Find Funding
Contract Topics
290 siRNA Resource for Synthetic Lethal Screening of DNA Repair and Damage Signaling Networks
Number of anticipated awards: 2
(Fast-Track proposals will be accepted.)
Budget (total costs): Phase I: $200,000;
Phase II: $1,000,000
(Note: It is strongly suggested that Proposals adhere to the above budget amounts. Proposals with budgets exceeding the above amounts may not be funded. Phase I project periods may last a maximum of 9 months.)
The deadline for receipt of all contract proposals submitted in response to this solicitation is: November 9, 2009.
Summary:
Human cancers appear to be highly and differentially vulnerable to targeted attack on individual gene expression within their DNA repair networks, especially those pathways that are closely associated with DNA replication. However such lethal combinations (i.e., synthetic lethals) are generally not obvious or easily predicted a priori. What is needed to establish the generality of synthetic lethality for DNA- repair- related genes in human cancers is a systematic screen of the major DNA repair and DNA damage pathways, ablating gene pairs (or larger combinations).
Cancer researchers use a variety of methods to detect these lethal combinations including pair-wise siRNA knockdown protocols, or a genotoxic insult (e.g., cist-Platinum, ionizing radiation) plus siRNA knockdown of individual genes, or other approaches that would yield the same information (e.g. binning combinations of genes followed by secondary screens of subsets of DNA-repair-related genes). Currently they must develop these siRNA resources themselves or piece them together from existing collections, often in different vectors with differing quality control methods.
To expedite the capability to detect synthetic lethal combinations in human, cancer biologists and clinical researchers need high quality, validated reagent sets targeting DNA-repair genes with minimal off-target effects and antibody reagents for detecting and typing DNA-repair and DNA-signaling defects within primary samples from individual patients. In this project an extensive set of such siRNA constructs would be validated in at least two different human cancer cell lines plus a normal reference (non-cancerous) control, representing different organ sites and demonstrate synthetic lethality in at least one of the tested reference cell lines.
Project Goals:
- Demonstrate siRNA knock down 400 chosen human DNA damage and damage signaling (DDR) genes with minimal off-target effects.
- Establish which pairs (or combinations) confer synthetic lethality in one or more of the reference the cell lines, 3 siRNA targets per gene, using an unbiased screening approach.
- Development of an extensible computer searching capability/database for potentially lethal siRNA combinations of human DDR genes using accepted eukaryotic ontologies conserved within the human DDR response network.
- 40 genes knocked down, genes may be from homologous recombination pathways, replication signaling complex, end joining, and/or mismatch repair networks (established genes from the literature). At least two different pathways or networks must be targeted.
- Show at least two examples of known synthetic lethal combination using the above-mentioned constructs in the synthetic lethal screen to be employed in phase II.
- Prototype database/data collection: genes mentioned above fully annotated as to their siRNA targets, pathways, and other available functional annotation as well as information on synthetic lethal partners.
Phase II activities and expected deliverables:
- 400 genes knocked down and annotated as in phase I.
- Extension of synthetic lethal screens, pair wise, or higher combinations of DDR genes, to an array of human established human cancer cell lines representing major malignancies (e.g., breast, prostate, pancreatic, brain, leukemias); targets should be tested in at least two different cell lines.
- Validation of synthetic lethal relationships in two reference human cancers that are known to demonstrate synthetic lethality, plus effects that may be lethal or non-lethal and that are produced in reference control (non-malignant) human cell lines.
