Display of Antibodies

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The evolution of phage and yeast display techniques have enabled a vast array of constructs that include bispecific antibodies, antibody-drug conjugates, immunotherapy constructs, T cell receptors, and membrane proteins with ever greater potency and target specificity. The 22nd Annual Display of Antibodies conference at the PEGS Summit convenes the premier leaders in antibody engineering every year to review the latest technology developments that are advancing the field of biologics forward. Don’t miss this significant milestone in the year to learn about new approaches to solving the challenges that remain in protein engineering and hear about the latest tools that are being deployed including structure-based drug design, deep sequencing and single cell analysis.

Final Agenda

 

Scientific Advisory Board

Andrew R.M. Bradbury, MB BS, PhD, CSO, Specifica, Inc.
Jennifer R. Cochran, PhD, Shriram Chair of Bioengineering; Professor of Bioengineering, and (by courtesy) Chemical Engineering, Stanford University
Gregory A. Weiss, PhD, Professor, Chemistry, Molecular Biology & Biochemistry, University of California, Irvine
K. Dane Wittrup, PhD, J.R. Mares Professor, Chemical Engineering & Bioengineering, Massachusetts Institute of Technology

5月3日(日)

Recommended Short Course(s)*

SC1: Clinical Assessment of Immunogenicity of New Modalities: Focus on Bispecific Antibodies, Gene Therapy and Oligonucleotides

SC8: Engineering Better Antibody Therapeutics Using Computational Approaches

*Separate registration required.

5月4日(一)

7:00 am Registration and Morning Coffee

STATE-OF-THE-ART IN ANTIBODY ENGINEERING

8:30 Chairperson’s Opening Remarks

K. Dane Wittrup, PhD, J.R. Mares Professor, Chemical Engineering & Bioengineering, Massachusetts Institute of Technology


8:40 Design of Bispecific Antibodies: From Heavy/Light Chain Pairing Preferences to Mitigating High Viscosity

Paul Carter, PhD, Senior Staff Scientist & Senior Director, Antibody Engineering, Genentech

Bispecific antibodies are of growing interest with two currently marketed and over 100 more in clinical development. This talk will offer some mechanistic understanding of antibody heavy/light chain pairing preference and application to the efficient production of bispecific IgG in single host cells. The second part of this talk will focus on elevated antibody viscosity at high concentration, which can be limiting for subcutaneous delivery, as well as manufacturing. Specifically, a novel mutational strategy was devised to mitigate high viscosity of monospecific and bispecific antibodies that may complement existing methods.

9:10 Addressing Antibody Developability by Mammalian Display

John McCafferty, PhD, CEO and Founder, IONTAS

As well as having appropriate binding affinity, it is important that clinical drug candidates are non-polyreactive and have optimal biophysical properties allowing formulation at high concentrations. Our mammalian display platform has allowed direct selection of antibody variants with reduced polyreactivity and aggregation propensity from large mammalian display libraries. Thus, mammalian display addresses developability issues during the earliest stages of lead discovery and significantly de-risks the future development of antibody drugs.

9:40 Next-Generation Platforms for Antibody Discovery

Andrew Bradbury, MB BS, PhD, CSO, Specifica, Inc.

Antibody display libraries have served as a rich source of therapeutic antibodies. However, antibody leads selected from display libraries usually require downstream affinity and developability optimization, extending lead development timelines and costs. Specifica has established a unique antibody discovery display platform based on natural antibody sequences in which sub-nanomolar antibodies, requiring minimal optimization, are routinely selected.

10:10 Networking Coffee Break

10:50 Choosing the Right Platform: Applications of in vivo and in vitro Systems across the Discovery Pipeline

Melissa Geddie, PhD, Senior Scientist, Antibody Discovery, Biogen

Deciding which platforms to use for new campaigns is an important step in the antibody discovery process. Some considerations include the purpose of the antibodies (reagents vs. therapeutics) as well as the difficulty of the target. Recent campaigns at Biogen will be discussed that highlight the advantages and disadvantages of our in vivo and in vitro platforms.

