Biology subjects

Brack, A.

Publications and source records attributed to Brack, A..

10 recordsLinked to original sources

bioRxiv2026

Environmental risk reshapes high-confidence schizophrenia risk genes during a developmental window of vulnerability

Rare coding variants and environmental exposures such as early-life stress contribute to schizophrenia risk, but whether environmental adversity alters the expression of genetically implicated genes remains unclear. Combining the limited bedding and nesting (LBN) model of early-life stress (ELS) with 24-plex single-cell mFISH registered to the Allen Mouse Brain Atlas, we profiled the ten genes identified in the original SCHEMA study, the complement gene C4b and activity markers in 1.29 million cells across four postnatal ages. Whole-brain risk-gene upregulation was greatest at postnatal day 21 (P21), with region- and cell-type-selective effects that prominently involved the hypothalamus. Sp4 and Cacna1g showed distinct temporal responses: Sp4 increased at P21 and decreased at P90 in hypothalamic oligodendrocytes, whereas Cacna1g decreased at P10. ELS-associated C4b upregulation extended across neuronal and glial populations, including oligodendrocytes and OPCs. Across regional cell types, P10 C4b effects were positively correlated with P21 Grin2a effects. These findings suggest that ELS perturbs the developmental expression of genes implicated in schizophrenia, identifying potential molecular links between environmental adversity and genetic vulnerability.

neuroscience↗

bioRxiv2025

Sex differences define the molecular and cellular phenotypes of pain resolution in dorsal root ganglia

The dorsal root ganglion (DRG), a key site for the initiation and maintenance of neuropathic pain, was examined for sex-dependent phenotypes in sensory neurons, satellite glial cells (SGCs), and local macrophages following traumatic nerve injury and during natural pain resolution. Systematic analysis of 7,495 DRG immunofluorescence images and 62 transcriptomes revealed pronounced sex-specific, multicellular DRG phenotypes, especially during pain resolution. System parameters, including tissue size and neuron density also showed sex-dependent differences. Neuropathic pain resolved without tissue or sensory neuron loss. After injury, macrophages invaded the space between sensory neurons and satellite glial cells (SGCs); this was partially reversed during pain resolution, particularly in males. In females, immune-related gene expression and macrophage phenotypes persisted longer, while SGC activation and contact to sensory neurons was more persistent in males. During resolution, synaptic and excitability-related processes were pronounced in both sexes. However, while injury responses were largely shared between sexes, the resolution phase displayed distinctly sex-specific molecular and cellular signatures. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=197 SRC="FIGDIR/small/691610v1_ufig1.gif" ALT="Figure 1"> View larger version (76K): org.highwire.dtl.DTLVardef@4063c7org.highwire.dtl.DTLVardef@156c0d2org.highwire.dtl.DTLVardef@8d4be4org.highwire.dtl.DTLVardef@7182bd_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefAnalysis of [~]7,500 bioimages and 62 transcriptomes reveals pronounced sex differences in rat dorsal root ganglia during pain resolution after peripheral nerve injury. HighlightsO_LIIn both female and male rats, peripheral nerve injury and subsequent pain resolution occur in the dorsal root ganglia (DRG) without neuronal or tissue loss. C_LIO_LISex influences DRG tissue size, neuron density, immune and glial phenotypes, and molecular-cellular responses to nerve injury and pain resolution. C_LIO_LIFollowing injury, macrophages infiltrate the space between sensory neurons and satellite glial cells (SGCs); this process reverses during pain resolution, particularly in males. C_LIO_LIIn females, immune phenotypes remain more stable throughout pain resolution, while SGC contact is reduced. C_LIO_LIPain resolution involves not only the reversal of injury-induced cell changes but also the activation of resolution-specific gene programs related to synaptic signaling, neuronal excitation, and cell-cell communication. C_LIO_LISex differences on the molecular-cellular level are less prevalent after nerve injury but become prominent during pain resolution. C_LI

neuroscience↗

bioRxiv2025

Control of Quiescence and Activation of Human Muscle Stem Cells by Cytokines

Skeletal muscle homeostasis and repair depend on the activation of tissue resident stem cells called satellite cells. To understand the early molecular basis of human satellite cell activation, epigenomics, transcriptomics and protein analysis were performed in quiescent and activated human satellite cells. Cytokine signaling pathways were enriched in stimulated human satellite cells revealing a high cytokine enrichment, including CCL2, CCL20, CXCL8, IL-6, TNFRSF12A, ILR1, CSF-1 and FGF2. Functional roles of these observed changes are supported by in vivo experiments showing that chemokine inhibitors increase engraftment and regeneration capacity of human satellite cells xenotransplants. Cytokines, chemokines and associated signaling pathways in the early stages of human satellite cell activation may underlie disparate muscle responses in neuromuscular inflammatory and degenerative disorders and consequently are potential entry points for clinical applications towards muscle repair.

