ETV5 is Essential for Neuronal Differentiation of Human Neural Progenitor Cells by Repressing NEUROG2 Expression

Integrative Multi-omics Analysis to Characterize Herpes Virus Infection Increases the Risk of Alzheimer's Disease

Evidence suggests that herpes virus infection is associated with an increased risk of Alzheimer's disease (AD), and innate and adaptive immunity plays an important role in the association. Although there have been many studies, the mechanism of the association is still unclear. This study aims to reveal the underlying molecular and immune regulatory network through multi-omics data and provide support for the study of the mechanism of infection and AD in the future. Here, we found that the herpes virus infection significantly increased the risk of AD. Genes associated with the occurrence and development of AD and genetically regulated by herpes virus infection are mainly enrichment in immune-related pathways. The 22 key regulatory genes identified by machine learning are mainly immune genes. They are also significantly related to the infiltration changes of 3 immune cell in AD. Furthermore, many of these genes have previously been reported to be linked, or potentially linked, to the pathological mechanisms of both herpes virus infection and AD. In conclusion, this study contributes to the study of the mechanisms related to herpes virus infection and AD, and indicates that the regulation of innate and adaptive immunity may be an effective strategy for preventing and treating herpes virus infection and AD. Additionally, the identified key regulatory genes, whether previously studied or newly discovered, may serve as valuable targets for prevention and treatment strategies.

Single-cell profiling coupled with lineage analysis reveals vagal and sacral neural crest contributions to the developing enteric nervous system

During development, much of the enteric nervous system (ENS) arises from the vagal neural crest that emerges from the caudal hindbrain and colonizes the entire gastrointestinal tract. However, a second ENS contribution comes from the sacral neural crest that arises in the caudal neural tube and populates the post-umbilical gut. By coupling single-cell transcriptomics with axial-level-specific lineage tracing in avian embryos, we compared the contributions of embryonic vagal and sacral neural crest cells to the chick ENS and the associated peripheral ganglia (Nerve of Remak and pelvic plexuses). At embryonic day (E) 10, the two neural crest populations form overlapping subsets of neuronal and glia cell types. Surprisingly, the post-umbilical vagal neural crest much more closely resembles the sacral neural crest than the pre-umbilical vagal neural crest. However, some differences in cluster types were noted between vagal and sacral derived cells. Notably, RNA trajectory analysis suggests that the vagal neural crest maintains a neuronal/glial progenitor pool, whereas this cluster is depleted in the E10 sacral neural crest which instead has numerous enteric glia. The present findings reveal sacral neural crest contributions to the hindgut and associated peripheral ganglia and highlight the potential influence of the local environment and/or developmental timing in differentiation of neural crest-derived cells in the developing ENS.

Methamphetamine-induced region-specific transcriptomic and epigenetic changes in the brain of male rats

Psychostimulant methamphetamine (METH) is neurotoxic to the brain and, therefore, its misuse leads to neurological and psychiatric disorders. The gene regulatory network (GRN) response to neurotoxic METH binge remains unclear in most brain regions. Here we examined the effects of binge METH on the GRN in the nucleus accumbens, dentate gyrus, Ammon's horn, and subventricular zone in male rats. At 24 h after METH, ~16% of genes displayed altered expression and over a quarter of previously open chromatin regions - parts of the genome where genes are typically active - showed shifts in their accessibility. Intriguingly, most changes were unique to each area studied, and independent regulation between transcriptome and chromatin accessibility was observed. Unexpectedly, METH differentially impacted gene activity and chromatin accessibility within the dentate gyrus and Ammon's horn. Around 70% of the affected chromatin-accessible regions in the rat brain have conserved DNA sequences in the human genome. These regions frequently act as enhancers, ramping up the activity of nearby genes, and contain mutations linked to various neurological conditions. By sketching out the gene regulatory networks associated with binge METH in specific brain regions, our study offers fresh insights into how METH can trigger profound, region-specific molecular shifts.

