Biology subjects

Schwamborn, J. C.

Publications and source records attributed to Schwamborn, J. C..

At least 19 recordsLinked to original sources

bioRxiv2026

Lab-on-a-chip device integrating a human stem cell-based blood-brain barrier model with neural organoids for translational research

For advanced biomedical research, complex, well-described human blood-brain barrier (BBB) models are crucial for studying central nervous system pathologies and brain targeting of nanotherapeutics. Our aim was to establish and characterize a complex lab-on-a-chip (LOC) system integrating a BBB model with neural organoids (NO). We optimized the conditions for BBB-NO models under static and dynamic circumstances. The combination of a human stem cell-derived BBB co-culture model with human midbrain organoids in a microfluidic LOC allowed the observation of BBB and neural tissue changes and the separate analysis of the barrier and brain units. The LOC design enabled phase contrast and fluorescent microscopy on the whole brain endothelial culture surface, barrier integrity and permeability measurements across the BBB model, and molecule passage into NOs. BBB-specific endothelial morphology, gene and protein expression, and good barrier integrity were demonstrated, corroborating the strength of the LOC engineering and cellular design. The transport of targeted nanoparticles across the BBB model followed by their entry to neural organoids validated the barrier integrity and transporter functionality of the dynamic integrated complex model. As a proof-of-concept experiment to confirm the translational value of the BBB-NO model integrated in the LOC device, we examined a clinically used hyperosmolar iodinated contrast agent, iopamidol, with confirmed neurological side effects. We corroborated that iopamidol induces transient BBB dysfunction and neural effects in the complex system, not only validating the complex dynamic BBB-NO model but also pointing to the necessity to study BBB changes together with NO functions.

cell biology↗

bioRxiv2026

Interpretable gene networks from single-cell foundation models reveal conserved neurogenic dysfunction in Parkinson's disease

Interpreting large-scale single-cell transcriptomic data remains a major challenge for understanding disease mechanisms. Recent single-cell foundation models learn rich representations of gene relationships across millions of cells, yet methods for translating these embeddings into biologically interpretable gene networks remain limited. Here we present scGENet, a computational framework that constructs context-specific gene interaction networks from foundation model-derived gene embeddings. By fine-tuning pretrained models on transcriptomic data from human midbrain organoids, scGENet generates transcriptome-scale gene modules that capture biologically meaningful cellular programs. Benchmarking across multiple foundation models demonstrates that networks derived from a fine-tuned scGPT brain model show the highest concordance with curated neuronal pathways, Parkinsons disease (PD) genetic risk loci, and independent patient-derived transcriptional signatures. Applying this framework to human iPSC-derived PD midbrain organoids reveals transcriptional modules associated with neuronal differentiation, synaptic signaling, and cell-cycle regulation. Single-nucleus RNA sequencing further links these programs to altered cellular composition, including reduced dopaminergic neurons, expansion of radial glia-like progenitors, and a dopaminergic neuron subtype expressing SNCA and VGLUT2. Integration with independent human substantia nigra datasets identifies a conserved neurogenic program disrupted across genetic and idiopathic PD. Together, these results establish a generalizable strategy for extracting interpretable gene networks from single-cell foundation models, enabling systematic discovery of disease-relevant molecular programs across diverse tissues and datasets.

neuroscience↗

bioRxiv2026

Replicative senescence of neural progenitors induces astrocyte senescence in 2D cultures and human midbrain organoids

Astrocyte senescence (astrosenescence) has emerged as a potential mechanism through which ageing may progressively impair glial homeostatic neuronal support and render the brain more vulnerable to neurodegenerative diseases such as Parkinsons disease (PD). Yet human experimental models that specifically recapitulate astrosenescence within a PD-relevant genetic background are lacking. Here, we applied passage-induced replicative exhaustion to human iPSC-derived neuroepithelial stem cells (NESCs) from a healthy donor and LRRK2-G2019S PD patients to establish an in vitro midbrain ageing model. Extended passaging induced senescence-associated changes in NESCs, including reduced proliferative capacity, decreased cleaved caspase 3 (CC3) and telomerase mRNA expression, and DNA damage response (DDR) activation, while preserving differentiation potential. Astrocytes derived from aged progenitors showed an increase in SA-{beta}-gal activity, loss of Lamin B1, DDR activation, and an altered mitochondrial morphology. In human midbrain organoids (hMOs), passage-induced ageing was associated with astrocyte-specific DDR activation and lipidomic remodelling. A multi-modal integrative analysis further revealed that, despite the variable penetrance of individual senescence-associated markers across lines, passage condition constitutes the primary discriminant of the collective cellular state, supporting the view that replicative senescence as a biological program is detectable only when individual readouts are aggregated across modalities. Together, this work establishes a human iPSC-based platform recapitulating key features of cellular senescence in both healthy and LRRK2-G2019S contexts and provides an in vitro platform to investigate the contribution of astrosenescence to PD-related neurodegeneration.

