Cambridge Healthtech Institute’s Inaugural
Informatics for Cancer Immunotherapies
Data Analytics in a Dynamic Landscape
August 6-7, 2019
Clinical success of immunomodulatory cancer therapies has sparked fast-paced growth in cancer research that converges at the intersection of cancer genomics, immunology, and informatics. Immuno-oncology is data-driven, yet the much-needed informatics
techniques for integrating tumor analysis, tumor microenvironment, systemic immunity, and therapeutic response are at the early stages of development. Cambridge Healthtech Institute’s Inaugural Informatics for Cancer Immunotherapies convenes
stakeholders that share their journey to this intersection of data and immuno-oncology – the place where breakthroughs happen.
Final Agenda
TUESDAY, AUGUST 6
12:00 pm Registration
1:25 Chairperson’s Opening Remarks
Doron Levy, PhD, Professor, Department of Mathematics, University of Maryland
1:30 Integrating Oncology Data for Models of Cancer Dynamics
Doron Levy, PhD, Professor, Department of Mathematics, University of Maryland
In this presentation, we will overview recent techniques for modeling the dynamics of cancer progression and the evolution of drug resistance. We will demonstrate how oncology data can be integrated into such models and focus on some of the questions
that can be potentially answered using these novel techniques.
2:00 High-Throughput Cancer Hypothesis Testing with an Integrated PhysiCell-EMEWS Workflow
Paul Macklin, PhD, Associate Professor, Intelligent Systems Engineering, Indiana University
We will present advances in simulating cancer-immune contact interactions, and how learning-guided exploration of these models on high-performance computing (HPC) resources can guide therapeutic design. We will use high-throughput model exploration to
understand the impact of biological and clinical constraints on treatments, while also ranking the importance of physical mechanisms. This is an ongoing collaboration between Indiana University, Argonne National Lab, and the University of Vermont
Medical Center.
2:30 NEW: KEYNOTE PRESENTATION: Driving the Drivers: Exploring Cancer Using Network Medicine
John Quackenbush, PhD, Henry Pickering Walcott Professor of Computational Biology and Bioinformatics; Chair, Department of Biostatistics, Harvard T.H. Chan School of Public Health
3:00 Network Biology and Complex Bioinformatics Enable Significant Novel Findings in Drug Development
Eske Rygaard-Hjalsted, MSc, Vice President, Sales, Marketing and BD, Intomics
The presentation will highlight how the application of complex bioinformatics and interpretation in a systems biology context can significantly improve the overall understanding of biology and lead to much higher success rates in pharma drug development
and precision medicine. Proprietary tools that are applied in Intomics projects and a case study on development of a multi-marker signature of drug response in oncology with an accuracy of more than 80% will be presented.
3:30 Refreshment Break in the Exhibit Hall with Poster Viewing
Harbor II & III
4:15 PLENARY KEYNOTE SESSION
PANEL DISCUSSION: Next-Generation Immunotherapies
CHI’s Immuno-Oncology Summit brings you the latest advances in immunotherapy every year. This panel of industry thought leaders will discuss the technology advances and implementation strategies for next-generation immunotherapies, including emerging
immunotherapy combinations, bispecific antibodies, oncolytic virotherapy, adoptive cell therapy, personalized vaccines and neoantigen targeted therapies, small molecules and ADCs, cytokines, and innate immunity targeted therapies.
Pamela Carroll, PhD
Senior Vice President, Immuno-Oncology, Genocea Biosciences
Rakesh Dixit
PhD, DABT, President & CEO, Bionavigen
Tara Arvedson, PhD
Director, Oncology Research, Amgen
Michael A. Curran, PhD
Associate Professor, MD Anderson Cancer Center; President, Immunogenesis, Inc.
