Inv(3) and t(3;3) have been documented in de novo AML (in all FAB subtypes except M3), therapy related AML (t-AML), MDS, CML, more often in accelerated phase or blast crisis, chronic myelomonocytic leukemia (CMML), and in other myeloproliferative disorders ^14-17.

AML with inv(3)(q21q26) or t(3;3)(q21;q26) is part of the new AML with MECOM rearrangement (WHO 2022 classification in the AML subgroup with defining genetic abnormalities ¹⁸).

Rare cases of lymphoid malignancies with inv(3) or t(3;3) have been described as well (acute lymphoblastic leukemia, chronic lymphocytic leukemia, among others) (Milteman Database or ^19-23). Nevertheless, most cases have not been characterized by FISH analysis. Only one t(3;3)(q21;q26) case is well documented with a EVI1 rearrangement identified by FISH in an acute lymphoblastic leukemia secondary to a myelodysplastic syndrome with 5q deletion ²⁴.

AML : inv(3)(q21q26) and t(3;3)(q21;q26) are the most common 3q abnormalities in AML (32%). The frequency of these rearrangements is estimated to range between 1.4% and 1.6% of AML in adults with no difference between sexes. These rearrangements are slightly more common in patients aged 60 years or younger, and extremely rare in pediatric AML.

MDS : inv(3)(21q26)/t(3;3)(q21;q26) occur approximatively in 1% of MDS ^25,26. These rearrangement are associated with aggressive disease and high risk of AML transformation.

CML : Chromosome 3 aberrations are described in ~1.5% of CML patients, of which 20-40% are in blast crisis. Among these abnormalities, inv(3) and t(3;3) were detected in 26% of the patients ^27,28.

GATA2::MECOM is a rare event in BCR::ABL1 negative myeloproliferative neoplasms and myelodysplastic/myeloproliferative neoplasms.

3q26 rearrangements were also reported in lymphoid malignancies but without evidence of MECOM involvement.

No specific clinical sign.

Patients may present a normal platelet count, however marked thrombocytosis may occur in 7% to 22% of patients ^29,30. 

Blasts present morphologic and cytochemical features of any AML subtypes other than M3. Multilineage dysplasia is frequently associated with dysmegakaryopoiesis (characterized by small monolobate or bilobate megakaryocytes that can be increased in number) ³¹. In peripheral blood, morphological abnormalities may be observed : hypogranular neutrophils, pseudo-Pelger anomaly, macrothrombocytes, circulating micromegakaryocytes.

Phenotype stem cell origin: Hematopoietic stem cell with multilineage potential is implicated.

Blasts express CD13, CD33, CD117, HLA-DR, CD56, CD34 and CD38; CD7 is aberrantly expressed in some cases, whereas the other lymphoid markers are uncommon; blasts may also express megakaryocytic markers such as CD41 or CD61 ^32,33.

Patients with inv(3)(q21q26) or t(3;3)(q21;26) present an aggressive course with short overall survival (OS) and poor response to conventional therapy, regardless of the pathology ³⁴. These anomalies are considered to have an adverse prognosis according to the European LeukemiaNet 2022 ³⁵. There is no difference in survival between inv(3) and t(3;3).

Table 1 : Pronostic significance of t(3;3)/inv(3) in myeloid malignancies, adapted from Summerer I et al ³⁶

OS is shortened when ACAs are present, especially with additional monosomy 7 or with 2 or more somatic mutations in particular with TP53, NRAS or U2AF1 mutations ³⁶. In CML, 3q26.2 rearrangement remains an independent adverse prognostic factor after adjusting other high-risk ACAs.

Inv(3)(q21q26) or t(3;3)(q21;q26) (Conventionnal Cytogenetics and FISH in Figure 1)

Inv(3)(q21q26) or t(3;3)(q21;q26) leads to an inappropriate expression of EVI1 and GATA2 genes, without gene fusion.

Figure 1 : chromosomal aspects on conventional cytogenetics and Fluorescence in situ hybridization for inv(3)(q21q26) GATA2::MECOM and t(3;3)(q21;q26) GATA2::MECOM

Top row : inv(3)(q21q26) G-banding - Courtesy Diane H. Norback, Eric B. Johnson, Sara Morrison-Delap Cytogenetics at the Waisman Center (left and middle) and Jean-Luc Lai and Alain Vanderhaegen (right), R-banding - Courtesy Nasséra Abermil, inv(3)(q21q26)x2 R-banding - Courtesy Claire Bracquemart

Second row : t(3;3)(q21;q26) G-banding - Courtesy Diane H. Norback, Eric B. Johnson, Sara Morrison-Delap - Courtesy Christiane Charrin; Adriana Zamecnikova, R-banding - Courtesy Nasséra Abermil

Fluorescence in situ hybridization with the EVI1 (MECOM) Breakapart MetaSystems probe showing MECOM rearrangement as a result of inv(3)(q21q26), t(3;3)(q21;q26) -Courtesy Nasséra Abermil; and inv(3)(q21q26)x2 - Courtesy Claire Bracquemart

Proportion among MECOM anomalies:

inv(3)(q21q26) are the most frequent anomalies (52%), ins(3;3)(q26;q21q26) (9%) are less frequent ¹.

