Antagonistic Ubiquitin Switching by USP7 and RNF40 Orchestrates KDM6A Homeostasis to License Coronavirus Susceptibility

Lysine demethylase 6A (KDM6A) is a critical epigenetic regulator implicated in development, cancer, and viral infection. Although KDM6A enhances coronavirus entry by modulating viral receptor expression, the mechanisms governing its protein stability remain unknown. Here, we show that ubiquitin-specific protease 7 (USP7) promotes diverse coronavirus infection, including SARS-CoV, SARS-CoV-2, MERS-CoV, and MHV, and represents a broad-spectrum anti-coronavirus target. Genetic and pharmacological inhibition of USP7 attenuates the expression of coronavirus receptors ACE2, DPP4, and Ceacam1, thereby impeding viral entry. Mechanistically, USP7 deubiquitinates KDM6A by removing K48-linked polyubiquitin chains to prevent its proteasomal degradation. Conversely, the E3 ubiquitin ligase RNF40 catalyzes K6- and K11-linked ubiquitination of KDM6A, which serves as a signal for recognition by TAX1BP1 for autophagic degradation, to restrict diverse coronavirus infection. Pharmacological inhibition of USP7 with FT671 and XL177A reduces KDM6A stability and viral receptor expression, and confers resistance to MERS-CoV, SARS-CoV, and all major SARS-CoV-2 variants of concern, including those resistant to remdesivir in primary human airway and intestinal epithelial cells. In mice, FT671 treatment was well tolerated, reduced Ceacam1 expression, and protected against MHV-A59 infection. Collectively, our findings unveil an antagonistic ubiquitin-mediated regulatory circuit that controls KDM6A stability, viral receptor levels, and coronavirus infection.