Raymond Tesi, MD
CEO/CMO, INmune Bio
David Kirn, MD
Co-Founder & Executive Chairman, IGNITE Immunotherapy
5:30 Welcome Reception in the Exhibit Hall with Poster Viewing
WEDNESDAY, AUGUST 7
7:30 am Registration Open and Morning Coffee
Harbor II
8:25 Chairperson’s Remarks
Litao Zhang, PhD, Vice President, Leads Discovery and Optimization, Bristol-Myers Squibb
8:30 KEYNOTE PRESENTATION: Dissecting the Tumor Microenvironment Using Multiplex Gene Profiling and Cellular Immune-Phenotyping
Litao Zhang, PhD, Vice President, Leads Discovery and Optimization, Bristol-Myers Squibb
Here we will describe and discuss several IO translational models that are regulated by distinct signaling pathways in the tumor microenvironment (TME). Using gene expression and cellular immune-phenotyping profiling as orthogonal and complementary
approaches, we uncover network signaling relationships that play a key role in the TME and its critical role in primary and secondary resistance in IO therapy.
Chairperson’s Remarks
Qinghua Song, PhD, Director, Biostatistics, Kite, a Gilead Company
9:00 Bioinformatics Accelerates Cancer Immunotherapy
Bolan Linghu, PhD, Principal Scientist, Oncology Bioinformatics, AstraZeneca
Bioinformatics methodologies play an important role in all aspects of cancer immunotherapy development. We will highlight several methodologies to advance IO drug discovery, such as transcriptome-profiling based gene signatures, integrating electronic
health records and cancer genomics, and AI applications.
9:30 Machine Learning in CAR T-Cell Therapy
Qinghua Song, PhD, Director, Biostatistics, Kite, a Gilead Company
We share some practical machine learning methods and experiences in translational medical science projects, where the focus is to understand and improve the efficacy and safety of the CAR T-Cell therapy.
10:00 The Role of Macrophage Differentiation in Triple-Negative Breast Cancer: A Multiscale Computational Modeling Approach
Kerri-Ann Norton, PhD, Assistant Professor, Computer Science Program, Department of Science, Mathematics, and Computing, Bard College
Triple-negative breast cancer (TNBC) progression is influenced by interactions between the breast tumor and immune system. To understand these interactions, a computational agent-based model of breast cancer progression was developed, including interactions
with stromal macrophages, cancer stem cells, cancer progenitor cells, and tumor vasculature. We investigate the interactions between macrophages that get recruited and differentiate and make predictions as to which therapeutic targets would most
reduce tumor growth.
10:30 Coffee Break in the Exhibit Hall with Poster Viewing
11:30 DeepTCR: A Deep Learning Framework for Revealing Structural Concepts within TCR Repertoire
John-William Sidhom, MSE, MD/PhD Candidate, Bloomberg-Kimmel Institute for Cancer Immunotherapy, Department of Biomedical Engineering, Johns Hopkins University School of Medicine
Deep learning algorithms have been utilized to achieve excellent performance in pattern-recognition tasks, such as in image and vocal recognition. The ability to learn complex patterns in data has tremendous implications in the genomics world, where
sequence motifs become learned features that can be used to predict functionality, guiding our understanding of disease and basic biology. We present DeepTCR, a broad collection of unsupervised an supervised deep learning methods able to uncover
structure in highly complex and large TCR sequencing data. We demonstrate its utility across multiple scientific examples, including learning antigen-specific motifs to viral and tumor-specific epitopes and understanding immunotherapy-related
shaping of repertoire.
12:00 pm Single Cell Genomics – Using a Finer Lens to Unravel Features of Human Immunity
Alexandra-Chloé Villani, PhD, Associate Scientist, Broad Institute of MIT and Harvard
Single-cell genomics analyses now provide an unbiased, data-driven way of systematically detecting cellular states and subtypes and can reveal diverse facets of cellular identity. Such an approach, which forms the basis for constructing a comprehensive
human immune cell atlas, will be discussed at the meeting. Collectively, our revised cell taxonomy will enable more accurate functional and developmental analyses, as well as immune monitoring in health and disease.
12:30 Enjoy Lunch on Your Own
1:55 Chairperson’s Remarks
Hans Bitter, PhD, Vice President, Data Sciences, bluebird bio
2:00 CD19 Chimeric Antigen Receptor Therapy for Refractory Aggressive B-Cell Lymphoma
Caron Jacobson, MD, Medical Director, Immune Effector Cell Therapy Program, Dana Farber Cancer Institute
I will be discussing the clinical data to date of second generation anti-CD19 CAR T cells in aggressive B cell non-Hodgkin lymphomas, comparing the three constructs most advanced in clinical development. I will also discuss ongoing unmet needs in
the field and approaches to meet them, including toxicity mitigation strategies, mechanisms of resistance, and the issues of time and cost with autologous CAR T-cell products.
