Immunotherapy can cure some cancers that until fairly recently were considered fatal. In addition to developing drugs that boost the immune system's cancer-fighting abilities, scientists are becoming expert at manipulating a patient's own immune cells, turning them into cancer-killing armies. But cancers have tricks to evade attack, so scientists are racing to outmaneuver cancer and boost the effectiveness of immune cell therapies. Today's scientists are skilled immune system engineers, but they're working off of an incomplete blueprint: while they know a great deal about how to reprogram immune cell pathways, they often can't determine precisely which circuits they should rewire in order to fabricate a more potent immune system.

Now, researchers have devised a CRISPR-based system called SLICE, which will allow scientists to rapidly assess the function of each and every gene in "primary" immune cells -- those drawn directly from patients. The new method, described in the journal Cell, provides researchers with a powerful tool that will guide their decision-making when determining how best to engineer immune cells to fight cancer and a host of other diseases.

"SLICE allows us to perform genome-wide screens in which we mutate every gene in the genome to see which genes have the biggest effect on the cellular behavior we're interested in," explained co-senior author of the new study. "We change one gene at a time in each cell and see which change causes the cell to do what we want it to do. SLICE is the discovery engine that will point us towards pathways that we can reprogram to generate the most effective next-generation cell therapies."

As a proof of principle, the researchers tested whether they could use SLICE to identify genes that make T cells -- a common type of immune cell -- replicate more effectively. This is especially important for cancer immunotherapy, which employs artificially stimulated and engineered T cells to kill cancer. So far, these therapies have only been effective against certain malignancies, but scientists believe that identifying genes that promote T cell proliferation can make cancer immunotherapy available to a wider range of patients.

Using SLICE, the researchers were able to identify genes that promote T cell replication, and others that suppress it. Though some of these genes had been previously characterized using other discovery methods, many were entirely new, demonstrating that SLICE could reveal key regulators of proliferation that other methods failed to capture.

After identifying these genes, the researchers obtained primary T cells from multiple human donors and deleted the genes that had been found to inhibit replication. When these CRISPR-modified T cells were cultured in the presence of cancer, they exhibited a markedly improved cancer-killing capacity, demonstrating that scientists could edit genes identified by SLICE and turn ordinary T cells into a potent potential therapy.

But cancer has tricks of its own. Cancer immunotherapy often fails because tumors thrive in so-called microenvironments that are teeming with compounds that suppress immune activity and prevent T cells from realizing their full cancer-killing potential.

"T cells seem to become 'suppressed' in tumor microenvironments," said co-first author of the new study. "We wanted to know if SLICE could help us find a way to help T cells overcome this suppression."

The researchers showed that SLICE can indeed be employed to invigorate suppressed T cells. Utilizing SLICE, the researchers identified genes targeted by adenosine, an immunosuppressor found in tumor microenvironments, and found that deleting these genes allowed T cells to proliferate, even in the presence of adenosine.

https://www.ucsf.edu/news/2018/11/412356/new-slice-tool-can-massively-expand-immune-systems-cancer-fighting-repertoire

http://www.cell.com/cell/fulltext/S0092-8674(18)31333-3