Display of Antibodies

 

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

SUNDAY, APRIL 7

Recommended Short Course*

SC3: Selection, Screening and Engineering for Affinity Reagents

Jonas V. Schaefer, PhD, Lab Head/Investigator II, Novartis Institutes for BioMedical Research (NIBR)

Christian Kunz, PhD, Director, MorphoSys AG

 

*Separate registration required.

MONDAY, APRIL 8

7:00 am Registration (Commonwealth Hall) and Morning Coffee (Harbor level)

NEW APPLICATIONS FOR PHAGE DISPLAY
Amphitheater

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

KroghJensen_MichaelMichael 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

Geyer_C_RonaldC. 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

Samavati_LobeliaLobelia 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

Weiss_GregoryGregory 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

Raines_RonaldRonald 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

Kay_BrianBrian 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

Molkenthin_VeraVera 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.

TWIST-Bioscience 1:50 Synthetic DNA Technologies Enable Antibody Discovery and Optimization

Sato_AaronAaron 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)

PLENARY KEYNOTE SESSION
Amphitheater & Harborview Ballroom

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

keynote-headshot-hastie-400x400Kathryn 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)

ENGINEERING SMALL PROTEINS AND CONSTRAINED PEPTIDES

Amphitheater

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

vanderDonk_WilfredWilfred 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

Kim_PhilipPhilip 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

Tavassoli_AliAli 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)

NOVEL TECHNOLOGIES
amphitheater

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

Kelly_RyanRyan 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

Zielonka_StefanStefan 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

Doranz_BenjaminBenjamin 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

Huston-Patterson_DuncanDuncan 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)

NGS IN NATURAL AND ARTIFICIAL ANTIBODY REPERTOIRES
amphitheater

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

Deane_CharlotteCharlotte 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

LuningPrak_ElineEline 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

Buick_RichardRichard 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

Wesemann_DuaneDuane 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

Ferrara_FortunatoFortunato 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)


Recommended Dinner Short Course*

SC11: Developability of Bispecific Antibodies: Formats and Applications

Nimish Gera, PhD, Director, Research and Development, Mythic Therapeutics

 

*Separate registration required.

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