Background/Objectives: Clear cell renal cell carcinoma (ccRCC), the predominant malignant subtype of kidney cancer, is the leading cause of death among renal cell carcinoma patients. Although a subset of ccRCC patients benefit from select immune checkpoint inhibitors (ICIs), prognosis remains poor. While PD-1 and PD-L1 have been extensively studied, the prevalence and distribution of other immune checkpoints (ICs) and their relationship with epithelial-to-mesenchymal transition (EMT) remain poorly characterised. Here, we investigated the interplay between twenty ICs and EMT markers and assessed their combined prognostic relevance in ccRCC patients. Methods: Transcriptomic profiling and integrated bioinformatic analyses were performed, including differential expression, correlation analyses, survival analyses, forest plot analyses, ROC curve evaluation, and OncoPrint visualisation, complemented by analysis of single-cell RNA sequencing data, immunohistochemistry, and multiplex secretory IC (LegendPlex) assays. Results: Transcriptomic profiling of over 500 ccRCC tumours versus normal kidney tissue revealed dysregulation of ICs, particularly LAG3 and NT5E. Notably, expression of ICs, including LAG3 and NT5E, was associated with poor overall survival in 415 ccRCC patients. ICs that synergised with the EMT phenotype provided improved prognostic discrimination compared to individual ICs. Correlation analyses, single-cell RNA sequencing, and immunohistochemistry demonstrated an association between EMT-associated tumours and expression of LAG3 and NT5E. ROC analysis indicated modest prognostic performance of LAG3 and NT5E. Conclusions: Collectively, this study identifies an EMT-IC axis in ccRCC and demonstrates its relevance to tumour biology and patient outcomes, highlighting LAG3 and NT5E as potential prognostic markers and therapeutic targets that warrant further investigation.
Cancers. 2026 Jul 14*** epublish ***
Arpita Poddar, Farah Ahmady-Nield, Revati Sharma, Seemadri Subhadarshini, Mohit Kumar Jolly, Suresh Ramakrishna, Ali Raza, Ravi Shukla, George Kannourakis, Aparna Jayachandran, Prashanth Prithviraj
Fiona Elsey Cancer Research Institute, Ballarat, VIC 3350, Australia., Department of Bioengineering, Indian Institute of Science, Bengaluru 560012, Karnataka, India., Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Republic of Korea., Ian Potter NanoBiosensing Facility, NanoBiotechnology Research Laboratory, School of Science, RMIT University, Melbourne, VIC 3000, Australia.