Neural Cells Research Articles

Hybrid improved fuzzy C-means and watershed segmentation to classify Alzheimer’s using deep learning

Brain damage and deficits in interactions among brain cells are the primary causes of dementia and Alzheimer’s disease (AD). Despite ongoing research, no effective medications have yet been developed for these conditions. Therefore, early detection is crucial for managing the progression of these disorders. In this study, we introduce a novel tool for detecting AD using non invasive medical tests, such as magnetic resonance imaging (MRI). Our method employs fuzzy C-means clustering to identify features that enhance image accuracy. The standard fuzzy C-means algorithm has been augmented with fuzzy components to improve clustering performance. This enhanced approach optimizes segmentation by extracting image information and utilizing a sliding window to calculate center coordinates and establish a stable group matrix. These critical features are subsequently integrated with a two-phase watershed segmentation process. The resulting segmented images are then used to train an optimal convolutional neural network (CNN) for AD classification. Our methodology demonstrated a 98.20% accuracy rate in the detection and classification of segmented MRI brain images, highlighting its efficacy in identifying disease types.

Electroacupuncture suppresses NK cell infiltration and activation in the ischemic mouse brain through STAT3 inhibition.

Electroacupuncture (EA) at Shuigou (GV26) and Baihui (GV20) has shown therapeutic benefits for stroke patients. Given that natural killer (NK) cell infiltration into the brain significantly contributes to the exacerbation of cerebral ischemic injury, this study investigated the impact of EA at Shuigou (GV26) and Baihui (GV20) on post-ischemic brain infiltration and activation of NK cells. Neurological deficit score, rotarod test, adhesive removal test, and TTC staining were used to evaluate the beneficial effects of EA in middle cerebral artery occlusion (MCAO) mice. The inhibitory effect of EA on STAT3 activation was assessed using Western blot. Flow cytometry was used to explore the impact of EA on post-ischemic brain infiltration of NK cells, as well as the activating receptor NKG2D expression and interferon-γ (IFN-γ) production by these infiltrated NK cells. EA significantly alleviated neurological functional deficits and reduced brain infarction in MCAO mice. Abundant NK cells infiltrated into the ischemic hemisphere, but this infiltration was significantly suppressed by EA. Furthermore, EA attenuated NKG2D levels and reduced production of IFN-γ by NK cells in the ischemic brain. Notably, EA's inhibitory effect on post-ischemic NK cell brain infiltration and activation was comparable to that of STAT3 inhibition. The combination of EA and STAT3 inhibition did not result in further enhancement of the inhibitory effect. Moreover, the protective effects of EA against MCAO injury were abolished when STAT3 was activated. Our findings suggest that EA at Shuigou (GV26) and Baihui (GV20) inhibits the post-ischemic brain infiltration and activation of NK cells through STAT3 inhibition, significantly contributing to its therapeutic effects against brain ischemia.

MiR-124 in Neuroblastoma: Mechanistic Insights, Biomarker Potential, and Therapeutic Prospects

: Neuroblastoma, a malignancy predominantly affecting young children, originates from neural crest cells in the sympathetic nervous system. It primarily appears in the adrenal gland but can also affect nerve tissues in regions, such as the chest, neck, abdomen, and pelvis. Despite advancements in treatment, high-risk neuroblastoma patients often face poor prognoses, underscoring the need for ongoing research. This review paper examines the numerous factors responsible for neuroblastoma, emphasizing the importance of approaching the disorder with more strategic therapeutic methods. MicroRNAs, particularly miR-124, play critical roles in gene regulation and cancer pathogenesis. Abundant in the brain, miR-124 functions as a tumor suppressor by inhibiting cell growth, migration, and invasion and is often dysregulated in neuroblastoma. This study investigates the molecular functions of miR-124 in neuroblastoma, its potential as a biomarker, and its application in targeted therapy. MiR-124 regulates key pathways in neuroblastoma, including PI3K/AKT, TGF-β, and p53 signaling, impacting cell proliferation, apoptosis, and metastasis. The study also explores the promise of miR-124 as a biomarker for neuroblastoma through liquid biopsy, enabling non-invasive diagnosis and disease monitoring. Therapeutic strategies targeting miR-124 pathways show potential for overcoming chemotherapy resistance and improving treatment efficacy. The research underscores the significance of miR-124 in neuroblastoma, aiming to enhance early diagnosis, identify specific drug targets, and expand treatment options, ultimately improving patient outcomes.

