The MLL recombinome of acute leukemias in 2013

Abstract

Chromosomal rearrangements of the human MLL (mixed lineage leukemia) gene are associated with high-risk infant, pediatric, adult and therapy-induced acute leukemias. We used long-distance inverse-polymerase chain reaction to characterize the chromosomal rearrangement of individual acute leukemia patients. We present data of the molecular characterization of 1590 MLL-rearranged biopsy samples obtained from acute leukemia patients. The precise localization of genomic breakpoints within the MLL gene and the involved translocation partner genes (TPGs) were determined and novel TPGs identified. All patients were classified according to their gender (852 females and 745 males), age at diagnosis (558 infant, 416 pediatric and 616 adult leukemia patients) and other clinical criteria. Combined data of our study and recently published data revealed a total of 121 different MLL rearrangements, of which 79 TPGs are now characterized at the molecular level. However, only seven rearrangements seem to be predominantly associated with illegitimate recombinations of the MLL gene (≈ 90%): AFF1/AF4, MLLT3/AF9, MLLT1/ENL, MLLT10/AF10, ELL, partial tandem duplications (MLL PTDs) and MLLT4/AF6, respectively. The MLL breakpoint distributions for all clinical relevant subtypes (gender, disease type, age at diagnosis, reciprocal, complex and therapy-induced translocations) are presented. Finally, we present the extending network of reciprocal MLL fusions deriving from complex rearrangements.

Figure 1

Age distribution of investigated patients. The age distribution of all analyzed patients (n=1690) is summarized. (Upper part) Diagram displaying ALL and AML patients. Age at diagnosis was for infants (0–1 year), pediatric (1–18 years) and adult patients (>18 years). The number of ALL, AML and other patients is listed below. We also added the information about TIL patients, the number of complex MLL rearrangements (CL) and specified the ‘Non-ALL' and ‘Non-AML' patients (MLL, myelodysplastic syndrome (MDS), primary myelofibrosis (PMF) and unknown) in more detail for each age group. The precise number of patient cases summarized on the right.

Figure 2

Classification of patients according to age classes and disease type. (Top) Frequency of most frequent TPGs in the investigated patient cohort of MLL-rearranged acute leukemia patients (n=1590). This patient cohort was divided into ALL (left) and AML patients (right). Gene names are written in black, and percentages are indicated as white numbers. Thirty-three patients could not be classified into the ALL or the AML disease types, respectively. (Middle) TPG frequencies for the infant, pediatric and adult patient group. (Bottom) Subdivision of all three age groups into ALL and AML patients. Negative numbers confer again to the number of patients who were neither classified to the ‘ALL' nor to the ‘AML' subgroup.

Figure 3

World distribution of patients. (Top) Worldmap grossly dividing the investigated patients into three distinct subgroups: American, European and Asian countries. The number of investigated patients is shown and the contribution of individual countries is given in patient numbers. Each country is indicated by its international country code. (Below) Information about the patient cohort. Mean age, age range and the amount of infants (I), pediatric (P) and adult patients (A) is indicated. In addition, we added the amount of therapy-induced malignancies in number and percentage. The breakpoint distribution for each subgroup within MLL exon 9/intron 9, MLL exon 10/intron 10 and MLL exon 11/intron 11 is displayed. Red mark in MLL intron 11: fragile site within MLL that is sensible to exogenous drug exposure.

Figure 4

General recombination mechanism and associated TPGs. (Top) Genes are categorized either by reciprocal chromosomal translocation (rCTL; n=51), spliced fusion (Spl; n=3), inversions at 11p/q (Inv; n=9), insertions (Ins1 and Ins2; n=12) or 11q deletions (Del; n=4). (Bottom) All identified recombination events, arranged according to the number of DNA double-strand breaks (DSBs) necessary to explain the recombination event. Green: Chromosome 11; red and orange: partner chromosomes involved in the recombination process. Green vertical bars: MLL; red, orange, blue and pink vertical bars: partner genes involved in recombination events; derivative 11 chromosomes is always depicted by ‘Der'. Black and white horizontal lines: recombination sites on wild-type and derivative chromosomes. rCTL: reciprocal chromosomal translocation; Del/Inv: deletion/inversion; 3 W-CTL: three-way chromosomal translocation; CTL+Δ: chromosomal translocation including deletion(s); Ins1: chromosomal fragment including portions of the MLL gene is inserted into a partner chromosome; Ins2: chromosomal fragment including portions of a partner gene is inserted into the MLL gene; cCTL: complex chromosomal translocations, for example, by chromothripsis.

Figure 5

Common pathways of the most frequent MLL fusions. The four most frequent MLL fusions, MLL-ENL, MLL-AF9, MLL-AF10 and AF4-MLL, are either interacting directly with the AF4 complex or are mimicking the AF4 complex in case of AF4-MLL. The crucial components within the AF4 complex are the P-TEFb kinase and the H3K79 HMT DOT1L protein. Hyperactive AF4 or AF4-MLL is strongly enhances the transcriptional processes. In addition, changes in the steady-state AF4 complex stability is causing extended H3K79me2/3 signatures. Future inhibitory strategies are indicated in red.