11:20 Selection and Optimization of Antibodies against Multipass Membrane Proteins in situ on Cell Surfaces

Robert Pejchal, PhD, Director, Antibody Engineering, Adimab LLC

Whole cell selections extend discovery of yeast-presented antibodies to integral membrane proteins, such as GPCRs. A case study from initial binder identification to functional characterization of affinity-optimized antagonist leads against a GPCR will be presented. Affinity optimization by selection as well as high-throughput selection-free screening of antibody variants will be discussed, along with takeaways for leveraging multiple cell lines in NGS-based enrichment analysis of highly-diverse library selection outputs.

11:50 Selected Poster Presentation

12:20 pm High-Quality Antibodies for Therapeutic Applications

Oleh Petriv, PhD, Vice President, New Technology Development, AbCheck

AbCheck discovers and optimizes monoclonal antibodies for therapeutic applications leveraging several proprietary platforms including in vivo and in vitro technologies. AbCheck developed a new approach to discover candidate leads based primarily on functional criteria which is assessed at single-cell level in cell-based assays. We will present data generated using high-throughput microfluidics to illustrate the potential of this new technology.

12:50 Session Break

12:55 LUNCHEON PRESENTATION I: Streamlined Discovery and Production of Therapeutic Antibodies

Birgit Viira, Key Account and Technology Officer, Icosagen

We take advantage of the universal HybriFree antibody discovery engine to efficiently discover therapeutic antibodies by direct cloning from B cells of immunized rabbit, chicken, human, or dog. HybriFree method is further powered by our patented QMCF expression platform to produce high-quality recombinant protein antigens, and antibodies cost-effectively for preclinical research (including afucosylated antibodies for enhanced ADCC). Technologies and case studies will be presented and discussed.

1:25 LUNCHEON PRESENTATION II: Synthetic DNA Technologies Enable Antibody Discovery and Optimization

Sato_AaronAaron Sato, PhD, CSO, Biopharma, Twist Bioscience

Utilizing its proprietary DNA technology to write synthetic libraries, Twist Biopharma provides end-to-end antibody discovery and optimization solutions for the biotechnology industry.  This solution includes (1) a panel of highly diverse synthetic naïve antibody phage display libraries, (2) several target class specific antibody phage display libraries against difficult-to-drug targets, (3) a Twist Antibody Optimization (TAO) platform for antibody affinity and developability optimization and (4) a high-throughput antibody expression service. 

1:55 Session Break

2:20 Problem-Solving Breakout Discussions - View All Breakout Discussion Topics

TABLE: Can Mammalian Display Compete with Yeast and Phage? Challenges and Benefits of Mammalian Selection Systems for Protein Engineering

Moderator: Jennifer Maynard, PhD, Henry Beckman Professor, McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at Austin

  • What are the trade-offs among reported mammalian systems?
  • What proteins are right for mammalian display? (GPCR, transport proteins and intramembrane proteases)
  • How can we design selections based on protein activity?
  • How to introduce and maintain a library – retroviral elements, CRISPR or others?
  • Can we simultaneously engineer glycosylation and proteins for desired functions?
  • How can we maximize library size, ensure just one variant per cell and maximize the dynamic range to separate populations of interest?

TABLE: Enabling Technologies to Enhance Selections Based on Immune Function

Moderator: Jamie Spangler, PhD, Assistant Professor, Biomedical and Chemical & Biomolecular Engineering, Johns Hopkins University

  • Interfacing new flow cytometry tools with directed evolution to facilitate functional selections
  • Yeast biopanning techniques to improve recognition of active signaling proteins
  • Choosing readouts to couple with selection process
  • Designing selection strategies to evolve proteins that enact therapeutic mechanisms of interest

3:20 Networking Refreshment Break

PLENARY KEYNOTE SESSION

4:00 Chairperson’s Remarks

K. Dane Wittrup, PhD, J.R. Mares Professor, Chemical Engineering & Bioengineering, Massachusetts Institute of Technology

4:10 From Energy to Machine Learning

George-ChurchGeorge Church, PhD, Professor of Genetics, Harvard Medical School; Professor of Health Sciences and Technology, Harvard and the Massachusetts Institute of Technology (MIT)

