Use of Single-Cell Data and scPagwas Analysis to Identify T Cell Subsets and Construct a Prognostic Model for Clear Cell Renal Cell Carcinoma

Clinical Snapshot

Key Findings

• P Value: Not specified in abstract

• Effect Size: Substantial survival advantage for low-risk patients (specific values not provided)

• Primary Outcome: Overall survival stratified by 7-gene prognostic signature

• Nnt Or Sensitivity: Excellent clinical predictive value by time-dependent ROC analysis (specific AUC values not provided)

• Confidence Interval: Not specified in abstract

Clinical Application

Requires single-cell RNA sequencing and computational analysis infrastructure, limiting immediate clinical implementation Relevant to Australian oncology practice given KIRC prevalence; however, implementation would require TGA consideration for companion diagnostics and integration with existing Cancer Australia guidelines Patients with clear cell renal cell carcinoma requiring prognostic stratification

Abstract

BACKGROUND: Clear cell renal cell carcinoma (KIRC), the most prevalent pathological renal cell carcinoma (RCC) subtype, makes up approximately 75%-84% of total cases. KIRC is characterized by high heterogeneity, high metastasis rates, and a poor prognosis. Its incidence rate has continued to rise in recent years. We sought to construct new prognostic models to optimize treatment decisions, improve clinical benefits, and explore potential therapeutic targets. METHODS: This study integrated various omics data including single-cell RNA seq (GSE171306), TCGA-KIRC, GWAS, and validation datasets (GSE29609 and E-MTAB-1980). The scPagwas algorithm combines GWAS with scRNA-seq to identify immune subgroups with high feature correlation. Key genes are identified through the combination of weighted correlation network analysis (WGCNA) with differentially expressed genes (DEGs). We built a clinical prognostic model by using machine learning algorithms and validated it through survival rate and receiver operating characteristic (ROC) analysis. We used cancer drug sensitivity genomics data to analyze drug sensitivity and performed molecular docking to identify potential therapeutic drugs. RESULTS: Using single-cell RNA seq data, we identified T cell subsets as characteristic cell subsets in KIRC through scPagwas analysis. In single-cell analysis, key genes in T cell subsets and genes with PCC values > 0.05 were combined with the core genes in DEGs and WGCNA modules, thus yielding 86 intersecting genes. These genes were significantly enriched in immune-related pathways. We established a clinical prognostic model containing seven risk genes. Low-risk patients exhibited substantial survival advantages. Time-dependent ROC analysis indicated the prognostic model's excellent clinical predictive value. Functional enrichment, immune infiltration, and somatic mutation analyses highlighted different biological mechanisms among risk populations. The SHAP values of the XGBoost and LightGBM machine learning algorithms indicated DOCK8 as a potential biomarker. Drug prediction and molecular docking predicted five potential drugs targeting DOCK8 (finasteride, nocodazole, palonosetron, pifithrin alpha, and topiramate). CONCLUSION: Our systematic analysis of the immune microenvironment, key genes, and prognosis of KIRC highlighted the critical roles of T cell subsets. We additionally established an effective clinical prognostic model. Our findings provide new insights and potential targets for the precise diagnosis and targeted KIRC therapy.

References

1. 1.Yi, X., Jia, Z., Wu, J., Wang, S., Yu, Y., Kong, Y., He, X., & Huang, Y. (2026). Use of Single-Cell Data and scPagwas Analysis to Identify T Cell Subsets and Construct a Prognostic Model for Clear Cell Renal Cell Carcinoma. Human Mutation. https://doi.org/10.1016/j.immuni.2004.09.002