scholarly journals Transcriptome Analysis of Effects of Folic Acid Supplement on Gene Expression in Liver of Broiler Chickens

2021 ◽  
Vol 8 ◽  
Author(s):  
Yujie Zhang ◽  
Ningbo Zhang ◽  
Lin Liu ◽  
Yan Wang ◽  
Jinyi Xing ◽  
...  
Keyword(s):  
Gene Expression ◽  
Folic Acid ◽  
Molecular Mechanisms ◽  
Acid Group ◽  
Abdominal Fat ◽  
Water Soluble ◽  
Receptor Interaction ◽  
Control Group ◽  
Snp Analysis ◽  
General Function

Folic acid is a water-soluble B vitamin, and plays an important role in regulating gene expression and methylation. The liver is the major site of lipid biosynthesis in the chicken. Nevertheless, how gene expression and regulatory networks are affected by folic acid in liver of broilers are poorly understood. This paper conducted the RNA-seq technology on the liver of broilers under folic acid challenge investigation. First, 405 differentially expressed genes (DEGs), including 157 significantly upregulated and 248 downregulated, were detected between the control group (C) and the 5 mg folic acid group (M). Second, 68 upregulated DEGs and 142 downregulated DEGs were determined between C group and 10 mg folic acid group (H). Third, there were 165 upregulated genes and 179 downregulated genes between M and H groups. Of these DEGs, 903 DEGs were successfully annotated in the public databases. The functional classification based on GO and KEEGG showed that “general function prediction only” represented the largest functional classes, “cell cycle” (C vs. M; M vs. H), and “neuroactive ligand-receptor interaction” (C vs. H) were the highest unique sequences among three groups. SNP analysis indicated that numbers of C, M and H groups were 145,450, 146,131, and 123,004, respectively. Total new predicted alternative splicing events in C, M, and H groups were 9,521, 9,328, and 8,929, respectively. A protein-protein interaction (PPI) network was constructed, and the top 10 hub genes were evaluated among three groups. The results of real time PCR indicated that mRNA abundance of PPARγ and FAS in abdominal fat of M and H groups were reduced compared with the C group (P < 0.05). Ultramicroscopy results showed that folic acid could reduce lipid droplets in livers from chickens. Finally, contents of LPL, PPARγ, and FAS in abdominal fat were decreased with the folic acid supplmented diets (P < 0.01). These findings reveal the effects of folic acid supplemention on gene expression in liver of broilers, which can provide information for understanding the molecular mechanisms of folic acid regulating liver lipid metabolism.

scholarly journals Effects of folic acid supplementation to basal diets of broilers on growth performance, slaughter performance, IGF2 gene expression and methylation

2021 ◽  
Author(s):  
Xiuling Li ◽  
Yujie Zhang ◽  
Wenqian Jing ◽  
Weiqi Tang ◽  
Jinyi Xing ◽  
...  
Keyword(s):  
Gene Expression ◽  
Folic Acid ◽  
Average Daily Gain ◽  
Regulation Of Gene Expression ◽  
Subcutaneous Fat ◽  
Water Soluble ◽  
Heart Weight ◽  
Control Group ◽  
Igf2 Gene ◽  
Positive Effects

Folic acid (FA) is an important water-soluble vitamin and plays an important role as a cofactor and coenzyme in animal growth and development, and regulation of gene expression and methylation. A total of 270 female broiler chickens (1-day-old) were randomly allotted to three dietary treatments supplemented with 0 mg/kg (control group), 5 mg/kg, and 10 mg/kg FA in basal diets for 42 days, respectively. Each treatment had six replicate cages with 15 birds per cage. Dietary supplementation of 5 mg/kg FA significantly enhanced average body weight and average daily gain of 21-day-old broilers (P < 0.05), but significantly reduced subcutaneous fat thickness and widths of an intermuscular fat band of 42-day-old broilers by dietary FA treatments (P < 0.05). Also, a diet with 10 mg/kg FA supplementation significantly increased the relative heart weight of 42-day-old chickens (P < 0.05). Furthermore, dietary FA supplementation significantly improved the serum insulin-like growth factor 2 (IGF2) concentrations (P < 0.01) and IGF2 mRNA expression in the abdominal fat (P < 0.05), but no statistical differences were found in the methylation of IGF2 promoter (P > 0.05). The present study demonstrated that dietary FA supplementation may have positive effects on chicken growth through increased IGF2 gene expression.  

scholarly journals Transcriptional profiling in the livers of rats after hypobaric hypoxia exposure

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6499 ◽  
Author(s):  
Zhenguo Xu ◽  
Zhilong Jia ◽  
Jinlong Shi ◽  
Zeyu Zhang ◽  
Xiaojian Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Altitude ◽  
Liver Tissue ◽  
Hypobaric Hypoxia ◽  
Cellular Response ◽  
Molecular Mechanisms ◽  
Receptor Interaction ◽  
Control Group ◽  
Acute Hypobaric Hypoxia ◽  
Genome Wide

