Expression and enrichment analysis of DEGs across distinct prognostic groups in adult AML
Based on the established screening criteria, a total of 662 up-regulated DEGs and 468 down-regulated DEGs were identified across various prognostic groups. The figure provided in the study highlights the significant variations in gene expression among adult AML patients belonging to different groups(Fig. S1). To explore the signaling pathways associated with these DEGs, separate analyses were conducted for up-regulated and down-regulated genes. The findings of the study revealed that the GO analysis of up-regulated DEGs primarily exhibited enrichment in tetrapyrrole binding, heme binding, hydrogen peroxide metabolic process, hydrogen peroxide catabolic process and peroxidase activity(Fig.1a). Furthermore, the KEGG analysis of up-regulated DEGs demonstrated enrichment in Olfactory transduction and Metabolism of xenobiotics by cytochrome P450(Fig.1b). Conversely, the GO analysis of down-regulated DEGs predominantly exhibited enrichment in pattern specification process, regionalization, embryonic organ development, collagen-containing extracellular matrix and embryonic organ morphogenesis(Fig.1c). Additionally, the KEGG analysis of down-regulated DEGs revealed enrichment in the Wnt signaling pathway and Complement and coagulation cascades(Fig.1d). Considering the association between the Wnt signaling pathway and AML, the study identified 14 DEGs (DAAM2, DKK2, FZD8, GPC4, NFATC4, PRICKLE1, PRICKLE2, PRICKLE4, RSPO2, SFRP5, SOX17, WNT5A, WNT9A, WNT6) that are related to the Wnt signaling pathway in AML. The heatmap analysis clearly depicted distinct expression patterns of these DEGs across different prognostic groups(Fig.1e). Notably, the gene expression within each group exhibited a high level of consistency, and the DEGs were effectively distinguished.
Key genes in the AML-associated Wnt signaling pathway DEGs
The PPI of the 14 AML-associated genes in the Wnt signaling pathway were examined using the online database STRING and visualized through the utilization of Cytoscape 3.9.1 software. The CytoHubba plug-in for Cytoscape was employed to identify the 7 most highly connected protein molecules. These proteins were identified as WNT5A, FZD8, SFRP5, WNT9A, DKK2, WNT6, and PRICKLE1(Fig.2a). Additionally, a T-test to compare the groups with high and low expression levels, resulting in the identification of 8 significant genes, namely FZD8, RSPO2, SFRP5, PRICKLE1, PRICKLE2, PRICKLE4, WNT6, and WNT9A(Fig.2h-o),and the other 6 genes were not statistically significant(Fig.2b-g). Among these, 5 genes were found to be common to both analyses, namely FZD8, SFRP5, PRICKLE1, WNT9A, and WNT6.
Prognostic evaluation of key genes in pediatric AML
To examine the prognostic implications of key genes in pediatric AML, we conducted an analysis to assess the impact of individual gene expression on the overall survival of AML patients. This investigation utilized the TARGET Pediatric Database and involved the collection of clinical samples from pediatric patients. Our analysis of the database revealed that pediatric AML patients with low expression of certain key genes, namely FZD8, SFRP5, PRICKLE1, WNT9A, and WNT6, exhibited more favorable overall survival rates. Notably, SFRP5 and WNT6 demonstrated particularly significant associations(Fig.3a). Furthermore, our examination of the clinical samples indicated that pediatric AML patients with low expression of the key gene WNT6 experienced improved overall survival. However, no statistically significant relationship between the remaining key genes and survival was observed(Fig.3b). Consequently, the disparity in WNT6 expression was found to be linked to the prognosis of AML in children, prompting further investigation into the underlying mechanisms.
WNT6 regulates the Wnt signaling pathway to influence drug resistance
The gene set enrichment analysis conducted on the Wnt signaling pathway in the dataset of WNT6 knockout mice (GSE160039) revealed a significant difference in scores between the WNT6 knockout group and the wild-type group(Fig.4a). Specifically, the scores for the Wnt signaling pathway were significantly lower after the knockout of WNT6. In the AML resistance dataset (GSE214158), a similar analysis was performed on the gene set enrichment results for the Wnt signaling pathway in the UTX knockout and wild-type groups. The scores for the Wnt signaling pathway were found to be lower in the UTX knockout group. Furthermore, the gene set enrichment analysis of the Wnt signaling pathway in the UTX wild group demonstrated a statistically significant difference in Wnt signaling pathway scores between the two groups(Fig.4b). Specifically, the UTX knockout group exhibited lower Wnt signaling pathway scores, indicating a significant reduction in drug resistance associated with KMT2A-rearranged AML after UTX knockout. Thus, when the Wnt signaling pathway scores were low, the likelihood of drug resistance in the Wnt signaling pathway was reduced. Additionally, it was observed that the Wnt signaling pathway scores significantly decreased when WNT6 was expressed at low levels. This decrease in Wnt signaling pathway score resulted in more effective drug treatment and a reduced likelihood of drug resistance. Therefore, it can be concluded that WNT6 plays a regulatory role in the Wnt signaling pathway and influences drug resistance.