Global metabolomic profiling of trastuzumab resistant gastric cancer cells reveals major metabolic pathways and metabolic signatures based on UHPLC-Q exactive-MS/MS

Resistance mechanism exploration has become an urgent need owing to the widespread trastuzumab resistance in gastric cancer. In this study, UHPLC-Q exactive MS/MS was carried out to characterize the metabolic profiles of human gastric cancer cell lines NCI N87, MKN45 (trastuzumab-sensitive) and NCI N87/R, MKN45/R (trastuzumab-resistant), respectively. Metabolic signatures and different metabolites were identified using multivariate in combination with univariate analysis. Integrated pathway enrichment analysis was executed using MetaboAnalyst and KEGG metabolic libraries to analyze the altered metabolic pathways in trastuzumab resistant cells. A total of 79 and 75 different metabolites were positively identified by utilizing authentic standards in NCI N87/R and MKN45/R cells, respectively. Furthermore, enrichment analysis demonstrated that seven metabolic pathways in NCI N87/R cells and five in MKN45/R cells were significantly changed. These pathways are involved in amino acid, nucleotide, carbohydrate, cofactor and vitamin metabolism, of which alanine, aspartate and glutamate metabolism displayed the highest pathway impact and lower P value both in NCI N87/R and MKN45/R cells. Moreover, we constructed a metabolomics–proteomics network between substantially altered metabolites and target genes which revealed citrate being regulated by citrate synthase and ACLY, while proline regulation was due to EPRS, PYCRL and PYCR1/2, respectively. Overall, our findings disclose prominent alterations of metabolic signatures in NCI N87/R and MKN45/R cells when compared with the parent cells which are crucial for understanding of underlying mechanisms of resistance and for developing strategies to overcome trastuzumab resistance.