cell biology↗

bioRxiv2025

Increased Complement C4 in a Sparse Neuronal Subset Induces Network-Wide Transcriptomic Alterations in the Prefrontal Cortex

The complement component C4 regulates synaptic refinement and plasticity in the brain and has been implicated in multiple neurological and psychiatric disorders, with especially strong genetic evidence linking elevated C4A expression to schizophrenia. However, it remains unclear whether localized C4 elevation in a small neuronal population is sufficient to reshape broader cortical gene-regulatory programs and cellular phenotypes. To address this question, we overexpressed mouse C4 in approximately 2% of prefrontal cortical neurons using in utero electroporation and performed bulk RNA sequencing on microdissected prefrontal cortex. Despite the sparse manipulation, C4 OE was associated with broad transcriptional remodeling across tissue composed predominantly of untransfected cells, including coordinated changes in cholesterol biosynthesis, axon and synaptic associated programs, vascular/ECM pathways, and immune and stress related responses. Comparison with a schizophrenia synaptic proteomic dataset identified limited global correspondence but selective gene and pathway level overlap in specific molecular programs. Reference based projection of directional DEG signatures onto a cortical single cell transcriptomic reference further identified cell type-associated structure, including prominent astrocyte and vascular associated axes and distinct lipid/metabolic, vascular/endothelial interferon associated, and immune/stress correlation domains. Spatial validation with MFISH showed increased Hmgcr expression in neighboring GFP-negative cells, while PLIN2 imaging revealed increased DAPI-associated/perinuclear lipid-droplet burden within the local C4 OE field. Together, these findings support a model in which sparse neuronal C4 elevation is associated with broader remodeling of the local cortical environment, including a non-cell-autonomous component involving neighboring cell lipid associated responses. These results expand the interpretation of C4 risk biology beyond synapse elimination alone and suggest that focal immune-gene dysregulation can engage lipid-homeostatic, stress-related, and cell-type-associated transcriptional programs relevant to cortical circuit vulnerability.

neuroscience↗

bioRxiv2024

TAM receptors mediate the Fpr2-driven pain resolution and fibrinolysis after nerve injury

Nerve injury causes neuropathic pain and multilevel nerve barrier disruption. Nerve barriers consist of perineurial, endothelial, and myelin barriers. So far, it is unclear whether resealing nerve barriers fosters pain resolution and recovery. To this end, we analysed the nerve barrier property portfolio, pain behaviour battery, and lipidomics for precursors of specialized pro-resolving meditators (SPMs) and their receptors in chronic constriction injury of rat sciatic nerve to identify targets for pain resolution by resealing the selected nerve barriers. Of the three nerve barriers - perineurium, capillaries, and myelin - only capillary tightness specifically against larger molecules, such as fibrinogen, recuperated with pain resolution. Fibrinogen immunoreactivity was not only elevated in rats at the time of neuropathic pain but also in nerve biopsies from patients with (but not without) painful polyneuropathy indicating that sealing of the vascular barrier might be novel approach in pain treatment. 15R-HETE (hydroxyeicosatetraenoic acid), a precursor of aspirin-triggered lipoxin A4, were specifically upregulated at the beginning of pain resolution. Repeated local application of resolvin D1-laden nanoparticles or Fpr2 agonists sex-independently resulted in accelerated pain resolution and fibrinogen removal. Clearing macrophages (Cd206) and fibrinolytic pathways (Plat) were also induced while inflammation (Tnf) and inflammasomes (Nlrp3) were unaffected by this treatment. Blocking TAM receptors (Tyro3, Axl, and Mer) and tyrosine kinase receptors linking haemostasis and inflammation completely inhibited all the effects. In summary, nanoparticles can be used as transporters for fleeting lipids, such as SPMs, and therefore expand the array of possible therapeutic agents. Thus, the Fpr2-Cd206-TAM receptor axis may be a suitable target for strengthening the capillary barrier, removing endoneurial fibrinogen, and boosting pain resolution in patients with chronic neuropathic pain.

neuroscience↗

bioRxiv2024

Overexpression of the schizophrenia risk gene C4 in PV cells drives sex-dependent behavioral deficits and circuit dysfunction.

Fast-spiking parvalbumin (PV)-positive cells are key players in orchestrating pyramidal neuron activity, and their dysfunction is consistently observed in myriad brain diseases. To understand how immune complement dysregulation - a prevalent locus of brain disease etiology - in PV cells may drive disease pathogenesis, we have developed a transgenic mouse line that permits cell-type specific overexpression of the schizophrenia-associated complement component 4 (C4) gene. We found that overexpression of mouse C4 (mC4) in PV cells causes sex-specific behavioral alterations and concomitant deficits in synaptic connectivity and excitability of PV cells of the prefrontal cortex. Using a computational network, we demonstrated that these microcircuit deficits led to hyperactivity and disrupted neural communication. Finally, pan-neuronal overexpression of mC4 failed to evoke the same deficits in behavior as PV-specific mC4 overexpression, suggesting that C4 perturbations in fast-spiking neurons are more harmful to brain function than pan-neuronal alterations. Together, these results provide a causative link between C4 and the vulnerability of PV cells in brain disease.

neuroscience↗

bioRxiv2023

C4 induces pathological synaptic loss by impairing AMPAR trafficking.

