Gene editing, particularly using the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 system, is now being extensively used as a research and functional screening tool in drug discovery. Cambridge Healthtech Institute’s second annual conference on Translational Gene Editing will bring together experts from all aspects of preclinical research, from early target discovery to drug delivery, to talk about the progress being made in gene editing and how it’s being applied. Learn about ways in which CRISPR/Cas9 is being used to identify targets, create relevant cell lines and in vivo disease models, set up functional screens, and for targeted drug delivery. What can you do to overcome some of the inherent challenges with design, delivery and off-target effects associated with CRISPR/Cas9? Hear from experts in pharma/biotech, academic and government labs who will share their experiences leveraging the utility of gene editing for diverse applications, particularly in oncology and immunotherapy.

Final Agenda

Thursday, June 16

11:00 am Registration.

12:00 pm Bridging Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

12:30 Session Break

1:00 Coffee and Dessert in the Exhibit Hall with Poster Viewing

1:45 PLENARY KEYNOTE SESSION

3:30 Refreshment Break in the Exhibit Hall with Poster Viewing

IMPROVING CRISPR FOR BETTER FUNCTIONAL SCREENING

4:15 Chairperson’s Opening Remarks

John Doench, Ph.D., Associate Director, Genetic Perturbation Platform, Broad Institute of Harvard and MIT

4:25 Optimized sgRNA Libraries for Genetic Screens with CRISPR-Cas9

John Doench, Ph.D., Associate Director, Genetic Perturbation Platform, Broad Institute of Harvard and MIT

CRISPR technology has proven to be a powerful means of determining gene function. Large-scale datasets coupled with machine learning approaches have enabled the optimization sgRNA on-target activity and prediction of off-target effects. Together, these advances have allowed the creation of more specific and effective genome-wide libraries for genetic screens.

4:55 Optimizing CRISPR for Pooled Genome-Wide Functional Genetic Screens

Paul Diehl, Ph.D., Director, Business Development, Cellecta, Inc.

While CRISPR/Cas9 knockout provides a convenient tool for genome-wide loss-of-function pooled screens, these screens require effective and efficient targeted gene interruption to generate robust results. We have leveraged our experience with pooled RNAi libraries to assess and optimize CRISPR guide RNA designs to increase knockout efficiency, analyze off target effects, and standardize controls to provide baseline metrics for quality CRISPR genetic screens.

5:10 A CRISPer Guide for Generating Superior sgRNA Libraries

Carsten Carstens, Ph.D., Research & Development, Sr. Scientist, Molecular Biology, Genomics, Agilent Technologies

Using a technologically advanced, array-based DNA synthesis platform, Agilent is one of the few companies that can generate high fidelity, low-bias, low-skew gRNA libraries to enable genome-wide gene KO screening or CAS-mediated transcriptional activation or repression. Example applications, catalog library formats and custom design options will be discussed.

5:25 CRISPR-Cas9 Whole Genome Screening: Going Where No Screen Has Gone Before

Ralph Garippa, Ph.D., Director, RNAi Core Facility, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center

For certain molecular targets, to unravel the underlying biology via loss-of-function studies, it is simply not enough to potently knock down the protein. In some cases, a complete functional knockout is called for. Here we summarize our early experiences with the Gecko v2, highlighting the strengths of this new powerful system but also calling attention to technical areas which need to be addressed and further improved as the technology moves deeper into the mainstream.

5:55 Cross-Species Synthetic Lethal Screens and Applications to Drug Discovery

Norbert Perrimon, Ph.D., Professor, Department of Genetics, Harvard Medical School and Investigator, Howard Hughes Medical Institute

We have developed a cross-species screening platform taking advantage of the robust RNAi screening methodologies available in Drosophila cell culture followed by filtering of the hits in mammalian systems. Such hits are likely to be reproducible between mammalian systems and more importantly between human patients. I will describe screens to identify synthetic lethal hits with the tumor suppressors TSC and NF1.

6:25 Close of Day

6:30 Dinner Short Course Registration.

7:00 - 9:30 Dinner Short Courses

Friday, June 17

7:15 am Registration.

