Integrated -Omics Analyses Demonstrate that Patient-Derived Colon Organoids Faithfully Recapitulate the Tumor Tissue of Origin, Highlighting Altered Pathways in Colorectal Cancer Progression

Purpose: methodically characterize colorectal cancer patient-derived organoids, at the molecular level, under different culturing conditions, by evaluating genomic, transcriptomic and phosphoproteomic profiles in order to define their ability to stably recapitulate patients-derived tissues features. Outcome: integrated molecular and bioinformatics analyses demonstrated that PDCOs faithfully recapitulate the tumor tissue of origin. Our results indicate that the in vitro culture of biopsy-derived organoids does not introduce substantial variation in the genomic landscape of CRC but still promotes the expansion of the more aggressive subset of cancer cells. In conclusion, our findings strongly support the use of CRC organoids as a novel and very promising and stable tool for personalized medicine that could represent a powerful alternative to animal experimentation in vivo. Patient-derived colon organoids (PDCOs) were obtained from surgical resected tissue of tumor and normal intestinal mucosa of patients affected by colon cancer (P12, P14 and P16). The crypts, derived from normal tissue, and the isolated cells derived from tumor were considered as primary tissues. From primary tissues, we generated normal (P12N, P14N, P16N) and tumor (P12T, P14T, P16T) PDCOs, respectively. Paired-end Whole Exome Sequencing allowed detecting the temporal acquisition of somatic variants, in a patient-specific manner, having deleterious effects on driving genes associated with colorectal cancer. Moreover, a targeted NGS approach confirmed that organoids faithfully recapitulated patients’ tumor tissue. Finally, using paired-end RNA-seq experiments, we identified differentially expressed genes in tumor versus normal organoids at different time points, underlining several pathways altered in a time-dependent fashion.