Clinical characteristics and comutational landscape of CSF3R mutations in acute myeloid leukemia

Abstract

Abstract Background Mutations in the colony stimulating factor 3 receptor (CSF3R) are the hallmark of chronic neutrophilic leukemia (CNL) and are rarely present in acute myeloid leukemia (AML). The low frequency of CSF3R mutations in AML has limited its characterization in AML to date. Therefore, we aimed to comprehensively characterize the clinical and comutational features of CSF3R mutations in a cohort of AML patients from our AMLSG reference laboratory in Hannover, Germany. Methods 3805 diagnostic AML patient samples obtained between 2010 and 2024 at our reference laboratory were included in our sequencing analysis. Sequencing of samples was performed using the customized TruSight myeloid sequencing panel (Illumina, San Diego, CA), which included 46 entire genes or hotspots recurrently found in myeloid leukemias. Mutations were annotated according to existing evidence on variant pathogenicity based on variant databases and verified by the use of genome browsers. Variants classified as pathogenic or likely pathogenic according to current data were included. Clinical and comutational characteristics of patients identified with CSF3R mutations were compared to a control cohort of without CSF3R mutated patients with available clinical and molecular data. Results Mutations in CSF3R were detected in 49 AML patients (1.29%). CSF3R mutations were most often present in the membrane proximal domain of the gene with hotspot mutations in c.1853C>T:p.T618I (26.5%) and c.1863A>G (16.1%) as previously described in CNL. The median age of patients with CSF3R mutations was 53.4 years (range 19 - 80 years), and 58.3% were male. Most cases with CSF3R mutations were de novo AML (58.9%), with secondary AML from myelodysplastic syndrome (18.4%) and AML from myeloproliferative neoplasms (10.5%) being less frequent. We found no significant difference regarding age, gender and type of AML between the CSF3R mutated and the comparison cohort. In addition, there were no significant differences in FAB classification, hemoglobin, leukocyte and platelet count nor in bone marrow blast percentage at diagnosis. However, patients with CSF3R mutations were significantly more frequently classified as adverse risk according to ELN 2022 criteria compared to the CSF3R wildtype (wt) cohort (68.8% vs 39.1%; p<0.001) and less commonly classified as favorable risk (8.3% vs 18.8%; p<0.05) or intermediate risk (18.8% vs 33.2%). By contrast, the analysis of cytogenetic profiles showed no statistically significant differences between cohorts. Principle component analysis primarily showed differences in comutational status: The total number of comutations of patients with CSF3R mutated AML was significantly higher (mean 4.5 vs 2.7, p<0.001). Also, CSF3R mutations were associated with mutations in RUNX1 (34.8%), TET2 (28.3%), AXSL1 (17.4%), STAG2 (15.2%) and SRSF2 (15.2%) which were observed significantly more often than in the comparison group (p<0.05%). 15% of CSF3R mutated cases also harbored mutations in TP53 which did not differ significantly from the control group. Strikingly, we observed multihit TET2 mutations in 36.1% of TET2 mutated patients (mean 2; range 1 – 6). In 22.2% of CSF3R mutated patients, the CSF3R mutation represented the dominant clone with a mean variant allele frequency (VAF) of 29.9% (range 5.5% - 95.65%). When comparing outcome for intensively treated patients between CSF3R mutated and CSF3R wt patients, we found no difference in overall survival or relapse free survival between cohorts. Conclusions Our findings demonstrate that CSF3R mutations are rare mutations only occurring in 1.29% of AML patients. Similar to germline CSF3R mutations in CNL, mutations in AML cluster in c.1853C>T:p.T618I and c.1863A>G, representing hotspot mutations of the gene. In CSF3R mutated AML patients, the number of mutated genes per sample was higher as compared to CSF3R wt patients. In a fifth of patients, the CSF3R mutation presented as the dominant clone. We identified an association between CSF3R mutations and myelodysplasia related gene mutations as well as multihit TET2 mutations. Thus, CSF3R mutated as compared to wt patients were significantly more often classified as adverse risk according to ELN 2022. Clinical data at diagnosis and outcome data did not show specific characteristics as compared to CSF3R wt patients.