Targeted deep sequencing improves outcome stratification in chronic myelomonocytic leukemia with low risk cytogenetic features

Abstract

Clonal cytogenetic abnormalities are found in 20-30% of patients with chronic myelomonocytic leukemia (CMML), while gene mutations are present in >90% of cases. Patients with low risk cytogenetic features account for 80% of CMML cases and often fall into the low risk categories of CMML prognostic scoring systems, but the outcome differs considerably among them. We performed targeted deep sequencing of 83 myeloid-related genes in 56 CMML patients with low risk cytogenetic features or uninformative conventional cytogenetics (CC) at diagnosis, with the aim to identify the genetic characteristics of patients with a more aggressive disease. Targeted sequencing was also performed in a subset of these patients at time of acute myeloid leukemia (AML) transformation. Overall, 98% of patients harbored at least one mutation. Mutations in cell signaling genes were acquired at time of AML progression. Mutations in ASXL1, EZH2 and NRAS correlated with higher risk features and shorter overall survival (OS) and progression free survival (PFS). Patients with SRSF2 mutations associated with poorer OS, while absence of TET2 mutations (TET2wt) was predictive of shorter PFS. A decrease in OS and PFS was observed as the number of adverse risk gene mutations (ASXL1, EZH2, NRAS and SRSF2) increased. On multivariate analyses, CMML-specific scoring system (CPSS) and presence of adverse risk gene mutations remained significant for OS, while CPSS and TET2wt were predictive of PFS. These results confirm that mutation analysis can add prognostic value to patients with CMML and low risk cytogenetic features or uninformative CC.

Keywords: chronic myelomonocytic leukemia; gene mutations; normal karyotype; prognostic factors; targeted deep sequencing.

Figure 1. Distribution of the affected genes across the 56 CMML patients at diagnosis

One gene is represented in each line and one patient in each column. Bars at the right represent the number of mutations present in each gene, while columns at the top represent the number of mutations per patient. At the bottom correlations of mutations with WHO, FAB, AML progression, CPSS and CFM model.

Figure 2. Prognostic impact of gene mutations

A. OS and PFS curves according to presence or absence of an adverse risk gene; B. OS and PFS curves according to number of mutations in an adverse risk gene. See Table 3 for 3-year percentage overall survival and progression free survival and confidence intervals. AR mutations: adverse risk gene mutations (ASXL1, EZH2, NRAS, SRSF2).