We currently have an unprecedented ability to profile the genetic- and pathway-level changes that occur in cancer. Yet, clinicians lack the diverse arsenal of drugs needed to treat subpopulations of patients more effectively, reduce side effects and offer second-line treatment when drug resistance emerges. There is a pressing need to dramatically increase the repertoire of drugs available to fight cancer. Advances in automated microscopy and computer vision, allow the widespread use of phenotypic profiling in early drug discovery. In this grant, we address two challenges. First, the power of phenotypic profiling has led to a growing number of large, disparate image datasets.
In aim 1, we will develop machine-learning approaches that combine disparate datasets to obtain accurate predictions of uncharacterized compound function. Second, phenotypic screens can identify candidate compounds across multiple, diverse pathways, but often only use a single cancer cell line.
In aim 2, we will develop strategies to identify minimal collections of cell lines that maximize detection of small molecule activities. Successful execution will: increase the power of phenotypic profiling by harnessing existing phenotypic screening datasets and providing a rational approach for selecting cell lines that maximize the chance of discovering hits in desired pathways.

Public Health Relevance

In this proposal, we will develop computational and experimental methods to maximize the power of high-throughput, microscopy-based phenotypic screens. Our studies will increase the power of phenotypic profiling by harnessing screens performed across the world, providing a rational approach for maximizing the chance of discovering hits for diverse pathways in future screens, and identifying novel compounds that expand our ability to perturb cancer-relevant pathways. Our proposal is designed to accelerate the pace of early drug discovery.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Project (R01)
Project #
2R01CA184984-06A1
Application #
9885647
Study Section
Drug Discovery and Molecular Pharmacology Study Section (DMP)
Program Officer
Forry, Suzanne L
Project Start
2014-08-01
Project End
2025-03-31
Budget Start
2020-04-01
Budget End
2021-03-31
Support Year
6
Fiscal Year
2020
Total Cost
Indirect Cost
Name
University of California San Francisco
Department
Pharmacology
Type
Schools of Pharmacy
DUNS #
094878337
City
San Francisco
State
CA
Country
United States
Zip Code
94118
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