New insights to the MLL recombinome of acute leukemias

Abstract

Chromosomal rearrangements of the human MLL gene are associated with high-risk pediatric, adult and therapy-associated acute leukemias. These patients need to be identified, treated appropriately and minimal residual disease was monitored by quantitative PCR techniques. Genomic DNA was isolated from individual acute leukemia patients to identify and characterize chromosomal rearrangements involving the human MLL gene. A total of 760 MLL-rearranged biopsy samples obtained from 384 pediatric and 376 adult leukemia patients were characterized at the molecular level. The distribution of MLL breakpoints for clinical subtypes (acute lymphoblastic leukemia, acute myeloid leukemia, pediatric and adult) and fused translocation partner genes (TPGs) will be presented, including novel MLL fusion genes. Combined data of our study and recently published data revealed 104 different MLL rearrangements of which 64 TPGs are now characterized on the molecular level. Nine TPGs seem to be predominantly involved in genetic recombinations of MLL: AFF1/AF4, MLLT3/ AF9, MLLT1/ENL, MLLT10/AF10, MLLT4/AF6, ELL, EPS15/AF1P, MLLT6/AF17 and SEPT6, respectively. Moreover, we describe for the first time the genetic network of reciprocal MLL gene fusions deriving from complex rearrangements.

The heterogeneity of pediatric MLL-rearranged acute myeloid leukemia

“…10 As GEP is not yet feasible for diagnostic purposes and long-distance inverse-PCR for MLL rearrangements is currently performed at one center, FISH is currently the state-of-the-art method for detection of MLL-rearranged leukemia, but could lead to false-negative results. Therefore, we would suggest that FISH and long-distance inverse-PCR are the methods of choice to detect MLL rearrangements.…”

“…9 Recent studies show that the MLL group itself is genetically and clinically heterogeneous, as more than 60 different translocation partners of the MLL gene with differences in outcome have been described to date. 6,10 The biological background of these differences remains unknown.…”

Detection of fusion genes at the protein level in leukemia patients via the flow cytometric immunobead assay

“…Thus far, at least 64 different MLL partner genes have been identified in acute leukemia patients [33,34]. Despite this exceptionally high number of different partner genes, only six different partner genes are found in w85% of acute leukemias with an MLL fusion gene: AF4, AF9, ENL, AF10, AF6 and ELL [34].…”

“…This multiplex immunobead assay can detect in a single step the most frequently occurring MLL fusion proteins in MLL þ acute leukemias. (Table 3) [33,34]. Also, the prognosis of these MLL gene aberrations ranges from mainly poor for most MLL gene aberrations to fairly good for, for instance, MLL-AF9 in AML.…”

Targeted next generation sequencing of clinically significant gene mutations and translocations in leukemia

“…Although FISH offers increased sensitivity over conventional cytogenetics, the identification of novel translocation partners, such as those involving the MLL locus, or variant breakpoints requires the use of multiple probes, again increasing the cost and complexity of testing. 13,14 Although the acquisition of next generation sequencing data is now relatively straightforward (see Mardis 15 for an excellent review), its analysis can be extremely complicated and time consuming due not only to the volume of data (often 4100 GB/ run), but also the computational difficulty in aligning short reads ( Figure 1). Next generation sequencing, as opposed to conventional Sanger sequencing, relies on massive parallelization of the sequencing process to generate large numbers of reads; however, these reads are generally much shorter (36-400 bp) than those obtained by Sanger sequencing.…”