Using a CRISPR screen, scientists at the Salk Institute have discovered a genetic “dial” to turn immune function up and down. The scientists suggest that the dial, which affects the development and function of regulatory T cells (Tregs), could be turned one way to fight autoimmune disease, and the other way to fight cancer.

Underactive Tregs are associated with autoimmune diseases where the immune system attacks the body, including rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease, and lupus. Some cancers, on the other hand, have higher-than-usual Treg activity, preventing the immune system from attacking a tumor and allowing its growth.

The Salk Institute scientists used a genome-wide CRISPR loss-of-function screen to identify Foxp3 regulators in mouse primary Tregs. The Foxp3 gene, the scientists knew, is a key player in the development and function of Tregs. If Tregs are like the lead peacekeepers, Foxp3 is like the United Nations, encouraging the peacekeeping force to organize. Without Foxp3, the body doesn’t form Tregs.

A group of scientists led by Ye Zheng, PhD, an associate professor in Salk’s NOMIS Center for Immunobiology and Microbial Pathogenesis, set out to find other genes that impacted levels of Foxp3. These scientists used CRISPR gene-editing technology to test which genes throughout the genome affected Foxp3. This screen turned up hundreds of genes, including a handful that encoded different subunits of the SWI/SNF complex, a group of proteins that plays a role in turning many other genes on and off by physically making DNA accessible to cellular machinery.

“Our ultimate goal,” said Zheng, “is to be able to use these genes that modulate regulatory T cells to interfere with autoimmune diseases and cancers.”

At Salk, another group of scientists, this one led by assistant professor Diana Hargreaves, PhD, was already studying a number of genes in the SWI/SNF complex, including a new variant that the lab identified in 2018 called the non-canonical BAF (ncBAF) complex. When this became clear, the Zheng group and the Hargreaves group joined forces to uncover the role of the complex in regulatory T cells.

Expanding on the work accomplished with the CRISPR screen, which was used to selectively remove the SWI/SNF complex genes from Tregs, the scientists found that the deletion of one gene in the ncBAF complex, called Brd9, had a particularly strong effect on the immune cells. Tregs without Brd9 had lower levels of Foxp3 and weakened function.

The scientists also studied another member of the SWI/SNF family of nucleosome remodeling complexes. This complex, called polybromo-associated BAF, or PBAF, appears to play a regulatory role opposed to that played by ncBAF. Deletion of one gene in the PBAF complex, Pbrm1, enhances Treg suppressor activity.

Additional details appeared July 7 in the journal Immunity, in an article titled, “A Genome-wide CRISPR Screen Reveals a Role for the Non-Canonical Nucleosome-Remodeling BAF Complex in Foxp3 Expression and Regulatory T Cell Function.”

“Foxp3 regulators were enriched in genes encoding subunits of the SWI/SNF nucleosome-remodeling and SAGA chromatin-modifying complexes,” the article’s authors wrote. “Among the three SWI/SNF-related complexes, the Brd9-containing ncBAF complex promoted Foxp3 expression, whereas the PBAF complex was repressive. Chemical-induced degradation of Brd9 led to reduced Foxp3 expression and reduced Treg cell function in vitro. Brd9 ablation compromised Treg cell function in inflammatory disease and tumor immunity in vivo.”

In mice with cancer, treatment with the weakened immune cells without Brd9 enabled other immune cells—the fighters and soldiers of the immune system—normally blocked by the regulatory T cells to infiltrate the tumors and shrink them. In mice with inflammatory bowel disease, however, the weakened Tregs left the immune system attacking the digestive tract unchecked. These results suggest that controlling the strength of Tregs has potential for treating both cancer and autoimmune diseases.

Using a genome-wide CRISPR screen, scientists at Salk found that Foxp3, a “peacekeeping” gene in immune cells, has its expression regulated by Brd9, a subunit of the ncBAF complex. Testing the in vivo relevance of this finding, the scientists disrupted Brd9 in regulatory T cells in mouse models of inflammatory bowel disease (IBD) and cancer. Brd9 deficiency exacerbates IBD and enhances antitumor immunity. The IBD finding is illustrated here. The histology image shows that weakening of regulatory T cell function induces infiltration of immune cells (small blue dots) into colon epithelium (blue layer) and causes colitis. [Salk Institute]
“The idea of manipulating this cell type for therapeutic purposes is very exciting,” said Hargreaves, who, like Zheng, is a co-corresponding author of the new paper. “Until now, it’s been very hard to fine-tune regulatory T cell activity in the body,” added Eric Chin-San Loo, a graduate student and co-first author of the new paper. “This complex allows us to do just that—turn up or down the activity of the immune cells, but not enough to cause other forms of disease.”

The Salk Institute researchers indicated that they’d like to dive deeper into the molecular mechanisms by which Brd9 is controlling Foxp3 expression and how the ncBAF complex might change the tumor environment in other ways.

Hargreaves added that future studies could look at whether small molecules can control the activity of the ncBAF complex; these would be more relevant for human therapeutics than genetic methods of altering the proteins. Such molecules might one day be able to turn down the activity of regulatory T cells to treat cancer, or turn up their activity to treat autoimmune disease.

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