scholarly journals Transcriptome Analysis Reveals Impaired Fertility and Immunity Under Salinity Exposure in Juvenile Grass Carp

2021 ◽  
Vol 8 ◽  
Author(s):  
Jingjing Zhang ◽  
Zhi Wu ◽  
Yujie He ◽  
Xinhui Li ◽  
Jie Li
Keyword(s):  
Signaling Pathway ◽  
Transcriptome Analysis ◽  
Grass Carp ◽  
Enrichment Score ◽  
Receptor Interaction ◽  
Receptor Signaling ◽  
Steroid Biosynthesis ◽  
Kegg Pathways ◽  
Risk Of Death ◽  
Receptor Signaling Pathway

Grass carp (Ctenopharyngodon idellus) is one of the most economically important aquaculture species and is widely cultured in China. However, its wild populations in many rivers are increasingly declining, and seawater intrusion is one of the most important threats to their survival. However, the mechanisms underlying the decline due to salinity pressure are still unknown. Here, we performed a comparative transcriptome analysis of C. idellus larvae in response to salinity exposures; a total of 481 differentially expressed genes (DEGs) were identified. These DEGs were significantly enriched in eight Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, among which steroid biosynthesis was the most important one, with the highest enrichment score. The pathway plays an important role in the development of the testes and ovary. Interestingly, all DEGs in steroid biosynthesis showed a down regulation, indicating that salinity exposure may pose damage to the fertility of C. idellus. Furthermore, three immunity-associated pathways (cytokine–cytokine receptor interaction, Toll-like receptor signaling pathway, and NOD-like receptor signaling pathway) were also significantly enriched, suggesting impaired immunity and a high risk of disease infection under salinity exposure. Overall, damage to both fertility and immunity would decrease the number of offspring and increase the risk of death due to disease infection. Our results provide a potential molecular mechanism underlying the decline of wild C. idellus populations in the Pearl River.

scholarly journals Identification of potential microRNAs and KEGG pathways in denervation muscle atrophy based on meta-analysis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xinyi Gu ◽  
Bo Jin ◽  
Zhidan Qi ◽  
Xiaofeng Yin
Keyword(s):  
Signaling Pathway ◽  
Muscle Atrophy ◽  
Meta Analysis ◽  
Cell Receptor ◽  
Differentially Expressed ◽  
Receptor Signaling ◽  
Denervated Muscle ◽  
Kegg Pathways ◽  
Receptor Signaling Pathway ◽  
Cell Receptor Signaling

AbstractThe molecular mechanism of muscle atrophy has been studied a lot, but there is no comprehensive analysis focusing on the denervated muscle atrophy. The gene network that controls the development of denervated muscle atrophy needs further elucidation. We examined differentially expressed genes (DEGs) from five denervated muscle atrophy microarray datasets and predicted microRNAs that target these DEGs. We also included the differentially expressed microRNAs datasets of denervated muscle atrophy in previous studies as background information to identify potential key microRNAs. Finally, we compared denervated muscle atrophy with disuse muscle atrophy caused by other reasons, and obtained the Den-genes which only differentially expressed in denervated muscle atrophy. In this meta-analysis, we obtained 429 up-regulated genes, 525 down-regulated genes and a batch of key microRNAs in denervated muscle atrophy. We found eight important microRNA-mRNA interactions (miR-1/Jun, miR-1/Vegfa, miR-497/Vegfa, miR-23a/Vegfa, miR-206/Vegfa, miR-497/Suclg1, miR-27a/Suclg1, miR-27a/Mapk14). The top five KEGG pathways enriched by Den-genes are Insulin signaling pathway, T cell receptor signaling pathway, MAPK signaling pathway, Toll-like receptor signaling pathway and B cell receptor signaling pathway. Our research has delineated the RNA regulatory network of denervated muscle atrophy, and uncovered the specific genes and terms in denervated muscle atrophy.

scholarly journals Analysis of transcriptomic changes in bovine endometrial stromal cells treated with lipopolysaccharide

2020 ◽  
Author(s):  
Xuefen Ding ◽  
Haimiao Lv ◽  
Lixin Deng ◽  
Wenju Hu ◽  
Zhan Peng ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Signaling Pathway ◽  
Stromal Cells ◽  
Interleukin 12 ◽  
Receptor Interaction ◽  
Control Group ◽  
Receptor Signaling ◽  
Toll Like Receptor ◽  
Endometrial Stromal Cells ◽  
Receptor Signaling Pathway

