Abstract 2701: Proteogenomic analysis of endoscopy biopsy identifies alterations in apoptotic pathways in trastuzumab-resistant gastric cancers

Although the combination of trastuzumab with cisplatin and fluoropyrimidine is standard therapy for metastatic HER2-positive gastric cancers, predictive biomarkers for this therapy need to be further refined. Given the multifactorial nature of clinical trastuzumab resistance, we performed nano-liquid chromatography (LC)-tandem mass spectrometry (MS/MS) proteomic analyses on 13 pairs of frozen HER2-positive tumors and adjacent normal tissue counterparts collected from patients who were treated with trastuzumab in combination with cisplatin and fluoropyrimidine (TCF). We quantified >6,000 protein groups per tumor on the average, and this number was almost comparable to those obtained by NCI9s Clinical Proteomic Tumor Analysis Consortium projects, which characterized resected tumors using similar nano-LC-MS/MS technologies. Nano-LC-MS/MS data for differentially expressed proteins were successfully validated by our immunostaining analyses. When we correlated proteomic data with clinical outcome, underexpression of apoptosis pathway proteins was the prominent proteomic signature in TCF-resistant tumors, as compared with TCF-sensitive tumors. Proapoptotic proteins in FAS signaling and mitochondrial apoptosis pathways were less abundant in TCF-resistant tumors than in sensitive tumors. When iTRAQ reporter ion ratios were compared between pretreatment and acquired-resistant tumors from clinical responders, apoptosis pathways were significantly enriched in proteins that were overexpressed in the acquired-resistant tumors. Assuming that the pretreatment tumors of clinical responders were mostly composed of chemosensitive clones, these antiapoptotic proteins may confer survival advantage on resistant clones, resulting in the repopulation of resistant clones overexpressing these antiapoptotic proteins. For the first time to our knowledge, therefore, our proteogenomic study of frozen endoscopic biopsy samples revealed that alterations in apoptotic pathway proteins were most significantly associated with clinical trastuzumab resistance. Our study is also the first to demonstrate that nano-LC-MS/MS technology can be applied to small biopsy tissue samples for precision medicine research. Citation Format: Jeong Won Kang, Il Ju Choi, Hark Kyun Kim. Proteogenomic analysis of endoscopy biopsy identifies alterations in apoptotic pathways in trastuzumab-resistant gastric cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2701.