Now some are adopting a new style: measure everything, ask questions later. This theme is being led by Harvard and MIT’s Broad Institute labs, where researchers are developing a way to generate more information about the inner workings of cells that they can release for years to come. The technique, known as cell painting, impressed scientists at several pharmaceutical companies—so much so that they formed a consortium and pooled resources to use the approach to create a large dataset that they began releasing to the public in November. The JUMP–Cell Imaging Consortium hopes the database will accelerate drug discovery by helping researchers identify promising compounds and better understand what works and what side effects they have. People.
Cell imaging uses up to six fluorescent dyes to illuminate major cell components such as the nucleus and mitochondria. The microscope captures various images of the stain, and the software measures morphological characteristics such as size, shape, intensity, and texture, creating an image-based profile of the sample. “It’s about the simplest imaging test you can manage,” said Anne Carpenter, a computational biologist who developed the method and leads the Broad Institute’s lab with Shantanu Singh. “Our mission was to choose the absolute cheapest light colors.”
Beyond ease of use, the power of cell imaging lies in the large amount of data that comes from a single experiment. The newly released database contains more than 140,000 images of cells responding to a perturbation—a drug treatment or other gene activity that turns gene activity up or down. Using this data set, Carpenter and some of her colleagues discovered a dozen compounds that affect the same structures that affect a key gene involved in fast-growing muscle cancer. Instead of putting hundreds of samples through multiple rounds of wet-lab tests, Broad researchers came up with the drug list years ago by typing the gene’s name into a database.
“It’s a completely different approach that has very small steps and doesn’t cost much,” said TS Karin Eisinger, a biologist at the University of Pennsylvania who studies muscle cancer. Her team worked with Carpenter to validate the compounds in wet-lab testing, and the two scientists are starting a company to further develop the most promising candidates. Others have stepped up a bit: Recursion Pharmaceuticals, a Salt Lake City-based company for which Carpenter is a consultant, has launched five clinical trials to test known candidates using cell imaging.
Following its official release, consortium members are preparing to work with the Washington, D.C.-based Institute of Health and Environmental Sciences to see if they can combine cell imaging results with other data to predict the toxicity of pharmaceuticals and agrochemicals. .
Esther Landhuis is a science and health journalist based in the San Francisco Bay Area.