(SC3) Functional Screening Strategies Using CRISPR and RNAi

This course will offer details on how the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas technology works, how to set up CRISPR-based screens and how to complement it with existing RNAi-based screens using proper analysis and follow-up studies. The instructors will share their experiences on how to go about evaluating reagents/libraries, designing and setting up assays, and interpreting results when dealing with complex biology and informatics. The applications of such functional genomics screens for drug discovery and disease modeling will be discussed, along with design and workflows when working with different model systems. Ideas and best practices will be shared in an informal, interactive setting and attendees will walk away with practical advice and resources.

18:30 Speaker Introductions

18:45 Michael Bassik, Ph.D., Assistant Professor, Department of Genetics, Stanford University

• Identification of drug targets and phenotypes for essential genes
• Screen design/common pitfalls
• Optimized protocols for sample prep, sequencing, and analysis

19:15 Roderick Beijersbergen, Ph.D., Group Leader, Netherlands Cancer Institute and Head, NKI Robotics and Screening Center

• Development of screening models for drug enhancers, re-sensitization screens
• Requirements of screening models for successful large scale pooled screening
• Analysis tools for CRISPR screens

19:45 Coffee and Dessert Break

20:05 Kaylene J. Simpson, Ph.D., Associate Professor and Head, Victorian Centre for Functional Genomics ACRF Translational RPPA platform, Peter MacCallum Cancer Centre, Australia

• Assay development requirements for arrayed screening
• Identification of appropriate controls, array plate layouts, weekly screen throughput considerations
• Data handling and analysis pipelines including off-target analysis
• Target validation strategies

20:40 Open Discussion

21:00 End of Course

Speaker Bios

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

Michael Bassik is an Assistant Professor in the Department of Genetics at Stanford University. He performed his Ph.D work in Stanley Korsmeyer’s lab at Harvard, exploring the role of BCL-2 phosphorylation in regulating cell death. As a postdoc in Jonathan Weissman’s lab at UCSF, he developed high-coverage shRNA screening libraries and mammalian genetic interaction maps, applying these to study the biology of retrograde toxins. His laboratory at Stanford focuses on the continued development of shRNA and CRISPR/Cas9 systems for high-throughput screening, and on application of these technologies to study endocytosis, stress, and the identification of novel drug targets.

Kaylene J. Simpson, Ph.D., Associate Professor and Head, Victorian Centre for Functional Genomics ACRF Translational RPPA Platform, Peter MacCallum Cancer Centre, Australia

Kaylene Simpson returned to Australia in late 2008 after a long postdoctoral period with Professor Joan Brugge at Harvard Medical School to establish the Victorian Centre for Functional Genomics (VCFG). The VCFG enables researchers Australia-wide to perform genome and boutique scale siRNA, shRNA, miRNA and long noncoding RNA screens and small compound screens, with an emphasis on quantitative phenotypic high content imaging. Most recently, the lab has established a complementary Reverse Phase Protein Array platform. Kaylene collaboratively engages with all researchers that utilise the facility to ensure they perform the most robust and novel screens possible. She is actively involved in numerous organisations, hosting an annual High Content and RNAi screening meeting in Melbourne, this year expanded to include CRISPR, RPPA and 3D screening technologies and she is the 2017 president of the Society of Biomolecular Imaging and Informatics (SBI2).

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

Roderick Beijersbergen is group leader at the Netherlands Cancer Institute and heads the NKI Robotics and Screening Center. His work evolves around the development and application of large-scale functional genomic technologies with the goal to identify more effective cancer treatments. His group pioneered the pooled shRNA screening technology which has been extended to CRIPSR/CAS9 genome editing based screening including CRISPRi and CRISPRa. These large-scale functional genomic screens have led to the identification of novel targets for cancer therapy, to the understanding of the mechanisms of action of novel drugs and the identification of novel mechanisms of acquired resistance to pathway targeted therapeutics. Based on these results treatment combinations have been identified currently in several clinical trials with promising results.