Genomic and Molecular Associations with Preoperative Immune Checkpoint Inhibition in Patients with Stage III Clear Cell Renal Cell Carcinoma

<b>Background and Objective</b>: Patients with stage III clear cell renal cell carcinoma (ccRCC) have a high risk for disease recurrence post-nephrectomy. To mitigate overtreatment, there is a pressing need to determine who benefits from immune checkpoint inhibition (ICI) around the time of surgical resection. We performed digital spatial analysis of both gene and protein expression in stage III ccRCC tumors, some of which had preoperative ICI exposure. <b>Methods</b>: Nephrectomy specimens from stage III ccRCC patients were analyzed using the Nanostring GeoMx Digital Spatial Profiler. Differential expression analysis was performed and validated using NCT02210117 trial data to identify genes associated with both ICI and clinical response. A gene score was then generated to predict overall survival in patients from The Cancer Genome Atlas (TCGA). <b>Key Findings and Limitations</b>: In a small cohort of 19 patients, RNA expression significantly differed based on preoperative ICI exposure and recurrence status-CD8+ effector and central-memory T-cell signatures were less prevalent in the treatment-naïve with recurrence group. Three out of four patients with preoperative immune checkpoint inhibition recurred. External validation yielded a four-gene set (<i>GZMK</i>, <i>GZMA</i>, <i>ITGAL</i>, and <i>IL7R</i>), where higher expression levels predicted better overall survival in the TCGA cohort (<i>p</i> = 0.005). <b>Conclusions and Clinical Implications</b>: Preoperative ICI favorably altered the tumor microenvironment to resemble that of treatment-naïve patients without recurrence but did not translate to improved survival. Upon external validation, the genes <i>GZMK</i>, <i>GZMA</i>, <i>ITGAL</i>, and <i>IL7R</i> were modifiable with ICI and associated with improved overall survival. Further investigation is needed to assess if patients with low baseline expression of these genes may benefit from ICI around the time of surgery.