Acute myeloid leukemia: Molecular genetics

INTRODUCTION — 

Acute myeloid leukemia (AML) develops as the consequence of a series of genetic changes in a hematopoietic precursor cell. These changes alter normal hematopoietic growth and differentiation, resulting in an accumulation of large numbers of abnormal, immature myeloid cells in the bone marrow and peripheral blood. These cells are capable of dividing and proliferating, but cannot differentiate into mature hematopoietic cells (ie, neutrophils).

Similar to other malignancies, the genetic alterations in AML include mutation of oncogenes as well as the loss of tumor suppressor genes. In contrast to most solid tumors, many hematologic malignancies are associated with a single characteristic cytogenetic abnormality (eg, the Philadelphia chromosome [t(9;22)] in chronic myeloid leukemia and t(15;17) in acute promyelocytic leukemia).

Advances in the identification of recurring chromosomal abnormalities and translocations have provided major insight into the pathobiology of AML. (See "Tools for genetics and genomics: Cytogenetics and molecular genetics".)

Specific cytogenetic abnormalities identified by karyotype analysis have considerable prognostic significance for patients with AML and affect treatment planning (table 1). Abnormalities in certain genes (eg, mutations in FLT3, NPM1, KIT) as well as gene expression profiles confer prognostic significance in adult patients with AML. Even those patients without obvious abnormalities detected by karyotypic analysis or gene expression profiles have acquired copy number alterations that may help to identify genes important for the pathogenesis of AML [1,2]. (See "Acute myeloid leukemia: Risk factors and prognosis".)

The focus of this topic review will be on the various molecular genetic events involved in the pathogenesis of AML. More general discussions of genetic events in hematologic malignancies are presented separately. (See "Genetic abnormalities in hematologic and lymphoid malignancies" and "General aspects of cytogenetic analysis in hematologic malignancies".)

GENE MUTATIONS — 

On average, de novo AML cases contain more than 10 significant gene mutations, many of which can be broadly grouped into nine categories of genes thought to participate in leukemogenesis: DNA methylation, tumor suppressors, transcription factor fusions, nucleophosmin, signaling molecules, chromatin modification, myeloid transcription factors, the cohesin complex, and the spliceosome complex [3]. The most commonly mutated genes are: FLT3 (28 percent), NPM1 (27 percent), DNMT3A (26 percent), IDH1 or IDH2 (20 percent), NRAS or KRAS (12 percent), RUNX1 (10 percent), TET2 (8 percent), TP53 (8 percent), CEBPA (6 percent), and WT1 (6 percent).

The nature of the genetic lesions that are required to establish AML is not well defined, but the combination of mutations in any given AML is not random [4,5]. As examples, mutations in genes that encode signaling molecules (eg, FLT3, RAS) often accompany chromosomal rearrangements that target hematopoietic transcription factors (eg, PML::RARA, CBFB::MYH11) or key hematopoietic transcription factors (eg, CEBPA, RUNX1). Conversely, mutations of genes in a single physiologic pathway are often mutually exclusive; as an example, it is uncommon to find mutations of more than one gene that regulates DNA demethylation (eg, TET2, IDH) in a given AML sample.

The pathogenetic effects of some of these mutations will be discussed here. The prognostic value of gene mutations in patients with AML is discussed separately. (See "Acute myeloid leukemia: Risk factors and prognosis".)

Mutations affecting DNA methylation — Gene mutations that affect DNA methylation have been identified in patients with AML. These mutations may result in the expression of genes that are normally silenced or in the silencing of genes that are normally expressed. DNA methylation patterns may also have prognostic significance [6].

DNA methylation involves the addition of a methyl group to cytosine or adenine residues within DNA. Hypermethylated genes are generally not expressed (ie, silenced); as such, DNA methylation provides an epigenetic method for altering gene expression. This process is an essential component of normal development and cell differentiation, and alterations in DNA methylation may impair cell differentiation, as is seen in AML [7].

Mutations associated with AML are found in genes that encode enzymes involved in both DNA methylation (eg, DNMTs) and DNA demethylation (eg, IDH, WT1, TET2). Deregulation of the IDH/WT1/TET2 axis is seen in as many as one-third of patients with AML, but mutations in genes associated with DNA demethylation are usually mutually exclusive in a given AML sample. The critical downstream targets of these changes in DNA methylation have not yet been identified.

