CSF3R Mutations Are Exceedingly Rare Genetic Events Associated with Inferior Survival and Sensitivity to Ruxolitinib across Myeloid Malignancies

BACKGROUND: CSF3R mutations are rare genetic events that have been associated with clinical response to the kinase inhibitors ruxolitinib and dasatinib according to the location and type of mutation observed. Although it has been reported that CSF3R mutations are exclusively associated with chronic neutrophil leukemia (CNL), the clinical relevance and response to therapy across the breadth of myeloid neoplasms is largely unknown. To address this, we report the first case series of CSF3R mutations across a large cohort of myeloid neoplasms.

METHODS: This study was approved by scientific and ethical review boards. Cases were profiled for all exons of CSF3R utilizing a CLIA-certified 54 gene myeloid Truseq panel or a commercial panel covering over 400 genes. All cases were sequenced on an Illumina instrument and had a target read depth of 200X and a variant allele frequency cut-off of 5%. Reads were aligned with Novoalign version 3.04.04 and variants called using Varscan version 2.3.6. Detected CSF3R variants were filtered through an analytic pipeline to include only those that have been previously reported as somatic and resulting in activated signaling. Clinical variables were abstracted from the medical record and analyzed using GraphPad Prism and SPSS. Kaplan-Meier curves were utilized to estimate overall survival. All cases were centrally reviewed by two expert hematopathologists.

RESULTS: Between April of 2014 and January of 2019, a total of 6182 patients with myeloid neoplasms were subjected to next generation sequencing (NGS) testing and only 18 (0.29%) harbored somatic activating CSF3R mutations. The CSF3R variants observed included T618I in 12 cases, T640N in 2 cases, T615A in 1 case and truncating mutations in 3 cases. CSF3R mutations were seen at diagnosis in 89% (16) of cases. The median age of CSF3R mutated cases was 77 years old (range 32-87 years), and 72% were male. Most cases were pathologically consistent with CNL (44.4%, 8 cases) but two cases were pathologically consistent with chronic myelomonocytic leukemia, one with myelodysplastic syndrome (MDS), one with myeloproliferative neoplasm unclassifiable (MPN-U), and one with MDS/MPN-U. Five patients were diagnosed with acute myeloid leukemia. Most patients were thrombocytopenic with a median platelet count of 69 x10³ cells/dL (range 19-428 x10³ cells/dL) and anemic with a median Hgb of 9.5 g/dL (range 7.7-14.1). Splenomegaly was observed in four cases (23.5%) by physical exam. The vast majority had normal cytogenetics (94.1%, 16 cases), and the most commonly co-mutated genes were ASXL1 (11 cases), TET2 (11 cases) and SRSF2 (7 cases).The median overall survival of CSF3R mutated cases was 13.8 months. Seven cases were treated with ruxolitinib, 5 of which harbored T618I mutations. When considering bone marrow myeloblast reduction, improvement in transfusion requirements, cytoreduction, improvement in splenomegaly, or improvement in constitutional symptoms, 100% of cases derived clinical benefit from ruxolitinib. This included two patients with clinically meaningful hematologic improvements as well as improvement in splenomegaly in 2 out of 3 patients with baseline splenomegaly. Further, one patient with serial NGS demonstrated CSF3R mutation clearance after 5 months of ruxolitinib therapy. The median overall survival was improved in ruxolitinib treated cases but did not reach statistical significance (16.5 vs. 10.9 months, p=0.27).

CONCLUSIONS: To our knowledge, this represents the largest collection of ruxolitinib treated CSF3R mutant myeloid neoplasms reported. Although enriched in CNL, CSF3R can occur in other myeloid neoplasms to include CMML and their overall prognosis is poor. Our data suggest that ruxolitinib should be considered in patients with membrane proximal CSF3R mutations.