A novel stop-loss variant in ISG15 causes C-terminal dysfunction and impairs USP18-mediated negative feedback

ISG15 is a type I interferon (IFN-I)-inducible ubiquitin-like protein that restrains IFN-I signaling. Classical ISG15 deficiency is thought to cause disease mainly by disrupting USP18 stabilization, which leads to sustained IFN-I signaling and interferon-driven autoinflammation. Whether patient-derived C-terminal ISG15 variants can impair IFN-I negative feedback through altered C-terminal functional presentation has remained unclear.

We studied a Chinese boy with early-onset recurrent fever, severe ulcerative skin lesions, and elevated liver enzymes. Whole-exome sequencing was performed to identify ISG15 variants. Patient peripheral blood mononuclear cells (PBMCs) and skin tissue were analyzed for IFN-I pathway activation. Functional effects of the identified variants were assessed in 293T cells, and structural analysis was performed. The patient was treated with the JAK inhibitor baricitinib.

Two novel compound heterozygous ISG15 variants were identified: c.234C>A, which produced a truncated ISG15 protein, and c.498A>T, a stop-loss variant predicted to extend the ISG15 C-terminus and associated with markedly impaired ISGylation. Patient PBMCs and skin tissue showed increased p-STAT1 signaling and IFN-I pathway activation, with decreased USP18 expression and altered ISG15-USP18 regulation in PBMCs. In 293T cells, c.498A>T alone did not reduce USP18 abundance, suggesting that this variant contributes to disease through impaired C-terminal functional presentation rather than USP18 loss alone. Structural analysis suggested that the C-terminal extension may alter LRLRGG motif presentation, weakening ISG15-USP18-mediated negative feedback. Baricitinib reduced IFN-I-related markers and was associated with improvement of ulcerative skin lesions and liver enzyme abnormalities.

This study expands the genetic and mechanistic spectrum of ISG15-associated type I interferonopathy, and supports that JAK-STAT inhibition with baricitinib can effectively control IFN-I-driven inflammation.