Biology subjects

Hof, P. R.

Publications and source records attributed to Hof, P. R..

At least 19 recordsLinked to original sources

bioRxiv2026

Cortical asymmetry and its developmental change have distinct relationships with brain connectivity

The two cerebral hemispheres specialize while remaining interconnected. Does greater structural asymmetry imply less connectivity, and does connectivity also relate to how asymmetry changes during development? We addressed these questions in three independent cohorts spanning birth to 22 years, measuring asymmetry as the magnitude of the left-right difference in association tract overlap across 74 homotopic cortical region pairs. The regional pattern of asymmetry was similar across cohorts. In all three cohorts, more asymmetric regions had lower connectional density to cortical and non-cortical targets. However, involvement of the corpus callosum, the major pathway connecting the hemispheres, showed no consistent inverse relationship with regional asymmetry across cohorts. Instead, callosal involvement conditioned the relationship between mean regional asymmetry and its age-related change. In the two older cohorts, greater mean asymmetry accompanied more positive age effects among regions with appreciable callosal overlap, whereas this relationship was weak or negative among regions with little callosal overlap (standardized interactions +0.42 and +0.56). The pattern replicated across the two cohorts at matched ages, and longitudinal region-mean estimates in the Adolescent Brain Cognitive Development cohort were similar in direction and magnitude. In the youngest cohort, regions converged toward the mean, narrowing the between-region spread by 12%, with no detected callosal moderation. More asymmetric regions have lower overall connectional density, whereas callosal involvement helps explain how regional asymmetry changes with age.

neuroscience↗

bioRxiv2026

A comparative framework for neocortical sulcal anatomy in pinnipeds

The transition of pinnipeds from terrestrial ancestors into marine environments provides a unique opportunity to examine how cortical organisation has changed with adaptation to life in water. Here, we examined neocortical sulcal anatomy in nine species representing all three extant pinniped families using cortical surfaces reconstructed from post-mortem MRI. Building on a standardised framework previously established for land-dwelling (fissiped) carnivorans, we developed identification criteria for major pinniped sulci and compared their configurations with those observed across fissipeds. Major sulci were broadly conserved, but pinnipeds exhibited characteristic modifications, including a complex, highly branched pseudosylvian configuration and distinct frontoparietal sulcal patterns, with further family-level variation in both territories. This observed variation in sulcal patterns may reflect pronounced differences in locomotor, tactile, and vocal specialisations, generating hypotheses about how cortical organisation may vary with adaptation to marine environments. Together, these findings establish a common anatomical framework across Carnivora for investigating how cortical organisation diversified in relation to behaviour and ecology.

neuroscience↗

bioRxiv2026

PS FAD mutants and γ-secretase inhibition accumulate VEGFR2-derived peptide VCTF1 suppressing brain VEGFR2 dimerization, angiogenesis and neuroprotection.

Efficient cerebrovasculature is vital to neuronal health and cognition and evidence shows that most dementia patients have cerebrovascular abnormalities. Brain vasculature is regulated by Vascular Endothelial Growth Factors (VEGFs) binding VEGF receptor2 (VEGFR2) and stimulating angiogenesis and neuroprotection. Here we show that an ADAM17 cleavage of extracellular VEGFR2 produces the membrane-bound {gamma}-secretase substrate VEGFR2/CTF1 (called VCTF1), comprising the transmembrane and intracellular domains of VEGFR2. VCTF1 binds full-length VEGFR2 monomers suppressing its dimerization a function that is required for VEGFR2 activation and downstream angiogenesis and neuroprotection. Presenilin1 (PS1) Familial Alzheimers disease (FAD) mutants exert dominant negative effects on the {gamma}-secretase processing of VCTF1 increasing its concentration and abolishing VEGF-A-induced VEGFR2 dimerization/activation and downstream VEGFR2 signaling, endothelial cell functions and angiogenesis. {gamma}-Secretase inhibitors or PS1 reduction have similar effects on VCTF1 accumulation and VEGFR2 dimerization/activation and downstream signaling and functions as PS1 FAD mutants. Moreover, PS1 FAD mutants increase vulnerability of brain neurons to ischemic stress and abolish VEGF-A-induced neuroprotection and cognition. Together, these data show that VCTF1 suppresses VEGFR2 dimerization and downstream signaling and functions of the brains VEGF-A-/VEGFR2 angiogenic and neuroprotection systems. Importantly, we detected molecular markers of decreased VEGFR2 dimerization and angiogenic dysfunction in human brain tissue from PS1 FAD mutant genotypes. Our data reveal a pathway through which FAD mutants may promote dementia by increasing accumulation of VCTF1 and decreasing angiogenesis, neuroprotection, and cognition, suggesting that PS1 FAD patients may benefit from therapeutic methods that decrease brain VCTF1.

