergence framework to mine unique and distinct VH lineages from rat anti-triggering receptor on myeloid cells 2 (TREM2) antibody repertoire datasets with high diversity in the third complementarity-determining loop region (CDR H3) to further affinity-optimize a high-affinity agonistic anti-TREM2 antibody while retaining critical functional properties. Structural analyses confirm a nearly identical binding mode of anti-TREM2 variants with subtle but significant structural differences in the binding interface. Parallel lineage repertoire mining is uniquely tailored to rationally explore the large CDR H3 sequence space in antibody repertoires and can be easily and generally applied to antibodies discovered in vivo.

Deep mining of antibody phage-display selections using Oxford Nanopore Technologies and Dual Unique Molecular Identifiers

Antibody phage-display technology identifies antibody-antigen interactions through multiple panning rounds, but traditional screening gives no information on enrichment or diversity throughout the process. This results in the loss of valuable binders. Next Generation Sequencing can overcome this problem. We introduce a high accuracy long-read sequencing method based on the recent Oxford Nanopore Technologies (ONT) Q20 + chemistry in combination with dual unique molecular identifiers (UMIs) and an optimized bioinformatic analysis pipeline to monitor the selections. We identified binders from two single-domain antibody libraries selected against a model protein. Traditional colony-picking was compared with our ONT-UMI method. ONT-UMI enabled monitoring of diversity and enrichment before and after each selection round. By combining phage antibody selections with ONT-UMIs, deep mining of output selections is possible. The approach provides an alternative to traditional screening, enabling diversity quantification after each selection round and rare binder recovery, even when the dominating binder was > 99% abundant. Moreover, it can give insights on binding motifs for further affinity maturation and specificity optimizations. Our results demonstrate a platform for future data guided selection strategies.

Open-source milligram-scale, four channel, automated protein purification system

Liquid chromatography purification of multiple recombinant proteins, in parallel, could catalyze research and discovery if the processes are fast and approach the robustness of traditional, "one-protein-at-a-time" purification. Here, we report an automated, four channel chromatography platform that we have designed and validated for parallelized protein purification at milligram scales. The device can purify up to four proteins (each with its own single column), has inputs for up to eight buffers or solvents that can be directed to any of the four columns via a network of software-driven valves, and includes an automated fraction collector with ten positions for 1.5 or 5.0 mL collection tubes and four positions for 50 mL collection tubes for each column output. The control software can be accessed either via Python scripting, giving users full access to all steps of the purification process, or via a simple-to-navigate touch screen graphical user interface that does not require knowledge of the command line or any programming language. Using our instrument, we report milligram-scale, parallelized, single-column purification of a panel of mammalian cell expressed coronavirus (SARS-CoV-2, HCoV-229E, HCoV-OC43, HCoV-229E) trimeric Spike and monomeric Receptor Binding Domain (RBD) antigens, and monoclonal antibodies targeting SARS-CoV-2 Spike (S) and Influenza Hemagglutinin (HA). We include a detailed hardware build guide, and have made the controlling software open source, to allow others to build and customize their own protein purifier systems.

High titer expression of antibodies using linear expression cassettes for early-stage functional screening

Antibody discovery processes are continually advancing, with an ever-increasing number of potential binding sequences being identified out of in vivo, in vitro, and in silico sources. In this work we describe a rapid system for high yield recombinant antibody (IgG and Fab) expression using Gibson assembled linear DNA fragments (GLFs). The purified recombinant antibody yields from 1 ml expression for this process are approximately five to ten-fold higher than previous methods, largely due to novel usage of protecting flanking sequences on the 5' and 3' ends of the GLF. This method is adaptable for small scale (1 ml) expression and purification for rapid evaluation of binding and activity, in addition to larger scales (30 ml) for more sensitive assays requiring milligram quantities of antibody purified over two columns (Protein A and size exclusion chromatography). When compared to plasmid-based expression, these methods provide nearly equivalent yield of high-quality material across multiple applications, allowing for reduced costs and turnaround times to enhance the antibody discovery process.