Ascent to high altitude feels uncomfortable in part because of a decreased partial pressure of oxygen due to the decrease in barometric pressure. The molecular mechanisms causing injury in liver tissue after exposure to a hypoxic environment are widely unknown. The liver must physiologically and metabolically change to improve tolerance to altitude-induced hypoxia. Since the liver is the largest metabolic organ and regulates many physiological and metabolic processes, it plays an important part in high altitude adaptation. The cellular response to hypoxia results in changes in the gene expression profile. The present study explores these changes in a rat model. To comprehensively investigate the gene expression and physiological changes under hypobaric hypoxia, we used genome-wide transcription profiling. Little is known about the genome-wide transcriptional response to acute and chronic hypobaric hypoxia in the livers of rats. In this study, we carried out RNA-Sequencing (RNA-Seq) of liver tissue from rats in three groups, normal control rats (L), rats exposed to acute hypobaric hypoxia for 2 weeks (W2L) and rats chronically exposed to hypobaric hypoxia for 4 weeks (W4L), to explore the transcriptional profile of acute and chronic mountain sickness in a mammal under a controlled time-course. We identified 497 differentially expressed genes between the three groups. A principal component analysis revealed large differences between the acute and chronic hypobaric hypoxia groups compared with the control group. Several immune-related and metabolic pathways, such as cytokine-cytokine receptor interaction and galactose metabolism, were highly enriched in the KEGG pathway analysis. Similar results were found in the Gene Ontology analysis. Cogena analysis showed that the immune-related pathways were mainly upregulated and enriched in the acute hypobaric hypoxia group.

scholarly journals Expression of NMDA receptor and microRNA-219 in rats submitted to cerebral ischemia associated with alcoholism

2017 ◽  
Vol 75 (1) ◽  
pp. 30-35 ◽  
Author(s):  
Cristiane Iozzi Silva ◽  
Paulo Cézar Novais ◽  
Andressa Romualdo Rodrigues ◽  
Camila A.M. Carvalho ◽  
Benedicto Oscar Colli ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cerebral Ischemia ◽  
Brain Tissue ◽  
Wistar Rats ◽  
Molecular Mechanisms ◽  
Inverse Correlation ◽  
Control Group ◽  
The Brain ◽  
Lower Expression ◽  
Control Sham

ABSTRACT Alcohol consumption aggravates injuries caused by ischemia. Many molecular mechanisms are involved in the pathophysiology of cerebral ischemia, including neurotransmitter expression, which is regulated by microRNAs. Objective: To evaluate the microRNA-219 and NMDA expression in brain tissue and blood of animals subjected to cerebral ischemia associated with alcoholism. Methods: Fifty Wistar rats were divided into groups: control, sham, ischemic, alcoholic, and ischemic plus alcoholic. The expression of microRNA-219 and NMDA were analyzed by real-time PCR. Results: When compared to the control group, the microRNA-219 in brain tissue was less expressed in the ischemic, alcoholic, and ischemic plus alcoholic groups. In the blood, this microRNA had lower expression in alcoholic and ischemic plus alcoholic groups. In the brain tissue the NMDA gene expression was greater in the ischemic, alcoholic, and ischemic plus alcoholic groups. Conclusion: A possible modulation of NMDA by microRNA-219 was observed with an inverse correlation between them.

scholarly journals An animal model study on the gene expression profile of meniscal degeneration

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yehan Fang ◽  
Hui Huang ◽  
Gang Zhou ◽  
Qinghua Wang ◽  
Feng Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pathway Analysis ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Control Group ◽  
Ion Binding ◽  
Endoplasmic Reticulum Membrane ◽  
Rt Pcr ◽  
Go Analysis ◽  
Meniscal Degeneration

AbstractMeniscal degeneration is a very common condition in elderly individuals, but the underlying mechanisms of its occurrence are not completely clear. This study examines the molecular mechanisms of meniscal degeneration. The anterior cruciate ligament (ACL) and lateral collateral ligament (LCL) of the right rear limbs of seven Wuzhishan mini-pigs were resected (meniscal degeneration group), and the left rear legs were sham-operated (control group). After 6 months, samples were taken for gene chip analysis, including differentially expressed gene (DEG) analysis, gene ontology (GO) analysis, clustering analysis, and pathway analysis. The selected 12 DEGs were validated by real time reverse transcription-polymerase chain reaction (RT-PCR). The two groups showed specific and highly clustered DEGs. A total of 893 DEGs were found, in which 537 are upregulated, and 356 are downregulated. The GO analysis showed that the significantly affected biological processes include nitric oxide metabolic process, male sex differentiation, and mesenchymal morphogenesis, the significantly affected cellular components include the endoplasmic reticulum membrane, and the significantly affected molecular functions include transition metal ion binding and iron ion binding. The pathway analysis showed that the significantly affected pathways include type II diabetes mellitus, inflammatory mediator regulation of TRP channels, and AMPK signaling pathway. The results of RT-PCR indicate that the microarray data accurately reflects the gene expression patterns. These findings indicate that several molecular mechanisms are involved in the development of meniscal degeneration, thus improving our understanding of meniscal degeneration and provide molecular therapeutic targets in the future.