In 1974, I adapted energy optimization methods for use in models of nucleic acids, protein and their interactions, and then for use in crystallographic refinement. In the last days of the second millennium, David Baker's team won the Critical Assessment of Structure Prediction (CASP) by an unbelievable margin. Since then, our labs exchanged 3 PhD students (Dantas, Raman, Lajoie), for Wannier from Mayo's group, Stranges from Kuhlman, and Mandell from Kortemme. We engineered new sensor proteins for metabolic engineering, essential proteins with non-standard amino acids for biocontainment, and polymerase-pore fusions for nanopore sequencing. None of this prepared us for the revolution following Gleb Kuznetsov joining our lab in 2012, joined soon by Surge Biswas, Pierce Ogden, Ethan Alley, and Sam Sinai. Together we abruptly moved to "sequence only" deep machine learning for protein design – ranging from fluorescent proteins to AAV capsids to antibodies. When combined with libraries of millions of designed gene segments from chip-synthesis and rapid testing, each design cycle can take large leaps in sequence space and function space.

4:55 The Case for Intelligent Design in Protein Engineering

Jamie Spangler, PhD, Assistant Professor, Biomedical Engineering and Chemical & Biomolecular Engineering, Johns Hopkins University

Directed evolution is in its prime, and it is deepening our understanding of biological systems and empowering therapeutic design. Recent breakthroughs in structural biology, computational design, and high-dimensional data analytics afford us the unprecedented opportunity to apply molecular, structural, and computational principles to guide protein engineering, employing a so-called “intelligent design” approach. This talk will highlight how my lab harnesses this interfacial approach to overcome the deficiencies of natural proteins.

5:40 Welcome Reception in the Exhibit Hall with Poster Viewing (Co-Sponsorship Opportunity Available)

7:15 End of Day

 

5月5日(二)

8:00 am Registration and Morning Coffee

PROTEIN STRUCTURE FOR ENGINEERING PROTEINS

8:25 Chairperson’s Remarks

Gregory Weiss, PhD, Professor, Chemistry, Molecular Biology & Biochemistry, University of California, Irvine


8:30 Mammalian Display Platform for Facile, FACS-Based Engineering of Antibodies, T Cell Receptors and Other Membrane Proteins of Interest

Jennifer Maynard, PhD, Henry Beckman Professor, McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at Austin

Engineering of antibodies and related receptors is most commonly performed using phage or yeast display, but mammalian cells are used for production. To streamline engineering of these and other membrane-bound proteins, we developed a mammalian screening platform which allows for variant selection in the manufacturing host. We have used this to identify human T cell receptors with low nanomolar affinities, select for chimeric antigen receptors lacking tonic signaling and modulate Fc binding to Fc receptors. Modifications allowing for selection based on protein activity as opposed to simple binding will be reported.

9:00 MicroED: Conception, Practice and Future Opportunities

Tamir Gonen, PhD, Professor, Biological Chemistry and Physiology, David Geffen School of Medicine, University of California, Los Angeles

In 2013, we unveiled the cryoEM method Microcrystal Electron Diffraction (MicroED). The CryoEM is used in diffraction mode for structural using crystals that are a billion times smaller than what is used for X-ray crystallography. In this seminar, I will describe the basics of this method, from concept to data collection, analysis and structure determination, and illustrate how samples that were previously unattainable can now be studied by MicroED.

9:30 Structure-Guided Design of Immunogens Based on Flavivirus Glycoprotein E Domain III (EDIII)