neuroscience↗

bioRxiv2026

Examining Action Potential Waveform Diversity in Neuronal Populations of Midbrain Organoid Models

Over the last decade, pre-clinical research has witnessed the advancement of human induced pluripotent stem-cell derived 3D brain organoid models and their differentiation into specific brain regions. In the realm of Parkinsons disease research, development of midbrain-specific organoids has enabled studies of this neurodegenerative disorder in patient derived 3D organoid models that attempt to recapitulate the human brain complexity. Within this line of research, neural functionality of the organoid models is established through electrophysiology. As a novel methodological approach, this study aimed to establish whether clustering of electrophysiological activity originating from midbrain organoids would aid in identifying different types of action-potential waveforms exhibited by neurons within the organoid model. Long-term extracellular electrophysiological recordings were conducted by use of a multi-electrode array device. The local field potential signal was spike-sorted, and the extracted putative neuron units were clustered into groups of spike waveform profiles. After establishing this methodological analysis pipeline, the clusters of waveform types were further analyzed in terms of electrophysiology. Results revealed that the clustering approach was successful at identifying three types of spike waveforms categories. Furthermore, it was proposed that one spike waveform profile potentially originated from dopaminergic neurons, which were one on the neural cells populating the organoid models. Overall, this study has successfully established a new methodological clustering approach to analyze electrophysiological data recoded from 3D organoid models in the context of Parkinsons disease modelling and organoid model development research.

neuroscience↗

bioRxiv2026

Microgravity enhances the viability of midbrain organoids on the International Space Station.

As human spaceflight becomes increasingly relevant, understanding how microgravity affects the human brain is an important but largely unexplored question, particularly in the context of neuronal function and vulnerability to neurodegeneration. Direct investigation of these processes in humans is not feasible, necessitating the use of physiologically relevant in vitro model systems. Three-dimensional human brain organoids recapitulate key aspects of brain development and organization and provide an experimentally accessible platform to study neuronal responses under controlled conditions. Here, within the framework of the student competition "Uberflieger 2", we investigated the effects of long-term microgravity on human midbrain organoids cultured for 40 days aboard the International Space Station (ISS). Midbrain organoids reproduce essential features of dopaminergic neuron development and are widely used to model Parkinsons disease and related neurodegenerative processes. To enable spaceflight experiments, we developed and implemented an autonomous culture system adapted to the constraints of the ISS environment. During the mission, a hardware malfunction impaired scheduled medium exchange, introducing an additional metabolic stress condition. Despite these limitations, ISS-cultured organoids remained viable and showed robust neurite outgrowth. Molecular and imaging analyses revealed that exposure to microgravity in combination with nutrient limitation induced a coordinated response involving cytoskeletal remodeling, neuronal plasticity, and selective vulnerability of dopaminergic neurons. These findings demonstrate that human midbrain organoids can maintain key structural and functional properties under prolonged spaceflight-associated stress while activating adaptive response programs. This work highlights the potential of organoid-based systems to investigate neurobiological effects of microgravity and provides a foundation for future studies addressing mechanisms relevant to neurodegenerative disease.

neuroscience↗

bioRxiv2026

Subthreshold membrane depolarization powerfully engages intracellular calcium dynamics in the brain

Membrane voltage (Vm) regulates spike timing and intracellular signaling. While Vm is extensively modulated by behavior, it is unclear how subthreshold Vm dynamics engage intracellular signaling in the awake mammalian brain. We developed a bicistronic viral vector to express genetically encoded and color compatible voltage and calcium (Ca2+) indicators in the same neuron, and simultaneously recorded cellular Vm and Ca2+ dynamics in awake mice. We report that prolonged subthreshold Vm depolarization is closely accompanied by prominent large amplitude Ca2+ elevation, whereas isolated spikes are coupled with weak Ca2+ rise. Additionally, individual spikes differentially engage intracellular Ca2+ dynamics depending on post-spiking Vm depolarization, consistent with a prominent role of slow Vm depolarization in regulating cellular signaling. While brief intracranial electrical stimulation consistently leads to Vm depolarization and Ca2+ increase, longer stimulation disrupts Vm and Ca2+ coupling, highlighting a tightly regulated cellular mechanism that relays slow Vm depolarization to intracellular signaling.

neuroscience↗

bioRxiv2025

Autophagy Dysfunction in iPSCs-Derived Neurons and Midbrain Organoids Carrying a SNCA Triplication

