The key differentially expressed genes and proteins related to immune response in the spleen of pufferfish (Takifugu obscurus) infected by Aeromonas hydrophila

2019 ◽  
Vol 91 ◽  
pp. 1-11 ◽  
Author(s):  
Shengli Fu ◽  
Mingmei Ding ◽  
Qingjian Liang ◽  
Yanjian Yang ◽  
Meng Chen ◽  
...  
Keyword(s):  
Immune Response ◽  
Differentially Expressed Genes ◽  
Aeromonas Hydrophila ◽  
Differentially Expressed ◽  
Takifugu Obscurus

scholarly journals Transcriptomic analysis of PPARα-dependent alterations during cardiac hypertrophy

2008 ◽  
Vol 36 (1) ◽  
pp. 15-23 ◽  
Author(s):  
Pascal J. H. Smeets ◽  
Heleen M. de Vogel-van den Bosch ◽  
Peter H. M. Willemsen ◽  
Alphons P. Stassen ◽  
Torik Ayoubi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Lipid Metabolism ◽  
Cardiac Hypertrophy ◽  
Signaling Pathways ◽  
Differentially Expressed Genes ◽  
Left Ventricular ◽  
Transcriptomic Analysis ◽  
Differentially Expressed ◽  
Wild Type

Peroxisome proliferator-activated receptor (PPAR)α regulates lipid metabolism at the transcriptional level and modulates the expression of genes involved in inflammation, cell proliferation, and differentiation. Although PPARα has been shown to mitigate cardiac hypertrophy, knowledge about underlying mechanisms and the nature of signaling pathways involved is fragmentary and incomplete. The aim of this study was to identify the processes and signaling pathways regulated by PPARα in hearts challenged by a chronic pressure overload by means of whole genome transcriptomic analysis. PPARα−/− and wild-type mice were subjected to transverse aortic constriction (TAC) for 28 days, and left ventricular gene expression profile was determined with Affymetrix GeneChip Mouse Genome 430 2.0 arrays containing >45,000 probe sets. In unchallenged hearts, the mere lack of PPARα resulted in 821 differentially expressed genes, many of which are related to lipid metabolism and immune response. TAC resulted in a more pronounced cardiac hypertrophy and more extensive changes in gene expression (1,910 and 312 differentially expressed genes, respectively) in PPARα−/− mice than in wild-type mice. Many of the hypertrophy-related genes were related to development, signal transduction, actin filament organization, and collagen synthesis. Compared with wild-type hypertrophied hearts, PPARα−/− hypertrophied hearts revealed enrichment of gene clusters related to extracellular matrix remodeling, immune response, oxidative stress, and inflammatory signaling pathways. The present study therefore demonstrates that, in addition to lipid metabolism, PPARα is an important modulator of immune and inflammatory response in cardiac muscle.

scholarly journals Fecal Host Transcriptomics for Non-invasive Human Mucosal Immune Profiling: Proof of Concept in Clostridium difficile Infection

2018 ◽  
Vol 3 (2) ◽  
pp. 164
Author(s):  
Robert Schlaberg ◽  
Amanda Barrett ◽  
Kornelia Edes ◽  
Michael Graves ◽  
Litty Paul ◽  
...  
Keyword(s):  
Immune Response ◽  
Clostridium Difficile ◽  
Differentially Expressed Genes ◽  
Clostridium Difficile Infection ◽  
Expression Profiles ◽  
Principal Component ◽  
Mucosal Immune Response ◽  
Differentially Expressed ◽  
Proof Of Concept ◽  
Non Invasive

