Sequential gain of mutations in severe congenital neutropenia progressing to acute myeloid leukemia

Abstract

Severe congenital neutropenia (SCN) is a BM failure syndrome with a high risk of progression to acute myeloid leukemia (AML). The underlying genetic changes involved in SCN evolution to AML are largely unknown. We obtained serial hematopoietic samples from an SCN patient who developed AML 17 years after the initiation of G-CSF treatment. Nextgeneration sequencing was performed to identify mutations during disease progression. In the AML phase, we found 12 acquired nonsynonymous mutations. Three of these, in CSF3R, LLGL2, and ZC3H18, co-occurred in a subpopulation of progenitor cells already in the early SCN phase. This population expanded over time, whereas clones harboring only CSF3R mutations disappeared from the BM. The other 9 mutations were only apparent in the AML cells and affected known AML-associated genes (RUNX1 and ASXL1) and chromatin remodelers (SUZ12 and EP300). In addition, a novel CSF3R mutation that conferred autonomous proliferation to myeloid progenitors was found. We conclude that progression from SCN to AML is a multistep process, with distinct mutations arising early during the SCN phase and others later in AML development. IntroductionSevere congenital neutropenia (SCN) is a BM failure syndrome characterized by strongly reduced neutrophil counts and recurrent, potentially life-threatening, opportunistic bacterial infections. Treatment with G-CSF elevates peripheral neutrophil counts and reduces the risk of infections. 1 Leukemic progression of SCN is a major concern, with an estimated overall cumulative incidence of approximately 20% after 15 years of G-CSF treatment. 2 Constitutional mutations in the gene encoding neutrophil elastase (ELANE) are common defects in SCN. 3 In addition, the acquisition of nonsense mutations in the gene encoding the G-CSF receptor (CSF3R) is a unique feature in SCN patients. [4][5][6][7] These mutations lead to the expression of truncated CSF3R proteins, also known as the ␦ forms. In cell-line models, truncated CSF3R proteins are hampered in transducing the signals required for proper neutrophil differentiation, confer increased proliferative responses to G-CSF treatment, but do not cause leukemia in mice. [4][5][6][8][9][10][11] CSF3R␦ mutations can be detected in approximately 30% of SCN patients. In some cases, distinct clones with different CSF3R␦ mutations are present for many years. 7,12 After evolution of SCN toward acute myeloid leukemia (AML), CSF3R␦ mutations are found in approximately 80% of patients. 12 Until now, all reported SCN/AML patients harboring a CSF3R␦ mutation in the SCN phase also carry this mutation in the leukemic phase. These observations suggest that leukemic progression in SCN follows a unique pattern, with CSF3R␦ mutations as an early event, followed by additional genetic and epigenetic events that are essential for full leukemic transformation. Chromosomal aberrations such as loss of chromosome 7 and gain of chromosome 21 are apparent in AML arising from SCN and other BM failure syndromes such as Fanconi anemia and Shwachman-Dia...

Chronic neutrophilic leukemia 2016: Update on diagnosis, molecular genetics, prognosis, and management

“…Recently an acquired CSF3R T618I was reported in a patient with SCN, after progression to AML. This mutation only involved the leukemic blasts, was present on the CSR3R allele carrying a truncation mutation, and led to fully autonomous proliferation of myeloid progenitors [27]. A very low prevalence (<0.5%) of the CSF3R T618I mutation was found in a recent study of 1500 consecutive de novo AML cases [28].…”

Prevalence of a new auto-activating colony stimulating factor 3 receptor mutation (CSF3R-T595I) in acute myeloid leukemia and severe congenital neutropenia

“…10,13 As germline material was not available we cannot confirm whether the mutations listed in Table 1 are acquired mutations. However, the fact that the T595I was acquired in the previously investigated SCN/AML patient 12 highly suggests that the identified mutations listed in Table 1 were acquired as well. In none of the AML patients carrying CSF3R-T595I, T617N or T617I, CSF3R truncating mutations were present ( Table 1).…”

“…[9][10][11] We recently identified a new extracellular CSF3R mutation (T595I) in the leukemic blasts of a SCN patient after progression to AML. 12 This mutation, located on the CSF3R allele that already carried the nonsense mutation, causes fully autonomous, i.e. colony-stimulating factor independent, proliferation of myeloid progenitors in semi-solid colony assays.…”

“…colony-stimulating factor independent, proliferation of myeloid progenitors in semi-solid colony assays. 12 Because most SCN patients receive life-long CSF3 therapy, we asked whether the acquisition of CSF3R-T595I mutations is unique for SCN/AML or whether this mutation can also be found in AML patients who did not receive CSF3 treatment. To address this, we investigated the prevalence of CSF3R-T595I mutations in 1446 consecutive de novo AML patients, none of whom had a documented history of CSF3 treatment.…”

Chemo-genomic interrogation of CEBPA mutated AML reveals recurrent CSF3R mutations and subgroup sensitivity to JAK inhibitors

“…CSF3R mutations comprise either the membrane-proximal missense mutations or C-terminal truncating mutations proposed to lead to ligand independence and ligand hypersensitivity, respectively. 4 CSF3R mutations have also been described in patients with congenital neutropenia treated with granulocyte colony-stimulating factor therapy upon acute myeloid leukemia (AML) transformation, 5,6 but they have only been reported in ,1% to 2% of AML. 3,7,8 Two major categories of collaborating CEBPA mutations have been described in human AML: (1) frameshift (FS) insertions or deletions affecting the N-terminal region resulting in a loss of the 42 kDa protein and overexpression of a shorter 30 kDa CEBPA protein proposed to exhibit a dominant negative activity, 9 and (2) in frame mutations in the C-terminal region that alter the basic leucine zipper domain.…”