The 21st Annual Display of Antibodies is the cornerstone conference of the PEGS Summit and convenes leaders in the field year after year. This year’s meeting showcases innovation in discovery, design and engineering of biologics
through molecular evolution using phage, yeast and other display methodologies. The proliferation of novel constructs is possible through methods to improve library design, pharmacological and biophysical properties to create drug molecules with greater
potency, modes of action, target specificity and activity than previously achievable.
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
MONDAY, APRIL 8
7:00 am Registration (Commonwealth Hall) and Morning Coffee (Harbor level)
8:30 Chairperson’s Opening Remarks
Gregory A. Weiss, PhD, Professor, Chemistry, Molecular Biology & Biochemistry, University of California, Irvine
8:40 Protein-Directed Evolution in Genomic Contexts Using Mutagenesis and CRISPR/Cas9
Michael Krogh Jensen, PhD, Senior Researcher & Co-Principal Investigator, Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability
Here we describe a method for robust directed evolution using mutagenesis in genomic contexts. The method employs error-prone PCR and Cas9-mediated genome integration of mutant libraries of 300-600 bp-sized donor variants into genomic sites with efficiencies
reaching 98-99% and >100K variants from a single transformation. To validate the method for directed evolution, we engineered two essential enzymes in the mevalonate pathway of Saccharomyces cerevisiae. Taken together, our method extends on existing
CRISPR technologies by facilitating efficient mutagenesis of hundreds of nucleotides in cognate genomic contexts.
9:10 Constructing a Synthetic Biology Toolbox Using Phage Display Parts
C. Ronald Geyer, PhD, Professor, Pathology and Lab Medicine, University of Saskatchewan
Antibody phage display is a powerful strategy for producing antibody fragments that can be used as parts for constructing synthetic antibody-like devices. Here we describe the construction and selection of antibody fragment libraries and the assembly
of selected antibody parts into devices useful for antibody therapy, imaging, and diagnostics.
9:40 Development of a Complex T7 Phage Display Library for Discovery of Biomarkers of Lung Diseases
Lobelia Samavati, MD, Associate Professor of Medicine, Department of Medicine, Center for Molecular Medicine and Genetics, Wayne State University School of Medicine
Chronic respiratory diseases of unknown etiology share similarities with various inflammatory and infectious diseases including tuberculosis. Currently, there is no test available to discriminate between active TB and sarcoidosis or between active, latent
TB and other respiratory diseases. Using a high throughput method, we developed two T7 phage display cDNA libraries derived from mRNA isolated from bronchoalveolar lavage (BAL) cells and leukocytes of sarcoidosis patients. We combined these two libraries
with two other libraries derived from embryonic lung fibroblasts and human monocytes, to build a complex library. Our studies indicate that our complex library contains diverse clones that can distinguish sera from healthy controls, sarcoidosis, cystic
fibrosis and tuberculosis.
10:10 Networking Coffee Break (Harbor & Mezzanine Level)
10:50 KEYNOTE PRESENTATION: Engineering Membrane Proteins with Phage Display
Gregory A. Weiss, PhD, Professor,
Chemistry, Molecular Biology & Biochemistry, University of California, Irvine
Phage display offers a power tool for remodeling proteins – their binding, catalysis, solubility and other properties. However, the technique has largely been confined to soluble proteins. My laboratory has demonstrated that membrane proteins can
also be displayed on the phage surface. In this talk, I’ll describe the limitations of membrane protein phage display and applying the approach to solubilize and engineer membrane proteins with powerful new functions.
11:20 Cytosolic Delivery of Proteins by Bioreversible Esterification
Ronald T. Raines, PhD, Firmenich
Professor of Chemistry, Department of Chemistry, Massachusetts Institute of Technology
The surface of mammalian cells is highly anionic. Accordingly, Coulombic repulsion prevents anionic molecules from entering cells. We have tuned the reactivity of a diazo compound to elicit the efficient O-alkylation of carboxylic acids in water. Such
esterification enables proteins (including a Fab fragment) to traverse the plasma membrane directly, like a small-molecule prodrug. As with prodrugs, the nascent esters are substrates for endogenous esterases that regenerate native proteins.
11:50 Generating Pairs of Affinity Reagents for Sandwich Assays through MegaSTAR
Brian K.
Kay, PhD, Professor & Head, Biological Sciences, University of Illinois, Chicago
The ‘sandwich’ assay is a robust, flexible and sensitive test that is widely employed in clinical diagnostics for monitoring human health and disease. Unfortunately, identifying pairs of antibodies takes time and luck. We have recently
developed a method to discover pairs of recombinant affinity reagents part of the phage-display process. We will present results of applying MegaSTAR to cell signaling proteins and biomarkers of heart disease.
