Biology subjects

Adolfs, Y.

Publications and source records attributed to Adolfs, Y..

10 recordsLinked to original sources

bioRxiv2026

High-Resolution 3D Mapping of Human Cortical Vasculature

A quantitative description of the three-dimensional organization of the human cortical vasculature at micron scale is critical for understanding the influence of the vascular architecture on cerebral blood flow, neurovascular coupling, neurological disease, and human neuroimaging signals. However, high-resolution volumetric vascular data from human cortex are scarce, as the acquisition relies on postmortem microscopy, and tissue-clearing and whole-mount immunolabeling approaches developed for rodent tissues are less effective in heavily crosslinked, pigment rich fixed human cortex. Here we introduce h-iDISCO+, a workflow that enables whole-mount immunolabeling and high-resolution light-sheet imaging of arteries, capillaries, and veins in long-term formalin fixed human brain tissue. By integrating extended oxidative and photobleaching prior to tissue staining, we achieve uniform sample transparency and full-depth antibody penetration. Applying this workflow to tissue samples from human primary visual cortex, we quantified vessel geometrical properties and vascular density across cortical depth. This approach allows quantitative reconstruction of human cortical vascular networks at micron resolution, enabling volumetric datasets of the human cortical vasculature that were previously unavailable.

neuroscience↗

bioRxiv2026

Ultra-high field microstructural MRI of living cortical organoids

Quantitative microstructural magnetic resonance imaging (MRI) can noninvasively characterize tissue configuration at micrometer scales, but clinical uptake is limited by validation and optimization in human-relevant scenarios. Organoids are powerful human-relevant tissue models, yet translation is hampered by lack of non-destructive, longitudinal microstructural assessment. Bridging these gaps, microstructural MRI of living organoids can accelerate MRI biomarker and organoid development and validation. Here, we address key obstacles to enable organoid microstructural MRI. First, we use a unique 28.2 T MRI system to achieve spatial resolution with adequate signal-to-noise ratio and feasible scan times. Second, we implement flexible acquisitions with fast readouts to expand multivariate experimental capacity. Third, we develop a workflow combining 3D MRI and 3D lightsheet microscopy for cross-modality anatomical comparison beyond 2D. Using this platform, we demonstrate microstructural MRI of cortical organoids with resolutions down to (20 {micro}m)3, revealing anisotropy, heterogeneity, maturation-dependent differences, and temporal changes in cortical organoids. Correlative lightsheet microscopy confirms correspondence to axonal and nuclear architecture. This platform enables live-organoid MRI as a complementary tool to human- and animal imaging for robust microstructural assessment.

biophysics↗

bioRxiv2025

MeCP2 binding and genome-lamina reorganization precede long gene activation during mouse corticogenesis

During corticogenesis, neural gene expression is tightly coordinated by chromatin and epigenetic changes, whose misregulation can lead to neurodevelopmental disorders1-4. The role of spatial genome organization--particularly interactions with the nuclear lamina--during these developmental programs remains poorly understood. Here, we combined in utero electroporation with scDam&T-seq to jointly profile genome-lamina contacts and transcriptomes in single cells of the mouse embryonic cortex. Interestingly, we find extensive genome-lamina reorganization during corticogenesis that is strongly biased towards long neuronal genes ([≥]100 kb), which are associated with neurodevelopmental disorders including autism spectrum disorder. Detachment of these genes frequently precedes transcriptional activation, positioning lamina disengagement as an early gene regulatory event. We identify the methyl CpG binding protein 2 (MeCP2)--mutated in Rett syndrome--as a candidate mediator of this process. MeCP2 binds lamina-associated, hydroxymethylated long genes before their repositioning, suggesting that MeCP2 may play a role in genome-lamina reorganization. These findings suggest a link between prevalent genome-lamina reorganization and MeCP2 regulation to ensure proper spatiotemporal activation of long neuronal genes during corticogenesis.

molecular biology↗

bioRxiv2025

Motor Cortex Modulates Ipsilateral Limb Movement Through a Direct Cortico-Cerebellar Circuit