CREB: A Promising Therapeutic Target for Treating Psychiatric Disorders.

Psychiatric disorders are complex, multifactorial illnesses. It is challenging for us to understand the underlying mechanism of psychiatric disorders. In recent years, the morbidity of psychiatric disorders has increased yearly, causing huge economic losses to the society. Although some progress, such as psychotherapy drugs and electroconvulsive therapy, has been made in the treatment of psychiatric disorders, including depression, anxiety, bipolar disorder, obsessive-compulsive and autism spectrum disorders, antidepressants and psychotropic drugs have the characteristics of negative effects and high rate of relapse. Therefore, researchers continue to seek suitable interventions. cAMP response element binding protein (CREB) belongs to a protein family and is widely distributed in the majority of brain cells that function as a transcription factor. It has been demonstrated that CREB plays an important role in neurogenesis, synaptic plasticity, and neuronal growth. This review provides a 10-year update of the 2013 systematic review on the multidimensional roles of CREB-mediated transcriptional signaling in psychiatric disorders. We also summarize the classification of psychiatric disorders and elucidate the involvement of CREB and related downstream signalling pathways in psychiatric disorders. Importantly, we analyse the CREB-related signal pathways involving antidepressants and antipsychotics to relieve the pathological process of psychiatric disorders. This review emphasizes that CREB signalling may have a vast potential to treat psychiatric disorders like depression. Furthermore, it would be helpful for the development of potential medicine to make up for the imperfection of current antidepressants and antipsychotics.

The Multitarget Action of Vitamins in the Ischemic Stroke

: A stroke, also known as a cerebral hemorrhage, occurs when there is an interruption in the blood supply to a part of the brain, resulting in damage to brain cells. This issue is one of the leading causes of death in developed countries, currently killing about 5 million people annually. Individuals who survive ischemic stroke often face serious vision problems, paralysis, dementia, and other sequelae. The numerous efforts to prevent and/or treat stroke sequelae seem insufficient, which is concerning given the increasing global elderly population and the well-known association between aging and stroke risk. In this review, we aim to present and discuss the importance of vitamins in stroke prevention and/or incidence. Vitamins from diet or dietary supplements influence the body at various levels; they are a relevant factor but are reported only in isolated articles. This review reports and updates the multitarget role of vitamins involved in reducing stroke risk.

A Snapshot of Early Transcriptional Changes Accompanying the Pro-Neural Phenotype Switch by NGN2, ASCL1, SOX2, and MSI1 in Human Fibroblasts: An RNA-Seq Study

Direct pro-neural reprogramming is a conversion of differentiated somatic cells to neural cells without an intermediate pluripotency stage. It is usually achieved via ectopic expression (EE) of certain transcription factors (TFs) or other reprogramming factors (RFs). Determining the transcriptional changes (TCs) caused by particular RFs in a given cell line enables an informed approach to reprogramming initiation. Here, we characterized TCs in the human fibroblast cell line LF1 on the 5th day after EE of the single well-known pro-neural RFs NGN2, ASCL1, SOX2, and MSI1. As assessed by expression analysis of the bona fide neuronal markers nestin and beta-III tubulin, all four RFs initiated pro-neuronal phenotype conversion; analysis by RNA-seq revealed striking differences in the resulting TCs, although some pathways were overlapping. ASCL1 and SOX2 were not sufficient to induce significant pro-neural phenotype switches using our EE system. NGN2 induced TCs indicative of cell phenotype changes towards neural crest cells, neural stem cells, mature neurons, as well as radial glia, astrocytes, and oligodendrocyte precursors and their mature forms. MSI1 mainly induced a switch towards early stem-like cells, such as radial glia.

