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R. Mishra
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P2.04 - Poster Session/ Biology, Pathology, and Molecular Testing (ID 234)
- Event: WCLC 2015
- Type: Poster
- Track: Biology, Pathology, and Molecular Testing
- Presentations: 1
- Moderators:
- Coordinates: 9/08/2015, 09:30 - 17:00, Exhibit Hall (Hall B+C)
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P2.04-046 - Kinome RNAi Screens Identify Essential Genes and Therapeutics In 'Driver Negative' Non-Small Cell Lung Cancer (ID 2970)
09:30 - 09:30 | Author(s): R. Mishra
- Abstract
Background:
Lung adenocarcinoma is a leading cause of cancer-related death worldwide. The discovery of “driver” mutations in genes such as the epidermal growth factor receptor (EGFR) which are required for malignant transformation have revolutionized lung cancer care as chemotherapy directed against these proteins has resulted in dramatic improvements in survival. Approximately 75% of the non-small cell lung cancer (NSCLC) patients harbor a driver gene (KRAS, EGFR, ALK, ROS etc) from the recent molecular characterization of lung adenocarcinomas by The Cancer Genome Atlas. Unfortunately, ~25% of the patients are “driver negative”. Therefore, identifying genes essential for malignant pathogenesis in these “driver negative” NSCLC may serve as new therapeutic targets for these patients.
Methods:
Four “driver negative” NSCLC cell lines – H292, H1703, H228, and H322C – were used in the kinome RNAi essential screen. Cells were transduced with a short-hairpin loop lentiviral kinome library (~3700 shRNAs targeting ~600 kinases) developed by The RNAi Consortium (TRC 1.0/1.5). Cells were cultured and harvested after 2, 7, and 14 days of transduction. ShRNAs from surviving cells were extracted, reverse transcribed and barcoded for individual replicates. These samples were sequenced on the Illumina HiSEQ 2000. BiNGS! software was used for analyzing and interpreting the essential screen. Kinases were considered essential if were present at day 2 but they were lost (i.e. knocked out causing cell death) at both day 7 and day 14. We then queried these essential kinases to K-Map, a bioinformatics platform that systematically connects a kinase profile with a reference kinase inhibitor database and predicts the most effective inhibitor for a queried kinase profile.
Results:
All samples from four cell lines had on average 85% of mapping rates (70% - 92%) with 5 to 24 million mapped reads per sample. In total, twenty kinases were identified as essential kinases for these “driver negative” cell lines. For example, MAPK4 for H292; ERBB3 for H322C; ATR for H228; and KDR for H1703. We queried the K-Map using the twenty essential and potentially transformative kinases to connect them to drugs. One of the top kinase inhibitors connected by K-Map was sunitinib. From published papers, we found that H1703 has been validated to be sensitive to sunitinib, supporting the K-Map prediction of inhibitors on the essential kinases. Further validation will be performed and presented in the conference.
Conclusion:
Functional genetic screens have the potential to identify genes essential for cancer cell survival and proliferation, providing a “functional” map in “driver negative” NSCLC. Using a series of novel bioinformatics analyses, specifically connecting the essential kinases with small molecules based on inhibition activities, we have identified that candidate drugs effectively inhibits the essential kinases in “driver negative” NSCLC cell lines resulting in cell death. Further investigation of these candidate drugs and the functional role of these essential kinases could provide personalized treatment for the “driver negative” lung cancer patients.
