Nanopore sequencing sheds a light on the FLT3 gene mutations complexity in acute promyelocytic leukemia

Abstract

Acute promyelocytic leukemia (APL) patients carry in 27% of cases an activating mutation of the fms-like tyrosine kinase-3 (FLT3) gene: internal tandem duplication (ITD) or tyrosine kinase domain (TKD) point mutation. The simultaneous presence of both types of mutations, so-called FLT3 dual mutations, has been reported in 2% of APL, but this circumstance has never been studied. We studied a cohort of 74 APL cases, performing an in-depth analysis of three FLT3 dual mutant cases. Nanopore sequencing (NS) allowed us to characterize their complex mutational profile, showing the occurrence of multiple activating FLT3 mutations on different alleles in the leukemic promyelocytes and suggesting a cumulative impact of these events on the constitutive activation of the FLT3 pathway in APL cells. NS approach not only sheds light on the FLT3 mutational complexity in APL, but may also be useful to better clarify the FLT3 mutations landscape in acute myeloid leukemia.

Keywords:

• FLT3 dual mutations
• acute promyelocytic leukemia
• nanopore sequencing
• phasing mutations

Acknowledgements

This work was supported by ‘Associazione Italiana contro le Leucemie (AIL)-BARI’.

Ethical approval

All mandatory laboratory health and safety procedures have been complied with in the course of conducting any experimental work reported in this paper.

Author contributions

CC, PO and FA conceived and designed the study, and wrote the manuscript. CC, LA and AZ performed the main experiments. PO and CFM performed all bioinformatics analysis. NC, GT, EP, MRC, LI, and IR performed diagnostic molecular analysis. PC and FT provided clinical data. GS, PM, and FA reviewed and edited the manuscript. FA supervised the manuscript preparation. All authors read and approved the final manuscript.

Disclosure statement

The authors report no conflict of interest.

Data availability statement

The sequence data from this study have been submitted to the National Center for Biotechnology Information (NCBI) Short Read Archive (https://www.ncbi.nlm.nih.gov/sra/) under accession Number PRJNA668375.