NUP98‐BPTF gene fusion identified in primary refractory acute megakaryoblastic leukemia of infancy

Abstract

The advent of large scale genomic sequencing technologies significantly improved the molecular classification of acute megakaryoblastic leukaemia (AMKL). AMKL represents a subset (∼10%) of high fatality pediatric acute myeloid leukemia (AML). Recurrent and mutually exclusive chimeric gene fusions associated with pediatric AMKL are found in 60%-70% of cases and include RBM15-MKL1, CBFA2T3-GLIS2, NUP98-KDM5A and MLL rearrangements. In addition, another 4% of AMKL harbor NUP98 rearrangements (NUP98r), with yet undetermined fusion partners. We report a novel NUP98-BPTF fusion in an infant presenting with primary refractory AMKL. In this NUP98r, the C-terminal chromatin recognition modules of BPTF, a core subunit of the NURF (nucleosome remodeling factor) ATP-dependent chromatin-remodeling complex, are fused to the N-terminal moiety of NUP98, creating an in frame NUP98-BPTF fusion, with structural homology to NUP98-KDM5A. The leukemic blasts expressed two NUP98-BPTF splicing variants, containing one or two tandemly spaced PHD chromatin reader domains. Our study also identified an unreported wild type BPTF splicing variant encoding for 2 PHD domains, detected both in normal cord blood CD34 cells and in leukemic blasts, as with the fly BPTF homolog, Nurf301. Disease course was marked by rapid progression and primary chemoresistance, with ultimately significant tumor burden reduction following treatment with a clofarabine containing regimen. In sum, we report 2 novel NUP98-BPTF fusion isoforms that contribute to refine the NUP98r subgroup of pediatric AMKL. Multicenter clinical trials are critically required to determine the frequency of this fusion in AMKL patients and explore innovative treatment strategies for a disease still plagued with poor outcomes.

Cryptic genomic lesions in adverse-risk acute myeloid leukemia identified by integrated whole genome and transcriptome sequencing

“…PHD domains of both NUP98-KDM5A and wild-type BPTF are essential in the activation of HOX family genes, which is associated with stemness and poor prognosis [12][13][14]. NUP98-BPTF fusion in case 6 retains the C-terminal PHD domains of BPTF, so we predict that it can activate HOX genes, as previously investigated by Roussy et al [11]. In addition, PICALM-MLLT10 in case 5 is another known activator of HOX [8], suggesting that HOX activation may be a common leukemogenic mechanism in the context of complex karyotype.…”

“…To our knowledge, case 6 represents the third reported leukemia patient with a NUP98-BPTF fusion (Supplementary Table 5). The first report of NUP98-BPTF was in a young adult with T-cell acute lymphoblastic leukemia (ALL) [10] and the second was in an infant with acute megakaryoblastic leukemia [11]; both fusions were identified via RNA-seq. Clinical presentations of these three NUP98-BPTF cases are in line with the observation that NUP98 fusions can occur in both myeloid neoplasms and T-cell ALL.…”

Cryptic recurrent ACIN1‐NUTM1 fusions in non‐KMT2A‐rearranged infant acute lymphoblastic leukemia

“…Total RNA was extracted from diagnosis BM aspiration and sequenced with Illumina Nextseq500 as previously described. 10 Library preparation and sequencing were performed at the Institute for Research in Immunology and Cancer's Genomics Platform Table S1. Sequences were subsequently analyzed using FusionCatcher 0.99.6a in order to identify potential gene fusions (Table S2).…”

Human models of NUP98-KDM5A megakaryocytic leukemia in mice contribute to uncovering new biomarkers and therapeutic vulnerabilities

“…Expression of SELP was confirmed at the protein level by flow cytometry on hCD45 1 CD41 1 GFP 1 blasts derived from the BM of an N5A AMKL primary xenograft recipient ( Figure 5E). The expression of NEO1 was validated by RT-PCR in 2 AMKL xenograft samples and in primary specimens of NUP98-BPTF AMKL 34 (diagnosis and measurable residual disease [MRD] monitoring), given the absence of commercially available antibodies robustly validated for flow cytometry (Figure 5F-G). Using proteomic analysis, we validated the expression of 411 proteins at the surface of NUP98-BPTF AMKL patient-derived xenograft (PDX) cells, including NEO1, MPIG6B, and SELP ( Figure 6A; supplemental Table 9).…”

“…These results corroborated recent studies in the field of pediatric AMKL, suggesting the importance of the JAK-STAT signaling pathway. 35,36 As proof of principle, we have thus tested in vitro sensitivity of AMKL cells to clinically approved JAK inhibitors (ruxolitinib, a JAK2/1 inhibitor, and tofacitinib, a JAK3/1 inhibitor), using our model NUP98-KDM5A AMKL along with a NUP98r AMKL PDX, 34 and gauged cross toxicity on normal CB cells. We chose the JAK inhibitors ruxolitinib and tofacitinib, as they are currently used in pediatrics in the context of cancer, graft-versus-host disease and rheumatoid arthritis.…”