12:20 pm High Quality Antibodies for Therapeutic Applications
Vera Molkenthin, PhD, Chief Scientist, AbCheck
AbCheck discovers and optimizes human antibodies for therapeutic applications leveraging several proprietary platforms including in vitro and in vivo technologies. AbCheck will present new technological developments regarding its versatile human antibody discovery and optimization platform with a focus on Rabbit Mass Humanization and AbAccelTM.. Both technologies can be combined with AbCheck’s yeast display platform AbSieveTM and deliver high quality leads with subnanomolar affinities and good stabilities which are compatible with different antibody designs including bispecifics.
12:50 Luncheon Presentation I: Integrated Solutions for Antibody Discovery and Beyond
Hua Tu, PhD, CEO and Founder, LakePharma
LakePharma focuses on providing complete solutions from antibody discovery to GMP manufacturing. In this talk, the biotech company will share its experience and case studies in antibody discovery and engineering using display technology. The presentation
provides solutions for the common problems encountered by display technology as well as rapid development to clinical manufacturing.
1:20 Luncheon Presentation II: Bruteforcing Hard Targets with Computationally Immuno-Engineered SuperHuman 2.0
Jacob G. Glanville, PhD, Co-Founder & CSO, Distributed Bio Inc.
Over the last decade, the iterative analysis and computational optimization of antibody repertoires has resulted in a 1000x improvement in antibody library functional sequence diversity. Here, we present a series of case studies against traditionally
hard targets that demonstrate the practical consequences of optimized library diversity. In GPCRs, we show a combination of a large library and high-throughput sequencing enables routine recovery of antibodies, including functionally active
antibodies, against GPCRs like CXCR5.
1:50 Synthetic DNA Technologies Enable Antibody Discovery and Optimization
Aaron Sato, PhD, CSO, Twist Bioscience
Utilizing its proprietary DNA writing technology to create oligo pools, genes, and synthetic libraries, Twist Pharma, a division of Twist Bioscience, provides the biotechnology industry with an end-to-end antibody discovery solution. This solution
includes (1) a panel of high diversity synthetic antibody libraries, (2) a proprietary human anti-GPCR antibody phage display library focused on this validated target class, and (3) a Twist Antibody Optimization (TAO) platform for antibody
affinity and developability optimization.
2:20 Problem-Solving Breakout Discussions - Click here for details(Commonwealth Hall)
3:20 Networking Refreshment Break (Harbor & Mezzanine Level)
4:00 Chairperson’s Remarks
Rakesh Dixit, PhD, DABT, Vice President, R&D, Global Head, Biologics Safety Assessment, Translational Sciences, AstraZeneca
PLENARY KEYNOTE SPEAKER
4:10 Vision for How Immunotherapy Will Shape Future of Cancer Care
Leena Gandhi, MD, PhD, Vice President, Immuno-Oncology Medical Development, Lilly Oncology
Immunotherapy is considered by many as a pillar of cancer care today, but in many ways we have only scratched the surface. Our knowledge and understanding of the complexities of immunotherapy and its mechanisms continue to evolve. The future of
cancer care will be defined by our ability to systematically identify and implement opportunities for combination therapy to improve and standardize patient response.
YOUNG SCIENTIST KEYNOTE
4:55 The Lassa Virus Glycoprotein: Stopping a Moving Target
Kathryn Hastie, PhD, Staff Scientist, Immunology and Microbiology, The Scripps Research Institute
Lassa virus causes ~5000 deaths from viral hemorrhagic fever every year in West Africa. The trimeric surface glycoprotein, termed GPC, is critical for infection, is the target for neutralizing antibodies, and a major component of vaccines. Structural
analysis of Lassa GPC bound to antibodies from human survivors reveals a major Achilles heel for the virus and provides the needed template for development of immunotherapeutics and improved vaccines.
5:40 Welcome Reception in the Exhibit Hall with Poster Viewing (Commonwealth Hall)
7:15 End of Day
TUESDAY, APRIL 9
8:00 am Registration (Commonwealth Hall) and Morning Coffee (Harbor Level)
8:25 Chairperson’s Remarks
K. Dane Wittrup, PhD, J.R. Mares Professor, Chemical Engineering & Bioengineering, Massachusetts Institute of Technology
8:30 Yeast Display of Post-Translationally Modified Polycyclic Peptides
Wilfred A. van der Donk, PhD, Richard E. Heckert Endowed Chair in Chemistry, Director of Graduate Studies, Howard Hughes Medical Institute Investigator, Department of Chemistry, University of Illinois
Ribosomally synthesized and post-translationally modified peptides (RiPPs) constitute a large class of natural products with vast structural diversity. Lanthionine-containing peptides (lanthipeptides) are examples of this growing class. They
contain multiple thioether crosslinks installed post-translationally by a single enzyme that typically forms 2-5 rings with high control over regio- and chemoselectivity. This presentation will discuss use of the biosynthetic machinery
to display libraries of such polycyclic peptides.
