Multiregional single-cell proteogenomic analysis of ccRCC reveals cytokine drivers of intratumor spatial heterogeneity

Intratumor heterogeneity (ITH) represents a major challenge for anticancer therapies. An integrated, multidimensional, multiregional approach dissecting ITH of the clear cell renal cell carcinoma (ccRCC) tumor microenvironment (TME) is employed at the single-cell level with mass cytometry (CyTOF), multiplex immunofluorescence (MxIF), and single-nucleus RNA sequencing (snRNA-seq) and at the bulk level with whole-exome sequencing (WES), RNA-seq, and methylation profiling. Multiregional analyses reveal unexpected conservation of immune composition within each individual patient, with profound differences among patients, presenting patient-specific tumor immune microenvironment signatures despite underlying genetic heterogeneity from clonal evolution. Spatial proteogenomic TME analysis using MxIF identifies 14 distinct cellular neighborhoods and, conversely, demonstrated architectural heterogeneity among different tumor regions. Tumor-expressed cytokines are identified as key determinants of the TME and correlate with clinical outcome. Overall, this work signifies that spatial ITH occurs in ccRCC, which may drive clinical heterogeneity and warrants further interrogation to improve patient outcomes. [Display omitted] •Integrated multiomic profiling and multiplex imaging of multiregional ccRCC biopsies•Heterogeneity in TME spatial architecture is detected across different tumor regions•MxIF analysis reveals 14 distinct cellular neighborhoods in multiregion ccRCC tumors•TME tumor-expressed cytokines are correlated with ccRCC clinical outcomes Using an integrated approach, including multiomic profiling and multiplex imaging, Miheecheva et al. identify heterogeneity within the tumor microenvironment (TME) spatial architecture of primary ccRCC tumors. Molecular analysis shows correlation of TME tumor-expressed cytokines with treatment response, which may drive clinical heterogeneity of ccRCC patient outcomes.