GENE EDITING FOR SCREENING DISEASE PATHWAYS AND DRUG TARGETS

8:35 Chairperson’s Remarks

Ralph Garippa, Ph.D., Director, RNAi & Gene Editing Core Facility, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center

8:45 Scouring the Non-Coding Genome by Saturating Edits

Daniel E. Bauer, M.D., Ph.D., Assistant Professor of Pediatrics, Harvard Medical School and Staff Physician in Pediatric Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Principal Faculty, Harvard Stem Cell Institute

Predicting the functional consequences of noncoding genetic variation is a major challenge to understand mechanisms of disease. Genome editing can prospectively perturb noncoding sequences to determine their biological importance. I describe a generalizable approach to uncover noncoding genome function. We apply custom CRISPR saturating guide RNA libraries to advance from a GWAS signal to novel mechanistic understanding of disease to a direct therapeutic strategy for clinical genome editing.

9:15 Parallel shRNA and CRISPR/Cas9 Screens Reveal Biology of Stress Pathways and Identify Novel Drug Targets

Michael Bassik, Ph.D., Assistant Professor, Department of Genetics, Stanford University

We are developing new high-complexity shRNA and CRISPR/Cas9-based libraries to interrogate key cellular pathways involved in endocytic trafficking, stress, cancer, and neurodegeneration. In addition, we have created a strategy to perform systematic pairwise genetic interaction maps to find functionally related gene groups and synergistic pairs. These tools allow us to elucidate basic cellular wiring mechanisms, and to identify novel drug targets and combinations.

9:45 Optimizing & Empowering the Revolution in Gene Editing & Regulation

Speaker to be Announced

Studying complex biological processes such as cancer development, stem cell differentiation, and drug interaction requires the ability to efficiently modulate multiple genes and subsequently isolate or enrich precisely modified cells. We will present novel technologies that facilitate complex genome engineering projects with direct relevance to pre-clinical research.

10:15 Coffee Break in the Exhibit Hall. Last Chance for Poster Viewing.

BUILDING THE CRISPR TOOLBOX

11:00 Beyond Cas9: Discovering Single Effector CRISPR Tools

Jonathan Gootenberg, Member, Laboratories of Dr. Aviv Regev and Dr. Feng Zhang, Department of Systems Biology, Harvard Medical School, and Broad Institute of Harvard and MIT

The RNA-guided endonuclease Cas9 has quickly gained prominence as a versatile genome editing tool, but is still limited by PAM inflexibility and inefficient insertion. I will discuss new research in discovering, characterizing, and utilizing new single effector CRISPR systems, including biochemical and in vivo characterization of Cpf1, a novel endonuclease, and computational approaches for mining new CRISPR enzymes from the existing wealth of bacterial genomes.

11:30 CRISPR-Cas9 Genome Editing Improves Subcellular Localization Studies

Netanya Y. Spencer, M.D., Ph.D., Research Fellow in Medicine, Joslin Diabetes Center, Harvard Medical School

Current approaches to identify subcellular localization signals in proteins are excellent for studies of monomeric proteins, but for multimeric proteins, these methods are unable to rule out artifacts from native protein subunits already present in the cells. Using CRISPR-Cas9 mediated genome engineering, we have developed a new gold standard approach for studies of subcellular localization signals in multimeric proteins.

12:00 pm TECHNOLOGY PANEL: Trends in CRISPR Technologies

Moderator:

Ralph Garippa, Ph.D., Director, RNAi & Gene Editing Core Facility, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center

Panelists:

Paul Diehl, Ph.D., Director, Business Development, Cellecta, Inc.

Carsten Carstens, Ph.D., Research & Development, Sr. Scientist, Molecular Biology, Genomics, Agilent Technologies

This panel will bring together 2-3 technical experts from leading technology and service companies to discuss trends and improvements in CRISPR libraries, reagents and platforms that users can expect to see in the near future. (Opportunities Available for Sponsoring Panelists)

12:30 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

1:00 Session Break

APPLICATIONS OF CRISPR FOR DRUG DISCOVERY

1:30 Chairperson’s Remarks

Myung Shin, Ph.D., Senior Principal Scientist, Genetics and Pharmacogenomics, Merck & Co. Inc.

1:35 SLENDR: High Throughput Mapping of Protein Localization in Mammalian Brain by In Vivo Genome Editing

Ryohei Yasuda, Ph.D., Scientific Director, Max Planck Florida Institute for Neuroscience

We developed a simple and generalizable technique to image endogenous proteins with high specificity, resolution and contrast in mammalian brain tissue. The technique, termed SLENDR, uses in vivo genome editing to insert a tage sequence to a gene of interest by CRISPR-Cas9-mediated homology-directed repair. SLENDR allows rapid determination of the localization and dynamics of many endogenous proteins in various cell types, regions and ages in the brain.

