High Throughput Sequencing Identifies MicroRNAs Mediating α-Synuclein Toxicity by Targeting Neuroactive-Ligand Receptor Interaction Pathway in Early Stage of Drosophila Parkinson's Disease Model

Red light-induced localized release of carbon monoxide for alleviating postoperative cognitive dysfunction

Inflammation within the central nervous system (CNS), which may be triggered by surgical trauma, has been implicated as a significant factor contributing to postoperative cognitive dysfunction (POCD). The relationship between mitigating inflammation at peripheral surgical sites and its potential to attenuate the CNS inflammatory response, thereby easing POCD symptoms, remains uncertain. Notably, carbon monoxide (CO), a gasotransmitter, exhibits pronounced anti-inflammatory effects. Herein, we have developed carbon monoxide-releasing micelles (CORMs), a nanoparticle that safely and locally liberates CO upon exposure to 650 nm light irradiation. In a POCD mouse model, treatment with CORMs activated by light (CORMs + hv) markedly reduced the concentrations of interleukin (IL)-6, IL-1β, and tumor necrosis factor-alpha (TNF-α) in both the peripheral blood and the hippocampus, alongside a decrease in ionized calcium-binding adapter molecule 1 in the hippocampal CA1 region. Furthermore, CORMs + hv treatment diminished Evans blue extravasation, augmented the expression of tight junction proteins zonula occludens-1 and occludin, enhanced neurocognitive functions, and fostered fracture healing. Bioinformatics analysis and experimental validation has identified Htr1b and Trhr as potential key regulators in the neuroactive ligand-receptor interaction signaling pathway implicated in POCD. This work offers new perspectives on the mechanisms driving POCD and avenues for therapeutic intervention.

The Role of miR-137 in Neurodegenerative Disorders

Neurodegenerative diseases affect an increasing part of the population of modern societies, burdening healthcare systems and causing immense suffering at the personal level. The pathogenesis of several of these disorders involves dysregulation of gene expression, which depends on several molecular processes ranging from transcription to protein stability. microRNAs (miRNAs) are short non-coding RNA molecules that modulate gene expression by suppressing the translation of partially complementary mRNAs. miR-137 is a conserved, neuronally enriched miRNA that is implicated in neurodegeneration. Here, we review the current body of knowledge about the role that miR-137 plays in five prominent neurodegenerative disorders, including Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and multiple sclerosis. The presented data indicate that, rather than having a general neuroprotective role, miR-137 modulates the pathology of distinct disorders differently.

A targeted CRISPR-Cas9 mediated F0 screen identifies genes involved in establishment of the enteric nervous system

The vertebrate enteric nervous system (ENS) is a crucial network of enteric neurons and glia resident within the entire gastrointestinal tract (GI). Overseeing essential GI functions such as gut motility and water balance, the ENS serves as a pivotal bidirectional link in the gut-brain axis. During early development, the ENS is primarily derived from enteric neural crest cells (ENCCs). Disruptions to ENCC development, as seen in conditions like Hirschsprung disease (HSCR), lead to the absence of ENS in the GI, particularly in the colon. In this study, using zebrafish, we devised an in vivo F0 CRISPR-based screen employing a robust, rapid pipeline integrating single-cell RNA sequencing, CRISPR reverse genetics, and high-content imaging. Our findings unveil various genes, including those encoding opioid receptors, as possible regulators of ENS establishment. In addition, we present evidence that suggests opioid receptor involvement in the neurochemical coding of the larval ENS. In summary, our work presents a novel, efficient CRISPR screen targeting ENS development, facilitating the discovery of previously unknown genes, and increasing knowledge of nervous system construction.

Expression and metabolism profiles of CVT associated with inflammatory responses and oxygen carrier ability in the brain

AIM

As the main type of stroke, the incidence of cerebral venous thrombosis (CVT) has been rising. However, the comprehensive mechanisms behind it remain unclear. Thus, the multi-omics study is required to investigate the mechanism after CVT and elucidate the characteristic pathology of venous stroke and arterial stroke.

METHODS

Adult rats were subjected to CVT and MCAO models. Whole-transcriptome sequencing (RNA-seq) and untargeted metabolomics analysis were performed to construct the transcriptome and metabolism profiles of rat brains after CVT and also MCAO. The difference analysis, functional annotation, and enrichment analysis were also performed.

RESULTS

Through RNA-seq analysis, differentially expressed genes (DEGs) were screened. 174 CVT specific genes including Il1a, Ccl9, Cxxl6, Tnfrsf14, etc., were detected. The hemoglobin genes, including both Hba and Hbb, were significantly downregulated after CVT, compared both to the MCAO and Sham groups. Metabolism analysis showed that CVT had higher heterogeneity of metabolism compared to MCAO. Metabolites including N-stearoyltyrosine, 5-methoxy-3-indoleaceate, Afegostat, pipecolic acid, etc. were specially regulated in CVT. Through the immune infiltration analysis, it was found that CVT had a higher immune response, with the abundance of certain types of immune cells increased, especially T helper cells. It was important to find the prevalence of the activation of inflammatory chemokine, cytokine, NOD-like pathway, and neutrophil extracellular trap.

CONCLUSION

We explored and analyzed the gene expression and metabolomic characteristics of CVT, revealed the specific inflammatory reaction mechanism of CVT and found the markers in transcriptome and metabolism levels. It points out the direction for CVT early diagnosis and treatment.

Transcriptional-profile changes in the medial geniculate body after noise-induced tinnitus

Tinnitus is a disturbing condition defined as the occurrence of acoustic hallucinations with no actual sound. Although the mechanisms underlying tinnitus have been explored extensively, the pathophysiology of the disease is not completely understood. Moreover, genes and potential treatment targets related to auditory hallucinations remain unknown. In this study, we examined transcriptional-profile changes in the medial geniculate body after noise-induced tinnitus in rats by performing RNA sequencing and validated differentially expressed genes via quantitative polymerase chain reaction analysis. The rat model of tinnitus was established by analyzing startle behavior based on gap-pre-pulse inhibition of acoustic startles. We identified 87 differently expressed genes, of which 40 were upregulated and 47 were downregulated. Pathway-enrichment analysis revealed that the differentially enriched genes in the tinnitus group were associated with pathway terms, such as coronavirus disease COVID-19, neuroactive ligand-receptor interaction. Protein-protein-interaction networks were established, and two hub genes (Rpl7a and AC136661.1) were identified among the selected genes. Further studies focusing on targeting and modulating these genes are required for developing potential treatments for noise-induced tinnitus in patients.

Comprehensive Analysis and Experimental Validation of the Parkinson's Disease Lysosomal Gene ACP2 and Pan-cancer

The pivotal role of lysosomal function in preserving neuronal homeostasis is recognized, with its dysfunction being implicated in neurodegenerative processes, notably in Parkinson's disease (PD). Yet, the molecular underpinnings of lysosome-related genes (LRGs) in the context of PD remain partially elucidated. We collected RNA-seq data from the brain substantia nigra of 30 PD patients and 20 normal subjects from the GEO database. We obtained molecular classification clusters from the screened lysosomal expression patterns. The lysosome-related diagnostic model of Parkinson's disease was constructed by XGBoost and Random Forest. And we validated the expression patterns of signature LRGs in the diagnostic model by constructing a PD rat model. Finally, the linkage between PD and cancer through signature genes was explored. The expression patterns of the 33 LRGs screened can be divided into two groups of PD samples, enabling exploration of the variance in biological processes and immune elements. Cluster A had a higher disease severity. Subsequently, critical genes were sieved through the application of machine learning methodologies culminating in the identification of two intersecting feature genes (ACP2 and LRP2). A PD risk prediction model was constructed grounded on these signature genes. The model's validity was assessed through nomogram evaluation, which demonstrated robust confidence validity. Then we analyzed the correlation analysis, immune in-filtration, biological function, and rat expression validation of the two genes with common pathogenic genes in Parkinson's disease, indicating that these two genes play an important role in the pathogenesis of PD. We then selected ACP2, which had a significant immune infiltration correlation, as the entry gene for the pan-cancer analysis. The pan-cancer analysis revealed that ACP2 has profound associations with prognostic indicators, immune infiltration, and tumor-related regulatory processes across various neoplasms, suggesting its potential as a therapeutic target in a range of human diseases, including PD and cancers. Our study comprehensively analyzed the molecular grouping of LRGs expression patterns in Parkinson's disease, and the disease progression was more severe in cluster A. And the PD diagnosis model related to LRGs is constructed. Finally, ACP2 is a potential target for the relationship between Parkinson's disease and tumor.

