Personalized chordoma organoids for drug discovery studies

Abstract

Chordomas are rare tumors of notochordal origin, most commonly arising in the sacrum or skull base. Primary treatment of chordoma is surgery, however complete resection is not always feasible due to their anatomic location, and recurrence rates remain high. Chordomas are considered insensitive to conventional chemotherapy, and their rarity complicates running timely and adequately powered trials to identify effective regimens. Therefore, there is a need for discovery of novel therapeutic approaches. Drug discovery efforts in chordoma have been mostly limited to cell line models. Patient-derived organoids can accelerate drug discovery studies and predict patient responses to therapy. In this proof-of-concept study, we successfully established organoids from seven chordoma tumor samples obtained from five patients presenting with tumors in different sites and stages of disease. The organoids recapitulated features of the original parent tumors and inter- as well as intra-patient heterogeneity. High-throughput screenings performed on the organoids highlighted targeted agents such as PI3K/mTOR, EGFR, and JAK2/STAT3 inhibitors among the most effective molecules. Pathway analysis underscored how the NF-κB and IGF-1R pathways are sensitive to perturbations and potential targets to pursue for combination therapy of chordoma.

Drug screening at single-organoid resolution via bioprinting and interferometry

“…Bioprinting enables seeding cells in conformations suitable for imaging applications. To address current limitations 3,15,16 and facilitate non-invasive, label-free, real time imaging of 3D organoids by HSLCI, we op-timized an automated cell printing protocol using an extrusion bioprinter. Our original platform takes advantage of seeding cells in mini-rings of Matrigel around the rim of 96-well plates 3,15,16 (Figure 1A).…”

“…Overall, we have optimized a protocol that generates bioprinted layers suitable for high-throughput HSLCI imaging without impacting cell viability. By having a cell-free well center, the mini-squares retain automation compatibility that is crucial for robust downstream applications 3,15,16,50,51 .…”

“…To address current limitations 3,15,16 and facilitate non-invasive, label-free, real time imaging of 3D organoids by HSLCI, we optimized an automated cell printing protocol using an extrusion bioprinter. Our original platform takes advantage of seeding cells in mini-rings of Matrigel around the rim of 96-well plates 3,15,16 ( Figure 1A ). The empty center allows for implementation of liquid handlers and automation, facilitating media exchanges and addition of perturbagens 3,15,16 .…”

“…Organoids were seeded manually according to our previously published protocols 3,15,16 . Briefly, single cells suspended in a 3:4 mixture of Mammocult (StemCell Technologies 05620) and Matrigel (Corning 354234) were deposited around the perimeter of the wells of either 24-well or 96-well plates.…”

“…They are physiologically-relevant, personalized cancer models well suited for drug development and clinical applications 13,14 . We previously developed a screening platform that takes advantage of patient-derived tumor organoids seeded in a mini-ring format to automate high-throughput drug testing, with results available within a week from surgery 3,15,16 . The key outstanding limitations to the broad adoption of organoid screening approaches remail the time-intensive and operator-to-operator susceptibility of the cell seeding steps and destructive, population-level approaches required to assay them 17 .…”