High WBP5 expression correlates with elevation of HOX genes levels and is associated with inferior survival in patients with acute myeloid leukaemia

Abstract

WW domain binding protein 5 (WBP5), also known as Transcriptional Elongation Factor A like 9 (TCEAL9) has been proposed as a candidate oncogene for human colorectal cancers with microsatellite instability and as a predictive indicator of small cell lung cancers. Furthermore, several independent studies have proposed WBP5, and its association with Wilms Tumor-1 (WT1) expression, as part of a gene expression-based risk score for predicting survival and clinical outcome in patients with Acute Myeloid Leukaemia (AML). To date, the prognostic significance of the sole WBP5 expression and its impact on the survival outcome in AML patients remains largely understudied. In the present study, we have made use of publicly available patient expression arrays and have developed an unbiased approach to classify AML patients into low versus high WBP5 expressers and to balance them for known mutations and cytogenetic findings. Interestingly, we found that patients characterized by high WBP5 expression displayed inferior overall and event-free survival rates. Notably, gene expression profiling showed that patients with high WBP5 had elevated expression of several HOX cluster genes, such as HOXA5, HOXA7, HOXA9 and HOXA10, and several of their partner proteins, such as MEIS1 and FOXC1, which have been demonstrated to be causative for AML. Taken together, our data suggest that WBP5 expression level could serve as an indicator for prognosis and survival outcome in patients with AML.

Figure 1

Flow chart showing the sequential steps for the identification of new molecular biomarkers from AML patient expression arrays.

Figure 2

High WBP5 expression is associated with unfavourable outcome in patients with AML. (A) Boxplot representation of WBP5 expression boundaries for patient samples from the Verhaak et al. dataset (0–30% low expression, 70–100% high expression). (B) Boxplot depicting the association of WBP5 expression with risk group categorization (poor, intermediate, good and unknown). (C) Kaplan-Meier representation of overall (OS) and event-free (EFS) survival for WBP5^low and WBP5^high AML patients prior to or (D) after balancing for age, sex, FAB and cytogenetic findings. The number of patients and the median OS and EFS are indicated in the plot. P-value was calculated using Wilcoxon rank-sum test.

Figure 3

WBP5^high and WBP5^low subgroups have distinct global gene expression profiles. (A) Hierarchical clustering of the Pearson correlation coefficient of mRNA expression showing distinct clusters for high and low WBP5 expressers from the Verhaak cohort. The mutational status of every patient is indicated by a colour coded graph on the top of the clustering map. A legend indicating each genetic subgroup is placed below the clustering map. (B) Heatmap indicating the gene expression profiles of WBP5^low and WBP5^high subgroups. (C) Hierarchical clustering of the Pearson correlation coefficient and (D) heatmap of mRNA values from the WBP5^low and WBP5^high subgroups of the patient cohort reported by Kohlmann et al. The cluster of low and high WBP5 expressers are indicated with blue and red boxes, respectively.

Figure 4

Correlation of high WBP5 expression with HOXA and HOXB clusters gene signatures. (A) Volcano plots indicating the most differentially more highly (red dots, above 1.5 log2 FC) and lowly expressed genes (blue dots, below −1.5 log2 FC) in the GSE6891 (Verhaak), GSE15434 (Kohlmann), GSE13204 (Haferlach), GSE1159 (Valk) and GSE22845 (Taskesen) datasets. The most highly differentially expressed HOXA, HOXB and HOX-TALE genes are indicated in each plot. (B) Gene Set Enrichment Analysis (GSEA) plots show enrichment of HOXA and HOXB clusters genes ranked using a signal-to-noise metric according to expression in WBP5 low versus high expressers.

Figure 5

Elevated expression of HOXA, HOXB and HOX partner genes across five different independent gene expression datasets. Expression of representative HOXA (HOXA9, HOXA7, HOAX10 and HOXA5) and HOXB (HOXB2, HOXB3, HOXB6) cluster genes and HOX partners (MEIS1, PBX1, PBX3 and FOXC1) or downstream effectors (MYB, GATA2, FLT3 and CEBPA). Data are represented as boxplots in which high expressers are indicated in red and low expressers are indicated in blue. Every plot presents a color-coded boxplot showing median and interquartile ranges. The statistical analysis reported indicates p-value adjusted for false discovery rates. ***<0.001, **<0.01, *<0.05.