With rapid advancements in gene editing tools like Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and single-cell analysis, genomics can prove to be a game-changer in driving decisions in drug discovery. Gene expression profiling, sequencing and editing can be used for identifying disease-associated genes and pathways, for functional screening and target identification, studying complex cell populations and for translating data for clinical applications. Cambridge Healthtech Institute’s conference on Next-Gen Genomics: Leveraging CRISPR & Single-Cells will bring together leading experts to talk about how to best apply CRISPR and other genomic technologies, how to utilize the data from single-cell analysis and how to exploit the power of machine learning and network analysis to make the right decisions in drug discovery.

Final Agenda

Wednesday, June 20

11:00 am Registration Open (America Foyer)

11:45 Enjoy Lunch on Your Own

12:20 pm Dessert and Coffee Break in the Exhibit Hall with Poster Viewing (America Ballroom)

Essex South

2:30 Refreshment Break in the Exhibit Hall with Poster Viewing (America Ballroom)


3:10 Chairperson’s Opening Remarks

Roderick L. Beijersbergen, PhD, Group Leader, Division of Molecular Carcinogenesis and Head, NKI Robotics and Screening Center, The Netherlands Cancer Institute

3:15 CRISPR Gene Editing for Drug Discovery

John_FederJohn Feder, PhD, Associate Director of Genome Biology and Emerging Technologies, Department of Genetically Defined Diseases and Genomics, Bristol-Myers Squibb

New CRISPR systems, modalities and methods are being discovered and published at an unprecedented pace such that unbiased and agnostic comparisons and protocol optimizations are warranted if the promise of genome engineering is to be realized in the pharmaceutical setting. We will present our results to date for generating an optimized method for performing homology directed repair gene editing in induced pluripotent stem cells.


3:45 Genomic Approaches for Functionally Dissecting a STAT-dependent Super-enhancer 

Warren J. Leonard, MD, NIH Distinguished Investigator, Chief, Laboratory of Molecular Immunology and Director, Immunology Center, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health

Super-enhancers regulate genes critical for cell-type specification, but studies of their function and regulation in vivo remain limited. We have studied the actions of IL-2 and IL-21, cytokines that activate transcription factors STAT5 and STAT3, respectively, and their binding to super-enhancers in a cytokine-specific manner. We focused on the immunologically critical Il2ra gene. By combining genomic approaches, including ChIA-PET and CRISPR/Cas9, we have identified IL-2-induced chromatin looping at the Il2ra locus and discovered that multiple super-enhancer elements cooperate to control gene expression. Our findings provide a detailed functional analysis of the Il2ra super-enhancer, with broader lessons for cytokine-dependent super-enhancer function as well.

4:15 Synthetic sgRNA Enables Efficient, Consistent CRISPR Editing of Cells for Automation and Therapeutic Applications

Ania_WronskiAnia Wronski, PhD, Product Manager, Engineered Cells, Product Management, Synthego

Achieving consistent and high editing efficiencies with CRISPR is critical for automation and therapeutic applications with primary cells, and remains a significant challenge. Through a collaborative effort, we demonstrate that use of synthetic sgRNA for CRISPR yields improved and consistent editing efficiencies that are required for such applications.

4:45 CRISPR-UMI: Single Cell Lineage Tracing of Pooled CRISPR/Cas9 Screens

Ulrich_EllingUlrich Elling, PhD, Principle Investigator, Institute of Molecular Biotechnology Austria (IMBA)

Pooled CRISPR screens are a powerful tool to assess gene function. We developed CRISPR-UMI (Unique Molecular Identifiers), a single cell lineage tracing methodology for pooled screening to account for cell heterogeneity. The added value of CRISPR-UMI both in positive and negative selection paradigms will be presented. CRISPR-UMI controls for inherent noise in genetic screens, increases reproducibility, and measures incident rates of phenotypes.

