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The Use of Reverse Phase Protein Arrays (RPPA) to Explore Protein Expression Variation within Individual Renal Cell Cancers
Published on: January 22, 2013
Multi-omics profiling highlights RPLP0 as a potential biomarker for prognosis and response to immunotherapy in clear
Bin Wang1,2, Hongquan Liu2, Yicheng Guo2
1School of Clinical Medicine, Shandong Second Medical University, Weifang, Shandong, 261053, China.
Background:
Clear cell renal cell carcinoma (ccRCC) is characterized by intratumoral heterogeneity and a complex immune microenvironment, which contribute to disease progression and therapeutic resistance. Although ribosomal proteins have been implicated in tumor biology, the clinical relevance, microenvironmental impact, and biological role of ribosomal protein lateral stalk subunit P0 (RPLP0) in ccRCC remain unclear.
Methods:
We performed a comprehensive investigation integrating bulk transcriptomics (TCGA, GEO, ICGC, ArrayExpress), proteomics (CPTAC, HPA), single-cell RNA sequencing, and spatial transcriptomics to characterize RPLP0 expression, prognostic value, immunological relevance, and spatial distribution in ccRCC. The biological functions of RPLP0 were validated experimentally using clinical tissues (qRT-PCR, immunofluorescence) and ccRCC cell lines. Proliferation, migration, and invasion were assessed via CCK-8, wound healing, and Transwell assays following siRNA-mediated knockdown, with epithelial-mesenchymal transition (EMT) markers evaluated by Western blot.
Results:
RPLP0 was ubiquitously expressed in normal tissues but significantly upregulated in ccRCC at both the mRNA and protein levels, which was validated in clinical specimens and cell lines. High RPLP0 expression was associated with advanced tumor stage, metastasis, and poor clinical outcomes, and was identified as an independent prognostic factor. Functional enrichment analyses revealed that RPLP0 was closely linked to ribosome-related processes, DNA damage response, cell cycle regulation, and epithelial-mesenchymal transition. Immune analyses demonstrated that elevated RPLP0 expression correlated with M2 macrophages, as well as with enhanced expression of immune checkpoint and antigen presentation-related genes. Single-cell and spatial transcriptomic analyses revealed the preferential enrichment of RPLP0 in the malignant compartment, with spatial transcriptomics further demonstrating a positive correlation with macrophages. Drug sensitivity analyses based on pRRophetic predictions showed that RPLP0-high tumors were associated with higher estimated IC50 values for several targeted therapies, suggesting a potential association between elevated RPLP0 expression and predicted reduced drug sensitivity. Mechanistically, RPLP0 knockdown in vitro significantly inhibited ccRCC cell proliferation, migration, and invasion, and reversed EMT progression by downregulating mesenchymal markers and upregulating the epithelial marker.
Conclusions:
These findings indicate that RPLP0 is aberrantly upregulated in ccRCC, promoting tumor progression, migration, and invasion by facilitating the EMT process. Furthermore, its close association with immune activation and spatial heterogeneity highlights its potential as a robust prognostic biomarker and a regulator of tumor-microenvironment interactions.