Cambridge Healthtech Institute’s Inaugural
Deep Sequencing and Single Cell Analysis for Antibody Discovery
Technologies and Best Practices for Applying Repertoire Analysis in the Discovery of Therapeutic Proteins
January 17-18, 2019
The rapid adoption of deep sequencing and single B cell analysis has given discovery scientists an extraordinary view into human and animal immune repertoires that is now informing all aspects of biopharmaceutical R&D. This dynamic field is bringing
together the disciplines of immunology, structural and computational biology, informatics and microfluidics to offer previously unimaginable perspectives that will drive discovery of the next generation of biologic drugs. PepTalk’s Inaugural
Deep Sequencing and Single Cell Analysis for Antibody Discovery explores the vast range of new science and technology in this field and how these new capabilities are being integrated with traditional discovery methods.
THURSDAY, JANUARY 17
7:45 am Registration and Morning Coffee (Sapphire West Foyer)
8:10 Organizer’s Welcome Remarks
Kent Simmons, Senior Conference Director, Cambridge Healthtech Institute
8:15 Chairperson’s Opening Remarks
Gabriel W.C. Cheung, PhD, Senior Director, BioMedicine Design, Medicinal Sciences, Worldwide Research and Development, Pfizer, Inc.
8:20 Leveraging Immune Repertoire Deep Sequencing to Extend Traditional Antibody Discovery Methods
Isidro Hotzel, PhD, Senior Scientist, Genentech
Hybridoma and B cell cloning remain the main technologies for antibody discovery in the industry. Although significantly improved over the years, these technologies still have a relatively limited repertoire sampling capacity which often results in relatively
limited panel sizes and antibody leads that require further optimization. Deep sequencing technologies have been integrated in the antibody discovery workflow to enhance the sampling of immune repertoires for rapid discovery of optimized antibody
9:00 Ultra-Deep Sequencing of the Baseline Human Antibody Repertoire
Bryan Briney, PhD, Assistant Professor, Immunology and Microbiology,
The Scripps Research Institute
In principle, humans can make an antibody response to any non-self-antigen molecule. We have examined the circulating B cell populations of ten healthy human subjects and present the largest single collection of human adaptive immune receptor sequences
described to date, comprising almost 3 billion nearly full-length antibody heavy chain sequences. This repertoire-scale dataset reveals a surprising degree of repertoire uniqueness, a subpopulation of public antibody clonotypes and exceptional repertoire
9:30 Combining High-Throughput Single-B Cell Screening with Ig-Seq for Comprehensive Analysis of Natural Immune Responses
Ester Falconer, PhD, Group Leader, Molecular Biology and Expression, AbCellera
The application of high-throughput sequencing to antibody repertoires (Ig-Seq) enables comprehensive analysis of natural immune responses. A key challenge to realizing its potential for vaccine development, antibody discovery, and diagnostics is connecting
sequence diversity with functional data. We present the combination of Ig-Seq with AbCellera’s microfluidic single-cell screening technology to enable deep profiling and functional annotation of human immune responses to viral pathogens.
10:00 Coffee Break in the Exhibit Hall with Poster Viewing (Sapphire Ballroom)
11:00 NEW: The Impact of Next Generation Sequencing on Antibody Library Production, Selection and Screening: Making an Effective Antibody Library from a Single Donor
Andrew M. Bradbury, PhD, MB BS, CSO, Specifica, Inc.
11:30 Rapid Functional Interrogation of Immune Repertoire
Gabriel W.C. Cheung, PhD, Senior Director, BioMedicine Design, Medicinal Sciences, Worldwide Research
and Development, Pfizer, Inc.
Numerous disruptive technologies, from NGS of BCRs to bottom-up serum Ig proteomic, have been developed to study B cell repertoires in the past decade. At Pfizer, we are further pushing the boundary of technologies to enable fast and comprehensive
interrogation of functionally relevant, antigen-specific B cells from both peripheral and bone marrow compartments through the use of proprietary high-throughput automation, novel single cell technology and deep sequencing.