neuroscience↗

bioRxiv2025

Human-specific features of the cerebellum and ZP2-regulated synapse development

Understanding the unique features of the human brain compared to non-human primates has long intrigued humankind. The cerebellum refines motor coordination and cognitive functions, contributing to the evolutionary development of human adaptability and dexterity. To identify shared and divergent features across primates, we conducted single-nucleus transcriptomic and chromatin accessibility profiling of the adult cerebellar cortex in humans, chimpanzees, macaques, and marmosets. We revealed human-specific transcriptomic and regulatory features, particularly those involved in synaptogenesis. Notably, we identified an enrichment of the sperm receptor zona pellucida glycoprotein 2 (ZP2) and its potential interactors, known for their roles in gamete interaction, in human granule cells. Experimental data show that ZP2 expression in human granule cells is induced by pontine mossy fibers, reducing synaptic proteins at pontocerebellar glomerular synapses, and decreasing cerebellar neuron electrophysiological activity. This unexpected co-option of ZP2 in human-specific synapse regulation provides insights into the evolutionary specialization of the human cerebellum.

neuroscience↗

bioRxiv2025

Myelinated fiber labeling and orientation mapping of the human brain with light-sheet fluorescence microscopy

The convoluted network of myelinated fibers that supports behavior, cognition, and sensory processing in the human brain is the source of its extraordinary complexity. Advancements in tissue optical clearing, 3D fluorescence microscopy, and automated image analysis have enabled unprecedented insights into the architecture of these networks. Here, we investigate the multiscale organization of myelinated fibers in human brain tissue from the brainstem, Brocas area, hippocampus, and primary visual cortex by exploiting a specific fiber staining method, light-sheet fluorescence microscopy (LSFM), and an advanced spatial orientation analysis tool. Using an optimized protocol that integrates tissue clearing with the lipophilic DiD probe to achieve uniform and deep myelinated fiber labeling, we generate micrometerresolution volumetric reconstructions of multiple brain regions through an inverted LSFM. Automated image processing, employing unsupervised 3D multiscale Frangi filters, provides orientation distribution functions and local orientation dispersion maps. This enables precise characterization of the directionality of white matter bundles, linking mesoscopic structural properties to orientation details computed at the native micrometric resolution of the LSFM apparatus. The presented workflow illustrates a robust platform for large-scale, high-resolution brain mapping, which may facilitate the investigation of pathological alterations with unparalleled spatial resolution and, furthermore, the validation of other neuroimaging modalities.

neuroscience↗

bioRxiv2025

Transcriptomic changes across subregions of the primate cerebellum support the evolution of uniquely human behaviors

BackgroundCompared to other primates, humans display unique behaviors including language and complex tool use. These abilities are made possible in part by the cerebellum. This region of the hindbrain, comprising the flocculus, vermis, and lateral hemispheres, has expanded throughout primate evolution, particularly in great apes. Given the cerebellums architecture--differing in connectivity, neuron content, and functions across subregions--examining subregional differences is crucial to understanding its evolutionary trajectory. ResultsWe performed bulk RNA-seq across samples from six primate species, representing 40-50 million years of evolutionary history, across four subregions of the cerebellum (vermis, flocculus, right lateral hemisphere, left lateral hemisphere). We analyzed changes in gene expression with respect to evolutionary relationships via the Ornstein-Uhlenbeck model and found that, on average, 8.5% of orthologous genes are differentially expressed in humans relative to other non-human primates. Subregion-specific gene expression patterns reveal that the primate lateral hemispheres exhibit significant differences in synaptic activity and glucose metabolism, which in turn are highly implicated in neural processing. ConclusionsThis study provides a novel perspective on gene expression divergences across cerebellar subregions in multiple primate species, offering valuable insights into the evolution of this brain structure. Our findings reveal distinct subregional transcriptomic patterns, with the lateral hemispheres emerging as key sites of divergence across the six primate species. The enrichment of genes related to synaptic activity, glucose metabolism, locomotion, and vocalization highlights the cerebellums crucial role in supporting the neural complexity underlying uniquely human and other species-specific primate behaviors.