Parkinsons disease (PD), characterized by -Synuclein aggregation and dopaminergic neuronal loss, has no current cure. Autophagy is critical for -Synuclein clearance, yet its real-time dynamics remain challenging to assess in human-relevant systems. Here, we used live-cell imaging to assess autophagy within human neuronal cultures and midbrain organoids (hMOs) derived from induced pluripotent stem cells (iPSCs) of PD patients carrying a triplication of the -Synuclein gene (3xSNCA). Using the LC3-Rosella dual-fluorescent reporter, we quantified autolysosomes dynamics in real time. In 3xSNCA neuronal cultures, we detected early autophagy defects. In 3xSNCA hMOs, reduced autolysosome area, increased total and phosphorylated -Synuclein (pS129), and decreased electrophysiological activity were observed at 50 days of differentiation (DoD). By 70 DoD, autophagy impairment became more pronounced, overlapping with dopaminergic neuron loss. These findings support the use of human iPSCs-derived models to study autophagy dysfunction in PD and demonstrate a temporal correlation between impaired autophagy, -Synuclein pathology and neuronal degeneration.

neuroscience↗

bioRxiv2025

Vascularized midbrain assembloids show neuroinflammation and dopaminergic neuron vulnerability in Parkinsons Disease

The use of micro-physiological systems has rapidly risen in the last years due to their translatability and complex cellular composition. Human midbrain-specific organoids contain neuroectoderm-derived cell types and are suitable for brain region-specific disease modeling. However, the lack of vasculature in these systems reduces oxygenation and nutrient supply. Furthermore, neurovascular interactions cannot be studied, and disease phenotypes affecting vascular and neurovascular structures cannot be assessed. To overcome these limitations, in this work, we successfully incorporated a vascular network into midbrain organoids by fusion with vascular organoids. Midbrain-vascular assembloids are enriched in vascular cells and microglia. We observed a decrease in hypoxia and cell death in these assembloids. Furthermore, microglia and endothelial cells increased their morphological complexity. Assembloids derived from a Parkinsons disease patient carrying a LRRK2-G2019S mutation displayed a pro-inflammatory phenotype and altered electrophysiological properties. Midbrain-vascular assembloids increase the midbrain model complexity and allow for neuroinflammation studies in Parkinsons disease.

neuroscience↗

bioRxiv2025

Parkinsons disease microglia induce endogenous alpha-Synuclein pathology in patient-specific midbrain organoids.

The accumulation of misfolded -synuclein and the loss of dopaminergic neurons are hallmarks of Parkinsons disease (PD), contributing to the development of synucleinopathies. Although considerable progress has been made in understanding -synucleins role in PD pathology, the precise mechanisms involved remain unclear. Human midbrain organoids (hMOs) have emerged as valuable models for studying PD, yet the lack of microglia limits the ability to investigate neuroimmune interactions. Recent studies show that integrating microglia into hMOs enhances neuronal maturation and functionality. Here, we generated a human midbrain assembloid model by incorporating iPSC-derived microglia into midbrain organoids from healthy control individuals and a PD patient carrying the SNCA triplication (3xSNCA) mutation. Our results show that 3xSNCA microglia alone are sufficient to induce early, endogenous formation of phosphorylated -synuclein (pS129) pathology in the absence of exogenous fibril seeding. This PD-pathology emerged as early as day 50 of culture and was not observed in models lacking microglia. These findings highlight a critical role for patient-derived microglia in driving - synuclein pathology and provide a physiologically relevant platform for studying early neuroimmune mechanisms in PD and testing potential therapeutic strategies.

neuroscience↗

bioRxiv2025

Reproducibility of PD patient-specific midbrain organoid data for in vitro disease modelling.

Midbrain organoids are advanced in vitro cellular models for disease modelling. They have been used successfully over the past decade for Parkinsons disease (PD) research and drug development. The three-dimensional structure and multicellular composition allow disease research under more physiological conditions than is possible with conventional 2D cellular models. However, there are concerns in the field regarding the organoid batch-to-batch variability and thus the reproducibility of the results. In this manuscript, we generate multiple independent midbrain organoid batches derived from healthy individuals or GBA-N370S mutation-carrying PD patients to evaluate the reproducibility of the GBA-N370S mutation-associated PD transcriptomic and metabolic signature as well as selected protein abundance. Our analysis shows that GBA-PD-associated phenotypes are reproducible across organoid generation batches and time points. This proves that midbrain organoids are not only suitable for PD in vitro modelling, but also represent robust and highly reproducible cellular models.

