Bi-Specific Synthetic Lethal (SL) DDR shRNA Libraries – Project Summary
Developed under an NCI-supported synthetic lethality RNAi screening and DDR database contract research project.
The primary objective of the 290 SBIR contract project was to develop a human pooled SL shRNA library targeting all annotated DDR genes (approximately 360) and to functionally/experimentally validate it in reference cancer cell models. The supporting tools, including a public SL DDR database, protocols, reagents, and software tools were developed along with a set of SL DDR bi-specific shRNA libraries. The contract goals and outline of the project are presented below:
- Development of technology and commercial reagents for combinatorial RNAi screen of 360 DDR genes
- Validation of combinatorial RNAi reagents in synthetic lethality screen in 3 cancer cell lines
- Development of annotated database of SL DDR gene interactions
Summary of SL DDR Validation Project
As a practical outcome of the HHSN261201200065C contract, we commercialized a comprehensive set of validated, standardized research tools, custom services, and software products for translational cancer research:
1. Bi-specific DDR shRNA libraries.
Under HHSN261201200065C contract support, we have developed an SL DDR RNAi screening platform. It comprises a standardized set of one 185K and two 55K bi-specific pooled lentiviral shRNA libraries targeting approximately 360 DDR genes.
- 185K Bi-Specific SL DDR Pooled Lentiviral shRNA Library
- Two 55K Bi-Specific SL DDR Pooled Lentiviral shRNA Sublibraries
- Development and Construction
- Gene List (TBA)
2. DDR Relational Database.
The 360 DDR Relational Database with the annotated gene information, reference SL gene interactions revealed in RNAi combinatorial screens, and predicted signaling pathway models are no longer available. The DDR database included the following types of open-access information: (i) DNA damage linked to environmental mutagenic and cytotoxic agents, (ii) pathways comprising individual processes and enzymatic reactions involved in the removal of damage, (iii) proteins participating in DNA repair, (iv) diseases correlated with mutations in genes encoding DNA repair proteins and a summary of experimentally and computationally predicted SL DDR interactions. Supporting interaction maps of the networks were previously made accessible through our data portal/accessible with Cytoscape. The data deposited in the SL DDR database is no longer available.
Custom bi-specific shRNA libraries designed for any rationally selected set of genes (e.g. cancer drug targets) can be generated by Cellecta. In addition, to provide researchers with easy access to the DECIPHER RNAi screening technology, Cellecta currently offers custom RNAi screening services in cancer cell models using premade (DECIPHER) or custom shRNA libraries targeting any specific set of genes.
We believe that the Bi-specific SL DDR shRNA libraries with supporting software tools for data analysis will stimulate significant interest and allow the scientific community to apply this novel, powerful technology to the discovery of new drug targets and development of anti-cancer therapies. This resource will facilitate the access to knowledge about human DDR signaling, correlation of human diseases with mutation in genes responsible for DNA integrity/stability, as well as information about the toxic and mutagenic agents causing DNA damage.
Furthermore, these integrative experimental and software tools will provide a platform for the expansion of our on-going, fee-based screening service by enabling us to provide therapeutic target discovery groups with RNAi screens focused on any specific set of pre-selected drug targets.
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