genomics↗

bioRxiv2024

Evaluation of near-infrared light therapy for the treatment of neurodegenerative diseases: Limited penetration depth into the brain likely hinders efficacy

BackgroundNear-infrared (NIR) light therapy is used to treat various musculoskeletal disorders. It has been proposed that transcranial NIR light treatment may also be beneficial for Alzheimers disease (AD). However, the ability of NIR light to penetrate the scalp and skull efficiently and induce cytoprotective responses in the brain parenchyma has not been sufficiently examined so far. This study aimed to evaluate whether the amount of NIR light that can penetrate through the human skull can cause a biological effect. MethodsThree commercially available devices (a medical laser emitting light at a wavelength of 905 nm and two LED helmets operating at wavelengths of 810 nm and 1070 nm, respectively) were used to measure the NIR light transmittance through human post-mortem skulls with a thermal power sensor. Furthermore, the biological effects of the fraction of light power that passed through the skull were investigated in a human neuronal cell line and in C. elegans. ResultsThe 905 nm laser achieved transmittances of up to 0.31% (173 {micro}W/cm2) of its input power, and the LED helmets 0.71% (41 {micro}W/cm2; 810 nm) and 0.45% (19 {micro}W/cm2; 1070 nm) of their respective input powers. NIR light exposure at a power density of 134 mW/cm2 was sufficient to activate mitochondrial metabolism in cultured human neurons and C. elegans, as demonstrated by increased cytochrome c oxidase activity and induction of mitochondrial chaperones. However, this stimulatory effect was no longer observed when the applied power density was reduced to 2.5 mW/cm2. ConclusionsMore than 99% of the NIR light emitted by the investigated devices was either absorbed or scattered by the human skull. The residual NIR light that would reach underlying brain structures was too weak to elicit biological effects. In conclusion, NIR light treatment is unlikely to be effective to treat brain diseases such as AD due to the low penetrability of the skull.

neuroscience↗

bioRxiv2023

Comparative basolateral amygdala connectomics reveals dissociable single-neuron projection patterns to frontal cortex in macaques and mice

Short abstractThe basolateral amygdala (BLA) projects to the frontal cortex (FC) in both rodents and primates, but the comparative organization of single-neuron BLA-FC projections is unknown. Using a barcoded connectomic approach, we found that BLA neurons are more likely to project to multiple distinct parts of FC in mice than in macaques. Further, while single BLA neuron projections to nucleus accumbens are similarly organized in mice and macaques, BLA-FC connections differ.

neuroscience↗

bioRxiv2023

Segmentation of supragranular and infragranular layers in ultra-high resolution 7T ex vivo MRI of the human cerebral cortex

Accurate labeling of specific layers in the human cerebral cortex is crucial for advancing our understanding of neurodevelopmental and neurodegenerative disorders. Lever-aging recent advancements in ultra-high resolution ex vivo MRI, we present a novel semi-supervised segmentation model capable of identifying supragranular and infragranular layers in ex vivo MRI with unprecedented precision. On a dataset consisting of 17 whole-hemisphere ex vivo scans at 120 {micro}m, we propose a multi-resolution U-Nets framework (MUS) that integrates global and local structural information, achieving reliable segmentation maps of the entire hemisphere, with Dice scores over 0.8 for supra- and infragranular layers. This enables surface modeling, atlas construction, anomaly detection in disease states, and cross-modality validation, while also paving the way for finer layer segmentation. Our approach offers a powerful tool for comprehensive neuroanatomical investigations and holds promise for advancing our mechanistic understanding of progression of neurodegenerative diseases.

neuroscience↗

bioRxiv2023

High-throughput sequencing of macaque basolateral amygdala projections reveals dissociable connectional motifs with frontal cortex

The basolateral amygdala (BLA) projects widely across the macaque frontal cortex1-4, and amygdalo-frontal projections are critical for optimal emotional responding5 and decision- making6. Yet, little is known about the single-neuron architecture of these projections: namely, whether single BLA neurons project to multiple parts of the frontal cortex. Here, we use MAPseq7 to determine the projection patterns of over 3000 macaque BLA neurons. We found that one-third of BLA neurons have two or more distinct targets in parts of frontal cortex and of subcortical structures. Further, we reveal non-random structure within these branching patterns such that neurons with four targets are more frequently observed than those with two or three, indicative of widespread networks. Consequently, these multi-target single neurons form distinct networks within medial and ventral frontal cortex consistent with their known functions in regulating mood and decision-making. Additionally, we show that branching patterns of single neurons shape functional networks in the brain as assessed by fMRI-based functional connectivity. These results provide a neuroanatomical basis for the role of the BLA in coordinating brain-wide responses to valent stimuli8 and highlight the importance of high- resolution neuroanatomical data for understanding functional networks in the brain.

