2014 Archived Content

Phage and Yeast Display of Antibodies and Recombinant Proteins

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Scientific Advisory Board
Andrew M. Bradbury, M.D., Ph.D., Staff Scientist, Biosciences, Los Alamos National Laboratory
Jennifer Cochran, Ph.D., Hitachi America Associate Professor, Bioengineering and Chemical Engineering, Stanford University
David C. Lowe, Ph.D., Fellow, R&D, MedImmune Ltd
Aaron K. Sato, Ph.D., Vice President of Research, Sutro Biopharma
Gregory A. Weiss, Ph.D., Professor, Departments of Chemistry, Molecular Biology & Biochemistry, University of California, Irvine
K. Dane Wittrup, Ph.D., J.R. Mares Professor, Chemical Engineering & Bioengineering, Massachusetts Institute of Technology




Phage and Yeast Display Libraries Alternate Display Technologies - Detailed Agenda 

*Separate registration required

7:00 am Registration and Morning Coffee

Plenary Keynote Session

8:30 Chairperson’s Opening Plenary Remarks

Kristi Sarno, Chair, Greater Boston Chapter, Women in Bio; Director, Business Development, Pfenex, Inc.

8:40 Harnessing the Patient’s Immune System to Combat Cancer

Peter CR Emtage, Ph.D., Vice President, Immune Mediated Therapies, MedImmune

With recent FDA approvals, modulation of the immune system is now a clinically validated approach in the treatment of some cancers. At MedImmune, the Oncology Department is developing assets and expertise in Immune Mediated Therapy of Cancer (IMT-C). The challenges from a drug development perspective are multi-fold. The talk will focus on the relevance of preclinical models and translational science to address key issues, including dose selection and rationale combinations.

9:25 Building Regeneron’s Pipeline: From Trap Technology to the VelocImmune Platform to Veloci-Next

George D. Yancopoulos, M.D., Ph.D., President, Regeneron Laboratories; CSO, Regeneron Pharmaceuticals, Inc.

George D. Yancopoulos will discuss how he and his colleagues exploited a commitment to science and technology to start the company, withstand years of challenges and failures, and emerge with a pipeline of promising technologies and novel/biologics that are beginning to bring hope to countless patients and their families.

10:10 Grand Opening Coffee Break in the Exhibit Hall with Poster Viewing


opening session 

11:05 Chairperson’s Remarks

Aaron K. Sato, Ph.D., Vice President of Research, Sutro Biopharma


Generating High-Quality Affinity Reagents through Phage Display

Brian KayBrian K. Kay, Ph.D., Professor and Head, Biological Sciences; LAS Distinguished Professor, University of Illinois, Chicago

Protein scaffolds are an attractive alternative to monoclonal and polyclonal antibodies as a source of high affinity and specific affinity reagents. I describe a method for incorporating mutagenesis into the phage-display pipeline and demonstrating that the resulting affinity reagents can be used for pull-down experiments.

11:40 Next-Generation Sequencing and Ultimate-Generation Peptide Phage Display

MichaelSzardeningsMichael Szardenings, Ph.D., Head, Ligand Development Unit, Fraunhofer Institute for Cell Therapy and Immunology; Coordinator JLCI, CNUHH, Hwasun, Korea

An innovative, highly diverse (>109) peptide phage library has been generated with a novel tri-nucleotide synthesis approach, with less than 20 codons per position, perfectly statistically distributed and a peptide diversity outnumbering most libraries. This diversity, in combination with next generation sequencing and novel software for in silico allows to determine epitopes after single round panning directly on complete sera from allergy patients or on polyclonal antibodies   

Avacta logo12:10 pm Biological Recognition Beyond the Antibody

Ko_Ferrigno_PaulPaul Ko Ferrigno, Ph.D., CSO, Avacta Life Sciences

Antibodies are ubiquitous in life science research; their high affinity and specificity have enabled biological detection in a range of settings, from basic research to clinical diagnostics. Antibodies, however, are not suitable for all applications, and have limitations around targets and applications. Engineered non-antibody protein binders, largely focused on therapeutics, have been developed more recently. Here, I will review existing alternatives to antibodies and present Affimers as next generation reagents for biological recognition.

12:40 Luncheon Presentation I: Antibody Library Display on a Mammalian Virus: Combining the Advantages of Panning and Cell Sorting in One Technology 

Smith_ErnestErnest S. Smith, Ph.D., CSO & Senior Vice President, Research, Vaccinex, Inc.

We have developed an antibody discovery platform that enables efficient mammalian cell based expression of a library of human antibodies in full length IgG format on the surface of vaccinia virus. Upon infection of mammalian cells the antibody is not only incorporated into newly produced virus, it is also displayed on the surface of the host cell. This technology allows us to combine the advantages of virus panning and cell sorting into one technology.

1:10 Luncheon Presentation II: Next-Generation Analysis of Deep Sequencing Data: Bringing Light into the Black Box of Phage Display Experiments

Michael Blank, Ph.D., CSO, AptaIT GmbH

We developed an innovative bioinformatic approach that allows to exploit NGS data with an unprecedented depth to improve the identification of phage display ligands. Besides quality control and optimization of libraries, early identification of rare but high quality ligands otherwise lost in the screening experiment or advanced screening strategies for difficult targets become possible. The wealth of comparative sequence data already obtained from the screening experiment is furthermore useful for subsequent lead optimization.

