Biallelic TP53 aberrations and double TP53 mutations are prevalent in AML/MDS patients with del(5q) complex karyotype - an NCI myelomatch and SWOG report Free

Introduction: Mutated TP53 has recently been incorporated into both the ICC and WHO classifications for AML and MDS due to its association with poor prognosis. ICC defined “AML with mutated TP53” as those with >20% blasts and TP53 mutation with VAF >10%; “MDS with mutated TP53” as multi-hit TP53 or TP53 mutation with VAF >10% plus complex karyotype; and “MDS/AML with mutated TP53” as those with 10-19% blasts and TP53 mutation VAF >10%. The WHO 5^th edition defined “MDS with biallelic TP53 inactivation” as those with <20% blasts with 2 or more TP53 mutations, or one mutation plus TP53 copy number loss or copy-neutral loss-of-heterozygosity (cnLOH). These different definitions led to confusion in classification. Also, venetoclax does not improve survival in AML patients with TP53 mutations. We aimed to assess the prevalence of TP53 aberrations in newly diagnosed AML and MDS patients enrolled in the NCI myeloMATCH clinical trial who underwent testing per SWOG master screening and reassessment protocol (MSRP).

Methods: All consecutive patients on MSRP from May 2024 to May 2025 were included in this analysis. We examined results from karyotype analysis, fluorescence in situ hybridization (FISH), chromosome genomic array testing (CGAT), and NCI Myeloid Assay (NMA) performed at the myeloMATCH Molecular Diagnostics Network (MDNet) labs to determine the prevalence of TP53 aberrations in cytogenetic subgroups. Patients with disqualifying diagnosis (including APL) and invalid karyotype results were excluded. Cytogenetics categories per ELN2017 were used to group patients. Biallelic TP53 aberrations are defined as (1) 17p deletion [del(17p)] plus TP53 mutation, (2) TP53 mutation with 17p cnLOH, (3) homozygous TP53 mutation (VAF >60%), and (4) compound heterozygous TP53 mutations with two different mutations in trans. When two TP53 mutations were identified without definitive knowledge of cis vs trans, they were considered double TP53 mutations instead of biallelic to be precise. TP53 mutation with VAF <5% was not counted. Incidence rates were compared with Fisher's exact test.

Results: Of 468 total patients enrolled in the first year of myeloMATCH, 61 (13.0%) with disqualifying diagnosis were excluded. Median age was 64.1 (18.4 to 95.8) at screening, with 43% female. Valid karyotype, FISH, and NMA results were obtained in 398 diagnostic AML (87.7%) and MDS (12.3%) samples, including 348 bone marrow and 50 peripheral blood. Karyotype was abnormal in 235 (59.0%) and FISH abnormal in 199 (50.0%). CGAT was abnormal in 244 of 364 (67.0%) samples; in 34 samples CGAT was not performed due to insufficient material. CGAT was the only test to detect 17p cnLOH, which was seen in 13 (3.6%). Complex karyotype (n=95) accounts for 23.9% of all cases; 72% of these (n=68) had 5q deletion [del(5q)]. Therefore, del(5q) complex karyotypes account for 17.1% of all diagnostic cases. Of these complex del(5q) cases, 35 (51%) showed del(17p), confirmed by FISH and/or CGAT. Among the non-del(5q) complex karyotype cases (n=27), only 4 (15%) showed del(17p). NMA results demonstrated TP53 mutations in 85% of complex del(5q) cases. Biallelic TP53 aberrations were present in 85.7% (n=30) of del(5q) complex cases with del(17p) (p=0.001). In del(5q) complex cases without del(17p), bi-allelic and double TP53 aberrations were demonstrated in 33.3% (p<0.001) and 36.4%, respectively. In contrast, other non-del(5q) complex cases with del(17p) showed biallelic TP53 aberrations in 25% (p=0.022), while other complex cases without del(17p) showed double TP53 mutations in 4.5% (p<0.011). None of the del(5q) patients without complex karyotype or non-complex samples showed biallelic TP53 aberrations.

Conclusions: The first year myeloMATCH study demonstrated that biallelic TP53 aberrations and double TP53 mutations were prevalent among AML/MDS patients with del(5q) complex karyotype, accounting for 78.0% overall, compared with 3.8% among those with non-del(5q) complex karyotype and 0% among those without a complex karyotype. Many publications include double TP53 mutations or multi-hit TP53 mutations as biallelic even though the assumption may not be accurate. Outcome data from each of the subgroups will further delineate the prognostic significance of these aberrations and help inform future clinical trial design for precision medicine. Our results also support the hypothesis that 5q loss cooperates with TP53 mutations to drive evolution to complex karyotype (Creamer 2024 ASH).