Characterization of gene expression and biological pathways in Wilms tumor

Abstract

Background

Although mortality for low stage (I/II) Wilms tumor (WT) has greatly improved with dose-intense multimodality and multi-agent interventions, advanced stage (III/IV) tumors remain associated with relapse, mortality and increased treatment-related morbidity. We aim to identify targets unique to the microenvironment of advanced stage WT to develop novel treatments.

Methods

Retrospective review of patients treated for WT at a single institution from 2000 to 2021. Following review by a pediatric pathologist, samples underwent bulk RNA-sequencing with differential gene expression and pathway enrichment analysis. Groups analyzed included low vs advanced stage and neoadjuvant chemotherapy-treated vs treatment-naïve tumors. In neoadjuvant chemotherapy-treated patients with subsequent recurrence, genes predictive of recurrence were identified using Boruta Random Forest Feature Selection and whole-exome DNA-Sequencing.

Results

Initial analysis of 15 samples showed enrichment for cell cycle progression E2F genes with downregulation of interferon alpha and KRAS signaling genes in advanced compared to low stage tumors. Subsequent analysis of 51 tumors with stratification of RNA-sequencing profiles by treatment status showed notable differences among neoadjuvant chemotherapy-treated tumors. A subcluster of advanced stage tumors lacked enrichment of immune-related genes and pathways observed within a subcluster of immune-enriched low stage tumors, including an activating variant of Catenin beta-1. Among patients with recurrence, transmembrane protein 31 was downregulated and flavin containing dimethylaniline monoxygenase 3 upregulated.

Conclusions

Genetic and cellular composition differ between low and advanced stage WT, most notably a significant reduction in immune-related genes/pathways in neoadjuvant chemotherapy-treated tumors. Significant variability exists between same stage tumors, requiring further investigation for reliable treatment targets.