Tumor protein p53 (TP53) is the most frequently mutated gene in cancer 1,2. In patients with myelodysplastic syndromes (MDS), TP53 mutations are associated with high-risk disease 3,4 , rapid transformation to acute myeloid leukemia (AML) 5 , resistance to conventional therapies 6-8 and dismal outcomes 9. Consistent with the tumor-suppressive role of TP53, patients harbor both mono-and biallelic mutations 10. However, the biological and clinical implications of TP53 allelic state have not been fully investigated in MDS or any other cancer type. We analyzed 3,324 patients with MDS for TP53 mutations and allelic imbalances and delineated two subsets of patients with distinct phenotypes and outcomes. One-third of TP53-mutated patients had monoallelic mutations whereas two-thirds had multiple hits (multi-hit) consistent with biallelic targeting. Established associations with complex karyotype, few co-occurring mutations, high-risk presentation and poor outcomes were specific to multi-hit patients only. TP53 multi-hit state predicted risk of death and leukemic transformation independently of the Revised International Prognostic Scoring System (IPSS-R) 11. Surprisingly, monoallelic patients did not differ from TP53 wild-type patients in outcomes and response to therapy. This study shows that consideration of TP53 allelic state is critical for diagnostic and prognostic precision in MDS as well as in future correlative studies of treatment response. In collaboration with the International Working Group for Prognosis in MDS (Supplementary Table 1), we assembled a cohort of 3,324 peridiagnostic and treatment-naive patients with MDS or closely related myeloid neoplasms (Extended Data Fig. 1 and Supplementary Fig. 1). Genetic profiling included conventional G-banding analyses (CBA) and tumor-only, capture-based, next-generation sequencing (NGS) of a panel of genes recurrently mutated in MDS, as well as genome-wide copy number probes. Allele-specific copy number profiles were generated from NGS data using the CNACS algorithm 7 (see Methods and Code availability). An additional 1,120 samples derived from the Japanese MDS consortium (Extended Data Fig. 2) were used as a validation cohort. To study the effect of TP53 allelic state on genome stability, clinical presentation, outcome and response to therapy, we performed a detailed characterization of alterations at the TP53 locus. First, we assessed genome-wide allelic imbalances in the cohort of 3,324 patients, to include arm-level or focal (~3 Mb) ploidy alterations and regions of copy-neutral loss of heterozygosity (cnLOH) (Extended Data Fig. 3, Supplementary Figs. 2-4 and Methods).

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Somatic mutations at methionine 41 (Met41) in UBA1, encoding the major E1 enzyme responsible for initiating ubiquitylation, were recently identified as the cause of a novel autoinflammatory disease, named VEXAS (Vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic). We sought to determine the prevalence of UBA1 mutations in a UK cohort of patients matching the VEXAS clinical phenotype. We identified 10 new patients with somatic mutations in UBA1, but only 8 had altered p.Met41. A novel variant, c.167C>T; p.Ser56Phe was identified, which was present in myeloid, and not lymphoid lineages and led to preferential loss of the catalytic activity of cytoplasmic UBA1. An additional novel variant, c.118-1G>C was identified at the splice acceptor site of exon 3 leading to altered splicing in vitro. Bone marrow biopsies from two patients with a Met41 substitution and the novel splice site variant were consistent with previously reported features of VEXAS. The bone marrow of the patient with the p.Ser56Phe variant was less similar, likely driven by a distinct but overlapping disease mechanism. Our study therefore confirms somatic p.Met41 substitutions in UBA1 as a major cause of VEXAS syndrome and identifies two new disease causing mutations.

and has received compensation from these companies in the form of stock; A.R.K. is a research collaborator of Ionis Pharmaceuticals and has received royalty income from Ionis through his employer, Cold Spring Harbor Laboratory. O.A.-W. has served as a consultant for H3 Biomedicine, Foundation Medicine Inc., Merck, and Janssen; O.A.-W. has received personal speaking fees from Daiichi Sankyo. O.A.-W. has received prior research funding from H3 Biomedicine unrelated to the current manuscript. D.I., R.K.B. and O.A.-W. are inventors on a provisional patent application (patent number FHCC.P0044US.P) applied for by Fred Hutchinson Cancer Research Center on the role of reactivating BRD9 expression in cancer by modulating aberrant BRD9 splicing in SF3B1 mutant cells.

Key Points The mutational profile of patients with preclinical MDS is distinct from that reported in healthy individuals. In the absence of morphologic disease, mutational analysis can predict those patients at high risk of disease progression.