Jonathan Lai, PhD, Professor, Biochemistry, Albert Einstein College of Medicine

Dengue virus is a mosquito-transmitted flavivirus that causes an estimated 390 million human infections each year. There are four serotypes of Dengue (DENV1-4) that can co-circulate in hyperendemic regions. Primary infection by a single serotype results in febrile illness and subsequent durable immunity to that serotype. Secondary infections by heterotypic serotypes can lead to severe shock syndrome and death. Severe Dengue disease is caused in part by cross-reactive antibodies elicited during primary infection that can bind heterologous DENV serotypes but cannot neutralize them. Instead, these non-neutralizing antibodies facilitate entry and infection in Fcg receptor positive cells thus causing "antibody-dependent enhancement" (ADE) of infection. The recent global emergence of Zika virus (ZIKV), a flavivirus that shares structural features with DENV, and the potential for ADE between DENV and ZIKV, raises concerns for vaccine strategies containing most or all epitopes in the E glycoprotein. The flavivirus E glycoprotein domain III (EDIII) is an attractive template for subunit vaccine design because it is relatively small (~100 residues) and is the target of potently neutralizing and protective antibodies for both DENV and ZIKV. However, there are limitations to the use of DENV and ZIKV EDIIIs as vaccines. For DENV EDIII, immunodominant regions lie outside of critical neutralizing epitopes, such as the broadly-neutralizing A/G-strand. Immunization of mice with ZIKV EDIII results in antibody responses to the neutralizing lateral ridge (LR) epitope, but also to the non-neutralizing ABDE sheet and CC'-loop epitopes. We have utilized structure-based protein engineering and phage display to mask unproductive epitopes of flavivirus EDIIIs by mutation while maintaining neutralizing epitopes. We have engineered these “resurfaced” EDIIIs from both DENV and ZIKV. Furthermore, we have developed protein nanoparticles containing EDIIIs from DENV and ZIKV using Spycatcher/Spytag conjugation technology. We will describe these design strategies and their potential for development of novel subunit vaccines.

10:00 Coffee Break in the Exhibit Hall with Poster Viewing

NGS AND MACHINE LEARNING IN ANTIBODY DISCOVERY

10:45 Chairperson’s Remarks

Andrew Bradbury, MB BS, PhD, CSO, Specifica, Inc.

10:50 Combining Machine Learning and Antibody Discovery

Simon Friedensohn, Researcher, Biosystems Science & Engineering, ETH Zurich

Next-generation sequencing of antibody repertoires has become a promising and powerful tool in the drug discovery process. However, its practical applications are often limited since selecting potential leads from sequencing data is challenging. Common approaches focus on screening the most abundant variants in a dataset or closely related variants of already known, functional antibodies. Thus, in many cases only a small fraction of the actual data is utilized. Modern machine learning methods are uniquely suited to unlock the true potential of antibody repertoire sequencing as they can fully utilize these large datasets to discover novel, previously hidden features. Here, we present a deep learning model that can be used to extract antigen-specific sequence patterns, that act as highly accurate, immunological biomarkers. Besides its diagnostic value, we show how this model not only facilitates antibody discovery, but also generates a large amount of rationally designed, novel in silico variants which can be used to identify promising lead candidates at an early stage during drug discovery.

11:20 Machine Learning and Antibody Repertoire Sequencing Harnessed for Antibody Discovery – A Case Study from HCV

Gur Yaari, PhD, Associate Professor, Bioengineering, Faculty of Engineering, Bar Ilan University

Hepatitis C virus is a major public health concern, with over 70 million people infected worldwide, and no vaccine currently available. Here, we present a machine learning approach to accurately predict infection outcome from antibody repertoire sequencing data. We further utilized a combinatorial antibody phage display approach and antibody repertoire analysis to construct two antibodies with high neutralization breadth, which is associated with disease clearance.

11:50 Semi-Supervised Machine Learning in the Identification of Antibody Leads from in vitro Selections

M. Frank Erasmus, PhD, Head, Bioinformatics, Specifica, Inc.

One important goal of therapeutic selection campaigns is to generate diverse antibody panels that comprehensively explore epitope space. While antibodies with very different sequences are expected to bind different epitopes, it is not clear what constitutes a “different antibody”. This seminar will describe a semi-supervised machine learning tool that utilizes low-to-moderate trained screening data coupled to unsupervised learning built around high-throughput next-generation sequence information to improve lead prediction accuracy.

