NUP98-NSD1 Fusion Gene Is Strongly Associated with a Poor Prognosis in Pediatric Acute Myeloid Leukemia: A Study of the Japanese Childhood AML99 Cooperative Study Group

Acute myeloid leukemia (AML) is a complex disease caused by mutations, deregulated gene expression, and epigenetic modifications of genes leading to increased proliferation and decreased differentiation of hematopoietic progenitor cells. In hematological malignancies with 11p15 translocations, the nucleoporin 98-kDa (NUP98) protein regulates nucleocytoplasmic transport of protein and RNA. More than 20 different chromosomal rearrangements involving NUP98 have been identified. The cryptic translocation t(5;11)(q35;p15.5), which creates a fusion gene between the NSD1 and the NUP98. The NUP98-NSD1 fusion gene has been associated with a deletion of the long arm of chromosome 5, del(5q), in pediatric AML patients. Recently, NUP98-NSD1 was identified in childhood AML by fluorescence in situ hybridization (FISH) with subtelomeric probes. However, the frequency and clinical impact of NUP98-NSD1 in pediatric AML remain uncertain.

To estimate the frequency and clinical impact of the NUP98-NSD1 in pediatric AML, we examined the NUP98-NSD1 fusion transcript in a consecutive series of 157 newly diagnosed AML patients enrolled in the AML99 protocol in Japan clinical trial. Total RNA extracted from the leukemia cells of the patient at diagnosis was reverse transcribed to cDNA. The PCR was performed using the primer sets for detection of NUP98-NSD1. The PCR amplification was performed with a DNA thermal cycler followed by direct sequencing with an ABI PRISM 310 Genetic Analyzer. We also examined somatic mutations of the FLT3, KIT, WT1, NPM1, NRAS, KRAS and MLL genes, which are prevalent in AML, in these AML patients with NUP98-NSD1.

In the current study, we identified the NUP98-NSD1 by RT-PCR followed by direct sequencing in 6 (3.8%) out of 157 AML patients, and clustered significantly in the cytogenetically normal AML subgroup (6/33, 18.2%). Significant differences between patients with and without NUP98-NSD1 were observed in 4-year OS (33.3% versus 80.0%), and EFS (33.3% versus 69.2%). NUP98-NSD1 was highly seen in males (5 males and 1 female). The statistical differences between patients with and without NUP98-NSD1 was not significant in age (median: 7 years [range: 2–15 years] versus 6 years [range: 0–15 years]), and the initial WBC count (median: 115.9 × 10⁹/L [range: 9.0–329 × 10⁹/L] versus 51.8 × 10⁹/L [range: 1.0–621 × 10⁹/L]). Interestingly, NUP98-NSD1 was observed in 4 patients with normal karyotype, and was observed in 2 patients with del(9q). NUP98-NSD1 could not be identified by conventional G-banding technique in any cases. Patients with NUP98-NSD1 had any mutation of FLT3 -ITD (66.7%), WT1 (50%), KIT (16.7%) or RAS (33.3%). Furthermore, NUP98-NSD1 was frequently found in M4 or M5 patients according to FAB classification.

We identified the NUP98-NSD1 in 6 out of 157 AML patients, and clustered significantly in the cytogenetically normal AML subgroup. Patients with NUP98-NSD1 had any FLT3 -ITD, WT1, KIT or RAS mutations. These results suggest that simultaneous occurrence of FLT3 -ITD, WT1, KIT mutations and RAS aberrations in NUP98 -related leukemia may be associated with poor prognosis. The NUP98-NSD1 was not identified by conventional G-banding technique, confirming that this translocation can exist as the only cytogenetic alteration. Therefore, FISH and RT-PCR analyses for NUP98-NSD1 fusion gene is recommended at the onset of disease in larger series of AML patients presenting an apparently normal karyotype, del(9q) or del(5q) to gain insight into the actual incidence and clinical features of patients with t(5;11)(q35;p15.5).

No relevant conflicts of interest to declare.