Spatial transcriptomic profiling of the tumor microenvironment associated with sunitinib response in metastatic renal cell carcinoma.

3119 Background: Metastatic clear cell renal cell carcinoma (ccRCC) exhibits heterogeneous clinical outcomes, and limited biomarkers are available to predict response to targeted therapies. This study evaluated cell compartment-specific transcriptional biomarkers predicting clinical response to the tyrosine kinase inhibitor (TKI) sunitinib. Methods: In this phase 2 single-arm clinical trial (NCT00715442), 46 patients with metastatic ccRCC received sunitinib pre- and post-cytoreductive nephrectomy. The primary endpoint was time-to-progression (TTP) and secondary endpoints included overall survival (OS) and sunitinib toxicity. To investigate spatial dynamics of therapeutic response to sunitinib, we applied whole-transcriptome digital spatial profiling (DSP) to tumor tissue to identify myeloid, endothelial, CD8+ T-cell and tumor compartment-specific transcriptional differences between responders (complete or partial response) and non-responders (stable or progressive disease). Results: For the 46 trial patients, the median duration of follow-up was 9.8 years (95% CI: 9.4 – NA). The median TTP was 8.2 months (95% CI: 6.1-19.3) and OS 36.3 months (95% CI: 19.7-70.5). Sunitinib-related adverse events occurred in 20% of patients, with grade 3 and 4 toxicities including hand-foot syndrome, fatigue, and hematologic abnormalities (thrombocytopenia, neutropenia). DSP analyses demonstrated that sunitinib responders display a tumor microenvironment enriched in pro-inflammatory and immunostimulatory programs. By contrast, non-responders displayed enrichment of immunosuppressive programs with elevated PD-L1 expression in myeloid cells and exhausted CD8+ T-cell signatures. Sunitinib resistance mechanisms involving pro-angiogenic VEGF-dependent and independent pathways were identified in non-responders, revealing potential therapeutic targets in combination with TKIs. Moreover, gene signatures developed based on DSP analysis of sunitinib response accurately predicted sunitinib response in an external patient cohort. Conclusions: Our findings underscore the relevance of spatial omics approaches to inform patient stratification and guide precision and combination treatment strategies aimed at mitigating TKI resistance in metastatic ccRCC. Clinical trial information: NCT00715442 .