Cross-cancer transcriptomic analysis reveals conserved developmental, ferroptosis, and immune remodeling modules in...

Wilms tumor (nephroblastoma) is a pediatric renal malignancy driven by disrupted nephrogenesis, yet its transcriptomic relationship with ferroptosis and immune remodeling remains poorly characterized.

We analyzed GSE66405 microarray data (28 Wilms tumor samples) together with an oral cancer 10X single-cell reference dataset to evaluate six biologically defined modules: developmental/nephrogenesis, Wnt/beta-catenin, ferroptosis/iron metabolism, immune/inflammatory, extracellular matrix, and cell-cycle. Module scores were calculated as mean z-scores across curated gene sets, and inter-module Pearson correlations, co-expression network analyses, and unsupervised clustering were performed in Python using scipy, scikit-learn, networkx, and matplotlib.

Developmental and Wnt programs formed the central transcriptomic axis of Wilms tumor, with WT1, SIX1, SIX2, PAX2, and CTNNB1 as hub genes (Pearson r = 0.868 between module scores, P < 0.001). The developmental module showed the strongest correlation with ferroptosis (r = 0.920, P < 0.001), while ferroptosis and immune modules were also tightly linked (r = 0.851, P < 0.001). Ferroptosis-related genes (HMOX1, FTL, SLC40A1, TFRC, GPX4, SLC7A11) and immune markers (CD68, CD163, CD8A, GZMB) were detected as secondary remodeling modules associated with the developmental core. Cross-cancer comparison revealed partial conservation of ferroptosis and immune module architecture in the oral cancer reference, whereas the developmental-Wnt axis remained Wilms tumor-specific. In vitro qRT-PCR validation in WiT49 (Wilms tumor) and CAL-27 (oral squamous cell carcinoma) cell lines confirmed differential ferroptosis gene expression: HMOX1 and TFRC were significantly upregulated in WiT49 cells (p < 0.001), while GPX4 and SLC7A11 were relatively higher in CAL-27 cells (p < 0.01), corroborating lineage-specific iron metabolism remodeling.

These results link developmental dysregulation, iron metabolism, and immune remodeling in Wilms tumor and identify candidate modules for future functional validation. The developmental-Wnt axis constitutes a Wilms tumor-specific transcriptomic core, while ferroptosis and immune programs represent partially conserved stress-response modules that may offer cross-lineage therapeutic relevance. In vitro qRT-PCR experiments in WiT49 and CAL-27 cells corroborated these transcriptomic findings, confirming lineage-differential expression of core ferroptosis regulators across the two cancer contexts.