The Display of Antibodies track is the cornerstone track of the PEGS Summit and is now in its twentieth year. This 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.

Scientific Advisory Board

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

Jennifer Cochran, PhD, Chair, Bioengineering, Stanford University School of Medicine and School of Engineering; and Chief Scientist, Lagunita Biosciences

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

Final Agenda

Sunday, April 29

Recommended Short Course(s)*

SC4: Selection, Screening and Engineering for Affinity Reagents

SC6: Practical Considerations for Biomarker Bioanalysis

*Separate registration required.

MONDAY, APRIL 30

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

PHAGE AT WORK
Amphitheater

8:30 Chairperson’s Remarks

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

8:40 KEYNOTE PRESENTATION: Phages and the Human Microbiome

Frederic D. Bushman, PhD, Chair and Professor, Microbiology, University of Pennsylvania

Humans harbor enormous communities of viruses that are important in health and disease. Many viral groups, particularly phage, are poorly represented in genome databases, and so difficult to recognize in sequence data. Metagenomic methods, however, allow these viral communities to be reconstructed and genomes tracked, permitting longitudinal quantification, analysis of variation over time, and tracking transfer during transplantation between human individuals. Results from recent studies will be presented.

9:10 Use of Engineered Phage in Cancer Therapy and Tissue Regeneration

Chuanbin Mao, PhD, Professor, Chemistry and Biochemistry, University of Oklahoma

Phages are biological nanostructures that can serve as therapeutics. They can be engineered to display functional peptides. As a result, they can target tumors and inhibit tumor growth when tumor-homing and inhibiting peptides are displayed. They can also instruct the stem cells to differentiate into functional bone forming cells and induce bone tissue formation when differentiation-inducing peptides are displayed.

9:40 A Phage Virus-Like Particle Display Platform for Identifying Vaccines for Chronic and Infectious Disease

Bryce Chackerian, PhD, Professor, Molecular Genetics and Microbiology, University of New Mexico School of Medicine

Display of antigens on virus-like particles (VLPs) is a valuable technique for enhancing the immunogenicity of targets that are poorly immunogenic in their native context. In this talk, I’ll describe how bacteriophage VLPs can be engineered to target molecules that play important roles in two chronic diseases, cardiovascular disease and Alzheimer’s.

10:10 Networking Coffee Break (Harbor & Mezzanine Level)

10:50 Single Domain Antibodies Targeting Membrane-Bound Glypicans in Cancer

Mitchell Ho, PhD, Senior Investigator, National Cancer Institute, NIH

The Ho laboratory studies cancer cell surface proteins, focusing primarily on the role of glypicans including GPC2 and GPC3 as a new family of tumor antigens, and designs ‘single domain antibodies’ that modulate Wnt and other glypican signaling processes responsible for the development of cancer. The talk will also include an update on new phage-displayed shark and camel single domain antibody libraries.

11:20 Deep Sequencing of Phage-Displayed Random Sequence and Genome-Derived Peptide Libraries for Norovirus Detection and Epitope Mapping

Timothy Palzkill, PhD, Professor, Chair, Pharmacology and Chemical Biology, Baylor College of Medicine

Norovirus infections are the leading cause of non-bacterial gastroenteritis, and there is a need for diagnostic tools to detect virus. In this study, a combination of phage display, deep sequencing, and computational analysis was used to identify peptides with specific binding to norovirus. In addition, deep sequencing and computational analysis of phage display libraries derived from norovirus genomic DNA was used to map antibody binding sites on norovirus proteins.

11:50 Identification of High Affinity HER2 Binding Fab Antibodies Using CHO Surface Display

Jennifer Maynard, PhD, Associate Professor, Chemical Engineering, University of Texas at Austin

Discovery of new antibodies is most commonly performed using phage or yeast display, but mammalian cells are used for large-scale production because of the complex antibody structure, including multiple disulfide bonds and a key glycosylation required for function. To circumvent problems associated with changing hosts, we developed a plasmid-based Fab screening platform on CHO cells which allows for antibody selection in the same host used for manufacturing. We further show that this method is generalizable to engineering other cell surface receptors, including T cell receptors and chimeric antigen receptors.

12:20 pm Further Advancement for Human Antibody Discovery

Vera Molkenthin, PhD, Chief Scientist, AbCheck s.r.o.

AbCheck has developed Mass Humanization to generate humanized libraries. This approach utilizes batch cloning of CDR3 immune repertoires from immunized rabbits into selected human frameworks containing specifically diversified CDR1 and CDR2 regions. For selecting high affinity binders from the resulting, highly diverse library, AbCheck routinely applies Phage or Yeast Display under various conditions. In this talk, AbCheck will present new technological developments regarding its human antibody discovery and optimization platform.

