Neurons depend on glucose to sustain their high energetic demands; yet, ketone bodies can serve as alternative substrates during ketogenic states. Here, we examined how β-hydroxybutyrate reshapes metabolism and function in human iPSC-derived neurons. Neurons generated from neuroepithelial stem cells were cultured in glucose-rich media or low-glucose media supplemented with β-hydroxybutyrate. We developed an electrochemical biosensor for ketone detection and validated its performance by cyclic voltammetry and amperometry, achieving linear sensitivity in the 0.01 to 0.1 mM range. Metabolic changes for neurons were assessed through glucose consumption and lactate production, and transcriptional profiling revealed reduced expression of selected metabolic and ketone-associated genes under ketone supplementation. Calcium imaging further showed lower firing rates in ketone exposed neurons compared with glucose conditions. Together, these results demonstrate how alternative energy substrates modulate neuronal metabolism and excitability, providing a framework to evaluate metabolic interventions for neurological disorders.

Nasiri R, Fayazbakhsh F, Sanei R, Wu T, Taebnia N, Habibey R, Fotouhi O, Cognetti J, Lauschke VM, Russom A, Herland A. (2026). Metabolic assessment of iPSC-derived neurons under ketone-enriched condition: Ketone sensor development and BHB-driven metabolic adaptation.

iScience. 2026 Apr 13;29(5):115702. doi: 10.1016/j.isci.2026.115702.

Retinal organoids are widely used to model human retinal development and disease, but their utility is limited by the absence of vascular networks and stable axonal projections, which contribute to retinal ganglion cell degeneration and loss of function. To address these challenges, we incorporated stem cell-derived endothelial cells to induce transient vascular-like networks and used microfluidic devices to stabilize axonal growth. The resulting organoids showed reduced hypoxia, increased size, and decreased apoptosis, indicating improved long-term survival and maturation of retinal ganglion cells. Integration with microfluidic-microelectrode arrays enabled stable recordings of spontaneous and optogenetically evoked activity, which persisted beyond the time when control organoids lost function. At later stages, these transiently vascularized organoids displayed photoreceptor-driven ON, OFF, and ON-OFF light responses, indicating circuit-level retinal activity. This bioengineered platform establishes a long-term, functional model of the human retina as a transformative tool for retinal research and therapeutic innovation.

Sharma K, Habibey R, Ribeiro MM, Cui B, Siwicki RA, Striebel J, Pawlick JS, Zorn J, Utz L, Renner M, Picelli S, Holz FG, Ruiz de Almodóvar C, Cowan CS, Busskamp V. (2026). Retinal ganglion cell survival and functional maturation in transiently vascularized human retinal organoids. Cell Stem Cell 33(2):253-271.e13. doi: 10.1016/j.stem.2025.12.013.

We developed a reproducible in vitro platform for engineering human neuronal circuits with single-cell precision by combining direct laser-written microtemplates, soft-lithography microscaffolds, and multielectrode array recordings. This system enables high-throughput fabrication of defined network architectures, precise neuronal placement, and controlled electrical or optogenetic stimulation. Using these bottom-up circuits, we quantitatively investigated ephaptic coupling by tuning axonal spacing and neuron number, validating predicted effects on conduction velocity, synchronization, and excitability. The platform provides a robust and versatile tool for studying synaptic and nonsynaptic interactions, disease mechanisms, and fundamental neural network dynamics.

Striebel J, Habibey R, Wendland D, Gehring H, Podoliak E, Pawlick JS, Sharma K, Ng AHM, Pernice W, Busskamp V. (2025). Reproducible Human Neural Circuits Printed with Single-Cell Precision Reveal the Functional Roles of Ephaptic Coupling. ACS Nano. 2025 Nov 11;19(44):38457-38471. doi: 10.1021/acsnano.5c11482

This review summarizes recent advances in organ-on-a-chip (OoC) models designed to replicate tissue barriers such as the blood-brain barrier, gut, lung, skin, kidney, retina, nasal epithelium, and placenta for applications in drug screening, transport studies, delivery, and disease modeling. We discuss key engineering strategies for barrier-on-a-chip platforms, including microfluidic chip and membrane fabrication methods-from two-channel porous membrane systems to hydrogel-based interfaces-and approaches for functional validation of engineered barriers. 

