Transcription Factors Form Continuous ‘Circuit’ That Regulates T-cell Exhaustion

Scientists have discovered how two transcription factors form a reciprocal regulatory circuit that controls T-cell exhaustion and migration during viral infection, which may inform future therapeutic strategies for managing infections and cancer, according to a recent Northwestern Medicine study published in Immunity.   

CD8+ T-cells are specialized white blood cells that are critical for destroying infected and cancerous cells. During viral infection, however, these cells can become exhausted and unable to effectively detect and control chronic pathogens.  

When exhausted, CD8+ T-cells differentiate into either cytotoxic effector-like T-cells that can migrate, or terminally exhausted T-cells that reside in tissue parenchyma. While commonly considered a negative event, this differentiation allows the T-cells to downregulate their killing abilities and prevent further damage to the tissue and other healthy cells. 

“This can be very important for their functional adaptation. They change their way of dealing with the virus and, at same time, they don’t want to cause trouble when they’re inside of vital organs so they downregulate their effector programs,” said Weiguo Cui, PhD, professor of Pathology in the Division of Experimental Pathology and a member of the Robert H. Lurie Comprehensive Cancer Center and the Center for Human Immunobiology of Northwestern University, who was senior author of the study.  

In the current study, investigators aimed to better understand how cellular localization influences the fate of exhausted T-cells. Using a combination of computation biology and single-cell multi-omics techniques, the scientists investigated CD8+ T-cells from mouse models of chronic viral infection.  

From this approach, the scientists found that the transcription factor Krüppel-like factor 2 (KLF2) promotes the expression and chromatin accessibility of T-cell migratory genes while Krüppel-like factor 3 (KLF3) limits these migratory programs by repressing KLF2 transcription and competing for shared genomic binding sites.  

KLF3 expression depends on KLF2, and together they create a reciprocal regulatory circuit that promotes T-cell exhaustion, according to Cui.  

“It’s almost like they’re counterbalancing each other,” Cui said. “You need KLF2 to turn on KLF3 and then KLF3 comes back to counteract KLF2 expression.”  

The findings suggest that the KLF2-KLF3 transcriptional circuit controls CD8+ T-cell cellular localization and differentiation during chronic viral infection. 

“We’re now starting to understand the complex transcriptional circuitry that is not as simple as we used to think,” Cui said. “Our work implies there are some important tissue-derived factors that will actively regulate T-cell differentiation and make sure their functions are being attenuated so that when they’re in the tissue. They appear functionally exhausted, but this state may accurately reflect adaptation to the local environmental constrains.”  

As for next steps, Cui said determining how long this circuit window lasts could inform therapeutic strategies that can target CD8+ T-cell exhaustion and manipulate their function, which may be beneficial in treating cancer.  

“We don’t know exactly how long this window of plasticity lasts. If we change the way the cell behaves by breaking this feed-forward loop at defined nodes, how might that reshape T-cell behavior in a way that preserves or improves their function? More broadly, could this enable us to redirect these cells toward an alternative T-cell fate?” Cui said.  

Jian Shen, a student in the Driskill Graduate Program in Life Sciences (DGP), was lead author of the study.  

Co-authors include Ryan Brown, Ashley Brown and Siying Lin, students in the Medical Scientist Training Program (MSTP); DGP students Yuqi Zhang, Arjun Kharel, Ashley Bauer and Gregory Cohen; Stephen Jameson, PhD, professor of Laboratory Medicine and Pathology at the University of Minnesota Medical School; and Nikhil Joshi, PhD, associate professor of Immunobiology at the Yale School of Medicine.  

This work was supported by National Institute of Health (NIH) grants R01AI148403, R21AI180877, and R56AI176611; the National Institute of General Medical Sciences training grant T32GM080202; National Cancer Institute training grant T32CA009560; and NIH training grant T32AI155387.