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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.

Final Agenda

THURSDAY, JANUARY 17

7:45 am Registration and Morning Coffee

Integrating Deep Sequencing with Traditional Antibody Discovery Methods

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.


KEYNOTE PRESENTATION

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 leads.

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 diversity.

9:30 Presentation to be Announced

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

11:00 Sequence-Based Prediction of Antibody Specificities

Sai Reddy, PhD, Associate Professor, Biosystems Science and Engineering, ETH Zurich, Switzerland

In this presentation, I will describe how we are decrypting antibody repertoires by identifying convergent antigen-associated molecular patterns. Molecular convergence is specifically identified by bioinformatic recoding of high-throughput sequencing data of antibody repertoires into constituent biochemical sequence space. By combining this approach with a statistical learning framework, we are able to accurately predict antigen exposure and antigen specificity based on antibody sequences alone.

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

Mining Human Antibody Repertoires

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 Sponsored Presentation (Opportunity Available)

3:35 Networking Refreshment Break

Single Cell Cloning and Screening Platforms

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 proliferation.

5:30 Close of Day

FRIDAY, JANUARY 18

8:00 am Registration

8:00 BuzZ Sessions with Continental Breakfast

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 trends.


Moderator: Vu Truong, PhD, CSO & CEO, R&D, Aridis Pharmaceuticals, Inc.

 

Application Case Studies

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

11:00 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.

11:30 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.

12:00 pm Conference Wrap-Up

Sam Wu, PhD, Principal Scientist, Janssen BioTherapeutics

12:30 Close of Conference

* The program is subject to change without notice, due to unforeseen reason.

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