5:15 Large Scale Pooled CRISPR Screening: Reversing Resistance

Roderick_BeijerbergenRoderick L. Beijersbergen, PhD, Group Leader, Division of Molecular Carcinogenesis and Head, NKI Robotics and Screening Center, The Netherlands Cancer Institute

A major challenge is the recurrence of cancers resistant to treatment thereby limiting long-term success in the clinic. We have applied genome scale CRISPR/Cas9 screens to identify genes that upon inactivation, re-sensitize cancer cells to standard cancer treatments. Identification of such genes allows for the development of novel drug combinations. The results of this work and the clinical implications will be discussed.

5:45 Close of Day and Dinner Short Course Registration*

*Separate registration required.

Thursday, June 21

7:30 am Registration Open (America Foyer) and Morning Coffee (Foyer)


8:00 Chairperson’s Remarks

John Doench, PhD, Associate Director, Genetic Perturbation Platform, Broad Institute of Harvard and MIT

8:05 Decoding T Cell Circuitry

Alexander_MarsonAlexander Marson, MD, PhD, Assistant Professor, Department of Microbiology and Immunology and Divisions of Infectious Diseases and Rheumatology, Department of Medicine; and Diabetes Center, University of California, San Francisco

Our research goal is to identify genetic circuits that control human immune cell functions and understand how sequence variation in the genome can contribute to immune-mediated diseases. To study and treat the biological effects of genetic disease variants in human immune cells, my lab has developed new CRISPR technologies. We can now advance from correlative studies of genome mapping to mechanistic studies of genome perturbations in primary cells. We can readily re-write specific sequences in T cells and interrogate the causal biological effects to understand disease.


8:35 Cell Engineering by CRISPR and the Impact of Single Cell Analysis in Drug Discovery

 Maryam_ClausenMaryam Clausen, PhD, Senior Research Scientist, Translational Genomics, Discovery Sciences, Innovative Medicines and Early Development Biotech Unit (iMed), AstraZeneca

9:05Combining Barcode Libraries with Targeted Gene Expression for Single-Cell Genetic Analysis

Alex_ChenchikAlex Chenchik, PhD, President, CSO, Cellecta, Inc.

Labeling of target cells with lentiviral barcode libraries offers an effective approach for monitoring cell phenotype in time course experiments using single-cell molecular analysis. While barcoding cells provides an effective way to group cells based on clonal origin in heterogeneous cell populations, comprehensive single-cell expression profiling of large numbers of cells remains challenging. The DriverMap assay combined with CellTracker lentiviral barcoded libraries can significantly improve phenotyping of distinct cell populations..

9:35 Find Your Table and Meet Your Moderator

9:40 Interactive Breakout Discussion Groups

This session features various discussion groups that are led by a moderator/s who ensures focused conversations around the key issues listed. Attendees choose to join a specific group and the small, informal setting facilitates sharing of ideas and active networking.

CRISPR/Cas9 for Drug Discovery Applications

Roderick Beijersbergen, Ph.D., Group Leader, Netherlands Cancer Institute and Head, NKI Robotics and Screening Center

Stephanie Mohr, PhD, Lecturer, Genetics & Director, Drosophila RNAi Screening Center at Harvard Medical School

  • Impact of CRISPR/Cas9 for drug discovery in pharma and academia
  • Applications for functional screens, creating cell lines and disease models
  • Design and optimization of low- and high-throughput screens using CRISPR approaches
  • Application of CRISPR-knockout, -activation and -inhibition
  • Impact of new CRISPR technologies and reagents

Exploiting CRISPR, RNAi and Single-Cell Analysis: What You Need to Know Before and After

Sarah Boswell, PhD, Director of Sequencing Technologies, Laboratory of Systems Pharmacology and Director, Single-Cell Sequencing Core, Harvard Medical School

Jennifer Smith, Ph.D., Deputy Director, ICCB-Longwood Screening Facility, Harvard Medical School

  • Understanding inherent limitations and need for using complementary techniques
  • Examples of how multiple techniques have been put to good use for addressing biological questions
  • Evaluating and testing the reagents and tools
  • Insights on inherent challenges and ways to overcome it
  • Tackling data analysis

10:20 Coffee Break in the Exhibit Hall with Poster Viewing (America Ballroom)

11:05 Combinatorial Genetic Screens with CRISPR-Cas9

John_DoenchJohn Doench, PhD, Associate Director, Genetic Perturbation Platform, Broad Institute of Harvard and MIT

CRISPR-Cas9 has enabled a new generation of genetic screens to interrogate gene function. Single gene knockout approaches, however, encounter limitations in exploring redundant genes and complex gene networks. Here I will discuss our ‘Big Papi’ approach, using orthogonal CRISPR-derived components to achieve efficient combinatorial screening, avoiding interference and maximizing gene targeting activity.

