Transcriptome Analysis of the Central Nervous System of Sea Slug (Onchidium reevesii) Exposed to Low-Frequency Noise

Low-frequency noise has become a marine pollutant that cannot be ignored, but most studies have focused on the behavioral and physiological effects on marine vertebrates, with few studies in marine mollusks. Therefore, sea slug was used in this study to investigate the effect of low-frequency noise on its physiological aspects. This experiment was designed with different low-frequency noise (0, 100, 300, and 500 Hz) and different stimulation times (0, 6, and 12 h) to measure superoxide dismutase (SOD), malondialdehyde (MDA), and catalase (CAT) activities in hemolymph and transcriptomics in the control (C) and 6 and 12 h groups (L1 and L2) with 500 Hz noise. The results showed a positive correlation between antioxidant enzyme activity and low-frequency noise frequency (P < 0.05) and no correlation with time (P > 0.05). In central nervous system (CNS) transcriptomics, 2,460 and 3,268 genes had upregulated expression and 2,765 and 2,783 genes had downregulated expression in the L1 and L2 groups, respectively, compared to the C group. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, low-frequency noise mainly affects signaling pathways such as cytokine-cytokine receptor interaction, the FoxO signaling pathway, natural killer cell-mediated cytotoxicity, apoptosis immune-related pathways, and energy metabolic pathways such as glycolysis, the TCA cycle, and glycerophospholipid metabolism, as well as neurological pathways such as GABAergic synapses, the synaptic vesicle cycle, amyotrophic lateral sclerosis (ALS) and other neurological pathways. This study would provide valuable reference information on the potential response of mollusks to low-frequency noise stress.

Protect Effects of Seafood-Derived Plasmalogens Against Amyloid-Beta (1–42) Induced Toxicity via Modulating the Transcripts Related to Endocytosis, Autophagy, Apoptosis, Neurotransmitter Release and Synaptic Transmission in SH-SY5Y Cells

To investigate the underlying mechanisms of decreased plasmalogens (Pls) levels in neurodegenerative diseases, here the effects of seafood-derived Pls on undifferentiated and differentiated human SH-SY5Y neuroblastoma cells exposed to amyloid-β1–42 was analyzed. Transcriptional profiles indicated that a total of 6,581 differentially expressed genes (DEGs) were significantly identified among different experimental groups, and KEGG analysis indicated that these DEGs were related to AD, endocytosis, synaptic vesicle cycle, autophagy and cellular apoptosis. After Pls treatment, the striking expression changes of ADORA2A, ATP6V1C2, CELF6, and SLC18A2 mRNA strongly suggest that Pls exerts a beneficial role in alleviating AD pathology partly by modulating the neurotransmitter release and synaptic transmission at the transcriptional level. Besides these, GPCRs are also broadly involved in Pls-signaling in neuronal cells. These results provide evidence for supporting the potential use of Pls as an effective therapeutic approach for AD.

A role for the Erk MAPK pathway in modulating SAX-7/L1CAM-dependent locomotion in Caenorhabditis elegans

L1CAMs are immunoglobulin cell adhesion molecules that function in nervous system development and function. Besides being associated with autism and schizophrenia spectrum disorders, impaired L1CAM function also underlies the X-linked L1 syndrome, which encompasses a group of neurological conditions, including spastic paraplegia and congenital hydrocephalus. Studies on vertebrate and invertebrate L1CAMs established conserved roles that include axon guidance, dendrite morphogenesis, synapse development, and maintenance of neural architecture. We previously identified a genetic interaction between the C. elegans L1CAM encoded by the sax-7 gene and RAB-3, a GTPase that functions in synaptic neurotransmission; rab-3; sax-7 mutant animals exhibit synthetic locomotion abnormalities and neuronal dysfunction. Here, we show that this synergism also occurs when loss of SAX-7 is combined with mutants of other genes encoding key players of the synaptic vesicle cycle. In contrast, sax-7 does not interact with genes that function in synaptogenesis. These findings suggest a post-developmental role for sax-7 in the regulation of synaptic activity. To assess this possibility, we conducted electrophysiological recordings and ultrastructural analyses at neuromuscular junctions; these analyses did not reveal obvious synaptic abnormalities. Lastly, based on a forward genetic screen for suppressors of the rab-3; sax-7 synthetic phenotypes, we determined that mutants in the ERK Mitogen-activated Protein Kinase (MAPK) pathway can suppress the rab-3; sax-7 locomotion defects. Moreover, we established that Erk signaling acts in a subset of cholinergic neurons in the head to promote coordinated locomotion. In combination, these results suggest a modulatory role for Erk MAPK in L1CAM-dependent locomotion in C. elegans.

