Uncovering the Genomic Landscape in Newly Diagnosed and Relapsed Pediatric Cytogenetically Normal FLT3‐ITD AML

Abstract

Fms-like tyrosine kinase 3 (FLT3) internal tandem duplication (ITD) mutations, common in pediatric acute myeloid leukemia (AML), associate with early relapse and poor prognosis. Past studies have suggested additional cooperative mutations are required for leukemogenesis in FLT3-ITD+ AML. Using RNA sequencing and a next-generation targeted gene panel, we broadly characterize the co-occurring genomic alterations in pediatric cytogenetically normal (CN) FLT3-ITD+ AML to gain a deeper understanding of the clonal patterns and heterogeneity at diagnosis and relapse. We show that chimeric transcripts were present in 21 of 34 (62%) of de novo samples, 2 (6%) of these samples included a rare reoccurring fusion partner BCL11B. At diagnosis, the median number of mutations other than FLT3 per patient was 1 (range 0-3), which involved 8 gene pathways; WT1 and NPM1 mutations were frequently observed (35% and 24%, respectively). Fusion transcripts and high variant allele frequency (VAF) mutants, which included WT1, NPM1, SMARCA2, RAD21, and TYK2, were retained from diagnosis to relapse. We did observe reduction in VAF of simple or single mutation clones, but VAFs were preserved or expanded in more complex clones with multiple mutations. Our data provide the first insight into the genomic complexity of pediatric CN FLT3-ITD+ AML and could help stratify future targeted treatment strategies.Pediatric acute myeloid leukemia (AML) is a rare heterogeneous disease that accounts for 30% of all childhood leukemia. 1,2 It is distinct from the adult counterpart in both their genomic alterations and therapeutic response. 3 However, in both settings, pediatric and adult AML have relatively low somatic mutation burden compared with other tumor types. 4,5 Fms-like tyrosine kinase 3 (FLT3) internal tandem duplication (ITD) mutations are among the most common

TP-0903 is active in models of drug-resistant acute myeloid leukemia

“…These primary human samples had 2 or more (up to 6) recurrent mutations that confer poor prognosis. Notably, some of these samples had NPM1 , DNMT3A , and FLT3 -ITD mutations co-occurring, which has a deleterious effect ( 1 ); ASXL1 , WT1 , and FLT3 mutations that carry a poor prognosis ( 1 , 4 , 15 , 16 ); BCOR , CBL , IDH1/2 , and RAS mutations that confer drug resistance ( 10 , 14 , 33 ); SRSF2 , EZH2 , and BCOR mutations that are associated with secondary AML ( 4 ); and more. TP-0903 retained near-equipotent activity against all samples, unlike other agents, where resistance was observed.…”

“…NPM1 mutations are considered recurrent in AML, and while harboring NPM1 mutations align with a favorable risk category, it is no longer considered favorable in the presence of an FLT3-ITD mutation (4). Although certain genetic mutations have not been classified in an unfavorable risk category, mutations in epigenetic modifiers (DNMT3A, IDH1/2, EZH2, BCOR), transcription factors (WT1, MLL-PTD), signaling genes (KRAS, NRAS), and splicing factors (SRSF2) among others have been associated with poorer risk, early relapse, or treatment resistance (4,(8)(9)(10)(11)(12)(13)(14)(15)(16). As such, clonal heterogeneity of the disease makes AML difficult to treat, and agents with selective activity are prone to clonal selection and drug resistance.…”

Midostaurin in combination with chemotherapy is most effective in patients with acute myeloid leukemia presenting with high FLT3‐ITD allelic ratio who proceed to allogeneic stem cell transplantation while in first complete remission

“…The role of companion genetic abnormalities in determining the prognosis of patients with mutated FLT3 is well acknowledged 13‐16 . However, the molecular mechanism that makes patients with a high FLT3‐ITD AR more susceptible to midostaurin is not clear.…”

“…However, the molecular mechanism that makes patients with a high FLT3‐ITD AR more susceptible to midostaurin is not clear. The distribution of major additional genetic aberrations associated with poor prognosis does not appear to be in concordance with the level of mutated FLT3 allele 15 . In addition, a general effect related to broad kinase inhibition has been ruled out due to disappointing results of the phase III prospective UNIFY trial.…”

What Is Abnormal in Normal Karyotype Acute Myeloid Leukemia in Children? Analysis of the Mutational Landscape and Prognosis of the TARGET-AML Cohort

“…Fortunately, the advent of Next-Generation sequencing (NGS) technologies has allowed more detailed genetic investigations of AML through targeted gene panel sequencing, whole exome sequencing, whole-genome sequencing (WGS), and transcriptomic RNA sequencing. Using these techniques, major efforts have been made to unravel the molecular landscape of pediatric AML and disease progression [ 10 , 15 , 16 ] including a study of focusing on normal karyotype FLT3 -ITD positive AML [ 17 ].…”