12:50 Discovery of Potent, Functional Anti-TIGIT Antagonists from Three Different Phage Display Platforms

Aaron Sato, PhD, CSO, Antibody Center, LakePharma

In a head-to-head study, we compared the performance of a synthetic scFv (Distributed Bio), a naïve Fab (XOMA), and an antigen-specific mouse immune library. Each library was panned against TIGIT (T cell immunoreceptor with Ig and ITIM domains) and screened using our high-throughput HighRes Biosolutions ELISA deck. All IgGs were tested for affinity, competition with TIGIT’s ligands, cell binding, and functional activity. Some commonalities as well as some striking differences amongst the leads were discovered.

1:20 Luncheon Presentation: 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. 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.

1:50 Session Break

2:00 Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification

Jeffrey J. Gray, PhD, Professor, Chemical & Biomolecular Engineering, Johns Hopkins University

Using repertoires of antibody sequences and structures, we re-examine the hypothesis that affinity maturation reduces the conformational flexibility of the antibody’s antigen-binding paratope to minimize entropic losses incurred upon binding. We used rigidity theory to estimate the structural flexibility of the CDR-H3 loop for thousands of recently-determined homology models of the human peripheral blood cell antibody repertoire. We found no clear delineation in the flexibility of naïve and antigen-experienced antibodies. Additional analysis of hundreds of human and mouse antibody structures with B-factors, rigidity theory, and molecular revealed a spectrum of changes in flexibility, suggesting that rigidification may be just one of many biophysical mechanisms for increasing affinity.

2:30 Problem-Solving Breakout Discussions (Commonwealth Hall)

Screening Libraries for Cancer Targeting Ligands

Moderator: Benjamin Umlauf, PhD, Post-Doctoral Fellow, Chemical and Biological Engineering Department, University of Wisconsin

• Targeting Ligand Format
• Cells versus Tissue Targeting
• Combining Selections and Screens
• Pairing Ligands with Therapeutic Strategy

Technologies for Efficient Screening of Binders Against Difficult Targets

Moderator: Balaji M. Rao, PhD, Associate Professor, Chemical and Biomolecular Engineering, North Carolina State University

• Hard to express targets (e.g. membrane proteins)
• Whole cell targets where a protein target is unknown
• Improving efficiency of the pipeline from combinatorial discovery to biophysical characterization

Single Domain Antibodies

Moderator: Mitchell Ho, PhD, Senior Investigator, National Cancer Institute, NIH

• Properties of single domain antibodies: camel, shark, human, or artificial
• How to engineer a better single domain antibody? Tissue (tumor, BBB) penetration, pharmacokinetics, or stability
• Clinical application of single domain antibodies: bispecific, ADC/immunotoxin, or CAR

Phage-Based Cancer Therapy:

Moderator: Chuanbin Mao, PhD, Professor, Chemistry and Biochemistry, University of Oklahoma

• Phage display
• Targeted Cancer therapy
• Immunotherapy

3:20 Networking Refreshment Break  (Harbor & Mezzanine Level)

PLENARY KEYNOTE SESSION        Amphitheater and Harborview Ballroom

 4:00 Chairperson’s Remarks

Peter Fung, PhD, Senior Manager Product Marketing, NanoTemper Technologies

4:10 Challenges and Opportunities in Engineering Protein Biopharmaceuticals

K. Dane Wittrup, PhD, C.P. Dubbs Professor, Chemical Engineering and Biological Engineering; Associate Director, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT)

Arthur C. Clarke’s First Law posits that “When a distinguished but elderly scientist states that something is possible, he is almost certainly right. When he states that something is impossible, he is very probably wrong.” Bearing this in mind, in this talk, I will highlight areas of protein drug development that appear poised for breakthroughs in the coming decade or so.

4:55 The Next Generation of Cancer Immunotherapy: Targeting Myeloid Immune Checkpoints

Kipp Weiskopf, MD, PhD, Resident Physician, Internal Medicine, Brigham and Women’s Hospital

Immune cells of the myeloid lineage hold tremendous potential as effectors of cancer immunotherapy. The CD47/SIRPα axis is a key molecular pathway that governs the interaction between myeloid cells and tumors. Therapies that target the interaction are effective across multiple preclinical models of cancer and are now under investigation in clinical trials. Further studies have revealed additional regulators of myeloid cell activation that can be exploited as myeloid immune checkpoints.