DNMT mutations — DNA methyltransferases (DNMTs) are enzymes responsible for initiating and/or maintaining DNA methylation in mammalian cells. Without DNMTs, cells would gradually lose methyl groups from their DNA, leading to the expression of genes that are usually silenced. In one study, DNMT3A mutations were found in 22 percent of 281 patients with de novo AML [8]. When compared with patients without such mutations, patients with DNMT3A mutations had a significantly shorter median survival (12 versus 41 months). Another DNA sequencing study suggested that the rate of DNMT3A mutations varies by AML subtype, with the highest rate (20 percent) seen among cases of acute monocytic leukemia (ie, FAB M5) [9].

TET mutations — The TET (ten-eleven translocation) genes encode proteins with enzymatic activity that initiate the multistep process of DNA demethylation [10]. Somatic mutations in TET2 occur in approximately 15 percent of myeloid cancers, including AML [11]. Mutations of TET2 result in increased methylation and silencing of genes that are normally expressed. In mice, ablation of TET2 alters the function of hematopoietic stem cells and induces myeloid leukemia [12]. WT1 (Wilms tumor 1) is an interaction partner of TET2, and regulates TET2 binding to DNA, thereby providing another mechanism that can alter DNA methylation [13,14]. (See 'Tumor suppressor genes' below.)

IDH mutations — IDH (isocitrate dehydrogenase) enzymes catalyze the conversion of isocitrate to alpha-ketoglutarate. Mutated IDH enzymes generate the "oncometabolite" 2-hydroxyglutarate, which inhibits TET2 function. Mutations of IDH1 and IDH2 are found in approximately 7 and 9 percent, respectively, of patients with AML, and are generally found in AML with a normal karyotype [15,16]. (See "Acute myeloid leukemia: Risk factors and prognosis", section on 'IDH1'.)

ASXL mutations — The function of ASXL (additional sex combs-like) proteins is poorly understood, but they may act as epigenetic regulators by serving as scaffolds for transcription activators, repressors, and related proteins [17]. (See "Acute myeloid leukemia: Risk factors and prognosis", section on 'ASXL1'.)

Tumor suppressor genes — Abnormalities of several tumor suppressor genes have been well characterized in myeloid leukemias. These are described in the following sections.

TP53 mutations — Progression to blast crisis in CML is commonly associated with acquisition of mutations in TP53 [18-20]. In AML, only approximately 7 percent of cases have known TP53 mutations at the time of diagnosis, although the incidence of TP53 abnormalities may be higher in patients with AML evolving from a prior myelodysplastic syndrome (MDS) [21], in AML associated with 11q23 translocations [22,23], and in AML with complex karyotype [24]. (See "Chronic myeloid leukemia-blast phase: Diagnosis and treatment" and "Acute myeloid leukemia: Risk factors and prognosis", section on 'TP53'.)

WT1 mutations — The Wilms tumor suppressor gene (WT1) is overexpressed in the leukemic blasts of approximately 75 percent of cases of newly diagnosed AML [25,26]. The WT1 gene, located at chromosome 11p13, encodes a transcription factor expressed mainly in kidneys and gonads [27,28], but it is also expressed in normal CD34+/CD38– hematopoietic progenitor cells [29]. In AML, high WT1 levels at diagnosis have, in some studies, been shown to correlate with lower remission rates and overall survival [25,26].

NF1 mutations — Patients with neurofibromatosis and mutations of the NF1 tumor suppressor gene have a high rate of developing neoplasms, including progression of MDS into AML [30,31].

Other tumor suppressor mutations — Some tumor suppressors that are commonly associated with other malignancies (eg, lymphomas) are infrequently found in AML, whereas certain as-yet-unidentified regulators may be located at chromosomal regions that are frequently deleted in AML.

Examples include the following:

●INK4 (ie, p16) is a cyclin dependent kinase inhibitor that is frequently deleted in acute lymphoblastic leukemia, but is only very rarely mutated in AML [32].

●BCL2 (B cell leukemia/lymphoma-2) is overexpressed in a wide variety of lymphoid malignancies as a result of t(14;18), which juxtaposes BCL2 with the Ig heavy chain locus. BCL-2 overexpression in AML has been reported only rarely, but in a study of patients with newly diagnosed AML, a multivariate analysis showed that BCL2 overexpression was associated with lower complete remission rates and a significantly shorter survival [33]. (See "Clinical manifestations, pathologic features, diagnosis, and prognosis of follicular lymphoma", section on 'Cytogenetics'.)

●Certain chromosomal deletions are closely associated with AML (eg, loss of the long arms of chromosomes 5, 7, and 20). These abnormalities occur commonly in therapy-related AML and AML associated with prior MDS, and are associated with a poor prognosis (table 2) [34-36]. The involved genes have not yet been identified, although novel tumor suppressor genes or other regulatory molecules are likely to be encoded at these loci.

