Impaired cytotoxic function and exhausted phenotype of natural killer cells in VEXAS syndrome

Abstract

VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome is an autoinflammatory disorder caused by acquired somatic ubiquitin like modifier activating enzyme 1 (UBA1) mutations in hematopoietic stem cells, affecting peripheral myeloid and natural killer (NK) cells. Given the high rate of severe infections in patients with VEXAS, we hypothesized that NK-cell dysfunction contributes to this susceptibility. We conducted a comprehensive immune characterization of peripheral NK cells in patients with VEXAS (n = 40), patients with autoinflammatory diseases without UBA1 mutations (n = 22), and older sex-matched healthy controls (n = 16). Multiparameter phenotyping used cytometry by time-of-flight, single-cell RNA sequencing (scRNA-seq), whole-blood stimulation assays, and in vitro NK-cell cytotoxic assay. Peripheral NK cells in VEXAS were quantitatively and qualitatively impaired. Mass cytometry revealed reduced frequencies of mature cytotoxic CD56dim NK cells and expansion of the CD56high CD16dim subset. NK cells exhibited exhaustion features, including increased programmed cell death protein 1 expression, and reduced cytotoxic markers such as NKp46 and CD8α. scRNA-seq analysis showed decreased signatures of cytotoxicity and interleukin-2 (IL-2) and interferon gamma (IFN-γ) production, alongside increased inflammatory signatures. Whole-blood stimulation assays confirmed impaired IL-2, IFN-γ, and granzyme B production following Toll-like receptor 3 (TLR3), TLR4, and TLR7/TLR8 agonist stimulation. Extended NK phenotyping by flow cytometry confirmed reduced activating receptors' expression and impaired IFN-γ production in VEXAS syndrome. Moreover, in vitro UBA1 inhibitors impaired NK-cell cytotoxic capacity and promote cell death. Finally, reduced NK-cell frequencies were independently associated with an increased risk of severe infections. These findings suggest that NK-cell dysfunction in VEXAS syndrome contributes to increased susceptibility to severe infections.