Microfluidic Chip-Based Automatic System for Sequencing Patient-Derived Organoids at the Single-Cell Level

Genetically sequencing patient-derived organoids (PDOs) at the single-cell level has emerged as a promising method to infer cell-level heterogeneity of original organs and improve cancer precision medicine. Unfortunately, because of the limited starting quantity and uncontrolled establishing process of PDOs, the existing single-cell sequencing technologies, either manual-operation-based or microfluid-based, are inefficient in processing PDOs originating from clinical tissue samples. To address such issues, this study presents a microfluidic chip-based automatic system for sequencing organoids at the single-cell level, named as MASSO. By performing all required procedures, including PDO establishment/culturing/digesting and single-cell isolation/lysis/whole-genome amplification, in a single microfluidic chip, the possible loss of precious PDO is avoided, and the high quality of on-chip whole-genome amplification of a single PDO cell is ensured. By automating the entire operation process, possible human error is eliminated, and the data repeatability is improved, therefore bridging the technical gap between laboratorial proof-of-concept studies and clinical practices. After characterizing the organoid single-cell whole-genome amplification chip (named as OSA-Chip) and the MASSO, the first successful attempt, to the best of our knowledge, on whole-genome sequencing lung cancer PDO at the single-cell level was performed by MASSO. The results reveal that the MASSO is capable of not only identifying common cancer-related mutations but also discovering specific mutations that affect drug responses, therefore laying the technical foundation for efficiently understanding the cell-level heterogeneities of PDOs and corresponding original organs.