1:40 Session Break

Rational Design 

2:00 Chairperson's Remarks

David C. Lowe, Ph.D., Fellow, R&D, MedImmune, Ltd.

2:05 Enhanced Identification of Antibodies Targeting Specific Structures

Dimiter DimitrovDimiter S. Dimitrov, Ph.D., Senior Investigator, Membrane Structure & Function, National Cancer Institute, NIH

Phage and yeast display methodologies to identify monoclonal antibodies targeting specific parts of a protein molecules will be discussed including sequential and competitive panning and sorting of antibody libraries.

2:35 Designing Antibodies to Bind to Integrin

AhuvaNissimAhuva Nissim, Ph.D., Senior Lecturer, Molecular Targeting, Biochemical Pharmacology, William Harvey Research Institute, Queen Mary University of London

To increase the likelihood of developing powerful bio-therapeutics, a structurally-guided scaffold library was engineered based on the NMR structure/function analysis of ligand to tumour cell surface receptor avb6. VH-CDR3 encoding RGD-helix hairpins with helices of differing pitch, length and amino acid composition were built. Lead scFv clones and their corresponding VH-CDR3 derived peptides demonstrated specific inhibition of avb6 mediated activity and selective retention by avb6-expressing, but not avb6-negative, human xenografts.

3:05 Integrating Therapeutic Target Identification with Rapid Yumab Generation

StefanDuebelStefan Duebel, Ph.D., Director, Institute for Biochemistry, Biotechnology & Bioinformatics, Technical University Braunschweig

Using parallel high-throughput generation of Yumabs (human single chain antibodies carrying an Fc part), new systematic screening approaches for the discovery of novel drug targets are now available - offering the additional advantage that the tools used for the discovery are drug lead candidates right away.

3:35 Structure-Based Design of Novel PTM-Specific Antibody Scaffolds

JT KoerberJames T. Koerber, Ph.D., Life Science Research Fellow, Pharmaceutical Chemistry, University of California, San Francisco

High-quality monoclonal PTM-specific antibodies have revolutionized our understanding of cell signaling. However, these reagents remain extremely challenging to generate by immunization methods, which are time consuming, expensive, and inefficient. I will discuss a novel method that combines structure-based design with display technologies to enable the rapid, high-throughput generation of renewable, recombinant PTM-specific antibodies.

4:05 Refreshment Break in the Exhibit Hall with Poster Viewing

4:45 Problem Solving Breakout Discussions 

These interactive discussion groups are open to all attendees, speakers, sponsors, & exhibitors. Participants choose a specific breakout discussion group to join. Each group has a moderator to ensure focused discussions around key issues within the topic. This format allows participants to meet potential collaborators, share examples from their work, vet ideas with peers, and be part of a group problem-solving endeavor. The discussions provide an informal exchange of ideas and are not meant to be a corporate or specific product discussion. 

Next-Generation Sequencing and Phage Display 

Michael Szardenings, Ph.D., Head, Ligand Development Unit, Fraunhofer Institute for Cell Therapy and Immunology; Coordinator JLCI, CNUHH, Hwasun, Korea 

• How to handle and search NGS data
• Quality vs quantity – share your experiences in generating phage libraries
• Do we still need scaffolds?
• What is next?

Enhanced Identification of Antibodies Targeting Specific Structures 

Dimiter S. Dimitrov, Ph.D., Senior Investigator, Membrane Structure & Function, National Cancer Institute, NIH  

• Need for such antibodies - virus neutralization, animal studies
• Conserved epitopes - sequential antigen panning
• Domains of interest - competitive antigen panning
• Specific structures and conserved epitopes - competitive antigen sorting other methods

In vivo Selection of Tumor-Specific Antibodies 

Luis Álvarez-Vallina, M.D., Ph.D., Associate Professor, BCE Protein Engineering, Aarhus University 

• How we can address the unmet need in oncology of discovering systemically accessible antigens preferentially overexpressed in the tumor microenvironment?
• In theory in vivo selection of combinatorial libraries could ensure the presence of antibodies against any potentially relevant target. However, there are several important issues to address:
• Which is the ideal library size?
• Which is the ideal antibody format?
• Which is the ideal displaying particle?
• Finally, it is important to discuss whether procedure is applicable to any disease for which an animal model exists (be it cancer, neurodegenerative diseases, etc.).

Generating High-Quality Affinity Reagents 

Brian K. Kay, Ph.D., Professor and Head, Biological Sciences; LAS Distinguished Professor, University of Illinois, Chicago 


• Recombinant affinity reagents versus antibodies
• Advantages and disadvantages of recombinant affinity reagents
• Technical hurdles in generating specific, high-affinity reagents
• Range of applications


Challenges in Generating PTM-Specific Detection Reagents 

James T. Koerber, Ph.D., Life Science Research Fellow, Pharmaceutical Chemistry, University of California, San Francisco 

• Antibodies versus other recombinant protein domains
• Which method should we be using? Immunization vs. in vitro methods
• What is the optimal antigen type and format?
• Challenges in obtaining specificity and validating


5:45 Welcome Reception in the Exhibit Hall with Poster Viewing

6:45 End of Day

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