Doganyigit, K. (BMEB) – Reimagining the petri dish, automated incubator-free organoid culture system for long term organoid maintenance and disease modeling

Organoids offer strong in vitro models for studying development and disease; however, traditional incubator-based culture methods hinder environmental regulation, elevate evaporation rates, and limit imaging and instrumentation access—restricting their effectiveness for prolonged, physiologically relevant research. To address these challenges, we created a compact, automated culture system that eliminates the need for an incubator by integrating microfluidic recirculation with gas exchange inspired by artificial lungs in intensive care medicine. The system employs a fluid impermeable gas-exchange membrane along with an aqueous buffer to passively stabilize oxygen, pH, and osmolarity. Automated media transfer and integrated sensing enable consistent, multi-week live imaging and accurate environmental control.

The First Aim of this proposal addresses the creation and execution of this organoid culture platform that does not require an incubator. In Aim 2, I validate the system utilizing mouse cerebral cortex organoids grown in the system, evaluating metabolic viability, tissue structure, and electrophysiological activity in comparison to shaker-incubator controls. I will also employ RNA sequencing to further analyze cell-type composition and transcriptional stress profiles. In Aim 3, I will modify the platform to simulate the prenatal stroke penumbra by incorporating spatially localized hypoxia and hypoglycemia through pressure-modulated perfusion. Combining real-time hypoxia imaging with transcriptomic analysis to facilitate investigation of ischemic damage and recovery within a regulated organoid model. Overall, this research seeks to create a flexible, and physiologically appropriate culture system that enhances experimental access and facilitates a better environment for new models of organoid development and disease research.

Event Host: Kivilcim Doganyigit, Ph.D Student, Biomolecular Engineering & Bioinformatics

Advisor: David Haussler