Characterization of clonal dynamics in VEXAS via integrated ECS bulk sequencing and single-cell proteogenomic analysis. (A) Patterns of clonal trajectories. In VEXAS, increased cell fitness is primarily driven by UBA1 loss-of-function. Considering that UBA1 gene is located on chromosome X and all patients are male, cooccurrence with heterozygous typical CH mutations follow 2 major patterns that can be inferred by their VAF at PB: (1) pattern 1 is seen when typical CH precedes UBA1^mut in a cell. Upon emergence of an UBA1 mutation, cells carrying both typical CH and UBA1 expand rapidly. Typical CH and UBA1 likely coexist in the same cell when their VAF follow a linear ratio of 1:2, or higher (Pattern 1). In contrast, pattern 2 is observed when UBA1^mut precedes the acquisition of typical CH in the same cell or independently coexist with typical CH clones. In this case, the VAF of typical CH mutations and UBA1^mut, which is commonly the dominant clone, follow no linear correlation at PB. (B) Clonal patterns of DNMT3A, TET2, and other typical CH mutations estimated based on their VAFs in the PB. Most DNMT3A mutations follow pattern 1, including the ones in the p.R882 hot spot. In contrast, TET2 and other typical CH mutations follow pattern 2.