12:20 pm Session Break

Isogenica_NEW

12:25 Luncheon Presentation I to be Announced

 

 

 

12:55 LUNCHEON PRESENTATION II: Self-Labelling Integral Membrane Display (SLIM): A Novel Strategy for Targeting Integral Membrane Proteins

Nathan Robertson, PhD, Group Leader, Antibody Discovery Team, OXGENE

We present a novel method of mammalian display. This involves expressing an antibody library in a population of mammalian cells, which each display the target polypeptide on the outer surface. This technology enables screening of large naive libraries against membrane proteins that display only physiological relevant epitopes.

1:25 Ice Cream Break in the Exhibit Hall with Poster Viewing and Poster Award

PHAGE AND YEAST DISPLAY FOR EMERGING AND CHALLENGING TARGETS

2:00 Chairperson’s Remarks

Jennifer Cochran, PhD, Shriram Chair of Bioengineering; Professor of Bioengineering, and (by courtesy) Chemical Engineering, Stanford University


2:05 KEYNOTE PRESENTATION: Attacking the Cancer Surfaceome with Recombinant Antibodies

James Wells, PhD, Professor, Departments of Pharmaceutical Chemistry and Cellular & Molecular Pharmacology, University of California, San Francisco

The cell surface proteome (surfaceome) is the primary hub for cells to communicate with the outside world. Oncogenes are known to cause huge changes in cells and we hypothesize transformation will lead to changes in the cancer surfaceome. Our lab uses proteomic technologies, both mass spectroscopy-based and a new multiplexed antibody method to systematically understand how cancer cells remodel their membrane proteomes. We then generate recombinant antibodies to detect and then attack these cells by toxifying the antibodies or recruiting immune cells to kill. I will describe our current studies in this area of attacking cancer from the outside.

2:35 Antibody Fragments as Tools to Investigate G Protein-Coupled Receptor Signaling

Andrew Kruse, PhD, Associate Professor, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School

G protein-coupled receptors (GPCRs) are critical regulators of most aspects of human physiology, including control of cardiovascular function and metabolic homeostasis. New methods for synthetic antibody fragment discovery allow targeting of GPCRs, offering new insights into receptor structure, function, and signaling. In particular, GPCR-targeted antibodies now enable structural studies of receptor activation mechanisms, revealing in atomic detail how agonists trigger conformational changes and thereby activate cellular signaling pathways.

3:05 Comparison of in silico and Mammalian Display Technologies for Affinity Screening

Richard BuickRichard Buick, PhD, CTO, Fusion Antibodies plc

We present a case study comparing in silico and mammalian display technologies. A library of variants for Trastuzumab was designed using both methods and the results were compared to achieve lead candidate selection.


3:35 Refreshment Break in the Exhibit Hall with Poster Viewing

4:25 From Nanobodies to Megabodies for Applications in Cryo-EM

Jan Steyaert, PhD, Francqui Research Professor, Vrije Universiteit Brussel (VUB); Director, VIB-VUB Center for Structural Biology, VIB

Nanobodies (Nbs) are highly popular and versatile tools for structural biology. Here we report the development of megabodies, whereby Nbs are rigidly grafted into selected protein scaffolds to increase their molecular weight while retaining the full antigen-binding specificity. The megabody design principles are applicable to other scaffolds without size limitations and expand cryo-EM analysis to proteins that are small and/or display preferential orientation in ice, two major factors that limit the resolution of reconstructed density maps. Such megabodies have been instrumental to solve the first structures of the human heteropentameric GABAA receptor in complex with well-known drugs.

4:55 Leveraging Next-Generation Yeast Display Libraries for Systems Immunology

Aaron Ring, MD, PhD, Assistant Professor, Immunobiology, Yale School of Medicine

Yeast have a remarkable capacity to functionally display a large fraction of the human exoproteome on their surface, including cytokines, growth-factors, and immunoreceptors. Using curated, genetically-barcoded yeast libraries of these proteins, we have developed high-throughput approaches for antibody discovery, detection of protein-protein interactions, and characterization of functional humoral responses in patient samples.

5:25 End of Display of Antibodies

5:30 Registration for Dinner Short Courses


6:00-8:30 pm Recommended Dinner Short Course*

SC11: Developability of Bispecific Antibodies: Assays and Case Studies

*Separate registration required.

* 活动内容有可能不事先告知作更动及调整。

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