5:40 Welcome Reception in the Exhibit Hall with Poster Viewing (Commonwealth Hall)

7:15 End of Day

TUESDAY, MAY 1

8:00 am Registration (Commonwealth Hall) and Morning Coffee (Harbor Level)

Novel Technologies
Amphitheater

8:25 Chairperson’s Remarks

Jennifer Cochran, PhD, Chair, Bioengineering, Stanford University School of Medicine and School of Engineering; Chief Scientist, Lagunita Biosciences

8:30 Inefficient Ribosomal Skipping for Simultaneous Cell Surface Display and Soluble Secretion of Proteins in Yeast

Balaji M. Rao, PhD, Associate Professor, Chemical and Biomolecular Engineering, North Carolina State University

We have developed a system for simultaneous cell surface display and soluble secretion of proteins in yeast Saccharomyces cerevisiae, based on inefficient ribosomal skipping. Application of this system to efficiently isolate and characterize binding proteins isolated from combinatorial protein libraries will be discussed.

9:00 Engineering Peptides and Peptidomimetics for Non-Invasive Disease Screening and Treatment Monitoring

Greg M. Thurber, PhD, Assistant Professor, Chemical Engineering and Biomedical Engineering, University of Michigan

Peptides hold a unique position between small molecule agents (less than 500 Da) and proteins (larger than ~5 kDa), endowing them with optimal properties for imaging agent development. However, their lack of structure and poor stability often result in low affinity and rapid clearance. Using bio-orthogonal chemistry and physicochemical property manipulation, we demonstrate how novel structures can be identified for non-invasive screening and disease monitoring.

9:30 Mammalian Display Platform Yields Cysteine-Dense Peptide that Blocks the Oncogenic YAP:TEAD Interaction with High Affinity

James M. Olson, MD, PhD, Sarah Hughes Chair for Pediatric Oncology; Member, Fred Hutchinson Cancer Research Center; Attending Physician, Seattle Children’s Hospital; Professor of Pediatrics, University of Washington

The hippo pathway drives proliferation during embryogenesis and, aberrantly, in some cancers. The hippo pathway’s YAP:TEAD interaction has eluded drug discovery efforts. Noting that some cysteine dense peptides (CDPs) act intracellularly despite the reducing environment and that CDPs naturally have other ideal properties for mid-sized medicines, we created and used a mammalian display platform which we used to select and evolve candidate therapeutics, ultimately yielding a 300 pM KD antagonist.

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

Improving Selection with NGS
Amphitheater

10:45 Chairperson’s Remarks

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

10:50 KEYNOTE PRESENTATION: Protein Engineering and Evolution to Create Base Editors for Precision Genome Editing without Double-Stranded DNA Breaks

David R. Liu, PhD, Richard Merkin Professor, Director, Merkin Institute of Transformative Technologies in Healthcare, Broad Institute Core Institute Member, Vice-Chair, Faculty, Director of the Chemical Biology and Therapeutic Sciences Program, Howard Hughes Medical Institute Investigator, Professor, Chemistry and Chemical Biology, Harvard University

In this lecture, I will describe the use of protein engineering and protein evolution to create base editing, a new approach to genome editing that enables programmable correction of point mutations efficiently without requiring DNA backbone cleavage or donor DNA templates. Base editing has the potential to advance the scope and effectiveness of genome editing of point mutations, which represent the substantial majority of known human genetic variants associated with disease but are difficult to correct cleanly and efficiently using standard genome editing methods.

11:20 Building a Single Donor Phage Antibody Library with NGS Validation

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

The traditional approach to generating natural phage antibody libraries has been to use as many donors as possible. However, given that naive B cells each have unique antibodies, it may be more important to use as many lymphocytes as possible, even if derived from a single donor. This talk will describe the creation of a highly functional antibody library from a single donor, in which all steps were quality controlled by next generation sequencing.

11:50 Deep Sequencing Analysis of Phage Selection Outputs: Leaving Conventional Screening Behind

Stefan Ewert, PhD, Senior Investigator, NIBR Biologics Center, Novartis Pharma AG 

We will show adaptations to library design and planning strategies exploiting the full potential of deep sequencing analysis of phage selection output pools to identify high affine antibodies without conventional screening.

12:20 pm Luncheon Presentation I
Discovery of Antagonist mAbs against the GPCR CB1 for Treating NASH

Ross Chambers, PhD, Vice President, Antibody Discovery, Integral Molecular

CB1 is a therapeutic target for non-alcoholic steatohepatitis (NASH), a metabolic disease with no approved treatment. Integral Molecular has discovered potent antagonist antibodies against this challenging GPCR using its MPS Antibody Discovery Engine. This approach yielded a large panel of CB1-reactive antibodies with diverse epitopes, increasing the likelihood of discovering rare antagonist antibodies. Lead candidates were affinity matured, resulting in high affinity, exquisite specificity, and potent inhibition of CB1 signaling.
High-Resolution Epitope Mapping and Specificity Profiling of MAbs Targeting Complex Proteins
Duncan Huston-Paterson, DPhil, Project Leader, Integral Molecular
Integral Molecular specializes in characterizing antibodies against structurally-complex targets, including GPCRs, ion channels, and immuno-oncology targets. Our Shotgun Mutagenesis technology maps conformational antibody epitopes at single-amino acid resolution with >95% success, generating critical intellectual property and detailed mechanistic insights. Our Membrane Proteome Array enables safety analysis of antibodies by testing each antibody against an expression array of 5,300 structurally-intact membrane proteins, providing a comprehensive assessment of off-target antibody interactions.

