Characterization of leukemias with ETV6-ABL1 fusion

Abstract

To characterize the incidence, clinical features and genetics of ETV6-ABL1 leukemias, representing targetable kinase-activating lesions, we analyzed 44 new and published cases of ETV6-ABL1-positive hematologic malignancies [22 cases of acute lymphoblastic leukemia (13 children, 9 adults) and 22 myeloid malignancies (18 myeloproliferative neoplasms, 4 acute myeloid leukemias)]. The presence of the ETV6-ABL1 fusion was ascertained by cytogenetics, fluorescence in-situ hybridization, reverse transcriptase-polymerase chain reaction and RNA sequencing. Genomic and gene expression profiling was performed by single nucleotide polymorphism and expression arrays. Systematic screening of more than 4,500 cases revealed that in acute lymphoblastic leukemia ETV6-ABL1 is rare in childhood (0.17% cases) and slightly more common in adults (0.38%). There is no systematic screening of myeloproliferative neoplasms; however, the number of ETV6-ABL1-positive cases and the relative incidence of acute lymphoblastic leukemia and myeloproliferative neoplasms suggest that in adulthood ETV6-ABL1 is more common in BCR-ABL1-negative chronic myeloid leukemia-like myeloproliferations than in acute lymphoblastic leukemia. The genomic profile of ETV6-ABL1 acute lymphoblastic leukemia resembled that of BCR-ABL1 and BCR-ABL1-like cases with 80% of patients having concurrent CDKN2A/B and IKZF1 deletions. In the gene expression profiling all the ETV6-ABL1-positive samples clustered in close vicinity to BCR-ABL1 cases. All but one of the cases of ETV6-ABL1 acute lymphoblastic leukemia were classified as BCR-ABL1-like by a standardized assay. Over 60% of patients died, irrespectively of the disease or age subgroup examined. In conclusion, ETV6-ABL1 fusion occurs in both lymphoid and myeloid leukemias; the genomic profile and clinical behavior resemble BCR-ABL1-positive malignancies, including the unfavorable prognosis, particularly of acute leukemias. The poor outcome suggests that treatment with tyrosine kinase inhibitors should be considered for patients with this fusion.

Figure 1.

Malignancy subtypes, age and gender distribution of the ETV6-ABL1-positive cases. In childhood, all cases were diagnosed as ALL (albeit one originally manifested as B-lymphoblastic lymphoma). Nine childhood ALL were of BCP and two of T-cell origin. Notably, there were two infants in this group; however, most of the childhood ALL were diagnosed in the preschool/early school age (5–10 years). ALL is dominant until the fourth decade and then it is replaced by MPN, which account for more than 70% of cases in the age categories over 35 years. Overall, the male to female ratio is 1.9: 1 (28:15). While gender distribution is almost even in ALL (M:F 12:10), patients with MPN were predominantly male (M:F 12:5) and all four AML cases were diagnosed in males. *The gender of one case of MPN was not reported.

Figure 2.

Overview and frequency of selected recurrent copy number aberrations in 22 samples (17 ALL, 3 MPN-LBC, 2 MPN-CP) from 18 ETV6-ABL1-positive cases. The most prevalent aberrations detected by the SNP array in ALL/MPN-LBC were deletions of CDKN2A/CDKN2B and deletions of IKZF1 followed by PAX5 (8/17; 47%) and BTG1 (7/17; 41%) deletions. CDKN2A and CDKN2B as well as BTLA and CD200 genes were co-deleted in all cases, thus the pairs are merged into one column. Deletion of ATP10A was recently shown to be a recurrent aberration in BCP-ALL, associated with decreased 10-year event-free survival. Gray indicates loss, black indicates a gain, deleted exons within IKZF1, ABL1 and ETV6 genes are indicated by numerals (for IKZF1 white numerals depict losses resulting in a dominant negative IKZF1 isoform or complete loss of IKZF1 expression, black numerals depict haploinsufficiency with the potential exception of combined 2–3/4–7 loss which can affect either a single allele or both gene alleles and thus can result in either haploinsufficiency or complete loss). For frequencies of the selected recurrent copy number aberrations in published ALL studies see Online Supplementary Figure S4. a: adult; ch: childhood; LBC: lymphoid blast crisis of MPN; CP: chronic phase of MPN. ^$In these cases some of the findings from the SNP array were further refined by multiplex ligation-dependent probe amplification. ^#ABL1 deletions were not found recurrently in the present study, thus, only ABL1 gains were considered for CNA frequency. * The relatively high frequency of ETV6 deletions in ETV6-ABL1-positive cases compared to that in BCR-ABL1-positive ALL probably does not reflect frequency of genuine secondary ETV6 loss but rather results from ETV6 loss during primary genomic rearrangement.

Figure 3.

Unsupervised hierarchical clustering of ETV6-ABL1 cases with a large cohort of BCP-ALL. Twelve ETV6-ABL1 cases clustered with a cohort of 1179 BCP-ALL cases using data from RMA normalized U133_Plus_2.0 arrays. The 1191 samples are shown in columns, while the 257 BCR-ABL1-like predicting probe sets (described previously) are in rows. The yellow box highlights the BCR-ABL1-like cluster. BCR-ABL1, ETV6-ABL1 and other ABL1 and ABL2 fusion (NUP214-ABL1, SNX2-ABL1, ZMIZ1-ABL1, RSCD1-ABL1, RSCD1-ABL2, PAG1-ABL2, ZC3HAV1-ABL2) status is shown with black, red and magenta bars, respectively, across the top of the heatmap. All other Ph-like cases are shown with blue bars using the status defined in their original report. The order of samples in the Ph-like cluster is enlarged on the top (with the same color coding). The order of the ETV6-ABL1 samples as shown in the figure, from left to right is 34-a-MPN (1^st LBC)/08-ch-ALL/10-ch-ALL/09-ch-ALL/06-ch-ALL/14-a-ALL/11-ch-ALL/12-ch-ALL/13-ch-LBL (1^st relapse)/05-ch-ALL (2^nd relapse)/05-ch-ALL (1^st relapse)/34-a-MPN (2^nd LBC).