Molecular studies reveal MLL-MLLT10/AF10 and ARID5B-MLL gene fusions displaced in a case of infantile acute lymphoblastic leukemia with complex karyotype

Abstract

The present report describes a unique infantile acute lymphoblastic leukemia (ALL) case with cryptic mixed-lineage leukemia (MLL) rearrangements with 11q23 chromosomal translocation. MLL break-apart signals were identified by fluorescence in situ hybridization, and transcriptome sequencing revealed MLL-myeloid/lymphoid or mixed-lineage leukemia; translocated To, 10 (MLLT10)/AF10 fusion transcripts. Analysis also revealed a previously unreported MLLT10/AF10-homeobox protein Mohawk (MKX) transcript, where the 5' portion of MLLT10/AF10 at 10p12.31 was fused out-of-frame with the 3' portion of MKX at 10p12.1, which is closely located to MLLT10/AF10. Furthermore, the reciprocal 3'-MLL gene segment was fused in-frame to AT-rich interaction domain (ARID)5B at 10q21. Previously, common allelic variants in ARID5B, which are directly associated with hematopoietic differentiation and development, have been repeatedly and significantly associated with childhood ALL. The heterozygous genotype in ARID5B (RefSNP: rs10821936) increased the risk for leukemia with MLL-rearrangement. In particular, single nucleotide polymorphisms of ARID5B conferred increased risk for MLL-MLLT3/AF9. Based on these findings, the authors propose that while the presence of reciprocal MLL alleles has been detected in this patient, different pathological disease mechanisms may be at play due to individual recombination events.

Keywords: ARID5B; MLL-MLLT10/AF10; acute lymphoblastic leukemia; molecular biology; transcriptome sequencing.

Figure 1.

Cytogenetic analysis suggested the evidence for 11q23 rearrangement. (A) G-banded karyogram from bone marrow cells at diagnosis showed to be 46, XY, t(2;14)(p11.2;q32), add(11)(q23) in 14 of 20 bone marrow cells. The arrow indicates the breakpoint at 11q23. (B) Fluorescence in situ hybridization analysis with MLL probe (Vysis) on interphase nuclei of bone marrow cells at diagnosis. A 11q23 split-signal type was observed: One green signal and one orange signal (divided arrows). A normal signal pattern for the MLL probe (green and red fusion signals) was also observed in the bone marrow cells (arrows). MLL, mixed-lineage leukemia.

Figure 2.

Validation of fusions. (A) Identification of MLL-MLLT10/AF10, MLLT10/AF10-MKX and ARID5B-MLL fusion transcripts in bone marrow cells from the patient using RT-PCR. Marker represents a 1 kb DNA ladder. M, size marker. (B-D) Schematic representation of reverse transcription-polymerase chain reaction products on der(10) and der(11) resulted in MLL-M14LLT10/AF10, MLLT10/AF10-MKX and ARID5B-MLL fusion genes. Sanger sequencing chromatograms showing the reading frame at the breakpoint and putative translation of the fusion protein in the patient's bone marrow cells. ARID5B, AT-rich interaction domain 5B; MLL, mixed-lineage leukemia; MLLT10, myeloid/lymphoid or mixed-lineage leukemia; translocated To, 10.

Figure 3.

Proposed chromosomal mechanism, which leads to MLL-MLLT10/AF10, ARID5B-MLL and MLLT10/AF10-MKX rearrangements in the patient. Paracentric inversion of 10p12.31-p12.1 with a breakpoint in the MLLT10/AF10 gene, followed by an additional break 3′ of MLL prior to translocation of the 11q segment into ARID5B located at 10q21. ARID5B, AT-rich interaction domain 5B; MLL, mixed-lineage leukemia; MLLT10, myeloid/lymphoid or mixed-lineage leukemia; translocated To, 10.