Etv5a Suppresses Neural Progenitor Cell Proliferation by Inhibiting sox2 Transcription

Neural progenitor cells are self-renewable, proliferative, and multipotent cell populations that generate diverse types of neurons and glia to build the nervous system. Transcription factors play critical roles in regulating various cellular processes; however, the transcription factors that regulate the development of neural progenitors are yet to be identified. In the present study, we demonstrated that zebrafish etv5a is expressed in the neural progenitor cells of the neuroectoderm. Downregulation of endogenous Etv5a function by etv5a morpholino or an etv5a dominant-negative variant increased the proliferation of sox2-positive neural progenitor cells, accompanied by inhibition of neurogenesis and gliogenesis. These phenotypes in Etv5a-depleted embryos could be rescued by a co-injection with etv5a cRNA. Etv5a overexpression reduced sox2 expression. Direct binding of Etv5a to the regulatory elements of sox2 was affirmed by chromatin immunoprecipitation. These data revealed that Etv5a directly suppressed sox2 expression to reduce the proliferation of neural progenitor cells. In addition, the expression of foxm1, a putative target gene of Etv5a and a direct upstream transcription factor of sox2, was upregulated in Etv5a-deficient embryos. Moreover, the suppression of Foxm1 function by the foxm1 dominant-negative construct nullified the phenotype of upregulated sox2 expression caused by Etv5a deficiency. Overall, our results indicated that Etv5a regulates the expression of sox2 via direct binding to the sox2 promoter and indirect regulation by inhibiting foxm1 expression. Hence, we revealed the role of Etv5a in the transcriptional hierarchy that regulates the proliferation of neural progenitor cells.

DNA Methylation Description of Hippocampus, Cortex, Amygdala, and Blood of Drug-Resistant Temporal Lobe Epilepsy

Epigenetic changes such as DNA methylation were observed in drug-resistant temporal lobe epilepsy (DR-TLE), a disease that affects 25-30% of epilepsy patients. The main objective is to simultaneously describe DNA methylation patterns associated with DR-TLE in hippocampus, amygdala, surrounding cortex to the epileptogenic zone (SCEZ), and peripheral blood. An Illumina Infinium MethylationEPIC BeadChip array was performed in 19 DR-TLE patients and 10 postmortem non-epileptic controls. Overall, 32, 59, and 3210 differentially methylated probes (DMPs) were associated with DR-TLE in the hippocampus, amygdala, and SCEZ, respectively. These DMP-affected genes were involved in neurotrophic and calcium signaling in the hippocampus and voltage-gated channels in SCEZ, among others. One of the hippocampus DMPs (cg26834418 (CHORDC1)) showed a strong blood-brain correlation with BECon and IMAGE-CpG, suggesting that it could be a potential surrogate peripheral biomarker of DR-TLE. Moreover, in three of the top SCEZ's DMPs (SHANK3, SBF1, and MCF2L), methylation status was verified with methylation-specific qPCR. The differentially methylated CpGs were classified in DMRs: 2 in the hippocampus, 12 in the amygdala, and 531 in the SCEZ. We identified genes that had not been associated to DR-TLE so far such as TBX5, EXOC7, and WRHN. The area with more DMPs associated with DR-TLE was the SCEZ, some of them related to voltage-gated channels. The DMPs found in the amygdala were involved in inflammatory processes. We also found a potential surrogate peripheral biomarker of DR-TLE. Thus, these results provide new insights into epigenetic modifications involved in DR-TLE.

E26 transformation-specific transcription variant 5 in development and cancer: modification, regulation and function

E26 transformation-specific (ETS) transcription variant 5 (ETV5), also known as ETS-related molecule (ERM), exerts versatile functions in normal physiological processes, including branching morphogenesis, neural system development, fertility, embryonic development, immune regulation, and cell metabolism. In addition, ETV5 is repeatedly found to be overexpressed in multiple malignant tumors, where it is involved in cancer progression as an oncogenic transcription factor. Its roles in cancer metastasis, proliferation, oxidative stress response and drug resistance indicate that it is a potential prognostic biomarker, as well as a therapeutic target for cancer treatment. Post-translational modifications, gene fusion events, sophisticated cellular signaling crosstalk and non-coding RNAs contribute to the dysregulation and abnormal activities of ETV5. However, few studies to date systematically summarized the role and molecular mechanisms of ETV5 in benign diseases and in oncogenic progression. In this review, we specify the molecular structure and post-translational modifications of ETV5. In addition, its critical roles in benign and malignant diseases are summarized to draw a panorama for specialists and clinicians. The updated molecular mechanisms of ETV5 in cancer biology and tumor progression are delineated. Finally, we prospect the further direction of ETV5 research in oncology and its potential translational applications in the clinic.

