Intragenic amplification of PAX5: a novel subgroup in B-cell precursor acute lymphoblastic leukemia?

Abstract

Intragenic PAX5 amplification defines a novel, relapse-prone subtype of B-cell precursor acute lymphoblastic leukemia with a poor outcome.

Graphical abstract

Figure 1.

MLPA and SNP6.0 profiles of patients with PAX5^AMP. (A) Example of MLPA results using the P335 IKZF1 MLPA kit. The plot shows the probe ratio for each target contained in the kit (EBF1, 4 probes; IKZF1, 8 probes; CDKN2A/B, 3 probes; PAX5, 6 probes; ETV6, 6 probes; BTG1, 4 probes; RB1, 5 probes; and the PAR1 region, CRLF2, CSF2RA, and IL3RA, 1 probe each). Probe ratio values between 0.75 and 1.3 were considered to be within the normal range, equivalent to the normal copy number of 2. Values <0.75 or >1.3 indicated loss or gain, respectively, and a value <0.25 indicated biallelic loss. These values correspond to copy numbers of 1, 3 and 4, and 0, respectively. A value ≥2.0 corresponds to a copy number of ≥4 and was interpreted as amplification. Approximate copy numbers of amplified exons ranged from 4 to 22 (median, 5.86). Ratio values of 1 representative patient (patient 64) showing amplification of PAX5 encompassing exons 2 and 5, gain of EBF1 consistent with trisomy 5 in this patient, monoallelic loss of IKZF1, and biallelic loss of CDKN2A/B. (B) Copy number profiles (log2ratio) of the PAX5 locus of 8 patients with PAX5^AMP processed on the SNP6.0 array. *In patient 79, PAX5 amplification was identified at relapse with no material available from diagnosis. **Patient 60 shows amplification of exon 5 only and gain of exons 1 to 4. (C) Exon and protein structure of PAX5; the amplified region encodes the DNA-binding paired domain and the octapeptid motif. PD, paired DNA-binding domain (amino acids 16-142); O, octapeptide (aa 179-186); H, homeodomain (aa 228-254); TA, transactivation domain (aa 304-391); I, inhibitory domain (aa 359-391).

Figure 2.

Genetic features of patients with PAX5^AMP. (A) Data for the 77 patients with intragenic amplification of PAX5 identified at diagnosis. The copy numbers for each PAX5 exon and the other genes targeted by the P335 IKZF1 MLPA kit are shown. Cytogenetic results were available for 57 patients, with abnormalities involving the short arm of chromosome 9, trisomy 5, and monosomy 7 being the most common recurrent chromosomal abnormalities. †In patient 31, the probe ratio values for exons 2 and 5 were just below the cutoff of 2 for ≥4 copies; because the percentage of blast cells was low at 83.5%, this result was interpreted as amplification. ‡In patient 69, MLPA showed that exon 2 had a ratio of 2.42 and exon 5 of 1.69; however on the single-nucleotide polymorphism array, exons 2 to 5 were amplified. (B) Data from 9 matched diagnosis-relapse pairs. *In patient 37, the difference in copy number of the amplified exons between diagnosis and relapse was due to reduced percentage of blasts at relapse. **P2RY8-CRLF2 fusion assessed by MLPA, FISH, and/or reverse-transcriptase polymerase chain reaction. ***Patient 16 presented with partial trisomy of chromosome 5 as a result of an unbalanced translocation involving chromosomes 1 and 5: 47,XY,der(1)(1qter-1p21::5q?34-5qter),+der(5)(5pter-5q15::1p21-1pter).