The Oncogenic Role of γ-Aminobutyrate Aminotransferase in Human Tumor: A Pan-Cancer Analysis

Emerging evidence supports the correlation between γ-aminobutyrate aminotransferase (ABAT) and tumors, but few research groups used pan-cancer analysis to verify it previously. Therefore, this study used the Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) to obtain information about the correlations between ABAT and tumor development, and to explore its potential effectiveness for genetic alterations in tumor prognosis. The reduced expression level of ABAT in a majority of tumors is significantly associated with the poor prognosis. The genetic alteration of ABAT seems linked to the favorable prognosis of Uterine Corpus Endometrial Carcinoma (UCEC). Immune infiltration analysis showed a significantly positive correlation between ABAT and cancer-associated fibroblasts in the majority of tumors, but a highly negative correlation with Kidney renal clear cell carcinoma (KIRC), Kidney Renal Papillary cell carcinoma (KIRP), and Prostate adenocarcinoma (PRAD). Enrichment analysis showed that cell junction organization, amino acids metabolism, and neuronal system-involved behaviors might affect the pathogenesis or etiology of cancer. This study is the first pan-cancer analysis that offers a detailed, comprehensive study of the process of the oncogenic roles of ABAT across different human tumors.

The Nerve Growth Factor Metabolic Pathway Dysregulation as Cause of Alzheimer’s Cholinergic Atrophy

The cause of the loss of basal forebrain cholinergic neurons (BFCNs) and their terminal synapses in the cerebral cortex and hippocampus in Alzheimer’s disease (AD) has provoked a decades-long controversy. The cholinergic phenotype of this neuronal system, involved in numerous cognitive mechanisms, is tightly dependent on the target-derived nerve growth factor (NGF). Consequently, the loss of BFCNs cholinergic phenotype in AD was initially suspected to be due to an NGF trophic failure. However, in AD there is a normal NGF synthesis and abundance of the NGF precursor (proNGF), therefore the NGF trophic failure hypothesis for the atrophy of BCNs was abandoned. In this review, we discuss the history of NGF-dependency of BFCNs and the atrophy of these neurons in Alzheimer’s disease (AD). Further to it, we propose that trophic factor failure explains the BFCNs atrophy in AD. We discuss evidence of the occurrence of a brain NGF metabolic pathway, the dysregulation of which, in AD explains the severe deficiency of NGF trophic support for the maintenance of BFCNs cholinergic phenotype. Finally, we revise recent evidence that the NGF metabolic dysregulation in AD pathology starts at preclinical stages. We also propose that the alteration of NGF metabolism-related markers in body fluids might assist in the AD preclinical diagnosis.

The S-palmitoylome and DHHC-PAT interactome of Drosophila melanogaster S2R+ cells indicate a high degree of conservation to mammalian palmitoylomes

ABSTRACTProtein S-palmitoylation, the addition of a long-chain fatty acid to target proteins, is among the most frequent reversible protein modification in Metazoa, affecting subcellular protein localization, trafficking and protein-protein interactions. S-palmitoylated proteins are abundant in the neuronal system and are associated with neuronal diseases and cancer. Despite the importance of this post-translational modification, it has not been thoroughly studied in the model organism Drosophila melanogaster.Here we present the palmitoylome of Drosophila S2R+ cells, comprising 198 proteins, an estimated 3.5% of expressed genes in these cells. Comparison of orthologs between mammals and Drosophila suggests that S-palmitoylated proteins are more conserved between these distant phyla than non-S-palmitoylated proteins. To identify putative client proteins and interaction partners of the DHHC family of protein acyl-transferases (PATs) we established DHHC-BioID, a proximity biotinylation-based method. In S2R+ cells ectopic expression of the DHHC-PAT dHip14-BioID in combination with Snap24 or an interaction-deficient Snap24- mutant, as a negative control, resulted in biotinylation of Snap24 but not the Snap24-mutant. DHHC-BioID in S2R+ cells using 10 different DHHC-PATs as bait identified 520 putative DHHC-PAT interaction partners of which 48 were S-palmitoylated and are therefore putative DHHC-PAT client proteins. Comparison of putative client protein/DHHC-PAT combinations indicates that CG8314, CG5196, CG5880 and Patsas have a preference for transmembrane proteins, while S-palmitoylated proteins with the Hip14-interaction motif are most enriched by DHHC-BioID variants of approximated and dHip14. Finally, we show that BioID is active in larval and adult Drosophila and that dHip14-BioID rescues dHip14 mutant flies, indicating that DHHC-BioID is non-toxic.In summary we provide the first systematic analysis of a Drosophila palmitoylome. We show that DHHC-BioID is sensitive and specific enough to identify DHHC-PAT client proteins and provide DHHC-PAT assignment for ca. 25% of the S2R+ cell palmitoylome, providing a valuable resource. In addition, we establish DHHC-BioID as a useful concept for the identification of tissue-specific DHHC-PAT interactomes in Drosophila.

