UBTF tandem duplications are rare but recurrent alterations in adult AML and associated with younger age, myelodysplasia, and inferior outcome

Abstract

Tandem-duplication mutations of the UBTF gene (UBTF-TDs) coding for the upstream binding transcription factor have recently been described in pediatric patients with acute myeloid leukemia (AML) and were found to be associated with particular genetics (trisomy 8 (+8), FLT3-internal tandem duplications (FLT3-ITD), WT1-mutations) and inferior outcome. Due to limited knowledge on UBTF-TDs in adult AML, we screened 4247 newly diagnosed adult AML and higher-risk myelodysplastic syndrome (MDS) patients using high-resolution fragment analysis. UBTF-TDs were overall rare (n = 52/4247; 1.2%), but significantly enriched in younger patients (median age 41 years) and associated with MDS-related morphology as well as significantly lower hemoglobin and platelet levels. Patients with UBTF-TDs had significantly higher rates of +8 (34% vs. 9%), WT1 (52% vs. 7%) and FLT3-ITD (50% vs. 20.8%) co-mutations, whereas UBTF-TDs were mutually exclusive with several class-defining lesions such as mutant NPM1, in-frame CEBPA^bZIP mutations as well as t(8;21). Based on the high-variant allele frequency found and the fact that all relapsed patients analyzed (n = 5) retained the UBTF-TD mutation, UBTF-TDs represent early clonal events and are stable over the disease course. In univariate analysis, UBTF-TDs did not represent a significant factor for overall or relapse-free survival in the entire cohort. However, in patients under 50 years of age, who represent the majority of UBTF-mutant patients, UBTF-TDs were an independent prognostic factor for inferior event-free (EFS), relapse-free (RFS) and overall survival (OS), which was confirmed by multivariable analyses including established risk factors such as age and ELN2022 genetic risk groups (EFS [HR: 2.20; 95% CI 1.52-3.17, p < 0.001], RFS [HR: 1.59; 95% CI 1.02-2.46, p = 0.039] and OS [HR: 1.64; 95% CI 1.08-2.49, p = 0.020]). In summary, UBTF-TDs appear to represent a novel class-defining lesion not only in pediatric AML but also younger adults and are associated with myelodysplasia and inferior outcome in these patients.

Fig. 1. Illustration of the effect of UBTF tandem duplications on the amino acid level.

A All patients showed typical inframe insertions and/or deletions leading to alterations in the coding sequence of exon 13. B 3D protein structure of UBTF (Source: Alphafold.ebi.ac.uk Sequence AF-P17480-F1). The highlighted amino acids represent the localization hotspots AA 445-449 of the observed InDel mutations.

Fig. 2. Clinical variables of UBTF-TD^pos patients.

A Age distribution of the 52 UBTF-TD^pos patients. Prevalence of UBTF-TDs shows a strong negative correlation with age. B Peripheral blood counts in UBTF-TD^pos vs. UBTF-TD^WT patients. Despite their young age, laboratory parameters revealed significantly lower hemoglobin levels and platelet counts at diagnosis for UBTF-TD^pos patients.

Fig. 3. Landscape of co-mutations in UBTF mutant AML and survival analysis according to UBTF mutant status.

A Alignment of additional gene mutations in 52 UBTF-TD^pos patients. B Frequency distribution of additional gene mutations identified in UBTF-TD^pos vs. UBTF-TD^WT patients. C Variant allele frequencies (VAFs) of UBTF-TDs and frequent co-mutations (frequency of at least 10% in UBTF-mut patients). Solid bars indicate VAF median and IQR.

Fig. 4. RNA-sequencing analysis in UBTF mutant AML and other well established AML subgroups.

A Principal component analysis (PCA) of the RNA-Sequencing data. B Heat map of RNA-Sequencing analysis indicates the top 50 differentially expressed genes ranked based on FDR between UBTF-TD^pos patients and references, with high levels of expression shown in red and low levels shown in blue. Color coding is based on standardized and normalized read counts accounting for the library size.

Fig. 5. Survival analysis according to UBTF mutant status.

Kaplan–Meier survival curves showing event-free, relapse-free and overall survival of UBTF-TD^pos and UBTF-TD^WT patients for A all patients and B for patients <50 years of age. p-values were calculated using the log-rank test. Numbers of patients at risk are provided below the x-axis.