A semi-supervised approach for the integration of multi-omics data based on transformer multi-head self-attention mechanism and graph convolutional networks

BACKGROUND AND OBJECTIVES

Comprehensive analysis of multi-omics data is crucial for accurately formulating effective treatment plans for complex diseases. Supervised ensemble methods have gained popularity in recent years for multi-omics data analysis. However, existing research based on supervised learning algorithms often fails to fully harness the information from unlabeled nodes and overlooks the latent features within and among different omics, as well as the various associations among features. Here, we present a novel multi-omics integrative method MOSEGCN, based on the Transformer multi-head self-attention mechanism and Graph Convolutional Networks(GCN), with the aim of enhancing the accuracy of complex disease classification. MOSEGCN first employs the Transformer multi-head self-attention mechanism and Similarity Network Fusion (SNF) to separately learn the inherent correlations of latent features within and among different omics, constructing a comprehensive view of diseases. Subsequently, it feeds the learned crucial information into a self-ensembling Graph Convolutional Network (SEGCN) built upon semi-supervised learning methods for training and testing, facilitating a better analysis and utilization of information from multi-omics data to achieve precise classification of disease subtypes.

RESULTS

The experimental results show that MOSEGCN outperforms several state-of-the-art multi-omics integrative analysis approaches on three types of omics data: mRNA expression data, microRNA expression data, and DNA methylation data, with accuracy rates of 83.0% for Alzheimer's disease and 86.7% for breast cancer subtyping. Furthermore, MOSEGCN exhibits strong generalizability on the GBM dataset, enabling the identification of important biomarkers for related diseases.

CONCLUSION

MOSEGCN explores the significant relationship information among different omics and within each omics' latent features, effectively leveraging labeled and unlabeled information to further enhance the accuracy of complex disease classification. It also provides a promising approach for identifying reliable biomarkers, paving the way for personalized medicine.

miRNA-137-5p improves spatial memory and cognition in Alzheimer's mice by targeting ubiquitin-specific peptidase 30

BACKGROUND

Alzheimer's disease (AD) is a prevalent neurodegenerative disorder causing progressive dementia. Research suggests that microRNAs (miRNAs) could serve as biomarkers and therapeutic targets for AD. Reduced levels of miR-137 have been observed in the brains of AD patients, but its specific role and downstream mechanisms remain unclear. This study sought to examine the therapeutic potential of miR-137-5p agomir in alleviating cognitive dysfunction induced in AD models and explore its potential mechanisms.

METHODS

This study utilized bioinformatic analysis and a dual-luciferase reporter assay to investigate the relationship between miR-137-5p and ubiquitin-specific peptidase 30 (USP30). In vitro experiments were conducted using SH-SY5Y cells to assess the impact of miR-137-5p on Aβ1-42 neurotoxicity. In vivo experiments on AD mice evaluated the effects of miR-137-5p on cognition, Aβ1-42 deposition, Tau hyperphosphorylation, and neuronal apoptosis, as well as its influence on USP30 levels.

RESULTS

It was discovered that miR-137-5p mimics efficiently counteract Aβ1-42 neurotoxicity in SH-SY5Y cells, a protective effect that is negated by USP30 overexpression. In vivo experiments demonstrated that miR-137-5p enhances the cognition and mobility of AD mice, significantly reducing Aβ1-42 deposition, Tau hyperphosphorylation, and neuronal apoptosis within the hippocampus and cortex regions. Mechanistically, miR-137-5p significantly suppresses USP30 levels in mice, though USP30 overexpression partially buffers against miR-137-5p-induced AD symptom improvement.

CONCLUSION

Our study proposes that miR-137-5p, by instigating the downregulation of USP30, has the potential to act as a novel and promising therapeutic target for AD.

Mesenchymal Stem Cell-Derived Exosomal Noncoding RNAs as Alternative Treatments for Myocardial Ischemia-Reperfusion Injury: Current Status and Future Perspectives

Ischemic cardiomyopathy is treated mainly with thrombolytic drugs, percutaneous coronary intervention, and coronary artery bypass grafting to recanalize blocked vessels. Myocardial ischemia-reperfusion injury (MIRI) is an unavoidable complication of obstructive revascularization. Compared with those of myocardial ischemic injury, few effective therapeutic options are available for MIRI treatment. The pathophysiological mechanisms of MIRI involve the inflammatory response, the immune response, oxidative stress, apoptosis, intracellular Ca2+ overload, and cardiomyocyte energy metabolism. These mechanisms exacerbate MIRI. Mesenchymal stem cell-derived exosomes (MSC-EXOs) can alleviate MIRI through these mechanisms and, to some extent, prevent the limitations caused by direct MSC administration. Therefore, using MSC-EXOs instead of MSCs to treat MIRI is a potentially beneficial cell-free treatment strategy. In this review, we describe the mechanism of action of MSC-EXO-derived noncoding RNAs in the treatment of MIRI and discuss the advantages and limitations of this strategy, as well as possible future research directions.

Preliminary study on toxicological mechanism of golden cuttlefish (Sepia esculenta) larvae exposed to cd

BACKGROUND

Cadmium (Cd) flows into the ocean with industrial and agricultural pollution and significantly affects the growth and development of economic cephalopods such as Sepia esculenta, Amphioctopus fangsiao, and Loligo japonica. As of now, the reasons why Cd affects the growth and development of S. esculenta are not yet clear.

RESULTS

In this study, transcriptome and four oxidation and toxicity indicators are used to analyze the toxicological mechanism of Cd-exposed S. esculenta larvae. Indicator results indicate that Cd induces oxidative stress and metal toxicity. Functional enrichment analysis results suggest that larval ion transport, cell adhesion, and some digestion and absorption processes are inhibited, and the cell function is damaged. Comprehensive analysis of protein-protein interaction network and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was used to explore S. esculenta larval toxicological mechanisms, and we find that among the 20 identified key genes, 14 genes are associated with neurotoxicity. Most of them are down-regulated and enriched to the neuroactive ligand-receptor interaction signaling pathway, suggesting that larval nervous system might be destroyed, and the growth, development, and movement process are significantly affected after Cd exposure.

CONCLUSIONS

S. esculenta larvae suffered severe oxidative damage after Cd exposure, which may inhibit digestion and absorption functions, and disrupt the stability of the nervous system. Our results lay a function for understanding larval toxicological mechanisms exposed to heavy metals, promoting the development of invertebrate environmental toxicology, and providing theoretical support for S. esculenta artificial culture.

Evaluation of developmental toxicity of safinamide in zebrafish larvae (Danio rerio)

Monoamine oxidase-B (MAO-B), as a principal metabolizing enzyme, plays important roles in the metabolism of catecholamines and xenobiotics in the central nervous system and peripheral tissues. Safinamide, the third-generation reversible MAO-B inhibitor, has potential to alleviate many neurological diseases such as Parkinson's disease (PD) and depression. Exposure to clinical psychotropic drugs often has adverse effects on fetuses. Currently, a variety of studies of safinamide focus on its curative effect and pharmacological effect, while its side effect of embryonic development is barely studied. In this study, we used zebrafish as a model to evaluate the embryonic developmental toxicity of safinamide. Our results revealed that higher concentrations (30 μM) of safinamide treatment caused a decrease in hatching rate and an increase in malformation and mortality in zebrafish larvae. Meanwhile, we observed that lower safinamide exposure (10 μM) increased the body length of zebrafish larvae and resulted in hyperactivity-like behaviors. In addition, an increased trend in dopamine (DA) level was found in 3.3 μM and 10 μM safinamide-exposed groups. Transcriptome analysis identified that safinamide exposure may disturb a variety of physiological processes such as neuroactive ligand-receptor interaction signaling pathway. In summary, our study reveals that safinamide may cause developmental defects in zebrafish larvae and provides insights into its toxic reactions in early develoment.

Dysregulated miRNA and mRNA Expression Affect Overlapping Pathways in a Huntington's Disease Model

Huntington's disease (HD) is a fatal neurodegenerative disorder caused by the expansion of a CAG trinucleotide repeat in the Huntingtin gene. Transcriptional dysregulation is one of the main cellular processes affected by mutant Huntingtin (mHtt). In this study, we investigate the alterations in miRNA and mRNA expression levels in a Drosophila model of HD by RNA sequencing and assess the functional effects of misregulated miRNAs in vivo. We found that in head samples of HD flies, the level of 32 miRNAs changed significantly; half of these were upregulated, while the other half were downregulated. After comparing miRNA and mRNA expression data, we discovered similarities in the impacted molecular pathways. Additionally, we observed that the putative targets of almost all dysregulated miRNAs were overrepresented among the upregulated mRNAs. We tested the effects of overexpression of five misregulated miRNAs in the HD model and found that while mir-10 and mir-219 enhanced, mir-137, mir-305, and mir-1010 ameliorated mHtt-induced phenotypes. Based on our results, we propose that while altered expression of mir-10, mir-137, and mir-1010 might be part of HD pathology, the upregulation of mir-305 might serve as a compensatory mechanism as a response to mHtt-induced transcriptional dysregulation.

