PB1656 TRIADIC FUSIONS AMONG ZNF384, EWSR1 AND EHMT1 GENES IN A PEDIATRIC B‐CELL PRECURSOR ACUTE LYMPHOBLASTIC LEUKEMIA PATIENT WITH PH LIKE CHROMOSOME
Authors: Chen X. , Cao P. , Wang F. , Zhang Y. , Ma X. , Liu M. , Teng W. , Yang J. , Zhang J. , Wang T. , Liu H. 
Published: June 2019

Background:

Fusion genes involving ZNF384 have recently been identified in B‐cell precursor acute lymphoblastic leukemia (BCP‐ALL), and 9 fusion partners have been reported. ZNF384 rearrangements have a distinct gene expression pattern and a characteristic immunophenotype with low CD10 expression and expression of the myeloid markers CD13 and/or CD33, while the clinical features depend on the functional properties of individual fusion partners. Among them, EWSR1‐ZNF384 fusion has been reported in a total of 7 cases to date.

Aims:

We report here triadic fusions among ZNF384, EWSR1 and EHMT1 genes in a 5‐year‐old girl who relapsed with Ph like chromosome eighteen months after initial diagnosis of normal karyotype BCP‐ALL.

Methods:

Conventional laboratory tests including morphologic, immunophenotypic, cytogenetic and molecular cytogenetic analysis were performed for the diagnosis and classification of BCP‐ALL. Whole transcriptome sequencing (WTS) and 30× whole genome sequencing (WGS) were then performed to clarify the atypical gene rearrangement in transcriptional and genomic levels.

Results:

The patient was diagnosed with BCP‐ALL based on laboratory, morphology and immunophenotypic analysis results. The blast cells were partially positive for CD13 and CD33, but negative for CD10. The chromosome karyotype was normal and none of the 36 fusion genes frequently reported in hematological malignancies was detected by reverse transcriptase (RT)‐PCR. The patient was treated with standard ALL chemotherapy and achieved a complete remission (CR). However, she relapsed with an infiltration by 45% blast cells in bone marrow (BM) 18 months after diagnosis. The blast cells were negative for CD10 and abnormally positive for CD13 and CD33. t(9;22)(q34;q11.2) translocation was identified by karyotyping with the ratio of 50% (10/20). However, BCR‐ABL1 fusion transcript was not detected by RT‐PCR, even with the use of a sophisticated designed panel that could theoretically detect all possible common and rare BCR‐ABL1 transcripts. Fluorescence in situ hybridization (FISH) using BCR/ABL1 dual color, dual fusion translocation probe showed atypical fusion signals with a significantly lower percentage (30/500, 6%) than the aberrant karyotypes. WTS analysis revealed triadic fusions involving 3 genes: in‐frame fusion of EWSR1 exon 6 to ZNF384 exon 7; out‐frame fusion of ZNF384 exon 6 to EHMT1 exon2; out‐frame fusion of EHMT1 exon1 to EWSR1 exon 7. We speculate that EWSR1‐ZNF384 is the key pathogenic fusion according to structural analysis and literature reports. WGS analysis revealed breakpoints in EWSR1 intron 6, ZNF384 intron 6, and EHMT1 intron 1, respectively. Fusion points in both EWSR1 and ZNF384 were differ from those of the 4 reported cases with known fusion points. The patient was treated with CD19‐directed CAR‐T cell therapy 20 days after relapse and achieved CR. She then underwent allogeneic hematopoietic stem cell transplantation and has survived for more than 10 months now.

Summary/Conclusion:

We identified unique triadic fusions among ZNF384, EWSR1 and EHMT1 genes in a relapsed pediatric BCP‐ALL patient with Ph like chromosome detected by karyotyping. WTS plays an important role in elucidating the key pathogenic and rare fusion pattern. Further studies involving a large series of patients should be conducted to elucidate the oncogenic properties of EWSR1‐ZNF384 and confirm the clinical and biological features of patients with BCP‐ALL harboring the EWSR1‐ZNF384 fusion gene.