The High-Throughput Drug Screening Core Facility (HTSCF) helps investigators discover and develop new chemical probes, identify novel genes or gene functions, and study biological processes.
Established in 2003, the facility seeks to facilitate research in chemical biology and functional genomics at Memorial Sloan Kettering. We also offer screening services to investigators at other institutions.
The HTSCF is a fee-for-service facility dedicated to providing the following services:
- Developing and optimizing biochemical and cell-based assays for high-throughput screening (HTS)
- Performing automated chemical and RNAi HTS, acquiring and analyzing screening data, and compiling and reporting the final results
- Resupplying identified hits for confirmatory studies and characterizing their activity in a non-HTS environment.
Chemical screening can be used to rapidly identify biologically active chemical scaffolds from libraries containing more than 400,000 discrete chemicals against a target. We have initiated a number of collaborations for the resupply of compounds and built a set of informatics tools to explore and design analogs or small libraries based on initial HTS hits.
In addition, we provide expertise in medicinal chemistry optimization through selected contract research organizations.
Chemical Screening Libraries
Our chemical library consists of approximately 400,000 chemicals — including synthetic compounds as well as natural products from plants, micro-organisms, fungi, and deep sea algae. The collection of synthetic chemicals was assembled from established vendors with some of the compounds filtered according to the Lipinski rules and additional criteria to eliminate reactive and otherwise undesirable functional groups/moieties.
These providers include Analyticon, BioFocus, ChemBridge, MicroSource, NCI, ChemDiv, Prestwick, SPECS, Sequoia, Tocris, GSK, Magellan, and the Sarawak Biodiversity Center, as well as other internal and external suppliers.
In RNAi screening, gene silencing by RNA interference technology is used to identify genes involved in a specific cellular pathway. We perform arrayed, genome-wide RNAi screening using both siRNA duplex– and shRNA hairpin–based technologies.
We have developed an analysis strategy through a stringent, five-step process called the Bhinder-Djaballah (BDA) analysis method. It involves the introduction of the H score as a measure of combined duplex activities toward hit nomination with a minimum score of 60.
In addition, we address off-target effects (OTEs) by performing a comprehensive analysis to eliminate duplexes from the analysis, or by flagging the activities of such duplexes as potential OTEs based on their seed sequence similarities to miRNAs or 3’UTR sequences.
When applied to random RNAi data, the BDA method filters out inherent noise due to the heterogeneous nature of RNAi screening and cell biology.
RNAi Screening Libraries
Below are the different types of libraries we provide for RNAi screening:
- Custom siRNA libraries including the druggable genome, the kinome, DNA damage response genes, and epigenetic genes
- MSKCC collection of siRNA duplexes, which were synthesized using our custom algorithm. This library covers approximately 7,000 human genes with an average coverage of 3 siRNA duplexes per gene.
- The Ambion (Life Technologies) Silencer Select V4.0 Library, which targets 22,000 human genes with an average coverage of 3 siRNA duplexes per gene. The siRNA duplex is chemically modified to help attenuate off-target effects.
- The Mission shRNA Library (The RNAi Consortium, the TRC1 library), purchased from Sigma-Aldrich, consists of 159,000 shRNA constructs targeting both the human and mouse genomes. This library covers approximately 16,000 genes with an average coverage of 5 shRNA hairpins per gene.
All our RNAi screening libraries are arrayed in 384-well microtiter plates.
Integrated Robotic Platforms
The High-Throughput Drug Screening Core Facility employs state-of-the-art integrated robotic platforms to screen our chemical, siRNA, and shRNA libraries, in combination with custom-built data management databases for storing and querying screening data.
Xanthus Robotic Platform
Xanthus, the first linear robotic platform built in 2003, is a Thermo CRS F3 robotic arm on a five meter linear track. The linear robotic track is surrounded by multiple instruments that can be used individually or as part of the robotic platform.
A GE Healthcare LEADseeker™ Multimodality Imaging System is primarily used to quantify light from radiometric, luminescence, and fluorescence technologies.
Perkin Elmer VICTOR3 V™ multilabel counters are used for fluorescence intensity, fluorescence polarization, time-resolved fluorescence, absorbance, and luminescence technologies.
A GE Healthcare IN Cell Analyzer 1000, in combination with four high humidity Cytomats CO2 incubators at a capacity of 1,389 plates, or two room temperature incubators at a capacity of 392 plates, enable live, high-content assays.
In addition, the platform includes two BioTek Elx405 plate washers, one ABgene 300 plate sealer, one LidPark lidding station with a capacity of up to seven sample plates, and three MultiDrop and two FlexDrop automated liquid dispensers.
Hestia Robotic Platform
Built in 2011, Hestia, our second robotic platform, is a Thermo F5 robotic arm on a four meter linear track specially designed for automated imaging and high content screening. Similarly to Xanthus, the linear track is surrounded by multiple instruments that can be used individually or as part of the robotic platform.
A GE Healthcare IN Cell Analyzer 2000 allows automated whole-well imaging in 384-well format. The GE Healthcare IN Cell Analyzer 3000 allows automated laser-scanning confocal microscopy in 384-well format. Three MultiDrop Combis and three Elx405 plate washers enable automated media swap for fixing or staining.
In addition, the platform includes one Cytomat CO2 incubator with a 504 plate capacity, one room temperature Cytomat hotel with a 189 plate capacity, one ABgene 3000 plate sealer, and one LidPark lidding station.
Project Evaluation and Procedures
All project requests are considered on a case-by-case basis following preliminary evaluation for suitability and amenability to screening. A prioritization committee then reviews the project to assess technical difficulties and determine priorities.
For each incoming project, our staff members will generate a proposal, workflow, and timelines, and an estimate for associated costs. We will work collaboratively with principal investigators and their team members through all stages of the project.
In addition, we provide opportunities for students and postdoctoral research fellows to gain experience and training in HTS.
If you are interested in working with us, please send an inquiry to core facility head Hakim Djaballah for consideration and evaluation of the proposed projects.
To learn more about how we work and collaborate with users outside of Memorial Sloan Kettering, e-mail us at firstname.lastname@example.org for chemical screening or at email@example.com for RNAi screening.