Mutual Exclusion Analysis Shows that DUSP9 Negatively Regulates PD‐L1 Expression and Acts as a Target to Enhance Anti‐PD‐1 Efficacy

Abstract The expression level of PD‐L1 is one of the most widely used predictive markers of immune checkpoint blockade (ICB) efficacy in the clinic, suggesting the importance of regulating PD‐L1 expression. However, no published reports have addressed the systematic exploration of the regulation of immune checkpoint molecules from the perspective of mutual exclusion (ME) in gene expression. The ME analysis, based on gene plasticity, provides a novel perspective on the intergenic regulatory paradigm. Here, multiple negative regulators of PD‐L1 expression are identified, and dual‐specificity phosphatase 9 (DUSP9) is selected for intensive study. DUSP9 negatively regulates PD‐L1 expression in multiple tumor cells, and mechanistically, DUSP9 dephosphorylates STAT3 to mediate the inhibitory role. In syngeneic tumor models, the combination of DUSP9 targeting and PD‐1 antibody can enhance therapeutic sensitivity. The clinical data demonstrated that elevated DUSP9 expression is correlated with diminished PD‐1/PD‐L1 antibody response rates. Consequently, DUSP9 emerges as a promising target for enhancing treatment response in combination with PD‐1 antibody, and functions as a potential marker for predicting the efficacy of tumor immunotherapy. This research demonstrates an efficient method for identifying negative regulators of highly plastic genes (HPGs), which can predict immunotherapy responses and identify new targets for combination therapy with ICB.