Biology subjects

Karayannis, T.

Publications and source records attributed to Karayannis, T..

12 recordsLinked to original sources

bioRxiv2026

Adolescent Astrocyte Dysregulation Impairs Prefrontal Interneuron Maturation and Adult Cognition

The prefrontal cortex (PFC), a brain region critical for executive and cognitive functions, is characterized by its protracted maturation extending through adolescence until early adulthood. During adolescence, the PFC undergoes substantial rearrangements, creating a window of heightened plasticity allowing experience-dependent refinement of neural networks. While this extended plasticity supports the development of higher-order cognitive functions, it also confers increased vulnerability to environmental and biological perturbations that can disrupt circuit development and contribute to cognitive and behavioral impairments relevant to psychiatric disorders. Astrocytes are central regulators of brain homeostasis and actively participate in developmental processes that shape postnatal brain maturation. Although astrocyte dysfunction has been increasingly linked to psychiatric pathophysiology, it remains unknown whether aberrant astrocyte activity can directly influence PFC development and cognitive maturation. Here, using selective modulation of astrocyte activity during defined developmental windows in the PFC, we show that abnormal astrocyte activity during adolescence induces transient synaptic loss through enhanced microglial phagocytosis, produces long-lasting alterations in fast-spiking parvalbumin (PV) interneurons, and results in persistent deficits in PFC-dependent behaviors. Together, these findings provide causal evidence that disrupted astrocyte function during adolescent PFC maturation can lead to persistent neuronal and cognitive deficits with relevance to major psychiatric disorders.

neuroscience↗

bioRxiv2025

Enhanced ex vivo 3D whole-brain mapping and automated analysis of Parkinson's disease pathologies in mice

The spatiotemporal relationships among -synuclein inclusion formation, dopaminergic degeneration, and white matter microstructural changes remain poorly defined. To address this, we unilaterally injected preformed fibrils (PFFs) or monomeric -synuclein into the substantia nigra pars compacta (SNc) of wild-type mice. At 12 and 20 weeks post-injection (wpi), we performed ex vivo magnetic resonance imaging (MRI) at 9.4T to assess microstructural, volumetric and paramagnetic changes, along with light-sheet microscopy (LSM) to map -synuclein aggregates, and dopaminergic neuron at single-cell resolution across the whole brain. We developed a Python-based, automated registration pipeline that achieves <40 {micro}m alignment error between ex vivo MRI and LSM and computes clearing-induced distortion, enabling scalable deformation analysis and multimodal multiscale data integration. Unilateral SNc injection of -syn PFFs induced dense phospho--syn pathology in the ipsilateral SNc at 12 wpi, which decreased by 20 wpi in parallel with the loss of tyrosine hydroxylase-positive dopaminergic neuron. Pathogenic -synuclein spreads along with dopaminergic denervation in the nigrostriatal pathway to the ipsilateral striatum and contralateral SNc. Our ex vivo MRI-LSM platform provides a scalable, open-source framework for understanding circuit-level and whole-brain propagation of pathology in an -synucleinopathy model and beyond. HighlightsO_LIOpen-source, automated pipeline aligns ex vivo 9.4T MRI with light-sheet microscopy (LSM) at <40 {micro}m error, quantifies clearing-induced tissue distortion, and enables multiscale, whole-brain multimodal analysis. C_LIO_LIWhole-brain, single-cell-resolution mapping of -synuclein pathology and dopaminergic neuron loss in an -synucleinopathy mouse model using an optimized iDISCO+ protocol that achieves uniform antibody penetration even in dense regions like the striatum. C_LIO_LIUnilateral SNc injection of -syn PFFs drives spread of p--syn pathology along the nigrostriatal pathway to the ipsilateral striatum, BST, CEA, and contralateral SNc, along with dopaminergic degeneration. C_LIO_LIIpsilateral SNc shows high pS129 pathology at 12 weeks post-injection but significant reduction by 20 wpi, concurrent with loss of tyrosine hydroxylase-positive neurons. C_LIO_LIMultiparametric MRI reveals microstructural and iron-related alterations in striatum, SNc, and VTA, with cross-modal correlations linking pS129 burden, TH loss, and magnetic susceptibility changes. C_LI

neuroscience↗

bioRxiv2024

MortX: A Domain Generalization Benchmark for Mouse Cortex Segmentation and Registration

