Cambridge Healthtech Institute’s Third Annual

Emerging Technologies for Antibody Discovery

Exploring the Intersection of Display Technologies, Next-Generation Sequencing and Informatics for the Discovery of Next-Generation Biotherapeutics

January 11-12, 2018


As large pharma continues its integration of biologic drugs into its product portfolios and discovery operations, it is imperative that industry companies identify truly novel drug targets for unmet medical needs – and that the biotherapeutics against these are selected and engineered to minimize development risk. For 2018, Cambridge Healthtech Institute’s Third Annual Emerging Technologies for Antibody Discovery meeting considers the intersection of traditional display-based screening and selection approaches with next-generation tools such as immune repertoire sequencing, in silico modeling and high resolution imaging.

Final Agenda


7:45 am Registration and Morning Coffee

8:15 Chairperson’s Opening Remarks

Andrew Bradbury, Ph.D., MB BS, CSO, Specifica, Inc.


8:20 Remodeling of Cell Surfaceomes in Cancer

Jim_WellsJames A. Wells, Ph.D., Professor, Pharmaceutical Chemistry, University of California, San Francisco

The cell surface proteome (surfaceome) is the primary hub for cells to communicate with the outside world. My lab studies how the surfaceome is remodeled in cancer. We find the new set of proteins promote enhanced cell growth and detachment from native tissues allowing metastasis. Our primary goal is to systematically understand how cancer cells remodel their membrane proteomes (surfaceomes) during cancer transformation and develop antibodies to detect and attack them.

Functional Screening

9:00 Combining Screening with Phenotypic Selection in Antibody Phage Display

Marcin_PaduchMarcin Paduch, Ph.D., Pipeline Director, Recombinant Antibody Network, University of Chicago

State-of-the-art methods for generating recombinant antibodies do not necessarily allow for targeting the particular cellular phenotype posing a fundamental challenge. A set of next generation high-throughput technologies that allow for phenotypic selection has to be developed. Intimate knowledge of conformation states and biochemistry of antigens can be exploited to mimic native-like environments and create the possibility of trapping physiologically-relevant states otherwise not accessible by current methods.

9:30 Phage-Displayed Ubiquitin Variant (UbV) Libraries to Rapidly Identify Potent and Highly Selective Protein-Based Inhibitors

Joan Teyra, Ph.D., Research Associate, University of Toronto, Canada

E3 ligases and deubiquitinases regulate diverse cellular processes and are implicated in numerous human diseases. However, targeting these enzymes potently and specifically remains a big challenge. We thus devised a screening platform to develop protein-based modulators for ubiquitin-proteasome system components. I will report how we design the ubiquitin variant library and phage selection strategies to generate inhibitors for USP15.

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

11:00 Efficient B Cell Cloning and Antibody Engineering Platform for Rare Ab Generation

Fang_ShuFeng Shu, Ph.D., Senior Researcher, Chugai Pharmabody Research, Singapore

Here we describe a high throughput antibody identification system by single B cell cloning, which can generate and evaluate a large number of antibodies with high diversity to identify the rare antibodies with required properties such as pH dependency. A robust antibody engineering system is also introduced, where thousands of antibodies with designed mutations can be generated and evaluated in 2 weeks’ time to further accelerate the antibody discovery process.

Rapid Novor11:30 Antibody Protein Sequencing with Mass Spectrometry

Mingjie_XieMingjie Xie, MSc, MBA, CEO, Rapid Novor Inc

Many applications in antibody engineering require the direct sequencing of antibody proteins. At Rapid Novor ( we have developed a robust workflow and routinely sequenced antibody proteins. Here we share the success experiences, examine common mistakes novices make, and present our practices to ensure the correctness of every amino acid.

  12:00 pm Session Break

12:15 Luncheon Presentation: Next-Generation Capillary Electrophoresis Technology for Protein Analysis

Wei-Chiang_ChenWei-Chiang Chen, Ph.D., Scientist, Analytical Development, Biogen

Recombinant adeno-associated virus (AAV) is a promising platform in human gene therapy. AAV vectors contain a protein outer shell called capsid, which is comprised of 60 subunits containing three viral proteins. To confirm the purity of the AAV capsids, we developed a CE-SDS method on the Maurice platform, which automates analysis of 96 samples in one batch. This assay demonstrates good separation of viral proteins (LOQ at 5e11 vg/ml), and comparable results with SDS-PAGE gels.