Establishment of Human-Induced Pluripotent Stem Cell-Derived Neurons—A Promising In Vitro Model for a Molecular Study of Rabies Virus and Host Interaction

Rabies is a deadly viral disease caused by the rabies virus (RABV), transmitted through a bite of an infected host, resulting in irreversible neurological symptoms and a 100% fatality rate in humans. Despite many aspects describing rabies neuropathogenesis, numerous hypotheses remain unanswered and concealed. Observations obtained from infected primary neurons or mouse brain samples are more relevant to human clinical rabies than permissive cell lines; however, limitations regarding the ethical issue and sample accessibility become a hurdle for discovering new insights into virus–host interplays. To better understand RABV pathogenesis in humans, we generated human-induced pluripotent stem cell (hiPSC)-derived neurons to offer the opportunity for an inimitable study of RABV infection at a molecular level in a pathologically relevant cell type. This study describes the characteristics and detailed proteomic changes of hiPSC-derived neurons in response to RABV infection using LC-MS/MS quantitative analysis. Gene ontology (GO) enrichment of differentially expressed proteins (DEPs) reveals temporal changes of proteins related to metabolic process, immune response, neurotransmitter transport/synaptic vesicle cycle, cytoskeleton organization, and cell stress response, demonstrating fundamental underlying mechanisms of neuropathogenesis in a time-course dependence. Lastly, we highlighted plausible functions of heat shock cognate protein 70 (HSC70 or HSPA8) that might play a pivotal role in regulating RABV replication and pathogenesis. Our findings acquired from this hiPSC-derived neuron platform help to define novel cellular mechanisms during RABV infection, which could be applicable to further studies to widen views of RABV-host interaction.

Identification of key genes involved in Brg1 mutation-induced cataract using bioinformatics analyses with publicly available microarray data

Background: Cataract is a common and frequently occurring disease in the elderly. The Brahma-related gene 1 (Brg1) is believed to be related to the formation of cataract, but its mechanisms still remain unclear. This study aimed to investigate how a Brg1 mutation affects lens development and promotes the formation of cataract in mice. Methods: We used mRNA profiles downloaded from the Gene Expression Omnibus (GEO) database to compare the tissue samples of lenses from 4 dominant-negative Brg1(dnBrg1) transgenic mice and 4 wild-type mice. Then, the NetworkAnalyst online tool was employed to screen for the significantly differentially expressed genes (DEGs). Gene Ontology (GO) annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome pathway analysis were examined in DEGs by using Metascape. In addition, we applied the STRING online tool and Cytoscape software to build the protein-protein interaction (PPI) network. Finally, the CytoNCA plug-in was used to choose the central modules from the PPI network. Results: 323 DEGs were filtered in total, 222 of which were up-regulated genes and enriched in the cell cycle process regulation, mitotic G1-G1/S phase, mRNA splicing, etc., while 101 of which were down-regulated genes and enriched in the organ hydroxy compound transport, synaptic vesicle cycle and neuron migration. Within this network of PPI, we found that the heat shock protein 90 alpha (cytosolic), class B member 1 (HSP90ab1), the polymerase (RNA) II (DNA directed) polypeptide E (Polr2e), the cell division cycle 20 (Cdc20) and the polymerase (RNA) II (DNA directed) polypeptide C (Polr2c) had higher connectivity degrees and may interact and influence each other. Conclusions: The Brg1 mutation affected expression of various genes in mice, such as HSP90ab1, Polr2e, Cdc20, and Polr2c. These genes may have some effects on the occurrence and development of cataract, and may serve as potential therapeutic targets for the cataract treatment.

