Biology subjects

Zagare, A.

Publications and source records attributed to Zagare, A..

10 recordsLinked to original sources

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↗

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↗

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↗

bioRxiv2019

Machine learning-assisted neurotoxicity prediction in human midbrain organoids

A major challenge in the field of neurodegenerative diseases is the poor translation of pre-clinical models to clinical applications. The human brain is an immensely complex structure, which makes it difficult to recapitulate its development, function and disorders. In the recent years, brain organoids derived from human induced pluripotent stem cells have risen as novel tools to study neurodegenerative diseases such as Parkinsons disease (PD). PD is a multifactorial disorder, with aging, genetics and environmental factors as key etiological elements. The majority of the PD cases are idiopathic and proposed to result from a complex interaction between genetic predisposition and environmental exposure. Consequently, the identification of potentially disease causing environmental factors is of critical importance. Organoids, as complex multi-cellular tissue proxies, are an ideal tool to study cellular response to environmental changes. However, with increasing complexity of the system, usage of quantitative tools becomes challenging. This led us to develop an automated high-content image analysis pipeline for image-based cell profiling in the organoid system. Here, we introduce a midbrain organoid system that recapitulates features of neurotoxin-induced PD, representing a platform for machine-learning-assisted prediction of neurotoxicity in high-content imaging data. This model is a valuable tool for advanced in vitro PD modeling and for the screening of putative neurotoxic compounds.

pharmacology and toxicology↗

bioRxiv2018

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

A multitude of factors contribute to complex diseases and can be measured with \"omics\" methods. Databases facilitate data interpretation for underlying mechanisms. Here, we describe the Virtual Metabolic Human (VMH, http://vmh.life) database encapsulating current knowledge of human metabolism within five interlinked resources \"Human metabolism\", \"Gut microbiome\", \"Disease\", \"Nutrition\", and \"ReconMaps\". The VMH captures 5,180 unique metabolites, 17,730 unique reactions, 3,288 human genes, 255 Mendelian diseases, 818 microbes, 632,685 microbial genes, and 8,790 food items. The VMHs unique features are i) the hosting the metabolic reconstructions of human and gut microbes amenable for metabolic modeling; ii) seven human metabolic maps for data visualization; iii) a nutrition designer; iv) a user-friendly webpage and application-programming interface to access its content; and v) user feedback option for community engagement. We demonstrate with four examples the VMHs utility. The VMH represents a novel, interdisciplinary database for data interpretation and hypothesis generation to the biomedical community.

systems biology↗