1:15 Ice Cream Break in the Exhibit Hall with Poster Viewing

Advances in Display Technologies and Library Design

2:00 Chairperson’s Remarks

Nicolas Fischer, Ph.D., Head, Research, Novimmune SA, Switzerland

2:05 Enhancing the Chemical Versatility of Yeast Display

James_VandeventerJames Van Deventer, Ph.D., Assistant Professor, Chemical and Biological Engineering, Tufts University

We have established a version of yeast display that supports the integration of chemical groups into displayed proteins using noncanonical amino acid incorporation. We are currently investigating strategies for positioning chemical groups within antibodies in order to enhance and change the molecular recognition capabilities of these proteins. This talk will highlight our recent progress in constructing, evaluating, and screening “hybrid” structures with potential applications in the tumor microenvironment.

2:35 How Big Are Antibody Libraries Really? And Are We Accessing the Full Diversity?

Andrew_BradburyAndrew Bradbury, Ph.D., MB BS, CSO, Specifica, Inc.

In vitro antibody libraries have been used to generate antibodies against many different therapeutic lead targets. Analyses indicate that one would expect to select 1-3 antibodies from a 1e7 library. However, this does not appear to scale to larger libraries with diversities estimated to be >1 billion, suggesting that libraries are less diverse than thought or selection methods do not tap the full diversity. This talk discusses the use of NGS to explore these issues and the application of NGS to the creation of improved antibody libraries.

3:05 Featured Poster Presentation: Mapping the Antibody Response to Vaccines Directly from Patient Serum

Michael_Szardenings Michael Szardenings, Ph.D., Vice Head Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, Germany

A novel phage display-based platform provides a promising alternative technology to determine epitopes of vaccines. Antibody epitope variations were studied over 6 years in the serum of a single patient (influenza, Hepatitis B vaccines and traces of other infections). Information about the natural antibodies’ epitopes may help to design vaccines and to clone or design antibodies for multiple therapeutic and diagnostic applications.

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

4:15 Dual Display Technology for “In Format” Selection and Screening of Bispecific Antibodies

Nicolas_FischerNicolas Fischer, Ph.D., Head, Research, Novimmune SA, Switzerland

The desired biological activity of bispecific antibodies is often dependent on the adequate geometry of the two antibody binding sites, thus requiring extensive combinatorial testing of isolated antibodies. Being able to evaluate candidates ‘in format’ as early as possible would greatly facilitate the development of bispecific antibodies. To achieve that goal, we have developed methodologies that allow ‘in format’ phage display selection and screening of candidates early in discovery.

4:45 Synthetic Human Antibody Fragment Libraries for CAR T Cell Therapy

Thomas_VanBlarcomThomas J. Van Blarcom, Ph.D., Associate Research Fellow, Rinat Laboratories, Oncology Research and Development, Pfizer, Inc.

Unlike most therapeutic antibodies, CAR T cells are typically generated with single chain variable fragment (scFv) antibodies. In this study, we present a human synthetic scFv antibody library that we use to simplify the generation and testing of large panels of antibodies for use as CAR T cells. The CAR T cells generated from these antibodies had desirable phenotypes and demonstrated robust and specific cytotoxic activity in vitro.

5:15 Highly Multiplexed Cell Surfaceomics Using Genetically Barcoded Antibody-Phage

Sam_PollockSamuel Pollock, Researcher, Pharmaceutical Chemistry, University of California, San Francisco

Cells express thousands of different surface proteins that can be used for their classification. We present a surface proteomic method using genetically barcoded antibodies called Phage-antibody Next Generation Sequencing. We use PhaNGS to reveal changes in surface protein abundance in the contexts of drug resistance, adaptation to oncogenes, and on the single-cell level. Linking selective, genetically encoded binders to NGS enables direct, multiplexed protein detection, comparable to RNAseq for mRNA.