Spatially Localized Visual Perception Estimation by Means of Prosthetic Vision Simulation

Retinal prosthetic devices aim to repair some vision in visually impaired patients by electrically stimulating neural cells in the visual system. Although there have been several notable advancements in the creation of electrically stimulated small dot-like perceptions, a deeper comprehension of the physical properties of phosphenes is still necessary. This study analyzes the influence of two independent electrode array topologies to achieve single-localized stimulation while the retina is electrically stimulated: a two-dimensional (2D) hexagon-shaped array reported in clinical studies and a patented three-dimensional (3D) linear electrode carrier. For both, cell stimulation is verified in COMSOL Multiphysics by developing a lifelike 3D computational model that includes the relevant retinal interface elements and dynamics of the voltage-gated ionic channels. The evoked percepts previously described in clinical studies using the 2D array are strongly associated with our simulation-based findings, allowing for the development of analytical models of the evoked percepts. Moreover, our findings identify differences between visual sensations induced by the arrays. The 2D array showed drawbacks during stimulation; similarly, the state-of-the-art 2D visual prostheses provide only dot-like visual sensations in close proximity to the electrode. The 3D design could offer a technique for improving cell selectivity because it requires low-intensity threshold activation which results in volumes of stimulation similar to the volume surrounded by a solitary RGC. Our research establishes a proof-of-concept technique for determining the utility of the 3D electrode array for selectively activating individual RGCs at the highest density via small-sized electrodes while maintaining electrochemical safety.

Abstract C002: CKLF attracts CCR4-expressing CD4+ cells to foster immune repression and tumor aggressiveness in MYCN-driven neuroblastoma

Abstract Neuroblastoma, especially those with aberrant MYCN activation, often harbor an immunosuppressive microenvironment to fuel malignant growth and trigger treatment resistance. Despite this knowledge, there are no effective strategies to tackle this problem. Here we combined analyses of human neuroblastoma with live tracking and functional studies of the tumor microenvironment (TME) in zebrafish. We identified chemokine-like factor (CKLF) as a key driver of MYCN-mediated immunosuppression and neuroblastoma aggression. We showed that human MYCN-activated neuroblastoma upregulates and secretes CKLF, which is a reliable predictor of poor patient survival. Analysis of primary patient samples demonstrates a strong positive association between MYCN and CKLF expression in neuroblastoma cells together with the enrichment of FOXP3+ T cells in the TME. Taking advantage of in vivo zebrafish models of MYCN-driven neuroblastoma that resemble human high-risk disease, we demonstrated that cklf overexpression in zebrafish neural crest cells induces an immunosuppressive TME while promoting rapid tumor onset and progression. We also demonstrated that as early as the premalignant stage, tumor cells secrete CKLF to attract CCR4-expressing Cd4+ cells to induce immunosuppression and tumor aggression. Conversely, genetic depletion of cklf in tumor cells reduces the recruitment of Cd4+ cells to the TME while increasing cytotoxic Cd8+ and natural killer cells infiltration, inhibiting neuroblastoma development in zebrafish. Our work provides the first example that MYCN can activate CKLF to allure CD4+ immune cells to the TME and incite immunosuppression, positioning CKLF as a potential novel immunotherapeutic target for the treatment of MYCN-driven high-risk neuroblastoma. Citation Format: Xiaodan Qin, Hui Feng, Andrew Lam, Xu Zhang, Satyaki Sengupta, Bryan Iorgulescu, Sanjukta Das, Zhenwei Zhou, Tao Zuo, Grace Meara, Madison Rager, Alexander Floru, Hongru Ni, Chinyere Kemet, Divya Veerapaneni, Daniel Kashy, Liang Lin, Kenneth Lloyd, Lauren Kwok, Kaylee Smith, Raghavendar Nagaraju, Rob Meijers, Craig Ceol, Ching-Ti Liu, Sanda Alexandrescu, Catherine J. Wu, Derin Keskin, Rani George. CKLF attracts CCR4-expressing CD4+ cells to foster immune repression and tumor aggressiveness in MYCN-driven neuroblastoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr C002.

Abstract A039: Characterization of the heterogeneous nature of the peritumoral zone of glioblastomas and its relevance for the clinical progression of the disease

Abstract Glioblastoma (GBM) is one of the most aggressive forms of cancer, with a recurrence rate of nearly 100% within 12 months of diagnosis. This is attributable to the persistence of residual tumor cells following surgical resection, which can repopulate the tumor even after the administration of aggressive chemoradiotherapy. These cells are embedded in a specific microenvironment in the peritumoral zone (PTZ), which is formed by their interaction with the brain parenchyma. The PTZ can be classified radiologically into two distinct categories: areas of clear tumor infiltration (non-contrast-enhancing (non-CE) tumor) and areas of vascular edema. Recent data suggest that the extent of surgical resection to non-CE regions may confer substantial benefits to patients with GBM. However, while the tumor core niche has been the subject of extensive study, there is a paucity of knowledge regarding the nature of the PTZ. In this study, we prospectively collected a large cohort of radiologically guided biopsies from GBM patients and performed a comprehensive cellular analysis. To this end, we initially integrated publicly available single-cell RNA sequencing (scRNA-seq) datasets from non-pathogenic human brains and gliomas, resulting in an integrated atlas representing the major cell types: immune (myeloid cells and T cells), astrocytic, oligodendroglial, and vascular. By means of a meticulous multi-stage examination of differentially expressed genes in glioma and cell type-specific markers, we were able to identify several genes that could serve to characterize the cellular content of the biopsies obtained from the tumor core and the periphery, comprising non-CE tumor, edema, and what was deemed "normal" tissue. The application of unsupervised clustering enabled the separation of the most pathogenic samples (including CE and non-CE tumor biopsies) based on the enrichment of proliferative markers and the pronounced absence of normal endothelial and oligodendrocyte expression. The tumorigenic samples were clustered into two main groups: one group that was enriched in astrocytic and proliferative markers and another one that was enriched in myeloid cells. Furthermore, our findings indicate the existence of inter- and intra-tumor heterogeneity in the cellular composition of the PTZ in GBM, with observed differences associated with the degree of tumor infiltration, but also patient age and gender. In particular, a distinct pathological pattern was discerned in select edema and normal biopsies from multiple patients, particularly those of an advanced age. Moreover, several markers of neural and immune cells associated with a favorable prognosis were identified, though only when expressed in the periphery. In conclusion, our study offers a comprehensive scRNA-seq resource for investigating the involvement of diverse cell types in the pathobiology of GBM. Additionally, it highlights the heterogeneous nature of the glioma periphery, which could explain the gender and age-related prognostic differences that have been observed among patients with GBM. Citation Format: Olaya de Dios, María de los Ángeles Ramírez-González, Beatriz Herranz, Juan Romero, Ana Ramos, Juan Manuel Sepúlveda-Sánchez, Ricardo Gargini, Aurelio Hernández-Laín, Pedro González, Luis Jiménez-Roldán, Guillermo García-Posadas, Ángel Pérez-Núñez, Pilar Sánchez-Gómez. Characterization of the heterogeneous nature of the peritumoral zone of glioblastomas and its relevance for the clinical progression of the disease [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr A039.

Abstract A021: HRI inhibition by hemin as a novel targeted therapy for glioblastoma via the integrated stress response

Abstract The treatment of glioblastoma (GBM), a highly malignant brain tumor, is critically hindered by the ineffectiveness of current modalities such as surgery, radiation, and chemotherapy. These traditional methods fail to completely remove the tumor mass and lack the ability to discriminate between cancerous and normal brain cells, often resulting in damage to healthy tissue and recurrence of the disease. This underscores an urgent necessity to develop novel therapeutic strategies that can target tumor cells with precision, offering hope for improved survival rates and quality of life for GBM patients. This study investigates targeted therapy, focusing on the Integrated Stress Response (ISR) that cancer cells harness to survive hypoxic stress. Specifically, it demonstrates that EIF2AK1, which encodes Heme-regulated eIF2α kinase (HRI), is activated under hypoxia and co-expressed with the glioma stem cell marker SOX2, which specifically happens in glioma cells, increasing the targeted accuracy of the repurposing drug. This correlation, indicating hypoxia-driven stemness, is confirmed at both the genetic level and through Gene Set Enrichment Analysis (GSEA). Furthermore, GSEA in Spatial Transcriptomics shows hypoxia-induced glycolysis, disrupting the tumor microenvironment and causing necrotic cell death. Stemness phenotype is induced in the peripheral cells due to the unfavorable hypoxic environment. Hemin, an HRI inhibitor, has been repurposed to inhibit ISR and mitigate hypoxia. Treatment with Hemin on the U87 cell line resulted in IC50 values of 23.50 µM and 52.46 µM at 24 and 48 hours, respectively, surpassing Temozolomide's efficacy. A decrease in HRI expression after the Hemin treatment suggests the and ISR activity and, potentially, hypoxia. This would reverse the unfavorable microenvironment so that the stemness phenotype doesn’t spread. Potentially, invasiveness and recurrences of GBM in clinic situation would decrease, thus potentially improving patient prognosis. The therapeutic potential of Hemin is enhanced by its ability to kill glioma cells directly and accurately in the glioma cell in original TME when cells are proliferating with adequate oxygen. Therefore, this study demonstrates the therapeutic potential of repurposing Hemin, an HRI inhibitor, to precisely target hypoxia-induced glioma stem cells in glioblastomas, disrupting the aggressive tumor microenvironment to potentially improve patient prognosis. Citation Format: Xingchuan Ma. HRI inhibition by hemin as a novel targeted therapy for glioblastoma via the integrated stress response [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr A021.

Neural Crest-Derived Mesenchymal Cells Support Thymic Reconstitution After Lethal Irradiation.

Reconstitution of the thymus is essential for assessing thymic function following injury. However, the currently employed cytoreductive regimes unvaryingly affect the thymic microenvironment, thereby impeding the recovery of T lymphopoiesis. The thymic stroma is composed of epithelial and mesenchymal cells. Thymic mesenchymal cells originate from the Neural crest (NC) and mesoderm and contribute to thymus organogenesis, yet their role in thymic regeneration is unclear. In this study, using transgenic mice expressing NC-specific Cre and Cre-driven DT receptors, we investigated the role of NC-derived mesenchymal cells in thymic regeneration following total body irradiation. We revealed that NC-derived mesenchymal cells have reduced susceptibility to irradiation and induce the upregulation of hematopoietic factors that promote thymus regeneration after irradiation. Additionally, using adult thymic organ culture and renal capsule transplantation, depletion of NC-derived mesenchymal cells resulted in a reduction of DN1-like early T-cell progenitors (ETP) and impaired thymic regeneration. Furthermore, among the numerous factors upregulated by NC-derived mesenchymal cells, Periostin and Flt3L were markedly increased after irradiation and promoted abundance of DN1-like ETPs during thymic reconstitution. Collectively, these findings highlight the importance of NC-derived mesenchymal cells in thymic regeneration.

Microglia in the spinal cord stem cell niche regulate neural precursor cell proliferation via soluble CD40 in response to myelin basic protein.

Neural stem cells (NSCs) are found along the neuraxis of the developing and mature central nervous system. They are found in defined niches that have been shown to regulate NSC behaviour in a regionally distinct manner. Specifically, previous research has shown that myelin basic protein (MBP), when presented in the spinal cord niche, inhibits NSC proliferation and oligodendrogenesis. Herein, we investigate the cell-based mechanism(s) underlying this spinal-cord niche derived MBP-mediated inhibition. We used reporter mice to sort for subpopulations of cells and found that spinal cord niche derived microglia release a soluble factor in response to MBP that is responsible for NSC inhibition. Microglia, but not other niche cells, release soluble CD40/TNFRSF5 (sCD40) in the presence of MBP which may indirectly reduce activation of transmembrane CD40/TNFRSF5 receptor on both spinal cord and brain NSCs. This is consistent with sCD40 binding to CD40 ligand (CD40L) thereby preventing CD40 receptor binding on NSCs and inhibiting NSC proliferation. The identification of the cell-based mechanism that regulates NSC behaviour in response to MBP, which is dysregulated in injury/disease, provides insight into a potential target for strategies to enhance neural repair through endogenous stem cell activation.

Membrane Budding Inspired Biomimetic Nanocarrier Delivers Brain‐derived Neurotrophic Factor to Improve AD Cognition

AbstractNeurotropic factors, crucial for neural cell maturation and proliferation, hold great therapeutic potential for treating neurodegenerative diseases but face challenges in brain delivery. This study introduces a novel membrane budding‐inspired lipoprotein biomimetic nanocarrier for efficient packaging and precise brain delivery of brain‐derived neurotrophic factor (BDNF). The nanocarrier is created by mixing protein‐loaded biomimetic gel with liposomes composed of lipids prone to forming liquid‐disordered and liquid‐ordered phases. This interaction triggers phase separation and lipid membrane rearrangement, enabling effective protein encapsulation. To enhance blood‐brain barrier permeability and target damaged cerebral vasculature in Alzheimer's Disease, the nanocarrier (RAP‐BHP‐rHDL) is functionalized with Apolipoprotein E3 and αRAP peptides. The obtained RAP‐BHP‐rHDL alleviates neuronal damage, promotes neurogenesis, normalizes the cerebral microvasculature, improves the function of neurovascular units, and restores memory function in 5 × FAD mice. This innovative packaging approach and biomimetic nanocarrier design offer a promising strategy for delivering neurotropic factors to the central nervous system, potentially advancing the management of neurodegenerative diseases.

In Vitro differentiation of hair-follicle bulge stem cells into synaptophysin-expressing neurons: a potential new approach for neuro-regeneration.

Stem cells, particularly bulge hair follicle stem cells (HFSCs), have recently attracted significant interest due to their potential for tissue repair and regeneration. These cells, marked by their expression of Nestin (a neural stem cell marker), suggest the possibility of neural differentiation into neurons. This study investigated the use of retinoic acid (RA) and epidermal growth factor (EGF) to induce HFSC transformation into mature neurons, identified by synaptophysin expression. Rat whisker follicles were cultured in a medium suitable for HFSC survival and proliferation. Immunostaining techniques were used to identify HFSCs and assess their differentiation into neural cells. The addition of RA and EGF to the culture medium aimed to induce this differentiation. Findings demonstrate that HFSCs expressed Nestin, indicating their pluripotent nature. Treatment with RA and EGF resulted in synaptophysin expression, a marker of mature neurons, which was absent in the control group. However, this treatment group also displayed a decrease in the expression of other neural markers (βIII tubulin and NeuN). This study suggests that a combination of RA and EGF can accelerate HFSC differentiation into synaptophysin-positive cells in vitro. This research paves the way for further exploration of its potential application in neuro-regeneration.

SMPD4-mediated sphingolipid metabolism regulates brain and primary cilia development.

Genetic variants in multiple sphingolipid biosynthesis genes cause human brain disorders. A recent study looked at people from 12 unrelated families with variants in the gene SMPD4, a neutral sphingomyelinase that metabolizes sphingomyelin into ceramide at an early stage of the biosynthesis pathway. These individuals have severe developmental brain malformations, including microcephaly and cerebellar hypoplasia. The disease mechanism of SMPD4 was not known and so we pursued a new mouse model. We hypothesized that the role of SMPD4 in producing ceramide is important for making primary cilia, a crucial organelle mediating cellular signaling. We found that the mouse model has cerebellar hypoplasia due to failure of Purkinje cell development. Human induced pluripotent stem cells lacking SMPD4 exhibit neural progenitor cell death and have shortened primary cilia, which is rescued by adding exogenous ceramide. SMPD4 production of ceramide is crucial for human brain development.