ETS transcription factors: Multifaceted players from cancer progression to tumor immunity

The E26 transformation specific (ETS) family comprises 28 transcription factors, the majority of which are involved in tumor initiation and development. Serving as a group of functionally heterogeneous gene regulators, ETS factors possess a structurally conserved DNA-binding domain. As one of the most prominent families of transcription factors that control diverse cellular functions, ETS activation is modulated by multiple intracellular signaling pathways and post-translational modifications. Disturbances in ETS activity often lead to abnormal changes in oncogenicity, including cancer cell survival, growth, proliferation, metastasis, genetic instability, cell metabolism, and tumor immunity. This review systematically addresses the basics and advances in studying ETS factors, from their tumor relevance to clinical translational utility, with a particular focus on elucidating the role of ETS family in tumor immunity, aiming to decipher the vital role and clinical potential of regulation of ETS factors in the cancer field.

GABAergic neurons maturation is regulated by a delicate network

Gamma-aminobutyric acid-expressing (GABAergic) neurons are implicated in a variety of neuropsychiatric disorders, such as epilepsy, anxiety, autism, and other pathological processes, including cerebral ischemia injury and drug addiction. Therefore, GABAergic neuronal processes warrant further research. The development of GABAergic neurons is a tightly controlled process involving the activity of multiple transcription and growth factors. Here, we focus on the gene expression pathways and the molecular modulatory networks that are engaged during the development of GABAergic neurons with the goal of exploring regulatory mechanisms that influence GABAergic neuron fate (i.e., maturation). Overall, we hope to provide a basis for clarifying the pathogenesis of neurodegenerative disorders.

Effects of Magnetite Nanoparticles and Static Magnetic Field on Neural Differentiation of Pluripotent Stem Cells

Neurodevelopmental processes of pluripotent cells, such as proliferation and differentiation, are influenced by external natural forces. Despite the presence of biogenic magnetite nanoparticles in the central nervous system and constant exposure to the Earth's magnetic fields and other sources, there is scant knowledge regarding the role of electromagnetic stimuli in neurogenesis. Moreover, emerging applications of electrical and magnetic stimulation to treat neurological disorders emphasize the relevance of understanding the impact and mechanisms behind these stimuli. Here, the effects of magnetic nanoparticles (MNPs) in polymeric coatings and the static external magnetic field (EMF) were investigated on neural induction of murine embryonic stem cells (mESCs) and human induced pluripotent stem cells (hiPSCs). The results show that the presence of 0.5% MNPs in collagen-based coatings facilitates the migration and neuronal maturation of mESCs and hiPSCs in vitro. Furthermore, the application of 0.4 Tesla EMF perpendicularly to the cell culture plane, discernibly stimulates proliferation and guide fate decisions of the pluripotent stem cells, depending on the origin of stem cells and their developmental stage. Mechanistic analysis reveals that modulation of ionic homeostasis and the expression of proteins involved in cytostructural, liposomal and cell cycle checkpoint functions provide a principal underpinning for the impact of electromagnetic stimuli on neural lineage specification and proliferation. These findings not only explore the potential of the magnetic stimuli as neural differentiation and function modulator but also highlight the risks that immoderate magnetic stimulation may affect more susceptible neurons, such as dopaminergic neurons.

Role of Calcium Signaling Pathway-Related Gene Regulatory Networks in Ischemic Stroke Based on Multiple WGCNA and Single-Cell Analysis

Background

This study is aimed at investigating the changes in relevant pathways and the differential expression of related gene expression after ischemic stroke (IS) at the single-cell level using multiple weighted gene coexpression network analysis (WGCNA) and single-cell analysis.

Methods

The transcriptome expression datasets of IS samples and single-cell RNA sequencing (scRNA-seq) profiles of cerebrovascular tissues were obtained by searching the Gene Expression Omnibus (GEO) database. First, gene pathway scoring was calculated via gene set variation analysis (GSVA) and was imported into multiple WGCNA to acquire key pathways and pathway-related hub genes. Furthermore, SCENIC was used to identify transcription factors (TFs) regulating these core genes using scRNA-seq data. Finally, the pseudotemporal trajectory analysis was used to analyse the role of these TFs on various cell types under hypoxic and normoxic conditions.

Results

The scores of 186 KEGG pathways were obtained via GSVA using microarray expression profiles of 40 specimens. WGCNA of the KEGG pathways revealed the two following pathways: calcium signaling pathway and neuroactive ligand-receptor interaction pathways. Subsequently, WGCNA of the gene expression matrix of the samples revealed the calcium signaling pathway-related genes (AC079305.10, BCL10, BCL2A1, BRE-AS1, DYNLL2, EREG, and PTGS2) that were identified as core genes via correlation analysis. Furthermore, SCENIC and pseudotemporal analysis revealed JUN, IRF9, ETV5, and PPARA score gene-related TFs. Jun was found to be associated with hypoxia in endothelial cells, whereas Irf9 and Etv5 were identified as astrocyte-specific TFs associated with oxygen concentration in the mouse cerebral cortex.