Nasiri R, Madadelahi M, Nikmaneshi MR, Gokce B, Bijarchi MA, Shah S, Tirpáková Z, Van Gastel D, Taebnia N, de Barros NR, Zhu Y, Morcimen ZG, Gulicli B, Habibey R, Sendemir A, Jain S, Enrico A, Lauschke VM, Dokmeci MR, Pratx G, Khademhosseini A, Herland A. (2025). Engineering biomimetic tissue barrier models on chips: From design and fabrication to applications in disease modeling and drug screening. Biomaterials. 327:123739. doi: 10.1016/j.biomaterials.2025.123739

We engineered microchannel-based devices to create reproducible 2D and 3D modular neuronal networks with predefined geometry and integrated multi-electrode array (MEA) recordings. Each circuit comprised 64 interconnected modules linked by micron-scale channels, enabling controlled structural organization and functional measurement. Compared with randomly assembled cultures, modular networks exhibited enhanced activity, stronger functional connectivity, higher clustering, greater global efficiency, and increased hub neuron formation. Neurons primarily interacted within their local modules, producing distinct functional communities while maintaining efficient global communication. These results demonstrate that physical architecture strongly shapes network dynamics and connectivity, establishing modular engineered circuits as a robust and physiologically relevant in vitro model of brain network organization.

Habibey R, Striebel J, Meinert M, Latiftikhereshki R, Schmieder F, Nasiri R, Latifi S. (2024). Engineered modular neuronal networks-on-chip represent structure-function relationship. Biosens Bioelectron. 2024 Oct 1;261:116518. doi: 10.1016/j.bios.2024.116518.

We investigate how altered gravity affects human neuronal function at both cellular and network levels to better understand the neurological risks of spaceflight. Using multi-electrode array technology, we recorded real-time electrophysiological activity of human iPSC-derived neural networks exposed to controlled microgravity and hypergravity conditions in specialized platforms, including a drop tower and human centrifuge. Our results demonstrate that gravity acts as a potent environmental modulator of neuronal activity: microgravity increases network firing rates, whereas hypergravity suppresses activity, with distinct responses across neuronal subpopulations. These findings reveal gravity-dependent adaptations in neural dynamics and provide a foundation for identifying underlying mechanisms and developing countermeasures to protect cognitive performance during human space missions.

Striebel J, Kalinski L, Sturm M, Drouvé N, Peters S, Lichterfeld Y, Habibey R, Hauslage J, El Sheikh S, Busskamp V, Liemersdorf C (2023). Human neural network activity reacts to gravity changesin vitro. Front Neurosci. doi: 10.3389/fnins.2023.1085282

An incubator-independent cell culture system including a double-wall perfusion chamber and ambient-conditioned culture media was engineered and integrated with compartmentalized microfluidic device and multi-electrode arrays (MEAs) electrophysiology devices. Compartmentalized device allowed guidance, tracking and recording from thin axonal branches. Incubator-independent perfusion system enabled continous recording and microscopy. This versatile self-contained system provides long-term and continuous access to the network data .

Habibey R (2023). Incubator-independent perfusion system integrated with microfluidic device for continuous electrophysiology and microscopy readouts. Biofabrication 15(2). doi: 10.1088/1758-5090/acb466

High-density micro-electrode arrays (HD-MEAs) offer non-invasive recording with the best spatial and temporal resolution possible to date. We tracked the morphology and activity features of developing networks derived from human induced pluripotent stem cell (hiPSC) for 3 months. Our morphological data revealed large-scale structural changes from homogeneously distributed neurons in the first month to the formation of neuronal clusters over time. Morphological changes and neuronal movement in the network structure was reflected in corresponding changes of network activity map over time.

Habibey R*, Striebel J*, Schmieder F, Czarske J, Busskamp V (2022). Long-term morphological and functional dynamics of human stem cell-derived neuronal networks on high-density MEAs. Front Neurosci. 16: 951964. 

doi: 10.3389/fnins.2022.951964

To obtain insights on long-term functional features, a glia–neuron co-culture protocol within MEAs was developed. Full-field optogenetic stimulation enhanced the number of active neurons and their firing rates. Compared with full-field stimulation, which evoked synchronized activity across all neurons, holographic stimulation of individual neurons resulted in local activity. Single-cell holographic stimulation facilitated to trace propagating evoked activities of 400 individually stimulated neurons that revealed precise functional neuronal connectivity motifs.

Schmieder F*, Habibey R*, Striebel J, Büttner L, Czarske J, Busskamp V (2022). Tracking connectivity maps in human stem cell-derived neuronal networks by holographic optogenetics. Life Sci Alliance. 5(7):e202101268. doi: 10.26508/lsa.202101268.

Optogenetic activation of human inducedpluripotent stemcell (hiPSC)-derived neurons facilitates the characterization of their functional properties at the single neuron and circuit level. Here we showcase the preparation of long-term hiPSC-derived neuronal networks expressing optogenetic actuators, in vitro optogenetic stimulation and simultaneous functional recordings using patch clamp and MEA electrophysiology.

Habibey R, Striebel J, Sharma K, Busskamp V (2022). Optogenetic Control of Human Stem Cell-Derived Neuron. Methods Mol Biol. 2501:339-360. doi: 10.1007/978-1-0716-2329-9_17.