Result of chromosome anomaly

Breakpoints of the inv(3) and t(3;3) differ. 3q21 breakpoints cluster in a 130 kb region between GATA2 and RPN1, and share a commonly translocated region of 18kb size before RPN1 for inv(3) and t(3;3) rearrangements that contains a distal GATA2 enhancer (G2DHE). In the 3q26 cytogenetic band, inversion breakpoints span the last intron or downstream of EVI1, whereas translocation breakpoints are located upstream of EVI1 in the MDS1 region (figure 2).

The relocation of the GATA2 enhancer located directly upstream of RPN1 causes EVI1 and GATA2 deregulation. This single enhancer rearrangement generates both EVI1 ectopic activation, by inappropriate transcriptional control, and GATA2 functional haploinsufficiency by removal of that same enhancer ².

Figure 2 : Schematic representation of GATA2 and MECOM loci. Boxes represent genes.

Top : GATA2, G2DHE (GATA2 distal hematopoietic enhancer), RPN1 are located in 3q21 cytogenetic band; MECOM is located in 3q26 cytogenetic band. Breakpoints in 3q26 band vary between translocations and inversions involving MECOM locus.

Bottom : Inversion(3) is a paracentric inversion of chromosome 3 with two breakpoints on the same chromosome 3 (3q21 and 3q26 upstream MECOM locus); Translocation t(3;3) between the two chromosomes 3, one breakpoint is in 3q21 and one downstream MECOM locus of the homologous chromosome 3.

Diagram is not in scale. Adapted from Thomas Smol diagram and Gröschel S et al. ²; courtesy Claire Bracquemart.

In myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), additional chromosomal anomalies (ACAs) are common (68% of cases) ³. The most frequent are monosomy 7 and deletion 7q, the first being more frequent, found in 40-70% of cases ⁴. Two major deleted regions in 7q35-36 have been identified ⁵. Deletion 5q occurs in 6-19% of cases ⁶. These anomalies are usually identified in a complex karyotype in 21% of cases, and monosomal karyotype in 68%.

Inv(3) and t(3;3) can be associated with t(9;22)(q34;q11) in blast phase of chronic myeloid leukemia (CML), often in a complex karyotype ⁶.

In some cases, both chromosomes 3 can be involved, presenting with a double inv(3)(q21q26) ⁶ (Figure 1).

Molecular profile

Gröschel and colleagues have shown among 41 inv(3)/t(3;3) cases (32 AML, 4 CML, 5 MDS), that the most common associated mutations were those in genes activating RAS/RTK signaling (98%). Among those mutations, 47% were directly affecting NRAS (27%), KRAS (11%), and also NF1 (9%), PTPN11. Their molecular analysis also showed mutations in a transcription factor (32%), most commonly GATA2 (15%), RUNX1 (12%), in splice factor-encoding genes (29%), such as SF3B1, epigenetic modifier genes (29%), tumor suppressor genes (10%), DNA methylation genes (10%) and cohesion-complex genes (5%). No discrimination difference was found between MDS and AML based on gene expression ^7,8.

MECOM = MDS1 and EVI1 complex locus, is a locus composed of two genes : EVI1 (Ecotropic Viral Integration Site 1) and MDS1 (Myelodysplastic Syndrome 1)

Figure 3 : Schematic representation of MECOM locus, from Maicas M et a. ⁹.

Location 3q26.2

Note Alias EVI1.

Dna rna description MDS1 has 3 exons. EVI1 has 16 exons, and five alternative mRNA 5-ends : EVI1-1A, EVI1-1B, EVI1-1C, EVI1-1D and EVI1-3L. A sixth mRNA 5-end exists and is a combination of MDS1 and EVI1 gene, it starts to the ATG codon of MDS1. Three MECOM protein isofroms have been described : EVI1-145kDa, EVI1-Δ324 and MDS1-EVI1 (⁹, Figure 3).

Protein description: EVI1 encodes a nuclear zinc finger protein that is a transcriptional regulator involved in cell proliferation, differentiation, and apoptosis. It plays a role in hematopoiesis ^10,11 with strong expression in CD34+ hematopoietic stem cells, with decreased expression during differentiation into myeloid lineages ¹². The role of Evi1 in hematopoiesis and Evi1 deregulation in leukaemogenesis have been well described, however, the roles of Mds1 and Mds1-Evi1 remain undefined ¹³.

GATA2 (GATA Biding Protein 2)

Location 3q21.3

Dna rna description GATA2 has 6 exons (NM_032638).

Protein description GATA2 encodes a zing finger transcription factor, member of the GATA family. Multiple transcripts variants exists. It has a key role in hematopoietic development.