Activated signaling — Mutations impacting signal activation are seen in approximately 60 percent of AML cases and include point mutations in FLT3, KIT, other tyrosine kinases, serine-threonine kinases, KRAS/NRAS, or protein-tyrosine phosphatases [3].

FLT3 — FLT3 is a transmembrane tyrosine kinase receptor that stimulates cell proliferation upon activation. Mutations in the FMS-like tyrosine kinase 3 gene producing internal transmembrane duplications (FLT3/ITD) and constitutive activation of the FLT3 receptor tyrosine kinase are quite common in AML, particularly in patients with normal karyotypes.

There are two main types of FLT3 mutations. The most common are internal tandem duplications of different length that result in ligand-independent activation of the FLT3 receptor and a proliferative signal. Alternatively, point mutations in the activating loop of the kinase domain of FLT3 may result in tyrosine kinase activation of FLT3 in 5 to 10 percent of patients [37,38].

The prognostic impact of FLT3 mutations is discussed in more detail separately. (See "Acute myeloid leukemia: Risk factors and prognosis", section on 'FLT3'.)

RAS mutations — Mutations of three closely related RAS (HRAS, KRAS, NRAS) proto-oncogenes occur in human malignancies. Each of these genes encodes a structurally similar 21 kilodalton protein which localizes to the inner plasma membrane and plays an important role in signal transduction [39]. Specific point mutations occur characteristically in each of the three genes, although no consistent karyotypic abnormalities have been associated with RAS mutation and activation [40].

Mutations of RAS have been identified in approximately 25 percent of cases of AML [40,41], and are observed with higher frequency in MDS (35 percent) [42,43]. The majority of the mutations in AML and MDS are in the NRAS gene; KRAS and HRAS mutations occur less frequently. In both AML and MDS, RAS mutations have been reported more frequently in cases with a monocytic morphology (eg, FAB M4 and chronic myelomonocytic leukemia) [44]. An association between AML in patients with a variety of occupational exposures and RAS mutations has also been observed [45].

The significance of RAS mutations in AML remains unclear. RAS mutations have been reported at diagnosis, but not at relapse in some AML cases [46]. Conversely, RAS mutations have been acquired at the time of relapse or disease progression [44,47]. However, the presence of RAS mutations has been associated with improved survival [41], possibly related to a lower leukemic cell burden at presentation, or an increased sensitivity to chemotherapy with cytarabine [48].

NPM1 mutations — Nucleophosmin (NPM1) is a ubiquitously-expressed phosphoprotein involved in ribosomal protein assembly and transport and regulation the tumor suppressor ARF (cyclin-dependent kinase inhibitor 2A). NPM1 shuttles between the nucleus and cytoplasm, but mutations associated with AML (typically four base pair insertions that cause a frameshift) eliminate the C-terminus amino acids responsible for nucleolar localization; as a result, mutant NPM1 is retained in the cytoplasm [49,50]. HOXA and HOX B cluster genes are consistently overexpressed in NPM1-mutated AML. In mouse models, NPM1-mutated cells can be targeted by menin inhibitors [51], and patients with NPM1-mutated AML have achieved remission with menin inhibitors [52].

NPM1 mutations are associated with improved outcomes in younger and older adults and in children with AML, although the mechanism for increased chemosensitivity is not known. The prognostic impact of NPM1 mutations in AML is discussed in more detail separately. (See "Acute myeloid leukemia: Risk factors and prognosis", section on 'NPM1'.)

Splicing factor mutations — Mutations involving the mRNA assembly system that cause aberrant mRNA splicing are highly specific to myeloid diseases that exhibit dysplastic features.

Splicing factor mutations are found in 85 percent of MDS with increased ring sideroblasts; 45 percent of MDS without increased ring sideroblasts; 55 percent of chronic myelomonocytic leukemia (CMML); and in 25 percent of secondary AML, therapy-related myeloid neoplasms (t-MN), or AML with myelodysplasia-related changes; these mutations are rare in de novo AML (5 to 10 percent) [53]. These mutations affect genes that are components of the premessenger RNA splicing machinery including SF3B1, SRSF2, U2AF1, U2AF35, ZRSR2, U2AF65, SF1, SF3A1, and PRPF40B and have, in several studies, been shown to mirror the clinical course of patients with secondary AML or t-MN (eg, inferior response to standard induction chemotherapy).

Distinct molecular subsets with specific alternative spliced isoforms of genes that are involved in innate immune and NF-kB signaling; these findings may provide insight into AML pathogenesis and provide therapeutic targets. As an example, IRAK4-L was the dominant isoform in AML with U2AF1 mutations [54,55]. IRAK4-L interacts with MyD88 to facilitate assembly of the myddosome complex and maximally activate NF-kB and MAPK. IRAK4-L was shown to be essential for leukemic cell function, and inhibition of IRAK4-L suppressed leukemic growth, particularly in AML cells with higher expression of the IRAK4-L isoform. Early phase trials of IRAK-4 inhibitors in MDS and AML have been initiated.

