TP53 mutation in therapy-related myeloid neoplasm defines a distinct molecular subtype

TO THE EDITOR:

Recent World Health Organization (WHO)¹ classifications (5^th edition), International Consensus Classification (ICC),² and the European LeukemiaNet (ELN) guidelines³ included new categories for TP53-mutated (TP53^mut) myeloid neoplasms (MNs) to acknowledge their uniformly poor outcomes and stimulate clinical research. However, there are critical differences in the details between these classifications, especially regarding single-hit TP53^mut status, and their significance relating to therapy-related myeloid neoplasm (t-MN), a rare but often fatal malignancy diagnosed following exposure to cytotoxic therapies, remains unclear. Here, we report an international cohort consisting of t-MN with full characterization of TP53^mut allele status and provide compelling evidence of poor outcome of TP53^mut t-MN irrespective of the allelic status of TP53.

The WHO defines a single category of myelodysplastic syndrome (MDS) with biallelic TP53 inactivation (MDS-biTP53) irrespective of the blast percentage¹ but excludes single-hit TP53^mut MDS with bone marrow (BM) blasts <20%. Likewise, in the ICC, single-hit TP53^mut MDS with blasts <10% is excluded from the definition of TP53^mut MN.² Similarly, the recent International Prognostic Scoring System-Molecular acknowledged the poor outcome of multi-hit TP53^mut but excluded single-hit TP53^mut.⁴ The ICC and ELN guidelines emphasize TP53^mut variant allele frequency (VAF) >10% regardless of single- or multi-hit status for MDS/acute myeloid leukemia (AML) and AML.^2,3 These critical differences in the classification of the TP53^mut MN reveal a lack of consensus among experts that is likely driven by limited evidence or conflicting results.^1-3 For example, in a large cohort consisting predominantly (93%) of de novo MDS, single-hit TP53^mut had outcomes similar to wild-type TP53 (TP53^wt), whereas the association with complex karyotype (CK), high risk of AML transformation, and poor overall survival (OS) were limited to multi-hit TP53^mut.⁵ In contrast, in another study the OS of TP53^mut AML and MDS with excess blasts were equally poor irrespective of single- or multi-hit TP53^mut.⁶ Notably, MDS <10% blasts were not included in this study. Similarly, survival of MDS and AML with CK was equally poor irrespective of single- or multi-hit TP53^mut status, and the distinction between MDS and AML by blast percentage did not hold any predictive value.⁷ Thus, the majority of the studies driving changes in classification are derived predominantly from de novo MDS and AML with only a small fraction of t-MN^5,7 or were restricted to MDS and AML with CK.⁷ Overall, this highlights a lack of data in the clinical context of t-MN to resolve the complex interactions between TP53^mut single- versus multi-hit status, blast percentage, and VAF.

To address these gaps, we performed a comprehensive analysis of an international cohort of 377 t-MN patients that included 245 t-MDS (65%) and 132 t-AML (35%) (supplemental Methods, available at the Blood website). The median age at t-MN diagnosis was 67 years. Somatic mutation analysis identified 185 putative oncogenic mutations in TP53 at VAF ≥2% in 132 (35%) patients (supplemental Figure 1 and Figure 1A). The majority of the TP53^mut patients with available information (n = 128; 96.9%) had a VAF >10% (n = 113; 88.2%), and only 15 (11.7%) had VAF ≤10% (supplemental Figure 1). Allelic imbalances overlapping the TP53 locus were detected in 56 (14.8%) patients, including TP53^mut VAF >10% (n = 46) and <10% (n = 2) and without TP53^mut (n = 8, supplemental Figure 1). In summary, 123 t-MN patients had TP53^mut VAF >10% or LOH or cnLOH involving the TP53 locus (supplemental Figure 1). Genomic instability including CK, monosomal karyotype, chromosome 5 aberrancies, and marker chromosomes were enriched in TP53^mut VAF >10% and/or LOH of TP53 locus compared with TP53^wt t-MN (supplemental Table 1). Median OS was significantly shorter in the TP53^mut cases compared with in TP53^wt cases (8.3 vs 19.4 months; P < .001) (Figure 1B). The OS in TP53^mut t-MN with VAF ≤10% was similar to TP53^wt (Figure 1B), although the number of cases with TP53^mut VAF ≤10% were limited and requires further validation.

