Implications of TP53 allelic state for genome stability, clinical presentation and outcomes in myelodysplastic syndromes

Abstract

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).

Mutated clones driving leukemic transformation are already detectable at the single cell level in CD34-positive cells in the chronic phase of primary myelofibrosis

“…TP53 loss-of-function is a crucial event in the activation of mechanisms underlying tumor progression 8 . In order to identify CNVs in TP53 gene, we analyzed this region by MLPA in bulk CD34+ cells of T2 and T3, because of the significant expansion of the clones carrying TP53 p.Cys238Ser mutation in these timepoints.…”

“…Since a recent work by Bernard et al demonstrated that TP53 impairment determines CNVs which correlate with poor prognosis in hematological malignancies8 , we deeply analyzed TP53 mutational state and identified a novel deletion at single cell level. Although this variant affects a small cell subpopulation, it could support the genomic instability that characterizes the accelerated phase of the disease.…”

From Clonal Hematopoiesis to Therapy-Related Myeloid Neoplasms: The Silent Way of Cancer Progression

“…Deeper sequencing of CHIP mutations within TP53-mutated samples demonstrated sub-clonal chromosome 5 and 7 copy number variations many years before the diagnosis of t-MN, suggesting that TP53 clones precede the development of cytogenetic abnormalities in t-MN. Moreover, TP53 clones expand over time and drive transformation to t-MN, being the bulk of the malignant clone at diagnosis [61]. This intrinsic advantage may be related to a specific TP53-related immune escape phenotype, as shown by a recent study where TP53 mutant cases showed an imbalance of checkpoint molecules and expansion of highly immunosuppressive regulatory T cells and myeloid-derived suppressor cells [62] (Figure 2).…”

The Genomics of Myelodysplastic Syndromes: Origins of Disease Evolution, Biological Pathways, and Prognostic Implications

“…Remarkably, TP53 mutations have the worst prognosis in MDS, including in patients who underwent HSC transplantation [82] and are linked to an increased risk of leukemic transformation [27]. A recent study from the International Working Group for Prognosis of MDS analyzed a large cohort (n = 3324) of de novo MDS and related myeloid neoplasms [105]. A comprehensive collection of cytogenetic data (G-banding analysis) and sequencing data (genome-wide copy number probes and capture-based NGS) were employed to resolve the clinical implications of TP53 mutations and their allelic status in MDS.…”