12:00 pm Session Break
12:10 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own
1:10 Ice Cream Break in the Exhibit Hall with Poster Viewing (Sapphire Ballroom)
2:15 Chairperson’s Remarks
Gregory C. Ippolito, PhD, Research Assistant Professor, Molecular Biosciences, Georgiou Lab, The University of Texas at Austin
2:20 Predicting Personal Immune Scenarios
Enkelejda Miho, PhD, Professor, Digital Life Sciences, FHNW
University of Applied Sciences and Arts Northwestern Switzerland, Switzerland
Antibodies protect against pathogens and are important diagnostics and therapeutics. Sequence diversity of antibody repertoires has been recently recorded from the advancement of high-throughput sequencing technologies. Antibody repertoires can now be
represented as large-scale networks where antibodies are sequence-nodes connected by similarity-edges. We show how this network model can serve as the base to track entire personalized antibody repertoires in the theoretical antibody sequence space,
thus predicting immune status scenarios.
2:50 High-Throughput Discovery of Patient-Specific, Immune-Selected, Anti-Tumor B Cells and Immunoglobulins in Breast Cancer
Gregory C. Ippolito, PhD, Research Assistant Professor, Molecular
Biosciences, Georgiou Lab, The University of Texas at Austin
The synergistic combination of Ig protein mass spectrometry (Ig-Seq) and a DNA sequencing method that preserves the natural pairing of heavy (VH) and light (VL) chain variable regions (VH:VL BCR-Seq) can prospectively identify tumor-reactive B cells and
also confirm the presence of functional, high-affinity, circulating anti-tumor Ig in cancer patients. This strategy capitalizes on the in vivo immune response and may provide an unbiased screening of antibody specificities
that have been immune-selected by cognate tumor antigens.
3:20 NEW: SELECTED POSTER PRESENTATION: Single B Cell Screening: A Versatile, High-Throughput Single Cell Screening Platform for the Discovery of Fully Human Antibodies from Natural Immune Repertoires
Kevin Heyries, PhD, Co-Founder – AbCellera
AbCellera's end-to-end antibody discovery platform screens millions of single B-cells from natural immune repertoires, from any species and from any immune tissue to generate hundreds of lead antibodies, including complex membrane protein targets. Optimized immunization strategies combined with complex single cell selection assays that include multiplexed binding, live cell binding, ligand blocking, affinity, competition and functional assays, enables the discovery of unique antibodies with desired properties.
3:35 Networking Refreshment Break (Sapphire & Aqua West Foyer)
4:00 Linked Experimental and Computational Analysis to Accelerate Antibody Discovery from Natively Paired VH:VL Antibody Libraries
Brandon DeKosky, PhD, Assistant Professor, Pharmaceutical Chemistry and Chemical Engineering, University of Kansas
Next-generation technologies have amplified the power of antibody screening technologies. Recent advances in paired heavy:light sequencing and native antibody library display offer new possibilities for discovering and annotating antibody functional
performance on a repertoire scale. We will discuss the application of these new technologies in combination with next-generation computational data analysis and precise screening methods to understand immune function and to discover and identify
new antibody molecules with desired functional properties.
4:30 Functional Antitumor Antibodies from Immunoglobulin Repertoires of Cancer Patients
Daniel Emerling, PhD, Senior Vice President, Research, Atreca, Inc.
We sequenced natively-paired, immunoglobulin (IgG) heavy and light chains from activated B cells of over 100 cancer patients and used sequence repertoire analyses to select specific IgGs for recombinant expression and characterization. Screened antibodies
bound non-autologous human-derived tumor tissues at a high rate, consistent with recognition of public tumor antigens. Some antibodies caused tumor regression in mouse cancer models. Starting from patient anti-tumor responses, we’ve established
a discovery strategy for novel cancer therapies.