TAD-dependent sub-TAD is required for enhancer-promoter interaction enabling the β-globin transcription.

Topologically associating domains (TADs) are chromatin domains in the eukaryotic genome. TADs often comprise several sub-TADs. The boundaries of TADs and sub-TADs are enriched in CTCF, an architectural protein. Deletion of CTCF-binding motifs at one boundary disrupts the domains, often resulting in a transcriptional decrease in genes inside the domains. However, it is not clear how TAD and sub-TAD affect each other in the domain formation. Unaffected gene transcription was observed in the β-globin locus when one boundary of TAD or sub-TAD was destroyed. Here, we disrupted β-globin TAD and sub-TAD by deleting CTCF motifs at both boundaries in MEL/ch11 cells. Disruption of TAD impaired sub-TAD, but sub-TAD disruption did not affect TAD. Both TAD and sub-TAD disruption compromised the β-globin transcription, accompanied by the loss of enhancer-promoter interactions. However, histone H3 occupancy and H3K27ac were largely maintained across the β-globin locus. Genome-wide analysis showed that putative enhancer-promoter interactions and gene transcription were decreased by the disruption of CTCF-mediated topological domains in neural progenitor cells. Collectively, our results indicate that there is unequal relationship between TAD and sub-TAD formation. TAD is likely not sufficient for gene transcription, and, therefore, sub-TAD appears to be required. TAD-dependently formed sub-TADs are considered to provide chromatin environments for enhancer-promoter interactions enabling gene transcription.

Mutant HTT protein decreases with CAG repeat expansion: implications for therapeutics and bioassays

Abstract Huntington’s disease is an inherited neurodegenerative disorder caused by a CAG repeat expansion that encodes a polyglutamine tract in the HTT protein. The mutant CAG repeat is unstable and expands in specific brain cells and peripheral tissues throughout life. Genes involved in the DNA mismatch repair pathways, known to act on expansion, have been identified as genetics modifiers, therefore, it is the rate of somatic CAG repeat expansion that drives the age of onset and rate of disease progression. In the context of an expanded CAG repeat, the HTT pre-mRNA can be alternatively processed to generate the HTT1a transcript, that encodes the aggregation prone and highly pathogenic HTT1a protein. This may be a mechanism through which somatic CAG repeat expansion exerts its pathogenic effects, as the longer the CAG repeat, the more HTT1a and HTT1a is produced. The allelic series of knock-in mouse models: HdhQ20, HdhQ50, HdhQ80, HdhQ111, CAG140 and zQ175 with polyglutamine expansions of 20, 50, 80, 111 140 and ∼190 can be used to model the molecular and cellular consequences of CAG repeat expansion within a single neuron. By western blot of cortical lysates, we found that mutant HTT levels decreased with increasing CAG repeat length; mutant HTT was only 23% and 10% of wild-type levels in CAG140 and zQ175 cortices, respectively. To identify the optimal bioassays for detecting the full-length HTT and HTT1a isoforms, we interrogated the pairwise combinations of seven well-characterized antibodies on both the ‘homogeneous time resolved fluorescence’ and ‘Meso Scale Discovery’ platforms. We tested 32 assays on each platform to detect ‘full-length mutant HTT’, HTT1a, ‘total mutant HTT’ (full-length HTT and HTT1a) and ‘total full-length HTT’ (mutant and wild type). None of these assays recapitulated the full-length mutant HTT levels as measured by western blot. We recommend using isoform- and species- specific assays that detect either full-length mutant HTT, HTT1a or wild-type HTT as opposed to those that detect more than one isoform simultaneously. Our finding that as the CAG repeat expands, full-length mutant HTT levels decrease, whilst HTT1a and HTT1a levels increase has implications for therapeutic strategies. If mutant HTT levels in cells containing (CAG)200 are only 10% of wild-type, HTT-lowering strategies targeting full-length HTT at sequences 3’ to intron 1 HTT will predominantly lower wild-type HTT, as mutant HTT levels in these cells are already depleted. These data support a therapeutic strategy that lowers HTT1a and depletes levels of the HTT1a protein.

