Integrative study of patient-derived in-vitro model toward pharmaco-proteogenomics

【Background】Pharmaco-proteogenomics using patient-derived cancer models is a promising approach for the development of predictive biomarkers as well as the discovery of therapeutic targets. The critical resource of pharmaco-proteogenomics is the patient-derived cancer models, which are established from tumor tissues and maintain the characteristics of original tumors. Various in-vitro models have been established from malignant tumors and applied for the study of cancer biology as well as translational research. Previous reports revealed that cancer stem cells played key roles in drug resistance, metastasis, and invasiveness of clinical tumors. With this regard, the organoids are widely used as in-vitro models for evaluating drug sensitivity. However, the clinical utility has not been established in any models, and further investigation is required to improve the quality of pharmaco-proteogenomics. The utility of cancer models depends on how their phenome, proteome, and genome recapitulate the features of original tumors.

【Object】This study aims to reveal the similarity of phenotype and proteotype among the in-vitro models derived from identical tumor tissue and cultured in different methods. Stemness, tumorigenicity, and drug sensitivity are examined and used to interpret the proteomic difference among the individual cell models.

【Methods】Tumor tissues of canine lung cancer were used to establish the monolayer, spheroid, and organoid cultures. The cells were exposed to multiple drugs, and the response to the treatments was observed. The population of stem cells in the cultured cells was examined by Fluorescence Activated Cell Sorting (FACS). The expression of proteins and mRNA in the molecular pathways were studied by mass spectrometry and next-generation sequencing, respectively. The protein expression was confirmed by immunohistochemistry. The tumorigenic potential was evaluated in xenograft models.

【Results and Discussion】We found that the population of stem cells and the response to drug treatments were diverse in the monolayer, spheroids, and organoids. Moreover, the cells exhibited the unique expression of proteins and mRNAs under different cultured conditions. These observations were consistent with the previous reports, where individual experiments were performed in the different studies. The integration of whole data in our experiment system will generate novel biology as well as clinical applications.