Evaluating the unfolded protein response as a therapeutic target in clear cell renal cell carcinoma patients

Metastatic clear cell renal cell carcinoma (ccRCC) is an incurable and lethal disease. While treatment of ccRCC has shifted toward antiangiogenic and immunotherapy combinations, long-term response is rare, underscoring the urgent need for novel therapeutic targets. We previously demonstrated in a murine model that therapeutic targeting of the unfolded protein response (UPR) via the mediator PKR-like ER kinase (PERK) can reverse tumor progression, immune suppression, and resistance to immune checkpoint blockade (ICB) (Mandula et al. Cancer Cell. 2022). Early-phase clinical studies are now evaluating PERK inhibition as a therapeutic strategy in solid tumors, including ccRCC. Here, we performed a retrospective analysis of patients with ccRCC using an analytical framework to estimate PERK activity from transcriptome data. We evaluated three independent ccRCC patient data sets - iATLAS patients treated with ICB (n = 296), ORIEN AVATAR patients treated with ICB (n = 85), and a TCGA treatment-naive cohort (n = 534). Across these datasets, PERK expression was associated with increased progression risk and worse overall survival. To evaluate the role of PERK in the context of endoplasmic reticulum (ER) stress, we generated a PERK knockout model using CRISPR gRNA in ccRCC cell lines and then challenged the cells with an ER stressor, thapsigargin. Interestingly, we found cytoplasmic vacuolization reminiscent of an unresolved unfolded protein response, ER swelling, and proteostasis disruption. Moreover, joint treatment with the PERK inhibitor AMG44 and thapsigargin significantly reduced viability in ccRCC cells. To further assess the therapeutic potential of PERK inhibition during standard-of-care therapy, we evaluated its impact during VEGF blockade. We observed decreased cell viability in PERK-silenced cells following cabozantinib (VEGF inhibitor) exposure, either through drug inhibition or genetic deletion. In summary, as clinical interest in PERK inhibition (PERKi) grows across multiple solid tumors, our findings highlight PERK as a potential therapeutic target in ccRCC and identify associated biomarkers that may inform future clinical strategies.