Identification of potentially deleterious mutations in gastric cancer using patient-derived xenograft models

Luke Kong¹Jie Wang¹Junqi Zheng¹Xihua Yang²Ruifang Sun³Jiahui Kou¹Yujie Yao¹Feng Li⁴Fuhua Wang^5*Sutang Guo^4*

• ¹Department of Biochemistry and Molecular Biology, School of Basic Medicine, Shanxi Medical University, Taiyuan, China
• ²Laboratory Animal Center, Shanxi Provincial Cancer Hospital, Taiyuan, Shanxi Province, China
• ³Department of Tumor Biobank, Shanxi Provincial Cancer Hospital, Taiyuan, Shanxi Province, China
• ⁴Central Laboratory,shanxi provincial cancer hospital, Taiyuan, China
• ⁵Department of Laboratory Medicine, Shanxi Provincial Cancer Hospital, Taiyuan, Shanxi Province, China

Background: This study aimed to identify novel mutations associated with the progression of gastric cancer by establishing patient-derived xenograft (PDX) models and performing comprehensive genomic characterization of these PDX models and their corresponding primary tumors. Methods: Fresh gastric cancer tissue samples were collected from 20 patients who underwent surgical resection at Shanxi Cancer Hospital and were subsequently implanted into NOD-SCID mice to establish PDX models. Histopathological features were evaluated using hematoxylin and eosin (H&E) staining. Whole-exome sequencing (WES) was performed on both primary tumors and their corresponding PDX tumors, focusing on mutations within 559 cancer-related genes. Predictive tools, including SIFT, Polyphen2_HVAR, Polyphen2_HDIV, and Mutation Taster, were utilized to identify potentially deleterious mutations, while I-Mutant and MUpro were employed to assess protein stability. Results: Nine gastric cancer PDX models were successfully established, with seven models propagated to the third generation (F3-PDX), achieving a success rate of 45%. The latency of tumor establishment significantly decreased with each successive generation, from a median of 56 days in F1 to 14 days in F3. The histological characteristics of the primary tumors were well preserved in the PDX models. Whole-exome sequencing revealed key mutated genes in primary tumors, including IRS2, BLM, PDE4DIP, NUMA1, MYH9, TP53, PIK3CD, ERCC5, and ASXL1. A total of 28 mutations were conserved between primary tumors (F0) and both F1-PDX and F3-PDX tumors. Among these, 10 mutations were identified as potentially deleterious, with mutations in PTPRK (p.L988S), PIK3CB (p.F934L), LRP1B (p.A1912T), and IGF2R (p.G2052R) showing the highest likelihood of impacting critical oncogenic pathways. Conclusions: This study demonstrated that PDX models effectively preserve the biological and genetic characteristics of primary gastric tumors, underscoring their utility in studying tumor heterogeneity and drug resistance in gastric cancer. The identified conserved and potentially deleterious mutations provide new insights into the genetic landscape of gastric cancer, informing the development of targeted therapeutic strategies. Key points: 1. Establishment of Patient-Derived Xenograft (PDX) Models for Gastric Cancer. 2. Identification of somatic mutations in Primary Gastric Tumors (F0) and PDX Models. 3. Prediction of four potentially deleterious mutations associated with gastric cancer.