Exome sequencing identifies recurring FLT3 N676K mutations in core-binding factor leukemia

Area of Science:

• Hematology
• Oncology
• Molecular Biology

Background:

• Core-binding factor (CBF) rearrangements, specifically t(8;21) and inv(16)/t(16;16), are common in adult de novo acute myeloid leukemia (AML).
• These genetic alterations involve RUNX1 and CBFB genes and are typically associated with a favorable prognosis.
• However, the expression of fusion genes alone is insufficient for leukemogenesis, suggesting the involvement of cooperating mutations.

Purpose of the Study:

• To identify cooperating mutations in CBF-AML by performing exome sequencing on an AML sample with an inv(16) rearrangement.
• To investigate the role of newly discovered mutations in the collaboration with CBF fusions during leukemogenesis.
• To characterize the functional impact and clinical relevance of identified mutations in a cohort of CBF-AML patients.

Main Methods:

• Exome sequencing was employed to identify mutations in an AML sample with an inv(16) rearrangement.
• A cohort of 84 de novo AML patients with CBFB/MYH11 rearrangement and 36 with RUNX1/RUNX1T1 rearrangement were screened for the identified mutation.
• Functional studies using Ba/F3 cells were conducted to assess the impact of the FLT3-N676K mutant on cell growth and drug resistance.
• Gene expression analysis was performed on AML patient samples.

Main Results:

• A novel N676K mutation in the adenosine triphosphate (ATP)-binding domain of the fms-related tyrosine kinase 3 (FLT3) gene was discovered.
• The FLT3 N676K mutation was identified in 5 out of 84 (6%) patients with CBFB/MYH11 rearrangement and 1 out of 36 (3%) patients with RUNX1/RUNX1T1 rearrangement.
• The FLT3-N676K mutant demonstrated factor-independent growth in Ba/F3 cells and conferred resistance to FLT3 protein tyrosine kinase inhibitors (PTKIs) when combined with FLT3-internal tandem duplication (ITD).
• Gene expression analysis revealed a trend toward a specific expression profile in AML patients with CBFB/MYH11 rearrangement and FLT3 N676K mutation.

Conclusions:

• This study reports the first recurring FLT3 N676 mutations in core-binding factor (CBF) leukemias.
• The findings suggest a distinct subgroup of CBF leukemias characterized by these specific FLT3 mutations.
• The FLT3 N676K mutation may play a collaborative role in leukemogenesis and contribute to therapeutic resistance in a subset of AML patients.