Motor cortex is traditionally associated with control of contralateral limb movements via corticospinal and cortico-ponto-cerebellar pathways. However, the contribution of ipsilateral motor cortical outputs on motor control remains unclear. Here, we identify and characterize a distinct population of cortico-cerebellar (C-C) neurons in the motor cortex that form monosynaptic projections to the ipsilateral cerebellar nuclei. The C-C neurons receive preferential local motor cortical inputs and exhibit projection patterns distinct from cortico-pontine projecting neurons. Using in vivo imaging and optogenetic perturbations, we show that these neurons are active during locomotion and transitions of volitional movements. Disruption of the C-C projection severely affects the locomotion and balancing. Interestingly, the C-C pathway is selectively involved in the initiation and coordination of ipsilateral forelimb movements, without affecting contralateral movement kinematics. These findings shed light on a non-canonical cortico-cerebellar pathway that supports ipsilateral motor control, complementing the traditional control mechanisms of the cerebral cortex over the contralateral motor domains.

neuroscience↗

bioRxiv2023

Generation and characterization of Sema6aΔcyt conditional knockout mice

The axon guidance molecule Semaphorin-6A (SEMA6A) plays a key role during nervous system development. SEMA6A, classically known as a ligand for Plexin-A2 and -A4, is a transmembrane protein that can also elicit signaling via its intracellular domain in vitro. However, the physiological relevance of this reverse signaling route is largely unknown. We generated a new transgenic mouse model, Sema6a{Delta}cytfl/fl, in which the cytosolic part of SEMA6A can be conditionally removed using Cre-recombination. Upon Sema6a{Delta}cyt mutation, SEMA6A can only act as a ligand and reverse signaling is perturbed. Germline deletion of SEMA6As intracellular part results in developmental defects in axon pathfinding and neuron migration that partially phenocopy defects observed in full Sema6a knockout mice. These defects include disorganization of the anterior commissure, piriform cortex, lateral olfactory tract, thalamocortical and corticospinal white matter tracts, and defected neuron migration in the neocortex and cerebellum. Intriguingly, the hippocampal malformation described in Sema6a full knockout mice was not reproduced, suggesting a specific role for SEMA6A forward signaling in hippocampal development. Our results indicate that the intracellular domain of SEMA6A is essential for proper axon targeting and neuron migration, and provide the first proof of a SEMA6A reverse signaling pathway in vivo.

developmental biology↗

bioRxiv2022

Molecular Signatures and Cellular Diversity During Mouse Habenula Development

The habenula plays a key role in various motivated and pathological behaviors and is composed of molecularly distinct neuron subtypes. Despite progress in identifying mature habenula neuron subtypes, how these subtypes develop and organize into functional brain circuits remains largely unknown. Here we performed single-cell transcriptional profiling of mouse habenular neurons at critical developmental stages instructed by detailed three-dimensional anatomical data. Our data reveal cellular and molecular trajectories during embryonic and postnatal development leading to different habenular subtypes. Further, based on this analysis our work establishes the distinctive functional properties and projection target of a previously uncharacterized subtype of Cartpt+ habenula neurons. Finally, we show how comparison of single-cell transcriptional profiles and GWAS data links specific developing habenular subtypes to psychiatric disease. Together, our study begins to dissect the mechanisms underlying habenula neuron subtype-specific development and creates a framework for further interrogation of habenular development in normal and disease states.

developmental biology↗

bioRxiv2021

Pipeline for 4D whole-brain microscopy preprocessing and analysis.

Acute stress leads to sequential activation of functional brain networks. The challenge is to get insight in whole brain activity at multiple scales, beyond the level of (networks of) nuclei. We developed a novel pre-processing and analytical pipeline to chart whole-brain immediate early genes expression - as proxy for cellular activity - after a single stressful foot-shock in 4 dimensions; that is, from functional networks up to 3D single-cell resolution, and over time. The pipeline is available as R-package. Most brain areas (96%) showed increased numbers of c-fos+ cells after foot-shock, yet hypothalamic areas stood out as being most active and prompt in their activation, followed by amygdalar, prefrontal, hippocampal and finally thalamic areas. At the cellular level, c-fos+ density clearly shifted over time across subareas, as illustrated for the basolateral amygdala. Moreover, some brain areas showed increased numbers of c-fos+ cells, while others dramatically increased c-fos intensity in just a subset of cells; this strategy changed after foot-shock in half of the brain areas. All single-cell data can be visualized for each of the 90 brain areas examined through our interactive web-portal.

neuroscience↗

bioRxiv2021

3D visualization of SARS-CoV-2 infection and receptor distribution in Syrian hamster lung lobes display distinct spatial arrangements

