Presence of Leukemia-Related Basophils and Mast Cells with Atypical Immunophenotype during Induction Should Not be Interpreted As Measurable Residual Disease in Children with Acute Myeloid Leukemia with <i>RUNX1</i>::<i>RUNX1T1</i>

In most study protocols for children with acute myeloid leukemia (AML), treatment response is assessed with flow cytometry (FCM) after one and/or two courses of induction treatment, impacting risk stratification. In AML with RUNX1::RUNX1T1, which is the most common subtype of pediatric AML and generally associated with good prognosis, assessment of treatment response is complicated by two factors: 1) Reverse transcription quantitative PCR (RT-qPCR-MRD) often shows high levels of RUNX1::RUNX1T1 fusion transcripts indicating residual disease. 2) FCM-MRD sometimes detects cells with immature markers such as CD34 or CD117 and atypical immunophenotype, leading to an interpretation as MRD. However, we have observed that such cells lack the diagnostic immunophenotype and instead display basophilic or mast cell markers. In this study, we aimed to improve interpretation of FCM-MRD by characterization of AML with RUNX1::RUNX1T1 with focus on basophils and mast cells. Our study included 45 of 46 children with AML with RUNX1::RUNX1T1 in Sweden, Finland, Norway, Denmark, Hong Kong and Israel during 2013-2020, comprising 22 females and 23 males with median age of 10 years (range 4-17). They were treated according to the NOPHO-DBH AML2012 protocol. FCM-MRD analysis utilized antibodies allowing for identification of basophils as CD123+, HLA-DR-, CD33+ and mast cells as CD117++, HLA-DR-, CD33+. FCM-MRD was performed at diagnosis, day 22 after induction 1, before start of induction 2, and before start of consolidation. Results were compared with 70 children treated in Sweden with the same protocol during the same time period for AML without RUNX1::RUNX1T1. When analyzing children with AML with RUNX1::RUNX1T1 on day 22 after induction 1, both basophils (median 0.64%, range 0-40%) and mast cells (0.44%, 0-29%) were elevated compared with regenerating bone marrow (basophils 0.32%, 0.04-0.69%; mast cells 0.01%, 0.006-0.06%). In 80% of cases, the basophils displayed atypical immunophenotype with lower expression of CD123, CD38, CD11b and CD13 and higher CD34 and CD117, and in 38% mast cells exhibited lower CD117. Levels normalized before consolidation treatment (basophils 0.12%, 0-0.7%; mast cells 0.04%, 0-1.2%). To investigate the impact of these cells, we divided children into those with notably high basophils on day 22, defined as ≥2% (n=16), and those with low basophils, &amp;lt;2% (n=29). The group with high basophils day 22 had more atypical basophils and mast cells already at diagnosis, as well as high levels of mast cells day 22 (median 1.87% vs 0.27%, p=0.007). Leukemic origin of atypical basophils and mast cells at diagnosis was verified using FCM cell sorting and RT-qPCR of RUNX1::RUNX1T1. Children with high basophils did not differ from low basophil cases regarding age, white blood cell count, leukemia-associated immunophenotype, KIT or FLT3 mutation status, or treatment intensity. The clinical outcome was favorable, with only five relapses (11%), with no difference between children with high and low basophils. Similar findings were seen when children were divided into groups of high (≥0.9%, n=18) and low (&amp;lt;0.9%, n=27) mast cells day 22, partly overlapping with basophil groups. This suggests that both basophils and mast cells have leukemic origin but not relapse potential. A comparison with children with other AML (n=70) showed that elevated levels and atypical immunophenotype of basophils and mast cells day 22 was unique to AML with RUNX1::RUNX1T1. To understand the reason for this phenomenon, we investigated the gene expression profile of cases with AML with RUNX1::RUNX1T1 using the TARGET (children), Beat AML 1.0 and TCGA-LAML (both adults) datasets. In all three datasets, AML with RUNX1::RUNX1T1 showed an enrichment of the signature genes of the common myeloid progenitor with eosinophil/mast cell/basophil potential, namely CSF2RB (CD131), CLC, HDC, EPX and IL5RA, compared to other types of AML. This suggests that RUNX1:::RUNX1T1 leukemia can originate in this progenitor. In conclusion, during induction treatment of children with AML with RUNX1::RUNX1T1, basophils and mast cells are often increased. Since they are leukemia-related and often have atypical immature immunophenotype, they might cause concern. However, such cells do not seem to be associated with a worse prognosis but rather reflect an inherent feature of this leukemia and should not be interpreted as MRD.