ATG2B and GSKIP: 2 new genes predisposing to myeloid malignancies

ABSTRACT

We have recently identified a 700-kb tandem duplication at locus 14q32.13-q32.2 involving 2 genes, autophagy-related protein 2 homolog B (ATG2B) and GSK3B interacting protein (GSKIP), that increases the predisposition to myeloid malignancies. Here, we discuss the clinical relevance of these findings.

Myeloid malignancies are hematologic malignancies that include 3 major groups: acute myeloid leukemia (AML), myelodysplasia (MDS), and myeloproliferative neoplasms (MPN). These clonal disorders arise from the transformation of hematopoietic stem cells (HSCs) with the exception of AML, which can also occur from transformation of more committed progenitors. These diseases are generally sporadic but some rare familial forms have been described. To date, 5 types of genetic predisposition to MDS and AML with autosomal dominant inheritance have been characterized at the molecular level. Three of them affect transcription factors regulating normal hematopoiesis: germline mutations in runt-related transcription factor 1 (RUNX1) in the familial platelet disorder predisposing to AML (FPD/AML)¹ and in CCAAT/enhancer-binding protein, alpha (CEBPA)² or GATA transcription factors (GATA2)³ in familial leukemia. Another corresponds to a mutation in the 5′ untranslated region of the ANKRD26 gene encoding ankyrin repeat domain 26, a protein associated with the inner part of the cell membrane, in familial thrombocytopenia 2 (THC2).⁴ Finally, mutations in the putative helicase DEAD (Asp-Glu-Ala-Asp) box polypeptide 41 (DDX41) involved in spliceosome regulation complexes have been identified more recently.⁵ Interestingly, all of these proteins except ANKRD26 are directly involved in the pathogenesis of sporadic AML and thus germline mutations are the first step in a multistep oncogenic process.

The frequency of familial forms of breakpoint cluster region-Abelson (BCR-ABL1)–negative MPNs, polycythemia vera, essential thrombocytemia (ET), and primary myelofibrosis (PMF) is much higher than that of other myeloid malignancies.⁶ BCR-ABL1–negative MPNs are the consequence of acquired genetic defects in HSCs that induce constitutive activation of the Janus activated kinases/signal transducer and activator of transcription (JAK/STAT) pathway and lead to increased proliferation of one or several myeloid lineages. In addition to familial forms, the presence of predisposition factors was evidenced by the occurrence of independent very rare genetic events acquired in the same patient. Susceptibility alleles corresponding to frequent polymorphisms, such as the 46/1 haplotype located on the JAK2 locus or an intronic polymorphism in telomerase reverse transcriptase (TERT) have been described and are associated with a higher risk of occurrence of a JAK2V617F mutated MPN.^7,8 However, these factors confer a very weak susceptibility to the occurrence of oncogenic mutations and barely explain the familial aggregations.

We have recently identified 4 families from the West Indies among which more than 30 members present with an autosomal dominant inheritance myeloid blood disorder including AML, MDS, myelomonocytic leukemia (CMML), and MPN. In two-thirds of the cases the patients develop an ET actively progressing to MF and leukemia.⁹ The median age of onset of the disease was 41 years, which appears to be later than onset due to GATA2 or CEBPA mutations. Moreover, the penetrance was relatively high (>80%) compared with GATA2 or RUNX1 mutations. The spectrum and frequency of molecular abnormalities in signaling molecules for 22 affected members from these families were identical to those found in sporadic ET: JAK2V617F (68%), thrombopoietin receptor MPL mutants (9%), calreticulin (CALR) mutants (18%), and triple negative (5%). In contrast, we observed enrichment in mutations in epigenetic molecules including ten-eleven translocation (TET2, 38%), isocitrate dehydrogenase (IDH1, 10%), IDH2 (19%), and additional sex combs-like 1 (ASXL1, 5%). In contrast to sporadic cases, no mutations in TP53 (best known as p53) were detected suggesting a different mechanism of transformation.

Through linkage analysis, we identified a 700-kb tandem duplication at the 14q32.13-q32.2 locus that segregated with all affected members of the 4 families. No mutation was found in this region, which contains 5 genes, T-cell leukemia/lymphoma (TCL1A), bradykinin receptor B (BDKRB1 and BDKRB2), ATG2B, and GSKIP, and the first exon of the adenylate cyclase (AK7) gene. We found that only ATG2B and GSKIP were expressed in myeloid hematopoiesis and that these genes were overexpressed in primary hematopoietic cells from patients compared with donor cells.

Currently, 2 mutually non-exclusive assumptions may explain a predisposition: either the predisposition locus or state could induce a hypermutability phenotype by deregulating genes involved in DNA repair or in the DNA damage response thus promoting the acquisition of mutations and/or it represents a fertile ground for the selection of pre-existing mutated clones by changing their fitness. The latter hypothesis seems likely since acquired mutations found in myeloid malignancies may be frequent in the general population, more particularly during aging, and are sometimes associated with clonal hematopoiesis but without disease.¹⁰

To understand the role of the predisposition and characterize the genes responsible, we used an original strategy based on induced pluripotent stem cell technology (iPSC). We generated 3 iPSC lines from 2 patients, one with predisposition alone and 2 with predisposition and JAK2V617F, with or without the TET2 mutation. After study of hematopoiesis of these iPSC lines, we showed that the duplication stimulates hematopoietic progenitors, in particular megakaryocytic progenitors, by increasing their sensitivity to thrombopoietin and cooperates with signaling mutations acquired as JAK2V617F or TET2 to modify the response of hematopoietic progenitors to erythropoietin. Through a silencing strategy involving simultaneous downregulation of ATG2B and GSKIP, we managed to reduce the spontaneous growth of megakaryocytic progenitors. The same results were obtained in primary cells, confirming the involvement of these genes in predisposition to the disease.

Overall, these results reveal a novel predisposition locus including 2 genes, ATG2B and GSKIP, that is responsible for the induction of myeloid malignancies. Moreover, whatever the molecular driver abnormality, this predisposition locus not only accelerates the disease onset, which is generally late in the cases of hematologic malignancies (>60 years), but also favors progression of MPN into leukemia (Fig. 1). However, the precise mechanism needs to be delineated since the roles of the proteins encoded by these genes are poorly understood but potentially involved in the Wnt pathway (GSKIP) and in autophagy (ATG2B). Similarly, it is unclear whether these genes are involved in sporadic NMP and other hematologic malignancies, including AML.

Figure 1.

Genomic duplication at chromosome 14 as a predisposition locus. We identified a 700-kb tandem duplication containing 5 genes and the first exon of a sixth gene in 4 families harboring myeloid hematologic malignancies. Only autophagy-related protein 2 homolog B (ATG2B) and GSK3B interacting protein (GSKIP) were found to be expressed in myeloid cells and overexpressed in cells of patients compared to donors. By functional studies, we found that these 2 genes were able to change the fitness of signaling mutated cells and may induce a clonal dominance that leads to disease. AK7, adenylate cyclase; BDKRB1 and BDKRB2, bradykinin receptor B1 and B2; TCL1A, T-cell leukemia/lymphoma 1A.

Disclosure of potential conflicts of interest

No potential conflicts of interest were disclosed.