During development, activation of the complement pathway, an extracellular proteolytic cascade, results in microglia-dependent synaptic elimination via complement receptor 3 (CR3). Here, we report that decreased connectivity caused by overexpression of C4 (C4-OE), a schizophrenia-associated gene, is CR3 independent. Instead, C4-OE triggers GluR1 degradation through an intracellular mechanism involving endosomal trafficking protein SNX27, resulting in pathological synaptic loss. Moreover, the connectivity deficits associated with C4-OE were rescued by increasing levels of SNX27, linking excessive complement activity to an intracellular endolysosomal recycling pathway affecting synapses.

neuroscience↗

bioRxiv2020

Chromatin potential identified by shared single cell profiling of RNA and chromatin

Cell differentiation and function are regulated across multiple layers of gene regulation, including the modulation of gene expression by changes in chromatin accessibility. However, differentiation is an asynchronous process precluding a temporal understanding of the regulatory events leading to cell fate commitment. Here, we developed SHARE-seq, a highly scalable approach for measurement of chromatin accessibility and gene expression within the same single cell. Using 34,774 joint profiles from mouse skin, we develop a computational strategy to identify cis-regulatory interactions and define Domains of Regulatory Chromatin (DORCs), which significantly overlap with super-enhancers. We show that during lineage commitment, chromatin accessibility at DORCs precedes gene expression, suggesting changes in chromatin accessibility may prime cells for lineage commitment. We therefore develop a computational strategy (chromatin potential) to quantify chromatin lineage-priming and predict cell fate outcomes. Together, SHARE-seq provides an extensible platform to study regulatory circuitry across diverse cells within tissues.

genomics↗

bioRxiv2019

Claudin-12 deficiency causes nerve barrier breakdown, mechanical hypersensitivity and painful neuropathy

Peripheral nerves and their axons are shielded by the blood-nerve and the myelin barrier, but understanding of how these barriers impact nociception is limited. Here, we identified a regulatory axis of the tight junction protein claudin-12, sex-dependently controlling perineurial and myelin barrier integrity. In nerve biopsies, claudin-12 in Schwann cells was lost in male and postmenopausal female patients with painful but not painless polyneuropathy. Global Cldn12 gene-knockout selectively increased perineurial/myelin barrier leakage, damaged tight junction protein expression and morphology, increased proinflammatory cytokines and induced mechanical hypersensitivity in naive and neuropathic male mice, respectively. Other barriers and neurological function remained intact. In vitro transfection studies documented claudin-12 plasma membrane localisation without interaction with other tight junction proteins or intrinsic sealing properties. Rather, claudin-12 had a regulatory tight junction protein function on the myelin barrier via the morphogen SHH in vivo in Cldn12-KO and after local siRNA knockdown. Fertile female mice were completely protected. Collectively, these studies reveal the critical role of claudin-12 maintaining the myelin barrier and highlight restoration of the claudin-12/SHH pathway as a potential target for painful neuropathy.

neuroscience↗

bioRxiv2017

Deep convolution neural networks allow analysis of cell motility during stem cell differentiation and neoplastic transformation

Cells in culture display diverse motility behaviors that may reflect differences in cell state and function, providing motivation to discriminate between different motility behaviors. Current methods to do so rely upon manual feature engineering. However, the types of features necessary to distinguish between motility behaviors can vary greatly depending on the biological context, and it is not always clear which features may be most predictive in each setting for distinguishing particular cell types or disease states. Convolutional neural networks (CNNs) are machine learning models allowing for relevant features to be learned directly from spatial data. Similarly, recurrent neural networks (RNNs) are a class of models capable of learning long term temporal dependencies. Given that cell motility is inherently spacio-temporal data, we present an approach utilizing both convolutional and long- short-term memory (LSTM) recurrent neural network units to analyze cell motility data. These RNN models provide accurate classification of simulated motility and experimentally measured motility from multiple cell types, comparable to results achieved with hand-engineered features. The variety of cell motility differences we can detect suggests that the algorithm is generally applicable to additional cell types not analyzed here. RNN autoencoders based on the same architecture are capable of learning motility features in an unsupervised manner and capturing variation between myogenic cells in the latent space. Adapting these RNN models to motility prediction, RNNs are capable of predicting muscle stem cell motility from past tracking data with performance superior to standard motion prediction models. This advance in cell motility prediction may be of practical utility in cell tracking applications.

bioinformatics↗