ISG20L2 as a Novel Prognostic Biomarker Facilitates the Progression of Pancreatic Cancer Via Glycolysis

Background: Longstanding type 2 diabetes mellitus (T2DM) is an increased risk of pancreatic cancer (PC) in western populations, and PC is also a cause of T2DM. However, the association of glucose metabolism between T2DM and PC remains unclear. Methods: Differentially expressed genes (DEGs) were identified by bioinformatic analysis from Gene Expression Omnibus (GEO) datasets GSE20966 and GSE16515, respectively. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, Gene Set Enrichment Analysis (GSEA), the Kaplan-Meier (KM) Plotter and Tumor Immune Estimation Resource (TIMER) database were applied. Pancreatic cancer cell lines and primary PDAC samples were used. Cell culture, immunohistochemistry (IHC), siRNA transfection, Western blot, RT-PCR, and migration assay, animal xenograft model studies and statistical analysis were performed in this study. Results: We identified 64 DEGs in GSE20966 of T2DM, and 296 DEGs were identified in GSE16515 of pancreatic cancer, respectively. T2DM-DEGs were mainly enriched in synaptic vesicle cycle, protein export. KEGG pathways in pancreatic cancer included spliceosome, RNA transport. Here, ISG20L2 was identified as only a co-expressed gene between T2DM and PDAC. We found that the expression of ISG20L2 was associated with tumor immune cell infiltration. ISG20L2 was significantly upregulated in PDAC and associated with prognosis of PDAC patients. Moreover, ISG20L2 expression was regulated by GLUT1 , HK2 , LDHA , PKM1 and PKM2 related with glycolysis in PDAC. ISG20L2 promoted PDAC cell proliferation and migration both in vitro and in vivo. Conclusion: This study showed that ISG20L2 promoted the progression and ISG20L2 may be a potential therapeutic strategy in PDAC.

Molecular Analysis of Prognosis and Immune Pathways of Pancreatic Cancer Based on TNF Family Members

Background. Tumor necrosis factor (TNF) family members play a vital role in anticancer therapy. This study aimed to screen the critical markers for the prognostic analysis of pancreatic adenocarcinoma (PAAD) by analyzing the clustering patterns of TNF family members in PAAD. Methods. In this study, the NMF clustering method was adopted to cluster samples from The Cancer Genome Atlas (TCGA) to acquire the clustering pattern of the TNF family in PAAD. Differential gene analysis was performed according to TNF family gene clusters. The support vector machine (SVM) method was conducted for further gene screening, and the risk score model of the screened genes was constructed by Lasso. The single sample gene set enrichment analysis (ssGSEA) method was adopted for immunoenrichment analysis and tumor immune cycle analysis. Genes associated with risk scores were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Results. We clustered PAAD into two groups based on TNF family genes. Nineteen TNF family genes were significantly associated with the clinical characteristics of PAAD patients. The risk score formula was composed of RHOD, UBE2C, KLHDC7b, MSLN, ADAM8, NME3, GNG2, and MCOLN3. GSE57495 and GSE62452 datasets verified that patients in the high-risk group had a worse prognosis than those in the low-risk group. The risk score-related genes analyzed by GO and KEGG were mainly involved in the modulation of chemical synaptic transmission and synaptic vesicle cycle pathway. There were significant differences in the expression of 15 immune cells between the high-risk group and the low-risk group. The risk score was positively correlated with HCK, interferon, MHC-I, and STAT1. The expression of genes relevant to chemokine, immunostimulator, MHC, and receptor was strongly associated with the risk score. Conclusion. The risk score model based on the TNF family can predict the prognosis and immune status of PAAD patients. Further research is needed to verify the clinical prognostic value of risk scores.

ISG20L2 as a Novel Prognostic Biomarker Facilitates the Progression of Pancreatic Cancer via Glycolysis

Background: Longstanding type 2 diabetes mellitus (T2DM) is an increased risk of pancreatic cancer (PC) in western populations, and PC is also a cause of T2DM. However, the association of glucose metabolism between T2DM and PC remains unclear. Methods: Differentially expressed genes (DEGs) were identified by bioinformatic analysis from Gene Expression Omnibus (GEO) datasets GSE20966 and GSE16515, respectively. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, Gene Set Enrichment Analysis (GSEA), the Kaplan-Meier (KM) Plotter and Tumor Immune Estimation Resource (TIMER) database were applied. Pancreatic cancer cell lines and primary PDAC samples were used. Cell culture, immunohistochemistry (IHC), siRNA transfection, Western blot, RT-PCR, and migration assay, animal xenograft model studies and statistical analysis were performed in this study. Results: We identified 64 DEGs in GSE20966 of T2DM, and 296 DEGs were identified in GSE16515 of pancreatic cancer, respectively. T2DM-DEGs were mainly enriched in synaptic vesicle cycle, protein export. KEGG pathways in pancreatic cancer included spliceosome, RNA transport. Here, ISG20L2 was identified as only a co-expressed gene between T2DM and PDAC. We found that the expression of ISG20L2 was associated with tumor immune cell infiltration. ISG20L2 was significantly upregulated in PDAC and associated with prognosis of PDAC patients. Moreover, ISG20L2 expression was regulated by GLUT1, HK2, LDHA, PKM1 and PKM2 related with glycolysis in PDAC. ISG20L2 promoted PDAC cell proliferation and migration both in vitro and in vivo. Conclusion: This study showed that ISG20L2 promoted the progression and ISG20L2 may be a potential therapeutic strategy in PDAC.

Synaptotagmin 7 is targeted to the axonal plasma membrane through γ-secretase processing to promote synaptic vesicle docking in mouse hippocampal neurons

Synaptotagmin 7 (SYT7) has emerged as a key regulator of presynaptic function, but its localization and precise role in the synaptic vesicle cycle remain the subject of debate. Here, we used iGluSnFR to optically interrogate glutamate release, at the single-bouton level, in SYT7KO-dissociated mouse hippocampal neurons. We analyzed asynchronous release, paired-pulse facilitation, and synaptic vesicle replenishment and found that SYT7 contributes to each of these processes to different degrees. ‘Zap-and-freeze’ electron microscopy revealed that a loss of SYT7 diminishes docking of synaptic vesicles after a stimulus and inhibits the recovery of depleted synaptic vesicles after a stimulus train. SYT7 supports these functions from the axonal plasma membrane, where its localization and stability require both γ-secretase-mediated cleavage and palmitoylation. In summary, SYT7 is a peripheral membrane protein that controls multiple modes of synaptic vesicle (SV) exocytosis and plasticity, in part, through enhancing activity-dependent docking of SVs.

Mechanism of Radix Rhei Et Rhizome Intervention in Cerebral Infarction: A Research Based on Chemoinformatics and Systematic Pharmacology

Objective. To explore the therapeutic targets, network modules, and coexpressed genes of Radix Rhei Et Rhizome intervention in cerebral infarction (CI), and to predict significant biological processes and pathways through network pharmacology. To explore the differential proteins of Radix Rhei Et Rhizome intervention in CI, conduct bioinformatics verification, and initially explain the possible therapeutic mechanism of Radix Rhei Et Rhizome intervention in CI through proteomics. Methods. The TCM database was used to predict the potential compounds of Radix Rhei Et Rhizome, and the PharmMapper was used to predict its potential targets. GeneCards and OMIM were used to search for CI-related genes. Cytoscape was used to construct a protein-protein interaction (PPI) network and to screen out core genes and detection network modules. Then, DAVID and Metascape were used for enrichment analysis. After that, in-depth analysis of the proteomics data was carried out to further explore the mechanism of Radix Rhei Et Rhizome intervention in CI. Results. (1) A total of 14 Radix Rhei Et Rhizome potential components and 425 potential targets were obtained. The core components include sennoside A, palmidin A, emodin, toralactone, and so on. The potential targets were combined with 297 CI genes to construct a PPI network. The targets shared by Radix Rhei Et Rhizome and CI include ALB, AKT1, MMP9, IGF1, CASP3, etc. The biological processes that Radix Rhei Et Rhizome may treat CI include platelet degranulation, cell migration, fibrinolysis, platelet activation, hypoxia, angiogenesis, endothelial cell apoptosis, coagulation, and neuronal apoptosis. The signaling pathways include Ras, PI3K-Akt, TNF, FoxO, HIF-1, and Rap1 signaling pathways. (2) Proteomics shows that the top 20 proteins in the differential protein PPI network were Syp, Syn1, Mbp, Gap43, Aif1, Camk2a, Syt1, Calm1, Calb1, Nsf, Nefl, Hspa5, Nefh, Ncam1, Dcx, Unc13a, Mapk1, Syt2, Dnm1, and Cltc. Differential protein enrichment results show that these proteins may be related to synaptic vesicle cycle, vesicle-mediated transport in synapse, presynaptic endocytosis, synaptic vesicle endocytosis, axon guidance, calcium signaling pathway, and so on. Conclusion. This study combined network pharmacology and proteomics to explore the main material basis of Radix Rhei Et Rhizome for the treatment of CI such as sennoside A, palmidin A, emodin, and toralactone. The mechanism may be related to the regulation of biological processes (such as synaptic vesicle cycle, vesicle-mediated transport in synapse, presynaptic endocytosis, and synaptic vesicle endocytosis) and signaling pathways (such as Ras, PI3K-Akt, TNF, FoxO, HIF-1, Rap1, and axon guidance).