scholarly journals Micro-Transcriptome Analysis Reveals Immune-Related MicroRNA Regulatory Networks of Paralichthys olivaceus Induced by Vibrio anguillarum Infection

2020 ◽  
Vol 21 (12) ◽  
pp. 4252
Author(s):  
Xianhui Ning ◽  
Li Sun
Keyword(s):  
Immune Response ◽  
Transcriptome Analysis ◽  
Regulatory Networks ◽  
Expression Profiles ◽  
Paralichthys Olivaceus ◽  
Vibrio Anguillarum ◽  
Japanese Flounder ◽  
Integrated Analysis ◽  
Immune Gene ◽  
Hub Genes

MicroRNAs (miRNAs) are non-coding regulatory RNAs that play a vital part in the host immune response to pathogen infection. Japanese flounder (Paralichthys olivaceus) is an important aquaculture fish species that has suffered from bacterial diseases, including that caused by Vibrio anguillarum infection. In a previous study, we examined the messenger RNA (mRNA) expression profiles of flounder during V. anguillarum infection and identified 26 hub genes in the flounder immune response. In this study, we performed the micro-transcriptome analysis of flounder spleen in response to V. anguillarum infection at 3 different time points. Approximately 277 million reads were obtained, from which 1218 miRNAs were identified, including 740 known miRNAs and 478 novel miRNAs. Among the miRNAs, 206 were differentially expressed miRNAs (DEmiRs), and 104 of the 206 DEmiRs are novel miRNAs identified for the first time. Most of the DEmiRs were strongly time-dependent. A total of 1355 putative target genes of the DEmiRs (named DETGs) were identified based on integrated analysis of miRNA-mRNA expressions. The DETGs were enriched in multiple functional categories associated with immunity. Thirteen key DEmiRs and 66 immune DETGs formed an intricate regulatory network constituting 106 pairs of miRNAs and DETGs that span five immune pathways. Furthermore, seven of the previously identified hub genes were found to be targeted by 73 DEmiRs, and together they formed interlinking regulatory networks. These results indicate that V. anguillarum infection induces complicated miRNA response with extensive influences on immune gene expression in Japanese flounder.

scholarly journals Impact of Ringer’s Solution Challenge Stress to Immunostimulatory Experiment, Insights From Japanese Flounder

2020 ◽  
Vol 11 ◽  
Author(s):  
Jinxiang Liu ◽  
Zan Li ◽  
Yujue Wang ◽  
Quanqi Zhang
Keyword(s):  
Immune Response ◽  
Intraperitoneal Injection ◽  
Expression Profiles ◽  
Paralichthys Olivaceus ◽  
Metabolic Process ◽  
Japanese Flounder ◽  
Innate Immune ◽  
Fundamental Information ◽  
Immune Related Genes ◽  
The Impact

Ringer’s or phosphate buffer saline (PBS) solution buffer usually was used as dilution butter in intraperitoneal injection. Stress could activate immune response, inflammatory response and glycogen metabolic process. The impact of solution buffer as a stressor to immune system was ignored in immunostimulatory experiment. In this report, we tested the hypothesis that the innate immune response and glycogen metabolic process were altered when it were challenged with Ringer’s in Japanese flounder (Paralichthys olivaceus). RNA-seq was performed after challenge with Ringer’s at 8 h and 48 h. The data revealed that the expression profiles of blood, gill, and kidney were significantly changed. Differentially expressed genes (DEGs) were identified, and energy metabolic and immune-related genes were up-regulated or down-regulated obviously. GO and KEGG analyses showed that DEGs were mainly enriched in innate immune terms and pathways. Weighted gene co-expression networks analysis (WGCNA) also indicated the highest association module with stress. A total of 16 genes were detected in the gray module, which were immune-related and metabolic-related genes. These results provided fundamental information on intraperitoneal injection with solution buffer. It offered useful clues to further explore the functional mechanism of stress and immunity.

scholarly journals Integrated Analysis of lncRNAs, mRNAs, and TFs to Identify Regulatory Networks Underlying MAP Infection in Cattle