Abstract Background: Endometritis adversely affects the ability of cattle to reproduce, and significantly reduces milk production. Consequently, it has great influence on the economic value of dairy cows. The endometrium is mainly composed of epithelial and stromal cells and they produce the first immune response to invading pathogens. Epithelial cells are the first cellular barrier through which bacteria enter the uterine endometrium. However, most of the epithelial cells are disrupted and stromal cells are exposed to an inflammatory environment when endometritis occurs, especially postpartum. A loss of the protective epithelium allows bacteria or toxins to access the underlying stromal cells. The activation of Toll-like receptor（TLRs）on stromal cells induces increased production of cytokines and chemokines. Understanding the genome-wide characterization of the bovine endometritis will be beneficial for prevention and treatment of endometritis. In this study, whole-transcriptomic gene changes in bovine stromal cells treated with LPS were compared with those treated with PBS (control group) and were analyzed by RNA sequencing (RNA-seq). Results: Compared with the control group, a total of 366 differentially expressed genes (DEGs) were identified in LPS-induced group (234 upregulated and 132 downregulated genes), with an adjusted P-value＜0.05 by DESeq. Gene ontology (GO) enrichment analysis revealed DEGs were most enriched in lymphocyte activation, interleukin-1 receptor binding, regulation of cell activation, and lymphocyte-activated interleukin-12 production. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed DEGs were most enriched in TNF signaling pathway, Toll-like receptor signaling pathway, cytokine-cytokine receptor interaction, nucleotide-binding oligomerization domain-like (NOD-like) receptor signaling pathway, NF-κB signaling pathway, and chemokine signaling pathway.Conclusion: The results of this study unraveled endometrial stromal cells transcriptome profile alterations in bovine affected by LPS which may have a significant effect on the eliminating or reducing inflammation by comprehending molecular mechanisms and authenticating unique genes related to endometritis.

scholarly journals Analysis of transcriptomic changes in bovine endometrial stromal cells treated with lipopolysaccharide

2020 ◽  
Author(s):  
Xuefen Ding ◽  
Haimiao Lv ◽  
Lixin Deng ◽  
Wenju Hu ◽  
Zhan Peng ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Signaling Pathway ◽  
Stromal Cells ◽  
Interleukin 12 ◽  
Receptor Interaction ◽  
Control Group ◽  
Receptor Signaling ◽  
Toll Like Receptor ◽  
Endometrial Stromal Cells ◽  
Receptor Signaling Pathway

Abstract Background: Endometritis adversely affects the ability of cattle to reproduce, and significantly reduces milk production. Consequently, it has great influence on the economic value of dairy cows. The endometrium is mainly composed of epithelial and stromal cells and they produce the first immune response to invading pathogens. Epithelial cells are the first cellular barrier through which bacteria enter the uterine endometrium. However, most of the epithelial cells are disrupted and stromal cells are exposed to an inflammatory environment when endometritis occurs, especially postpartum. A loss of the protective epithelium allows bacteria or toxins to access the underlying stromal cells. The activation of Toll-like receptor（TLRs）on stromal cells induces increased production of cytokines. Understanding the genome-wide characterization of the bovine endometritis will be beneficial for prevention and treatment of endometritis. In this study, whole-transcriptomic gene changes in bovine stromal cells treated with LPS were compared with those treated with PBS (control group) and were analyzed by RNA sequencing (RNA-seq). This was done in a cell culture model in vitro.Results: Compared with the control group, a total of 366 differentially expressed genes (DEGs) were identified in LPS-induced group (234 upregulated and 132 downregulated genes), with an adjusted P-value＜0.05 by DESeq. Gene ontology (GO) enrichment analysis revealed DEGs were most enriched in lymphocyte activation, interleukin-1 receptor binding, regulation of cell activation, and lymphocyte-activated interleukin-12 production. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed DEGs were most enriched in TNF signaling pathway, Toll-like receptor signaling pathway, cytokine-cytokine receptor interaction, nucleotide-binding oligomerization domain-like (NOD-like) receptor signaling pathway, NF-κB signaling pathway, and chemokine signaling pathway.Conclusion: The results of this study unraveled bovine endometrial stromal cells affected with LPS transcriptome profile alterations，which may have a significant effect on the treatment inflammation by comprehending molecular mechanisms and authenticating unique genes related to endometritis.

scholarly journals Identification of hub genes and pathways in psoriasis through bioinformatics and validation by RT-qPCR