9:00 Integrating Computational Design with Screening in Mammalian Cells for Novel Peptide Therapeutics
Philip M. Kim, PhD, Associate
Professor, The Donnelly Centre for Cellular and Biomolecular Research, Departments of Molecular Genetics and Computer Science, University of Toronto
I will present our technology platform that integrates computational library design with modern in-cell selection strategies to uncover novel peptide therapeutics. I will cover a number of different library designs and selection methodologies,
including selections for phenotype or using genetic reporter systems and cell sorting, as well as methods to obtain highly stable mirror image peptides.
9:30 Platforms for the Generation and Screening of Cyclic Peptide Libraries
Ali Tavassoli, PhD, Professor, Chemical Biology, University of Southampton
Cyclic peptide libraries have demonstrated significant potential when employed against challenging targets such as protein-protein interactions. SICLOPPS is a genetically encoded method for the intracellular generation of cyclic peptide libraries
of over a hundred million members. SICLOPPS libraries can be interfaced with a variety of cell-based assays. Here, we will report the use of this approach for the identification of inhibitors of a variety of challenging targets.
10:00 Coffee Break in the Exhibit Hall with Poster Viewing (Commonwealth Hall)
10:45 Chairperson’s Remarks
Jennifer R. Cochran, PhD, Shriram Chair of Bioengineering; Professor of Bioengineering, and (by courtesy) Chemical Engineering, Stanford University
10:50 Specificity and Polyreactivity: Designing Antibodies Against Receptor Families for Desired Reactivity
Christilyn Graff, PhD, Director, Antibody Discovery and Engineering, Biogen
Targeting receptor families can present a challenge depending on the level of sequence and structural homology. From highly conserved to more divergent families, in vitro display libraries can be used
to focus the antibody response to the desired specificity. Antigen optimization, in concert with knowledge of ligand/receptor interactions across the family, can also be used to direct the response. This talk will highlight our efforts
to isolate antibodies that are either highly specific or polyreactive, in order to better understand the implication of targeting one or more members of the receptor family.
11:20 A Platform Enabling High-Throughput Functional Screening of Antibody Libraries
Ryan Kelly, PhD, Research
Scientist, xCella Biosciences
We present a novel platform for rapid antibody discovery based on cell binding and functional activity readouts. Our microcapillary array technology allows us to screen antibody libraries, displayed on or secreted by yeast and mammalian
cells, using a wide variety of assay formats. This proprietary hardware and software platform combined with xEmplar™, our human-inspired synthetic antibody library, have enabled the isolation of antibodies against multiple clinically
relevant targets.
11:50 A Novel Strategy for the Generation of Yeast Surface Display Antibody Fab Libraries
Stefan Zielonka, PhD, Group Leader & Principal Scientist, Protein Engineering & Antibody Technologies, Discovery Technologies, Global Research and Development, Merck KGaA
Yeast surface display emerged as a promising platform technology for antibody engineering. Still, generation of libraries comprising heavy chain as well as light chain diversities is a cumbersome process involving multiple steps. We recently
implemented a focused approach for the construction of Fab antibody libraries using type IIs restriction enzymes. This method seems to be valid for the generation of YSD diversities with adequate qualities.
12:20 pm Luncheon Presentation I: Highly Specific Claudin6 Antibodies for Targeting Solid Tumors
Benjamin Doranz, PhD, MBA, President and CEO, Integral Molecular
Claudin6 is upregulated in tumors, but unlike other claudins, is not expressed in normal tissue. Using our MPS Antibody Discovery platform, we have discovered lead candidate antibodies that bind unique residues on Claudin6 (creating novel
IP) and do not bind any other membrane protein in the human proteome.
Specificity Profiling and High-Resolution Epitope Mapping of mAbs Targeting Membrane Proteins
Duncan Huston-Paterson, DPhil, Product Manager, Integral Molecular
Specificity testing across the proteome de-risks lead selection and has been applied to hundreds of mAbs using our Membrane Proteome Array of 5,300 membrane proteins. Conformational epitopes generate novel IP and mechanistic insights,
and we have mapped >1,000 such epitopes with >95% success rate using our Shotgun Mutagenesis platform.
