Work

Integrative SMR and single cell & spatial analysis reveals the spatial heterogeneity and prognostic value of CASP9-mediated apoptotic pathways in clear cell renal cell carcinoma

Year: 2025

Type: book-chapter

Abstract: BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is the most common histological subtype of renal cancer and remains a clinical challenge due to its frequent resistance to therapy and poor prognosis in advanced stages. Apoptosis, a fundamental tumor-suppressive mechanism, exhibits paradoxical roles in cancer, wherein apoptotic tumor cells can also contribute to immunosuppression and tumor progression. However, the spatial dynamics, transcriptional heterogeneity, and prognostic relevance of apoptosis-related gene programs in ccRCC remain poorly defined. METHODS: We performed an integrative analysis combining single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, and summary-based Mendelian randomization (SMR) to dissect apoptosis-related malignant cell states in ccRCC. Cancer cells were stratified based on apoptosis gene signatures and CASP9 expression. Cell-cell communication was assessed using CellChat and spatial interaction networks were constructed using RCTD and mistyR. SMR was employed to link genetically regulated CASP9 expression with renal cancer risk. A CASP9-associated prognostic model was developed using LASSO Cox regression and DeepSurv on TCGA and E-MTAB-1980 cohorts. RESULTS: We identified transcriptionally and spatially distinct apoptosis-high and apoptosis-low malignant cell subpopulations. Apoptosis-high tumor cells, characterized by elevated CASP9 expression, preferentially localized near macrophage-enriched stromal regions and exhibited stronger spatial clustering. Ligand-receptor modeling revealed directional signaling via the SPP1-CD44 axis between CASP9-high cancer cells and macrophages. SMR analysis provided genetic evidence supporting CASP9 as a causal gene for renal cancer. CASP9-high cells demonstrated distinct developmental trajectories and formed multicellular spatial modules with macrophages and cycling cells. A five-gene apoptosis-related signature derived from CASP9-stratified tumor cells robustly predicted patient survival across both training and validation cohorts. Low-risk patients exhibited enriched immune infiltration, increased immune checkpoint expression, and enhanced immune pathway activity. CONCLUSIONS: Our study reveals that apoptosis, particularly CASP9-driven programs, defines a spatially organized, immunosuppressive malignant cell state in ccRCC. CASP9 acts as both a genetic driver and spatial regulator of tumor-macrophage interactions, contributing to disease progression. The CASP9-associated risk model demonstrates strong prognostic utility and highlights apoptosis as a promising therapeutic axis in ccRCC.

Source: Discover Oncology

DOI: 10.1007/s12672-025-03798-0