2021 ◽  
Author(s):  
Ling Ai Zou ◽  
Qichao Jian
Keyword(s):  
Signaling Pathway ◽  
Quantitative Polymerase Chain Reaction ◽  
Cytokine Receptor ◽  
Receptor Interaction ◽  
Hacat Cells ◽  
Receptor Signaling ◽  
Ppi Network ◽  
Hub Genes ◽  
Network Analyses ◽  
Receptor Signaling Pathway

Abstract Background Although several studies have attempted to investigate the aetiology and mechanism of psoriasis, the precise molecular mechanism remains unclear. Our study aimed to identify the hub genes and associated pathways that promote its pathogenesis in psoriasis, which would be helpful for the discovery of diagnostic and therapeutic markers. Methods GSE30999, GSE34248, GSE41662, and GSE50790 datasets were extracted from the Gene Expression Omnibus (GEO) database. The GEO profiles were integrated to obtain differentially expressed genes (DEGs) using the affy package in R software, with |logFC|> 1.5 and adjusted P < 0.05. The DEGs were utilised for Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein-protein interaction (PPI) network analyses. Hub genes were identified using Cytoscape and enriched for analysis in www.bioinformatics.com.cn. These hub genes were validated in the four aforementioned datasets and M5-induced HaCaT cells using real-time quantitative polymerase chain reaction (RT-qPCR). Results A total of 359 DEGs were identified, which were mostly associated with responses to bacterium, defence responses to other organism, and antimicrobial humoral response. These DEGs were mostly enriched in the steroid hormone biosynthesis pathway, NOD-like receptor signaling pathway, and cytokine-cytokine receptor interaction. PPI network analysis indicated seven genes (CXCL1, ISG15, CXCL10, STAT1, OASL, IFIT1, and IFIT3) as the probable hub genes of psoriasis; CXCL10 had a positive correlation with the other six hub genes. The chord plot results further supported the GO and KEGG analysis results of the 359 DEGs. Seven predicted hub genes were validated to be upregulated in four datasets and M5-induced HaCaT cells using RT-qPCR. Conclusions The pathogenesis of psoriasis may be associated with seven hub genes (CXCL1, ISG15, CXCL10, STAT1, OASL, IFIT1, and IFIT3) and pathways, such as the NOD-like receptor signaling pathway and cytokine-cytokine receptor interaction. These hub genes, especially CXCL10, can be used as potential biomarkers in psoriasis.

scholarly journals SUMOylation of GMFB regulates the stability and function of GMFB in RPE cells under oxidative stress and inflammation

2021 ◽  
Author(s):  
Wan Sun ◽  
Juan Wang ◽  
Jieping Zhang ◽  
Furong Gao ◽  
Qingjian Ou ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Quantitative Polymerase Chain Reaction ◽  
Age Related Macular Degeneration ◽  
Receptor Interaction ◽  
Receptor Signaling ◽  
Post Translational Modification ◽  
Nf Kappa B ◽  
Age Related ◽  
Receptor Signaling Pathway ◽  
And Function

AbstractGlia maturation factor beta (GMFB) is a growth and differentiation factor that act as an intracellular regulator of signal transduction pathways. The SUMOylation is a post-translational modification (PTM) that plays a key role in protein subcellular localization, stability, transcription, and enzymatic activity. Recent studies have highlighted the importance of SUMOylation in the inflammation and progression of numerous diseases. But little is known about the relationship between GMFB and SUMOylation. Here we first report that GMFB can be mono-SUMOylated at multiple sites by the covalent addition of a single SUMO1 protein, and identified K20, K35, K58, and K97 as major SUMO acceptor sites. We also found that SUMOylation leading to increased stability and trans-localization of GMFB. Furthermore, RNA-seq data and Real-time quantitative polymerase chain reaction (rt-qPCR) also indicated that the SUMOylated GMFB upregulated multiple pathways, including the cytokine-cytokin receptor interaction, NOD-like receptor signaling pathway, TNF signaling pathway, RIG-I-like receptor signaling pathway, and NF-kappa B signaling pathway. Our studies intend to provide a novel direction for the study into the biofunction of GMFB, SUMOylated GMFB and the mechanism, clinical therapy, and prognosis of inflammation-related RPE disorders like age-related macular degeneration (AMD) and diabetic retinopathy (DR).

scholarly journals Analysis of transcriptomic changes in bovine endometrial stromal cells treated with lipopolysaccharide

