NeoGenomics Laboratories, Aliso Viejo, CA
Frank J Scarpa , Rachel Daringer , Wendy A. Wolfson , Fernando Lopez Diaz , Sally Agersborg , Vincent Anthony Funari , Lawrence Martin Weiss , Forrest Blocker , Madhuri Paul
Background: TP53-mutated acute myeloid leukemia (AML) is a distinct disease entity associated with a dismal prognosis. This disease group is distinguishable by its low frequency of SNVs, unremarkable transcriptional signatures, and lower leukocyte and myeloblast counts compared to TP53 wildtype disease. Response to gold-standard hypomethylating agents is typically transient. NPM1 mutations in this disease subset are rare despite the fact that NPM1c has been shown to negatively regulate the tumor suppressive functions of p53.Methods: Bone marrow, peripheral blood, or FFPE tissue samples from 10,118 patients with suspected myeloid disease were sequenced using a dual DNA/RNA 297 gene myeloid panel. Results were validated in a separate independent dataset using a 54 gene TruSight myeloid panel (N = 2463). FISH/cytogenetic data was analyzed across myeloid disease. Patients with confirmed AML (n = 460) were included in the NGS portion of this study. Statistics were performed using Fisher’s exact test for categorical variables and two-tailed T-test for continuous variables. Results: All TP53-mutated myeloid disease (n = 1282 / 10,118) was associated with fewer co-mutations except DNMT3A (13.4%; n = 172), and complex cytogenetics (36.4%; n = 134/381). TP53+/NPM1+ status across all myeloid disease was not associated with a complex karyotype (7.6% vs 38.5%; 1/13 vs. 133/368, p = 0.02). Among AML patients, NPM1+/TP53+ patients (n = 18) were more co-mutated with DNMT3A (33.3% vs. 10.3%, P = 0.01), FLT3 (33.33% vs. 2.5%, P < 0.0001), IDH1 (27.8% vs. 4.4%, P = 0.002), IDH2 (22.2% vs. 6.4%, P = 0.03); and PTPN11 (22.2% vs. 2.5%, P = 0.003) when compared to TP53+/NPM1- patients. NPM1+/TP53+ AML had more mutations in recurrently mutated genes (4.5 vs 2.1; P < 0.0001) than TP53+/NPM1- AML. Conclusions: TP53+/NPM1+ AML harbors molecular signatures which clearly distinguish it from ordinary TP53-mutated AML, and is more reflective of de novo and NPM1+ AML. Further clinical outcome studies are needed to determine the therapeutic and prognostic implications of this subset, and whether other TP53-mutated patients can be better risk stratified.
Cohort: | TP53+/NPM1- | TP53+/NPM1+ | TP53-/ NPM1+ | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
297 panel | (n = 203) | TruSight | (n = 215) | 297 panel | (n = 18) | TruSight | (n = 14) | 297 panel | (n = 239) | TruSight | (n = 272) | |
Prevalence: | ||||||||||||
DNMT3A | 10.3% (21) | - | 12.6% (27) | - | 33.33% (6) | P < 0.01 | 57.1% (8) | P = 0.0002 | 47.3% (113) | P = 0.0001 | 46.3% (126) | P = 0.0001 |
FLT3 | 2.5% (5) | - | 1.4% (3) | - | 33.33% (6) | P = 0.0001 | 21.4% (3) | P = 0.003 | 54.4% (130) | P = 0.0001 | 29.0% (79) | P = 0.0001 |
IDH1 | 4.4% (9) | - | 2.3% (5) | - | 27.8% (5) | P = 0.002 | 14.3% (2) | P = 0.06 | 14.6% (35) | P = 0.0004 | 14.0% (38) | P = 0.0001 |
IDH2 | 6.4% (13) | - | 4.2% (9) | - | 22.2% (4) | P = 0.03 | 7.1% (1) | P = 0.05 | 25.1% (60) | P = 0.0001 | 21.0% (57) | P = 0.0001 |
PTPN11 | 2.5% (5) | - | 1.4% (3) | - | 22.2% (4) | P = 0.003 | 14.3% (2) | P = 0.06 | 14.6% (35) | P = 0.0001 | 13.6% (37) | P = 0.0001 |
MUTATION COUNT | 2 - 2.6 | - | 2-2.1 | - | 4.6 - 5 | P = 0.0001 | 4.5 – 5 | P = 0.0001 | 4 – 4.3 | P = 0.0001 | 3 – 3.1 | P = 0.0001 |
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