Distribution of different classes of CSF3R mutations and co-mutational pattern in 360 myeloid neoplasia

Abstract

The colony-stimulating factor 3 receptor (CSF3R) plays an essential role in differentiation, growth, and survival of granulocytes. Driver mutations in CSF3R gene represent a diagnostic marker of chronic neutrophilic leukemia (CNL). Less commonly, these mutations are observed in other myeloid neoplasms but their pathogenetic and prognostic role is still unclear. Here, we analyzed a large cohort of myeloid neoplasms to evaluate the incidence of CSF3R mutations and co-mutational profile. Mutational analysis was performed using targeted NGS myeloid panel in a consecutive cohort of 360 patients with myeloid neoplasms. Mutations in CSF3R were identified in 20/360 (5.6%) cases. A CSF3R gene mutation was present in 13/179 AML cases (7.3%), in 2/27 (7.4%) CMML cases, in 1/94 (1.1%) MDS cases and in 4/60 (6.7%) other myeloid neoplasms. The frequencies of patients with CSF3R mutations lowered to 2.8% in all cases and 3.4% in AML, excluding cases with variants of uncertain significance (VUS). A total of 23 mutations of CSF3R gene were detected, half localized in the extracellular domain, 5 in the transmembrane region (type I) and 6 mutations in the cytoplasmic domain (type II). In AML, CSF3R mutations were more frequent in patients harboring CBF alterations (25.0%) and CEBPA mutations (11.8%). Two cases with AML harboring pathogenic CSF3R variants were primary refractory to induction therapy. CMML cases with T618I variant showed a myeloproliferative phenotype. Overall, our findings support the notion that CSF3R variants, particularly type I and II pathogenic mutations, may modulate the phenotypic features of leukemic cells in myeloid neoplasia.

Keywords: CSF3R; Co-mutational pattern; Disease outcome; Myeloid neoplasia.

Fig. 1

Frequencies of CSF3R mutated cases in a cohort of 360 patients with myeloid neoplasia. (A) Flow-chart shows the distribution of CSF3R mutated cases among patients with AML or MDS/AML, MDS, MPN or CMML. For 179 AML cases frequencies are reported, as percentage compared to all AML cases, among subsets i.e., TP53-mutated, NPM1-mutated, CEBPA-mutated, AML with CBL alterations, AML with MDS-related mutations. (B) Histograms show frequencies of cases harboring pathogenetic (P) or likely pathogenetic (LP) variants or variants of uncertain significance (VUS) among different myeloid neoplasia

Fig. 2

Characteristics and distribution of CSF3R mutations in patients with myeloid neoplasia. (A) Pie-chart depicts the frequencies of different types of CSF3R mutations i.e., missense, frameshift, nonsense, delins and splice-donor variants. (B) Distribution of pathogenic/likely pathogenic (P/LP) mutations and variants of uncertain significance (VUS) in extracellular, proximal membrane, C-terminal domains of CSF3R gene or splice-donor mutations. (C) Pictures show the different domains of CSF3R gene and distribution of mutations in AML (above) and CMML (below). In red, pathogenic/likely pathogenic (P/LP) mutationsand in black, variants of unknown significance (VUS).

Fig. 3

Co-mutational pattern of CSF3R-mutated cases. (A) Histogram show the frequencies of co-occurring mutations in other genes related to myeloid neoplasia in AML cases with CSF3R-mutated gene. (B) Allele frequencies (VAF%) of mutated genes in AML and CMML cases with pathogenic/likely pathogenic mutations of CSF3R gene are depicted. (C, D) Heatmaps depict co-mutational profile of CSF3R-mutated cases. Each row represents a different gene and each column an individual patient with de novo or relapsed AML (C) or other myeloid neoplasm (D). A colored cell indicates the presence of mutation, and a blank cell indicates wild-type. Color legends are depicted below