Application of germline antibody features to vaccine development, antibody discovery, antibody optimization and disease diagnosis

Although the efficacy and commercial success of vaccines and therapeutic antibodies have been tremendous, designing and discovering new drug candidates remains a labor-, time- and cost-intensive endeavor with high risks. The main challenges of vaccine development are inducing a strong immune response in broad populations and providing effective prevention against a group of highly variable pathogens. Meanwhile, antibody discovery faces several great obstacles, especially the blindness in antibody screening and the unpredictability of the developability and druggability of antibody drugs. These challenges are largely due to poorly understanding of germline antibodies and the antibody responses to pathogen invasions. Thanks to the recent developments in high-throughput sequencing and structural biology, we have gained insight into the germline immunoglobulin (Ig) genes and germline antibodies and then the germline antibody features associated with antigens and disease manifestation. In this review, we firstly outline the broad associations between germline antibodies and antigens. Moreover, we comprehensively review the recent applications of antigen-specific germline antibody features, physicochemical properties-associated germline antibody features, and disease manifestation-associated germline antibody features on vaccine development, antibody discovery, antibody optimization, and disease diagnosis. Lastly, we discuss the bottlenecks and perspectives of current and potential applications of germline antibody features in the biotechnology field.

Western Blot as a Support Technique for Immunohistochemistry to Detect Programmed Cell Death Ligand 1 Expression

Antibody selection and optimization are crucial to guarantee accurate and reproducible results when using such antibodies for applications such as western blot analysis and immunohistochemistry (IHC). This is especially important when selecting good candidate antibodies that will be used for cancer immunotherapy diagnostics and research. In this chapter, we describe a Western Blot technique as support methodology for the selection and validation of Programmed Cell Death Ligand 1 (PD-L1) antibodies that can be subsequently used in immunohistochemistry applications. Western Blot is a sensitive, specific, and widely available protein characterization technique, used for the detection of specific antigens. PD-L1 is a major immune checkpoint protein that mediates antitumor immune suppression and response, which is routinely detected using IHC in formalin-fixed and paraffin-embedded tissues as part of cancer clinical diagnostic workflows. For this reason, it is critical to define and select the best antibody clones and validate them using different techniques in order to have a reliable detection of positive staining when these antibodies are used in IHC.

Detection of Programmed Cell Death Ligand 1 Expression in Lung Cancer Clinical Samples by an Automated Immunohistochemistry System

Programmed cell death 1 (PD-1) plays an important role in subsiding immune responses, in promoting self-tolerance through suppressing the activity of T-cells, and in promoting differentiation of regulatory T-cells. One of its ligands, programmed cell death ligand 1 (PD-L1) acts as a checkpoint regulator in immune cells and is also expressed in a wide range of cancer types. Anti-PD therapy modulates immune responses at the tumor site, targets tumor-induced immune defects, and repairs ongoing immune responses. Since drugs that target the PD-1/PD-L1 pathways became available as a cancer treatment, there is need for the use of different antibodies to detect the presence of these proteins in tumoral samples by immunohistochemistry or other assays. Because the detection of these antigens in tumor samples is highly clinically informative for guiding treatment decisions, especially to establish the aptness of a patient to receive anti-PD therapy, it is necessary to have a validation process that guaranties that the test results obtained when using antibodies against these proteins are specific, selective, reproducible, and conducive to quantification of antigen abundance in cancer tissue sections. Here we describe an automated immunohistochemistry staining procedure that can be applied for the validation of multiple anti-PD-L1 antibody clones when used for the staining of formalin-fixed, paraffin-embedded lung cancer tissue sections.

Round optimization for improved discovery of native bispecific antibodies

The assembly of bispecific antibodies (bsAb) that retain the structure of a standard IgG can be challenging as the correct pairing of the different heavy and light chains has to be ensured while unwanted side products kept to a minimum. The use of antibodies sharing a common chain facilitates assembly of such bsAb formats but requires additional efforts during the initial discovery phase. We have developed a native bsAb format called κλ body based on antibodies that, while being specific for different antigens, share the same heavy chain. Such antibodies can readily be isolated from antibody libraries incorporating a single VH combined with light chain diversity. However, in order to improve the discovery process of such fixed VH antibodies, we developed a method to optimize populations of light chains by recovering and shuffling CDRL3 sequences that have been enriched for antigen binding by phage display selection. This approach allowed for the isolation of a more diverse and potent panel of antibodies blocking the interaction between PD-1 and PD-L1 when compared to our standard in vitro selection approach, thus providing better building blocks for subsequent bsAb generation.

Modular Construction of Large Non-Immune Human Antibody Phage-Display Libraries from Variable Heavy and Light Chain Gene Cassettes

Monoclonal antibodies and antibody-derived therapeutics have emerged as a rapidly growing class of biological drugs for the treatment of cancer, autoimmunity, infection, and neurological diseases. To support the development of human antibodies, various display techniques based on antibody gene repertoires have been constructed over the last two decades. In particular, scFv-antibody phage display has been extensively utilized to select lead antibodies against a variety of target antigens. To construct a scFv phage display that enables efficient antibody discovery, and optimization, it is desirable to develop a system that allows modular assembly of highly diverse variable heavy chain and light chain (Vκ and Vλ) repertoires. Here, we describe modular construction of large non-immune human antibody phage-display libraries built on variable gene cassettes from heavy chain and light chain repertoires (Vκ- and Vλ-light can be made into independent cassettes). We describe utility of such libraries in antibody discovery and optimization through chain shuffling.