High throughput purification of monoclonal recombinant antibodies using a Protein-A coated membrane plate system

The therapeutic use of monoclonal antibodies (mAbs) ranges from cancer treatment to immune-mediated conditions, covering infectious and cardiovascular disorders, among others. The development of improved methods for therapeutic antibody discovery has accelerated the identification of numerous mAbs: a discovery campaign can be deeply mined, resulting in hundreds, even thousands, of potential antibody leads for a given target of interest. High throughput mAb expression and purification methods are required for the rapid validation of those leads. In this work, we describe the implementation of a Protein-A coated membrane plate system, the Purexa™ AHT membrane plate, for robust preparative purification of hundreds of recombinant mAbs, without the need for automation. The high efficiency (>80%) recovery generated sufficient mAb for downstream screening analyses such as ELISA and surface plasmon resonance (SPR). This new system allows the functional validation of hundreds of lead antibodies from discovery campaigns in a timely manner regardless of operational size.

Development of a robust and semi-automated two-step antibody purification process

Advances in antibody discovery technologies, especially with the availability of humanized mice and phage/yeast library approaches, enable the generation of a large diversity of antibodies against nearly any target of interest. As a result, there is an increasing demand for the production of larger numbers of purified antibodies at quantities (10s-100s of milligrams) sufficient for functional screening assays, drug-ability/develop-ability studies and immunogenicity assessments. To accommodate this need, new methods are required that bridge miniature high throughput/plate-based purification and conventional, one at a time, two-step purification at much larger scales. Thus, we developed a semi-automated, mid-scale (i.e., 1-75 mg) purification process that uses a combination of parallel affinity capture and automated sequential polishing to provide substantially improved throughput while delivering high purity. We optimized the affinity capture step to perform 24 monoclonal antibody purifications in parallel using a Protein Maker for 20-200 mL culture media. The eluant is transferred directly to an AKTA pure system equipped with an autosampler for sequential preparative size exclusion chromatography to remove aggregates and undesirable impurities, as well as exchange the antibody into a buffer suitable for most uses, including cell-based assays. This two-step purification procedure, together with plate-based protein analytical methods, can purify 24-48 monoclonal antibodies in <20 hours and generate up to 80 mg per sample. A stringent clean-in-place protocol for both systems and column maintenance was designed and established to minimize endotoxin contamination. This process has proven to be very reliable and robust, enabling the production of thousands of antibodies of sufficient quality and quantity that are suitable for cell-based assays, biochemical/biophysical characterization, and in vivo animal models.

Dramatic activation of an antibody by a single amino acid change in framework

Antibody function is typically entirely dictated by the Complementarity Determining Regions (CDRs) that directly bind to the antigen, while the framework region acts as a scaffold for the CDRs and maintains overall structure of the variable domain. We recently reported that the rabbit monoclonal antibody 4A11 (rbt4A11) disrupts signaling through both TGFβ2 and TGFβ3 (Sun et al. in Sci Transl Med, 2021. https://doi.org/10.1126/scitranslmed.abe0407). Here, we report a dramatic, unexpected discovery during the humanization of rbt4A11 where, two variants of humanized 4A11 (h4A11), v2 and v7 had identical CDRs, maintained high affinity binding to TGFβ2/3, yet exhibited distinct differences in activity. While h4A11.v7 completely inhibited TGFβ2/3 signaling like rbt4A11, h4A11.v2 did not. We solved crystal structures of TGFβ2 complexed with Fab fragments of h4A11.v2 or h4A11.v7 and identified a novel interaction between the two heavy chain molecules in the 2:2 TGFb2:h4A11.v2-Fab complex. Further characterization revealed that framework residue variations at either position 19, 79 or 81 (Kabat numbering) of the heavy chain strikingly converts h4A11.v2 into an inhibitory antibody. Our work suggests that in addition to CDRs, framework residues and interactions between Fabs in an antibody could be engineered to further modulate activity of antibodies.