2:05 Application of Genome Editing Tools to Model Human Genetics Findings in Drug Discovery

Myung Shin, Ph.D., Senior Principal Scientist, Genetics and Pharmacogenomics, Merck & Co. Inc.

Human genetic findings have provided great hope that novel therapeutics will be developed with above average chances of clinical success for biotechnology and pharma. In this talk, we will discuss how recent advances in genome editing tools have greatly expanded our ability to model these human genetics for drug discovery programs.

2:35 In vivo Application of the CRISPR/Cas9 Technology for Translational Research

Danilo Maddalo, Ph.D., Lab Head, ONC Pharmacology, Novartis Institutes for BioMedical Research

Genome-wide analysis studies and advancements in genome editing technology have expanded the possibility of identifying and modeling genetic lesions recurrent in cancer development. In this talk we will discuss the strategies to generate preclinical models of cancer by in vivo delivery of the CRISPR/Cas9 system to induce genetic perturbations in somatic cells. Such models represent an important platform for drug discovery, and translational medicine studies.

3:05 Refreshment Break

DEVELOPING TOOLS FOR BETTER TRANSLATION

3:20 Improving CRISPR-Cas9 Precision through Tethered DNA-Binding Domains

Scot A. Wolfe, Ph.D., Associate Professor, Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School

Type II CRISPR/Cas9 systems have the potential to revolutionize gene therapy applications. However, the standard CRISPR-Cas9 system is sub-optimal for many clinical-level genome editing applications due to insufficient precision. We have developed a CRISPR-Cas9 platform fused to a programmable DNA-binding domain that increases the design density of Cas9 target sites and provides dramatically improved on- vs off-target selectivity. This novel platform can generate site-specific nucleases with single-site precision for targeted-genome editing.

3:50 Nucleic Acid Delivery Systems for RNA Therapy and Gene Editing

Daniel G. Anderson, Ph.D., Professor, Department of Chemical Engineering, Institute for Medical Engineering & Science, Harvard-MIT Division of Health Sciences & Technology and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology

High throughput, combinatorial approaches have revolutionized small molecule drug discovery. We describe our high throughput methods for developing and characterizing RNA delivery and gene editing systems. Libraries of degradable polymers and lipid-like materials have been synthesized, formulated and screened for their ability to deliver RNA, both in vitro and in vivo, and show potential therapeutic application for the treatment of genetic disease, viral infection, and cancer.

4:20 Envisioning a Gene Editing Approach to Treat Inherited Blindness

Alexandra Glucksmann, Ph.D., COO, Editas Medicine

Recent successes in clinical trials highlight the potential to treat genetic retinal disorders using viral gene delivery. While subretinal injection of adeno-associated viruses (AAVs) encoding transgenes has been shown to be safe and efficacious, there are many inherited retinal dystrophies that are not amenable to gene augmentation approaches. Gene editing may be capable of addressing inherited forms of blindness resulting from mutations in genes that exceed the packaging size limit of AAV. In addition, mutations in genes that are toxic when overexpressed or must be regulated by their endogenous control elements, as well as autosomal dominant mutations where removal of the dominant allele is required to produce a wild-type phenotype, may also be well-suited to gene editing approaches. The CEP290 gene, mutations in which account for ~20% of Leber Congenital Amaurosis, far exceeds the packaging limit of AAV and has been suggested to be toxic when overexpressed in retinal cells. The most common mutation in CEP290 is an intronic point mutation that creates an aberrant splice site, resulting in a premature stop codon. We have developed a gene editing approach, using the CRISPR/Cas9 system, to delete this disease-causing, intronic mutation. Using a dual-guide RNA approach, we demonstrate that targeted deletions result in increased expression of wild-type CEP290 transcripts and decreased expression of mutant transcripts, as well as increased expression of wild-type CEP290 protein. We have also established improvements and modifications to the CRISPR/Cas9 technology that may allow for alternative targeting strategies which may be used to develop CRISPR-based gene editing approaches for a broad range of currently untreatable, inherited forms of blindness.

4:50 Close of Conference