Local generation and efficient evaluation of numerous drug combinations in a single sample

We develop a method that allows one to test a large number of drug combinations in a single-cell culture sample. We rely on the randomness of drug uptake in individual cells as a tool to create and encode drug treatment regimens. A single sample containing thousands of cells is treated with a combination of fluorescently barcoded drugs. We create independent transient drug gradients across the cell culture sample to produce heterogeneous local drug combinations. After the incubation period, the ensuing phenotype and corresponding drug barcodes for each cell are recorded. We use these data for statistical prediction of the treatment response to the drugs in a macroscopic population of cells. To further application of this technology, we developed a fluorescent barcoding method that does not require any chemical drug(s) modifications. We also developed segmentation-free image analysis capable of handling large optical fields containing thousands of cells in the sample, even in confluent growth condition. The technology necessary to execute our method is readily available in most biological laboratories, does not require robotic or microfluidic devices, and dramatically reduces resource needs and resulting costs of the traditional high-throughput studies.