SARS-CoV-2 attaches to angiotensin-converting enzyme 2 (ACE2) to gain entry into cells after which the spike protein is cleaved by the transmembrane serine protease 2 (TMPRRS2) to facilitate viral-host membrane fusion. ACE2 and TMPRRS2 expression profiles have been analyzed at the genomic, transcriptomic, and single-cell RNAseq level, however, biologically relevant protein receptor organization in whole tissues is still poorly understood. To describe the organ-level architecture of receptor expression, related to the ability of ACE2 and TMPRRS2 to mediate infectivity, we performed a volumetric analysis of whole Syrian hamster lung lobes. Lung tissue of infected and control animals were stained using antibodies against ACE2 and TMPRRS2, combined with fluorescent spike protein and SARS-CoV-2 nucleoprotein staining. This was followed by light-sheet microscopy imaging to visualize expression patterns. The data demonstrates that infection is restricted to sites with both ACE2 and TMPRRS2, the latter is expressed in the primary and secondary bronchi whereas ACE2 is predominantly observed in the terminal bronchioles and alveoli. Conversely, infection completely overlaps at these sites where ACE2 and TMPRSS2 co-localize. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/435771v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@150fc65org.highwire.dtl.DTLVardef@1ea6a56org.highwire.dtl.DTLVardef@eb3c43org.highwire.dtl.DTLVardef@1c1877e_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2019

Anatomical development of the cerebellothalamic tract in embryonic mice

Cerebellar projections to the thalamus are a pivotal connection in cerebello-cerebral interactions. Apart from its role in coordinating sensorimotor integration in the adult brain, the cerebello-thalamic projection has also been implemented in developmental disorders, such as autism spectrum disorders. Although the development of the cerebellum, thalamus and cerebral cortex have been studied in many species, a detailed description of the ontogeny of the mammalian cerebello-thalamic tract (CbT) is currently missing. Here we investigated the development of the CbT at embryonic stages using transgenic Ntsr1-Cre/Ai14 mice and in utero electroporation (IUE) of wild type mice. Wide-field, confocal and 3D light-sheet imaging of immunohistochemical stainings showed that CbT fibers arrive in the prethalamus between E14.5 and E15.5, but only invade the thalamus after E16.5. We quantified the spread of CbT fibers throughout the various thalamic nuclei and found that at E17.5 and E18.5 the ventrolateral, ventromedial and parafascicular nuclei, but also the mediodorsal and posterior complex become increasingly innervated. Several CbT fiber varicosities colocalize with vGluT2, indicating that already from E18.5 the CbT synapse in various thalamic nuclei. Our results contribute to the construction of a frame of reference on the anatomical development of the CbT, which will help to guide future experiments investigating neurodevelopmental disorders.\n\nSignificance statementUsing various microscopic approaches, we investigated the anatomical development of the fiber tract between the cerebellum and thalamus, one of the major mammalian brain connections. Our results show that in mice cerebellar axons wait outside of the thalamus from embryonic day (E)15.5 until E17.5 before invading the thalamic complex. Cerebellar axons establish vGluT2-positive synapses at E18.5 throughout various thalamic nuclei, each of which subsequently develops its connections with dedicated cerebral cortical regions. Our data thereby advocate the cerebellar influence on the maturation of the thalamus and connected cerebral cortex. This knowledge can help to guide future experiments into neurodevelopmental disorders affecting cerebello-thalamo-cortical networks.

neuroscience↗

bioRxiv2018

TRPC3 is essential for functional heterogeneity of cerebellar Purkinje cells

Despite the canonical homogenous character of its organization, the cerebellum plays differential computational roles in distinct types of sensorimotor behaviors. However, the molecular and cell physiological underpinnings are unclear. Here we determined the contribution of transient receptor potential cation channel type C3 (TRPC3) to signal processing in different cerebellar modules. Using gain-of-function and loss-of-function mouse models, we found that TRPC3 controls the simple spike activity of zebrin-negative (Z-), but not of zebrin-positive (Z+), Purkinje cells. Moreover, in vivo TRPC3 also regulated complex spike firing and its interaction with simple spikes exclusively in Z- Purkinje cells. Finally, we found that eyeblink conditioning, related to Z- modules, but not compensatory eye movement adaptation, linked to Z+ modules, was affected in TRPC3 loss-of-function mice. Together, our results indicate that TRPC3 is essential for the cellular heterogeneity that introduces distinct physiological properties in an otherwise homogeneous population of Purkinje cells, conjuring functional heterogeneity in cerebellar sensorimotor integration.

neuroscience↗