Gut brain regulation using psychobiotics for improved neuropsychological illness

"Psychobiotics" are a novel class of probiotics that are beneficial to the health and functional efficiency of our brain and psychology. The main hold on command in ill conditions of the brain and psychology is overtaken by these psychobiotic bacteria (a dietary supplement) via the action/determined role of bacterial neurochemicals or neuroactive substances that are released by them in the intestinal epithelium after their ingestion. Although these psychobiotics flourish in the gut of the host consuming them, the effect is widely spread to the brain due to the communication between the gut and the brain via the bidirectional gut-brain axis. The nervous system involved in this directional process includes both the enteric nervous system and the central nervous system. With time, several corroborations have proved the effectiveness of psychobiotics in terms of mental illnesses and brain disorders. In the prevailing situation of the coronavirus pandemic, psychobiotics may serve as an aid because a majority of the population worldwide is already suffering from psychological issues due to changes in lifestyle and dietary habits, and in need of an immediate solution to cope with it. Moreover, the in silico approach is also vital for the development of biological relevance to neurosubstances.

PPIGCF: A Protein-Protein Interaction-Based Gene Correlation Filter for Optimal Gene Selection

Biological data at the omics level are highly complex, requiring powerful computational approaches to identifying significant intrinsic characteristics to further search for informative markers involved in the studied phenotype. In this paper, we propose a novel dimension reduction technique, protein-protein interaction-based gene correlation filtration (PPIGCF), which builds on gene ontology (GO) and protein-protein interaction (PPI) structures to analyze microarray gene expression data. PPIGCF first extracts the gene symbols with their expression from the experimental dataset, and then, classifies them based on GO biological process (BP) and cellular component (CC) annotations. Every classification group inherits all the information on its CCs, corresponding to the BPs, to establish a PPI network. Then, the gene correlation filter (regarding gene rank and the proposed correlation coefficient) is computed on every network and eradicates a few weakly correlated genes connected with their corresponding networks. PPIGCF finds the information content (IC) of the other genes related to the PPI network and takes only the genes with the highest IC values. The satisfactory results of PPIGCF are used to prioritize significant genes. We performed a comparison with current methods to demonstrate our technique's efficiency. From the experiment, it can be concluded that PPIGCF needs fewer genes to reach reasonable accuracy (~99%) for cancer classification. This paper reduces the computational complexity and enhances the time complexity of biomarker discovery from datasets.

Systematic Selection Signature Analysis of Chinese Gamecocks Based on Genomic and Transcriptomic Data

Selection pressures driven by natural causes or human interference are key factors causing genome variants and signatures of selection in specific regions of the genome. Gamecocks were bred for cockfighting, presenting pea-combs, larger body sizes, stronger limbs, and higher levels of aggression than other chickens. In this study, we aimed to explore the genomic differences between Chinese gamecocks and commercial, indigenous, foreign, and cultivated breeds by detecting the regions or sites under natural or artificial selection using genome-wide association studies (GWAS), genome-wide selective sweeps based on the genetic differentiation index (F_ST), and transcriptome analyses. Ten genes were identified using GWAS and F_ST: gga-mir-6608-1, SOX5, DGKB, ISPD, IGF2BP1, AGMO, MEOX2, GIP, DLG5, and KCNMA1. The ten candidate genes were mainly associated with muscle and skeletal development, glucose metabolism, and the pea-comb phenotype. Enrichment analysis results showed that the differentially expressed genes between the Luxi (LX) gamecock and Rhode Island Red (RIR) chicken were mainly related to muscle development and neuroactive-related pathways. This study will help to understand the genetic basis and evolution of Chinese gamecocks and support the further use of gamecocks as an excellent breeding material from a genetic perspective.

Melatonin Mitigates Rotenone-Induced Oxidative Stress and Mitochondrial Dysfunction in the Drosophila melanogaster Model of Parkinson's Disease-like Symptoms

Parkinson's disease (PD) is the second most common neurodegenerative disorder; however, its etiology remains elusive. Antioxidants are considered to be a promising approach for decelerating neurodegenerative disease progression owing to extensive examination of the relationship between oxidative stress and neurodegenerative diseases. In this study, we investigated the therapeutic effect of melatonin against rotenone-induced toxicity in the Drosophila model of PD. The 3-5 day old flies were divided into four groups: control, melatonin alone, melatonin and rotenone, and rotenone alone groups. According to their respective groups, flies were exposed to a diet containing rotenone and melatonin for 7 days. We found that melatonin significantly reduced the mortality and climbing ability of Drosophila because of its antioxidative potency. It alleviated the expression of Bcl 2, tyrosine hydroxylase (TH), NADH dehydrogenase, mitochondrial membrane potential, and mitochondrial bioenergetics and decreased caspase 3 expression in the Drosophila model of rotenone-induced PD-like symptoms. These results indicate the neuromodulatory effect of melatonin, and that it is likely modulated against rotenone-induced neurotoxicity by suppressing oxidative stress and mitochondrial dysfunctions.

miRNA in Parkinson's disease: From pathogenesis to theranostic approaches

Parkinson's disease (PD) is an age associated neurological disorder which is specified by cardinal motor symptoms such as tremor, stiffness, bradykinesia, postural instability, and non-motor symptoms. Dopaminergic neurons degradation in substantia nigra region and aggregation of αSyn are the classic signs of molecular defects noticed in PD pathogenesis. The discovery of microRNAs (miRNA) predicted to have a pivotal part in various processes regarding regularizing the cellular functions. Studies on dysregulation of miRNA in PD pathogenesis has recently gained the concern where our review unravels the role of miRNA expression in PD and its necessity in clinical validation for therapeutic development in PD. Here, we discussed how miRNA associated with ageing process in PD through molecular mechanistic approach of miRNAs on sirtuins, tumor necrosis factor-alpha and interleukin-6, dopamine loss, oxidative stress and autophagic dysregulation. Further we have also conferred the expression of miRNAs affected by SNCA gene expression, neuronal differentiation and its therapeutic potential with PD. In conclusion, we suggest more rigorous studies should be conducted on understanding the mechanisms and functions of miRNA in PD which will eventually lead to discovery of novel and promising therapeutics for PD.

Non-coding RNAs as key players in the neurodegenerative diseases: Multi-platform strategies and approaches for exploring the Genome's dark matter

A growing amount of evidence in the last few years has begun to unravel that non-coding RNAs have a myriad of functions in gene regulation. Intensive investigation on non-coding RNAs (ncRNAs) has led to exploring their broad role in neurodegenerative diseases (NDs) owing to their regulatory role in gene expression. RNA sequencing technologies and transcriptome analysis has unveiled significant dysregulation of ncRNAs attributed to their biogenesis, upregulation, downregulation, aberrant epigenetic regulation, and abnormal transcription. Despite these advances, the understanding of their potential as therapeutic targets and biomarkers underpinning detailed mechanisms is still unknown. Advancements in bioinformatics and molecular technologies have improved our knowledge of the dark matter of the genome in terms of recognition and functional validation. This review aims to shed light on ncRNAs biogenesis, function, and potential role in NDs. Further deepening of their role is provided through a focus on the most recent platforms, experimental approaches, and computational analysis to investigate ncRNAs. Furthermore, this review summarizes and evaluates well-studied miRNAs, lncRNAs and circRNAs concerning their potential role in pathogenesis and use as biomarkers in NDs. Finally, a perspective on the main challenges and novel methods for the future and broad therapeutic use of ncRNAs is offered.

The Effective Components, Core Targets, and Key Pathways of Ginseng against Alzheimer's Disease

Background

Panax ginseng C. A. Mey (ginseng) is a traditional Chinese medicinal herb used for the treatment of nervous system disorders, such as Alzheimer's disease (AD). However, the pharmacological mechanisms of ginseng involved in AD have not been systematically investigated. Here, a network pharmacology approach was adopted to explore the effective components, core targets, and key pathways of ginseng against AD.

Methods

TCMSP database was used to screen the active ingredients of ginseng. Prediction of the targets of ginseng and AD-related genes was performed using online public databases. "Compound-Target," "Compound-Target-Disease," "Protein-Protein Interaction (PPI)," "Compound-Target-Pathway," and "Compound-Target-GO-Pathway" networks were constructed with Cytoscape 3.7.2 software. Gene Ontology (GO) function annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were performed by using the DAVID database.

Results

A total of 22 bioactive compounds were identified from ginseng, and 481 targets of ginseng and 763 AD-related targets were obtained from public databases. The PPI network screened out 19 hub genes of ginseng against AD. According to GO function enrichment, ginseng influenced cell proliferation, death, the nitric oxide biosynthetic process, hypoxia response, and synaptic transmission. Neuroactive ligand-receptor interaction, serotonergic synapse, calcium signaling, cAMP signaling, FoxO signaling, Ras signaling, and PI3K-AKT signaling were among the most key regulatory pathways. The compound-target-GO-route network found EGFR, MAPK1, MAPK14, AKT1, CASP3, and PRKACA as key genes, with PI3K-AKT signaling being the most important pathway for ginseng's anti-AD activity.

