KIT mutations in pediatric, core binding factor (CBF), acute myeloid leukemia (AML) 

Core binding factor (CBF)* acute myeloid leukemia (AML) is present in 20–30% of pediatric cases and is associated with favorable outcomes. The co-occurrence of KIT mutations, found in 20–40% of patients, has been reported to be a negative prognostic factor in some studies, however, other contradictory studies reported no association between KIT mutation and clinical outcome.¹ Whilst the European Leukemia Network (ELN) 2017 guidelines recognize that CBF AML with KIT mutations appear to be associated with a poorer prognosis, they do not recommend patients are assigned to a different genetic risk category.²

To better determine whether KIT mutations are of prognostic significance in CBF AML, Katherine Tarlock, Fred Hutchinson Cancer Research Center and Seattle Children’s Hospital, Seattle, US, and colleagues conducted a study, recently published in Clinical Cancer Research.¹ They aimed to:

• Identify the functional impact of distinct KIT mutation subsets
• Analyze the response of different KIT mutants to tyrosine kinase inhibitors (TKIs) in vitro
• Define the prognostic impact of KIT ⁺ CBF AML using data from a phase III trial, COG AAML0531 (NCT01407757)

_{* CBF AML is associated with the cytogenetic abnormalities translocation (t)(8;21)(q22;q22) and inversion(16)(p13;1q22)/t(16;16)(p13;q22)}

Background¹

The KIT proto-oncogene encodes a transmembrane glycoprotein type III receptor tyrosine kinase (RTK). KIT mutations cause significant oncogenic events as they affect RTK activity. In some malignancies with KIT mutations, such as gastrointestinal stromal tumors, melanomas, and mastocytosis. TKIs have proven effective and have become standard-of-care for first-line therapeutic approaches.

Study design and patient characteristics¹

• Evaluated two KIT mutations:
  • Immunoglobulin G (IgG) domain - exon 8 (E8)
  • Tyrosine kinase domain (TKD) - exon 17 (E17)
• Used data from the phase III study COG AAML0531 (NCT01407757) to analyze patient outcomes by mutation status (KIT⁺ vs KIT^-) and mutation location (E8 vs E17)
  • Study compared the use of the CD33-targeted antibody-drug conjugate, gemtuzumab ozogamicin (GO) in combination with conventional chemotherapy, to conventional chemotherapy alone
  • Of the total patient population (N= 1,022), 247 eligible patients were identified with CBF AML, of whom 205 had available bone marrow (BM) or peripheral blood specimens for KIT analysis
  • KIT mutations were identified in 63 patients (31%). These were located in:
    • E8 only: 22 (35%)
    • E17 only: 32 (51%)
    • Both E8 and E17: 6 (10%)
    • Alternative exons: 3 (5%)
  • Outcomes of patients with KIT⁺ (n= 63) were compared to those who were KIT^- (n= 142)
    • No significant differences in baseline characteristics between two groups and no difference in treatment assignment
    • KIT⁺ patients had a higher percentage of BM blast cells and peripheral blasts cells

Results¹

Growth characteristics of transduced cells in vitro

• HEK293 cells transduced with E8 mutations in the IgG domain (D419G, D419del) showed:
  • No KIT phosphorylation
  • No interleukin-3 (IL-3) independent proliferation when transduced into Ba/F3 cells
• HEK293 cells transduced with E17 mutations in the TKD (D816V, N822K) showed:
  • Autonomous receptor phosphorylation
  • IL-3 independent proliferation in Ba/F3 cells

Response of transduced cells to TKI in vitro

• Ba/F3 cells (E17 variants): uniquely susceptible to the TKIs, dasatinib and crenolanib
  • Both dasatinib and crenolanib provided an apoptotic effect
  • Supports E17 mutations as therapeutic targets in AML
• Ba/F3 cells (parental or KIT^-): no response to TKIs with IC₅₀s > 10,000 nmol/L
  • Cells transduced with E8 KIT mutations were insensitive to the cytotoxic effects of TKIs
• These results support the investigation of using TKIs in patients with E17, but not E8, CBF AML

Clinical analysis

The prognostic significance of KIT mutations was analyzed by comparing outcomes between patients with KIT⁺ and KIT^- CBF AML (Table 1).

