PI3/Elafin expression predicts recurrence after chemotherapy with DNA-damaging drugs in gastric cancer

Despite recent advances in gastric cancer therapy, chemotherapy resistance and lack of methods for selecting combination regimens remain major problems. Organoids, which recapitulate the in vivo micro-environment, can be established from surgical specimens with a high success rate, and are widely used for drug sensitivity assays. In this study, we aimed to discover a novel biomarker for predicting multidrug resistance using gastric cancer organoids (GCOs), which provide in vivo-like culture system that more closely resembles tumor cell organization than traditional cell lines. We evaluated 5-fluorouracil or oxaliplatin-resistant GCOs to find novel biomarkers that reflect multidrug resistance in gastric cancer. To examine the resistance mechanisms, RNA-seq analysis and ex vivo drug sensitivity testing were performed. The association of biomarkers with patient prognosis and chemotherapy efficacy was evaluated using three original cohorts with a total of 230 cases. The results were also validated with two independent public cohorts and a single-cell RNA sequence data. Increased expression of PI3/Elafin was detected in all 5-fluorouracil or oxaliplatin-resistant GCOs. Our findings suggest a potential association of PI3/Elafin expression with ribosome biosynthesis and RNA metabolism under organoid conditions. We also found that PI3/Elafin overexpression promotes 5-fluorouracil/oxaliplatin/cisplatin resistance but not paclitaxel resistance. Immunohistochemical evaluation of Elafin expression revealed that the Elafin-positive gastric cancer group had a poorer outcome, especially in terms of time-to-recurrence. Elafin positivity was also an independent predictor of relapse after chemotherapy with DNA-damaging agents. PI3/Elafin promotes DNA-damaging drug resistance through multiple downstream regulations related to RNA and ribosomal metabolism. PI3/Elafin may be useful as a biomarker for therapeutic selection of non-DNA-damaging agents. We performed PI3/Elafin overexpression (PI3OE) and control vector transfection (Ctrl) in three gastric cancer cell lines and three GCOs to investigate the effect of Elafin expression. Gene expression was comprehensively analyzed using RNA sequencing.