Conclusion

Ginseng exerts neuroprotective effects in AD patients through multicomponent, multitarget, and multipathway modes, providing novel insight into the pharmacological and experimental research on ginseng against AD.

A Network Pharmacology-Based Study on the Mechanism of Dibutyl Phthalate of Ocimum basilicum L. against Alzheimer's Disease through the AKT/GSK-3β Pathway

Background

Ocimum basilicum L. (OBL) is mainly used to treat neurological diseases in China. The preliminary work of this group showed that OBL improves cognitive impairment in Alzheimer's disease (AD). However, the underlying pharmacological mechanism remains unclear.

Methods

The components of OBL were compiled by literature search, and their active ingredients were screened by online database. The drug targets of OBL in the treatment of AD were predicted and analyzed using information derived from sources such as the SwissTargetPrediction tool. And through the network visual analysis function of Cytoscape software and protein-protein interaction analysis (PPI), the core targets of OBL treatment of AD are predicted. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were employed to analyze the related signaling pathways affected by OBL. Moreover, AutoDock software was used to assess the potential binding affinity between the core targets and the active compounds. Subsequently, in vivo experiment was conducted to verify the findings of network pharmacology.

Results

A total of 35 active compounds and 188 targets of OBL were screened, of which 43 common targets were related to AD. The active compounds of 35 OBLs induced 118 GO and 78 KEGG. The results of PPI and network topology parameter analysis show that targets such as MAPK1, GSK3B, NR3C2, ESR1, and EGFR are known as the core targets for the treatment of AD by OBL and are docked with the active ingredients of OBL. Molecular docking results suggest that diterbutyl phthalate (DBP) may be the main active component of OBL for the treatment of AD. Flow cytometry analysis results showed that apoptosis decreased with increasing DBP dose. In addition, DBP significantly decreased the levels of lactate dehydrogenase (LDH) and reactive oxygen species (ROS) in the supernatant of Aβ _25-35-induced injury HT22 cell cultures, and it can be speculated that DBP has the ability to protect the stability of injured neuronal cells and improve the permeability of cell membranes, thus stabilizing the intracellular environment. Mechanistically, DBP may increase the mRNA levels of AKT, GSK-3β, etc. in AD cell models and regulate the phosphorylation of AKT/GSK-3β pathway-related.

Conclusions

Conclusively, our study suggests that DBP, the main active component of OBL, has potential in the prevention or treatment of AD.

Gastrodin ameliorates the lipopolysaccharide-induced neuroinflammation in mice by downregulating miR-107-3p

Background: Neuroinflammation plays a pivotal role in the pathogenesis of Central Nervous System (CNS) diseases. The phenolic glucoside gastrodin (GAS), has been known to treat CNS disorders by exerting anti-inflammatory activities. Our aim was to investigate the potential neuroprotective mechanisms of GAS on lipopolysaccharide (LPS)-induced mice. Methods: Male C57BL/6J mice were treated by LPS, before which GAS was adminisrated. The behavior tests such as forced swim test, tail suspension test, and elevated plus maze were performed to evaluate depressive-anxiety-like behaviors. A high-throughput sequencing (HTS) analysis was performed to screen out distinctive miRNAs which were validated using quantitative real-time PCR. Then, miRNA agomir or NC was injected stereotaxically into hippocampus of mice to explore the role of miRNA on GAS in response to LPS. Furthermore, Immunofluorescence and the hematoxylin and eosin (H&E) staining were employed to observe the cellular morphology. The protein levels of pro-inflammatory factors were evaluated by western blot. Finally, the target mRNA of miRNA was predicted using bioinformatics analysis. GO and KEGG enrichment analyses were conducted to clarify the potential function of target protein, which were visualized by bubble charts. Results: The behavioral data showed that mice in the LPS group had obvious depressive-anxiety-like behaviors, and 100 mg/kg GAS could improve these behavioral changes and alleviate the levels of pro-inflammatory cytokines in the hippocampus when mice were exposed to LPS for 6 h. Meanwhile, LPS-induced microglia and astrocyte activation in the CA1, CA2, CA3, and DG regions of the hippocampus were also reversed by GAS. Furthermore, miR-107-3p were screened out and verified for GAS in response to LPS. Importantly, miR-107-3p overexpression negatively abrogated the neuroprotective effects of GAS. Moreover, KPNA1 might be the target molecular of miR-107-3p. KPNA1 might regulate 12 neuroinflammation-related genes, which were mainly involved in cytokine-mediated signaling pathway. Conclusion: These results suggested that GAS might alleviate the LPS-induced neuroinflammation and depressive-anxiety-like behaviors in mice by downregulating miR-107-3p and upregulating the downstream target KPNA1. The indicates miR-107-3p may provide a new strategy for the treatment of CNS diseases.

Defining Specific Cell States of MPTP-Induced Parkinson's Disease by Single-Nucleus RNA Sequencing

Parkinson's disease (PD) is a neurodegenerative disease with an impairment of movement execution that is related to age and genetic and environmental factors. 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) is a neurotoxin widely used to induce PD models, but the effect of MPTP on the cells and genes of PD has not been fully elucidated. By single-nucleus RNA sequencing, we uncovered the PD-specific cells and revealed the changes in their cellular states, including astrocytosis and endothelial cells' absence, as well as a cluster of medium spiny neuron cells unique to PD. Furthermore, trajectory analysis of astrocyte and endothelial cell populations predicted candidate target gene sets that might be associated with PD. Notably, the detailed regulatory roles of astrocyte-specific transcription factors Dbx2 and Sox13 in PD were revealed in our work. Finally, we characterized the cell-cell communications of PD-specific cells and found that the overall communication strength was enhanced in PD compared with a matched control, especially the signaling pathways of NRXN and NEGR. Our work provides an overview of the changes in cellular states of the MPTP-induced mouse brain.

Network pharmacology-based approach to investigate the mechanisms of Zingiber officinale Roscoe in the treatment of neurodegenerative diseases

Neurodegenerative diseases (NDDs) are chronic neurological disorders associated with cognitive or motor dysfunction. As a common spice, Zingiber officinale Roscoe has been used as a medicine to treat a variety of NDDs. However, at the molecular level, the mechanisms of Z. officinale in treating of NDDs have not been deeply investigated. In this study, network pharmacology method, molecular docking, Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were used to predict the mechanisms of Z. officinale in the treatment of NDDs. After a series of biological information analyses, five core targets were obtained, including heme oxygenase 1 (HMOX1), acetylcholinesterase (AChE), nitric oxide synthase (NOS), catechol-O-methyl-transferase (COMT), and metabotropic glutamate receptor 5 (mGluR5). Compounds 75, 68, 46, 67, 69, 49, 66, 50, 34, and 64 were identified as the main components of Z. officinale in the treatment of NDDs. The crucial pathways mainly include neuroactive ligand-receptor signaling pathways, cyclic adenosine monophosphate signaling pathways, dopamine synaptic signaling pathways, and so on. Besides, in vitro experiments by AChE inhibitory activities assay and neuroprotective activities against H2 O2 -induced injury in human neuroblastoma SH-SY5Y cells validated the reliability of the results of network analysis. PRACTICAL APPLICATIONS: Zingiber officinale Roscoe is widely used as a traditional spice and herbal medicine. It contains a number of active ingredients, which have shown activities on anti-neurodegenerative diseases (NDDs). In this paper, the potential mechanism of Z. officinale in the treatment of NDDs is explored through network pharmacology, and it was verified by in vitro experiments. The mechanism was not only clarified at the system level but also proved to be effective at the biological level. The results can be used as a reference for Z. officinale in the treating of NDDs.

A co-expression network based molecular characterization of genes responsive for Braak stages in Parkinson's disease

The progression of Parkinson's disease (PD) is defined by six Braak stages. We used transcriptome data from PD patients with Braak stage information to understand underlying molecular mechanisms for the progress of the disease. We created networks of genes with decreased/increased co-expression from control group to Braak 5-6 stages. These networks are significantly associated with PD related mechanisms such as mitochondrial dysfunction and synaptic signaling among others. Applying Weighted Gene Correlation Network Analysis (WGCNA) algorithm to the co-expression networks led to more specific modules enriched with neurodegeneration related disease pathways, seizure, abnormality of coordination, and hypotonia. Furthermore, we showed that one of the co-expression networks is clustered into three major communities with dedicated molecular functions: (i) tubulin folding pathway, gap junction related mechanisms, neuronal system (ii) synaptic vesicle, intracellular vesicle, proteasome complex, PD genes (iii) energy metabolism, mitochondrial mechanisms, oxidative phosphorylation, TCA cycle, PD genes. The co-expression relations we identified in this study as crucial players in the disease progression cover several known PD-associated genes and genes whose products are known to physically interact with alpha-synuclein protein.

Combination of Stem Cells with Chinese Herbs for Secondary Depression in Neurodegenerative Diseases Based on Traditional Chinese Medicine Theories

Depression is a common secondary symptom in neurodegenerative diseases (NDs) caused by the loss of neurons and glial cells. Recent research focuses on stem cell therapy to replace dead nerve cells, but the low efficiency of stem cell differentiation and short survival time are obstacles limiting the therapy's effectiveness. Clinically, patients with different diseases cannot obtain the same effect by using the same cell therapy. However, traditional Chinese medicine (TCM) often uses syndrome differentiation to determine the treatment plan for NDs. Based on TCM syndrome differentiation and treatment, this article summarizes the advantages of Chinese herbal medicine combined with stem cell therapy, mainly for the effects of various herbs on diseases and stem cells, including prolonging the survival time of stem cells, resisting inflammation, and antidepressant-like effects. In particular, it analyzes the unique pathways of the influence of drugs and acupuncture on different therapies, seeking to clarify the scientific TCM system. This review mainly elaborates on the treatment of secondary depression in TCM and the advantages of a herbal combined stem cell therapy in various methods. We believe it can provide a new clinical concept for secondary depression to obtain good clinical effects and reduce the risks borne by patients.

Significant Association of Variable Number Tandem Repeat Polymorphism rs58335419 in the MIR137 Gene With the Risk of Gastric and Colon Cancers

The purpose of the article: The MIR137 gene acts as a tumor-suppressor gene in colon and gastric cancers. The aim of this study was to investigate the association of functional variable number tandem repeat (VNTR) polymorphism rs58335419 locating in the upstream of the MIR137 gene with the risk of colon and gastric cancers.

Materials and methods: Totally, 429 individuals were contributed in the study, including 154 colon and 120 gastric cancer patients and 155 healthy controls. The target VNTR was genotyped using PCR and electrophoresis for all samples. Statistical analysis was performed using SPSS 21.0 software and by T, χ2 and logistic regression tests.

Results: Excluding the rare genotypes, our results showed that genotype 3/5 (95% CI = 1.08–3.73, OR = 2.01, p = 0.026) significantly increased the risk of colon cancer but not gastric cancer (95% CI = 0.88–3.30, OR = 1.70, p = 0.114). Also, in the stratification analysis for VNTRs and sex, genotypes 3/4 (95% CI = 1.00–6.07, OR = 2.46, p = 0.049) and 3/5 (95% CI = 1.25–7.18, OR = 2.99, p = 0.014) significantly increased the risk of colon cancer in men but not in women. In addition, all genotypes including the rare genotypes as a group, significantly increase the risk of gastric (95% CI = 1.14–3.00, OR = 1.85, p = 0.012) and colon (95% CI = 1.38–3.43, OR = 2.17, p = 0.001) cancers compared to the genotype 3/3 as a reference.

Conclusion: The results show that increasing the copy of VNTR in the MIR137 gene, increases the risk of colon and gastric cancers and can serve as a marker for susceptibility to colon and gastric cancers.

Long non-coding RNA Opa interacting protein 5-antisense RNA 1 promotes mitochondrial autophagy and protects SH-SY5Y cells from 1-methyl-4-phenylpyridine-induced damage by binding to microRNA-137 and upregulating NIX

Parkinson's disease (PD) is a leading cause of disability. Long noncoding RNA (LncRNA) OIP5-AS1 alleviates the accumulation and toxicity of 1-methyl-4-phenylpyridine (MPP⁺ )/-induced α-synuclein in human neuroblastoma SH-SY5Y cells, which may be involved in the pathological process of PD. This study explored the neuroprotective effect of lncRNA OIP5-AS1 on MPP⁺ /-induced SH-SY5Y cell model of PD, so as to provide a theoretical basis for PD treatment. The PD cell model was established (MPP⁺ group). The overexpression vector oe-OIP5-AS1 was constructed and transfected into MPP+/-induced SH-SY5Y cells, which were further transfected with miR-137 mimic or si-NIX plasmids. The localization of OIP5-AS1 and its binding sites with miR-137 were predicted by subcellular isolation and fluorescence in situ hybridization analysis. The targeting relationships between OIP5-AS1 and miR-137, and miR-137 and NIX were detected by dual-luciferase reporter assays. The mitochondrial membrane potential (Δψm) and total reactive oxygen species (ROS) levels, and expressions of α-synuclein, inflammatory cytokines, and microglia-activated chemokines, cell activity, and apoptosis were assessed. OIP5-AS1 was downregulated in MPP⁺ cells. After OIP5-AS1 overexpression, miR-137 was downregulated and NIX was upregulated in MPP⁺ cells, inflammatory factors and chemokines were downregulated. There were target relationships between OIP5-AS1 and miR-137, and miR-137 and NIX. After OIP5-AS1 overexpression, miR-137 overexpression or NIX downregulation inhibited mitochondrial autophagy and ROS levels and aggravated mitochondrial vacuolation; and partially reversed the effect of OIP5-AS1 overexpression on promoting mitochondrial autophagy and protection on MPP+ cells. Collectively, lncRNA OIP5-AS1 promoted NIX expression through competitively binding to miR-137, and promoted mitochondrial autophagy, thus protecting neurons from degeneration which might be seen in patients with PD.

Long Non-coding RNAs Gabarapl2 and Chrnb2 Positively Regulate Inflammatory Signaling in a Mouse Model of Dry Eye

Purpose: To elucidate the expression profile and the potential role of long non-coding ribonucleic acids (RNAs) (lncRNAs) in a dry eye disease (DED) model.

Methods: A DED model was established in C57BL/6J mice with 0.2% benzalkonium chloride (BAC) twice a day for 14 days. The differentially expressed lncRNAs were detected by RNA-seq technology (Gene Expression Omnibus, GEO GSE186450) and the aberrantly expressed lncRNAs were further verified by RT-qPCR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to predicate the related candidate genes and potential pathological pathways. Cells from a human corneal epithelial cell line (HCECs) were cultured under hyperosmolarity. The regulation of inflammatory factors by silencing potential targeted lncRNAs was verified in vitro in HCECs.

Results: In our study, a significant increase in corneal fluorescence staining and a reduction in tear production were observed in DED mice at all follow-ups compared with the controls, and the differences were increasing over time. In total, 2,649 upregulated and 704 downregulated lncRNAs were identified in DED mice. We selected six aberrantly expressed and most abundant lncRNAs and performed RT-qPCR using the samples for RNA-seq. Chrnb2, Gabarapl2, and Usp31 were thereby confirmed as the most significantly altered lncRNAs. Pathway analysis revealed that the neuroactive ligand–receptor interaction signaling pathway was the most enriched, followed by the calcium signaling pathway and cytokine–cytokine receptor interaction. Following treatment of Gabarapl2 siRNA and Chrnb2 siRNA, tumor necrosis factor-α (TNF-α), interleukin (IL)-1β, and IL-6 were significantly downregulated in the HCECs.

Conclusion: Our study suggests that Chrnb2 and Gabarapl2 may be involved in the inflammation response by regulating TNF-α, IL-1β, and IL-6 in DED. These candidate lncRNAs may be both potential biomarkers and therapeutic targets for DED.

Unraveling the Neuroprotective Effect of Tinospora cordifolia in a Parkinsonian Mouse Model through the Proteomics Approach

Stress-induced dopaminergic (DAergic) neuronal death in the midbrain region is the primary cause of Parkinson's disease (PD). Following the discovery of l-dopa, multiple drugs have been developed to improve the lifestyle of PD patients; however, none have been suitable for clinical use due to their multiple side effects. Tinospora cordifolia has been used in traditional medicines to treat neurodegenerative diseases. Previously, we reported the neuroprotective role of Tc via inhibition of NF-κB-associated proinflammatory cytokines against MPTP-intoxicated Parkinsonian mice. In the present study, we investigated the neuroprotective molecular mechanism of Tc in a rotenone (ROT)-intoxicated mouse model, using a proteomics approach. Mice were pretreated with Tc extract by oral administration, followed by ROT intoxication. Behavioral tests were performed to check motor functions of mice. Protein was isolated, and label-free quantification (LFQ) was carried out to identify differentially expressed protein (DEP) in control vs PD and PD vs treatment groups. Results were validated by qRT-PCR with the expression of target genes correlating with the proteomics data. In this study, we report 800 DEPs in control vs PD and 133 in PD vs treatment groups. In silico tools demonstrate significant enrichment of biochemical and molecular pathways with DEPs, which are known to be important for PD progression including mitochondrial gene expression, PD pathways, TGF-β signaling, and Alzheimer's disease. This study provides novel insights into the PD progression as well as new therapeutic targets. More importantly, it demonstrates that Tc can exert therapeutic effects by regulating multiple pathways, resulting in neuroprotection.

Parkinson's disease and microRNAs - Lessons from model organisms and human studies

Parkinson's disease (PD) is a progressive, age-associated neurodegenerative disorder that affects an estimated 10 million people worldwide. PD is characterized by proteinaceous, cytoplasmic inclusions containing α-synuclein, called Lewy Bodies, which form in dopaminergic neurons in an age-dependent manner, and are associated with the emergence of characteristic PD symptoms such as resting tremor, rigidity, slow movements and postural instability. Although considerable progress has been made in recent years in identifying genetic and environmental factors that are associated with PD, early diagnosis and therapeutic options remain severely lacking. Recently, microRNAs (miRNAs) have emerged as novel therapeutic targets in various diseases, such as cancer and neurodegenerative diseases. MiRNAs have been shown to play roles in various aging and neurodegenerative disease models across phyla. More recently, studies have identified specific roles for miRNAs and their targets in the pathogenesis and progression of PD in several model organisms. Here, we discuss the evolving field of miRNAs, their association with PD, and the outlook for the future.

Identification of hub genes and functional modules in colon adenocarcinoma based on public databases by bioinformatics analysis

Background

Colon adenocarcinoma (COAD) is one of the most common cancers in the world. Although an extensive effort has been made to elucidate its pathogenesis, the underlying molecular mechanisms and genetic characteristics remain elusive.

Methods

In this study, protein-coding transcript expression profiles of COAD were downloaded from the Cancer RNA-Seq Nexus (CRN) database. They were then integrated to identify the overlapping transcripts expressed in every COAD RNA sequencing (RNA-seq) subset. The functional annotation of these overlapping genes (OLGs) involved noting their biological process (BP), cellular components (CC), molecular function (MF) for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway in the Database for Annotation, Visualization and Integrated Discovery (DAVID). Protein-protein interaction (PPI) networks were then constructed and analyzed using Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Cytoscape 3.8.2.

Results

A total of 10 hub genes and 3 functional modules were screened by the plugin cytoHubba and MCODE, respectively. The plugin ClueGO and DAVID were used for the functional enrichment analyses of both hub genes and modules. The expression of hub genes was verified through the gene expression profiling interactive analysis (GEPIA) database. Survival analysis of the hub genes revealed that low expressions of ADCY5, GNG2, and PTPRC were significantly associated with an improved COAD prognosis. Furthermore, the expression level of ADCY5 in stages I/II was lower than that in stages III/IV, which seems to explain why the low expression of ADCY5 results in a better prognosis.

Conclusions

The identification of hub genes, functional modules, and pathways have the potential to improve our understanding of the causes and underlying molecular events of COAD. The hub gene ADCY5 could also be a prognostic monitoring indicator or therapeutic target in the treatment of COAD.

The Role of Gut Microbiota in Aging and Aging Related Neurodegenerative Disorders: Insights from Drosophila Model

Aging is characterized by a time dependent impairment of physiological function and increased susceptibility to death. It is the major risk factor for neurodegeneration. Neurodegenerative disorders including Alzheimer's disease (AD) and Parkinson's disease (PD) are the main causes of dementia in the old population. Gut microbiota is a community of microorganisms colonized in the gastrointestinal (GI) tract. The alteration of gut microbiota has been proved to be associated with aging and aging related neurodegeneration. Drosophila is a powerful tool to study microbiota-mediated physiological and pathological functions. Here, we summarize the recent advances using Drosophila as model organisms to clarify the molecular mechanisms and develop a therapeutic method targeting microbiota in aging and aging-related neurodegenerative disorders.

Toxic effects of Decabromodiphenyl ether (BDE-209) on thyroid of broiler chicks by transcriptome profile analysis

The wide usage of decabromodiphenyl ether (BDE-209) results in its increasing occurrence in the environment and increasing attention in regard to human and animal health. BDE-209 is an endocrine disruptor for hypothyroidism, but the toxicity mechanism is unclear. Here, the histopathology and transcriptome sequencing of thyroid tissue from broiler chicks were investigated by supplemental feeding with different concentrations of BDE-209 for 42 days (0-4 g/kg in basal diet), followed by determining the levels of thyroid hormones in serum. The results showed ruptured and even hyperplastic follicular epithelial cells in the thyroid, and a total of 501 differentially expressed genes were screened out: 222 upregulated and 279 downregulated. Based on the Kyoto Encyclopedia of Genes and Genomes database, neuroactive ligand-receptor interaction pathway was significantly enriched, and α1D-adrenergic receptor, follicle-stimulating hormone receptor, thyroid stimulating hormone receptor, and somatostatin receptor type 2 were shown to be candidate biomarkers. Thyroxine was a possible biomarker due to clear reduction in serum and significant correlation with exposure concentrations. These results suggested that oral intake of BDE-209 can cause structural injuries and even hyperplasia, and affect gene transcription involved in the neuroactive ligand-receptor interaction pathway of thyroid, as well as thyroid hormones in serum.

Elevated plasma miR-133b and miR-221-3p as biomarkers for early Parkinson's disease

Blood circulating microRNAs (miRNAs) are proposed to be promising biomarkers for many neurodegenerative disorders, including Parkinson’s disease (PD). However, there is a lack of identified differentially expressed miRNAs in PD from different studies. The aim of this study was to evaluate miRNAs expression in PD. We measured plasma circulating miRNA expression in three independent sets with a total of 151 PD patients, 21 multiple system atrophy (MSA) patients and 138 healthy controls using high-throughput RT-PCR. We identified that elevated miR-133b and miR-221-3p discriminated early-stage PD from controls with 94.4% sensitivity and 91.1% specificity. Elevated miR-133b and miR-221-3p distinguished PD from controls with 84.8% sensitivity and 88.9% specificity. In addition, miR-4454 distinguished PD from MSA with 57.1% sensitivity and 82.6% specificity. Hence, elevated miR-133b and miR-221-3p potentially represent good biomarkers for early PD, and a combination of miR-133b, miR-221-3p and miR-4454 has the potential to serve as a non-invasive biomarker for PD diagnosis.

Evolutionary Changes in Pathways and Networks of Genes Expressed in the Brains of Humans and Macaques

As the key organ that separates humans from nonhuman primates, the brain has continuously evolved to adapt to environmental and climatic changes. Although humans share most genetic, molecular, and cellular features with other primates such as macaques, there are significant differences in the structure and function of the brain between humans and these species. Thus, exploring the differences between the brains of human and nonhuman primates in the context of evolution will provide insights into the development, functionality, and diseases of the human central nervous system (CNS). Since the genes involved in many aspects of the human brain are under common pressures of natural selection, their evolutionary features can be analyzed collectively at the pathway level. In this study, the molecular mechanisms underlying human brain capabilities were explored by comparing the evolution features of pathways enriched in genes expressed in the human brain and the macaque brain. We identified 31 pathways with differential evolutionary properties, including those related to neurological diseases, signal transduction, immunological response, and metabolic processes. By analyzing genes differentially expressed in brain regions or development stages between humans and macaques,  9 and 4 pathways with differential evolutionary properties were detected, respectively. We further performed crosstalk analysis on the pathways to obtain an intuitive correlation between the pathways, which is helpful in understanding the mechanisms of interaction between pathways. Our results provide on a comprehensive view of the evolutionary pathways of the human CNS and can serve as a reference for the study of human brain development.

miRNAs of Aedes aegypti (Linnaeus 1762) conserved in six orders of the class Insecta

Aedes aegypti L. is the most important vector of arboviruses such as dengue, Zika, chikungunya, Mayaro, and yellow fever, which impact millions of people's health per year. MicroRNA profile has been described in some mosquito species as being important for biological processes such as digestion of blood, oviposition, sexual differentiation, insecticide resistance, and pathogens dissemination. We identified the miRNAs of Ae. aegypti females, males and eggs of a reference insecticide susceptible strain New Orleans and compared them with those other insects to determine miRNA fingerprint by new-generation sequencing. The sequences were analyzed using data mining tools and categorization, followed by differential expression analysis and conservation with other insects. A total of 55 conserved miRNAs were identified, of which 34 were of holometabolous insects and 21 shared with hemimetabolous insects. Of these miRNAs, 32 had differential expression within the stages analyzed. Three predominant functions of miRNA were related to embryonic development regulation, metamorphosis, and basal functions. The findings of this research describe new information on Ae. aegypti physiology which could be useful for the development of new control strategies, particularly in mosquito development and metamorphosis processes.

System biology and bioinformatics pipeline to identify comorbidities risk association: Neurodegenerative disorder case study

Alzheimer's disease (AD) is the commonest progressive neurodegenerative condition in humans, and is currently incurable. A wide spectrum of comorbidities, including other neurodegenerative diseases, are frequently associated with AD. How AD interacts with those comorbidities can be examined by analysing gene expression patterns in affected tissues using bioinformatics tools. We surveyed public data repositories for available gene expression data on tissue from AD subjects and from people affected by neurodegenerative diseases that are often found as comorbidities with AD. We then utilized large set of gene expression data, cell-related data and other public resources through an analytical process to identify functional disease links. This process incorporated gene set enrichment analysis and utilized semantic similarity to give proximity measures. We identified genes with abnormal expressions that were common to AD and its comorbidities, as well as shared gene ontology terms and molecular pathways. Our methodological pipeline was implemented in the R platform as an open-source package and available at the following link: https://github.com/unchowdhury/AD_comorbidity. The pipeline was thus able to identify factors and pathways that may constitute functional links between AD and these common comorbidities by which they affect each others development and progression. This pipeline can also be useful to identify key pathological factors and therapeutic targets for other diseases and disease interactions.

Network Pharmacology Analysis on Zhichan Powder in the Treatment of Parkinson's Disease

AIMS AND OBJECTIVE

Effective components and the mechanism of action of Zhichan powder for the treatment of Parkinson's disease were researched at a systematic level.

MATERIALS AND METHODS

Screening of active components in Zhichan powder for the treatment of Parkinson's disease was conducted using the Traditional Chinese Medicine Systems Pharmacology database, and a medicine-target-disease network was established with computational network pharmacology.

RESULTS

By using network pharmacology methods, we identified 18 major active components in Zhichan powder through screening, indicating a connection between chemical components of this Traditional Chinese Medicine and Parkinson's disease-related targets.

CONCLUSION

The medicine-target-disease system of Zhichan powder established by network pharmacology permitted visualization of clustering and differences among chemical components in this prescription, as well as the complex mechanism of molecular activities among those effective components, relevant targets, pathways, and the disease. Thus, our results provide a new perspective and method for revealing the mechanism of action of Traditional Chinese Medicine prescriptions.

mRNA and miRNA profiles in the nucleus accumbens are associated with psychological stress-induced susceptible and resilient mice

BACKGROUND

Stress may be one of the main causes of fear and anxiety. Previous studies have shown that the nucleus accumbens is involved in emotional responses. However, in the nucleus accumbens, the mRNA and miRNA profiles of stress susceptibility and resilience of psychological stress still need to be studied.

MATERIALS AND METHODS

In this study, by observing the conspecific being attacked, the witness group experienced psychological stress. After five days of psychological stress, the fear memory of mice was measured by social interaction test, and the degree of anxiety was measured by elevated plus maze. mRNA and miRNA profiles in the nucleus accumbens tissue of control, susceptible and resilient mice were established by high-throughput sequencing.

RESULTS

In susceptible mice versus resilient mice, the Differentially expressed genes (DEGs) may be related to psychological stress-induced susceptibility. DEGs enriched in Cell adhesion molecules, Neuroactive ligand-receptor interaction, Gap junction, PI3K-Akt, VEGF, Jak-STAT, Ras, and Chemokine pathways were up-regulated. DEGs enriched in cGMP-PKG, B cell receptor, and NOD-like receptor pathways were down- regulated. The sequencing results of mRNAs and miRNAs were verified by qRT-PCR and dual luciferase reporter assay.

CONCLUSION

The imbalance of different synapses and pathways in the nucleus accumbens may be related to susceptibility and resilience caused by psychological stress.

The Role of Exosomal microRNAs and Oxidative Stress in Neurodegenerative Diseases

Neurodegenerative diseases including Alzheimer's disease and Parkinson's disease are aging-associated diseases with irreversible damage of brain tissue. Oxidative stress is commonly detected in neurodegenerative diseases and related to neuronal injury and pathological progress. Exosome, one of the extracellular vesicles, is demonstrated to carry microRNAs (miRNAs) and build up a cell-cell communication in neurons. Recent research has found that exosomal miRNAs regulate the activity of multiple physiological pathways, including the oxidative stress response, in neurodegenerative diseases. Here, we review the role of exosomal miRNAs and oxidative stress in neurodegenerative diseases. Firstly, we explore the relationship between oxidative stress and neurodegenerative diseases. Secondly, we introduce the characteristics of exosomes and roles of exosome-related miRNAs. Thirdly, we summarized the crosstalk between exosomal miRNAs and oxidative stress in neurodegenerative diseases. Fourthly, we discuss the potential of exosomes to be a biomarker in neurodegenerative diseases. Finally, we summarize the advantages of exosome-based delivery and present situation of research on exosome-based delivery of therapeutic miRNA. Our work is aimed at probing and reinforcing the recognition of the pathomechanism of neurodegenerative diseases and providing the basis for novel strategies of clinical diagnosis and treatment.

Noncoding RNAs and Midbrain DA Neurons: Novel Molecular Mechanisms and Therapeutic Targets in Health and Disease

Midbrain dopamine neurons have crucial functions in motor and emotional control and their degeneration leads to several neurological dysfunctions such as Parkinson's disease, addiction, depression, schizophrenia, and others. Despite advances in the understanding of specific altered proteins and coding genes, little is known about cumulative changes in the transcriptional landscape of noncoding genes in midbrain dopamine neurons. Noncoding RNAs-specifically microRNAs and long noncoding RNAs-are emerging as crucial post-transcriptional regulators of gene expression in the brain. The identification of noncoding RNA networks underlying all stages of dopamine neuron development and plasticity is an essential step to deeply understand their physiological role and also their involvement in the etiology of dopaminergic diseases. Here, we provide an update about noncoding RNAs involved in dopaminergic development and metabolism, and the related evidence of these biomolecules for applications in potential treatments for dopaminergic neurodegeneration.

Integrated Microarray and RNAseq Transcriptomic Analysis of Retinal Pigment Epithelium/Choroid in Age-Related Macular Degeneration

We report for the first time an integrated transcriptomic analysis of RPE/choroid dysfunction in AMD (mixed stages) based on combining data from publicly available microarray (GSE29801) and RNAseq (GSE135092) datasets aimed at increasing the ability and power of detection of differentially expressed genes and AMD-associated pathways. The analysis approach employed an integrating quantitative method designed to eliminate bias among different transcriptomic studies. The analysis highlighted 764 meta-genes (366 downregulated and 398 upregulated) in macular AMD RPE/choroid and 445 meta-genes (244 downregulated and 201 upregulated) in non-macular AMD RPE/choroid. Of these, 731 genes were newly detected as differentially expressed (DE) genes in macular AMD RPE/choroid and 434 genes in non-macular AMD RPE/choroid compared with controls. Over-representation analysis of KEGG pathways associated with these DE genes mapped revealed two most significantly associated biological processes in macular RPE/choroid in AMD, namely the neuroactive ligand-receptor interaction pathway (represented by 30 DE genes) and the extracellular matrix-receptor interaction signaling pathway (represented by 12 DE genes). Furthermore, protein-protein interaction (PPI) network identified two central hub genes involved in the control of cell proliferation/differentiation processes, HDAC1 and CDK1. Overall, the analysis provided novel insights for broadening the exploration of AMD pathogenesis by extending the number of molecular determinants and functional pathways that underpin AMD-associated RPE/choroid dysfunction.

Enhancing and Complementary Mechanisms of Synergistic Action of Acori Tatarinowii Rhizoma and Codonopsis Radix for Alzheimer's Disease Based on Systems Pharmacology

Materials and Methods

In this study, a systems pharmacology-based strategy was used to elucidate the synergistic mechanism of Acori Tatarinowii Rhizoma and Codonopsis Radix for the treatment of AD. This novel systems pharmacology model consisted of component information, pharmacokinetic analysis, and pharmacological data. Additionally, the related pathways were compressed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and the organ distributions were determined in the BioGPS bank.

Results

Sixty-eight active ingredients with suitable pharmacokinetic profiles and biological activities were selected through ADME screening in silico. Based on 62 AD-related targets, such as APP, CHRM1, and PTGS1, systematic analysis showed that these two herbs were mainly involved in the PI3K-Akt signaling pathway, MAPK signaling pathway, neuroactive ligand-receptor interaction, and fluid shear stress and atherosclerosis, indicating that they had a synergistic effect on AD. However, ATR acted on the KDR gene, while CR acted on IGF1R, MET, IL1B, and CHUK, showing that they also had complementary effects on AD. The ingredient contribution score involved 29 ingredients contributing 90.14% of the total contribution score of this formula for AD treatment, which emphasized that the effective therapeutic effects of these herbs for AD were derived from both ATR and CR, not a single herb. Organ distribution showed that the targets of the active ingredients were mainly located in the whole blood, the brain, and the muscle, which are associated with AD.

Conclusions

In sum, our findings suggest that the systems pharmacology methods successfully revealed the synergistic and complementary mechanisms of ATR and CR for the treatment of AD.

Small regulatory noncoding RNAs in Drosophila melanogaster: biogenesis and biological functions

RNA interference (RNAi) is an important phenomenon that has diverse genetic regulatory functions at the pre- and posttranscriptional levels. The major trigger for the RNAi pathway is double-stranded RNA (dsRNA). dsRNA is processed to generate various types of major small noncoding RNAs (ncRNAs) that include microRNAs (miRNAs), small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs) in Drosophila melanogaster (D. melanogaster). Functionally, these small ncRNAs play critical roles in virtually all biological systems and developmental pathways. Identification and processing of dsRNAs and activation of RNAi machinery are the three major academic interests that surround RNAi research. Mechanistically, some of the important biological functions of RNAi are achieved through: (i) supporting genomic stability via degradation of foreign viral genomes; (ii) suppressing the movement of transposable elements and, most importantly, (iii) post-transcriptional regulation of gene expression by miRNAs that contribute to regulation of epigenetic modifications such as heterochromatin formation and genome imprinting. Here, we review various routes of small ncRNA biogenesis, as well as different RNAi-mediated pathways in D. melanogaster with a particular focus on signaling pathways. In addition, a critical discussion of the most relevant and latest findings that concern the significant contribution of small ncRNAs to the regulation of D. melanogaster physiology and pathophysiology is presented.

Scleral HIF-1α is a prominent regulatory candidate for genetic and environmental interactions in human myopia pathogenesis

BACKGROUND

Myopia is a good model for understanding the interaction between genetics and environmental stimuli. Here we dissect the biological processes affecting myopia progression.

METHODS

Human Genetic Analyses: (1) gene set analysis (GSA) of new genome wide association study (GWAS) data for 593 individuals with high myopia (refraction ≤ -6 diopters [D]); (2) over-representation analysis (ORA) of 196 genes with de novo mutations, identified by whole genome sequencing of 45 high-myopia trio families, and (3) ORA of 284 previously reported myopia risk genes. Contributions of the enriched signaling pathways in mediating the genetic and environmental interactions during myopia development were investigated in vivo and in vitro.

RESULTS

All three genetic analyses showed significant enrichment of four KEGG signaling pathways, including amphetamine addiction, extracellular matrix (ECM) receptor interaction, neuroactive ligand-receptor interaction, and regulation of actin cytoskeleton pathways. In individuals with extremely high myopia (refraction ≤ -10 D), the GSA of GWAS data revealed significant enrichment of the HIF-1α signaling pathway. Using human scleral fibroblasts, silencing the key nodal genes within protein-protein interaction networks for the enriched pathways antagonized the hypoxia-induced increase in myofibroblast transdifferentiation. In mice, scleral HIF-1α downregulation led to hyperopia, whereas upregulation resulted in myopia. In human subjects, near work, a risk factor for myopia, significantly decreased choroidal blood perfusion, which might cause scleral hypoxia.

INTERPRETATION

Our study implicated the HIF-1α signaling pathway in promoting human myopia through mediating interactions between genetic and environmental factors.

FUNDING

National Natural Science Foundation of China grants; Natural Science Foundation of Zhejiang Province.

Comprehensive phenotyping and transcriptome profiling to study nanotoxicity in C. elegans

Engineered nanoparticles are used at an increasing rate in both industry and medicine without fully understanding their impact on health and environment. The nematode Caenorhabditis elegans is a suitable model to study the toxic effects of nanoparticles as it is amenable to comprehensive phenotyping, such as locomotion, growth, neurotoxicity and reproduction. In this study, we systematically evaluated the effects of silver (Ag) and five metal oxide nanoparticles: SiO₂, CeO₂, CuO, Al₂O₃ and TiO₂. The results showed that Ag and SiO₂ exposures had the most toxic effects on locomotion velocity, growth and reproduction, whereas CeO₂, Al₂O₃ and CuO exposures were mostly neurotoxic. We further performed RNAseq to compare the gene expression profiles underlying Ag and SiO₂toxicities. Gene set enrichment analyses revealed that exposures to Ag and SiO₂consistently downregulated several biological processes (regulations in locomotion, reproductive process and cell growth) and pathways (neuroactive ligand-receptor interaction, wnt and MAPK signaling, etc.), with opposite effects on genes involved in innate immunity. Our results contribute to mechanistic insights into toxicity of Ag and SiO₂ nanoparticles and demonstrated that C. elegans as a valuable model for nanotoxicity assessment.

A joint study of whole exome sequencing and structural MRI analysis in major depressive disorder

BACKGROUND

Major depressive disorder (MDD) is a leading cause of disability worldwide and influenced by both environmental and genetic factors. Genetic studies of MDD have focused on common variants and have been constrained by the heterogeneity of clinical symptoms.

METHODS

We sequenced the exome of 77 cases and 245 controls of Han Chinese ancestry and scanned their brain. Burden tests of rare variants were performed first to explore the association between genes/pathways and MDD. Secondly, parallel Independent Component Analysis was conducted to investigate genetic underpinnings of gray matter volume (GMV) changes of MDD.

RESULTS

Two genes (CSMD1, p = 5.32×10-6; CNTNAP5, p = 1.32×10-6) and one pathway (Neuroactive Ligand Receptor Interactive, p = 1.29×10-5) achieved significance in burden test. In addition, we identified one pair of imaging-genetic components of significant correlation (r = 0.38, p = 9.92×10-6). The imaging component reflected decreased GMV in cases and correlated with intelligence quotient (IQ). IQ mediated the effects of GMV on MDD. The genetic component enriched in two gene sets, namely Singling by G-protein coupled receptors [false discovery rate (FDR) q = 3.23×10-4) and Alzheimer Disease Up (FDR q = 6.12×10-4).

CONCLUSIONS

Both rare variants analysis and imaging-genetic analysis found evidence corresponding with the neuroinflammation and synaptic plasticity hypotheses of MDD. The mediation of IQ indicates that genetic component may act on MDD through GMV alteration and cognitive impairment.

Systems pharmacology based approach to investigate the in-vivo therapeutic efficacy of Albizia lebbeck (L.) in experimental model of Parkinson's disease

Background

Parkinson’s disease (PD) is a progressive neurodegenerative disorder characterized by loss of dopaminergic neurons in substantia nigra pars compacta and clinically manifested mainly with motor dysfunctions. Plants are rich source of medicinally important bioactive compounds and inhabitants of underdeveloped countries used plants for treatment of various ailments. Albizia lebbeck has been reported to possess antioxidant and neuroprotective properties that suggest the evaluation of its traditional therapeutic potential in neurodegenerative diseases.

The aim of present study was to validate the traditional use of Albizia lebbeck (L.) and delineate its mechanism of action in PD. The systems pharmacology approach was employed to explain the Albizia lebbeck (L.) mechanism of action in PD.

Methods

The haloperidol-induced catalepsy was adopted as experimental model of PD for in-vivo studies in wistar albino rats. The systems pharmacology approach was employed to explain the Albizia lebbeck (L.) mechanism of action in PD.

Results

In-vivo studies revealed that Albizia lebbeck improved the motor functions and endurance as demonstrated in behavioral studies which were further supported by the rescue of endogenous antioxidant defense and reversal of ultrastructural damages in histological studies. System pharmacology approach identified 25 drug like compounds interacting with 132 targets in a bipartite graph that revealed the synergistic mechanism of action at system level. Kaemferol, phytosterol and okanin were found to be the important compounds nodes with prominent target nodes of TDP1 and MAPT.

Conclusion

The therapeutic efficiency of Albizia lebbeck in PD was effectively delineated in our experimental and systems pharmacology approach. Moreover, this approach further facilitates the drug discovery from Albizia lebbeck for PD.

Competitive Endogenous RNA Network Construction and Comparison of Lung Squamous Cell Carcinoma in Smokers and Nonsmokers

Background

Lung squamous cell carcinoma (LUSC) is a subtype of highly malignant lung cancer with poor prognosis, for which smoking is the main risk factor. However, the underlying genetic and molecular mechanisms of smoking-related LUSC remain largely unknown.

Methods

We mined existing LUSC-related mRNA, miRNA, and lncRNA transcriptome data and corresponding clinical data from The Cancer Genome Atlas (TCGA) database and divided them into smoking and nonsmoking groups, followed by differential expression analysis. Functional enrichment analysis of the unique differentially expressed mRNAs of the two groups was performed using the DAVID database. Subsequently, the lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network of LUSC in smoking and nonsmoking groups was constructed. Finally, survival analyses were performed to determine the effects of differentially expressed lncRNAs/mRNAs/miRNAs that were involved in the ceRNA network on overall survival and to discover the hub genes.

Results

A total of 1696 lncRNAs, 125 miRNAs, and 3246 mRNAs and 1784 lncRNAs, 96 miRNAs, and 3229 mRNAs with differentially expressed profiles were identified in the smoking and nonsmoking groups, respectively. The ceRNA network and survival analysis revealed four lncRNAs (LINC00466, DLX6-AS1, LINC00261, and AGBL1), one miRNA (hsa-mir-210), and two mRNAs (CITED2 and ENPP4), with the potential as biomarkers for smoking-related LUSC diagnosis and prognosis.

Conclusion

Taken together, our research has identified the differences in the ceRNA regulatory networks between smoking and nonsmoking LUSC, which could lay the foundation for future clinical research.