An intelligent magnetic resonance imagining-based multistage Alzheimer's disease classification using swish-convolutional neural networks.

Alzheimer's disease (AD) refers to a neurological disorder that causes damage to brain cells and results in decreasing cognitive abilities and memory. In brain scans, this degeneration can be seen in different ways. The disease can be classified into four stages: Non-demented (ND), moderate demented (MoD), mild demented (MiD), and very mild demented (VMD). To prepare the raw dataset for analysis, the collected magnetic resonance imaging (MRI) images are subjected to several pre-processing techniques in order to improve the performance accuracy of the proposed model. Medical images generally have poor contrast and get affected by noise, which ends up with inaccurate diagnosis. For the different phases of AD to be detected, a clear image is necessary. To address this issue, the influence of the artefacts must be reduced, enhance the contrast, and reduce the loss of information. A novel framework for image enhancement is suggested to increase the accuracy in the detection and identification of AD. In this study, the raw MRI dataset from the Alzheimer's disease neuroimaging initiative (ADNI) database is subjected to skull stripping, contrast enhancement, and image filtering followed by data augmentation to balance the dataset with four types of Alzheimer's classes. The pre-processed data are subjected to five different pre-trained models such as AlexNet, ResNet, VGG 16, EfficientNet, and Inceptionv3 achieving a testing accuracy rate of 91.2%, 88.21%, 92.34%, 93.45%, and 85.12%, respectively. These pre-trained models are compared with the proposed CNN (convolutional neural network) model designed with Adam optimizer and Flatten Swish activation function which reaches the highest accuracy of 96.5% with a learning rate of 0.000001. The five pre-trained CNNmodels along with the proposed swish-based AD-CNN were tested using various performance metrics to evaluate the model efficiency in classifying and identifying the AD classes. From the result analysis, it is evident that the proposed AD-CNN model outperforms all the other models.

Synergistic Activation of VDR-RXR Heterodimers by Vitamin D and Rexinoids in Human Kidney and Brain Cells

Synergistic Activation of VDR-RXR Heterodimers by Vitamin D and Rexinoids in Human Kidney and Brain Cells

Chronobiological disruptions: unravelling the interplay of shift work, circadian rhythms, and vascular health in the context of stroke risk.

Shift work, particularly night shifts, disrupts circadian rhythms and increases stroke risk. This manuscript explores the mechanisms connecting shift work with stroke, focusing on circadian rhythms, hypertension, and diabetes. The circadian system, controlled by different mechanisms including central and peripheral clock genes, suprachiasmatic nuclei (SCN), and pineal gland (through melatonin production), regulates body functions and responds to environmental signals. Disruptions in this system affect endothelial cells, leading to blood pressure issues. Type 2 diabetes mellitus (T2DM) is significantly associated with night shifts, with circadian disturbances affecting glucose metabolism, insulin sensitivity, and hormone regulation. The manuscript examines the relationship between melatonin, insulin, and glucose balance, highlighting pathways that link T2DM to stroke risk. Additionally, dyslipidemia, particularly reduced HDL-c levels, results from shift work and contributes to stroke development. High lipid levels cause oxidative stress, inflammation, and endothelial dysfunction, increasing cerebrovascular risks. The manuscript details the effects of dyslipidemia on brain functions, including disruptions in blood flow, blood-brain barrier integrity, and neural cell death. This comprehensive analysis emphasizes the complex interplay of circadian disruption, hypertension, diabetes, and dyslipidemia in increasing stroke risk among shift workers. Understanding these mechanisms is essential for developing targeted interventions to reduce stroke susceptibility and improve cerebrovascular health in this vulnerable population.