Abstract Introduction Clear cell renal cell carcinoma (ccRCC) is a highly heterogeneous cancer with complex tumor and immune microenvironment interactions influencing progression and therapy response. Advances in spatial technologies now allow for simultaneous spatial mapping of transcriptomic and proteomic features from patient tissue and phenotyping of blood cells, enabling detailed assessment of disease biology. This study highlights a multi-omic approach to characterizing systemic immune responses, tumor microenvironment niches, immune states and tumor heterogeneity in ccRCC patient samples. Methods We profiled ccRCC patient samples using peripheral blood mononuclear cells (PBMC) and tumor-derived cells (TDCs) by CyTOF™ technology with a 50-plus-antibody panel. Matched formalin-fixed tumor tissue was examined by a spatial transcriptomic platform, hematoxylin and eosin (H&E) assessment, and Imaging Mass Cytometry™ (IMC™) technology with a 43-marker panel sequentially on the same tissue section. These datasets were analyzed to explore immune and tumor signatures linked to disease states. Results We demonstrate compatibility of IMC workflows with H&E and spatial transcriptomic modalities. IMC technology identified spatial distribution and activation states of immune and tumor cells in ccRCC. Combining spatial transcriptomics and proteomics enabled detailed phenotyping of tumor metabolic and signaling states and immune cytokine and transcription factor expression. Comparison of PBMC and TDC composition provided insights into systemic and localized immune responses. Conclusion This study highlights the power of spatial multi-omic profiling to unravel the immune and oncologic landscape of ccRCC with high resolution. Identification of spatially defined immune cell states and niches offered insights into tumor immune evasion and resistance mechanisms. These findings pave the way for spatially informed biomarkers and potential precision therapies for ccRCC. For Research Use Only. Not for use in diagnostic procedures. Funding Source n/a Topic Categories Tumor Immunology: Cellular Responses and Tumor Microevironment (TIME)
Cohen et al. (2026) studied this question.