Among patients with TP53^mut VAF >10% (n = 113), 75% had single TP53^mut plus loss of TP53 locus or cnLOH (n = 39; 34.5%) or ≥2 TP53^mut (n = 45; 39.8%), whereas 25% (n = 29) had single TP53^mut (Figure 1C). Of the 29 patients with single TP53^mut, 18 (62%) and 11 (37.9%) patients had VAF >50% and 10% to 50%, respectively (supplemental Figure 1). Additionally, 10 patients had loss of the TP53 locus without evidence of TP53^mut (n = 8) or TP53^mut VAF ≤10% (n = 2) (Figure 1D and supplemental Figure 1). Loss or cnLOH of TP53 locus was more prevalent in cases with single TP53^mut compared with ≥2 TP53^mut (57.4% vs 15.5%, P < .0001) (Figure 1D).

Integrating data from next generation sequencing, copy number, cytogenetic banding, fluorescence in situ hybridization, and single nucleotide polymorphism microarray analyses, TP53^mut were classified as multi- or single-hit following ICC² (supplemental Methods). In total, 21 (17.1%) of the 123 patients with TP53^mut and/or loss of TP53 locus were considered single-hit and 102 (82.9%) were considered multi-hit (supplemental Figure 1). The clinical parameters and OS of t-MN with single-hit TP53^mut and 17p loss across the TP53 locus were comparable (8.3 vs 6.3 months, P = .58) (supplemental Figure 2A and supplemental Table 2) and were combined for subsequent analyses.

We next compared the clinical features, profiles of genome stability, and patterns of co-mutation for each TP53 state. In contrast to the findings for predominantly de novo MDS,⁵ no difference in the frequency of structural chromosomal aberrancies including CK, monosomal karyotype, chromosome 5 aberrancy, or comutation pattern between single- and multi-hit TP53^mut t-MN were observed (Table 1). Similarly, no significant differences were observed in age, latency, blood counts, BM blast percentage, and cytogenetic aberrancies. Critically, OS was not significantly different between the single- and multi-hit TP53^mut in the whole t-MN cohort and for the t-MDS subgroup or the t-AML subgroup or when stratified by blast percent categories (Figure 1E-H and supplemental Figure 2B). There was also no difference in the incidence of progression to AML between single- vs multi-hit TP53^mut t-MDS (supplemental Figure 2C). The striking enrichment of CK in single-hit TP53^mut t-MN (85.7%) compared with reported frequency of 13% in de novo MDS⁵ and VAF cut-off >10% vs 2% could partly explain the difference between the 2 studies. Single nucleotide polymorphism microarray analyses and copy number analysis were unavailable for 7 cases with single-hit TP53^mut with VAF 10% to 50%, and thus few cases of multi-hit TP53^mut could have been missed. However, the OS between single- and multi-hit TP53^mut was still not significantly different after excluding these cases (supplemental Figure 2D).

These findings are highly relevant considering the changes proposed in the recent classifications. The ICC² and the ELN³ removed the subcategory of “therapy-related,” substituting it with diagnostic qualifiers instead. The WHO¹ has grouped t-MN with secondary MN and renamed it as “myeloid neoplasm post-cytotoxic therapy,” with the assertion that the majority of MDS and AML occurring post–cytotoxic therapy have TP53^mut and that multi-hit TP53^mut have poor outcome compared with single-hit.¹ The underlying assumption of these changes is that TP53^mut MNs, regardless of the underlying etiology, have similar genomic characteristics and outcomes.

Our results provide compelling evidence that neither the allelic status nor the BM blast percentage of t-MDS provides meaningful prognostic information and that the TP53 VAF of 10% is a clinically useful threshold to identify patients with poor survival. Underestimation of the poor prognosis of single-hit TP53^mut t-MDS, by exclusion from TP53^mut MN, has significant implications on patient management such as consideration for allogeneic transplantation and exclusion from clinical trials. Our findings, therefore, warrant reconsideration of the allelic status in TP53^mut t-MN.