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Genomic landscape of B-other ALL
Table 3. PAX5-involving fusion genes. UPN PAX5 exons
(NM_016734)
Gene symbol
1768 1-6 PML 1826 1-8 PROC 2188 1-5 NOL4L 2319 1-5 CBFA2T3 2415 1-7 CBFA2T2
2544 1-5 CBFA2T3 2548 1-8 PIK3AP1
2564 1-7 ESRRB
2578 1-6 MPRIP
2621 1-8 DNAJA1
2663 1-8 ARHGAP22
2701 1-5 ARHGAP22
2486 2-10 ZCCHC7
Fusion partner Reference Exons
NM_033238 3-9
NM_000312 3-9 NM_080616 3-8 NM_005187 2-12 NM_005093 8-12
NM_005187 4-12
NM_152309 14-17
NM_004452 5-11
NM_015134 11-23
NM_001539 4-9 NM_021226 4-10 NM_021226 5-10 NM_032226 1-2 NM_032226 1-2
Locus
15q24
2q14 20q11.21 16q24 20q11.21
16q24
10q24
14q24
17p11.2
9p13.3 10q11.23 10q11.23 9p21.1 9p21.1
Fusion-related chromosomal imbalances
None
None
dic(9;20)
deletion of 3' part of PAX5
deletion of 3' part of PAX5 and deletion of 5' part of CBFA2T2
None at PAX5 locus, CBFA2T3 locus unclear (multiple CNA across 16q) deletion of 5' part of PIK3AP1 deletion of 3' part of PAX5 and deletion of 5' part of ESRRB
deletion of 3' part of PAX5 and deletion of 5' part of MPRIP
deletion of 5' part of DNAJA1 deletion of 3' part of PAX5 deletion of 3' part of PAX5
None
None
2596 2-10 ZCCHC7
PAX5 fusion partners newly identified in the present study are shown in bold.
In total, we found 11 different PAX5-involving in-frame fusions in 14 patients (Table 3). There were 2 types of fusions (Online Supplementary Figure S3). The more com- mon type was comprised of the 5’ part of PAX5 (exons 1- 5/6/7/8) with the (partially) absent PAX5 transactivation domain (TAD), fused to various partner genes. This type was present in 12 patients, representing 11% of the total B-other cohort (Figure 2). The second type, represented only by the ZCCHC7-PAX5 fusion [generated by intra- chromosomal inversion (Online Supplementary Figure S3)], involved the 3’ part of PAX5 including both the DNA- binding domain and complete TAD (exons 2-10). We iden- tified four novel PAX5 partner genes: ARHGAP22 (n=2), MPRIP, PIK3AP1, and PROC. To the best of our knowl- edge, except for PIK3AP1 (whose deletions were reported in adult ALL40), none of these genes have previously been reported as recurrently affected in BCP-ALL. Interestingly, we found rearrangement of the second PIK3AP1 allele resulting in an in-frame PIK3AP1-WDR5 fusion in the PAX5-PIK3AP1-positive patient.
Intragenic PAX5 amplification was found in six B-rest ALL patients, representing 5% of total B-other cohort (Figure 2). In five out of six patients, amplification encom- passed exons 2-5 (n=4) or exon 5 (n=1), and thus corre- sponded to the recurrent type of amplification, PAX5AMP, which was recently characterized in detail;41 the remain- ing patient had atypical amplification encompassing exons 4-8 (Online Supplementary Figure S5). RNA-sequencing revealed aberrant PAX5 transcripts containing amplified exons in all six patients (Online Supplementary Figure S6). In line with the previous study,41 PAX5AMP was accompanied by the trisomy 5 in three out of five patients.
The PAX5 P80R mutation was found in five patients from the B-rest subset who co-clustered tightly together in
unsupervised HCA (Figure 1D) and represented 5% of the total B-other cohort (Figure 2). The variant allele frequen- cy (VAF) of PAX5 P80R ranged from 32% to 100%. The second PAX5 allele was deleted/lost in four out of five patients and likely inactivated in the remaining patient, with VAF 32% at the genomic but 98% at the mRNA level. We did not find any other genetic lesion which could explain co-clustering of these patients, which sug- gests that the specific expression signature was triggered by PAX5 P80R.
Unlike those with PAX5 P80R, patients with PAX5 fusions or PAX5AMP did not form clear clusters in unsuper- vised HCA; however, via an analysis of differential gene expression, we identified a gene set which distinguished patients with PAX5AMP from the remaining patients in supervised HCA (Online Supplementary Figure S7).
Two and three patients from the B-rest subset co-clus- tered together with ZNF384r and MEF2Dr ALL subtypes, respectively (Figure 1 and Online Supplementary Figure S7). We did not find any common genetic lesion in patients co- clustering with ZNF384r ALL; however, two out of three patients co-clustering with MEF2Dr ALL harbored the ZNF618-NUTM1 fusion. The NUTM1-gene involving fusions were recently shown to occur recurrently in child- hood ALL, outside the established ALL subtypes.7
Frequency and distribution of therapeutically relevant aberrations
The IKZF1plus pattern was found in 14 out of 103 B-other ALLs (BCR-ABL1-like, n=8; ETV6-RUNX1-like, n=2; B- rest ALLs, n=4) and was significantly enriched in the BCR- ABL1-like subtype (Table 2). It has been shown that IKZF1plus has a negative prognostic impact only in patients with detectable MRD at the end of induction.17 All but two
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