5:45 Close of Day


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.

Table Moderator: James Van Deventer, Ph.D., Assistant Professor, Chemical and Biological Engineering, Tufts University

Table Moderator: Marcin Paduch, Ph.D., Pipeline Director, Recombinant Antibody Network, University of Chicago


Integrated Discovery Platforms

9:00 Chairperson’s Remarks

Sagar Kathuria, Ph.D., Senior Scientist, Protein Engineering, Sanofi Genzyme

9:05 Generation of Mono and Bispecific Antibodies from Immunized Transgenic Rodents and the Potential to Engineer Multi-Specific Entities Using Common Light Chain Paratopes

Simon_KrahSimon Krah, Ph.D., Senior Scientist, Protein Engineering and Antibody Technologies, Merck KGaA, Germany

We demonstrate that by using Yeast Surface Display (YSD), a more effective coverage of the antibody diversity generated during the course of an immunization can be realized in comparison to classical hybridoma technology. Moreover, we show that bispecific antibodies can also be readily engineered via such YSD approaches in combination with the application of common light chains. In addition, we established a methodology which facilitates the tedious and time-consuming process of YSD library generation.

9:35 Discovery Platform for Antibody Generation and Screening for Different Applications

Anne_MarcilAnne Marcil, Team Lead, Monoclonal Antibodies, National Research Council, Canada

The National Research Council of Canada has a strong history in target discovery, antibody generation and characterization, resulting in the production of new antibodies against hundreds of targets. An overview of our antibody discovery pipeline which includes bioinformatics and MS analysis for target discovery, monoclonal, single-domain and antibody library screening, in vitro screening for function (ADCs, Blood-brain barrier crossers, electrophysiology, etc.) and in vivo screening will be presented.

10:05 A Patient-Centric Function F.I.R.S.T™ Approach to Cancer Immunotherapy Discovery

Björn Frendéus, Ph.D., CSO, Bioinvent, Sweden

We have developed a patient-centric phenotypic discovery approach (F.I.R.S.T) that utilizes primary cancer patients’ cells from the initial steps of isolating antibodies from a naïve human antibody library through POC studies and subsequent identification of targeted receptors. A lead candidate which blocks FcgRIIB internalization and acts in synergy with rituximab to boost responses and help overcome resistance in the background of emerging targeted therapies as well as conventional chemotherapy in vivo, is now in clinical phase testing.

10:35 Coffee Break with a Poster Pavilion

PepTalk is proud to support and recognize the protein scientists of tomorrow during the Poster Pavilion. This time has been set aside to view the Student Fellowship posters and interact with presenters one on one. This opportunity gives job seekers the chance to share their expertise with future/potential employers or develop contacts to further their research.

11:15 Tool and Platform Development for Antibody Developability Assessment and Mitigation

Sagar_KathuriaSagar Kathuria, Ph.D., Senior Scientist, Protein Engineering, Sanofi Genzyme

Antibodies have emerged as very successful biological drugs in the recent past. The growth of this industry has highlighted a need for a comprehensive set of non-redundant assays and corresponding threshold values to identify likely candidates early during research and prioritize their development. We make use of several high-throughput biophysical and biochemical tools for antibody characterization towards achieving this goal. Results from some test cases will be discussed.

11:45 High Content Confocal for Antibody Selection and Potency Screening

Tianyi_WangTianyi Wang, Ph.D., Scientist, R&D, Sorrento Therapeutics

This talk outlines applications of high content confocal and cell-by-cell metrics for selection and potency of antibodies with applications toward intracellular targets. 3D spheroids and high content confocal in vitro system are used to screen the phenotypic effects of selected intracellular-targeting antibodies. 3D spheroids, by mimicking tumor microenvironment, are a better predictor of clinical potential of antibody therapeutics. Our method proposes multiparametric analyses of spheroids to elucidate mechanism of action.


12:15 pm Conference Wrap-Up

Tilman Schlothauer, Ph.D., Principal Scientist, Biochemical and Analytical Research, Large Molecule Research, Roche Innovation Center Munich


12:45 Close of Conference


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