Clonal Hematopoiesis in Vexas Syndrome

Abstract

Background VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome is a recently described systemic inflammatory disease of older men, due to somatic mutations in UBA1 (UBA1mut). VEXAS predisposes to myelodysplastic syndrome (MDS) and plasma cell dyscrasia (PCD). A few studies have reported concomitant somatic mutations in genes associated with myeloid neoplasia but their true prevalence and the clonal landscape is unknown in UBA1mut cases. We hypothesized that clonal hematopoiesis in myeloid-related genes (typical CH) may be linked to heterogenous clinical phenotypes and progression to MDS seen in VEXAS. Methods We performed error-corrected DNA sequencing (ECS) in 80 VEXAS patients and correlated findings with clinical outcomes in 77 patients. Targeted single-cell proteogenomic sequencing (scDNA) was performed on three patients to define clonal architectures. DNA methylation was also investigated in 38 cases. ResultsUBA1mut p.M41T c.122T>C (n=52; 65%) was most frequent followed by p.M41V c.121A>G (n=15;18%), p.M41L c.121A>C (n=10,12%), and three (4%) splice site mutations (c.118-1G>C); one patient had two UBA1mut in independent clones: a p.M41T and c.118-2A>C. Median variant allele frequency (VAF) of UBA1 mut variant was 75%. Forty-eight patients (60%) had one (n=28; 35%) or ≥2 typical CH mutations (n=20; 23%) concomitant with UBA1mut, a frequency much higher than in healthy age-matched controls (>50% in VEXAS patients ³40 years vs. 18% in controls). Mutations in DNMT3A and TET2 were most frequent, DNMT3A mutations at high VAF (median 27%), in contrast to TET2 (median 1.5%; Figure 1). Patients with typical CH were divided into 4 subgroups: with DNMT3A or TET2 mutations alone (D/T, n=19), concomitant DNMT3A and TET2 mutations (D&T; n=7), mutations in other genes regardless of DNMT3A/TET2 mutations (Others; n=20), and no typical CH mutations (n=31). UBA1mut genotype and co-occurring CH mutations did not predict inflammatory or hematologic manifestations (MDS, PCD, thrombosis, cytopenia). An MDS diagnosis was only associated with transfusion-dependent anemia and thrombocytopenia but not with typical CH mutation subgroups, UBA1 VAF or abnormal karyotype. Overall survival was 60% at 10 years. MDS diagnosis did not confer poorer prognosis but transfusion-dependent anemia, thrombocytopenia, and the presence of typical CH mutation at VAF>2% (particularly DNMT3A/TET2) increased the risk of mortality (Figure 2). VEXAS patients had marked epigenetic age acceleration with a median of 11 years (range 7-23), especially in those with DNMT3A or TET2 mutations. By scDNA, >90% of myeloid but not lymphoid cells were UBA1mut. The majority (60-90%) of HSPC in the marrow were also UBA1mut. There was a shift towards increased neutrophils (with typically high CD16/CD62L/CD10 expression), plasmacytoid DC and classical monocytes in PB, compared to a healthy control. In UPN1, a TET2 and DNMT3A mutations preceded UBA1mut in the same clone, resulting in striking clonal expansion after acquisition of UBA1mut; all variants were at VAF >45% by ECS. In UPN2, UBA1mut was a driver of a clone that dominated the clonal landscape; subclones with SF3B1 and TET2 mutations in the same cell remained stable at lower VAF by ECS (<5%). In UPN3, UBA1mut itself resulted in clonal expansion of mutated cells. Conclusions In VEXAS, UBA1mut cells are the primary cause of inflammatory and hematological manifestations, defining a new molecularly defined somatic entity that is associated with MDS. scDNA data demonstrate that UBA1mut clones have competitive proliferative advantage, therefore, the expansion of clones with typical CH mutations is dependent on co-occurrence with UBA1mut. In VEXAS, typical CH mutations may serve as a biomarker of shortened overall survival, without an increased rate of myeloid neoplastic transformation. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal