Stimulus-specific combinatorial functionality of neuronal c-fos enhancers

Transcription and epigenetic factor dynamics in neuronal activity-dependent gene regulation

Neuronal activity, including sensory-evoked and spontaneous firing, regulates the expression of a subset of genes known as activity-dependent genes. A key issue in this process is the activation and accumulation of transcription factors (TFs), which bind to cis-elements at specific enhancers and promoters, ultimately driving RNA synthesis through transcription machinery. Epigenetic factors such as histone modifiers also play a crucial role in facilitating the specific binding of TFs. Recent evidence from epigenome analyses and imaging studies have revealed intriguing mechanisms: the default chromatin structure at activity-dependent genes is formed independently of neuronal activity, while neuronal activity modulates spatiotemporal dynamics of TFs and their interactions with epigenetic factors (EFs). In this article we review new insights into activity-dependent gene regulation that affects brain development and plasticity.

Mechanism of arsenic regulation of mitochondrial damage and autophagy induced synaptic damage through SIRT1 and protective effect of melatonin in HT22 cell

Arsenic (As), a widespread environmental pollutant, can induce severe neurological damage worldwide; however, the underlying mechanisms remain unclear. Sirtuin 1 (SIRT1) has been reported to exert neuroprotective effects against various neurological diseases by resisting mitochondrial damage and autophagy through deacetylation. In this study, we established a model of HT22 cells exposed to NaAsO2 and examined the levels of mitochondrial, autophagy, and synaptic damage in HT22 cells and HT22 cells with high expression of SIRT1 (pre-treated with the agonist SRT1720) 24 h after exposure. Our results suggest that NaAsO2 exposure induces down-regulation of SIRT1, causing mitochondrial damage and activation of autophagy, which in turn leads to synaptic damage. Notably, melatonin (Mel) intervention upregulated SIRT1 and attenuated mitochondrial damage and autophagy, restoring synaptic damage. In conclusion, the results of the present study indicate that As causes neurotoxicity by decreasing SIRT1 production, causing mitochondrial damage and activating autophagy, which provides fundamental data for further study of arsenic neurotoxicity. In addition, blocking this pathway attenuated the synaptic damage of arsenic exposure, which provides a new therapeutic avenue for arsenic neurotoxicity.

Molecular and genetic mechanisms of plasticity in addiction

Drugs of abuse result in well-characterized changes in synapse function and number in brain reward regions such as the nucleus accumbens. However, recent reports demonstrate that only a small fraction of neurons in the nucleus accumbens are activated in response to psychostimulants such as cocaine. While these "ensemble" neurons are marked by drug-related transcriptional changes in immediate early genes, the mechanisms that ultimately link these early changes to enduring molecular alterations in the same neurons are less clear. In this review, we 1) describe potential mechanisms underlying regulation of diverse plasticity-related gene programs across drug-activated ensembles, 2) discuss factors conferring ensemble recruitment bias within seemingly homogeneous populations, and 3) speculate on the role of chromatin and epigenetic modifiers in gating metaplastic state transitions that contribute to addiction.

Chromatin regulation of neuronal activity-dependent gene programs in circuit formation and plasticity

Neuronal activity-dependent transcription is crucial for the development and plasticity of neuronal circuits. At the chromatin level, the induction of neuronal activity-regulated genes is orchestrated through various mechanisms, including the deposition of histone modifications at regulatory elements, the binding of transcriptional activators and repressors, chromatin remodeling, and the control of 3D genome architecture. Here, we review our current understanding of how chromatin mechanisms regulate temporally distinct transcriptional waves following neuronal stimulation and allow neurons to mount cell type-specific and stimulus-specific transcriptional responses. We also highlight a specific epigenetic mechanism in developing neurons that maintains immediate early genes (IEGs) in an inactive though poised state, while simultaneously preparing them for rapid activation in response to sensory stimulation. We discuss how chromatin regulation mechanisms play a crucial role in controlling activity-regulated gene expression, enabling the implementation of precise gene expression programs during different stages of neural circuit development and plasticity.

Analgesic Mechanism of Emodin in Neuropathic Pain Through Inhibiting P2X4 Purinoceptor Signaling

Neuropathic pain (NeP) is a most intractable health problem due to its unsatisfactory treatment effect. Emodin, a natural anthraquinone derivative extracted from Rheum palmatum and Polygonam cuspidatum, exhibits the analgesic effects in various NeP models. However, the underlying mechanisms remain elusive. This study employed whole transcriptome sequencing and metabolomics to elucidate emodin's analgesic mechanism in the spinal cord of chronic constriction injury (CCI) rats. Fifteen-day emodin treatment reversed hyperalgesia and deficit of sciatic nerve function induced by CCI and significantly decreased the concentrations of TNF-α, IL- 1β, IL- 6, IL- 18, and BDNF in the spinal cord of the CCI rats. Transcriptome sequencing revealed altered expression of 85 mRNAs in the spinal cord of emodin-treated and CCI rats, with 53 mRNAs upregulated and 32 mRNAs downregulated. Notably, seven genes (P2RX4, CXCL10, ALOX5, SCN4 A, AURKB, AQP9) overlapped with established NeP targets. Untargeted metabolomic analyses identified 67 significantly altered metabolites (46 upregulated, 32 downregulated) in the spinal cord upon emodin treatment. Integrative analysis highlighted shared pathways between differentially expressed genes and metabolites, including arachidonic acid metabolism, cAMP signaling pathway, and Fc epsilon RI signaling pathway. Western blot and immunofluorescent staining further proved the decreased expression of IBA1, P2X4R, p38 MAPK, p-p38 MAPK, NF-κB, p-NF-κB, and TNF-α, IL- 1β. In conclusion, this study demonstrated that emodin played the analgesic effect in the CCI rats, possibly through suppression of P2X4 purinoceptor signaling in spinal microglia, suggesting a potential therapeutic target for NeP.

Activation of GABAergic neurons in the dorsal raphe nucleus alleviates hyperalgesia induced by ovarian hormone withdrawal

ABSTRACT

Menopausal and postmenopausal women, characterized by a significant reduction in ovarian hormones, have a high prevalence of chronic pain with great pain intensity. However, the underlying mechanism of hyperalgesia induced by ovarian hormone withdrawal remains poorly understood. Here, we report that decreases in the activity and excitability of GABAergic neurons in the dorsal raphe nucleus (DRN) are associated with hyperalgesia induced by ovariectomy in mice. Supplementation with 17β-estradiol, but not progesterone, is sufficient to increase the mechanical pain threshold in ovariectomized (OVX) mice and the excitability of DRN GABAergic (DRN GABA ) neurons. Moreover, activation of the DRN GABA neurons projecting to the lateral parabrachial nucleus was critical for alleviating hyperalgesia in OVX mice. These findings show the essential role of DRN GABA neurons and their modulation by estrogen in regulating hyperalgesia induced by ovarian hormone withdrawal, providing therapeutic basis for the treatment of chronic pain in physiological or surgical menopausal women.

Compensatory enhancement of orexinergic system functionality induced by amyloid-β protein: a neuroprotective response in Alzheimer's disease

Background

Amyloid-β protein (Aβ) accumulation is a defining characteristic of Alzheimer's disease (AD), resulting in neurodegeneration and a decline in cognitive function. Given orexin's well-documented role in enhancing memory and cognition, this study investigates its potential to regulate Aβ-induced neurotoxicity, offering new perspectives into AD management.

Methods

This paper simulated Aβ accumulation in the hippocampus of AD patients by administering Aβ1-42 oligomers into the bilateral hippocampal dentate gyrus of ICR mice. Inflammatory cytokines (IL-6, TNF-α) and orexin-A levels were measured by ELISA. Additionally, the excitability of orexinergic neurons was assessed by IHC targeting c-Fos expression. These methodologies evaluated the Aβ-induced neuroinflammation, orexinergic system functionality, and dexamethasone's (Dex) effects on these processes.

Results

Injection of Aβ1-42 oligomer resulted in elevated levels of IL-6, TNF-α, and orexin-A in the hippocampus, as well as increased excitability of orexinergic neurons in the lateral hypothalamus (LH). Dex treatment reduced neuroinflammation, causing a reduction in orexin-A levels and the excitability of orexinergic neurons.

Conclusion

Aβ-induced neuroinflammation is accompanied by enhanced levels of orexin-A and orexinergic neuron excitability. These findings suggest that the enhanced functionality of the orexinergic system may become a compensatory neuroprotective mechanism to counteract neuroinflammation and enhance cognitive function.

Scopolamine affects fear learning and social recognition in adult zebrafish

Scopolamine is the secondary metabolite of the Datura stramonium and act as a muscarinic receptor antagonist. Previous studies showed that scopolamine caused attention and memory deficit. However, the effects of scopolamine on specific cognitive functions, such as fear learning and social recognition, remain poorly understood. Here, we demonstrate the effects of scopolamine on fear learning, social memory, and neural activity in zebrafish, providing a novel perspective on its impact on cognitive and social behaviors. Here, we used equal number of male and female zebrafish as an animal model and performed a series of behavioral tests after treatment with scopolamine (100 µM and 200 µM) for 1 h to evaluate social and cognitive functions. Treatment with scopolamine increased locomotion activity, reduced the level of anxiety in the novel tank diving test, and impaired memory retrieval in the active avoidance test. Scopolamine also increased the preference for newly introduced fish in the social recognition test. In situ hybridization of c-fos mRNA showed that scopolamine decreased the neural activity of the telencephalic regions that are crucial for social, cognitive, and memory functions. Our results demonstrate the effects of scopolamine on fear learning and social recognition in adult zebrafish.

Dorsal bed nucleus of the stria terminalis GABA neurons are necessary for chronic unpredictable stress-induced depressive behaviors in adolescent male mice

BACKGROUND

Previous studies have shown that neurons in the Bed Nucleus of the Stria Terminalis (BNST) respond to stress and play a key role in mental health. However, the cellular bases of BNST in adolescent depression remain elusive.

METHODS

Male C57BL/6 mice were randomly assigned to the control (Ctrl) or chronic unpredictable stress (CUS) groups. The CUS mice, aged 28 days, were subjected to diverse stressors at various times of the day for 12 days. Depression-like behaviors were assessed through the sucrose preference test (SPT) and tail suspension test (TST). Immunostaining was used to investigate the neural activity and subtypes in the brain. A chemogenetic tool was conducted to examine the role of specific neural activity in CUS-induced depression-like behaviors.

RESULTS

CUS led to a significant decrease in preference for sucrose solution in the SPT and increased immobility time in the TST. C-Fos immunostaining showed hyperactivity of the GABAergic neurons within the dorsal BNST (dBNSTGABA). Chemogenetic activation of dBNSTGABA neurons increased depression-like behaviors. Conversely, chemogenetic inhibition of dBNSTGABA neurons led to a decrease in CUS-induced depression.

CONCLUSIONS

These results suggest that adolescent CUS induces hyperactivity of dBNSTGABA neurons, subsequently giving rise to depression-like behaviors and that reducing dBNSTGABA neuronal activity might constitute a novel and efficacious therapeutic approach for adolescent depression.

Epigenetics in Learning and Memory

In animals, memory formation and recall are essential for their survival and for adaptations to a complex and often dynamically changing environment. During memory formation, experiences prompt the activation of a selected and sparse population of cells (engram cells) that undergo persistent physical and/or chemical changes allowing long-term memory formation, which can last for decades. Over the past few decades, important progress has been made on elucidating signaling mechanisms by which synaptic transmission leads to the induction of activity-dependent gene regulation programs during the different phases of learning (acquisition, consolidation, and recall). But what are the molecular mechanisms that govern the expression of immediate-early genes (IEGs; c-fos, Npas4) and plasticity-related genes (PRGs; Dlg4/PSD95 and Grin2b/NR2B) in memory ensemble? Studies in relatively simple in vitro and in vivo neuronal model systems have demonstrated that synaptic activity during development, or when induced by chemical stimuli (i.e., cLTP, KCl, picrotoxin), activates the NMDAR-Ca2+-CREB signaling pathway that upregulates gene expression through changes in the epigenetic landscape (i.e., histone marks and DNA methylation) and/or 3D chromatin organization. The data support a model in which epigenetic modifications in promoters and enhancers facilitate the priming and activation of these regulatory regions, hence leading to the formation of enhancer-promoter interactions (EPIs) through chromatin looping. The exploration of whether similar molecular mechanisms drive gene expression in learning and memory has presented notable challenges due to the distinct phases of learning and the activation of only sparse population of cells (the engram). Consequently, such studies demand precise temporal and spatial control. By combining activity-dependent engram tagging strategies (i.e., TRAP mice) with multi-omics analyses (i.e., RNA-seq, ChiP-seq, ATAC-seq, and Hi-C), it has been recently possible to associate changes in the epigenomic landscape and/or 3D genome architecture with transcriptional waves in engram cells of mice subjected to contextual fear conditioning (CFC), a relevant one-shot Pavlovian learning task. These studies support the role of specific epigenetic mechanisms and of the 3D chromatin organization during the control of gene transcription waves in engram cells. Advancements in our comprehension of the molecular mechanisms driving memory ensemble will undoubtedly play a crucial role in the development of better-targeted strategies to tackle cognitive diseases, including Alzheimer's disease and frontotemporal dementia, among other information-processing disorders.

Therapeutic Potential of Cinnamon Oil: Chemical Composition, Pharmacological Actions, and Applications

Cinnamon oil, an essential oil extracted from plants of the genus Cinnamomum, has been highly valued in ancient Chinese texts for its medicinal properties. This review summarizes the chemical composition, pharmacological actions, and various applications of cinnamon oil, highlighting its potential in medical and industrial fields. By systematically searching and evaluating studies from major scientific databases including Web of Science, PubMed, and ScienceDirect, we provide a comprehensive analysis of the therapeutic potential of cinnamon oil. Research indicates that cinnamon oil possesses a wide range of pharmacological activities, covering antibacterial, anti-inflammatory, anti-tumor, and hypoglycemic effects. It is currently an active ingredient in over 500 patented medicines. Cinnamon oil has demonstrated significant inhibitory effects against various pathogens comprising Staphylococcus aureus, Salmonella, and Escherichia coli. Its mechanisms of action include disrupting cell membranes, inhibiting ATPase activity, and preventing biofilm formation, suggesting its potential as a natural antimicrobial agent. Its anti-inflammatory properties are evidenced by its ability to suppress inflammatory markers like vascular cell adhesion molecules and macrophage colony-stimulating factors. Moreover, cinnamon oil has shown positive effects in lowering blood pressure and improving metabolism in diabetic patients by enhancing glucose uptake and increasing insulin sensitivity. The main active components of cinnamon oil include cinnamaldehyde, cinnamic acid, and eugenol, which play key roles in its pharmacological effects. Recently, the applications of cinnamon oil in industrial fields, including food preservation, cosmetics, and fragrances, have also become increasingly widespread. Despite the extensive research supporting its medicinal value, more clinical trials are needed to determine the optimal dosage, administration routes, and possible side effects of cinnamon oil. Additionally, exploring the interactions between cinnamon oil and other drugs, as well as its safety in different populations, is crucial. Considering the current increase in antibiotic resistance and the demand for sustainable and effective medical treatments, this review emphasizes the necessity for further research into the mechanisms and safety of cinnamon oil to confirm its feasibility as a basis for new drug development. In summary, as a versatile natural product, cinnamon oil holds broad application prospects and is expected to play a greater role in future medical research and clinical practice.

A long noncoding eRNA forms R-loops to shape emotional experience-induced behavioral adaptation

Emotional experiences often evoke neural plasticity that supports adaptive changes in behavior, including maladaptive plasticity associated with mood and substance use disorders. These adaptations are supported in part by experience-dependent activation of immediate-early response genes, such as Npas4 (neuronal PAS domain protein 4). Here we show that a conserved long noncoding enhancer RNA (lnc-eRNA), transcribed from an activity-sensitive enhancer, produces DNA:RNA hybrid R-loop structures that support three-dimensional chromatin looping between enhancer and proximal promoter and rapid Npas4 gene induction. Furthermore, in mouse models, Npas4 lnc-eRNA and its R-loop are required for the development of behavioral adaptations produced by chronic psychosocial stress or cocaine exposure, revealing a potential role for this regulatory mechanism in the transmission of emotional experiences.

Enriched Environment Reduces Seizure Susceptibility via Entorhinal Cortex Circuit Augmented Adult Neurogenesis

Enriched environment (EE), characterized by multi-sensory stimulation, represents a non-invasive alternative for alleviating epileptic seizures. However, the mechanism by which EE exerts its therapeutic impact remains incompletely understood. Here, it is elucidated that EE mitigates seizure susceptibility through the augmentation of adult neurogenesis within the entorhinal cortex (EC) circuit. A substantial upregulation of adult hippocampal neurogenesis concomitant with a notable reduction in seizure susceptibility has been found following exposure to EE. EE-enhanced adult-born dentate granule cells (abDGCs) are functionally activated during seizure events. Importantly, the selective activation of abDGCs mimics the anti-seizure effects observed with EE, while their inhibition negates these effects. Further, whole-brain c-Fos mapping demonstrates increased activity in DG-projecting EC CaMKIIα+ neurons in response to EE. Crucially, EC CaMKIIα+ neurons exert bidirectional modulation over the proliferation and maturation of abDGCs that can activate local GABAergic interneurons; thus, they are essential components for the anti-seizure effects mediated by EE. Collectively, this study provides compelling evidence regarding the circuit mechanisms underlying the effects of EE treatment on epileptic seizures, shedding light on the involvement of the EC-DG circuit in augmenting the functionality of abDGCs. This may help for the translational application of EE for epilepsy management.

The Involvement of the Ventral Tegmental Area in the Electroacupuncture Alleviation of Anxiety-Like Behaviors Induced by Chronic Restraint Stress in Mice

Emotional stress is a significant environmental risk factor for various mental health disabilities, such as anxiety. Electroacupuncture (EA) has been demonstrated to have pronounced anxiolytic effects. However, the neural mechanisms underlying these effects and their contribution to behavioral deficits remain poorly understood. Here, we addressed these issues using a classical mouse anxiety model induced by chronic restraint stress (CRS).Anxiety-like behaviors were evaluated with the open field test and elevated plus maze. Neuronal activation in various brain regions was marked using c-Fos, followed by calculations of interregional correlation to characterize a network that became functionally active following EA at the HT7 acupoint (EA-HT7). We selected the hub regions and further investigated their functions and connections in regulating anxiety-like behaviors by using a combination of chemogenetic manipulations and behavioral testing. CRS exposure induced anxiety-like behaviors. Interestingly, EA-HT7 mitigated these behavioral abnormalities. The c-Fos expression in 30 brain areas revealed a vital brain network for acupuncture responsiveness in naïve mice. Neural activity in the NAcSh (nucleus accumbens shell), BNST (bed nucleus of the stria terminalis), VMH (Ventromedial Hypothalamus), ARC (arcuate nucleus), dDG (dorsal dentate gyrus), and VTA (ventral tegmental area) was significantly altered following acupuncture. Notably, both c-Fos immunostaining and brain functional connectivity analysis revealed the significant activation of VTA following EA-HT7. Interestingly, blocking the VTA eliminated the anxiolytic effects of EA-HT7, whereas chemogenetic activation of the VTA replicated the therapeutic effects of EA-HT7. EA-HT7 has demonstrated benefits in treating anxiety and enhances brain functional connectivity. The VTA is functionally associated with the anxiolytic effects of EA-HT7.

Effect of Voluntary Wheel Running on Anxiety- and Depression-Like Behaviors in Fluoride-Exposed Mice

Fluoride, an environmental toxicant, could induce endoplasmic reticulum stress (ERS) in neuronal cells ultimately leading to apoptosis and emotional dysfunction. Meanwhile, voluntary wheel running contributes to mitigate anxiety and depression. Our investigation aimed to study the effect of voluntary wheel running on anxiety- and depression-like behaviors in fluoride-exposure mice. The results showed that exposure to 100 mg/L sodium fluoride (NaF) for 6 months can induce anxiety- and depression-like behavior in mice. Fluorosis mice subjected to voluntary wheel running have less anxiety- and depression-like behaviors. Nissl and TUNEL staining demonstrated that fluoride led to a reduced proportion of Nissl body area in the cerebral cortex and an increased apoptotic ratio of nerve cells in the cerebral cortex. In contrast, these pathologic damages were improved in voluntary wheel running mice exposed to NaF. Moreover, the expressions of mRNA in the cerebral cortex GABA, GAD65, GAD67, DR, vGLU, 5-HT1A, BDNF, NMDAR1, and Bcl2 were downregulated and the levels of c-fos, GRP78, PERK, eIF2α, CHOP, Caspase-12, and Caspase-3 mRNA were upregulated in mice exposed to fluoride. NaF treatment had increased the PERK, ATF6, IRE1, p-eIF2α, and Caspase-3 protein levels and reduced the expressions of proteins, including GAD67, VGAT, BDNF, NMDAR1, PSD95, and SYN. By contrast, fluorosis mice subjected to voluntary wheel running enhanced the expression of GAD65, GAD67, VGAT, and neuroplasticity-related proteins in mice and inhibited the PERK-CHOP pathway. It is worth noting that the correlation between the amount of exercise and the behavioral indicators as well as neurotransmitter levels was found. In conclusion, voluntary wheel running inhibits the fluoride-induced ERS and GRP78 expression through the PERK-CHOP pathway and plays an anti-apoptotic role, ultimately ameliorating emotional dysfunction in NaF-exposed mice.

Large-scale analysis of the integration of enhancer-enhancer signals by promoters

Genes are often regulated by multiple enhancers. It is poorly understood how the individual enhancer activities are combined to control promoter activity. Anecdotal evidence has shown that enhancers can combine sub-additively, additively, synergistically, or redundantly. However, it is not clear which of these modes are more frequent in mammalian genomes. Here, we systematically tested how pairs of enhancers activate promoters using a three-way combinatorial reporter assay in mouse embryonic stem cells. By assaying about 69,000 enhancer-enhancer-promoter combinations we found that enhancer pairs generally combine near-additively. This behaviour was conserved across seven developmental promoters tested. Surprisingly, these promoters scale the enhancer signals in a non-linear manner that depends on promoter strength. A housekeeping promoter showed an overall different response to enhancer pairs, and a smaller dynamic range. Thus, our data indicate that enhancers mostly act additively, but promoters transform their collective effect non-linearly.

A tissue bandage for pelvic ganglia injury

Neurogenic bladder often occurs after pelvic ganglia injury. Its symptoms, like severe urinary retention and incontinence, have a significant impact on individuals' quality of life. Unfortunately, there are currently no effective treatments available for this type of injury. Here, we designed a fiber-enhanced tissue bandage for injured pelvic ganglia. Tight junctions formed in tissue bandages create a mini tissue structure that enhances resistance in an in vivo environment and delivers growth factors to support the healing of ganglia. Strength fibers are similar to clinical bandages and guarantee ease of handling. Furthermore, tissue bandages can be stored at low temperatures over 5 months without compromising cell viability, meeting the requirements for clinical products. A tissue bandage was applied to a male rat with a bilateral major pelvic ganglia crush injury. Compared to the severe neurogenic bladder symptoms observed in the injury and scaffold groups, tissue bandages significantly improved bladder function. We found that tissue bandage increases resistance to mechanical injury by boosting the expression of cytoskeletal proteins within the major pelvic ganglia. Overall, tissue bandages show promise as a practical therapeutic approach for ganglia repair, offering hope for developing more effective treatments for this thorny condition.

Transcriptome-Wide Profiling of Nascent RNA in Neurons with Enriched H3K27ac Signal Elevates eRNA Identification Efficiency

Growing evidence suggests that activity-dependent gene expression is crucial for neuronal plasticity and behavioral experience. Enhancer RNAs (eRNAs), a class of long noncoding RNAs, play a key role in these processes. However, eRNAs are highly dynamic and are often present at lower levels than their corresponding mRNAs, making them difficult to detect using total RNA-seq techniques. Nascent RNA sequencing, which separates nascent RNAs from the steady-state RNA population, has been shown to increase the ability to detect activity-induced eRNAs with a higher signal-to-noise ratio. However, there is a lack of bioinformatic tools or pipelines for detecting eRNAs utilizing nascent RNA-seq and other multiomics data sets. In this study, we addressed this gap by developing a novel bioinformatic framework, e-finder, for finding eRNAs and have made it available to the scientific community. Additionally, we reanalyzed our previous nascent RNA sequencing data and compared them with total RNA-seq data to identify activity-regulated RNAs in neuronal cell populations. Using H3K27 acetylome data, we characterized activity-dependent eRNAs that drive the transcriptional activity of the target genes. Our analysis identified a subset of eRNAs involved in mediating synapse organization, which showed increased activity-dependent transcription after the potassium chloride stimulation. Notably, our data suggest that nascent RNA-seq with an enriched H3K27ac signal exhibits high resolution to identify potential eRNAs in response to membrane depolarization. Our findings uncover the role of the eRNA-mediated gene activation network in neuronal systems, providing new insights into the molecular processes characterizing neurological diseases.

Identification of Potential Key Genes for the Comorbidity of Myasthenia Gravis With Thymoma by Integrated Bioinformatics Analysis and Machine Learning

Background

Thymoma is a key risk factor for myasthenia gravis (MG). The purpose of our study was to investigate the potential key genes responsible for MG patients with thymoma.

Methods

We obtained MG and thymoma dataset from GEO database. Differentially expressed genes (DEGs) were determined and functional enrichment analyses were conducted by R packages. Weighted gene co-expression network analysis (WGCNA) was used to screen out the crucial module genes related to thymoma. Candidate genes were obtained by integrating DEGs of MG and module genes. Subsequently, we identified several candidate key genes by machine learning for diagnosing MG patients with thymoma. The nomogram and receiver operating characteristics (ROC) curves were applied to assess the diagnostic value of candidate key genes. Finally, we investigated the infiltration of immunocytes and analyzed the relationship among key genes and immune cells.

Results

We obtained 337 DEGs in MG dataset and 2150 DEGs in thymoma dataset. Biological function analyses indicated that DEGs of MG and thymoma were enriched in many common pathways. Black module (containing 207 genes) analyzed by WGCNA was considered as the most correlated with thymoma. Then, 12 candidate genes were identified by intersecting with MG DEGs and thymoma module genes as potential causes of thymoma-associated MG pathogenesis. Furthermore, five candidate key genes (JAM3, MS4A4A, MS4A6A, EGR1, and FOS) were screened out through integrating least absolute shrinkage and selection operator (LASSO) regression and Random forest (RF). The nomogram and ROC curves (area under the curve from 0.833 to 0.929) suggested all five candidate key genes had high diagnostic values. Finally, we found that five key genes and immune cell infiltrations presented varying degrees of correlation.

Conclusions

Our study identified five key potential pathogenic genes that predisposed thymoma to the development of MG, which provided potential diagnostic biomarkers and promising therapeutic targets for MG patients with thymoma.

Neuronal enhancers fine-tune adaptive circuit plasticity

Neuronal activity-regulated gene expression plays a crucial role in sculpting neural circuits that underpin adaptive brain function. Transcriptional enhancers are now recognized as key components of gene regulation that orchestrate spatiotemporally precise patterns of gene transcription. We propose that the dynamics of enhancer activation uniquely position these genomic elements to finely tune activity-dependent cellular plasticity. Enhancer specificity and modularity can be exploited to gain selective genetic access to specific cell states, and the precise modulation of target gene expression within restricted cellular contexts enabled by targeted enhancer manipulation allows for fine-grained evaluation of gene function. Mounting evidence also suggests that enduring stimulus-induced changes in enhancer states can modify target gene activation upon restimulation, thereby contributing to a form of cell-wide metaplasticity. We advocate for focused exploration of activity-dependent enhancer function to gain new insight into the mechanisms underlying brain plasticity and cognitive dysfunction.

Noninvasive closed-loop acoustic brain-computer interface for seizure control

Rationale: The brain-computer interface (BCI) is core tasks in comprehensively understanding the brain, and is one of the most significant challenges in neuroscience. The development of novel non-invasive neuromodulation technique will drive major innovations and breakthroughs in the field of BCI. Methods: We develop a new noninvasive closed-loop acoustic brain-computer interface (aBCI) for decoding the seizure onset based on the electroencephalography and triggering ultrasound stimulation of the vagus nerve to terminate seizures. Firstly, we create the aBCI system and decode the onset of seizure via a multi-level threshold model based on the analysis of wireless-collected electroencephalogram (EEG) signals recorded from above the hippocampus. Then, the different acoustic parameters induced acoustic radiation force were used to stimulate the vagus nerve in a rat model of epilepsy-induced by pentylenetetrazole. Finally, the results of epileptic EEG signal triggering ultrasound stimulation of the vagus nerve to control seizures. In addition, the mechanism of aBCI control seizures were investigated by real-time quantitative polymerase chain reaction (RT-qPCR). Results: In a rat model of epilepsy, the aBCI system selectively actives mechanosensitive neurons in the nodose ganglion while suppressing neuronal excitability in the hippocampus and amygdala, and stops seizures rapidly upon ultrasound stimulation of the vagus nerve. Physical transection or chemical blockade of the vagus nerve pathway abolish the antiepileptic effects of aBCI. In addition, aBCI shows significant antiepileptic effects compared to conventional vagus nerve electrical stimulation in an acute experiment. Conclusions: Closed-loop aBCI provides a novel, safe and effective tool for on-demand stimulation to treat abnormal neuronal discharges, opening the door to next generation non-invasive BCI.

Light-Dependent Circadian Rhythm Governs O-GlcNAc Cycling to Influence Cognitive Function in Adult Zebrafish

This study explores the 24-h rhythmic cycle of protein O-GlcNAcylation within the brain and highlights its crucial role in regulating the circadian cycle and neuronal function based on zebrafish as an animal model. In our experiments, disruption of the circadian rhythm, achieved through inversion of the light-dark cycle or daytime melatonin treatment, not only impaired the rhythmic changes of O-GlcNAcylation along with altering expression patterns of O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA) in zebrafish brain but also significantly impeded learning and memory function. In particular, circadian disruption affected rhythmic expression of protein O-GlcNAcylation and OGT in the nuclear fraction. Notably, the circadian cycle induces rhythmic alterations in O-GlcNAcylation of H2B histone protein that correspond to changes in H3 trimethylation. Disruption of the cycle interfered with these periodic histone code alterations. Pharmacological inhibition of OGT with OSMI-1 disrupted the wake-sleep patterns of zebrafish without affecting expression of circadian rhythm-regulating genes. OSMI-1 inhibited the expression of c-fos, bdnf, and calm1, key genes associated with brain function and synaptic plasticity, and decreased the binding of O-GlcNAcylated H2B and OGT to promoter regions of these genes. The collective findings support the potential involvement of circadian cycling of the O-GlcNAc histone code in regulating synaptic plasticity and brain function. Overall, data from this study provide evidence that protein O-GlcNAcylation serves as a pivotal posttranslational mechanism integrating circadian signals and neuronal function to regulate rhythmic physiology.

Modulation of Comorbid Chronic Neuropathic Pain and Anxiety-Like Behaviors by Glutamatergic Neurons in the Ventrolateral Periaqueductal Gray and the Analgesic and Anxiolytic Effects of Electroacupuncture

Comorbid chronic neuropathic pain and anxiety is a common disease that represents a major clinical challenge. The underlying mechanisms of chronic neuropathic pain and anxiety are not entirely understood, which limits the exploration of effective treatment methods. Glutamatergic neurons in the ventrolateral periaqueductal gray (vlPAG) have been implicated in regulating pain, but the potential roles of the vlPAG in neuropathic pain-induced anxiety have not been investigated. Herein, whole-cell recording and immunofluorescence showed that the excitability of CamkIIα neurons in the vlPAG (vlPAGCamkIIα+ neurons) was decreased in mice with spared nerve injury (SNI), while electroacupuncture (EA) activated these neurons. We also showed that chemogenetic inhibition of vlPAGCamkIIα+ neurons resulted in allodynia and anxiety-like behaviors in naive mice. Furthermore, chemogenetic activation of vlPAGCamkIIα+ neurons reduced anxiety-like behaviors and allodynia in mice with SNI, and EA had a similar effect in alleviating these symptoms. Nevertheless, EA combined with chemogenetic activation failed to further relieve allodynia and anxiety-like behaviors. Artificial inhibition of vlPAGCamkIIα+ neurons abolished the analgesic and anxiolytic effects of EA. Overall, our study reveals a novel mechanism of neuropathic pain-induced anxiety and shows that EA may relieve comorbid chronic neuropathic pain and anxiety by activating vlPAGCamkIIα+ neurons.

HyperCas12a enables highly-multiplexed epigenome editing screens

Interactions between multiple genes or cis-regulatory elements (CREs) underlie a wide range of biological processes in both health and disease. High-throughput screens using dCas9 fused to epigenome editing domains have allowed researchers to assess the impact of activation or repression of both coding and non-coding genomic regions on a phenotype of interest, but assessment of genetic interactions between those elements has been limited to pairs. Here, we combine a hyper-efficient version of Lachnospiraceae bacterium dCas12a (dHyperLbCas12a) with RNA Polymerase II expression of long CRISPR RNA (crRNA) arrays to enable efficient highly-multiplexed epigenome editing. We demonstrate that this system is compatible with several activation and repression domains, including the P300 histone acetyltransferase domain and SIN3A interacting domain (SID). We also show that the dCas12a platform can perform simultaneous activation and repression using a single crRNA array via co-expression of multiple dCas12a orthologues. Lastly, demonstrate that the dCas12a system is highly effective for high-throughput screens. We use dHyperLbCas12a-KRAB and a ~19,000-member barcoded library of crRNA arrays containing six crRNAs each to dissect the independent and combinatorial contributions of CREs to the dose-dependent control of gene expression at a glucocorticoid-responsive locus. The tools and methods introduced here create new possibilities for highly multiplexed control of gene expression in a wide variety of biological systems.

Integrating hydrogels manipulate ECM deposition after spinal cord injury for specific neural reconnections via neuronal relays

A bioinspired hydrogel composed of hyaluronic acid-graft-dopamine (HADA) and a designer peptide HGF-(RADA)4-DGDRGDS (HRR) was presented to enhance tissue integration following spinal cord injury (SCI). The HADA/HRR hydrogel manipulated the infiltration of PDGFRβ+ cells in a parallel pattern, transforming dense scars into an aligned fibrous substrate that guided axonal regrowth. Further incorporation of NT3 and curcumin promoted axonal regrowth and survival of interneurons at lesion borders, which served as relays for establishing heterogeneous axon connections in a target-specific manner. Notable improvements in motor, sensory, and bladder functions resulted in rats with complete spinal cord transection. The HADA/HRR + NT3/Cur hydrogel promoted V2a neuron accumulation in ventral spinal cord, facilitating the recovery of locomotor function. Meanwhile, the establishment of heterogeneous neural connections across the hemisected lesion of canines was documented in a target-specific manner via neuronal relays, significantly improving motor functions. Therefore, biomaterials can inspire beneficial biological activities for SCI repair.

Nongenetic Precise Neuromodulation and Spatiotemporal Neuroprotection for Epilepsy Therapy via Rationally Designed Multifunctional Nanotransducer

The precise modulation of electrical activity in specific neuronal populations is paramount for rectifying abnormal neurological functions and is a critical element in the therapeutic arsenal for neurological disorders. However, achieving a balance between minimal invasiveness and robust neuroprotection poses a considerable challenge. Herein, we present a nanoneuromodulation strategy integrating neuroprotective features to effectively address epilepsy with minimal invasiveness and enable wireless functionality. Strategically engineered nanotransducer, adorned with platinum (Pt) decoration with titanium disulfide (TiS2) (TiS2/Pt), enables precise modulation of neuronal electrical activity in vitro and in vivo, ensuring exceptional temporal fidelity under millisecond-precision near-infrared (NIR) light pulses irradiation. Concurrently, TiS2/Pt showcase a pronounced enhancement in enzyme-mimicking activity, offering a robust defense against oxidative neurological injury in vitro. Nanotransducer-enabled wireless neuromodulation with biocatalytic neuroprotective capacity is highly effective in alleviating epileptic high-frequency neural activity and diminishing oxidative stress levels, thereby restoring redox equilibrium. This integrated therapeutic approach reduces the severity of epilepsy, demonstrating minimal invasiveness and obviating the requirements for genetic manipulation and optical fiber implantation, while providing an alternative avenue for neurological disorder treatment.

Spinal bestrophin-1 and anoctamin-1 channels have a pronociceptive role in the tactile allodynia induced by REM sleep deprivation in rats

Bestrophin-1 and anoctamin-1 are members of the calcium-activated chloride channels (CaCCs) family and are involved in inflammatory and neuropathic pain. However, their role in pain hypersensitivity induced by REM sleep deprivation (REMSD) has not been studied. This study aimed to determine if anoctamin-1 and bestrophin-1 are involved in the pain hypersensitivity induced by REMSD. We used the multiple-platform method to induce REMSD. REM sleep deprivation for 48 h induced tactile allodynia and a transient increase in corticosterone concentration at the beginning of the protocol (12 h) in female and male rats. REMSD enhanced c-Fos and α2δ-1 protein expression but did not change activating transcription factor 3 (ATF3) and KCC2 expression in dorsal root ganglia and dorsal spinal cord. Intrathecal injection of CaCCinh-A01, a non-selective bestrophin-1 blocker, and T16Ainh-A01, a specific anoctamin-1 blocker, reverted REMSD-induced tactile allodynia. However, T16Ainh-A01 had a higher antiallodynic effect in male than female rats. In addition, REMSD increased bestrophin-1 protein expression in DRG but not in DSC in male and female rats. In marked contrast, REMSD decreased anoctamin-1 protein expression in DSC but not in DRG, only in female rats. Bestrophin-1 and anoctamin-1 promote pain and maintain tactile allodynia induced by REM sleep deprivation in both male and female rats, but their expression patterns differ between the sexes.

Molecular insights into regulatory RNAs in the cellular machinery

It is apparent that various functional units within the cellular machinery are derived from RNAs. The evolution of sequencing techniques has resulted in significant insights into approaches for transcriptome studies. Organisms utilize RNA to govern cellular systems, and a heterogeneous class of RNAs is involved in regulatory functions. In particular, regulatory RNAs are increasingly recognized to participate in intricately functioning machinery across almost all levels of biological systems. These systems include those mediating chromatin arrangement, transcription, suborganelle stabilization, and posttranscriptional modifications. Any class of RNA exhibiting regulatory activity can be termed a class of regulatory RNA and is typically represented by noncoding RNAs, which constitute a substantial portion of the genome. These RNAs function based on the principle of structural changes through cis and/or trans regulation to facilitate mutual RNA‒RNA, RNA‒DNA, and RNA‒protein interactions. It has not been clearly elucidated whether regulatory RNAs identified through deep sequencing actually function in the anticipated mechanisms. This review addresses the dominant properties of regulatory RNAs at various layers of the cellular machinery and covers regulatory activities, structural dynamics, modifications, associated molecules, and further challenges related to therapeutics and deep learning.

An upstream enhancer and MEF2 transcription factors fine-tune the regulation of the Bdnf gene in cortical and hippocampal neurons

The myocyte enhancer factor (MEF2) family of transcription factors, originally discovered for its pivotal role in muscle development and function, has emerged as an essential regulator in various aspects of brain development and neuronal plasticity. The MEF2 transcription factors are known to regulate numerous important genes in the nervous system, including brain-derived neurotrophic factor (BDNF), a small secreted neurotrophin responsible for promoting the survival, growth, and differentiation of neurons. The expression of the Bdnf gene is spatiotemporally controlled by various transcription factors binding to both its proximal and distal regulatory regions. While previous studies have investigated the connection between MEF2 transcription factors and Bdnf, the endogenous function of MEF2 factors in the transcriptional regulation of Bdnf remains largely unknown. Here, we aimed to deepen the knowledge of MEF2 transcription factors and their role in the regulation of Bdnf comparatively in rat cortical and hippocampal neurons. As a result, we demonstrate that the MEF2 transcription factor-dependent enhancer located at -4.8 kb from the Bdnf gene regulates the endogenous expression of Bdnf in hippocampal neurons. In addition, we confirm neuronal activity-dependent activation of the -4.8 kb enhancer in vivo. Finally, we show that specific MEF2 family transcription factors have unique roles in the regulation of Bdnf, with the specific function varying based on the particular brain region and stimuli. Altogether, we present MEF2 family transcription factors as crucial regulators of Bdnf expression, fine-tuning Bdnf expression through both distal and proximal regulatory regions.

Alleviation of migraine related pain and anxiety by inhibiting calcium-stimulating AC1-dependent CGRP in the insula of adult rats

BACKGROUND

Recent animal and clinical findings consistently highlight the critical role of calcitonin gene-related peptide (CGRP) in chronic migraine (CM) and related emotional responses. CGRP antibodies and receptor antagonists have been approved for CM treatment. However, the underlying CGRP-related signaling pathways in the pain-related cortex remain poorly understood.

METHODS

The SD rats were used to establish the CM model by dural infusions of inflammatory soup. Periorbital mechanical thresholds were assessed using von-Frey filaments, and anxiety-like behaviors were observed via open field and elevated plus maze tests. Expression of c-Fos, CGRP and NMDA GluN2B receptors was detected using immunofluorescence and western blotting analyses. The excitatory synaptic transmission was detected by whole-cell patch-clamp recording. A human-used adenylate cyclase 1 (AC1) inhibitor, hNB001, was applied via insula stereotaxic and intraperitoneal injections in CM rats.

RESULTS

The insular cortex (IC) was activated in the migraine model rats. Glutamate-mediated excitatory transmission and NMDA GluN2B receptors in the IC were potentiated. CGRP levels in the IC significantly increased during nociceptive and anxiety-like activities. Locally applied hNB001 in the IC or intraperitoneally alleviated periorbital mechanical thresholds and anxiety behaviors in migraine rats. Furthermore, CGRP expression in the IC decreased after the hNB001 application.

CONCLUSIONS

Our study indicated that AC1-dependent IC plasticity contributes to migraine and AC1 may be a promising target for treating migraine in the future.

Anatomical Substrates of Rapid Eye Movement Sleep Rebound in a Rodent Model of Post-sevoflurane Sleep Disruption

BACKGROUND

Previous research suggests that sevoflurane anesthesia may prevent the brain from accessing rapid eye movement (REM) sleep. If true, then patterns of neural activity observed in REM-on and REM-off neuronal populations during recovery from sevoflurane should resemble those seen after REM sleep deprivation. In this study, the authors hypothesized that, relative to controls, animals exposed to sevoflurane present with a distinct expression pattern of c-Fos, a marker of neuronal activation, in a cluster of nuclei classically associated with REM sleep, and that such expression in sevoflurane-exposed and REM sleep-deprived animals is largely similar.

METHODS

Adult rats and Targeted Recombination in Active Populations mice were implanted with electroencephalographic electrodes for sleep-wake recording and randomized to sevoflurane, REM deprivation, or control conditions. Conventional c-Fos immunohistochemistry and genetically tagged c-Fos labeling were used to quantify activated neurons in a group of REM-associated nuclei in the midbrain and basal forebrain.

RESULTS

REM sleep duration increased during recovery from sevoflurane anesthesia relative to controls (157.0 ± 24.8 min vs. 124.2 ± 27.8 min; P = 0.003) and temporally correlated with increased c-Fos expression in the sublaterodorsal nucleus, a region active during REM sleep (176.0 ± 36.6 cells vs. 58.8 ± 8.7; P = 0.014), and decreased c-Fos expression in the ventrolateral periaqueductal gray, a region that is inactive during REM sleep (34.8 ± 5.3 cells vs. 136.2 ± 19.6; P = 0.001). Fos changes similar to those seen in sevoflurane-exposed mice were observed in REM-deprived animals relative to controls (sublaterodorsal nucleus: 85.0 ± 15.5 cells vs. 23.0 ± 1.2, P = 0.004; ventrolateral periaqueductal gray: 652.8 ± 71.7 cells vs. 889.3 ± 66.8, P = 0.042).

CONCLUSIONS

In rodents recovering from sevoflurane, REM-on and REM-off neuronal activity maps closely resemble those of REM sleep-deprived animals. These findings provide new evidence in support of the idea that sevoflurane does not substitute for endogenous REM sleep.

EDITOR’S PERSPECTIVE

Cellular and molecular mechanisms involved in the analgesic effects of botulinum neurotoxin: A literature review

Botulinum neurotoxins (BoNTs), derived from Clostridium botulinum, have been employed to treat a range of central and peripheral neurological disease. Some studies indicate that BoNT may be beneficial for pain conditions as well. It has been hypothesized that BoNTs may exert their analgesic effects by preventing the release of pain-related neurotransmitters and neuroinflammatory agents from sensory nerve endings, suppressing glial activation, and inhibiting the transmission of pain-related receptors to the neuronal cell membrane. In addition, there is evidence to suggest that the central analgesic effects of BoNTs are mediated through their retrograde axonal transport. The purpose of this review is to summarize the experimental evidence of the analgesic functions of BoNTs and discuss the cellular and molecular mechanisms by which they can act on pain conditions. Most of the studies reviewed in this article were conducted using BoNT/A. The PubMed database was searched from 1995 to December 2022 to identify relevant literature.

Role of Qufeng Tongqiao Prescription in the protection of cerebral ischemia and associated molecular network mechanism

To explore the of Qufeng Tongqiao Prescription in the treatment of cerebral ischemia-reperfusion (CIR) and associated molecular network mechanism. Venny diagram, gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analysis, protein-protein interaction (PPI), hub genes mining, molecular docking, combined with animal experiments and Nissl stain were performed to determine the molecular network mechanism of Qufeng Tongqiao Prescription for CIR treatment. Fifty three intersecting genes between Qufeng Tongqiao Prescription and cerebral ischemia reperfusion were acquired from Venny analysis. GO analysis showed that the main biological process (BP) was response to lipopolysaccharide, and the main cell localization (CC) process was membrane raft, while the most important molecular function (MF) process is Cytokine receptor binding. Moreover, AGE-RAGE signaling pathway in diabetic complications is the most important signaling pathway in KEGG pathway. Through molecular docking, it was found that Astragalus membranaceus was docked with MAPK14, IL4, FOS, IL6, and JUN; pueraria membranaceus was directly docked with JUN and IL4; Acorus acorus was linked to JUN and MAPK14; Ganoderma ganoderma and human were involved in JUN docking, and Ligusticum chuanqi and pueraria could not be docked with MAPK14, respectively. The results of animal experiments showed that Qufeng Tongqiao Prescription significantly improved behavioral performance and reduced the number of neuronal deaths in rats subjected to CIR, and molecular mechanisms are associated with FOS, IL-6, IL4, JUN, and MAPK14, of there, IL-6, as a vital candidator, which has been confirmed by immunostaining detection. Together, Qufeng Tongqiao Prescription has positive therapeutic effect on CIR, and the underlying mechanism is involved MAPK14, FOS, IL4, and JUN network, while IL-6 may be as a vital target.

Age-related decline in social interaction is associated with decreased c-Fos induction in select brain regions independent of oxytocin receptor expression profiles

Social behavior decreases with aging, and we have previously found a substantial decline in social investigative behavior of old female rats. In this study we examined the neural activation pattern (c-Fos mRNA) of young (3 month) and old (18 month) female rats after brief 10 min exposure to a novel female rat in order to identify forebrain regions that show selective age-related alterations in their neural response to social investigation. We also measured relative oxytocin receptor expression (Oxtr mRNA) as a possible factor in age-related declines in c-Fos induction after social interaction. Young rats exposed to a social partner had a greater c-Fos mRNA response than those exposed to novel context alone in the lateral septum and septohypothalamic area, with blunted increases evident in old rats. In addition, c-Fos mRNA levels in the lateral septum were positively correlated with social investigative behavior. Interestingly, age-related differences in c-Fos gene induction were unrelated to the local amount of Oxtr expression within specific brain regions, although we found an age-related decline in Oxtr expression in the ventromedial hypothalamus. This functional neuroanatomical characterization may point to certain brain regions that are especially sensitive to age-related declines associated with social interaction behavior.

Repetitive CREB-DNA interactions at gene loci predetermined by CBP induce activity-dependent gene expression in human cortical neurons

Neuronal activity-dependent transcription plays a key role in plasticity and pathology in the brain. An intriguing question is how neuronal activity controls gene expression via interactions of transcription factors with DNA and chromatin modifiers in the nucleus. By utilizing single-molecule imaging in human embryonic stem cell (ESC)-derived cortical neurons, we demonstrate that neuronal activity increases repetitive emergence of cAMP response element-binding protein (CREB) at histone acetylation sites in the nucleus, where RNA polymerase II (RNAPII) accumulation and FOS expression occur rapidly. Neuronal activity also enhances co-localization of CREB and CREB-binding protein (CBP). Increased binding of a constitutively active CREB to CBP efficiently induces CREB repetitive emergence. On the other hand, the formation of histone acetylation sites is dependent on CBP histone modification via acetyltransferase (HAT) activity but is not affected by neuronal activity. Taken together, our results suggest that neuronal activity promotes repetitive CREB-CRE and CREB-CBP interactions at predetermined histone acetylation sites, leading to rapid gene expression.

Current advances in biomaterials for inner ear cell regeneration

Inner ear cell regeneration from stem/progenitor cells provides potential therapeutic strategies for the restoration of sensorineural hearing loss (SNHL), however, the efficiency of regeneration is low and the functions of differentiated cells are not yet mature. Biomaterials have been used in inner ear cell regeneration to construct a more physiologically relevant 3D culture system which mimics the stem cell microenvironment and facilitates cellular interactions. Currently, these biomaterials include hydrogel, conductive materials, magneto-responsive materials, photo-responsive materials, etc. We analyzed the characteristics and described the advantages and limitations of these materials. Furthermore, we reviewed the mechanisms by which biomaterials with different physicochemical properties act on the inner ear cell regeneration and depicted the current status of the material selection based on their characteristics to achieve the reconstruction of the auditory circuits. The application of biomaterials in inner ear cell regeneration offers promising opportunities for the reconstruction of the auditory circuits and the restoration of hearing, yet biomaterials should be strategically explored and combined according to the obstacles to be solved in the inner ear cell regeneration research.

Unraveling the role of Xist RNA in cardiovascular pathogenesis

Understanding the molecular pathways behind cardiovascular illnesses is crucial due to the enormous worldwide health burden they impose. New insights into the role played by Xist (X-inactive specific transcript) RNA in the onset and progression of cardiovascular diseases have emerged from recent studies. Since its discovery, Xist RNA has been known for its role in X chromosome inactivation during embryogenesis; however, new data suggest that its function extends well beyond the control of sex chromosomes. The regulatory roles of Xist RNA are extensive, encompassing epigenetic changes, gene expression, cellular identity, and sex chromosomal inactivation. There is potential for the involvement of this complex regulatory web in a wide range of illnesses, including cardiovascular problems. Atherosclerosis, hypertrophy, and cardiac fibrosis are all conditions linked to dysregulation of Xist RNA expression. Alterations in DNA methylation and histones are two examples of epigenetic changes that Xist RNA orchestrates, leading to modifications in gene expression patterns in different cardiovascular cells. Additionally, Xist RNA has been shown to contribute to the development of cardiovascular illnesses by modulating endothelial dysfunction, inflammation, and oxidative stress responses. New treatment approaches may become feasible with a thorough understanding of the complex function of Xist RNA in cardiovascular diseases. By focusing on Xist RNA and the regulatory network with which it interacts, we may be able to slow the progression of atherosclerosis, cardiac hypertrophy, and fibrosis, thereby opening novel therapeutic options for cardiovascular diseases amenable to precision medicine. This review summarizes the current state of knowledge concerning the impact of Xist RNA in cardiovascular disorders.

Dorsoventral hippocampus distinctly modulates visceral sensitivity and anxiety behaviors in male IBS-like rats

Accumulating evidences suggest dysfunctions in the hippocampus are associated with chronic pain. Nevertheless, the role of hippocampal circuitry in pain memories and emotional responses is not yet fully understood. In this study, we utilized a comprehensive approach that combined electromyography (EMG), photochemical genetic techniques, and anxiety-related behavioral paradigms to investigate the involvement of dorsal hippocampus (DH) and ventral hippocampus (VH) in visceral sensitivity and anxiety behaviors in male rats. Our results demonstrated that IBS-like rats exhibited comorbid visceral hypersensitivity and anxiety, along with the number of activated neurons in the VH was higher than that in the DH. Manipulation of glutamatergic neurons in the hippocampus was identified as a crucial mechanism underlying the mediation of both visceral sensitivity and anxiety behaviors. Specifically, optogenetic activation of the DH induced both visceral hypersensitivity and anxiety, while activation of the VH induced anxiety but did not affect visceral sensitivity. Conversely, chemogenetic inhibition of the DH reduced both visceral hypersensitivity and anxiety, whereas inhibition of the VH alleviated anxiety but did not alleviate visceral hypersensitivity in IBS-like rats. Our study highlights the important role of early life stress in inducing visceral hypersensitivity and anxiety, and further elucidates the distinct functional contributions of the DH and VH to these behavioral changes. These findings provide a theoretical basis for the diagnosis and treatment of IBS, and suggest that targeting specific hippocampal neuron subtypes may represent a promising therapeutic approach.

An 840 kb distant upstream enhancer is a crucial regulator of catecholamine-dependent expression of the Bdnf gene in astrocytes

Brain-derived neurotrophic factor (BDNF) plays a fundamental role in the developing and adult nervous system, contributing to neuronal survival, differentiation, and synaptic plasticity. Dysregulation of BDNF synthesis, secretion or signaling has been associated with many neurodevelopmental, neuropsychiatric, and neurodegenerative disorders. Although the transcriptional regulation of the Bdnf gene has been extensively studied in neurons, less is known about the regulation and function of BDNF in non-neuronal cells. The most abundant type of non-neuronal cells in the brain, astrocytes, express BDNF in response to catecholamines. However, genetic elements responsible for this regulation have not been identified. Here, we investigated four potential Bdnf enhancer regions and based on reporter gene assays, CRISPR/Cas9 engineering and CAPTURE-3C-sequencing we conclude that a region 840 kb upstream of the Bdnf gene regulates catecholamine-dependent expression of Bdnf in rodent astrocytes. We also provide evidence that this regulation is mediated by CREB and AP1 family transcription factors. This is the first report of an enhancer coordinating the transcription of Bdnf gene in non-neuronal cells.

Neuroepigenetic Editing

Epigenetic regulation is intrinsic to basic neurobiological function as well as neurological disease. Regulation of chromatin-modifying enzymes in the brain is critical during both development and adulthood and in response to external stimuli. Biochemical studies are complemented by numerous next-generation sequencing (NGS) studies that quantify global changes in gene expression, chromatin accessibility, histone and DNA modifications in neurons and glial cells. Neuroepigenetic editing tools are essential to distinguish between the mere presence and functional relevance of histone and DNA modifications to gene transcription in the brain and animal behavior. This review discusses current advances in neuroepigenetic editing, highlighting methodological considerations pertinent to neuroscience, such as delivery methods and the spatiotemporal specificity of editing and it demonstrates the enormous potential of epigenetic editing for basic neurobiological research and therapeutic application.

Effects of Multiple High-Dose Methamphetamine Administration on Enteric Dopaminergic Neurons and Intestinal Motility in the Rat Model

Several studies have identified the effects of methamphetamine (MA) on central dopaminergic neurons, but its effects on enteric dopaminergic neurons (EDNs) are unclear. The aim of this study was to investigate the effects of MA on EDNs and intestinal motility. Male Sprague-Dawley rats were randomly divided into MA group and saline group. The MA group received the multiple high-dose MA treatment paradigm, while the controls received the same saline treatment. After enteric motility was assessed, different intestinal segments (i.e., duodenum, jejunum, ileum, and colon) were taken for histopathological, molecular biological, and immunological analysis. The EDNs were assessed by measuring the expression of two dopaminergic neuronal markers, dopamine transporter (DAT) and tyrosine hydroxylase (TH), at the transcriptional and protein levels. We also used c-Fos protein, a marker of neural activity, to detect the activation of EDNs. MA resulted in a significant reduction in TH and DAT mRNA expression as well as in the number of EDNs in the duodenum and jejunum (p < 0.05). MA caused a dramatic increase in c-Fos expression of EDNs in the ileum (p < 0.001). The positional variability of MA effects on EDNs paralleled the positional variability of its effect on intestinal motility, as evidenced by the marked inhibitory effect of MA on small intestinal motility (p < 0.0001). This study found significant effects of MA on EDNs with locational variability, which might be relevant to locational variability in the potential effects of MA on intestinal functions, such as motility.

Acoustofluidic Engineering of Functional Vessel-on-a-Chip

Construction of in vitro vascular models is of great significance to various biomedical research, such as pharmacokinetics and hemodynamics, and thus is an important direction in the tissue engineering field. In this work, a standing surface acoustic wave field was constructed to spatially arrange suspended endothelial cells into a designated acoustofluidic pattern. The cell patterning was maintained after the acoustic field was withdrawn within the solidified hydrogel. Then, interstitial flow was provided to activate vessel tube formation. In this way, a functional vessel network with specific vessel geometry was engineered on-chip. Vascular function, including perfusability and vascular barrier function, was characterized by microbead loading and dextran diffusion, respectively. A computational atomistic simulation model was proposed to illustrate how solutes cross the vascular membrane lipid bilayer. The reported acoustofluidic methodology is capable of facile and reproducible fabrication of the functional vessel network with specific geometry and high resolution. It is promising to facilitate the development of both fundamental research and regenerative therapy.

Impact and Role of Hypothalamic Corticotropin Releasing Hormone Neurons in Withdrawal from Chronic Alcohol Consumption in Female and Male Mice

Worldwide, alcohol use and abuse are a leading risk of mortality, causing 5.3% of all deaths (World Health Organization, 2022). The endocrine stress system, initiated by the peripheral release of corticotropin releasing hormone (CRH) from primarily glutamatergic neurons in the paraventricular nucleus of the hypothalamus (PVN), is profoundly linked with alcohol use, abuse, and relapse (Blaine and Sinha, 2017). These PVN CRH-releasing (PVNCRH) neurons are essential for peripheral and central stress responses (Rasiah et al., 2023), but little is known about how alcohol affects these neurons. Here, we show that two-bottle choice alcohol consumption blunts the endocrine-mediated corticosterone response to stress during acute withdrawal in female mice. Conversely, using slice electrophysiology, we demonstrate that acute withdrawal engenders a hyperexcitable phenotype of PVNCRH neurons in females that is accompanied by increased glutamatergic transmission in both male and female mice. GABAergic synaptic transmission was unaffected by alcohol history. We then tested whether chemogenetic inhibition of PVNCRH neurons would restore stress response in female mice with a history of alcohol drinking in the looming disk test, which mimics an approaching predator threat. Accordingly, inhibition of PVNCRH neurons reduced active escape in hM4Di alcohol history mice only. This study indicates that stress-responsive PVNCRH neurons in females are particularly affected by a history of alcohol consumption. Interestingly, women have indicated an increase in heavy alcohol use to cope with stress (Rodriguez et al., 2020), perhaps pointing to a potential underlying mechanism in alcohol-mediated changes to PVNCRH neurons that alter stress response.SIGNIFICANCE STATEMENT Paraventricular nucleus of the hypothalamus neurons that release corticotropin releasing hormone (PVNCRH) are vital for stress response. These neurons have been understudied in relation to alcohol and withdrawal despite profound relations between stress, alcohol use disorders (AUD), and relapse. In this study, we use a variety of techniques to show that acute withdrawal from a history of alcohol impacts peripheral stress response, PVNCRH neurons, and behavior. Specifically, PVNCRH are in a hyperactive state during withdrawal, which drives an increase in active stress coping behaviors in female mice only. Understanding how alcohol use and withdrawal affects stress responding PVNCRH neurons may contribute to finding new potential targets for the treatment of alcohol use disorder.

