Biology subjects

Vörös, J.

Publications and source records attributed to Vörös, J..

12 recordsLinked to original sources

bioRxiv2026

Progressive neuronal network reorganisation in glioblastoma drives pathological activity in vitro

Glioblastoma (GBM) is the most aggressive primary brain tumour and is frequently accompanied by severe neurological symptoms, including epilepsy and cognitive impairment. Neurological symptoms often persist after surgical resection, indicating that GBM induces durable and self-sustaining changes in the surrounding neuronal networks. However, the mechanisms by which GBM reshapes network structure and function in the tumour periphery remain poorly understood. We present a compartmentalised in vitro platform enabling long-term coculture of iPSC-derived neurons and primary GBM cells to investigate these changes. Placed on high-density microelectrode arrays, the platform permits longitudinal electrophysiological recordings at single-neuron resolution. Using effective network inference, we find that GBM drives a reproducible structural progression: first toward a hyperconnected, hub-dominated architecture, then a collapse of community structure accompanied by a widespread neuron loss. This evolving structure shapes population dynamics, constraining features such as network burst rate and instantaneous synchrony. The reorganisation also carries computational consequences: signal propagation becomes progressively redundant and synergistic rather than unique. As a result, neurons lose the capacity to encode distinct input combinations independently, and the repertoire of accessible network states contracts. Together, these findings reframe GBM as a driver of neuronal network reorganisation rather than uniform hyperexcitability, and establish a compartmentalised, single-neuron-resolution platform for the longitudinal observation, dissection, and ultimately targeting of the network processes that underlie disease progression.

neuroscience↗

bioRxiv2026

Reinforcement learning for closed-loop optimisation of spatiotemporal stimulation in patterned neuronal networks

Understanding how neuronal circuits transform inputs into outputs requires systematic perturbation under controlled conditions. In vitro neuronal networks can be cultured on microelectrode arrays (MEAs) that allow stimulation and recording, and microfluidic patterning can constrain network topology to yield stable stimulation-evoked responses. Yet, the space of possible spatiotemporal stimulation patterns remains too large for exhaustive exploration. Additionally, the evoked responses depend on prior stimulation history. Here, we embedded topologically constrained biological neuronal networks in a closed-loop reinforcement learning (RL) framework that sends electrical stimuli to the MEA and evaluates the evoked responses to efficiently identify stimulation patterns that evoke specific target activity motifs. We extend inkube, a low-cost, open-source electrophysiology system from off-the-shelf components, with closed-loop electrophysiology. This enables reliable delivery of stimulation at single-sample precision with millisecond-range round-trip times. It also allows independent RL agents to control multiple networks simultaneously. We first demonstrated that stimulation-evoked responses in engineered recurrent networks were stable and separable across the action space over hours of continuous operation. We characterised the dependency of responses on prior stimulation history, finding state dependence in a subset of stimulus pairs. We then benchmarked different RL agents, multi-armed bandits (MABs) and linear contextual bandits (LCBs), on the task of identifying stimulation patterns that maximise the length of clockwise-circular firing sequences. All agents learned to improve reward during training with respect to random stimulation. Agents converged on non-trivial stimulation patterns that span the full action space rather than mirroring the target motif. LCBs exploited the identified state dependence through action switching, yielding measurable reward benefits for specific action pairs, though this did not translate into overall performance gains over MABs. All hardware designs and software are publicly available, providing an accessible platform for goal-directed functional characterisation of engineered neuronal networks at single-spike resolution.

neuroscience↗

bioRxiv2026

A water compartment cell culture lid enables stable longitudinal recording of neuronal networks in vitro

Longitudinal electrophysiological recordings of neuronal networks are essential for studying network maturation, plasticity, and pharmacological responses. Yet current microelectrode array (MEA) approaches are limited by evaporation-induced drift in culture conditions, exacerbated by heat dissipation from active recording electronics on CMOS-based high-density MEAs. We present a cell culture lid featuring a water compartment at its interface that eliminates evaporation whilst maintaining gas exchange. Combined with a custom incubator that uses independent temperature control of the MEA to prevent condensation, the system enables stable, un-interrupted recordings for weeks. We show that perturbations in firing rate and functional connectivity following medium exchange are significantly reduced by suppressing evaporation. We demonstrate continuous 35-day recordings of patterned human iPSC-derived neuronal networks with a single medium exchange, revealing the spontaneous emergence and consolidation of spatiotemporal firing patterns during maturation. All design files are provided to facilitate adoption across culturing platforms, enabling un-interrupted longitudinal interfacing with network dynamics for studies of plasticity, chronic pharmacology, and developmental trajectories in individual cultures.