2:30 Integrating Genomic and Immunologic Data to Accelerate Translational Discovery at the Parker Institute for Cancer Immunotherapy
Danny Wells, PhD, Lead Bioinformatics Scientist, Parker Institute for Cancer Immunotherapy
Immunotherapy is rapidly changing how we treat both solid and hematologic malignancies, and combinations of these therapies are quickly becoming the norm. For any given treatment strategy, only a subset of patients will respond, and an emerging challenge
is how to effectively identify the right treatment strategy for each patient. This challenge is compounded by a concomitant explosion in the amount of data collected from each patient, from high dimensional single cell measurements to whole exome
tumor sequencing. In this talk, I will discuss translational research at the Parker Institute, and how we are integrating multiple molecular and clinical data types characterize the tumor-immune phenotype of each patient.
3:00 Patient Outcomes Tracking through Registries: Understanding the Role in Adoptive Cell Therapies, Present and Future
Marcelo Pasquini, MD, MS, Senior Scientific Director, CIBMTR Clinical Trials Support; Associate Professor of Medicine, Medical College of Wisconsin
CIBMTR is partnering with Be The Match BioTherapies® to drive standardization across the cell therapy industry, including the registration and tracking of patient outcomes of adoptive cell therapies worldwide. We’ve built a Cellular Therapy
Registry that accurately captures the nature, sequence and effects of modern cellular therapies, including CAR-T cells. From this vantage point, we have a unique window into the ACT industry, and evidence showing how such a database can be utilized
to advance both academic research and industry R&D.
3:30 Refreshment Break in the Exhibit Hall with Poster Viewing
4:15 Decoding Human Immune System: Real Life Implications for Drug Development
Setareh Shamsili, MD, PhD, CMO, Selvita
The recent convergence of technological advances in biomedical research, computer sciences, artificial intelligence and machine learning, are enabling generation and analysis of unprecedented scales of data. This presentation will focus on advances
in decoding the human immune system and how these data are being used to transform drug development.
4:45 NEW: Relevance of Patient Tumor Heterogeneity Defined by Robust Data Analytics
Patrice M. Milos, PhD, Co-Founder/President and CEO, Medley Genomics, Inc.
Immunotherapies show promising results in some patients; however, it is difficult to predict whether immunotherapy will be effective for a particular patient. This challenge results from the fact that tumors are highly heterogeneous, with a tumor
from a patient containing a mixture of cancerous cells with different complements of mutations. Medley Genomics’ novel data analytics and software platform describe this diverse, heterogeneous mixture of tumor cells and their unique molecular
underpinnings. With these insights, we have the opportunity to improve understanding of immunotherapy response.
5:15 PANEL DISCUSSION: Breaking Down Immuno-Oncology Data Silos
The dynamic data sets from cancer progression, immune response, and patient therapy are each computationally complex. How then can they be integrated to provide actionable IO drug discovery? Panelists discuss promising computational tools from modeling
to artificial intelligence that are shaping and defining the intersection of data and immuno-oncology.
Moderator: Hans Bitter, PhD, Vice President, Data Sciences, bluebird bio
Panelists: Caron Jacobson, MD, Medical Director, Immune Effector Cell Therapy Program, Dana Farber Cancer Institute
Danny Wells, PhD, Lead Bioinformatics Scientist, Parker Institute for Cancer Immunotherapy
Marcelo Pasquini, MD, MS, Senior Scientific Director, CIBMTR Clinical Trials Support; Associate Professor of Medicine, Medical College of Wisconsin
John Quackenbush, PhD, Henry Pickering Walcott Professor of Computational Biology and Bioinformatics; Chair, Department of Biostatistics, Harvard T.H. Chan School of Public Health
5:45 Close of Informatics for Cancer Immunotherapies
5:45 Dinner Short Course Registration
6:30 Dinner Short Course: Development of Bioassays for Checkpoint Immunotherapy and Other Immuno-Oncology Leads*
*Separate registration required.