12:50 Luncheon Presentation II: Design and Validation of Alexandria™, a Fully Synthetic Human Fab Library

Guy Hermans, PhD, CSO, Isogenica Ltd.

We will present validation data on Alexandra™, our recently developed fully synthetic human Fab library. The diverse set of heavy and light chain germlines, combined with the fully synthetic nature of the randomized CDR1, -2 and -3 regions ensures many issues with immune and naïve libraries can be overcome. Use of Colibra™ DNA library build technology allowed for the removal of CMC liability motifs from both the framework as well as CDR regions.

1:20 Ice Cream Break in the Exhibit Hall with Poster Viewing (Commonwealth Hall)

Display as a Tool for Discovery
Amphitheater

2:00 Chairperson’s Remarks

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

2:05 High-Throughput Synthetic Antibody Discovery at the Institute for Protein Innovation (IPI)

Joseph Jardine, PhD, Head, Antibody Discovery, Institute for Protein Innovation

The mission statement for the Institute for Protein Innovation is to produce high quality, highly validated open source antibodies against human cell surface proteins. We are building high-throughput pipelines for mammalian protein production, yeast Fab display for antibody selection and receptor-ligand deorphaning for novel target identification, details of which will be presented in this talk.

2:35 Multi-Tasking for Multi-Specific Targets at Sanofi

Leila Sevigny, PhD, Senior Scientist, Sanofi Genzyme

In the present case study, we show how Sanofi increased the efficiency of bi- and multi-specific screening, antigen creation and engineering. We show how we have benefited from the use of the fully integrated workflow platform, Genedata Biologics, which enables molecule, sample and assay data tracking from generation to final candidates. Not only does the underlying database system provide a shared repository to track all the pertinent data associated with the project from start to finish, but it also allows us to draw conclusions from the cross-project data mining and learn from our experience for future multi-specific antibody discovery and optimization campaigns.

3:05 Screening Smarter to Derive Data Driven Decisions Faster

Ben Schenker, Director, TTP Labtech

There’s a smart way to increase the pace of therapeutic antibody and vaccine discovery. Derive data driven decisions faster with no-wash, cell, or bead-based immunoassay screening workflows that can be multiplexed to combine hit identification with selectivity, species cross-reactivity, viability, infectivity, or titer for accelerated decision making.

3:20 Accurate Low-Volume Liquid Handling for Cost-Effective NGS Library Preparation and Single Cell Genomics

Ben Schenker, Director, TTP Labtech Inc.

Deliver more data by removing sample preparation bottlenecks. Alleviate 90% of your costs per sample & improve your throughput through automation. Our liquid handling solutions are designed for discovery: accurate & precise at low volumes, compatible with 384-well microplates and zero potential for cross-contamination! Join us to learn more.

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

4:25 Engineering Alternative Scaffolds via Yeast Display

Benjamin Hackel, PhD, Associate Professor, Chemical Engineering and Materials Science, University of Minnesota

Small protein scaffolds provide an efficient basis for ligand discovery with potential advantages in molecular imaging, ex vivo diagnostics, and multi-functional protein fusions. We have merged computational analysis of scaffold biophysical properties, yeast display sorting of scaffold libraries, and deep sequencing of phenotypic populations to discover novel scaffolds and elucidate the characteristics that dictate evolvability. The discovery platform and case studies will be presented.

4:55 Identification and Development of Variable Lymphocyte Targeting Ligands for Glioblastoma

Benjamin Umlauf, PhD, Post-Doctoral Fellow, Chemical and Biological Engineering Department, University of Wisconsin

The median survival for patients presenting with the brain tumor Glioblastoma Multiforme (GBM) remains less than two years despite clinical intervention. Here we present a screening paradigm, identification of lead candidates, and a functional application for identifying Variable Lymphocyte Receptors that serve as targeting ligands for GBM therapies by binding to pathologically exposed brain extracellular matrix.

5:25 End of Display of Antibodies

5:30 Registration for Dinner Short Courses* (Commonwealth Hall) 

*Separate registration required.