Background: Host factors play an important role in pathogenesis and disease outcome in Clostridium difficile infection (CDI), and characterization of these responses could uncover potential host biomarkers to complement existing microbe-based diagnostics.Methods: We extracted RNA from fecal samples of patients with CDI and profiled human mRNA using amplicon-based next-generation sequencing (NGS). We compared the fecal host mRNA transcript expression profiles of patients with CDI to controls with non-CDI diarrhea.Results: We found that the ratio of human actin gamma 1 (ACTG1) to 16S ribosomal RNA (rRNA) was highly correlated with NGS quality as measured by percentage of reads on target. Patients with CDI could be differentiated from those with non-CDI diarrhea based on their fecal mRNA expression profiles using principal component analysis. Among the most differentially expressed genes were ones related to immune response (IL23A, IL34) and actin-cytoskeleton function (TNNT1, MYL4, SMTN, MYBPC3, all adjusted P-values <1×10-3).Conclusions: In this proof-of-concept study, we used host fecal transcriptomics for non-invasive profiling of the mucosal immune response in CDI. We identified differentially expressed genes with biological plausibility based on animal and cell culture models. This demonstrates the potential of fecal transcriptomics to uncover host-based biomarkers for enteric infections.

The impact of a moderate chronic temperature increase on spleen immune-relevant gene transcription depends on whether Atlantic cod (Gadus morhua) are stimulated with bacterial versus viral antigens

Genome ◽  
2013 ◽  
Vol 56 (10) ◽  
pp. 567-576 ◽  
Author(s):  
Tiago S. Hori ◽  
A. Kurt Gamperl ◽  
Gord Nash ◽  
Marije Booman ◽  
Ashoktaru Barat ◽  
...  
Keyword(s):  
Immune Response ◽  
Elevated Temperature ◽  
Differentially Expressed Genes ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Aeromonas Salmonicida ◽  
Differentially Expressed ◽  
Important Species ◽  
Transcriptome Response ◽  
The Impact

Exposure to elevated temperature is an inherent feature of Atlantic cod (Gadus morhua) sea-cage culture in some regions (e.g., Newfoundland) and may also become an increasingly prevalent challenge for wild fish populations because of accelerated climate change. Therefore, understanding how elevated temperatures impacts the immune response of this commercially important species may help to reduce the potential negative impacts of such challenges. Previously, we investigated the impacts of moderately elevated temperature on the antiviral responses of Atlantic cod (Hori et al. 2012) and reported that elevated temperature modulated the spleen transcriptome response to polyriboinosinic polyribocytidylic acid (pIC, a viral mimic). Herein, we report a complementary microarray study that investigated the impact of the same elevated temperature regime on the Atlantic cod spleen transcriptome response to intraperitoneal (IP) injection of formalin-killed Aeromonas salmonicida (ASAL). Fish were held at two different temperatures (10 °C and 16 °C) prior to immune stimulation and sampled 6 and 24 h post-injection (HPI). In this experiment, we identified 711 and 666 nonredundant ASAL-responsive genes at 6HPI and 24HPI, respectively. These included several known antibacterial genes, including hepcidin, cathelicidin, ferritin heavy subunit, and interleukin 8. However, we only identified 15 differentially expressed genes at 6HPI and 2 at 24HPI (FDR 1%) when comparing ASAL-injected fish held at 10 °C versus 16 °C. In contrast, the same comparisons with pIC-injected fish yielded 290 and 339 differentially expressed genes (FDR 1%) at 6HPI and 24HPI, respectively. These results suggest that moderately elevated temperature has a lesser effect on the Atlantic cod spleen transcriptome response to ASAL (i.e., the antibacterial response) than to pIC (i.e., antiviral response). Thus, the impacts of high temperatures on the cod’s immune response may be pathogen dependent.

scholarly journals FCN3 Is a Prognostic Biomarker Correlated with Immune Response in Liver Cancer

2020 ◽  
Author(s):  
Zhongxiao Lu ◽  
Jian Wu ◽  
Yi-ming Li ◽  
Wen-xiang Chen ◽  
Qiang-feng Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Liver Cancer ◽  
Differentially Expressed Genes ◽  
Kegg Pathway ◽  
Differentially Expressed ◽  
Ppi Network ◽  
Hub Genes ◽  
R Software ◽  
Hub Gene