• Five-year overall survival (OS) was comparable between both groups
• There was an overall trend for decreased event-free survival (EFS) and disease-free survival (DFS), and increased relapse rate (RR) in KIT⁺ patients
• In patients who received traditional chemotherapy, those with KIT mutations had inferior EFS, DFS and a higher RR
• When comparing outcomes by location of KIT mutation and treatment type (Tables 2–4)
  • E8 KIT⁺ patients: no improvement in outcome when treated with GO
  • E17 KIT⁺ patients: DFS and RR were comparable to KIT^- patients indicating a trend towards improved outcomes in this subset of patients. Indicates GO abrogated the negative impact of E17 KIT mutation

In the Tables below, statistically significant results are indicated in a bold font.

Table 1. Comparison of outcomes to evaluate the impact of KIT mutations

	KIT+ (%)	KIT- (%)		p value
Five-year OS	78 ± 12	81% ± 7		0.905
Patients in CR
DFS	55 ± 14	73 ± 8		0.040
RR	43 ± 14	21 ± 8		0.005
Treatment with conventional chemotherapy only
EFS	44 ± 20		70 ± 11	0.021
DFS	43 ± 20		69 ± 12	0.034
RR	57 ± 21		28 ± 12	0.013

Table 2. Comparison of outcomes in patients with E17 KIT mutations, overall and by treatment

	KIT+ (%)	KIT- (%)	p value
E17 KIT+ versus KIT-
OS	72 ± 17	81 ± 7	0.478
DFS	51 ± 18	73 ± 8	0.027
RR	46 ± 19	21 ± 8	0.007
E17 KIT+ versus KIT- treated with GO
DFS	67 ± 24	78 ± 11	0.396
RR	27 ± 24	13 ± 9	0.207
E17 KIT+ versus KIT- treated with conventional chemotherapy
DFS	35 ± 25	69 ± 12	0.021
RR	65 ± 27	28 ± 12	0.010

Table 3. Comparison of outcome in E17 KIT⁺ by treatment type

	GO (%)	Conventional chemotherapy	p value
DFS	67 ± 24	35 ± 25	0.161
RR	27 ± 24	65 ± 27	0.062

Table 4. Comparison of outcomes in patients with E8 KIT mutations, overall and by treatment

	KIT+ (%)	KIT- (%)	p value
E8 KIT+ versus KIT-
OS	91 ± 12	81 ± 7	0.302
DFS	60 ± 22	73 ± 8	0.305
RR	40 ± 23	21 ± 8	0.072
E8 KIT+ versus KIT- treated with GO
OS	100 ± 0	77 ± 10	0.092
DFS	64 ± 29	78 ± 11	0.456
RR	36± 31	13 ± 9	0.082

Advantages and limitations of analysis¹

Advantages

• Patients were homogenously treated with the same chemotherapy backbone
  • Provides an insight into distinct functional properties of KIT mutations in context of GO treatment
• Large scale analysis: allowed investigation by location of KIT mutation
• Investigated CD33-targeted therapy in KIT⁺ CBF AML
  • Provides an insight into the potential therapeutic efficacy of anti-CD33 agents in this population

Limitations

• Prognostic impact of KIT mutations may be influenced by therapy (inclusion of GO and no GO patients)
• A larger cohort size would be required to definitively confirm these results

Conclusions¹

In vitro:

• KIT mutations in E17 were associated with aberrant KIT phosphorylation, and a higher sensitivity to KIT-directed TKIs in vitro
• KIT mutations in E8 had no functional impact

In vivo

• Patients with E17-mutated CBF AML form a high-risk subgroup
• Despite a lower CD33 expression than other AML subgroups, this study supports the use of CD33-targeted, intensive treatment for the E17 KIT⁺ subgroup
• Adding a TKI to pediatric CBF AML treatment may be an important strategy
  • TKIs have been shown to be safe when combined with intensive chemotherapy