Treatment optimization and genomic outcomes in refractory severe aplastic anemia treated with eltrombopag

Abstract

Eltrombopag (EPAG) received approval from the US Food and Drug Administration for the treatment of refractory severe aplastic anemia (rSAA) based on treatment of 43 patients with doses escalating from 50 to 150 mg daily for 12 weeks. Response kinetics suggested that more prolonged administration of EPAG at a dose of 150 mg could speed and improve response rates. We enrolled 40 patients with rSAA in a study of EPAG 150 mg daily, with a primary end point of response at 24 weeks. Twenty (50%) of 40 patients responded at 24 weeks; 5 (25%) of 20 would have been deemed nonresponders at 12 weeks, the end point of the previous study. Fifteen of the 19 responding patients continuing on EPAG had drug discontinued for robust response; 5 of the 15 required EPAG re-initiation for relapse, with all recovering response. To analyze risk of clonal progression, we combined long-term data from the 83 patients with rSAA enrolled in both studies. Evolution to an abnormal karyotype occurred in 16 (19%), most within 6 months of EPAG initiation. Targeted deep sequencing/whole-exome sequencing was performed pre-EPAG and at primary response end point and/or time of clonal evolution or longest follow-up. Cytogenetic evolution did not correlate with mutational status, and overall mutated allele fractions of myeloid cancer genes did not increase on EPAG. In summary, extended administration of EPAG at a dose of 150 mg for 24 weeks rescued responses in some patients with rSAA not responding at 12 weeks. The temporal relationship between clonal evolution and drug exposure suggests that EPAG may promote expansion of dormant preexisting clones with an aberrant karyotype. The studies were registered at www.clinicaltrials.gov as #NCT00922883 and #NCT01891994.

Graphical abstract

Figure 1.

Response summary and timelines. Twenty of 40 patients on study 2 met primary response criteria at the defined end point of 24 weeks on EPAG (solid green bars after 24-week response assessment). Note that 5 patients achieved response only after the 12-week interim assessment (UPN3, UPN4, UPN8, UPN12, and UPN18; gray bars between first and second response assessments). UPN7 achieved response criteria at 12 weeks but not at the primary end point of 24 weeks. UPN14 reached response criteria at 12 weeks but was taken off study at that time point due to clonal evolution, and thus was a nonresponder at the primary end point of 24 weeks. Nineteen responders continued EPAG on the extension arm of the protocol. EPAG administration was stopped in 14 patients for robust response and one when blood cell counts appeared to reach a plateau (UPN16), with continuing response off EPAG designated by the green striped bars. The drug was restarted in 5 patients for declining blood cell counts off EPAG, and all responded a second time (UPN8, UPN9, UPN16, UPN37, and UPN38; solid yellow bars). *Off study for patient choice. **Off study for cytogenetic evolution.

Figure 2.

Clonal cytogenetic evolution. Results from all 83 patients treated with EPAG on both study 1 and study 2. Patients are grouped according to presence or absence of chr7 abnormalities. Timing of cytogenetic evolution is shown in relation to initial treatment with IST as well as EPAG treatment. Further details are given in supplemental Table 5. Cytogenetic evaluations after initial clonal progression were performed off-study and in some cases not at the study site. HSCT, hematopoietic stem cell transplantation.

Figure 3.

Acquired somatic mutations in myeloid cancer and AA-related genes in relation to EPAG treatment. Targeted deep sequencing and/or WES was performed on bone marrow cells from 64 patients. Detection of acquired variants in a panel of genes with somatic mutations associated with myeloid cancer or AA are shown. Each row indicates a specific MC/AA gene and each column a patient, with results shown for baseline and primary end point (3 months for study 1, 6 months for study 2). The panel of MC/AA genes is given in the supplemental Methods, and the mutations detected are listed in supplemental Table 8.

Figure 4.

Impact of EPAG treatment on candidate gene mutations. The percentage of variant alleles is shown on the y-axis at baseline and the primary end point (3 months for study 1, 6 months for study 2) for mutations detected in 63 candidate genes in all analyzed patients (n = 64; A), responding patients (n = 26; B), cytogenetic evolvers (n = 12; C), and nonresponding patients (n = 26; D). P values for paired Student t tests comparing baseline and end point are shown.

Figure 5.

Individual patient-mutated clone size in response to EPAG. (A) UPN1, a 30-year-old woman diagnosed 8 years before EPAG treatment and failing multiple IST cycles, had mutations in SETBP1 and RUNX1 detected at baseline before EPAG. At the time of detection of monosomy 7 at 3 months, the percentage of variant alleles for both genes increased concurrently with the monosomy 7 clone, suggesting the transformed monosomy 7 clone also harbored the abnormal genetic variants. (B) UPN24, an 8-year-old boy with super SAA, responded to EPAG and remained stable. Analysis at baseline did not detect mutations, but at the primary end point of 6 months, 2 RUNX1 mutations and 1 SETBP1 mutation were detected. Bone marrow morphology and karyotype have remained normal for >3 years, including after EPAG was discontinued for a robust response.

Figure 6.

Longitudinal follow-up of mutated clone size in responding patients on and off EPAG. Candidate gene mutations were analyzed at baseline, primary end point, the longest time point on continuous EPAG, and the longest time point after EPAG was discontinued for robust response in 12 responding patients. Each panel shows the results in a single patient, with mutated clone size off EPAG (at baseline and at longest follow-up time point off EPAG after robust response) designated by open symbols, and clone size on EPAG (at primary end point and at longest follow-up on EPAG) designated by closed symbols. Specific mutations are listed in supplemental Table 8.