Characterization of Leukemias with ETV6-ABL1 Fusion
Authors: Zaliova Marketa , Moorman Anthony V. , Cazzaniga Giovanni , Stanulla Martin , Harvey Richard C. , Roberts Kathryn G. , Heatley Sue L. , Loh Mignon L. , Konopleva Marina , Chen I-Ming , Zimmermannova Olga , Schwab Claire , Smith Owen , Mozziconacci Marie-Joelle , Chabannon Christian , Kim Myungshin , Falkenburg J.H. Frederik , Norton Alice , Marshall Karen , Haas Oskar A. , Starkova Julia , Stuchly Jan , Hunger Stephen P. , White Deborah , Mullighan Charles G. , Willman Cheryl L , Stary Jan , Trka Jan , Zuna Jan 
Published: October 2019

Abstract
Introduction
The ETV6-ABL1 (TEL-ABL) fusion gene is a rare but recurrent genetic aberration found in various hematological malignancies in children and adults. Due to the inverse orientation of ETV6 (12p13) and ABL1 (9q34) an in-frame fusion cannot be produced by a simple balanced translocation and thus results from a complex rearrangement. Alternative splicing generates two fusion transcripts - type A and B without and with ETV6 exon 5, respectively. Both transcripts encode a constitutively active chimeric tyrosine kinase. The effect of ETV6-ABL1 on cellular proliferation, cell survival and transforming capacity mirrors that seen in BCR-ABL1-positive cases. There is a renewed interest in ETV6-ABL1 since the discovery of a "BCR-ABL1-like" (or "Ph-like") gene expression profile (GEP) among B-cell precursor (BCP) ALL cases lacking an established chromosomal abnormality (so-called "B-other ALL"). The BCR-ABL1-like GEP resembles the BCR-ABL1 GEP because both are driven by the activation of kinase signaling. In vitro studies suggest that many of these kinase fusions, including ETV6-ABL1, are sensitive to specific tyrosine kinase inhibitors (TKI), thus representing a promising and relevant therapeutic target, especially given the reported unfavorable prognosis of BCR-ABL1-like ALL. The aim of this study was to characterize the incidence, clinical features and genetic profile of ETV6-ABL1 leukemias with a focus on ALL as an example of a targetable kinase-activating lesion.
Patients and methods
The cohort totals 44 ETV6-ABL1 patients and comprises newly identified cases (n=9), published cases with additional new data (n=11) and cases with re-examined published data (n=24). Half of the patients (n=22) was diagnosed with ALL (13 children, 9 adults) while 22 had a myeloid malignancy (18 CML-like myeloproliferative neoplasm (MPN), 4 AML). Besides routine diagnostic examinations, we analyzed the presence of fusion transcript variants, genomic profile using MLPA and SNP-array, gene expression profile on microarrays and the presence of BCR-ABL1-like expression signature using quantitative PCR-based low density expression arrays.
Results
Systematic screening of >3500 cases revealed that ETV6-ABL1 is rare in childhood ALL (0.17% cases) and slightly more prevalent in adult ALL (0.38%). The equal number of MPN and ALL cases and the relative incidence of ALL and MPN in adulthood suggests ETV6-ABL1 is more common in MPN. The type B variant (including ETV6 exon 5) is the dominant transcript and its detection by PCR screening is a more reliable diagnostic approach than FISH with commercial probes for ETV6-RUNX1 and BCR-ABL1. In BCP ALL, ETV6-ABL1 fusion always localized to the der(12) whereas in T-ALL and myeloid cases the fusion localized to the der(9), der(12) or a third chromosome. The genomic profile of ETV6-ABL1 ALL resembled BCR-ABL1 and BCR-ABL1-like ALL with 80% cases having concurrent CDKN2A/B and IKZF1 deletions. The gene expression signature of ETV6-ABL1 ALL cases was more similar to BCR-ABL1 than BCR-ABL1-like principally due to low CRLF2 expression. Nonetheless, 11/12 ETV6-ABL1 ALL cases were classified as BCR-ABL1-like by a standardized qPCR-based expression array. Survival of ETV6-ABL1-positive ALL is 46% in children (6/13 alive) and 13% in adults (1/8 alive). While prognosis of childhood ALL patients responding well to initial treatment seems to be favorable (3/3 with end-induction MRD < 5x10e-5 are in the 1st remission >4 years from diagnosis), children with inferior response have very poor prognosis. Survival of MPN is 50% (9/18 alive) and depends on the disease status at diagnosis (chronic vs. blastic phase).
Conclusion
ETV6-ABL1 fusion occurs in lymphoid and myeloid leukemia. Its genomic and expression profile, spectrum of malignancies and clinical behavior resemble BCR-ABL1, including the unfavorable prognosis, particularly in acute leukemias. Systematic screening confirmed low frequency of ETV6-ABL1 fusion in ALL. Due to high false-negative rate of FISH, PCR diagnostics are recommended for systematic screening of ALL and FISH-negative CML-like MPN. Despite the generally poor outcome, childhood ALL cases with favorable early treatment response can be treated with standard modern therapeutic protocols. To improve prognosis of the others, early diagnostics of ETV6-ABL1 and treatment with TKI should be considered.
Supported by grants IGA MZ NT/13170-4 and GAUK 694414.

Disclosures
Mullighan: Amgen: Honoraria; Incyte: Consultancy.