Integrated proteogenomics of primary tumoroid models for precision oncology

The availability of scalable primary oncology models remains an impediment to preclinical evaluation of new therapeutic strategies. Recently, primary tumoroid models have been developed to aid in early-phase evaluation of drug compounds. These models are generated from dissociated primary tumors and can be expanded through numerous passages, from a conventional, embedded dome stage through a suspension state, which allows for the generation of a large number of tumoroids for comprehensive studies. The tumoroid lines maintain the underlying genomic and transcriptomic signatures of the parent tumor from the initial, early-passage embedded stage to later-passage suspension cultures. These models are highly amendable to in vitro evaluation of cell-intrinsic therapeutic interventions, as well as cell-extrinsic modalities, since tumor-resident immune and stromal cells from the parent tissue are preserved in the cryopreserved dissociated tissue. Proteogenomics is the integration of genomic, transcriptomic, and proteomic datasets to uncover novel biological insights that cannot be uncovered with a single data set alone. Tumoroids represent the most physiologically relevant oncology models to understand the relationship between DNA variants, RNA expression, and protein expression. Mass spectrometry-based proteomic data were generated from the tumoroid models and searched against sample-specific databases generated from whole exome sequencing as well as whole transcriptome data for a comprehensive overview of the biology of the tumoroids. This robust analysis was further supported by drug response data of the tumoroids exposed to a standard set of classical chemotherapeutic compounds and small-molecule inhibitors. We identified a colorectal cancer tumor model with a pathogenic KRAS-G12C mutation, and how treatment with the clinical KRAS-G12C inhibitor sotorasib altered global protein expression was further evaluated. Additionally, high mutational burden tumoroids generated from deficient DNA mismatch repair endometrial tumors were analyzed to better understand how DNA hypermutation affects global protein expression. Collectively, these studies establish a pipeline to generate a holistic view of tumor cell biology, enabling for the discovery of new biomarkers and drug targets.