Clonal evolution revealed by whole genome sequencing in a case of primary myelofibrosis transformed to secondary acute myeloid leukemia

Abstract

Clonal architecture in myeloproliferative neoplasms (MPNs) is poorly understood. Here we report genomic analyses of a patient with primary myelofibrosis (PMF) transformed to secondary acute myeloid leukemia (sAML). Whole genome sequencing (WGS) was performed on PMF and sAML diagnosis samples, with skin included as a germline surrogate. Deep sequencing validation was performed on the WGS samples and an additional sample obtained during sAML remission/relapsed PMF. Clustering analysis of 649 validated somatic single nucleotide variants revealed four distinct clonal groups, each including putative driver mutations. The first group (including JAK2 and U2AF1), representing the founding clone, included mutations with high frequency at all three disease stages. The second clonal group (including MYB) was present only in PMF, suggesting the presence of a clone that was dispensable for transformation. The third group (including ASXL1) contained mutations with low frequency in PMF and high frequency in subsequent samples, indicating evolution of the dominant clone with disease progression. The fourth clonal group (including IDH1 and RUNX1) was acquired at sAML transformation and was predominantly absent at sAML remission/relapsed PMF. Taken together, these findings illustrate the complex clonal dynamics associated with disease evolution in MPNs and sAML.

Changes in allele frequencies of CSF3R and SETBP1 mutations and evidence of clonal evolution in a chronic neutrophilic leukemia patient treated with ruxolitinib

“…KIT is involved in activated signaling, 8 while GATA2 and RUNX1 are myeloid transcription factors; in addition, RUNX1 has been identified as a driver mutation in the evolution of a myeloproliferative neoplasm to acute myeloid leukemia. 9 The proportional decreased allele frequenices for CSF3R and SETBP1 after treatment with ruxolitnib (Table 1) suggest that a single sub-clone harbored these mutations and was suscepitble to inhibition of the JAK/STAT signaling pathway, as was predicted. Although a previous case report did not show a reduction in CSF3R-T618I allele frequency in a patient who clinically responded to ruxolitinib, 5 it is possible that depth of responses may vary, and that this patient experienced a deeper response.…”

“…After four months of treatment, the patient had stabilization of the blood counts, with a WBC of 5.5x10 9 /L, hemoglobin 10.2 g/dL and platelets of 137x10 9 /L (Figure 1), he no longer had a palpable spleen and, clinically, had returned to his usual baseline with respect to energy and activity tolerance. He declined a follow up bone marrow examination to formally assess his response.…”

“…He had no significant past medical history and, four months prior to presentation, developed increasing fatigue, abdominal distention, and easy bruising. He was noted to have a WBC of 100.1x10 9 /L with an absolute neutrophil count (ANC) of 93.1x10 9 /L, a hemoglobin of 10.0 g/dL, and a platelet count of 102x10 9 /L (Figure 1). His peripheral blood smear showed marked leukocytosis, predominately neutrophils ( Figure 2a).…”

Correlation of mutation profile and response in patients with myelofibrosis treated with ruxolitinib

“…In recent years, with the explosion of whole genome sequencing efforts, a number of rare, but recurrent, mutations have been identified in myeloproliferative neoplasms (MPNs), suggesting that there may be several paths to the development of MPNs, which have heterogeneous clinical presentations and treatment responses. [3][4][5] To detect genes that may be correlated with response to ruxolitinib and other clinicopathologic features, we performed a comprehensive mutation profile of 29 genes recurrently mutated in primarily myeloid malignancies 6 in a cohort of 95 patients with MF who were treated with ruxolitinib in a phase 1/2 study. 7 …”

Acute promyelocytic leukemia co-existing with JAK2 V617F positive myeloproliferative neoplasm: a case report

“…JAK-2 inhibition by ruxolitinib in the in vitro studies on NB-4 APL cells treated with ATRA did not affect CLL-2 and IL-8 levels, supporting the importance of JAK2 in downstream activation as previously described (1,2). However, the role of JAK-2 inhibition in the management of differentiation syndrome has not been (23)(24)(25). Since splenomegaly and FLT3-TKD were also present at the time of diagnosis, we hypothesize that the JAK2 V617F mutated MPN clone (likely PMF) was present first and that additional mutations like FLT3 and PML/RARa took place later and then led to the development of APL (26)(27)(28)(29)(30)(31)(32).…”