CHROMOSOMAL TRANSLOCATIONS — 

Chromosomal translocations are common in AML. They can affect the cell by one of two mechanisms [56]:

●Juxtaposition of an intact transcription unit from one chromosome to an enhancer element from a gene on another chromosome. As an example, in t(14;18), the BCL2 gene translocates into the immunoglobulin heavy chain (IgH) locus, leading to the inappropriate expression of a normal BCL2 gene product. (See "Clinical manifestations, pathologic features, diagnosis, and prognosis of follicular lymphoma", section on 'Cytogenetics'.)

●Formation of chimeric fusion proteins. Chromosomal translocations can disrupt two different genes within their coding sequences, leading to the creation of a chimeric protein. For example, the t(9;22) in CML results in the formation of a chimeric BCR::ABL1 fusion protein. (See "Chronic myeloid leukemia: Pathogenesis, clinical manifestations, and diagnosis".)

In AML, the vast majority of chromosomal translocations result in the generation of chimeric fusion genes that are never expressed in wild type cells. Characterization of the genes involved in these translocations has led to the elucidation of many transcriptional regulatory pathways in hematopoiesis [57-60]. For example, the alpha and beta subunits of core-binding factor (CBF) have been found to be required for definitive hematopoiesis; both of these subunits are involved in chromosomal translocations in AML.

The involvement in chromosomal translocations of several other classes of transcription factors has been recognized, including those that contain zinc fingers, ring fingers, leucine zippers, basic helix-loop-helix motifs, and ETS domains [61]. Homologues of these transcription factors have been well characterized in animal models such as Drosophila, including the RUNX1 (AML1) homologue "runt," and the KMT2A (MLL) homologue "trithorax." Several other proteins with well-defined hematopoietic functions have been recognized at chromosomal translocation breakpoints, including retinoic acid receptors and Hox genes. However, structural proteins that do not appear to be specific to myeloid cells have also been identified, including members of the nuclear pore complex and nucleolar phosphoproteins. The functions of many other genes involved in chromosomal translocations remain to be elucidated.

Many genes are capable of participating in translocations that involve multiple alternative partner genes. As an example, KMT2A (MLL) forms chimeric fusion genes with >80 known partners. These various fusions provide an opportunity to contrast the contributions of each component of the fusion gene and thus dissect the motifs within these genes that are critical to tumorigenesis. The fusion of nucleophosmin (NPM) to ALK is a frequent recurring abnormality in anaplastic large cell lymphoma. NPM also fuses to RARalpha in acute promyelocytic leukemia and to MLF1 in other subtypes of AML. (See "Clinical manifestations, pathologic features, and diagnosis of systemic anaplastic large cell lymphoma (sALCL)", section on 'Pathogenesis'.)

In the following sections, we will discuss specific fusion genes in the context of families of fusions that share common features. The recurring involvement of the same genes in multiple different translocations has two important implications:

●The genomic structure of these genes may contain "hot spots" for chromosomal breakage.

●Disruption of the pathways regulated by these genes results in malignant transformation, rather than cell death.

Involvement of core binding factor — Chromosomal aberrations in AML commonly involve subunits of the core-binding factor (CBF) group of transcription factors [62,63]. Members of the CBF group function as heterodimeric complexes regulating diverse target genes involved in tissue differentiation [64]. CBF factors consist of an alpha subunit that binds DNA, and a beta subunit that does not bind DNA directly but enhances binding by the alpha subunit. Three alpha subunits have been identified: RUNX1 (AML1/CBFA2/PEBP2aB), RUNX2 (AML3/CBFA1/PEBP2aA), and RUNX3 (AML2/CBFA3/PEBP2aC). As will be described below, both the alpha and beta subunits of CBF are disrupted in common subtypes of AML and form chimeric fusion transcripts with genes not normally expressed in hematopoietic cells [65].

In hematopoietic cells, CBF binding sites have been observed in genes specific to both the lymphoid lineage (T-cell receptor enhancers, CD3E, and LCK proximal promoter) and myeloid lineage (M-CSF receptor, IL-3, GM-CSF, myeloperoxidase, granzyme B, and neutrophil elastase) [57,66].

