CRISPR news: Cancer immunotherapy gets a boost from a knockout that reversed T cell exhaustion

The takeaway: T cell exhaustion occurs when immune cells lose the ability to kill other cells, like cancer. Now, researchers have found that a CRISPR knockout can reverse T cell exhaustion and perhaps offer a solution to cancer immune evasion. 

In chronic infections—and especially in cancer—nonstop antigen stimulation during difficult conditions can create what is called “T cell exhaustion.” Exhausted T cells are bad news for the body—they show increased inhibitory markers and progressive loss of function. Perhaps most importantly, exhausted T cells can’t proliferate and are unable to clear tumors. 

T cell exhaustion has been well documented in the literature, but until recently, figuring out how to keep those cells peppy and high functioning has been a mystery. Thanks to CRISPR, that may be changing. 

What is T cell exhaustion and why is it important? 

Scientists first identified T cell exhaustion more than two decades ago. In T cell exhaustion, T cells, under prolonged stress, lose their ability to fight against virus and tumors. It was hoped that T cell exhaustion could be reversed relatively simple, perhaps when the T cells are taking a break from fighting a particular virus or tumor. 

A paper by researchers from the University of Pennsylvania in 2021 went deeper into the problem of T cell exhaustion and what can be done about it—and why finding a solution was not as easy as had been hoped for at first. 

“Our findings suggest that once T cells become exhausted, they remain fundamentally ‘wired’ to be exhausted—thus it may be hard to get them to become effective virus- and cancer-fighters again,” said study senior author E. John Wherry, PhD, chair of the department of Systems Pharmacology and Translational Therapeutics and director of the Penn Institute of Immunology in the Perelman School of Medicine at the University of Pennsylvania, in a press release. 

Wherry was one of the early investigators of T cell exhaustion. He and others had hoped that they could reinvigorate T cells in individuals with cancer by blocking some of the activity-inhibiting receptors found on the spend T cells. 

Gene editing and exhausted T cells: Enabling genome-wide CRISPR-Cas9 investigation

Now, there may be a new tack that researchers can take to reinvigorate exhausted T cells—CRISPR. 

Writing in the journal Cancer Cell, Stanford University School of Medicine researcher Ansuman Satpathy, MD, PhD, spelled out new home for cancer immunotherapy efforts: using CRISPR to reverse T cell exhaustion. 

In their work, researchers identified chromatin remodeling factor Arid1A as a key regulator of T cell dysfunction. They then showed that CRISPR could be used to knock out Arid1A, which reversed the exhausted state of T cells. Sapathy and colleagues created a model that recapitulated T cells in an exhausted state. Then they ran those cells through genome-wide CRISPR-Cas9 experiments. They then sought to improve T cell persistence using a series of smaller screens to find the target that could reverse the exhausted state. Working in mice, they used a single-cell RNA sequencing platform that permitted the analysis of large CRISPR experiments in order to explore transcriptional profiles in cells after the genetic perturbation. 

Eventually, Arid1A was identified as a target. Using CRISPR-Cas9 to knock out Arid1A improved T cell activity in several ways, including enhanced persistence, better expression of inhibitory receptors, and improved anti-tumor responses. 

“Arid1A depletion limited the acquisition of exhaustion-associated chromatin accessibility,” the authors wrote, “and led to improved antitumor immunity.” 

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