11:35 TECHNOLOGY PANEL: What to Use & When: Finding the Right Tool for the Right Application

Scientists from pharma and academia come together with service providers to discuss current choices as well as gaps in know-how and technology for matching technology with the biological question that needs to be addressed. They will discuss current challenges, share best practices and their experiences using some of the new tools available for gene editing, expression profiling and sequencing such as, CRISPR and single cells.

Moderator: John Doench, PhD, Associate Director, Genetic Perturbation Platform, Broad Institute of Harvard and MIT


Kevin Holden, PhD, Head, Synthetic Biology, Synthego

Alex Chenchik, PhD, President, CSO, Cellecta Inc.

12:35 Networking Luncheon in the Exhibit Hall with Poster Viewing (America Ballroom)


1:55 Chairperson’s Remarks

Gus Frangou, PhD, Assistant Professor of Oncology, Department of Cancer Genetics, Roswell Park Cancer Institute; Senior Fellow, Harvard T.H. Chan School of Public Health

2:00 Genome-Wide CRISPR Screens and Single-Cell Analysis Identify New Genes and Pathways Driving Breast Cancer Development and Progression

Gus Frangou, PhD, Assistant Professor of Oncology, Department of Cancer Genetics, Roswell Park Cancer Institute; Senior Fellow, Harvard T.H. Chan School of Public Health

Identifying genetic drivers of metastatic breast cancer and the timing during which these lesions occur is critical to developing effective therapeutics. Using novel modifications of CRISPR/Cas9 we have developed high-efficiency in vivo phenotypic screens and inducible gene targeting, to interrogate the functions of cancer-driver mutations. These CRISPR/Cas9-based genetic screens provide a systematic phenotypic measurement of loss-of-function lesions in disease progression and provide novel insights into the molecular underpinnings of metastasis.

2:30 Single-Cell RNA Sequencing and CRISPR/Cas9-Mediated Gene Deletion Reveals an Altered Gene Expression Pattern in Human Lung Epithelial Cells

Dazhong Xu, PhD, Assistant Professor of Pathology, Vice Chair of Research, Department of Pathology, New York Medical College School of Medicine

We used single-cell RNA-Seq to compare gene expression profiles between BEAS-2B lung epithelial cells chronically treated with Cr(VI), with or without CRISPR/Cas9-mediated deletion of ERRFI1. We identified 83 significantly differentially expressed genes with cellular functions such as cell adhesion, oxidative stresses, and protein ubiquitination. Upregulation of some neuro-specific genes was also evident in ERRFI1-deleted cells, particularly UCHL-1, a deubiquitinase and potential marker for lung cancer.

3:00 Challenges Within the Shadows of CRISPR

Geoffrey Bartholomeusz, PhD, Associate Professor and Director, Target Identification and Validation Program, Department of Experimental Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center

The benefits of CRISPR-based editing are far reaching. There are however, accompanying challenges that can slow down progress of CRISPR-based studies. It is therefore necessary to be aware of these underlying challenges both in study design and data interpretation. CRISPR-based challenges experienced by my group will be discussed.

3:30 Using CRISPR/Cas9-Based Approaches to Analyze Cell Division and Cell Biological Phenotypes

Kuan-Chun_SuKuan-Chun Su, PhD, Post-doctoral Fellow, Laboratory of Iain Cheeseman, Department of Biology, MIT and Whitehead Institute

CRISPR/Cas9 has enabled rapid knock out of genes to allow study of their function. We are developing these approaches to conduct microscopy-based visual analyses of phenotypes from gene disruption for diverse cell biological processes. Our work has generated robust strategies to rapidly and efficiently screen to identify novel factors in human cells with roles in core cell biological processes, with a focus on cell division.

4:00 Close of Conference

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