Clonal Evolution in NPM1 Mutated Acute Myeloid Leukemia (AML)
Authors: Kapp-Schwoerer Silke , Cocciardi Sibylle , Kroenke Jan , Dolnik Anna , Blätte Tamara J. , Corbacioglu Andrea , Gaidzik Verena I. , Paschka Peter , Teleanu Maria-Veronica , Holzmann Karlheinz , Göhring Gudrun , Thol Felicitas , Heuser Michael , Ganser Arnold , Schlenk Richard F. , Döhner Hartmut , Bullinger Lars , Döhner Konstanze 
Published: October 2019

Abstract
Background: Mutations in the nucleophosmin (NPM1) gene represent one of the most common gene mutations in AML, and are considered a founder event in the pathogenesis of AML. Recently, we gained novel insights into clonal architecture and clonal evolution in 53 NPM1 mutated (NPM1mut) AML patients (pts). Here, we showed the highest stability for DNMT3A mutations (DNMT3Amut) suggesting that these mutations represent an early event in leukemogenesis as well as an increase in genomic complexity.
Aims: To validate our previous results on clonal evolution in a larger cohort of NPM1mut AML pts and to define relapse specific mutation patterns.
Methods: Paired samples at diagnosis and relapse from 129 NPM1mut AML pts were assessed for additional mutations by comprehensive mutation analysis (FLT3-ITD, FLT3-TKD, DNMT3A, IDH1/2, NRAS, ASXL1, TP53, MLL-PTD). In addition, 11 AML cases with loss of NPM1mut at the time of relapse and 12 cases with persisting NPM1mut were subjected to whole exome sequencing (WES).
Results: At diagnosis, the incidence of concurrent gene mutations was as follows: FLT3-ITDmut 32% (40/126), FLT3-TKDmut 19% (22/118), DNMT3Amut 69% (78/113), NRASmut 19% (22/117), IDH1mut 21% (26/123) and IDH2mut 19% (22/118). None of the pts analyzed exhibited a TP53 (n=53), MLL-PTD (n=63) or ASXL1 (n=59) mutation. At relapse, a significant shift in the genetic pattern was found in 74 pts (57%). FLT3-ITDmut was lost in 10 pts and newly acquired in 24 pts,16 pts lost FLT3-TKDmut. DNMT3Amut was lost in 2 pts and gained in 1 pt. NRASmut was lost in 12 pts and gained in 4 pts. IDH1mut was lost in 3 pts and acquired in 4 pts, while IDH2mut was lost in 2 pts and gained in only one pt. ASXL1mut and TP53mut were gained in 2 and 1 pts, respectively; gain of MLL -PTDmut (n=4) was restricted to pts with loss of NPM1mut at the time of relapse. Based on these findings we calculated the following stabilities: FLT3-ITDmut 75%, FLT3-TKDmut 27%, DNMT3Amut 97%, NRASmut 45%, IDH1mut 88% and IDH2mut 91%, respectively. In total, 11 pts (9%) lost NPM1mut at relapse while DNMT3Amut was present in 9/11 pts at diagnosis and remained stable at relapse; 4/11 pts gained MLL-PTDmut, one pt ASXL1mut and 3 pts acquired RUNX1mut.
By WES we observed a persistence of mutations known to be involved in clonal hematopoiesis, such as DNMT3A and TET2 mutations. These were usually seen during all analyzed time points (diagnosis, remission and relapse). In addition, we found distinct mutational patterns at the time of relapse compared to the time of diagnosis. For example, relapse- and diagnosis-specific mutations in NPM1mut loss cases were significantly enriched for different signaling pathways.
Conclusions: 74 (57%) of 129 NPM1mut AML pts showed clonal evolution at the time of relapse. DNMT3Amut demonstrated the highest stability (97%) confirming our previous findings that DNMT3Amut constitutes an early event which persists in preleukemic hematopoietic stem cells. High-resolution sequencing of selected cases is ongoing and will further unravel the clonal hierarchy in NPM1mut AML.
Those authors equally contributed to work: SKS, SC, LB and KD.

Disclosures
Heuser: Karyopharm: Research Funding.