rnai screening 2009 - Seventh Annual RNAi: For Screening Cellular Pathways and Targets - Discovery On Target

MONDAY, NOVEMBER 2
7:00 am Registration and Morning Coffee
EXPLORING GENOME-WIDE RNAI SCREENS

8:30 Chairperson’s Opening Remarks
Norbert Perrimon, Ph.D., Professor, Department of Genetics, Harvard Medical School
8:40 Efficient Vectors for in vivo RNAi and Construction of a Drosophila Genome-wide Transgenic RNAi Collection
Norbert Perrimon, Ph.D., Professor, Department of Genetics, Harvard Medical School
Conditional expression of hairpin constructs in Drosophila is a powerful method to disrupt the activity of single genes with a spatial and temporal resolution that is impossible, or exceedingly difficult, using classical genetic methods. We have developed new RNAi vector systems that allow efficient RNAi in all tissues including the germ line. I will describe these various vectors and their applications at building a Drosophila genome wide transgenic RNAi collection for in vivo studies.???????????????

9:10 Genome-wide siRNA Gain-of-Function Screen for Modulators of the miRNA Pathway
Hakim Djaballah, Ph.D., Director, HTS Core Facility, Memorial Sloan Kettering Cancer Center
The group has developed and validated a high content gain-of-function cell-based assay to screen for modulators of the miRNA pathway. The validated assay was used to screen a genome-wide siRNA library. Several parameters were utilized to score obtained hits and to assess for potential off-target effects. I will present and discuss our findings.???????????????

9:40 Genome-scale RNAi-based Screening to Identify Flavivirus Host Factors in Insects and Humans
James L. Pearson, Ph.D., Manager, RNAi Screening Facility, Center for RNA Biology, Duke University Medical Center
The arthropod borne flaviviruses, Dengue and Yellow Fever, pose a significant health threat to almost half of the world’s population. Our studies focus on the identification of factors required for flavivirus propagation in both insect and human hosts by genome-scale siRNA screening using drosophila and human libraries.???????????????

10:10 Grand Opening Coffee Break in the Exhibit Hall
10:40 Title to be Announced
Stephen Elledge, Ph.D., Department of Genetics, Center for Genetics and Genomics, Harvard Medical School
Oncogenic mutations in the small GTPase Ras are highly prevalent in cancer, but an understanding of the vulnerabilities of these cancers is lacking. We undertook a genome-wide RNAi screen to identify synthetic lethal interactions with the KRAS oncogene. We discovered a diverse set of proteins whose depletion selectively impaired the viability of Ras mutant cells. Among these we observed a strong enrichment for genes with mitotic functions.

11:10 Genome-wide shRNA Search for Effector Function of mTOR Addicted Growth
Christoph Moroni, M.D., Professor, Department of Biochemistry, University of Basel
A genome wide search using shRNA expressing lentiviruses has been conducted aimed at identifying genes mediating mTORC1 and mTORC2 dependent growth. 0-5% of genes had a high score, with a predominance of genes in energy metabolism, growth control and apoptosis. We present an original strategy to identify functions mediating mTOR addicted growth based on cellular mutants defective in Pten or TSC2 tumor suppressor genes. The search revealed an interesting list of potential drug targets and their evaluation is in progress.???????????????

11:40 Title to be Announced
Michael Green, M.D., Ph.D., Professor, Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School
We have been performing genome-wide loss-of-function screens using pools of shRNAs to address a variety of questions relevant to the initiation and progression of cancer. The results of these screens have led to the identification of novel genes that either promote or antagonize cancer development. Our experiments have also revealed new regulatory pathways that contribute to malignant transformation and are potential therapeutic targets. In addition, some components of these pathways may have a role as cancer therapeutics.

Sponsored by
12:10 pm Genome-scale RNAi Screens Identify Loss of Function Phenotypes
James Goldmeyer, Ph.D., Field Application Scientist, Thermo Fisher Scientific
Negative selection screens to interrogate networks and pathways of genetic interactions have proven difficult to carry out. By combining lentiviral shRNAmir libraries with barcode microarray technology, it is now possible to screen thousands of genes and identify not only those that enrich for a phenotype, but more importantly, genes that cause anti-proliferation or cell death. Such a tool is vital in understanding the mechanisms of action for drugs, genetic events that lead to cell transformation and identifying elements involved in gene pathways & networks. This talk will focus on the new Thermo Scientific Open Biosystems’ Decode RNAi platform for genome-scale multiplex RNAi screening. This methodology has been successfully used to identify cancer cell specific vulnerabilities in response to suppression of specific genes or biological pathways.