5:00 Isolation of Single Antigen Specific T Cells for Rapid TCR Sequencing and Cloning
Paul Armistead, MD, PhD, Associate Professor, Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill
Cloning cancer-antigen specific T cells is important for immunotherapeutic development. Because of the inefficiencies of limiting dilution and tetramer-FACS based T cell cloning, we have developed a cellular microarray-based platform that can identify,
isolate and clonally expand individual T cells from a large population based upon their antigen specific cytotoxicity. Ongoing studies will further develop this platform to select and isolate antigen specific T cells based upon clonal, antigen-specific
5:30 Close of Day
FRIDAY, JANUARY 18
8:00 am Registration (Sapphire West Foyer)
8:00 BuzZ Sessions with Continental Breakfast (Sapphire Foyer)
Protein therapeutics is a fast-growing global market. As the science improves, so does the complexity of the R&D organization. Ensuring product quality plus speed to market requires insights from stakeholders working across the stages of protein
science R&D. Join experts representing this PepTalk pipeline, peers, and colleagues for an interactive roundtable discussion. Topics include highlights from the week’s presentations, new technologies and strategies, challenges, and future
Click here for more details
Moderator: Vu Truong, PhD, CSO & CEO, R&D, Aridis Pharmaceuticals, Inc.
9:00 Chairperson’s Remarks
Marcin Paduch, PhD, Senior Staff Scientist, Product Development, GRAIL, Inc.
9:05 Recombinant Human B Cell Repertoires Enable Screening for Rare, Specific and Natively-Paired Antibodies
Sarav Rajan, PhD, Scientist, Antibody Discovery & Protein Engineering, MedImmune
We present an approach to encapsulate millions of primary B cells into picoliter-sized droplets, where their cognate V genes are fused in frame to form a library of scFv cassettes. We used this approach to construct natively-paired phage-display libraries
and rapidly drove selection towards cross-reactive antibodies targeting influenza hemagglutinin. Most antibodies were not detected by next-generation sequencing of the paired repertoire, illustrating how this method can isolate extremely rare leads
not likely found by existing technologies.
9:35 Engineered Virus-Like-Particles for GPCR-Specific Therapeutic Antibody Discovery
Mart Ustav, Jr., PhD, Postdoctoral Fellow, Sidhu Lab, University of Toronto
We have established a robust method for the expression of GPCRs on HIV-1 gag Virus-Like-Particles (VLPs). We engineered the gag protein of HIV-1 to enable tight interaction with a short peptide fused to the C-terminal tail of therapeutically relevant GPCRs. We used these engineered VLPs for the isolation of mAbs from large phage- libraries and through Next-Generation-Sequencing (NGS) were able to identify mAbs binding therapeutically relevant GPCRs.
10:05 Sequencing Cancer Genome Data for Diagnostic Discovery and Development
Marcin Paduch, PhD, Senior Staff Scientist, Product Development, GRAIL, Inc.
Large-scale cancer genome sequencing efforts are rapidly increasing our power to identify tumor genetic and epigenetic biomarkers with unprecedented precision. Expanded knowledge of tumor biology, genetics, cfNAs and other types of cancer-related molecules open up uncharted paths to discovery of new diagnostic and therapeutic markers. I will discuss the development of approaches that capture complexity of disease states such as cancer and take advantage of extensive data sets being generated.
10:35 Networking Coffee Break (Sapphire & Aqua West Foyer)
11:00 SPEAKER CANCELLED Identification of Therapeutic Antibodies and Orphan TCR Targets by Microfluidics Based Single Cell Analysis
George Wu, PhD, CEO, Amberstone
It remains to be a major bottleneck to efficiently discover a functional antibody lead for a therapeutic target. Here we present a case study to show the power of a cutting-edge microfluidic based single cell platform technology in the discovery of a functional antibody against immunotherapeutic targets. We also show the platform’s usefulness in the antigen discovery for an orphan T cell receptor (TCR) with therapeutic applications.
11:00 Comprehensive B Cell Repertoire Screening and Stabilization of Selected B Cell Using Novel Cell Fusion Technology
Vu Truong, PhD, CSO & CEO, R&D, Aridis Pharmaceuticals, Inc.
Development of monoclonal antibody therapeutics derived from B cell repertoire screening of infected hosts has been limited by two barriers: 1) how to comprehensively screen the entire repertoire which typically comprises over 1 million of unique B cells generated against the pathogen and 2) how to rapidly manufacture mAbs without employing traditional recombinant DNA and cell line process development steps. We will present a novel approach to addressing these two barriers.
11:30 pm Conference Wrap-Up
Sam Wu, PhD, Principal Scientist, Janssen BioTherapeutics
12:00 Close of Deep Sequencing Conference (delegates may attend programs in other rooms; Peptalk ends at 12:30)