Vortex flow reactor assessment for the purification of monoclonal antibodies from unclarified broths

The vortex flow reactor (VFR) can be used in many chemical engineering applications. This paper assesses its novel use in the purification of monoclonal antibodies from cell broth. To this end, the IgG2a antibody was purified from the unclarified fermentation broth of transgenic mouse 55/6 hybridoma cells. Visual experiments showed that the VFR worked in the laminar vortices flow regime and the vortices displaced slightly faster than the axial flow. The VFR has the advantage of creating two sorts of flows: axial flow to produce the expanded bed and an extra vortex flow to avoid channeling and stabilize the expanded bed, the hydrodynamic behavior of which is plug flow with an experimental Pèclet number higher than 20. The pH was adjusted in the untreated fermentation broth, which was directly introduced into the reactor thus reducing the number of stages. The IgG2a purification was carried out in a single device via two steps: antibody adsorption in the expanded bed and antibody elution in the settled bed using Streamline rProtein A. A thirty-fold increase in the high-purity antibody concentration was achieved at the top of the pH5 elution peak with a total recovery of 93.1% (w/w) between elution peaks pH 5 and 3.

Process analytics 4.0: A paradigm shift in rapid analytics for biologics development

Analytical testing of product quality attributes and process parameters during the biologics development (Process analytics) has been challenging due to the rapid growth of biomolecules with complex modalities to support unmet therapeutic needs. Thus, the expansion of the process analytics tool box for rapid analytics with the deployment of cutting-edge technologies and cyber-physical systems is a necessity. We introduce the term, Process Analytics 4.0; which entails not only technology aspects such as process analytical technology (PAT), assay automation, and high-throughput analytics, but also cyber-physical systems that enable data management, visualization, augmented reality, and internet of things (IoT) infrastructure for real time analytics in process development environment. This review is exclusively focused on dissecting high-level features of PAT, automation, and data management with some insights into the business aspects of implementing during process analytical testing in biologics process development. Significant technological and business advantages can be gained with the implementation of digitalization, automation, and real time testing. A systematic development and employment of PAT in process development workflows enable real time analytics for better process understanding, agility, and sustainability. Robotics and liquid handling workstations allow rapid assay and sample preparation automation to facilitate high-throughput testing of attributes and molecular properties which are otherwise challenging to monitor with PAT tools due to technological and business constraints. Cyber-physical systems for data management, visualization, and repository must be established as part of Process Analytics 4.0 framework. Furthermore, we review some of the challenges in implementing these technologies based on our expertise in process analytics for biopharmaceutical drug substance development.

Restricted epitope specificity determined by variable region germline segment pairing in rodent antibody repertoires

Antibodies from B-cell clonal lineages share sequence and structural properties as well as epitope specificity. Clonally unrelated antibodies can similarly share sequence and specificity properties and are said to be convergent. Convergent antibody responses against several antigens have been described in humans and mice and include different classes of shared sequence features. In particular, some antigens and epitopes can induce convergent responses of clonally unrelated antibodies with restricted heavy (V_H) and light (V_L) chain variable region germline segment usage without similarity in the heavy chain third complementarity-determining region (CDR H3), a critical specificity determinant. Whether these V germline segment-restricted responses reflect a general epitope specificity restriction of antibodies with shared V_H/V_L pairing is not known. Here, we investigated this question by determining patterns of antigen binding competition between clonally unrelated antigen-specific rat antibodies from paired-chain deep sequencing datasets selected based solely on V_H/V_L pairing. We found that antibodies with shared V_H/V_L germline segment pairings but divergent CDR H3 sequences almost invariably have restricted epitope specificity indicated by shared binding competition patterns. This epitope restriction included 82 of 85 clonally unrelated antibodies with 13 different V_H/V_L pairings binding in 8 epitope groups in 2 antigens. The corollary that antibodies with shared V_H/V_L pairing and epitope-restricted binding can accommodate widely divergent CDR H3 sequences was confirmed by in vitro selection of variants of anti-human epidermal growth factor receptor 2 antibodies known to mediate critical antigen interactions through CDR H3. Our results show that restricted epitope specificity determined by V_H/V_L germline segment pairing is a general property of rodent antigen-specific antibodies.