Abstract AimLiver cancer is a common malignant tumor whose molecular pathogenesis remains unclear. This study attempts to identify key genes related to liver cancer by bioinformatics analysis and analyze their biological functions.MethodsThe gene expression data of the microarray were downloaded from the Gene Expression Omnibus(GEO) database. The differentially expressed genes (DEGs) were then identified by the R software package “limma” and were subjected to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses using DAVID. The protein-protein interaction (PPI) network was constructed via String, and the results were visualized in Cytoscape. Modules and hub genes were identified using the MCODE plugin, while the expression of hub genes and its effects were analyzed by GEPIA2. Additionally, the co-expression of the hub gene was explored in String, while the GO results were visualized using the R software. Finally, the targets of the hub gene were predicted through an online website. ResultsIn total, 43 differentially expressed genes were obtained. The GO analysis was mainly concentrated in the redox process and nuclear mitosis, while the KEGG pathway analysis was mainly enriched in retinol metabolism and the cell cycle. Moreover, four hub genes were identified in the PPI network, however, the Kaplan-Meier risk curve showed that only ECT2 and FCN3 affected the survival of liver cancer. ECT2 was found to be high expressed in liver cancer, carrying out signal transduction and targeting hsa-miR-27a-3p. FCN3 was observed to be lowly expressed in liver cancer and related to the immune response, targeting hsa-miR132-5p.ConclusionThe obtained findings suggest that two genes are significantly related to the prognosis of liver cancer, and the analysis of their biological function provided novel insight into the pathogenesis of liver cancer. Furthermore, FCN3 may serve as a promising biomarker for patients with liver cancer.

scholarly journals Gene Expression Pattern and Regulatory Network of α-Toxin Treatment in Bombyx mori

2019 ◽  
Vol 2019 ◽  
pp. 1-11
Author(s):  
Tieshan Feng ◽  
Ping Lin ◽  
Jiao Gong ◽  
Dong Cheng ◽  
Xi Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Bombyx Mori ◽  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Metabolic Process ◽  
Differentially Expressed ◽  
Potential Candidate ◽  
Upregulated Genes ◽  
Catabolic Process

Bacillus bombyseptieus is a pathogen of Bombyx mori; it can cause bacterial septicemia in silkworm. One of the components of the parasporal crystal toxin of B. bombyseptieus, α-toxin, plays an important role in the process of infection in silkworm. In this study, we investigated the immune response of silkworm induced by α-toxin by using RNA-seq. We compared the changes in gene expression in the midgut, fatbody, and hemocytes of silkworm and in the B. mori embryonic cell line (BmE) after treatment with α-toxin and identified 952 differentially expressed genes and 353 differentially expressed long noncoding RNAs (lncRNAs). These regulated genes in different tissues were found to be enriched in different pathways. The upregulated genes in the midgut were mainly involved in peptidoglycan catabolic process and tyrosine kinase signaling pathway, whereas the downregulated genes were mainly involved in chitin metabolic pathways. The upregulated genes in fatbody were also involved in peptidoglycan catabolic process, but they were for a different peptidoglycan subtype. Further, genes encoding cecropins were enriched in the fatbody. The downregulated genes were mainly involved in the metabolic pathways of fundamental substances such as cellular protein metabolic process and nucleobase-containing compound metabolic process. These results suggest that α-toxin can induce various immune responses in silkworm, and further studies are warranted to understand the mechanism of α-toxin action in silkworm. Further, lncRNAs and differentially expressed genes were correlated using coexpression network analysis. Our findings revealed potential candidate genes and lncRNAs that might play important physiological functions in the immune response to α-toxins in silkworm.

scholarly journals Deduction of Novel Genes Potentially Involved in Keratinocytes of Type 2 Diabetes Using Next-Generation Sequencing and Bioinformatics Approaches

2019 ◽  
Vol 8 (1) ◽  
pp. 73 ◽  
Author(s):  
En-Shyh Lin ◽  
Wei-An Chang ◽  
Yang-Yi Chen ◽  
Ling-Yu Wu ◽  
Yi-Jen Chen ◽  
...  
Keyword(s):  
Immune Response ◽  
Next Generation Sequencing ◽  
Differentially Expressed Genes ◽  
Defense Response ◽  
Wound Repair ◽  
Immune Defense ◽  
Differentially Expressed ◽  
Diabetic Patients ◽  
Next Generation ◽  
Generation Sequencing