neuroscience↗

bioRxiv2025

Released mitochondrial DNA and neurofilament light chain as Parkinson's disease phenotypes in patient-specific midbrain assembloids

Parkinsons Disease is the second most common neurodegenerative disorder worldwide, with growing numbers and considerable societal and economic concerns. Human cell culture systems are efficient models for neurodegenerative disorders and allow for personalized, non-invasive analysis of cellular and molecular disease mechanisms. Midbrain organoids and assembloids are advanced 3D culture systems that recapitulate the human midbrain, which is highly affected by Parkinsons disease. Here, we used healthy control and patient-specific midbrain assembloids to assess mitochondrial DNA phenotypes and NfL levels alongside neurodegeneration and alpha-synuclein phosphorylation. Importantly, alterations in mitochondrial DNA homeostasis and NfL levels can be assayed in the supernatant and therefore are particularly suitable as biomarkers and for high throughput screening approaches.

neuroscience↗

bioRxiv2024

DJ-1 mediates regulation of metabolism and immune response in Parkinsons disease astrocytes and Glioblastoma cells

An inverse correlation for the expression of Parkinsons disease (PD)- and cancer-associated genes has been previously reported. Genes that are upregulated in cancer are frequently downregulated in PD and vice versa. PARK7, encoding DJ-1, was initially identified as an oncogene, but loss of DJ-1 causes early-onset PD. However, it remains elusive how differential DJ-1 levels contribute to opposite cell fates in cancer and PD. Here, we demonstrate specific effects of differential DJ-1 protein levels on the energy metabolism and cell growth in patient-derived cellular models of PD and glioblastoma (GBM) cell lines. Impaired energy metabolism was associated with an increased immune response upon IL-1{beta} stimulation and increased apoptosis and decreased cell growth in models of PD, whereas in GBM cells increased metabolic activity translated into a reduced immune response and increased cell growth. Furthermore, we found decreased glutathione (GSH) synthesis and therefore increased levels of reactive oxygen species (ROS) and oxidized glutathione (GSSG) in models of DJ-1 deficiency and decreased ROS levels in GBM cell lines. Thus, the mechanism by which DJ-1 modulates these phenotypes is the same in both diseases. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/621212v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@4eccb4org.highwire.dtl.DTLVardef@161669corg.highwire.dtl.DTLVardef@197bfc3org.highwire.dtl.DTLVardef@1aecb36_HPS_FORMAT_FIGEXP M_FIG C_FIG DJ-1 levels modulate GSSG/GSH ratio and ROS levels, which results in divergent effects on cell growth and immune response in DJ-1-dependent glial pathologies in glioblastoma and PD. In models of PD, DJ-1 level dependent phenotypes can be rescued by antioxidant treatment that reduces the GSSG/GSH ratio and ROS levels.

neuroscience↗

bioRxiv2024

Deciphering shared molecular dysregulation across Parkinson's disease variants using a multi-modal network-based data integration and analysis

Parkinsons disease (PD) is a progressive neurodegenerative disorder with no effective treatment. Advances in neuroscience and systems biomedicine now enable the use of complex patient-specific in vitro disease models and cutting-edge computational tools for data integration, enhancing our understanding of complex PD mechanisms. To explore common biomedical features across monogenic PD forms, we developed a knowledge graph (KG) by integrating previously published high-content imaging and RNA sequencing data of PD patient-specific midbrain organoids harbouring LRRK2-G2019S, SNCA triplication, GBA-N370S or MIRO1-R272Q mutations with publicly available biological data. Furthermore, we generated a single-cell RNA sequencing dataset of midbrain organoids derived fromidiopathic PD patients (IPD) to stratify IPD patients towards genetic forms of PD. Despite high PD heterogeneity, we found that common transcriptomic dysregulation in monogenic PD forms is reflected in IPD glial cells. In addition, dysregulation in ROBO signalling might be involved in shared pathophysiology between monogenic PD and IPD cases.

systems biology↗

bioRxiv2024

Insulin resistance compromises midbrain organoid neural activity and metabolic efficiency predisposing to Parkinsons disease pathology

Growing evidence indicates that Type 2 Diabetes (T2D) is associated with an increased risk of developing Parkinsons disease through shared disease mechanisms. Studies show that insulin resistance, which is the driving pathophysiological mechanism of T2D plays a major role in neurodegeneration by impairing neuronal functionality, metabolism, and survival. To investigate insulin resistance caused pathological changes in the human midbrain, which could predispose a healthy midbrain to PD development, we exposed iPSC-derived human midbrain organoids from healthy individuals to either high insulin concentrations, promoting insulin resistance, or to more physiological insulin concentrations restoring insulin signalling function. We combined experimental methods with metabolic modelling to identify the most insulin resistance-dependent pathogenic processes. We demonstrate that insulin resistance compromises organoid metabolic efficiency, leading to increased levels of oxidative stress. Additionally, insulin-resistant midbrain organoids showed decreased neural activity and reduced amount of dopaminergic neurons, highlighting insulin resistance as a significant target in PD prevention.

