Adult AML Patients with NUP98 Fusions Are Frequently Therapy-Related, and Are Associated with Monocytic Differentiation, Recurring Mutations in NRAS, DNMT3A and WT1 and Poor Outcome

NUP98 related AML and other myeloid neoplasm (MN) are recognized as a distinct subgroup of AML with unique pathological features and poor outcomes primarily in pediatric patients, whereas NUP98 translocations in adult AML are rarer and its pathological and genetic features, and clinical outcome remain to be defined.

Using cytogenetic, FISH and targeted RNA sequencing (RNA-Seq) techniques, we identified 23 adult patients with NUP98 rearrangement MN at our institution since 2016. The cohort included 15 females and 8 males, with ages ranging from 23 to 79 years (median 62 years). There were 11 de novo AML (including 2 myeloid sarcoma, MS), 1 AML progressing from MDS, 2 MDS (one with increased blasts, 8 therapy related t-MN, and 1 uncharacterized MN with refractory T-ALL. Skin and CNS involvement was observed in 1 patient each. All 8 patients with prior hematologic or other malignancies were treated with topo II inhibitors (4/8) and alkylating agents (5/8), and often with radiotherapy (7/8).

Most patients had low hemoglobin and platelets, with white blood cell count ranging from 1.9 to 365.55 K/uL (median 9.3 K/uL). Blast percentages in peripheral blood and bone marrow ranged widely from 0% to 87% (median 20%) and 1% to 93% (median 29%), respectively. Auer rods were observed in 1 case. Blasts consistently express CD13, CD33 and CD117, whereas lack of CD34 was observed in 8 cases (34.8%). Monocytic differentiation was present in 17 patients (73.9%) with CD11b (7/21) and/or CD64 expression (15/21).

Cytogenetic analysis was performed in 21 patients. Of 6 patients with NUP98::NSD1, a normal karyotype was observed in 5 patients, and deletion of 9q as sole abnormality in 1 patient. NGS based genomic copy number alterations were observed in 2 patients including 1 MS. All other patients (except 1 MS) show clonal chromosome abnormalities (CA), and a complex karyotype with ≥3 CA were observed in 6 patients, including 1 with MS and 2 with t-MN. Clonal evolution was observed in 5 patients. FISH analysis using NUP98 break-apart probes was performed in 21 patients and confirmed a split signal pattern in 19 patients, and deletion of the 3’ NUP98 region in 2 patients.

NUP98 translocations and fusions were defined in 19 patients by combining chromosome, FISH and molecular findings, including RNA-Seq confirmation in 16 patients: NUP98::NSD1 (n=6, all with AML), NUP98::DDX10 (n=4, all with t-MN), NUP98::KMT2A (n=2, both with MDS, 1 harboring germline BRCA2 mutations), NUP98::KDM5A (n=2, both with MS), NUP98::HOXD13 (n=1), NUP98::TOP1 (n=1) and NUP98::PRRX2 (n=1, coexisting with ETV6::PDE3A). Two novel NUP98 fusions were detected: NUP98::KAT6B t(10;11) in a t-MDS with history of T-ALL, and NUP98::SATB1 t(3;11) in t-AML with history of breast cancer; both partner genes are implicated in epigenetic regulation. In the remaining 4 patients without defined NUP98 partners,11p15 abnormalities were detected by karyotyping and NUP98 split was confirmed by FISH testing. The presumptive NUP98 partner in 1 patient could be HOXA1 or HOXA9 (7p15). The NUP98 fusions were at exons 9-14 with exon 12 consistently in NUP98::NSD1, exon13 in NUP98::KDM5A, and exon 14 in NUP98::DDX10 and NUP98::TOP1.

NGS testing were performed in 21 patients and pathogenic somatic mutations were detected in 19 patients. The recurrent genetic alterations are NRAS (n=9, 47.3%, including 1 G12, 5 G13, 2 Q61, and 1 A146 codons ), DNMT3A (n=7, 36.8%), FLT3 ITD (n=7, 36.8%), WT1 (n=7, 36.8%), TP53 (n=4, 21%), IDH1/2 (n=3, 15.8%), RUNX1 (n=2, 10.5%), FAT1 (n=2, 10.5%). Other mutations include ASXL1, BCOR, CHEK1, EZH2, KDM6A, GATA2, KMT2D, KRAS, NF1, NPM1, NUP93, SETD2, and STAG2, one each. WT1 mutations are frequent, with 5 cases showing 2 to 5 mutations and 3 of them with bi-allelic WT1 alterations, and in 3 patients WT1 mutations likely acquired during disease progression.

The median follow-up was 13 months. At the last follow-up, 6 patients were alive, while 14 had died (10 died of disease complications), with a median survival of 9 months. Of the 8 cases with blasts <20% at initial presentation, 3 died within 6 months due to causes related or unrelated to the myeloid neoplasm, and 4 progressed to AML despite treatment with a median time to progression of 5.5 months (range: 1 to 27 months).

In summary, adult AML patients with NUP98 fusions are enriched for t-AML/MDS, often have monocytic differentiation, and featured with high prevalence of NRAS, DNMT3A and WT1 mutations, and portend poor outcome.