Keratinocytes constitute the major cell type of epidermis, which participates in re-epithelialization during wound repair and the immune defense response to pathogens. The aim of the current study was to explore the differentially expressed genes and novel microRNA (miRNA) regulations that are potentially involved in diabetic keratinocytes through next-generation sequencing (NGS) and bioinformatics approaches. A total of 420 differentially expressed genes between normal and diabetic keratinocytes were identified, and systematic bioinformatics analyses indicated that these differentially expressed genes were functionally enriched in interferon-alpha signaling, viral defense response, and immune response. Additionally, the potential miR-340-3p-DTX3L interaction that has been systematically validated in miRNA prediction databases was proposed to participate in the disrupted skin homeostasis, altering the defense and immune response of diabetic skin. The findings may provide new insights into understanding the pathogenesis of epidermal pathologies in diabetic patients and targeting novel molecules to advance diabetic skin care in clinical practice.

scholarly journals Dynamics of rumen gene expression, microbiome colonization, and their interplay in goats

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiangyu Pan ◽  
Zongjun Li ◽  
Bibo Li ◽  
Chen Zhao ◽  
Yu Wang ◽  
...  
Keyword(s):  
Immune Response ◽  
Differentially Expressed Genes ◽  
Microbial Colonization ◽  
Differentially Expressed ◽  
Metagenomic Data ◽  
Second Phase ◽  
Functional Interactions ◽  
Rumen Microbiome ◽  
Rumen Development ◽  
Gene Modules

Abstract Background Preweaned rumen development is vital for animal health and efficient fermentation. In this study, we integrated ruminal transcriptomic and metagenomic data to explore the dynamics of rumen functions, microbial colonization, and their functional interactions during the first 8 weeks of life in goats. Results The dynamic rumen transcriptomic and microbial profiles both exhibited two distinct phases during early rumen development. The differentially expressed genes of the rumen transcriptome between the two phases showed that the immune-related response was enriched in the first phase and nutrient-related metabolism was enriched in the second phase, whereas the differentially expressed genes of the rumen microbiome were enriched in bacteriocin biosynthesis and glycolysis/gluconeogenesis activities. The developmental shift in the rumen transcriptome (at d 21) was earlier than the feed stimulus (at d 25) and the shift in the rumen microbiome (at d 42). Additionally, 15 temporal dynamic rumen gene modules and 20 microbial modules were revealed by coexpression network analysis. Functional correlations between the rumen and its microbiome were primarily involved in rumen pH homeostasis, nitrogen metabolism and the immune response. Rumen gene modules associated with the microbial alpha diversity index were also enriched in the immune response process. Conclusions The present study touched the critical developmental process of rumen functions, microbial colonization and their functional interactions during preweaned development. Taken together, these results demonstrated that rumen development at the first phase is more likely a programmed process rather than stimulation from feed and the microbiome, while the shift of rumen metagenomes was likely regulated by both the diet and host. The intensive functional correlations between rumen genes and the microbiome demonstrated that synergistic processes occurred between them during early rumen development.

scholarly journals Mating Stimulates the Immune Response and Sperm Storage-Related Genes Expression in Spermathecae of Bumblebee (Bombus terrestris) Queen

2021 ◽  
Vol 12 ◽  
Author(s):  
Yueqin Guo ◽  
Qi Zhang ◽  
Xiao Hu ◽  
Chunxiu Pang ◽  
Jilian Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Differentially Expressed Genes ◽  
Bombus Terrestris ◽  
Immunofluorescence Assay ◽  
Sperm Storage ◽  
Differentially Expressed ◽  
Immune Genes ◽  
Real Time Quantitative Pcr ◽  
Spermathecal Gland