Characterization of Pathogenesis and Inflammatory Responses to Experimental Parechovirus Encephalitis

Human parechovirus type 3 (PeV-A3) infection has been recognized as an emerging etiologic factor causing severe nerve disease or sepsis in infants and young children. But the neuropathogenic mechanisms of PeV-A3 remain unknown. To understand the pathogenesis of PeV-A3 infection in the neuronal system, PeV-A3-mediated cytopathic effects were analyzed in human glioblastoma cells and neuroblastoma cells. PeV-A3 induced interferons and inflammatory cytokine expression in these neuronal cells. The pronounced cytopathic effects accompanied with activation of death signaling pathways of apoptosis, autophagy, and pyroptosis were detected. A new experimental disease model of parechovirus encephalitis was established. In the disease model, intracranial inoculation with PeV-A3 in C57BL/6 neonatal mice showed body weight loss, hindlimb paralysis, and approximately 20% mortality. PeV-A3 infection in the hippocampus and cortex regions of the neonatal mouse brain was revealed. Mechanistic assay supported the in vitro results, indicating detection of PeV-A3 replication, inflammatory cytokine expression, and death signaling transduction in mouse brain tissues. These in vitro and in vivo studies revealed that the activation of death signaling and inflammation responses is involved in PeV-A3-mediated neurological disorders. The present results might account for some of the PeV-A3-associated clinical manifestations.

Tet1 Regulates Astrocyte Development and Cognition of Mice Through Modulating GluA1

Tet (Ten eleven translocation) family proteins-mediated 5-hydroxymethylcytosine (5hmC) is highly enriched in the neuronal system, and is involved in diverse biological processes and diseases. However, the function of 5hmC in astrocyte remains completely unknown. In the present study, we show that Tet1 deficiency alters astrocyte morphology and impairs neuronal function. Specific deletion of Tet1 in astrocyte impairs learning and memory ability of mice. Using 5hmC high-throughput DNA sequencing and RNA sequencing, we present the distribution of 5hmC among genomic features in astrocyte and show that Tet1 deficiency induces differentially hydroxymethylated regions (DhMRs) and alters gene expression. Mechanistically, we found that Tet1 deficiency leads to the abnormal Ca2+ signaling by regulating the expression of GluA1, which can be rescued by ectopic GluA1. Collectively, our findings suggest that Tet1 plays important function in astrocyte physiology by regulating Ca2+ signaling.

Foreground Estimation in Neuronal Images With a Sparse-Smooth Model for Robust Quantification

3D volume imaging has been regarded as a basic tool to explore the organization and function of the neuronal system. Foreground estimation from neuronal image is essential in the quantification and analysis of neuronal image such as soma counting, neurite tracing and neuron reconstruction. However, the complexity of neuronal structure itself and differences in the imaging procedure, including different optical systems and biological labeling methods, result in various and complex neuronal images, which greatly challenge foreground estimation from neuronal image. In this study, we propose a robust sparse-smooth model (RSSM) to separate the foreground and the background of neuronal image. The model combines the different smoothness levels of the foreground and the background, and the sparsity of the foreground. These prior constraints together contribute to the robustness of foreground estimation from a variety of neuronal images. We demonstrate the proposed RSSM method could promote some best available tools to trace neurites or locate somas from neuronal images with their default parameters, and the quantified results are similar or superior to the results that generated from the original images. The proposed method is proved to be robust in the foreground estimation from different neuronal images, and helps to improve the usability of current quantitative tools on various neuronal images with several applications.

Resilience of Nematode Connectomes Based on Network Dimension-reduced Method

The whole map of nematode connectomes provides important structural data for exploring the behavioral mechanism of nematodes, but to further reveal the functional importance and resilience pattern of nematode neurons, it is necessary to effectively couple the regulatory relationship between neurons and their topology. Here, with a typical signal excitation function we propose a model to capture the interacting relationship between the neurons, because a differential equation depicts the activity of a neuron, n neurons mean we need high-D differential equations to capture the neural network. With mean-field theory, we decouple this N-dimension question into a one-dimension problem mathematically. In our framework, we emphatically analyze the characteristics, similarities and differences of the structure and dynamical behaviors of the neuronal system for Caenorhabditis elegans and Pristionchus pacificus. The comparing results of simulating method and theoretical approach show that the most important homologous neurons between C.elegans and P.pacificus are I2 and NSM, which may lead to their different behavior characteristics of predation and prey. At the same time, we expect that the xeff index can be used to reveal the importance of neurons for the functional evolution and degeneration of neural networks from a dynamic perspective. In the hermaphroditic and male C.elegans, we test the control level of the intermediate neuron groups over the output neuron groups and the single neuron. These results suggest that our theoretical approach can be used to reveal the effects of bio-connectivity groups, potentially enabling us to explore the interaction relationship of neural networks in humans and animals.

Histochemical characteristics of nitrergic neuronal system during acute alcohol intoxication and nNOS blockage in the rat lateral septum

Annotation. Alcohol is a one of the most frequently consumed substances of abuse, which can cause addiction or alcohol use disorders (AUDs). Alcohol addiction leads to decrease of the life quality of patients and considerable economic burden. Neuronal mechanisms of addiction are intensively studied. One of the most important systems involved in this process is a brain reward system that includes lateral septum (LS). Additionally alcohol consumption changes activity of the neurotransmitter systems including the nitric oxide (NO). Recent studies for blockage of nitric oxide synthase (NOS) for cocaine addiction and late stages of AUDs demonstrated that a group of the substances known as blockers of NOS can be referred to as candidates for alcohol addiction therapy. The aim of our research was to investigate histochemical characteristics of NO-system in LS, its response to acute alcohol intoxication including or excluding neuronal NOS (nNOS) blockage with selective inhibitor – 7-nitroindazole (7-NI). This study involved three experimental groups of animals (control group (n=4), group with acute alcohol intoxication (n=4), group of nNOS blockage with acute alcohol intoxication (n=4)). For statistical analysis, one-way Kruskal-Wallis test was implemented to reveal differences between groups (Matlab, Mathworks). We have identified NOS-positive structures in LS consisting of big neurons, medium/small neurons and nerve fibers. Acute alcohol intoxication activated subpopulations of NOS-positive medium/small neurons and nerve fibers. Moreover, we determined that ethanol-induced changes can be blocked with selective nNOS inhibitor 7-NI.

Chaotic Resonance in Izhikevich Neural Network Motifs Under Electromagnetic Induction

Chaotic resonance (CR) is the response of a nonlinear system to weak signals enhanced by internal or external chaotic activity (such as the signal derived from Lorenz system). In this paper, the triple-neuron feed-forward loop (FFL) Izhikevich neural network motifs with eight types are constructed as the nonlinear systems, and the effects of EMI on CR phenomenon in FFL neuronal network motifs are studied. It is found that both the single Izhikevich neural model under electromagnetic induction (EMI) and its network motifs exhibit CR phenomenon depending on the chaotic current intensity. There exists an optimal chaotic current intensity ensuring the best detection of weak signal in single Izhikevich neuron or its network motifs via CR. The EMI can enhance the ability of neuron to detect weak signals. For T1-FFL and T2-FFL motifs, the adjustment of EMI parameters makes T2-FFL show a more obvious CR phenomenon than that for T1-FFL motifs, which is different from the impact of system parameters (e.g., the weak signal frequency, the coupling strength, and the time delay) on CR. Another interesting phenomenon is that the variation of CR with time delay exhibits quasi periodic characteristics. Our results showed that CR effect is a robust phenomenon which is observed in both single Izhikevich neuron and network motifs, which might help one understand how to improve the ability of weak signal detection and propagation in neuronal system.