Sponsored by
12:40 Luncheon Presentation
Next Generation siRNAs?Do They Really Improve RNAi Screening Results?
Susan Magdaleno, Ph.D., Sr. Manager, Scientists, Life Technologies, Applied Biosystems
First generation siRNA technologies can yield confusing results due to incomplete knockdown and off-target effects. Novel siRNA technologies address these issues, but how well do they work? We investigated the impact of siRNA sequence and chemical modifications on siRNA potency, specificity, and RISC compatibility. Using an SVM approach, a novel hyperpotent siRNA designer was generated. We also screened >100 siRNA modification patterns and identified a unique configuration that efficiently eliminated off-target effects measured by microarray and HCS. We show that these improvements translate to improved RNAi screening results.





FOCUSED RNAI SCREENS FOR IDENTIFYING TARGETS

2:20 Chairperson’s Remarks
Alex Gaither Ph.D., Research Investigator II, Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research
2:25 Using Targeted siRNA Screens to Identify Novel Regulators of Viral Replication
Alex Gaither, Ph.D., Biomedical Research Investigator II, Novartis Institutes for Biomedical Research
We performed a focused siRNA screen in an A549 dengue type 2 New Guinea C subgenomic replicon cell line (Rluc-replicon) that contains a Renilla luciferase cassette. We found that siRNA mediated knock down of mevalonate diphospho decarboxylase (MVD) inhibited viral replication of the Rluc-replicon and DEN-2 NGC live virus replication in A549 cells. When the Rluc-replicon A459 cells were grown in delipidated media the replicon expression was suppressed and MVD knock down could further sensitize Renilla expression. Our data suggest genetic and pharmacological modulation of cholesterol biosynthesis can regulate dengue virus replication.

2:55 Combining Parallel Chemical and RNAi Screens in Physiologically Relevant Cell Models to Identity Drug Targets
John N. Feder, Ph.D., Associate Director, Genome Biology, Applied Genomics, Bristol Myers Squibb Co.
3:25 Strengthening Oncology Pipeline Using RNAi Technology: From Target Discovery to Therapy
Yu Shen, Ph.D., Senior Group Leader, siRNA Therapeutics, Abbott Laboratories
RNAi is widely used to study gene functions in cell and animals. It also holds promise as a novel therapeutic modality to tackle unmet medical needs. Over the last 8 year, we have been applying the RNAi technology to facilitate drug discovery in the oncology area via carrying out large-scale siRNA library screen for target identification, developing RNAi-based strategy for cancer target validation, and more recently, developing siRNA-based cancer therapeutics. In this presentation, we will update on the progress and lessons learned in these areas.

3:55 Networking Refreshment Break in the Exhibit Hall
4:30 From RNAi Screens to Molecular Function: A Systematic Pipeline for Gene Function in Mammalian Cells
Frank Buchholz, Ph.D., Group Leader, Max Planck Institute for Molecular Cell Biology and Genetics
RNAi screens typically deliver a large number of candidate genes that play a role in a biological process. We have developed a pipeline using BAC recombineering technology and tissue culture transgenesis to streamline the analysis of hits identified in large scale RNAi screens. Examples from this pipeline will be presented.???????????????

5:00 Identification of Synthetic Lethal Targets of Oncogenic KRAS Using Systematic RNA Interference
David Barbie, M.D., Assistant in Medicine, Massachusetts General Hospital and Dana-Farber Cancer Institute
An alternative strategy for targeting KRAS-driven cancers is to identify secondary genetic dependencies created by the oncogenic allele. Through meta-analysis of RNA interference screens, we identified synthetic lethality between oncogenic KRAS and TBK1. These observations identify a KRAS-specific therapeutic target and a systematic method to identify genetic co-dependencies in cancer.???????????????


5:30 Genome-Wide Screening with a Pooled shRNA Library for the
Surface Receptor of Murine IgG3
Andre Nicola, MD, Research Associate, Department of Microbiology and Immunology, Albert Einstein College of Medicine