Mesoscale understanding of human brain development is crucial for understanding neurodevelopmental disorders. By applying AI techniques to analyze high-resolution, multi-modal brain imaging datasets across postnatal ages, researchers can study cortical development at the granular level. We introduce MortX, a benchmark dataset of the developing mouse cortex that captures multiple postnatal stages with annotations for distinct anatomical and functional subregions and layers. MortX features high-resolution imaging data including bright-field and fluorescence-labeled neuronal markers. We developed a standardized cortical atlas of genetic markers and manually registered it to brain section images for ground-truth labeling. The dataset serves as a benchmark for domain generalization in neuroimaging, enabling both classical and deep learning models to be trained on source brains and tested on unseen targets. Our results demonstrate generalized model performance and structural invariance across ages. We open-source MortX as a community resource for mouse brain segmentation and registration, emphasizing domain adaptation. This dataset addresses key challenges in mouse brain imaging and advances machine learning models that will help unravel neurodevelopmental disorders.

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bioRxiv2024

Progressive engagement of SST+ interneurons via Elfn1 regulates the barrel-septa response identity in the somatosensory cortex of mice

Just as separated digits and repeated sampling enhance somatosensation in humans, mice sense objects through multiple segregated whiskers through successive contacts. Individual whisker identity is maintained through the somatotopic organization of the Whisker[->]Brainstem[->]Thalamus[->]Cortex axis, culminating in distinct cortical domains: barrels and the surrounding septa. By performing simultaneous recordings using in-vivo electrophysiology in wild-type (WT) mice, we identify a progressive divergence in spiking activity between these domains upon repeated behaviorally relevant (10Hz) single- and multi-whisker stimulation. While the spiking activity ratio of multi- to single-whisker stimulation remains stable in barrels, it increases progressively in septa, suggesting inhibitory cell recruitment. Using genetic fate-mapping and tissue clearing, we indeed reveal that SST+ and VIP+ interneurons exhibit distinct laminar and regional distributions in barrel and septa domains. Further, calcium imaging of SST+ and VIP+ interneurons shows that while both neuron types respond to single-whisker stimulus, SST+ interneurons preferentially engage more in 10Hz multi-whisker stimulation, indicating their critical role in progressive stimulus preference. Genetic removal of Elfn1, which regulates the incoming excitatory synaptic dynamics onto SST+ interneurons, leads to the loss of the progressive increase in septal spiking ratio (MWS/SWS) upon stimulation. The importance of the loss of functional segregation of barrels, versus septa is revealed by cumulative temporal decoding analysis, supporting the notion that SST+ interneuron-mediated inhibition contributes to temporal encoding and stimulus integration. Finally, viral tracing combined with whole brain clearing and imaging reveals that barrel and septa domains project differentially to secondary somatosensory (S2) and motor (M1) cortices. These distinct projection patterns suggest that differential inhibitory processing in barrels and septa may contribute to functionally specialized downstream signaling. Together, our findings indicate that the progressive engagement of SST+ interneurons, mediated by Elfn1-dependent synaptic facilitation, underlies the preferential integration of multi-whisker stimuli in septa. This local inhibitory mechanism likely contributes to the functional segregation of barrel and septa domains and their distinct cortical projections, shaping how sensory information is processed and relayed to higher-order brain regions.

