Development of a high-throughput 3D culture microfluidic platform for multi-parameter phenotypic and omics profiling of patient-derived organoids

Patient-derived organoids (PDOs) are poised to become central tools in clinical practice, to preemptively identify patient optimal treatments, and in drug discovery, overcoming the limitations of cancer cell lines. However, the implementation of PDOs in both these settings has been hampered by several bottlenecks including sample requirements, assay time and handling in the context of high-throughput-based drug assays. We report here the development of a microfluidic-based device ( M icrofluidic P latform for O rganoids culture, MPO) that miniaturises and greatly simplifies PDO cultures in a 384-plate format. Both retrospective and prospective clinical studies demonstrate its predictive value and the swift and straightforward implementation in the clinical setting. Obtaining comprehensive functional and molecular information on the response to drugs is becoming a requirement in drug discovery. MPO allows subcellular phenotypic and imaging screenings, target engagement for the assessment of the efficacy of therapies, alongside the ability to comprehensively and concomitantly define PDOs genomic, transcriptomic, proteomic, lipidomic and metabolomic landscape. In all, we demonstrate the potential of our platform to impact clinical practice generating relevant information on drug sensitivity within a time frame that could inform treatment decisions alongside exploration of the mechanisms underlying compound response and resistance in drug discovery efforts.