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M. Zaliova et al.
Figure 4. Frequency and distribution of kinase aberrations. The graphs are proportional to (sub)cohort sizes (number of patients in the total B-other cohort and in individual subtypes). *The one patient who was analyzed by RNA-sequencing only at relapse is not included in this analysis.
immunophenotype and these were significantly enriched in ZNF384r ALL [MPALs comprised 67% (4 out of 6) of ZNF384r vs. 3% (3 out of 104) of non-ZNF384r ALLs; P<0.0001].
Genomic characterization of the study cohort
Genomic aberrations were analyzed by SNPa, WES, RNA-sequencing and PCR. On average, we found 9 CNAs/UPDs per patient by SNPa (range 0-35) and 14 mutations [single nucleotide variants (SNVs), insertions/deletions (indels)] by WES (range 1-65) (Online Supplementary Tables S7 and S8). In total, we identified 18 recurrently (in ≥2 patients) mutated genes by WES, and 43 recurrent chromosomal imbalances and CNAs subtracted to genes by SNPa; all had already been reported to occur in ALL. In addition to IGH-DUX4, we found 41 different fusion transcripts including 23 that were novel: 24 were in- frame (13 out of 24 novel), 9 contained a full coding sequence of one partner gene (3 out of 9 novel), and 8 were out-of-frame (7 out of 8 novel) (Online Supplementary Table S9). Subclonal deletions of ERG and P2RY8-CRLF2 fusions were detected by PCR in 11 and ten patients negative for these lesions by SNPa and RNA-sequencing, respectively. All recurrent findings are shown together with clinical parameters in Figure 3 and Online Supplementary Table S6.
Specific genetic features of the B-other-derived acute lymphoblastic leukemia subtypes
No significant differences were observed in numbers of CNAs/UPDs or SNVs/indels comparing individual ALL
subtypes except for a significantly lower number of CNAs/UPDs in DUX4r versus remaining ALL cases (4±0.5 vs. 10±0.9; P<0.0001) (Online Supplementary Figure S2). Apart from the MEF2Dr and iAMP21 ALL, which were represent- ed by a very low number of patients, each of the remaining subtypes was significantly enriched for specific genetic aberrations (Table 2). ERGdel occurred in 63% of DUX4r ALL but not in non-DUX4r ALL patients. Aberrations of TBLXR1 and DMD genes were also enriched in DUX4r ALL. BCR-ABL1-like ALL was enriched for the CRLF2 fusions, IKZF1del, both constitutional and somatic trisomy 21, and deletions of EBF1. Mutations in the KMT2D and SETD2 genes (encoding histone methyltransferases) were mutually exclusive and occurred in 5 out of 6 ZNF384r ALL patients. In agreement with our previous study, all ETV6- RUNX1-like patients harbored an ETV6 aberration (5 out of 5 had a deletion and 2 out of 5 had a fusion). This subtype was also enriched for ARPP21 deletions, deletions of his- tone gene cluster on 6p22.2, and BTG1 aberrations.
Specific genetic features of the B-rest acute lymphoblastic leukemia subset
The B-rest subset was significantly enriched for the PAX5 fusions, PAX5 amplifications, PAX5 P80R mutation, CDKN2A/B deletions, dic(9;20), and TOX deletions com- pared to remaining B-other ALLs. It is worthy of note that the PAX5 fusions, amplifications and P80R mutations and TOX deletions occurred exclusively in the B-rest subset; 6 out of 8 TOX deletions occurred together with the PAX5 fusions (Table 2).
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haematologica | 2019; 104(7)