The RUNX1 (AML1) subunit has been studied extensively in hematopoiesis. Multiple splice variants have been identified; AML1B contains the runt domain and a transactivation domain, whereas AML1A lacks the transactivation domain [67]. Disruption of RUNX1 by gene targeting in embryonic stem cells results in embryonic lethality due to an absence of fetal liver hematopoiesis and to central nervous system hemorrhage [68]. The knockout of CBFbeta results in a similar phenotype, indicating that both the alpha and beta subunits of CBF are essential for definitive but not primitive hematopoiesis [62,69]. The role of CBF in later stages of hematopoietic differentiation is not yet clear.

Familial AML — Abnormalities in several genes are known to cause inherited forms of myelodysplastic syndrome (MDS) or acute leukemia that can present throughout the lifespan. These include abnormalities in RUNX1, ANKRD26, CEBPA, GATA2, TERC, TERT, SRP72, PAX5, SH2B3, and TP53. These are discussed in more detail separately. (See "Familial disorders of acute leukemia and myelodysplastic syndromes".)

AML and MDS and myeloproliferative neoplasms — Point mutations of RUNX1 (AML1) have been infrequently reported in de novo AML or MDS, at incidences varying from zero to 12 percent [70-72].

●In one study of 132 patients with primary MDS, the presence of these mutations was associated with a significantly higher frequency of chromosome 7/7q deletion as well as shortened overall survival [72].

●In a study from Japan, RUNX1 (AML1) mutations were found in 6 of 13 Atom-bomb survivors who developed MDS, and in 5 of 13 patients who developed AML/MDS following alkylating agent treatment with or without supplementary radiation [70].

●In a study of 18 patients with myeloproliferative neoplasms (eg, polycythemia vera, essential thrombocythemia, primary myelofibrosis) who progressed from chronic phase (CP) to acute leukemia, point mutations of RUNX1 were detected in five at the time of leukemic transformation but not while they were still in CP [73]. Consistent with the leukemogenic potential of RUNX1 point mutations, when the AML1D171N mutation was transduced into CD34+ cells from patients in the CP of MPNs, this resulted in proliferation of immature myeloid cells, enhanced self-renewal capacity, and proliferation of primitive progenitors.

Abnormalities in RUNX1 are also seen in patients with familial platelet disorder with propensity to myeloid malignancies. (See "Familial disorders of acute leukemia and myelodysplastic syndromes", section on 'Familial platelet disorder with propensity to myeloid malignancies'.)

Cooperating mutations in AML — t(8;21)(q22;q22) (picture 1) was the first recurring chromosomal translocation in AML to be identified [74]. The clinical and morphologic correlations of this subtype of AML include a high propensity to develop extramedullary collections of leukemic blasts (granulocytic sarcomas). Another hallmark of t(8;21) leukemia is the relatively high rate of responsiveness to chemotherapy, particularly to high dose Ara-C [75].

Leukemic myeloblasts in this subtype have a characteristic morphology, including prominent Auer rods, large cytoplasmic granules, and vacuoles. When the characteristic histologic appearance of these cells is identified in AML blasts that do not contain a t(8;21), the RUNX1::RUNX1T1 (ETO) fusion can be identified by polymerase chain reaction techniques, indicating that the formation of the molecular fusion is responsible for the morphologic and clinical features of this subtype of AML [76].

In t(8;21), RUNX1 fuses to the RUNX1T1 (ETO) gene on the der(8) chromosome to form a chimeric fusion protein [77]. The chimeric protein fuses the N-terminus of RUNX1 including the runt homology domain, but excluding the transactivation domain, to nearly all of RUNX1T1. The RUNX1::RUNX1T1 fusion gene has pleiotropic effects in reporter gene assays as it appears to repress several RUNX1 target genes [78,79], but to activate the M-CSF receptor promoter [80,81]. (See "Regulation of myelopoiesis", section on 'Transcription factors'.)

RUNX1::EAP, MDS1, EVI1 in t(3;21) — The t(3;21)(q26;q22) has been observed in the blast crisis of CML and therapy-related MDS and AML [82]. The RUNX1 (AML1) gene has been found to be rearranged in these cases, leading to the formation of alternative fusion transcripts involving the EAP, MDS1, and EVI1 genes [83,84]. These fusions contain the N-terminus of RUNX1, including its runt homology domain, fused to alternative C-terminal sequences derived from partner genes on 3q26. EVI1 is also involved in the inv(3)(q21q26) and t(3;3)(q21;q26) in AML [85]. However, the consequence of these chromosome aberrations is the inappropriate expression of the EVI1 transcription unit, whereas in the t(3;21), EVI1 participates in the formation of a fusion gene with RUNX1. Sequences from another transcription unit, MDS1, are also observed in t(3;21). Although mapping data indicate that the exons of MDS1 and EVI1 are separated by several hundred kilobases, they have been found to be spliced together not only in cases with the t(3;21), but also in normal tissues.