neuroscience↗

bioRxiv2023

Human-specific features and developmental dynamics of the brain N-glycome

Comparative "omics" studies have revealed unique aspects of human neurobiology, yet an evolutionary perspective of the brain N-glycome is lacking. Here, we performed multi-regional characterization of rat, macaque, chimpanzee, and human brain N-glycomes using chromatography and mass spectrometry, then integrated these data with complementary glycotranscriptomic data. We found that in primates the brain N-glycome has evolved more rapidly than the underlying transcriptomic framework, providing a mechanism for generating additional diversity. We show that brain N-glycome evolution in hominids has been characterized by an increase in complexity and (2-6)-linked N-acetylneuraminic acid along with human-specific cell-type expression of key glycogenes. Finally, by comparing the prenatal and adult human brain N-glycome, we identify region-specific neurodevelopmental pathways that lead to distinct spatial N-glycosylation profiles in the mature brain. One-Sentence SummaryEvolution of the human brain N-glycome has been marked by an increase in complexity and a shift in sialic acid linkage.

neuroscience↗

bioRxiv2022

Neuronal TIMP2 regulates hippocampus-dependent plasticity and extracellular matrix complexity

The functional output of the hippocampus, a brain region subserving memory processes, depends on highly orchestrated cellular and molecular processes that regulate synaptic plasticity throughout life. The structural requirements of such plasticity and molecular processes involved in this regulation are poorly understood. Specific molecules, including tissue inhibitor of metalloproteinases-2 (TIMP2) have been implicated in processes of plasticity in the hippocampus, a role that decreases with brain aging as expression is lost. Here, we report that TIMP2 is highly expressed by neurons within the hippocampus and its loss drives changes in cellular programs related to adult neurogenesis and dendritic spine turnover with corresponding impairments in hippocampus-dependent memory. Consistent with the accumulation of ECM in the hippocampus we observe with aging, we find that TIMP2 acts to reduce accumulation of extracellular matrix (ECM) around synapses in the hippocampus. Moreover, its removal results in hindrance of newborn neuron migration through a denser ECM network. A novel conditional TIMP2 KO mouse reveals that neuronal TIMP2 regulates adult neurogenesis, accumulation of ECM, and ultimately hippocampus-dependent memory. Our results define a mechanism whereby hippocampus- dependent function is regulated by TIMP2 and its interactions with the ECM to regulate diverse processes associated with synaptic plasticity.

neuroscience↗

bioRxiv2022

Transcriptomic cytoarchitecture reveals principles of human neocortex organization

Variation in cortical cytoarchitecture is the basis for histology-based definition of cortical areas, such as Brodmann areas. Single cell transcriptomics enables higher-resolution characterization of cell types in human cortex, which we used to revisit the idea of the canonical cortical microcircuit and to understand functional areal specialization. Deeply sampled single nucleus RNA-sequencing of eight cortical areas spanning cortical structural variation showed highly consistent cellular makeup for 24 coarse cell subclasses. However, proportions of excitatory neuron subclasses varied strikingly, reflecting differences in intra- and extracortical connectivity across primary sensorimotor and association cortices. Astrocytes and oligodendrocytes also showed differences in laminar organization across areas. Primary visual cortex showed dramatically different organization, including major differences in the ratios of excitatory to inhibitory neurons, expansion of layer 4 excitatory neuron types and specialized inhibitory neurons. Finally, gene expression variation in conserved neuron subclasses predicts differences in synaptic function across areas. Together these results provide a refined cellular and molecular characterization of human cortical cytoarchitecture that reflects functional connectivity and predicts areal specialization.

neuroscience↗

bioRxiv2022

The BRAIN Initiative Cell Census Data Ecosystem: A User's Guide

Characterizing cellular diversity at different levels of biological organization across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also required to manipulate cell types in controlled ways, and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data generating centers, data archives and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain and demonstration of prototypes for human and non-human primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed, and to accessing and using the BICCN data and its extensive resources, including the BRAIN Cell Data Center (BCDC) which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted by the BICCN toward FAIR (Wilkinson et al. 2016a) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.

