Association of enriched <i>YES1</i> tumor expression at the stromal interface with overall survival in clear cell renal cell carcinoma when treated with first-line immune checkpoint blockade.

Abstract

522 Background: Immune checkpoint blockade (ICB) has improved response rates for patients with advanced clear cell renal cell carcinoma (ccRCC). However, most ccRCC patients develop resistance. Prior studies have shown YES1 expression is upregulated in malignant cells at the tumor-stromal interface of treatment resistant primary tumors. Our objective was to validate YES1 upregulation in an expanded cohort of ICB and tyrosine kinase inhibitor (TKI) exposed patients, develop a bulk RNA sequencing (RNAseq) gene signature, and test for overall survival (OS) in the Oncology Research Information Exchange Network’s (ORIEN) multi-institutional molecular database of patients treated with ICB. Methods: Tissue microarrays were constructed using one-millimeter cores from the tumor-stromal interface of surgically excised primary ccRCC tumors and normal controls. Single-cell spatial transcriptomics (scST) was obtained using a 6,000 gene panel. Malignant cell YES1 expression was compared between treatment-naïve and treatment-exposed samples. Genes of known related proteins to YES1 were tested for correlation within tumor cells, and also compared between the two groups. Same patient RNAseq data were used to construct a signature using genes that correlated with YES1 expression on scST. We tested OS in treatment-naïve patients with a metastatic diagnosis who received any systemic therapy and a subgroup of patients who received a first-line ICB regimen in the multi-institutional ORIEN cohort. Optimal cut off was determined using the survminer package in R, and rank sum test was performed on Kaplan-Meier curves. Cox regression was also performed and YES1 score was treated as a continuous variable. Results: 209,255 cells were analyzed from 21 treatment-naïve and 11 treatment-exposed patients (ICB only, TKI only, or ICB/TKI). On linear mixed effect modeling, YES1 expression was higher in ICB-exposed patients but not TKI-exposed patients (p = 0.001 and p = 0.634). In ORIEN, significantly elevated YES1 score was associated with worse OS in 130 patients with treatment naïve metastatic ccRCC who received systemic therapy (rank sum p-value 0.047). In the subgroup of 69 patients who received first line ICB, elevated YES1 score was associated with worse OS (p = 0.019), but not in the 69 patients who received first line TKI therapy (p = 0.296). Seven genes of proteins known to interact with YES1 were correlated within tumor cells and expressed at higher levels within ICB-exposed patients in both the single-cell and bulk RNA sequencing data ( GRB2, CRK, PAK2, MAPK1, NCK1, MAPK14, and NRAS ). Conclusions: We found that a spatially informed bulk RNA gene signature associated with malignant YES1 upregulation at the tumor-stromal interface was associated with worse OS in a cohort of patients who received first-line ICB treatment.