Identification of New Antibodies Targeting Malignant Plasma Cells for Immunotherapy by Next-Generation Sequencing-Assisted Phage Display

Novel Strategy of Antibody Affinity Maturation and Enhancement of Nucleolin-Mediated Antibody-Dependent Cellular Cytotoxicity Against Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) is a clinically aggressive subtype of breast cancer that remains an unmet medical need. Because TNBC cells do not express the most common markers of breast cancers, there is an active search for novel molecular targets in triple-negative tumors. Additionally, this subtype of breast cancer presents strong immunogenic characteristics which have been encouraging the development of immunotherapeutic approaches against the disease. In this context, nucleolin arises as a promising target for immunotherapy against TNBC. Our group has previously developed an anti-nucleolin VHH-Fc antibody capable of eliciting antibody-dependent cellular cytotoxicity (ADCC). Moreover, we constructed and characterized an antibody library, that was screened against nucleolin-overexpressing cells, originating an enriched anti-nucleolin antibody pool. In this work, a strategy to select individual clones from the pool was designed, combining NGS data with 3D modeling. Two antibodies demonstrated a significant 4.4- and 6.1-fold increase in binding to nucleolin-overexpressing and TNBC cells, and an improvement in affinity to the sub-micromolar range (0.19 µM and 83.69 nM). Additionally, an increment in 4.6- and 3.1-fold in ADCC activity against respective cell lines was observed for the M2 antibody clone. Herein, the affinity maturation strategy developed was validated and corroborated a positive, but not proportional, correlation between antibody binding, affinity, and ADCC.

Single-Stranded Variable Fragment Gene Libraries Built for Phage Display: An Updated Review of Design, Selection and Application

The development of the phage display technique has brought practicality and speed when selecting high-affinity molecules. It is used to obtain single-chain variable fragments (scFvs) and has revolutionized several branches of research and industry. These are developed from gene libraries that differ in their construction strategies, which causes a diversity of sequences, specificity and binding strength of the projected molecule to its antigen. In this review, we present the recent studies that demonstrate methods and approaches using immune, naïve, synthetic and semi-synthetic libraries to construct and select scFvs. Subsequently, the characteristics of these libraries, the functionality of the scFvs and the cost-benefits of production will be discussed. In addition, we highlight the methodological trends and challenges to be overcome in order to optimize the production and application of these antibody fragments.

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.

Combining Cellular Immunization and Phage Display Screening Results in Novel, FcγRI-Specific Antibodies

Antibodies that specifically bind to individual human fragment crystallizable γ receptors (FcγRs) are of interest as research tools in studying immune cell functions, as well as components in bispecific antibodies for immune cell engagement in cancer therapy. Monoclonal antibodies for human low-affinity FcγRs have been successfully generated by hybridoma technology and are widely used in pre-clinical research. However, the generation of monoclonal antibodies by hybridoma technology that specifically bind to the high-affinity receptor FcγRI is challenging. Monomeric mouse IgG2a, IgG2b, and IgG3 bind human FcγRI with high affinity via the Fc part, leading to an Fc-mediated rather than a fragment for antigen binding (Fab)-mediated selection of monoclonal antibodies. Blocking the Fc-binding site of FcγRI with an excess of human IgG or Fc during screening decreases the risk of Fc-mediated interactions but can also block the potential epitopes of new antibody candidates. Therefore, we replaced hybridoma technology with phage display of a single-chain fragment variable (scFv) antibody library that was generated from mice immunized with FcγRI-positive cells and screened it with a cellular panning approach assisted by next-generation sequencing (NGS). Seven new FcγRI-specific antibody sequences were selected with this methodology, which were produced as Fc-silent antibodies showing FcγRI-restricted specificity.

Identification of New Antibodies Targeting Tumor Cell Surface Antigens by Phage Display

The majority of therapeutic antibodies, bispecific antibodies, and chimeric antigen receptor (CAR) T cells in cancer therapy are based on an antibody or antibody fragment that specifically binds a target present on the surface of a tumor cell. Suitable antigens that can be used for immunotherapy are ideally tumor-specific or tumor-associated and stably expressed on the tumor cell. The identification of new target structures to further optimize immunotherapies could be realized by comparing healthy and tumor cells using "omics" methods to select promising proteins. However, differences in post-translational modifications and structural alterations that can be present on the tumor cell surface are difficult to identify or even not accessible by these techniques. In this chapter, we describe an alternative approach to potentially identify antibodies targeting novel tumor-associated antigens (TAA) or epitopes by using cellular screening and phage display of antibody libraries. Isolated antibody fragments can be further converted into chimeric IgG or other antibody formats to investigate the anti-tumor effector functions and finally identify and characterize the respective antigen.