neuroscience↗

bioRxiv2025

An Integrated In Vitro Platform and Biophysical Modeling Approach for Studying Synaptic Transmission in Isolated Neuronal Pairs

Studying synaptic transmission and plasticity is facilitated in experimental systems that isolate individual neuronal connections. We developed an integrated platform combining polydimethylsiloxane (PDMS) microstructures with high-density microelectrode arrays to isolate and record single neuronal pairs from human induced pluripotent stem cell (hiPSC)-derived neurons. The system maintained hundreds of parallel neuronal pairs for over 100 days, demonstrating functional synapses through pharmacological validation and long-term potentiation studies. We coupled this platform with a biophysical Hodgkin-Huxley model and simulation-based inference to extract mechanistic parameters from electrophysiological data. The analysis of long-term potentiation stimulation using a biophysical model revealed (-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) AMPA and (N-methyl-D-aspartate) NMDA receptor-specific alterations, providing quantitative insights into synaptic plasticity mechanisms. This integrated approach represents the first system combining isolated synaptic pairs, long-term stability, and mechanistic modeling, offering unprecedented opportunities for studying human synaptic function and plasticity.

neuroscience↗

bioRxiv2024

Engineered biological neural networks as basic logic operators

We present an in vitro neuronal network with controlled topology capable of performing basic Boolean computations, such as NAND and OR. Neurons cultured within polydimethylsiloxane (PDMS) microstructures on high-density microelectrode arrays (HD-MEAs) enable precise interaction through extracellular voltage stimulation and spiking activity recording. The architecture of our system allows for creating non-linear functions with two inputs and one output. Additionally, we analyze various encoding schemes, comparing the limitations of rate coding with the potential advantages of spike-timing-based coding strategies. This work contributes to the advancement of hybrid intelligence and biocomputing by offering insights into neural information encoding and decoding with the potential to create fully biological computational systems.

neuroscience↗

bioRxiv2024

Unveiling the evolutionary history of European vipers and their venoms from a multi-omic approach

Snake genomes attract significant attention from multiple disciplines, including medicine, drug bioprospection, and evolutionary biology, due to the unique features found in snakes, especially, the evolution of venom. However, genomic research within the family Viperidae has mostly focused to date on the subfamily Crotalinae, while overlooking Viperinae, the Old World vipers. Among Viperinae, European vipers (Vipera) have been the subject of extensive research because of their venoms, phylogeographic, and ecological diversification. Nevertheless, venom research in this group has been conducted using mostly proteomes alone, while phylogeography and systematics in the genus have relied on biased information from mitochondrial phylogenies. Here, we generated chromosome-level genome assemblies for three Vipera species and whole-genome sequencing data for 94 samples representing 15 Vipera taxa. This comprehensive dataset has enabled us to disentangle the phylogenomic relationships of this genus, affected by mito-nuclear discordance and pervaded by ancestral introgression. Population-level analyses in the Iberian Peninsula, where the three oldest lineages within Vipera meet, revealed signals of recent adaptive introgression between ecologically dissimilar species, whereas chromosomal rearrangements isolate species occupying similar niches. Finally, using transcriptomic and proteomic data, we characterized the Vipera toxin-encoding genes, in which opposing selective forces were unveiled as common drivers of the evolution of venom as an integrated phenotype.

genomics↗

bioRxiv2024

Constructing well-defined neural networks of multiple cell types by picking and placing of neuronal spheroids using FluidFM

Controlled placement of single cells, spheroids and organoids is important for in vitro research, especially for bottom-up biology and for lab-on-a-chip and organ-on-a-chip applications. This study utilised FluidFM technology in order to automatically pick and place neuronal spheroids and single cells. Both single cells and spheroids of interest could be selected using light microscopy or fluorescent staining. A process flow was developed to automatically pick and pattern these neurons on flat surfaces, as well as to deposit them into polydimethylsiloxane microstructures on microelectrode arrays. It was shown that highly accurate and reproducible neuronal circuits can be built using the FluidFM automated workflow.

