Adverse genetic alterations and their prognostic impact in Chinese b-ALL patients with DUX4 rearrangement Free

B-cell acute lymphoblastic leukemia (B-ALL) is a heterogeneous group of hematological malignancy with many molecular subtypes. It generally occurs in children and adolescents, but it can also appear in adults with significantly poorer outcome. Recent omics studies have classified B-ALL into more than 20 subtypes with distinct oncogenic lesions or gene expression profiles, further promoted the risk-adapted treatment strategies. Among them, both pediatric and adult patients of DUX4-r subtype were generally considered to have good prognosis. However, the recent report with relapsed DUX4-r cases (n=5) experienced a high mortality rate of 80%, and suggested TP53 mutation or IKZF1^plus might be adverse genetic factors. Large scale verification, further discovery of molecular features, and prognostic biomarkers of DUX4-r B-ALL patients are still urgently needed.

Retrospective analyses were performed for more than 1,000 B-ALL cases tested in our lab between January, 2019 and July, 2025. Gene fusions were detected from the RNA-seq data, while B-ALL subtypes were determined by integrating the gene expression profiles. Totally, 52 DUX4-r B-ALL cases were identified, including 36 newly diagnosed patients without relapse during the whole observation period, and the other 16 relapsed patients (including 11 relapsed after HSCT) admitted to Beijing GoBroad Boren hospital for further therapy. Genetic mutations were detected from their corresponding targeting sequencing data, or retrieved from original diagnosing reports. Clinical and molecular features of these non-relapsed and relapsed DUX4-r cases were then characterized, and adverse genetic alterations associated with poor prognosis were explored.

The incidence of female (n=29, 55.8%) was higher than male (n=23, 44.2%) among the total 52 DUX4-r B-ALL cases, which was more notably in the relapsed group (12 females vs. 4 males) though not significant enough (p=0.06). The median age of all the DUX4-r patients was 12.5 years (IQR: 8.0-17.0 years), similar to previous reports. However, the median age of the relapsed patients was 21.5 years (IQR: 18.5-28.3 years), significantly higher than the value (median: 6.5 years, IQR: 4.8-7.3 years) of the other non-relapsed patients (p < 0.01).

51 of the DUX4-r B-ALL patients carried the IGH::DUX4 gene fusion, while the other 1 carried TCL1A::DUX4 gene fusion. The most frequent mutated genes were KMT2D (n=18, 34.6%), NRAS (n=16, 30.8%), TP53 (n=8, 15.4%), FLT3 (n=6, 11.5%), and KRAS (n=5, 9.6%). The widely known ERG gene deletion was observed in 14 patients (26.9%), and the IKZF1 gene deletion especially IK6 (exon 4-7 deletion) was observed in 16 patients (30.8%). And lower incidence of TBL1XR1 gene mutation (n=2, 3.8%) were observed, which was different from previous western studies. Meanwhile, we also observed enrichment of KMT2D gene mutations (9/16 vs. 9/36, p=0.02) and TP53 gene mutations (6/16 vs. 2/36, p<0.01) in the relapsed group.

Survival analyses were performed, with a median follow-up time of 24.4 (95% CI: 18.3-34.9) months. And it was observed that the 2-year cumulative incidence rate (CIR) of patients with KMT2D gene mutations was significantly higher than the others (62.3% vs. 18.1%, p=0.02), further confirming their poor prognosis impact.

DUX4-r B-ALL were generally considered to have good prognosis, however, high mortality rate of the relapsed patients was also reported. Clinical characteristics of females and elder age were discovered to be associated with the relapsed DUX4-r patients. KMT2D and TP53 gene mutations were enriched in the relapsed group, and KMT2D mutation positive patients were observed with higher 2-year CIR, further indicated that they were adverse genetic alterations in Chinese B-ALL patients with DUX4 rearrangement.