Summary: The study aimed to identify transcriptomic biomarkers for Wilms tumor (WT), irrespective of histological type, stage and risk group. Next-generation sequencing (NGS) was used to analyze the miRNA profiles of 74 kidney samples in two groups: fresh-frozen tissue (FFT) and formalin-fixed, paraffin-embedded tissue (FFPE). The analysis revealed 41 differentially expressed miRNAs in WT versus adjacent kidney tissue, with 27 downregulated and 14 upregulated miRNAs, regardless of tissue preservation. Further mRNA profiling and pathway analysis identified the interaction between miRNA and mRNA in WT. Identified set of genes is potentially regulated by the differentially expressed miRNAs. This comprehensive NGS and bioinformatics approach provides deeper insight into WT pathogenesis and highlights potential miRNA biomarkers, which could serve as universal biomarkers for WT, irrespective of risk group.
Introduction: WT is the most common childhood kidney cancer of embryonic origin. MiRNAs regulate gene expression and play a key role in cancer biology. Despite extensive research on miRNA expression in various cancers, including embryonal neoplasms, these findings are not yet part of routine clinical practice. This study aimed to identify universal transcriptomic biomarkers for the WT. We conducted an epidemiological analysis and compared treatment outcomes with international studies. The molecular analysis used NGS to compare miRNA expression in WT and adjacent kidney tissue. Additionally, mRNA expression profiling and pathway analysis were performed to understand the interplay between miRNAs and mRNAs in WT.
Methods: Patients treated for WT at the Clinical Department of Hematology and Oncology, Pediatric Clinic, University Medical Centre Ljubljana (2000–2019) were include Age at diagnosis, gender, histological subtype, tumor stage, and risk group were determined. Kidney tissue was examined following International Society of Pediatric Oncology (SIOP) guidelines. NGS was used to analyze the miRNA expression in 74 kidney samples, which were divided into two groups: FFT and FFPE samples. Following this, mRNA expression profiling was carried out, and in-silico analysis was performed to predict miRNA-mRNA interactions.
Results: Epidemiological results were consistent with findings from international multicentre randomized trials. Out of 43 children treated for WT, 37 patients were included in the study, 18 boys (age at diagnosis 3.17 ± 2.65 years) and 19 girls (age at diagnosis 3.28 ± 2.70 years). Most patients (97 %) received preoperative chemotherapy, one child underwent primary surgery. WT was stage I in 18 children (49 %), stage II in 6 (16 %), stage III in 3 (8 %), stage IV in 7 (19 %) and stage V in 3 (8 %), with a median age at nephrectomy of 3.17 ± 2.67 years. Among patients, 76% were intermediate risk. No germline variants in WT-related genes were foun Survival was 100%, with relapse in 8% and late effects in 19%. MiRNA analysis identified 41 differentially expressed miRNAs (27 downregulated, 14 upregulated), independent of histology, stage, or risk group. In-silico analysis predicted 10 oncogenesis-related genes (AKT1, BCL-2, CCND1, CDKN1B, ERBB2, FAS, HIF1A, IGF1R, ITGA3, MDM2). Differential mRNA analysis revealed 7207 altered transcripts, mostly in metabolic pathways with reduced activity in WT.
Conclusion: Altered miRNA biogenesis plays a key role in WT. This study revealed transcriptomic differences, irrespective of histology, stage, or risk. Specifically, 27 miRNAs were downregulated and 14 upregulate These findings underscore their role in WT pathogenesis and possible clinical applications. Further studies are needed to confirm their biomarker and therapeutic potential.
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