Molecular and clinical characteristics of NUP98 rearrangements and their therapeutic responses in 6,000 patients with hematologic malignancies

Abstract Background: Translocations involving nucleoporin 98 (NUP98) and over 30 fusion partner genes are well-characterized drivers of hematologic malignancies and have long been associated with poor prognosis. Although progress has been made in understanding the molecular mechanisms underlying NUP98 translocations, the literature primarily focuses on pediatric AML, leaving a gap in understanding their clinical significance in adult AML cohorts. Here, we analyzed the molecular and clinical characteristics of 128 NUP98 fusion-positive patients (including 87 adults). Material and Methods Bone marrow or peripheral blood samples from 6,000 patients with hematological malignancies (collected between 2020 and 2025 at a single center) were screened for fusion genes using whole-transcriptome sequencing (RNA-seq). Gene mutations (364 genes) and copy number variations (CNVs) were assessed using targeted DNA sequencing. All patients underwent routine testing and risk assessment, including analysis of age, WBC count, cytogenetic/molecular classification, immunophenotyping, and measurable residual disease (MRD). Results RNA-seq analysis identified 128 patients with NUP98 fusions involving 23 partner genes. Among these, 18 were known partners (e.g., NSD1, HOXA9, RAP1GDS1, PRRX2, DDX10), and 5 were novel (BRWD3, HOXA7, MLLT1, WT1, ZNF215). Abnormal karyotypes were present in 53.9% of patients with NUP98 rearrangements, primarily in non-NSD1 cases. Breakpoints in NUP98 were predominantly in intron 12 (93/128), preserving the N-terminal FG-rich domain; all NUP98::NSD1 fusions (n=67) shared this breakpoint. Diagnoses included AML (108 cases, mainly NSD1 and HOXA9 fusions), T-ALL (11 cases, mainly RAP1GDS1), MDS (7 cases, mostly non-NSD1), and one case each of CMML and MPAL. Male predominance was observed in NUP98::NSD1-positive patients (62.7% vs. 37.3% female; p<0.05), whereas the non-NSD1 group had a balanced sex ratio (50.8% vs. 49.2%). Adults comprised a significantly higher proportion of NUP98 fusion patients than children/adolescents (68% vs. 32%; p<0.001), with non-NSD1 patients tending to be older. The most frequent co-mutations were FLT3 (48%), WT1 (41.6%), NRAS (24%), RUNX1 (14.4%), and CEBPA (10.4%). FLT3 (especially ITD) and WT1 mutations were significantly more prevalent in the NUP98::NSD1 group than in non-NSD1 patients (FLT3: 63.6% vs. 30.5%, p<0.001; WT1: 53% vs. 28.8%, p<0.01). CEBPA mutations occurred almost exclusively in the NUP98::NSD1 group (18.2% vs. 1.7%, p<0.01). Trisomy 8 was detected in 15 patients, 13 of whom had NUP98::NSD1. After one cycle of conventional chemotherapy, the complete remission rate was significantly lower in the NUP98::NSD1 group than in the non-NSD1 group (50.8% vs. 72.5%, p<0.05). Forty-two patients received allogeneic hematopoietic stem cell transplantation (allo-HSCT); all achieved sustained MRD negativity except for two recurring cases. One young NUP98::NSD1-positive patient with persistent disease achieved MRD negativity and long-term disease-free survival after receiving a menin inhibitor (via clinical trial) following chemotherapy failure. This suggests that targeted inhibitors (e.g., menin, KMT2A, or NSD1 inhibitors), though not FDA-approved, represent potential therapeutic options beyond allo-HSCT for NUP98-rearranged patients. Conclusion Our data indicate that NUP98 rearrangements confer a poor prognosis, particularly in NUP98::NSD1-positive patients, attributable to distinct breakpoints and mutational spectra compared to non-NSD1 fusions. Allo-HSCT remains the recommended therapy, but prospective evaluation of targeted inhibitors (e.g., menin, KMT2A, or NSD1 inhibitors) is warranted.