Conclusions

Calcium signaling pathway-related genes (AC079305.10, BCL10, BCL2A1, BRE-AS1, DYNLL2, EREG, and PTGS2) and TFs (JUN, IRF9, ETV5, and PPARA) were identified to play a key role in IS. This study provides a new perspective and basis for investigating the pathogenesis of IS and developing new therapeutic approaches.

Cell-type-specific effects of genetic variation on chromatin accessibility during human neuronal differentiation

Common genetic risk for neuropsychiatric disorders is enriched in regulatory elements active during cortical neurogenesis. However, it remains poorly understood as to how these variants influence gene regulation. To model the functional impact of common genetic variation on the noncoding genome during human cortical development, we performed the assay for transposase accessible chromatin using sequencing (ATAC-seq) and analyzed chromatin accessibility quantitative trait loci (QTL) in cultured human neural progenitor cells and their differentiated neuronal progeny from 87 donors. We identified significant genetic effects on 988/1,839 neuron/progenitor regulatory elements, with highly cell-type and temporally specific effects. A subset (roughly 30%) of chromatin accessibility-QTL were also associated with changes in gene expression. Motif-disrupting alleles of transcriptional activators generally led to decreases in chromatin accessibility, whereas motif-disrupting alleles of repressors led to increases in chromatin accessibility. By integrating cell-type-specific chromatin accessibility-QTL and brain-relevant genome-wide association data, we were able to fine-map and identify regulatory mechanisms underlying noncoding neuropsychiatric disorder risk loci.

3D promoter architecture re-organization during iPSC-derived neuronal cell differentiation implicates target genes for neurodevelopmental disorders

Neurodevelopmental disorders are thought to arise from interrupted development of the brain at an early age. Genome-wide association studies (GWAS) have identified hundreds of loci associated with susceptibility to neurodevelopmental disorders; however, which noncoding variants regulate which genes at these loci is often unclear. To implicate neuronal GWAS effector genes, we performed an integrated analysis of transcriptomics, epigenomics and chromatin conformation changes during the development from Induced pluripotent stem cell-derived neuronal progenitor cells (NPCs) into neurons using a combination of high-resolution promoter-focused Capture-C, ATAC-seq and RNA-seq. We observed that gene expression changes during the NPC-to-neuron transition were highly dependent on both promoter accessibility changes and long-range interactions which connect distal cis-regulatory elements (enhancer or silencers) to developmental-stage-specific genes. These genome-scale promoter-cis-regulatory-element atlases implicated 454 neurodevelopmental disorder-associated, putative causal variants mapping to 600 distal targets. These putative effector genes were significantly enriched for pathways involved in the regulation of neuronal development and chromatin organization, with 27 % expressed in a stage-specific manner. The intersection of open chromatin and chromatin conformation revealed development-stage-specific gene regulatory architectures during neuronal differentiation, providing a rich resource to aid characterization of the genetic and developmental basis of neurodevelopmental disorders.

HOTAIRM1 regulates neuronal differentiation by modulating NEUROGENIN 2 and the downstream neurogenic cascade

Neuronal differentiation is a timely and spatially regulated process, relying on precisely orchestrated gene expression control. The sequential activation/repression of genes driving cell fate specification is achieved by complex regulatory networks, where transcription factors and noncoding RNAs work in a coordinated manner. Herein, we identify the long noncoding RNA HOTAIRM1 (HOXA Transcript Antisense RNA, Myeloid-Specific 1) as a new player in neuronal differentiation. We demonstrate that the neuronal-enriched HOTAIRM1 isoform epigenetically controls the expression of the proneural transcription factor NEUROGENIN 2 that is key to neuronal fate commitment and critical for brain development. We also show that HOTAIRM1 activity impacts on NEUROGENIN 2 downstream regulatory cascade, thus contributing to the achievement of proper neuronal differentiation timing. Finally, we identify the RNA-binding proteins HNRNPK and FUS as regulators of HOTAIRM1 biogenesis and metabolism. Our findings uncover a new regulatory layer underlying NEUROGENIN 2 transitory expression in neuronal differentiation and reveal a previously unidentified function for the neuronal-induced long noncoding RNA HOTAIRM1.