Validation of ITPR2, DPF3, EPAS1 and PVT1 -associated SNPs as biomarkers for RCC in an independent case-control cohort

Abstract

Introduction: Renal cell carcinoma (RCC) is a heterogeneous malignancy influenced by genetic and environmental factors. Previous genome-wide association studies (GWAS) have identified risk single nucleotide polymorphisms (SNPs) associated with RCC susceptibility, particularly within genes such as ITPR2, DPF3, EPAS1, PVT1, and MYC. These SNPs are in regions implicated in key cellular processes like calcium signaling, chromatin remodeling, hypoxia response, and oncogenesis. These pathways are highly relevant to RCC pathogenesis, although the functional significance of these genetic variations in sporadic RCC remains insufficiently characterized. Methods: This study analyzed five GWAS-identified SNPs—rs1049380 and rs10771279 (ITPR2), rs4903064 (DPF3), rs7579899 (EPAS1), and rs35252396 (PVT1/MYC)—in a Spanish case-control cohort comprising 168 RCC patients and 259 healthy controls. Genotyping was performed from buccal swabs, and gene expression levels were assessed in 33 paired formalin-fixed paraffin-embedded (FFPE) tumor and adjacent normal kidney tissue samples. Associations between SNPs, overall survival, and expression of quantitative trait loci (eQTLs) were evaluated in relation to RCC risk and RCC progression in the case of survival curves. Results: The C/C genotype of ITPR2 rs10771279 was associated with a protective effect (OR:0.41), with higher ITPR2 expression observed in healthy tissues than in RCC. The C/C risk genotype of DPF3 rs4903064 was correlated with increased RCC risk (OR: 2.21) and higher DPF3 expression, potentially linked to hypoxia-inducible pathways. Similarly, EPAS1 rs7579899 A/A genotype was significantly associated with RCC risk (OR:1.78) While PVT1/MYC rs35252396 demonstrated a risk trend, it was not statistically significant; however, both genes showed upregulated expression in RCC tissue. In survival analyses, the G allele of rs1049380 (ITPR2) was associated with reduced overall survival in both metastatic and non-metastatic patients and remained significant in 5-year survival analyses. Additionally, the AC genotype of rs35252396 showed the highest risk in 5-year survival models. Conclusion: This study identifies key SNPs and genes, including ITPR2, DPF3, EPAS1, and PVT1/MYC, as potential predictive factors for renal cell carcinoma (RCC) at both diagnostic and prognostic levels, underscoring the importance of using independent validation cohorts to propose new potential biomarkers.