Genetic Approaches for Neural Circuits Dissection in Non-human Primates

Genetic tools, which can be used for the morphology study of specific neurons, pathway-selective connectome mapping, neuronal activity monitoring, and manipulation with a spatiotemporal resolution, have been widely applied to the understanding of complex neural circuit formation, interactions, and functions in rodents. Recently, similar genetic approaches have been tried in non-human primates (NHPs) in neuroscience studies for dissecting the neural circuits involved in sophisticated behaviors and clinical brain disorders, although they are still very preliminary. In this review, we introduce the progress made in the development and application of genetic tools for brain studies on NHPs. We also discuss the advantages and limitations of each approach and provide a perspective for using genetic tools to study the neural circuits of NHPs.

Electroacupuncture alleviates depression-like behaviours via a neural mechanism involving activation of Nucleus Accumbens Shell

OBJECTIVES

This study investigated the effects of electroacupuncture (EA) on the depression-like behaviours in a mouse model of chronic restraint stress (CRS) and explored the underlying neural mechanisms.

METHODS

Depression-like behaviours including sucrose preference test (SPT), open field test (OFT) and tail suspension test (TST) were carried out to evaluate the effects of CRS and EA treatment. Using immunohistochemistry to measure the expression of c-Fos. The Nucleus Accumbens Shell (NAc Shell) in C57BL/6J mice were activated or inhibited using Chemogenetics.

RESULTS

All the CRS stimulated groups showed lower sucrose preference in the SPT and decreased centre times in the OFT, and increased immobility time in the TST when compared to the normal control. Interestingly, EA at LR3 or HT7 exerted anti-depressant effects, and LR3 EA exhibited a more significant restoration than HT7. Furthermore, EA at LR3 increased expression of c-Fos in the NAc Shell. Chemogenetic inhibition of NAc Shell blocked the effects of EA, whereas enhancement of NAc Shell activity profoundly reversed depressive phenotypes.

CONCLUSIONS

LR3 EA was effective in alleviating the depressive-like behaviours, and this therapeutic effect was associated with the activation of NAc Shell. Collectively, these findings revealed that EA may represent a promising therapeutic strategy for depression.

Single genomic enhancers drive experience-dependent GABAergic plasticity to maintain sensory processing in the adult cortex

Experience-dependent plasticity of synapses modulates information processing in neural circuits and is essential for cognitive functions. The genome, via non-coding enhancers, was proposed to control information processing and circuit plasticity by regulating experience-induced transcription of genes that modulate specific sets of synapses. To test this idea, we analyze here the cellular and circuit functions of the genomic mechanisms that control the experience-induced transcription of Igf1 (insulin-like growth factor 1) in vasoactive intestinal peptide (VIP) interneurons (INs) in the visual cortex of adult mice. We find that two sensory-induced enhancers selectively and cooperatively drive the activity-induced transcription of Igf1 to thereby promote GABAergic inputs onto VIP INs and to homeostatically control the ratio between excitation and inhibition (E/I ratio)-in turn, this restricts neural activity in VIP INs and principal excitatory neurons and maintains spatial frequency tuning. Thus, enhancer-mediated activity-induced transcription maintains sensory processing in the adult cortex via homeostatic modulation of E/I ratio.

The midnolin-proteasome pathway catches proteins for ubiquitination-independent degradation

Cells use ubiquitin to mark proteins for proteasomal degradation. Although the proteasome also eliminates proteins that are not ubiquitinated, how this occurs mechanistically is unclear. Here, we found that midnolin promoted the destruction of many nuclear proteins, including transcription factors encoded by the immediate-early genes. Diverse stimuli induced midnolin, and its overexpression was sufficient to cause the degradation of its targets by a mechanism that did not require ubiquitination. Instead, midnolin associated with the proteasome via an α helix, used its Catch domain to bind a region within substrates that can form a β strand, and used a ubiquitin-like domain to promote substrate destruction. Thus, midnolin contains three regions that function in concert to target a large set of nuclear proteins to the proteasome for degradation.

Acoustofluidic Engineering Functional Vessel-on-a-Chip

Construction of in vitro vascular models is of great significance to various biomedical research, such as pharmacokinetics and hemodynamics, thus is an important direction in tissue engineering. In this work, a standing surface acoustic wave field was constructed to spatially arrange suspended endothelial cells into a designated patterning. The cell patterning was maintained after the acoustic field was withdrawn by the solidified hydrogel. Then, interstitial flow was provided to activate vessel tube formation. Thus, a functional vessel-on-a-chip was engineered with specific vessel geometry. Vascular function, including perfusability and vascular barrier function, was characterized by beads loading and dextran diffusion, respectively. A computational atomistic simulation model was proposed to illustrate how solutes cross vascular lipid bilayer. The reported acoustofluidic methodology is capable of facile and reproducible fabrication of functional vessel network with specific geometry. It is promising to facilitate the development of both fundamental research and regenerative therapy.

Ultrasound stimulation of the vagal nerve improves acute septic encephalopathy in mice

Septic encephalopathy (SE) is characterized by symptoms such as coma, delirium, and cognitive dysfunction, and effective therapeutic interventions for SE remain elusive. In this study, we aimed to investigate the potential alleviating effects of vagal nerve stimulation (VNS) on SE-associated signs. To evaluate our hypothesis, we utilized a mouse model of SE induced by intraperitoneal injection of lipopolysaccharide (0.3 mg per mouse) and administered noninvasive, high-frequency ultrasound VNS. To assess the efficacy of ultrasound VNS, we measured inflammation-related molecules, including the α7 nicotinic acetylcholine receptor (α7nAChR) expression in peritoneal macrophages and plasma interleukin 1β (IL-1β) levels. Consistent with our hypothesis, SE mice exhibited reduced α7nAChR expression in macrophages and elevated IL-1β levels in the blood. Remarkably, VNS in SE mice restored α7nAChR expression and IL-1β levels to those observed in control mice. Furthermore, we evaluated the effects of VNS on survival rate, body temperature, and locomotor activity. SE mice subjected to VNS demonstrated a modest, yet significant, improvement in survival rate, recovery from hypothermia, and increased locomotor activity. To investigate the impact on the brain, we examined the hippocampus of SE mice. In control mice, VNS increased the expression of c-fos, a marker of neuronal electrical excitability, in the hippocampus. In SE mice, VNS led to the restoration of aberrant firing patterns in hippocampal neurons. Additionally, proteomic analysis of hippocampal tissue in SE mice revealed abnormal increases in two proteins, tissue factor (TF) and acyl-CoA dehydrogenase family member 9 (ACAD9), which returned to control levels following VNS. Collectively, our findings support the value of exploring the beneficial effects of ultrasound VNS on SE.

Differential expression of Dusp1 and immediate early response genes in the hippocampus of rats, subjected to forced swim test

The forced swim test (FST) is widely used to screen for potential antidepressant drugs and treatments. Despite this, the nature of stillness during FST and whether it resembles "depressive-like behavior" are widely debated issues. Furthermore, despite being widely used as a behavioral assay, the effects of the FST on the brain transcriptome are rarely investigated. Therefore, in this study we have investigated changes in the transcriptome of the rat hippocampus 20 min and 24 h after FST exposure. RNA-Seq is performed on the hippocampus tissues of rats 20 min and 24 h after an FST. Differentially expressed genes (DEGs) were identified using limma and used to construct gene interaction networks. Fourteen differentially expressed genes (DEGs) were identified only in the 20-m group. No DEGs were identified 24 h after the FST. These genes were used for Gene Ontology term enrichment and gene-network construction. Based on the constructed gene-interaction networks, we identified a group of DEGs (Dusp1, Fos, Klf2, Ccn1, and Zfp36) that appeared significant based on multiple methods of downstream analysis. Dusp1 appears especially important, as its role in the pathogenesis of depression has been demonstrated both in various animal models of depression and in patients with depressive disorders.