TEL(ETV6) and RUNX1 in t(12;21) — RUNX1 (AML1) is involved in the t(12;21)(p13;q22), resulting in the generation of a chimeric protein with the TEL(ETV6) gene [86]. The t(12;21) fusion is observed commonly in pre-B-cell ALL. The TEL (ETV6) gene was originally cloned from a t(5;12)(q33;p13) in CMML where it fuses to PDGFRB and it has also been found to fuse to the ABL1 gene in t(12;22) in AML [87,88].

CBFb/MYH11 in inv(16) and t(16;16) — inv(16)(p13q22) and t(16;16)(p13;q22) are seen in AML (picture 2). These patients, like those with the t(8;21), have a relatively good prognosis and a high likelihood to respond to high dose cytosine arabinoside-containing chemotherapy regimens [89]. The CBFB subunit located at 16q22 is disrupted as a result of either the chromosomal inversion or translocation, leading to the formation of a fusion transcript with the gene for smooth muscle myosin heavy chain, MYH11, located at 16p13 [90].

Involvement of the KMT2A (MLL) locus — The mixed lineage leukemia gene, KMT2A (also known as MLL), located at chromosome band 11q23, is frequently involved in translocations in both AML and ALL and is associated with a poor prognosis. Translocations involving 11q23 are the single most common cytogenetic abnormality in infants with acute leukemia, regardless of phenotype, and occur in approximately 70 to 80 percent of cases. 11q23 translocations are also observed frequently in therapy-related leukemias in patients who have previously been treated with drugs that inhibit topoisomerase II, especially the epipodophyllotoxins. This syndrome differs from the therapy-related myeloid leukemias that occur in patients exposed to alkylating agents, which are commonly associated with deletional events on chromosomes 5 and 7. (See "Acute myeloid leukemia: Cytogenetic abnormalities", section on 'Therapy-related myeloid neoplasms'.)

Partner chromosomes — There were at least 121 different partner loci involved in recurring reciprocal 11q23 translocations in a molecular analysis of 1590 KMT2A (MLL)-rearranged biopsy samples from adults and children with AML and ALL with KMT2A gene rearrangements [91-95]. This exceeds the number of known translocations affecting the immunoglobulin loci, suggesting that the 11q23 breakpoint region may contain genomically unstable sequences leading to recombination events.

The chromosomal partners in 11q23 translocations are usually lineage specific. In AML, t(9;11)(p22;q23), t(11;19)(q23;p13.1) and t(6;11)(q27;q23) are the most common, and in ALL, t(4;11)(q21;q23) and t(11;19)(q23;p13.3) occur predominantly. Translocations at 11q23 have been observed in several FAB subtypes, but occur most commonly in the FAB-M4 myelomonocytic and FAB-M5 monoblastic leukemias [92,96,97]. Myeloid leukemias with 11q23 translocations often coexpress lymphoid markers, whereas 11q23 lymphoid leukemias often express myeloid or monocytoid markers in addition to B-cell markers. These observations suggest that rearrangements of KMT2A may affect a pluripotent stem cell or, alternatively, that disruption of KMT2A may affect a common differentiation pathway shared by lymphoid and myeloid progenitor cells.

In a subset of patients with AML and either trisomy 11 or a normal karyotype, a unique pattern of rearrangement of the KMT2A gene has been observed. As in the translocations that affect KMT2A, a fusion occurs involving one of the exons in its breakpoint cluster region. However, rather than fusing to a partner gene, the fusion is to 5' sequences from KMT2A itself [98,99]. These partial duplications of KMT2A appear to occur primarily in older patients and are infrequent in childhood and therapy-related leukemias. The morphology of the leukemias also differs in that the partial duplication patients usually are classified as FAB M1 or M2, rather than the M4 or M5 typically observed in cases with KMT2A translocations.

Mechanism of action — The KMT2A (MLL) gene was isolated from the 11q23 breakpoint by several groups and has been referred to by other names including HRX, ALL-1, and Htrx [100-103]. KMT2A encodes a large protein (predicted molecular weight of 430 kD) that contains two regions of extensive homology to the Drosophila trithorax gene [104]. KMT2A is a histone methyltransferase that plays a critical role in normal embryonic development and hematopoiesis, mainly regulating transcription via epigenetic mechanisms [105]. Translocations create KMT2A fusion proteins that induce aberrant expression of downstream mediators, including HOXA proteins and myeloid ecotropic viral integration site 1 (MEIS1) [106-109]. KMT2A fusion proteins also appear to deregulate the RNA polymerase II elongation factor, thereby disrupting checkpoints for transcription elongation [110,111]. Both Menin and lens epithelium-derived growth factor (LEDGF) appear to be key elements in the interaction between the KMT2A histone methyltransferase and the nonmethylated CpG DNA to which it binds [112]. A selective inhibitor of the KMT2A-Menin interaction was shown to inhibit growth of cell lines harboring KMT2A fusions and prolong survival in mouse models of KMT2A leukemia [113]. Menin inhibitors have demonstrated complete remissions in patients with relapsed/refractory KMT2A-rearranged leukemias [52]. Like treatment with all trans retinoic acid in acute promyelocytic leukemia and the use of IDH inhibitors in IDH1- and IDH2-mutant AML, menin inhibitors can induce differentiation syndrome. Resistance to menin inhibitors is associated with the development of acquired mutations in the MEN1 gene [114].

