Adaptive immunity is driven by the ability of lymphocytes to undergo V(D)J recombination and generate a highly diverse set of adaptive immune receptors [B cell receptors (BCRs)/secreted antibodies and T cell receptors (TCRs)], and their subsequent clonal selection and expansion upon molecular recognition of foreign antigens. These principles lead to remarkable, unique, and dynamic immune receptor repertoires. This presentation will explain how our group is using genome editing, deep sequencing, and machine learning to identify patterns of antigen specificity in adaptive immune receptors. Furthermore, I will explain how these approaches can be used for antibody drug discovery and T cell immunotherapy. 

Antibody repertoires are instrumental in both fighting and causing disease. Past and current immune events are recorded in the antibody repertoire throughout an individual's lifetime. Computational immunology is increasingly used to decipher the immune record in antibody repertoires. We will show how computational and machine learning methods may be used to analyse fundamental aspects of adaptive immunity, predict immune events and antigen binding, as well as generate antibodies in silico.

In 23 days, AbCellera identified 24 lead candidate antibodies for the treatment and prevention of COVID-19 directly from a blood sample of a convalescent patient. AbCellera is a technology company that searches, decodes, and analyzes natural immune systems to find antibodies that its partners can develop into drugs to prevent and treat disease.

Computational tools are becoming increasingly important in the field of therapeutic antibody discovery. Our SAbDab-SAbPred platform is a toolbox of software applications and databases that can be used at various points along the development pipeline to inform decisions; for example, TAP, our developability prediction software, can be used to select candidate molecules that are more likely to be successful. The latest addition to the platform is our humanisation tool, which exploits the rapidly growing amount of antibody repertoire data that is becoming available. Given a starting sequence, the tool aims to minimally mutate that sequence, such that it does not elicit an immune response in humans, without impacting its efficacy as a therapeutic. Testing the protocol on previously humanised therapeutics indicates that the tool replicates many of the mutations proposed experimentally in a fraction of the time.

Recombinant expression of botulinum neurotoxins enables protein engineering to exploit the modularity of these proteins, with potential for an increased range of indications. Enhanced strategies around protein modelling, engineering, and characterization have been exploited to increase the numbers of novel neurotoxins produced, extending the early exploration of design space and supporting selection of candidates with optimal function and improved developability.

A core research goal of my lab is to study the macromolecular machines that contribute to genome organization and structure. To this end we have been focused on understanding the DNA rearrangements that occur during transposition. Here I will talk about recent work from our lab to understand the mechanism of action of DNA-transposases as they carry out the reactions that result in their replication and to modify the host genome. 

Antibodies are cornerstones of modern biotechnology, but antibody properties, including chemical reactivity and mode of target binding, can be constrained by the limited chemistries found in the genetic code. In this work, we describe our yeast display-based approach to identifying antibody variable domains with properties augmented by noncanonical amino acids. This presentation will highlight proof-of-principle demonstrations of how this approach provides important opportunities for discovering and engineering more “druglike” antibodies.

We will demonstrate Icosagen's contribution to battle the global pandemic in developing SARS-CoV-2 neutralizing antibodies. We have developed a panel of highly potent virus neutralizing antibodies. Through biochemical, functional and structural analysis we characterize the properties of our lead molecules and demonstrate in-vivo efficacy of the developed lead molecules.

Antibody effector functions are often undesired for therapeutic antibodies when only antigen binding or neutralization would be ideal. By switching the native glycosylation site from position 297 to 298, we created alternative antibody glycosylation variants as a novel strategy to eliminate the effector functions. The lead mutant called “NNAS” (N297/S298N/T299A/Y300S) with the engineered glycosylation site at Asn298 shows no detectable binding to all mouse or human FcγRs by SPR analyses. The effector functions of the mutant are completely eliminated when measured in antibody-dependent cellular cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC) assays. No in vivo cell depletion was observed with NNAS mutant in transgenic mice. Structural study confirmed the successful glycosylation switch to the engineered Asn298 site would cause a clash of N-glycans with FcγRs, resulting in loss of binding. In addition, the NNAS mutants of multiple antibodies retain binding to antigens and FcRn, exhibit comparable purification yields and thermal stability, and display normal circulation half-life in mice and non-human primates. Our work provides a novel approach for generating therapeutic antibodies devoid of any effector function with potentially lower immunogenicity.

Multi-spanner receptors, including GPCRs, constitute a therapeutically interesting yet technically challenging target class for therapeutic antibodies. Factors contributing difficulty of targeting these receptors include high homology across species resulting in immune silencing during immunization, relatively low or transient cell-surface expression levels, and difficulty in formulation as a soluble protein applicable to immunogen and screening reagent applications. This talk will cover some examples of approaches to overcome these challenges.

Human mAbs are ideal diagnostic reagents for infectious disease and auto-immunity, but diagnostic Abs must meet different performance criteria than therapeutic antibodies. On-Cell mAb Screening (OCMS™) is a hybridoma method in which patient-derived B cells express their antibodies on their cell surface. OCMS mAbs are screened for binding to fluorescent antigens using high throughput imaging techniques. OCMS accelerates diagnostic mAb discovery because it simplifies multiplex screening, epitope binning, and off-rate measurement.  Case studies will be shown with antibodies to poliovirus, the NMDAR receptor, and SARS-CoV-2 Spike protein. 

A deeper understanding of protective humoral immunity to SARS-CoV-2 should aid in the discovery and design of therapeutic interventions. Here, I will present a molecular, functional, and structural analysis of convalescent-phase IgG monoclonal antibodies mined from the blood of COVID-19 survivors. The talk will include a comparative analysis of these serological repertoires vs. B cell repertoires described by other research groups.

Synbio Technologies provides fast and customized one-stop solutions for antibody discovery. SynoAb platform is a structure-based in silico antibody discovery method and can screen hits for antigens for wet-lab evaluation, followed by affinity maturations using controlled permutation libraries. The SynoAb will offer highly flexible supports and services for antibody discovery.

mAb candidates identified from high-throughput screening or binding affinity optimization often present liabilities for developability, such as aggregation-prone regions or poor solution behavior. In this work, we developed a method for modeling proteins and performing pH-dependent conformational sampling, which can enhance property calculations such as hydrophobic patches, charge and pI. A retrospective data analysis demonstrates that these 3D descriptors, averaged over conformational sampling and stochastic titration, can accurately predict pI values, screen candidates and enrich libraries with favorable developability properties for a range of biotherapeutics. The clinical landscape of antibodies is also analyzed and its property profile and insights thereof are presented.

My laboratory has established unique, large, single-domain antibody (also called “nanobody”) phage display libraries from camels (Camelus dromedarius) and sharks (Ginglymostoma cirratum) to develop nanobodies against SARS-CoV-2 and other disease antigens. In my talk, I will discuss: (i) construction and sequencing analysis of our camel (V_HH) and shark (V_NAR) nanobody phage libraries; (ii) screening of nanobodies to SARS-CoV-2 spike (S) protein; and (iii) binding features of these novel nanobodies.

Our novel, automated high-throughput engineering platform enables the fast generation of large panels of multi-specific biotherapeutics (up to 10.000), giving rise to large data sets (more than 100.000 data points). By combining data science and structure-based design workflows, we leverage the potential of our unique data sets to guide the engineering of our next-generation antibody therapeutics.