2019 ◽  
Author(s):  
Xuefen Ding ◽  
Haimiao Lv ◽  
Lixin Deng ◽  
Wenju Hu ◽  
Zhan Peng ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Signaling Pathway ◽  
Stromal Cells ◽  
Molecular Mechanisms ◽  
Interleukin 12 ◽  
Receptor Interaction ◽  
Control Group ◽  
Receptor Signaling ◽  
Endometrial Stromal Cells ◽  
Receptor Signaling Pathway

Abstract Background: Endometritis adversely affects the ability of cattle to reproduce, and significantly reduces milk production. Consequently, it has great influence on the economic value of dairy cows. The endometrium is mainly composed of epithelial and stromal cells and they produce the first immune response to invading pathogens. Epithelial cells are the first cellular barrier through which bacteria enter the uterine endometrium. However, most of the epithelial cells are disrupted and stromal cells are exposed to an inflammatory environment when endometritis occurs, especially postpartum. Inflammation in endometrial stromal cells is thus activated, immune-related cytokines and signaling pathways are activated. This indicates that endometritis is becoming more and more serious. However, inflammatory response in bovine endometrial stromal cells is yet to be studied in detail. Understanding the genome-wide characterization of the bovine endometritis will be beneficial for prevention and treatment of endometritis. In this study, whole-transcriptomic gene changes in bovine stromal cells treated with LPS were compared with those treated with PBS (control group) and were analyzed by RNA sequencing (RNA-seq). Results: Compared with the control group, a total of 366 differentially expressed genes (DEGs) were identified in LPS-induced group (234 upregulated and 132 downregulated genes), with an adjusted P -value＜0.05 by DESeq. Gene ontology (GO) enrichment analysis revealed DEGs were most enriched in lymphocyte activation, interleukin-1 receptor binding, regulation of cell activation, and lymphocyte-activated interleukin-12 production. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed DEGs were most enriched in TNF signaling pathway, Toll-like receptor signaling pathway, cytokine-cytokine receptor interaction, nucleotide-binding oligomerization domain-like (NOD-like) receptor signaling pathway, NF-κB signaling pathway, and chemokine signaling pathway. Conclusion: Our results proved and expanded findings of previous studies on bovine endometritis. These results will be useful to propose new therapeutic targets and eliminate or reduce inflammation by comprehending molecular mechanisms and authenticating unique genes related to endometritis.

scholarly journals Diagnostic Value of DHX58 - IRF7 Involved in RIG-I-Like Receptor Signaling Pathway in Tuberculosis

2021 ◽  
Author(s):  
Chong-hui Li ◽  
Yu-rong Fu ◽  
zhengjun yi
Keyword(s):  
Dendritic Cell ◽  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Diagnostic Value ◽  
Receptor Interaction ◽  
Receptor Signaling ◽  
Hub Genes ◽  
Roc Curve Analysis ◽  
Diagnostic Efficacy ◽  
Receptor Signaling Pathway

Abstract Background: Tuberculosis (TB) is an infectious disease that endangers human health. This study set out to search for key genes and related pathways in dendritic cell (DC) from TB patients to reveal the potential molecular mechanisms and identify potential biomarkers for TB.Method: DC data GSE34151 related to TB was downloaded from GEO data sets for analysis. Differentially expressed genes (DEGs) were obtained by employing an online tool, GEO2R. PPI network of DEGs and gene module were visualized and calculated applying STRING and Cytoscape, respectively. GO analysis and KEGG pathway were utilized to annotate the functions of DEGs. ROC curve analysis was applied to screen the most diagnostic hub genes associated with TB. Furthermore, their expression was validated in blood data (GSE83456), which were further compared to the T-spot·TB test.Results: A total of 290 DEGs were screened, which were significantly enriched in Cytokine-cytokine receptor interaction, Toll-like receptor signaling pathway, and RIG-I-like receptor signaling pathways. Among them, 27 candidate hub genes with the most significant cluster in PPI were enriched in RIG-I-like receptor signaling pathway, which has been known to be associated with TB. We further found that the top 10 hub genes(DHX58, ISG20, IRF1, IRF7 and RSAD2, etc) showed high performance for TB diagnosis, among which both DHX58 and IRF7 were enriched in the RIG-I-like receptor signaling pathway. Moreover, DHX58 and IRF7 were also increased in blood, which were consistent with that in dendritic cell. Interestingly, DHX58 and IRF7 display higher diagnostic efficacy than T-spot·TB test.Conclusion: In this study, we revealed that both DHX58 and IRF7 with high diagnostic value in blood and dendritic cells, potentially involved in RIG-I-like receptor signaling pathway, may serve as a marker for TB diagnosis.

Sign in / Sign up

Export Citation Format

Share Document