Clonal Hematopoiesis in Vexas Syndrome

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 (UBA1^mut). 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 UBA1^mut 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.

Results

UBA1^mut 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 UBA1^mut 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 UBA1^mut, 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). UBA1^mut 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 UBA1^mut. The majority (60-90%) of HSPC in the marrow were also UBA1^mut. 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 UBA1^mut in the same clone, resulting in striking clonal expansion after acquisition of UBA1^mut; all variants were at VAF >45% by ECS. In UPN2, UBA1^mut 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, UBA1^mut itself resulted in clonal expansion of mutated cells.

Conclusions

In VEXAS, UBA1^mut 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 UBA1^mut clones have competitive proliferative advantage, therefore, the expansion of clones with typical CH mutations is dependent on co-occurrence with UBA1^mut. In VEXAS, typical CH mutations may serve as a biomarker of shortened overall survival, without an increased rate of myeloid neoplastic transformation.