Case Report: Diagnosis and Management of Myeloid/Lymphoid Neoplasms with
ETV6::FLT3
Rearrangement
Authors: Pastor Loyola Victor B , Liu Yen-Chun , Blackburn Patrick R. , Neary Jennifer L. , Furtado Larissa B. , Wang Lu , Ross Mary Elizabeth Elizabeth , Ribeiro Raul C. , Eldomery Mohammad K. 
Published: December 2024

Introduction
Myeloid/lymphoid neoplasms with eosinophilia and tyrosine kinase gene fusion is an emerging entity in the fifth edition of WHO Hematolymphoid Tumors. This entity is characterized by tyrosine kinase (TK)-driven genetic alterations and encompasses those with FLT3 rearrangement. The ETV6::FLT3 rearrangement is relatively rare, with approximately 16 documented cases, predominantly affecting adults with myeloid or lymphoid neoplasms associated with eosinophilia (MLN-Eo), MPN-like phenotypes, or MDS-like conditions. In this study, we report a case of an adolescent patient with a myeloid/lymphoid neoplasmdisorder with a complex ETV6::FLT3 rearrangement detected by whole transcriptome (RNA) sequencing.
Material and Methods
Chromosomal analysis and fluorescence in situ hybridization (FISH) were conducted following established diagnostic protocols. Comprehensive genomic testing was performed using a multi-platform approach, which includes whole RNA sequencing genome sequencing, and exome sequencing, as previously detailed by our institution.
Results
The patient is a 13-year-old male who presented with leukocytosis (WBC: 97 - 10*3/mm3). Bone marrow examination showed trilineage hematopoiesis with cytologic atypia in a subset of myeloid cells, but without a definitive increase in blast counts. Cytogenetic analysis of 20 metaphase cells revealed an abnormal karyotype: 46,XY,add(9)(p22),add(12)(p11.2),del(13)(q12)[6]/46,XY[14]. Sequential metaphase FISH using an ETV6 break-apart probe suggested a complex t(12;13) translocation. Transcriptome sequencing detected an in-frame fusion between ETV6 (NM_001987.5) exon 4 and FLT3 (NM_004119.2) exon 14, which included an insertion of 11 amino acids creating a cryptic splice site. This fusion preserved the HLH domain of ETV6 and the TK domains of FLT3, with these findings subsequently confirmed by whole genome sequencing. Diagnosis of myeloid/lymphoid neoplasm with FLT3 rearrangement was established and the patient was started on Gilteritinib targeted therapy and is scheduled to undergo allogeneic hematopoietic stem cell transplantation.
Discussion
Myeloid/lymphoid neoplasmwithETV6::FLT3 is a rare finding in pediatric cases, with only one previous report of a pediatric patient besides 15 adult cases exhibiting MPN, MPN-like, or MDS-Like phenotype. In the reported pediatric case, an 8-month-old with MLN-Eo achieved remission following a treatment regimen that included type-1 FLT3 inhibitors and subsequent hematopoietic stem cell transplantation (HSCT). Recent studies, including comprehensive reviews and patient case reports, suggest that combining FLT3 inhibitors with HSCT offers a promising therapeutic strategy. The reported cases predominantly lack additional somatic/acquired alterations, except for two adult instances with STAG2 alterations related to clonal hematopoiesis. Detection methods for ETV6::FLT3 fusion typically include chromosomal analysis, RT-PCR, genomic testing. In the present case, cytogenetic analysis initially indicated t(12;13). While sequential FISH pointed towards an ETV6 rearrangement, the actual significance of ETV6 (in-frame vs. out-of-frame) could not be determined. Definitive clarification was achieved through whole transcriptome RNA sequencing, which identified the ETV6::FLT3 in-frame fusion.
Whole transcriptome sequencing data aid to establish the diagnosis and timely initiation of therapeutic interventions. Although tyrosine kinase inhibitor (TKI) therapy alone, or combined with chemotherapy, often fails to provide long-term disease control, its use as an initial treatment to reduce disease burden may be beneficial in facilitating successful outcomes. In conclusion, rapid detection of FLT3 rearrangements represents a valuable diagnostic and therapeutic advantage.