UBTF duplication — Tandem duplications of UBTF (upstream binding transcription factor) may define a unique subset of AML with a poor prognosis. UBTF encodes a nucleolar protein that is a key regulator of the epigenetic status of ribosomal DNA and RNA transcription. Tandem duplications of UBTF are found in 1 to 3 percent of adults with AML and appear to be significantly enriched in younger adults (median age of 41 years) [115,116].

UBTF tandem duplications appear to be mutually exclusive with other class-defining lesions in AML and display a unique computational signature associated with morphologic dysplasia with trisomy 8, internal tandem duplication of FLT3 (FLT3-ITD), mutations in WT1, and poor prognosis. Moreover, HOX and MEIS genes seem to be overexpressed in AML with UBTF tandem duplication, suggesting potential sensitivity to menin inhibitors.

Retinoic acid receptor — The cytogenetic hallmark of acute promyelocytic leukemia (APL), is a translocation involving the retinoic acid receptor-alpha (RARA) locus on chromosome 17 [117]. The vast majority of these cases contain a t(15;17)(q22;q11-12), although several variant translocations involving RARA have been identified. These include PLZF in t(11;17)(q23;q11-12) and NPM in t(5;17)(q35;q11-12). These translocations lead to the formation of chimeric fusion transcripts from each of the derivative chromosomes. The pathobiology of APL is discussed in detail separately. (See "Molecular biology of acute promyelocytic leukemia".)

Other fusion genes in AML

DEK::CAN in t(6;9) and SET::CAN — The t(6;9)(p23;q34) is observed usually in the M2 and M4 subtypes of AML but has also been identified in the M1 subtype and MDS. This translocation is associated with a younger age and a poor prognosis. The CAN gene was also found to be rearranged in a patient with acute undifferentiated leukemia and a normal karyotype. A chimeric transcript containing an alternative CAN partner gene, named SET, was isolated in this case [118]. The SET gene was also localized to 9q34, suggesting that this fusion results from an inversion of chromosome 9 or a cryptic translocation.

TLS/FUS/ERG and t(16;21) — The t(16;21)(p11;q22) has been observed in several AML subtypes, blast phase of CML, and MDS [119,120]. In this translocation, the TLS::FUS gene at 16p11 fuses to the ERG gene at 21q22 to generate a chimeric protein. Both TLS::FUS and ERG are involved in chromosomal translocations with other partner genes in sarcomas [121-123]. The striking similarity of the TLS/FUS/ERG fusion gene in AML to the sarcoma associated fusion genes suggests that disruption of a common differentiation pathway may lead to transformation in multiple cell types.

NPM::MLF1 in t(3;5) — The t(3;5)(q25.1;q35) has been observed in AML and MDS [124]. The NPM gene at 5q35 was found to be rearranged in patients with this translocation, resulting in the formation of a fusion gene with MLF1 at 3q25.1. Previously, the involvement of NPM had been identified in the t(2;5)(p23;q35) in anaplastic large cell lymphoma, where it fuses to ALK [125]. NPM is also rearranged in the t(5;17)(q35;q21) in APL, where it fuses to RARA.

The MLF1 protein normally localizes to the cytoplasm, whereas in leukemia cells with t(3;5), the NPM::MLF1 fusion protein is observed primarily in nucleoli. The involvement of NPM in chromosome translocations involving three different partner genes, resulting in three discrete types of hematologic malignancies, suggests that NPM plays an important role in normal hematopoietic differentiation.

EVI1 in inv(3) and t(3;3) — EVI1 (Ecotropic Virus Integration 1) was initially cloned as the gene at a common site of retroviral integration in murine myeloid leukemia. The EVI1 gene is normally expressed only in kidney and ovary. In mice, the retroviral integration at the murine Evi1 locus leads to its inappropriate expression in hematopoietic cells. A similar phenomenon occurs in human AML with inv(3)(q21q26) and t(3;3)(q21;q26) [126]. As a result of these cytogenetic aberrations, the EVI1 gene is juxtaposed to enhancer elements of the Ribophorin gene leading to inappropriate activation of the EVI1 transcription unit, a component of the complex fusion transcripts that involve the RUNX1 gene in t(3;21).