Bumblebee queens have remarkable spermathecae that store sperm for year-round reproduction. The spermathecal gland is regarded as a secretory organ that could benefit sperm storage. Queen mating provokes substantial physiological, behavioral, and gene expression changes. Here, the transcriptomes of spermathecae were compared between virgins and mated queens of the bumblebee, Bombus terrestris L., at 24 h post mating. Differentially expressed genes were further validated by real time quantitative PCR and immunofluorescence assay. In total, the expression of 11, 069 and 10, 862 genes were identified in virgins and mated queens, respectively. We identified that 176 differentially expressed genes between virgin and mated queen spermathecae: 110 (62.5%) genes were upregulated, and 66 (37.5%) genes were downregulated in mated queens. Most of the differentially expressed genes validated by RT-qPCR were concentrated on immune response [i.e., leucine-rich repeat-containing protein 70 (35.8-fold), phenoloxidase 2 (41.9-fold), and defensin (4.9-fold)] and sperm storage [i.e., chymotrypsin inhibitor (6.2-fold), trehalose transporter Tret1 (1.7-, 1.9-, 2.4-, and 2.4-fold), and heterogeneous nuclear ribonucleoprotein A3 (1.2-, and 2.6-fold)] functions in the spermathecae of mated queens. Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 (PLOD1) was hypothesized to promote the mating behavior according to RT-qPCR and immunofluorescence assay. The expression levels of most upregulated immune genes were decreased significantly at 3 days post mating. In conclusion, the external sperm transfer into spermathecae led to the significantly upregulated immune response genes in bumblebees. These gene expression differences in queen spermathecae contribute to understanding the bumblebee post mating regulatory network.

scholarly journals Identification of differentially expressed genes for fescue toxicosis in high and low tolerant Angus cows

2019 ◽  
Author(s):  
Piush Khanal ◽  
Leticia P Sanglard ◽  
Kyle Mayberry ◽  
Jeffery Sommer ◽  
Matthew H Poore ◽  
...  
Keyword(s):  
Immune Response ◽  
Differentially Expressed Genes ◽  
Gene Networks ◽  
Cardiovascular Function ◽  
Cellular Growth ◽  
Differentially Expressed ◽  
Fescue Toxicosis ◽  
Biological Processes ◽  
Q Value ◽  
Beef Industry

Abstract Background Fescue toxicosis (FT) is the multifaceted syndrome that causes the major loss of revenue in beef industry. Management of FT has been substantial challenge for the beef industry. Little research has been conducted to identify host genetic variation for FT response. Therefore, the objectives of this study were 1) to identify differentially expressed genes (DEG) in animals with contrasting response to fescue toxicosis, 2) to assess the biological relevance of DEG and 3) to investigate the relationships of DEG through gene networks in Angus cows. Results Genotype-by-location-by-time interaction was evident, with one location (2,296) having much greater number of DEG (q-value < 0.1) between HT and LT animals than the other (554). In addition, there was a greater number of DEG (q-value < 0.1) between HT and LT animals on week 5 (3,892) than on weeks 1(1,413), 9 (1,384), and 13 (573). So, further analyses focused on DEG between HT and LT animals on week 5 at the most toxic location. The most significant DEG between HT and LT animals had relevant functions associated with FT: cellular growth (SPDYC, HEYL, ANXA13), cardiovascular function (FGB, HBA, WNT11, BPIFB4, MESP2), protein metabolism (ENPP6, MMP8), and immune response (CTBS, SDC2, CXCL13, IL-13, JAKMIP2). The strongest positive partial correlation (0.99) was between CTBS and CXCL13, where CTBS is involved in carbohydrate metabolism and immune function, and CXCL13 is involved in immune, inflammatory, and defense response, and G-protein coupled pathway. The regulation of the most significant DEG between HT and LT animals on week 5 are highly correlated, indicating a complex interaction between. When all DEG were analyzed, the enriched biological processes associated with fescue toxicosis included immune response, cardiovascular function and development, metabolic, cellular and biological processes, and fertilization. Conclusions These findings provide potential biomarkers that should be evaluated for selection of cattle with greater tolerance to fescue toxicosis which will help to establish the herd with fescue tolerant cows in regions where high endophyte infected pasture is present.

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