12:50 Luncheon Presentation II: Efficient Membrane Protein Targeting Antibodies Discovery Using Synthetic Antibody Libraries and CIS Display
Guy Hermans, PhD, CSO, Isogenica Ltd.
Isogenica’s llamdA™ library is a highly diverse, fully synthetic VHH library. It can be used to discover VHHs in phage display format, as well as through our proprietary CIS display selection process. In this talk, we will
briefly discuss the benefits this library design brings and illustrate some of the unique benefits of VHH technology over conventional antibodies. Also, we will share recent data demonstrating isolation of VHHs to membrane proteins.
1:20 Ice Cream Break in the Exhibit Hall with Poster Viewing (Commonwealth Hall)
2:00 Chairperson’s Remarks
Andrew R.M. Bradbury, MB BS, PhD, CSO, Specifica, Inc.
2:05 Using Structural Information to Aid in silico Therapeutic Design from Next-Generation Sequencing Repertoires of Antibodies
Charlotte
Deane, PhD, Professor of Structural Bioinformatics & Head of Department, Department of Statistics University of Oxford; Head of the Oxford Protein Informatics Group, University of Oxford
We have built the freely available Observed Antibody Space database of over half-a-billion antibody sequences. Using this data, I will show how predicted structural information can enrich data from next-generation sequencing experiments.
In particular, ABOSS, our novel method for filtering Ig-seq data, which considers the structural viability of each sequence and TAP, our novel therapeutic antibody profiler that provides five computational developability guidelines.
2:35 Analysis of Human Antibody Repertoires
Eline T. Luning Prak, MD, PhD, Associate Professor, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania
This talk will focus on different methods for the analysis of antibody repertoires including RNA- and DNA-based methods in bulk populations as well as single cell analysis. I will describe the strengths and limitations of each
method and which methods are most useful for different types of research questions.
3:05 Rational Library Design for the Affinity Maturation of Antibodies
Richard Buick, PhD, CTO, Fusion Antibodies plc
A case study will be shown for the affinity maturation of an anti-Cathepsin S antibody by rational library design followed by molecular docking of variants in a step-wise combinatorial fashion.
3:20 Use of Mammalian Virus Display to Select Antibodies Specific for Complex Membrane Antigens
Ernest Smith, CSO, Senior Vice President, Research, Vaccinex, Inc.
We have developed a technology to enable direct incorporation of multipass membrane proteins such as GPCRs and ion channels into the membrane of a mammalian virus. Antigen expressing virus can be readily purified and used for antibody
selection using either vaccinia, phage or yeast display methods. This method is rapid, does not require any detergents or refolding, and can be applied to multiple cell types in order to maximize protein expression and to provide
properly folded protein that is necessary for antibody selection.
3:35 Refreshment Break in the Exhibit Hall with Poster Viewing (Commonwealth Hall)
4:25 Shaping of Primary Ig Repertoires
Duane
R. Wesemann, MD, PhD, Principal Investigator, Assistant Professor of Medicine, Harvard Medical School; Associate Physician, Brigham and Women’s Hospital
B cell immunoglobulin (Ig) repertoire composition shapes immune responses. The generation of Ig diversity begins with Ig variable region exon assembly from gene segments, random inter-segment junction sequence diversity, and combinations
of Ig heavy and light chain. This generates vast preemptive sequence freedom in early developing B lineage cell Ig genes that can anticipate a great diversity of threats. This freedom is met with large restrictions that ultimately
define the naïve (i.e. preimmune) Ig repertoire. Activation-induced somatic hypermutation (SHM), which further diversifies Ig V regions, is also met with strong selection that shapes Ig affinity maturation. While individual
repertoire features, such as affinity for self and competition for foreign antigen, are known to drive selection, the selection filters themselves may be regulatable. Large sequence freedom coupled with strong selection for
each diversification process provides flexibility for demand-driven regulation to dynamically balance antigen recognition capacities and associated autoimmune risks according to host needs. We use single B cell culture, antibody
specificity testing, and deep Ig sequencing analysis to investigate Ig tolerance filter porosity.
4:55 Going Directly from Sequence to Clone: Isolation of Antibodies after Identifying Them by NGS
Fortunato Ferrara, PhD, Vice President, Specifica, Inc.
Going easily from sequence to clones presently represents the primary bottleneck in the full exploitation of next-generation sequencing (NGS) applied to in vitro antibody selection. We have devised
and tested a number of different methods to generate antibody clones identified by NGS. This talk will describe the success we obtained with the different methods, how effective they were to reach into the abundance rank, and
the affinities and binding properties of antibodies derived at different abundance depths.
5:25 End of Display of Antibodies
5:30 Registration for Dinner Short Courses (Commonwealth Hall)