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bioRxiv2023

Distinct hypothalamus-habenula circuits govern risk preference

Appropriate risk evaluation is essential for survival in complex, uncertain environments. Confronted with choosing between certain (safe) and uncertain (risky) options, animals show strong preference for either option consistently across extended time periods. How such risk preference is encoded in the brain remains elusive. A candidate region is the lateral habenula (LHb), which is prominently involved in value-guided behavior. Here, using a balanced two-alternative choice task and longitudinal two-photon calcium imaging, we identify LHb neurons with risk-preference-selective activity reflecting individual risk preference prior to action selection. By employing whole-brain anatomical tracing, multi-fiber photometry, and projection- and cell-type-specific optogenetics, we find that glutamatergic LHb projections from the medial (MH) but not lateral (LH) hypothalamus provide behavior-relevant synaptic input before action selection. Optogenetic stimulation of MH{lozenge}LHb axons evoked excitatory and inhibitory postsynaptic responses, whereas LH{lozenge}LHb projections were excitatory. We thus reveal functionally distinct hypothalamus-habenula circuits for risk preference in habitual economic decision-making.

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bioRxiv2021

Human neural networks with sparse TDP-43 pathology reveal NPTX2 misregulation in ALS/FTLD

Human cellular models of neurodegeneration require reproducibility and longevity, which is necessary for simulating these age-dependent diseases. Such systems are particularly needed for TDP-43 proteinopathies1,2, which involve human-specific mechanisms3-6 that cannot be directly studied in animal models. To explore the emergence and consequences of TDP-43 pathologies, we generated iPSC-derived, colony morphology neural stem cells (iCoMoNSCs) via manual selection of neural precursors7. Single-cell transcriptomics (scRNA-seq) and comparison to independent NSCs8, showed that iCoMoNSCs are uniquely homogenous and self-renewing. Differentiated iCoMoNSCs formed a self-organized multicellular system consisting of synaptically connected and electrophysiologically active neurons, which matured into long-lived functional networks. Neuronal and glial maturation in iCoMoNSC-derived cultures was similar to that of cortical organoids9. Overexpression of wild-type TDP-43 in a minority of iCoMoNSC-derived neurons led to progressive fragmentation and aggregation, resulting in loss of function and neurotoxicity. scRNA-seq revealed a novel set of misregulated RNA targets coinciding in both TDP-43 overexpressing neurons and patient brains exhibiting loss of nuclear TDP-43. The strongest misregulated target encoded for the synaptic protein NPTX2, which was consistently misaccumulated in ALS and FTLD patient neurons with TDP-43 pathology. Our work directly links TDP-43 misregulation and NPTX2 accumulation, thereby highlighting a new pathway of neurotoxicity.

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bioRxiv2021

Layer 1 NDNF+ interneurons control bilateral sensory processing in a layer-dependent manner

Bilateral sensory information is indispensable for navigating the world. In most mammals, signals sensed by either side of the midline will ultimately reach the cortex where they will be integrated for perception and appropriate action selection. Even though information transferred across the hemispheres is routed through the corpus callosum, how and which microcircuits are key in integrating it is not well understood. Here we identify an essential role for layer 1 NDNF+ inhibitory cells of mice in integrating bilateral whisker-evoked information in an NMDA receptor-dependent manner. Direct connections from the contralateral cortex and the ipsilateral side activate NDNF+ neurons, which subsequently inhibit the late spiking activity of underlying layer 2/3 neurons, but not layer 5. Our results identify a feed-forward regulatory pathway for bilateral cortical sensory processing of upper layer cortical neurons actuated via layer 1 NDNF+ interneurons.

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bioRxiv2021

Identification of a developmental switch in information transfer between whisker S1 and S2 cortex in mice

The whiskers of rodents are a key sensory organ that provides critical tactile information for animal navigation and object exploration throughout life. Previous work has explored the developmental sensory-driven activation of the primary sensory cortex processing whisker information (wS1), also called barrel cortex. This body of work has shown that the barrel cortex is already activated by sensory stimuli during the first post-natal week. However, it is currently unknown when over the course of development these stimuli begin being processed by higher order cortical areas, such as secondary whisker somatosensory area (wS2). Here we investigate for the first time the developmental engagement of wS2 by sensory stimuli and the emergence of cortico-cortical communication from wS1 to wS2. Using in vivo wide-field imaging and electrophysiological recordings in control and conditional knock-out mice we find that wS1 and wS2 are able to process bottom-up information coming from the thalamus already right after birth. We identify that it is only at the end of the first post-natal week that wS1 begins to provide excitation into wS2, a connection which begins to acquire feed-forward inhibition characteristics after the second post-natal week. Therefore, we have uncovered a developmental window during which excitatory versus inhibitory functional connectivity between wS1 and wS2 takes place.