2021 ◽  
Vol 12 ◽  
Author(s):  
Maryam Heidari ◽  
Abbas Pakdel ◽  
Mohammad Reza Bakhtiarizadeh ◽  
Fariba Dehghanian
Keyword(s):  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Johne's Disease ◽  
Johne’S Disease ◽  
Functional Enrichment ◽  
Integrated Analysis ◽  
Complex Nature ◽  
Hub Genes ◽  
Cis And Trans

Johne’s disease is a chronic infection of ruminants that burdens dairy herds with a significant economic loss. The pathogenesis of the disease has not been revealed clearly due to its complex nature. In order to achieve deeper biological insights into molecular mechanisms involved in MAP infection resulting in Johne’s disease, a system biology approach was used. As far as is known, this is the first study that considers lncRNAs, TFs, and mRNAs, simultaneously, to construct an integrated gene regulatory network involved in MAP infection. Weighted gene coexpression network analysis (WGCNA) and functional enrichment analysis were conducted to explore coexpression modules from which nonpreserved modules had altered connectivity patterns. After identification of hub and hub-hub genes as well as TFs and lncRNAs in the nonpreserved modules, integrated networks of lncRNA-mRNA-TF were constructed, and cis and trans targets of lncRNAs were identified. Both cis and trans targets of lncRNAs were found in eight nonpreserved modules. Twenty-one of 47 nonpreserved modules showed significant biological processes related to the immune system and MAP infection. Some of the MAP infection’s related pathways in the most important nonpreserved modules comprise “positive regulation of cytokine-mediated signaling pathway,” “negative regulation of leukocyte migration,” “T-cell differentiation,” “neutrophil activation,” and “defense response.” Furthermore, several genes were identified in these modules, including SLC11A1, MAPK8IP1, HMGCR, IFNGR1, CMPK2, CORO1A, IRF1, LDLR, BOLA-DMB, and BOLA-DMA, which are potentially associated with MAP pathogenesis. This study not only enhanced our knowledge of molecular mechanisms behind MAP infection but also highlighted several promising hub and hub-hub genes involved in macrophage-pathogen interaction.

scholarly journals Systematic and integrated analysis of tRNA-derived small RNAs reveals novel potential pathogenesis targets of sarcoidosis

2022 ◽  
Author(s):  
Min Zhao ◽  
Chang Tian ◽  
Xin Di ◽  
Xin Jin ◽  
Shan Cong ◽  
...  
Keyword(s):  
Visual Analysis ◽  
Expression Profiles ◽  
Target Prediction ◽  
Integrated Analysis ◽  
Hub Genes ◽  
Bioinformatics Analyses ◽  
Deep Sequencing Technology ◽  
Non Coding Rnas ◽  
Polymerase Chain ◽  
Regulatory Functions

Abstract The pathogenesis of sarcoidosis, which involves several systems, is unclear, and its pathological type is non-caseating epithelioid granulomas. tRNA-derived small RNA (tsRNA) is a novel class of short non-coding RNAs with potential regulatory functions. However, whether tsRNA contributes to sarcoidosis pathogenesis remains unclear. Deep sequencing technology was used to identify alterations in tsRNA expression profiles between patients with sarcoidosis and healthy controls. A total of 360 tsRNAs were identified for exact matches. Among them, the expression of three tRNAs (tiRNA-Glu-TTC-001, tiRNA-Lys-CTT-003, and tRF-Ser-TGA-007) was markedly regulated in sarcoidosis and validated by quantitative real-time polymerase chain reaction. The expression of various tsRNAs was significantly correlated with age, the number of affected systems, and calcium levels in the blood. Additionally, target prediction and bioinformatics analyses revealed that these tsRNAs may play roles in chemokine, cAMP, cGMP-PKG, retrograde endorphin, and FoxO signalling pathways. The Cytoscape software was used for visual analysis to obtain 10 hub genes of each target tsRNA. Among the hub genes, APP, PRKACB, ARRB2, and NR5A1 finding may participate in the occurrence and development of sarcoidosis through immune inflammation. This study provides novel insights to explore tsRNA as a novel and efficacious pathogenic target of sarcoidosis.

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