Benjamin Izar is trying to work out what happens when immune cells encounter cancer cells. He starts with large molecular profiling studies, such as whole-exome sequencing and RNA-seq. “They give dozens of putative targets or mechanisms that may play a role in disease or drug response, but it is impossible to functionally validate each of them individually,” he laments.
To help, Izar, a physician-scientist at Columbia University’s Herbert Irving Comprehensive Cancer Center in New York, turned to CRISPR screens. CRISPR allows researchers to precisely alter cells’ DNA sequences, and modify gene function. With high-throughput screens, the effects of thousands of perturbations can be assessed in a single experiment. These tools aid research and drug discovery efforts by helping scientists identify the genetic variations, in both coding and non-coding regions, that contribute to disease.
However, until now, typical read-outs of CRISPR screens under different conditions, such as drug treatment or viral infection, have been quite simple cell growth and survival assays. These read-outs reveal genes that, when disturbed, either sensitize or confer a selective advantage to the challenged cells — but with no indication of how they do so. Newly developed techniques provide single-cell, multi-omic readouts of CRISPR-modified cells. “Any large-scale profiling or screening effort may benefit from such methods as they help drill down to what might be functionally relevant,” says Izar. With these ‘high-content’ CRISPR screens, researchers can start to evaluate the myriad nominated mechanisms and targets.