MOZ::CBP in t(8;16) — The t(8;16)(p11;p13) has been recognized in the M4 and M5 subtypes of AML that exhibit a characteristic erythrophagocytosis [127]. This translocation has been observed in both de novo and therapy-related leukemias. Several variant translocations involving 8p11 have been recognized in monocytic leukemias with erythrophagocytosis, but the genes involved in these translocations have not yet been cloned. CBP is also involved with a fusion to KMT2A in t(11;16)(q23;p13) [128].

PICALM/MLLT10CALM/AF10 in t(10;11) — t(10;11)(p13;q14) has been recognized in both ALL and AML [129]. In ALL, PICALM/MLLTT10 is associated with T cell acute lymphoblastic leukemia. Outcomes for T-ALL in children with PICALM::MLLT10 are comparable to those without this fusion. However, outcomes for AML in children with PICALM::MLLT10 are very poor [130].

NUP98::HOXA9 in t(7;11) and NUP98::DDX10 in inv(11) — The t(7;11)(p15;p15) is observed in AML and CML. HOXA9 was identified at the 7p15 breakpoint and NUP98 at the 11p15 break [131]. In BXH-2 mice, the Hoxa9 gene has been implicated in myeloid leukemia as a result of its activation via proviral insertion. NUP98 has been found to be involved in the inv(11)(p15q22) in AML. This cytogenetic aberration has been recognized in both de novo and therapy-related MDS and AML.

In addition, a t(10;11)(q23;p15) translocation involving the NUP98 gene at 11q15 and the hematopoietically expressed homeobox gene (HHEX) at 10q23 has been implicated in AML [132]. Other cases of AML have been identified that demonstrate a NUP98-KMT2A fusion protein with low levels of HOXA gene expression [94].

INFORMATION FOR PATIENTS — 

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Here are the patient education articles that are relevant to this topic. We encourage you to print or e-mail these topics to your patients. (You can also locate patient education articles on a variety of subjects by searching on "patient info" and the keyword(s) of interest.)

●Beyond the Basics topics (see "Patient education: Acute myeloid leukemia (AML) treatment in adults (Beyond the Basics)")

SUMMARY

●Acute myeloid leukemia (AML) – AML develops as the consequence of genetic changes in a hematopoietic precursor cell that alters normal growth and differentiation, resulting in an accumulation of large numbers of abnormal, immature myeloid cells in the bone marrow and blood. These aberrant cells can divide and proliferate, but they cannot differentiate normally into mature, fully functional hematopoietic cells.

●Prognostic significance – Many of the chromosomal abnormalities and gene mutations are associated with prognosis in AML (table 1 and table 2).

●Mutations of oncogenes and tumor suppressors – Cases of AML may demonstrate mutations in oncogenes (eg, NRAS, FLT3) and/or loss of tumor suppressor genes (eg, TP53, WT1 [Wilms tumor suppressor gene]). (See 'Gene mutations' above.)

●Chromosomal translocations – Many hematologic malignancies are associated with specific chromosomal translocations that generate chimeric fusion genes that are never expressed in wild type cells. Chromosomal aberrations in AML commonly involve transcription factors that regulate hematopoiesis. (See 'Chromosomal translocations' above.)

●Core binding factor abnormalities – The chromosomal aberrations t(8;21)(q22;q22) and the inv(16)(p13q22) in AML involve subunits of the core-binding factor (CBF) group of transcription factors. Members of the CBF group function as heterodimeric complexes regulating diverse target genes involved in tissue differentiation. (See 'Involvement of core binding factor' above.)

●KMT2A (MLL) – The mixed lineage leukemia gene, KMT2A (MLL), located at chromosome band 11q23, is frequently involved in translocations in AML with different partner chromosomes. KMT2A is a histone methyltransferase that plays a critical role in normal embryonic development and hematopoiesis, mainly regulating transcription via epigenetic mechanisms. Translocations involving KMT2A result in KMT2A fusion proteins that induce the aberrant expression of downstream mediators. (See 'Involvement of the KMT2A (MLL) locus' above.)

●Acute promyelocytic leukemia (APL) – The cytogenetic hallmark of APL is a translocation involving the retinoic acid receptor-alpha (RARA) locus on chromosome 17. These translocations lead to the formation of chimeric fusion transcripts from each of the derivative chromosomes. The pathobiology of acute promyelocytic leukemia is discussed in detail separately. (See "Molecular biology of acute promyelocytic leukemia".)