neuroscience↗

bioRxiv2023

Parkinson's disease-related Miro1 mutation induces mitochondrial dysfunction and loss of dopaminergic neurons in vitro and in vivo

The complex and heterogeneous nature of Parkinsons disease (PD) is still not fully understood, however, increasing evidence supports mitochondrial impairments as a major driver of neurodegeneration in PD. Recently, the regulator of mitochondrial homeostasis Miro1 has been linked genetically and pathophysiologically to PD. Using 2D and 3D patient-based induced pluripotent stem cells models, including an isogenic control, showed that the Miro1 p.R272Q mutation leads to mitochondrial impairments including increased oxidative stress, disrupted mitochondrial bioenergetics and altered metabolism. This was accompanied by increased -synuclein levels in 2D dopaminergic neurons and by a significant reduction of dopaminergic neurons within midbrain organoids. Knock-in mice expressing mutant p.R285Q Miro1 (orthologue of the human p.R272Q mutation) confirmed the PD-specific dopaminergic neuronal loss in the substantia nigra, accumulation of striatal phosphorylated -synuclein accompanied by behavioral alterations. These findings demonstrate that mutant Miro1 is sufficient to comprehensively model PD-relevant phenotypes in vitro and in vivo, reinforcing its pivotal role in PD pathogenesis.

neuroscience↗

bioRxiv2023

Age-induced midbrain-striatum assembloids model early phenotypes of Parkinsons disease

Parkinsons disease (PD), one of the most common aging-associated neurodegenerative disorders, is characterised by nigrostriatal pathway dysfunction, caused by the gradual loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) of the midbrain and the dopamine depletion in the striatum. State of the art, human in vitro models are enabling the study of the dopaminergic neurons loss, but not the dysregulation of the dopaminergic network in the nigrostriatal pathway. Additionally, these models do not incorporate aging characteristics which potentially contribute to the development of PD. Therefore, it is conceivable that research conducted using these models overlooked numerous processes that contribute to diseases phenotypes. Here we present a nigrostriatal pathway model based on midbrain-striatum assembloids with inducible aging. We show that these assembloids are capable of developing characteristics of the nigrostriatal connectivity, with catecholamine release from the midbrain to striatum and synapse formation between midbrain and striatal neurons. Moreover, Progerin-overexpressing assembloids acquire aging traits that lead to early phenotypes of PD. This new model shall help to reveal the contribution of aging as well as nigrostriatal connectivity to the onset and progression of PD.

neuroscience↗

bioRxiv2023

Highly scalable and standardized organ-on-chip platform with TEER for biological barrier modeling

The development of new therapies is hampered by the lack of predictive, and patient-relevant in vitro models. Organ-on-chip (OOC) technologies can potentially recreate physiological features and hold great promise for tissue and disease modeling. However, the non-standardized design of these chips and perfusion control systems has been a barrier to quantitative high-throughput screening (HTS). Here we present a scalable OOC microfluidic platform for applied kinetic in vitro assays (AKITA) that is applicable for high, medium, and low throughput. Its standard 96-well plate and 384-well plate layouts ensure compatibility with existing laboratory workflows and high-throughput data collection and analysis tools. The AKITA plate is optimized for the modeling of vascularized biological barriers, primarily the blood-brain barrier, skin, and lung, with precise flow control on a custom rocker. The integration of trans-epithelial electrical resistance (TEER) sensors allows rapid and repeated monitoring of barrier integrity over long time periods. Together with automated confocal imaging and compound permeability testing analyses, we demonstrate the flexibility of the AKITA platform for establishing human-relevant models for preclinical drug and precision medicines efficacy, toxicity, and permeability under physiological conditions.

bioengineering↗

bioRxiv2023

SARS-CoV-2 infection induces dopaminergic neuronal loss in midbrain organoids during short and prolonged cultures

COVID-19 is mainly associated with respiratory symptoms, although several reports showed that SARS-CoV-2 affects the nervous system. We evaluated the effects of infection in prolonged culture of midbrain organoids, showing that the virus induces changes in gene expression, and fragmentation and loss of dopaminergic neurons. Our findings highlight the direct viral-induced damage to midbrain organoids indicating the relevance of assessing the neurological long-term evolution of COVID-19 patients.

neuroscience↗