neuroscience↗

bioRxiv2024

An implantable biohybrid nerve model towards synaptic deep brain stimulation

Restoring functional vision in blind patients lacking a healthy optic nerve requires bypassing retinal circuits, ideally, by directly stimulating the visual thalamus. However, available deep brain stimulation electrodes do not provide the resolution required for vision restoration. We developed an implantable biohybrid nerve model designed for synaptic stimulation of deep brain targets. The interface combines a stretchable stimulation array with an aligned microfluidic axon guidance system seeded with neural spheroids to facilitate the development of a 3 mm long nerve-like structure. A bioresorbable hydrogel nerve conduit was used as a bridge between the tissue and the biohybrid implant. We demonstrated stimulation of spheroids within the biohybrid structure in vitro and used high-density CMOS microelectrode arrays to show faithful activity conduction across the device. Finally, implantation of the biohybrid nerve onto the mouse cortex showed that neural spheroids grow axons in vivo and remain functionally active for more than 22 days post-implantation.

bioengineering↗

bioRxiv2024

Code Multiplexed Nanocapacitor Arrays for Scalable Neural Recordings

Large scale neural recordings are redefining our understanding of the brain. However, simultaneously recording potentials from thousands of microelectrodes remains challenging. We overcome this limitation by measuring activity-induced changes in mutual capacitance. Code division multiplexing enabled simultaneous recordings of neural activity from 1,024 nanocapacitor electrodes at a density of 10k electrodes/mm.2 Features of neural activity i.e., action potentials, bursts, and local field potentials were measured in recordings, benchmarking our device against the state-of-the-art. SummaryCapacitive sensing of neural activity improves the scalability, fabrication, and miniaturization of microelectrode arrays.

neuroscience↗

bioRxiv2022

Engineering circuits of human iPSC-derived neurons and rat primary glia

Novel in vitro platforms based on human neurons are needed to improve early drug testing and address the stalling drug discovery in neurological disorders. Topologically controlled circuits of human induced pluripotent stem cell (iPSC)-derived neurons have the potential to become such a testing system. In this work, we build in vitro co-cultured circuits of human iPSC-derived neurons and rat primary glial cells using microfabricated polydimethylsiloxane (PDMS) structures on microelectrode arrays (MEAs). Such circuits are created by seeding either dissociated cells or pre-aggregated spheroids at different neuron-to-glia ratios. Furthermore, an antifouling coating is developed to prevent axonal overgrowth in undesired locations of the microstructure. We assess the electrophysiological properties of different types of circuits over more than 50 days, including their stimulation-induced neural activity. Finally, we demonstrate the effect of magnesium chloride on the electrical activity of our iPSC circuits as a proof-of-concept for screening of neuroactive compounds.

neuroscience↗

bioRxiv2021

Nanoscale patterning of in vitro neuronal circuits

Methods for patterning neurons in vitro have gradually improved and are used to investigate questions difficult to address in or ex vivo. Though these techniques guide axons between groups of neurons, multiscale control of neuronal connectivity, from circuits to synapses, is yet to be achieved in vitro. As studying neuronal circuits with synaptic resolution in vivo poses significant challenges, an in vitro alternative could serve as a testbed for in vivo experiments or as a platform for validating biophysical and computational models. In this work we use a combination of electron beam and photolithography to create polydimethylsiloxane (PDMS) structures with features ranging from 150 nanometers to a few millimeters. Leveraging the difference between average axon and dendritic spine diameters, we restrict axon growth while allowing spines to pass through nanochannels to guide synapse formation between small groups of neurons (i.e. nodes). We show this technique can be used to generate large numbers of isolated feed-forward circuits where connections between nodes are restricted to regions connected by nanochannels. Using a genetically encoded calcium indicator in combination with fluorescently tagged post synaptic protein, PSD-95, we demonstrate functional synapses can form in this region. Although more work needs to be done to control connectivity in vitro, we believe this is a significant step in that direction.

neuroscience↗

bioRxiv2021

Topologically controlled circuits of human iPSC-derived neurons for electrophysiology recordings

Bottom-up neuroscience, which consists of building and studying controlled networks of neurons in vitro, is a promising method to investigate information processing at the neuronal level. However, in vitro studies tend to use cells of animal origin rather than human neurons, leading to conclusions that might not be generalizable to humans and limiting the possibilities for relevant studies on neurological disorders. Here we present a method to build arrays of topologically controlled circuits of human induced pluripotent stem cell (iPSC)-derived neurons. The circuits consist of 4 to 50 neurons with mostly unidirectional connections, confined by microfabricated polydimethylsiloxane (PDMS) membranes. Such circuits were characterized using optical imaging and microelectrode arrays (MEAs). Electrophysiology recordings were performed on circuits of human iPSC-derived neurons for at least 4.5 months. We believe that the capacity to build small and controlled circuits of human iPSC-derived neurons holds great promise to better understand the fundamental principles of information processing and storing in the brain.

neuroscience↗