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bioRxiv2020

SpineS: An interactive time-series analysis software for dendritic spines

Live fluorescence imaging has shown the dynamic nature of dendritic spines, with changes in shape occurring both during development and in response to activity. The structure of a dendritic spine positively correlates with its functional efficacy. Learning and memory studies have shown that great deal of the information stored by a neuron is contained in the synapses. High precision tracking of synaptic structures can give hints about the dynamic nature of memory and help us to understand how memories evolve both in biological and artificial neural networks. Experiments that aim to investigate the dynamics behind the structural changes of dendritic spines require the collection and analysis of large time-series datasets. In this paper, we present an open-source software called SpineS for the automatic longitudinal structural analysis of dendritic spines with additional features for manual intervention to ensure optimal analysis. Our extensive experimental analyses on multiple datasets demonstrate that SpineS can achieve a high-level performance on samples collected both by two-photon and confocal imaging systems.

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bioRxiv2020

Post-mitotic Prox1 expression controls the final specification of cortical VIP interneuron subtypes

Neuronal identity is controlled in multiple developmental steps by key transcription factors that determine the unique properties of a cell. During embryogenesis, the transcription factor Prox1 has been shown to regulate VIP interneuron migration, survival, and as a result, circuit integration. Here, we explore the role of Prox1 as a regulator of genetic programs that guide the final specification of VIP interneuron subtypes in early post-natal life. Using in-vitro electrophysiology we find that post-natal removal of Prox1 differentially affects the synaptic integration of VIP bipolar and multipolar subtypes. RNA sequencing reveals that one of the downstream targets of Prox1 is the postsynaptic protein Elfn1, a constitutive regulator of presynaptic release probability. Genetic, pharmacological and electrophysiological experiments demonstrate that knocking out Prox1 reduces Elfn1 function in VIP multipolar but not in bipolar cells. Thus, in addition to the activity-dependent and contextual processes that finalize developmental trajectories, genetic programs engaged by Prox1 control the differentiation and connectivity of VIP interneuron subtypes.

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bioRxiv2020

Developmental Divergence of Sensory Stimulus Representation in Cortical Interneurons

Two inhibitory cell types involved in modulating barrel cortex activity and perception during active whisking in adult mice, are the VIP+ and SST+ interneurons. Here we identify a developmental transition point of structural and functional rearrangements onto these interneuron types around the start of active sensation at P14. Using in vivo two-photon Ca2+ imaging, we find that before P14, both interneuron types respond stronger to a multi-whisker stimulus, whereas after P14 their responses diverge, with VIP+ cells losing their multi-whisker preference and SST+ neurons enhancing theirs. Rabies virus tracings followed by tissue clearing, as well as photostimulation-coupled electrophysiology reveal that SST+ cells receive higher cross-barrel inputs compared to VIP+ at both time points. In addition, we also uncover that whereas prior to P14 both cell types receive direct input from the sensory thalamus, after P14 VIP+ cells show reduced inputs and SST+ cells largely shift to motor-related thalamic nuclei.

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bioRxiv2019

The mesoSPIM initiative: open-source light-sheet mesoscopes for imaging in cleared tissue

Over the course of the past decade, tissue clearing methods have reached a high level of sophistication with a wide variety of approaches now available1. To image large cleared samples, light-sheet microscopes have proven to be ideal due to their excellent optical sectioning capability in transparent tissue2. Such instruments have recently seen extensive technological and commercial development. However, despite this progress, the community is lacking instruments capable of exploring large samples with near-isotropic resolution within minutes. Here, we introduce the mesoscale selective plane-illumination microscopy (mesoSPIM) initiative, an open-hardware project that provides researchers with instructions and software to easily build and operate light-sheet microscopes for centimeter-sized cleared samples (http://www.mesospim.org).\n\nA wide range of commercial light-sheet microscopes have ...

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