Parallel sample processing using dispersive INtip micro-purification on programmable multichannel pipettes

Automation gives researchers the ability to process and screen orders of magnitude higher numbers of samples than manual experimentation. Current biomacromolecule separation methodologies suffer from necessary manual intervention, making their translation to high-throughput automation difficult. Herein, we present the first characterization of biomacromolecule affinity purification via dispersive solid-phase extraction in a pipette tip (INtip). We use commercially available resin and compare efficiency with batch and spin column methodologies. Moreover, we measure the kinetics of binding and evaluate resin binding capacities. INtip technology is effective on, and scalable for, an automated platform (INTEGRA ASSIST). The results suggest that high-throughput biomolecular workflows will benefit from the integration of INtip separations.

Massively parallel single-cell B-cell receptor sequencing enables rapid discovery of diverse antigen-reactive antibodies

Obtaining full-length antibody heavy- and light-chain variable regions from individual B cells at scale remains a challenging problem. Here we use high-throughput single-cell B-cell receptor sequencing (scBCR-seq) to obtain accurately paired full-length variable regions in a massively parallel fashion. We sequenced more than 250,000 B cells from rat, mouse and human repertoires to characterize their lineages and expansion. In addition, we immunized rats with chicken ovalbumin and profiled antigen-reactive B cells from lymph nodes of immunized animals. The scBCR-seq data recovered 81% (n = 56/69) of B-cell lineages identified from hybridomas generated from the same set of B cells subjected to scBCR-seq. Importantly, scBCR-seq identified an additional 710 candidate lineages not recovered as hybridomas. We synthesized, expressed and tested 93 clones from the identified lineages and found that 99% (n = 92/93) of the clones were antigen-reactive. Our results establish scBCR-seq as a powerful tool for antibody discovery.

Immune repertoire mining for rapid affinity optimization of mouse monoclonal antibodies

Traditional hybridoma and B cell cloning antibody discovery platforms have inherent limits in immune repertoire sampling depth. One consequence is that monoclonal antibody (mAb) leads often lack the necessary affinity for therapeutic applications, thus requiring labor-intensive and time-consuming affinity in vitro engineering optimization steps. Here, we show that high-affinity variants of mouse-derived mAbs can be rapidly obtained by testing of somatic sequence variants obtained by deep sequencing of antibody variable regions in immune repertories from immunized mice, even with a relatively sparse sampling of sequence variants from large sequence datasets. Affinity improvements can be achieved for mAbs with a wide range of affinities. The optimized antibody variants derived from immune repertoire mining have no detectable in vitro off-target binding and have in vivo clearance comparable to the parental mAbs, essential properties in therapeutic antibody leads. As generation of antibody variants in vitro is replaced by mining of variants generated in vivo, the procedure can be applied to rapidly identify affinity-optimized mAb variants.

Susceptibility of Antibody CDR Residues to Chemical Modifications Can Be Revealed Prior to Antibody Humanization and Aid in the Lead Selection Process

A critical part of the clinical development path for a therapeutic antibody involves evaluating the physical and chemical stability of candidate molecules throughout the manufacturing process. In particular, the risks of chemical liabilities that can impact antigen binding, such as deamidation, oxidation, and isomerization in the antibody CDR sequences, need to be controlled through formulation development or eliminated by replacing the amino acid motif displaying the chemical instability. Commonly, the antibody CDR sequence contains multiple sequence motifs (potential hotspots) for chemical instability. However, only a subset of these motifs results in actual chemical modification, and thus, experimental assessment of the extent of instability is necessary to identify positions for potential sequence engineering. Ideally, this information should be available prior to antibody humanization at the stage of parental rodent antibody identification. Early knowledge of liabilities allows for ranking of clones or the mitigation of liabilities by concurrent engineering with the antibody humanization process instead of time-consuming sequential activities. However, concurrent engineering of chemical liabilities and humanization requires translatability of the chemical modifications from the rodent parental antibody to the humanized. We experimentally compared the stability of all sequence motifs by mass spectrometric peptide mapping between the rodent parental antibody and the final humanized antibody and observed a linear correlation. These results have enabled a streamlined developability assessment process for therapeutic antibodies from lead discovery to clinical development.