bioinformatics↗

bioRxiv2021

A multimodal imaging and analysis pipeline for creating a cellular census of the human cerebral cortex

Cells are not uniformly distributed in the human cerebral cortex. Rather, they are arranged in a regional and laminar fashion that span a range of scales. Here we demonstrate an innovative imaging and analysis pipeline to construct a reliable cell census across the human cerebral cortex. Magnetic resonance imaging (MRI) is used to establish a macroscopic reference coordinate system of laminar and cytoarchitectural boundaries. Cell counting is obtained with both traditional immunohistochemistry, to provide a stereological gold-standard, and with a custom-made inverted confocal light-sheet fluorescence microscope (LSFM) for 3D imaging at cellular resolution. Finally, mesoscale optical coherence tomography (OCT) enables the registration of the distorted histological cell typing obtained with LSFM to the MRI-based atlas coordinate system.

neuroscience↗

bioRxiv2021

Exploring the human cerebral cortex using confocal microscopy

Cover-all mapping of the distribution of neurons in the human brain would have a significant impact on the deep understanding of brain function. Therefore, complete knowledge of the structural organization of different human brain regions at the cellular level would allow understanding their role in the functions of specific neural networks. Recent advances in tissue clearing techniques have allowed important advances towards this goal. These methods use specific chemicals capable of dissolving lipids, making the tissue completely transparent by homogenizing the refractive index. However, labeling and clearing human brain samples is still challenging. Here, we present an approach to perform the cellular mapping of the human cerebral cortex coupling immunostaining with SWITCH/TDE clearing and confocal microscopy. A specific evaluation of the contributions of the autofluorescence signals generated from the tissue fixation is provided as well as an assessment of lipofuscin pigments interference. Our evaluation demonstrates the possibility of obtaining an efficient clearing and labeling process of parts of adult human brain slices, making it an excellent method for morphological classification and antibody validation of neuronal and non-neuronal markers.

neuroscience↗

bioRxiv2021

Cellular resolution anatomical and molecular atlases for prenatal human brains

Increasing interest in studies of prenatal human brain development, particularly using new single-cell genomics and anatomical technologies to create cell atlases, creates a strong need for accurate and detailed anatomical reference atlases. In this study, we present two cellular-resolution digital anatomical atlases for prenatal human brain at post-conceptional weeks (PCW) 15 and 21. Both atlases were annotated on sequential Nissl-stained sections covering brain-wide structures on the basis of combined analysis of cytoarchitecture, acetylcholinesterase staining and an extensive marker gene expression dataset. This high information content dataset allowed reliable and accurate demarcation of developing cortical and subcortical structures and their subdivisions. Furthermore, using the anatomical atlases as a guide, spatial expression of 37 and 5 genes from the brains respectively at PCW 15 and 21 was annotated, illustrating reliable marker genes for many developing brain structures. Finally, the present study uncovered several novel developmental features, such as the lack of an outer subventricular zone in the hippocampal formation and entorhinal cortex, and the apparent extension of both cortical (excitatory) and subcortical (inhibitory) progenitors into the prenatal olfactory bulb. These comprehensive atlases provide useful tools for visualization, targeting, imaging and interpretation of brain structures of prenatal human brain, and for guiding and interpreting the next generation of cell census and connectome studies.

neuroscience↗

bioRxiv2021

Tempo and mode of gene expression evolution in the brain across Primates

Primate evolution has led to a remarkable diversity of behavioral specializations and pronounced brain size variation among species 1,2. Gene expression provides a promising opportunity for studying the molecular basis of brain evolution, but it has been explored in very few primate species to date e.g. 3,4. To understand the landscape of gene expression evolution across the primate lineage, we generated and analyzed RNA-Seq data from four brain regions in an unprecedented eighteen species. Here we show a remarkable level of variation in gene expression among hominid species, including humans and chimpanzees, despite their relatively recent divergence time from other primates. We found that individual genes display a wide range of expression dynamics across evolutionary time reflective of the diverse selection pressures acting on genes within primate brain tissue. Using our sample that represents an unprecedented 190-fold difference in primate brain size, we identified genes with variation in expression most correlated with brain size and found several with signals of positive selection in their regulatory regions. Our study extensively broadens the context of what is known about the molecular evolution of the brain across primates and identifies novel candidate genes for study of genetic regulation of brain development and evolution.

evolutionary biology↗