scholarly journals Functional Modules Analysis and Hub Gene Prognostic Values Evaluation Based on Co-Expression Network in Gastric Cancer

2021 ◽  
Author(s):  
Yujia Liu ◽  
Xiaoping Hu ◽  
Zongfu Pan ◽  
Yuchen Jiang ◽  
Dandan Guo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gastric Cancer ◽  
Regulatory Network ◽  
Molecular Mechanisms ◽  
Transcriptional Regulatory Network ◽  
Receptor Interaction ◽  
Ppi Network ◽  
Hub Gene ◽  
Transcriptional Regulatory ◽  
Key Nodes

Abstract Background: Gastric cancer is one of the most common fatal disease worldwide, but its mechanism and therapeutic targets are still unclear. In this study, we have analyzed the differences in gene modules and key pathways in gastric cancer patients, then elaborated the mechanism and effective treatment of gastric cancer with microarray data from the gene expression omnibus(GEO) database. Methods: GEO2R tools were used to identify differential expression genes (DEGs), String database was employed to construct a protein-protein interaction (PPI) network. We imported the PPI network into the Cytoscape software to find key nodes, and employed statistical approach of MCODE to cluster genes. After that the ClueGO was used to enrich and annotate the pathways of key modules. To investigate the relationship between the upstream regulator and hub genes, the transcriptional regulatory network was built based on TFCAT database. Results: 63 characteristic genes of gastric cancer are involved in regulation of ECM-receptor interaction, focal adhesion and protein digestion and absorption. SPARC, FN1, BGN and COL1A2 are four key nodes relating to tumor proliferation and metastasis, and their expression were strongly associated with poor survival (p<0.05). 13 transcription factors including PRRX1 have remarkable changes in gastric cancer, which may play a key role in hub gene regulation. Conclusions: The present study defined the gene expression characteristics and transcriptional regulatory network that promote our understanding of the molecular mechanisms underlying the development of gastric cancer, and might provide new insights into targeted therapy and prognostic markers for the personalized treatment of gastric cancer.

scholarly journals Identification of core genes and pathways in melanoma metastasis via bioinformatics analysis

2020 ◽  
Author(s):  
Yumei Li ◽  
Bifei Li ◽  
Fan Chen ◽  
Weiyu Shen ◽  
Vladimir L. Katanaev ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metastatic Melanoma ◽  
Molecular Mechanisms ◽  
Therapeutic Targets ◽  
Primary Melanoma ◽  
Melanoma Cells ◽  
Receptor Interaction ◽  
Melanoma Metastasis ◽  
Hub Genes ◽  
Core Genes

Abstract Background Metastasis is the leading cause of melanoma mortality. Current therapies are rarely curative for metastatic melanoma, revealing the urgent need to identify more effective preventive and therapeutic targets. This study aimed to screen for the key core genes and molecular mechanisms related to the metastasis of melanoma. Methods Gene expression profile, GSE8401 including 31 primary melanoma and 52 metastatic melanoma clinical samples, was downloaded from the Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) between metastatic melanoma and primary melanoma were screened using GEO2R. Assays of gene ontology (GO), Kyoto Encyclopedia of Gene and Genome (KEGG) pathway and protein-protein interaction (PPI) were performed to visualize these DEGs through Database for Annotation, Visualization and Integrated Discovery (DAVID) software and Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape with Molecular Complex Detection (MCODE) plug-in tools. Top 10 genes with high degree were defined as hub genes. Furthermore, paired post-metastatic melanoma cells and pre-metastatic melanoma cells were established by experimental mouse model of melanoma metastasis to verify the expression of these hub genes. Results 424 DEGs between the metastatic melanoma and primary melanoma were screened, including 60 upregulated genes enriched in ECM-receptor interaction and progesterone-mediated oocyte maturation and 364 downregulated genes enriched in amoebiasis, melanogenesis, and ECM-receptor interaction. CDH1, EGFR, KRT5, COL17A1, KRT14, IVL, DSP, DSG1, FLG and CDK1 were defined as the hub genes. . In addition, paired post-metastatic melanoma cells (A375M) and pre-metastatic melanoma cells (A375) were established and qRT-PCR analysis confirmed the expression of the hub genes during melanoma metastasis. Conclusion This bioinformatic study has provided a deeper understanding of the molecular mechanisms of melanoma metastasis. KRT5, IVL and COL17A1 have emerged as possible biomarkers and therapeutic targets in metastasis of melanoma.

scholarly journals Transcriptomic Signatures and Functional Network Analysis of Chronic Rhinosinusitis With Nasal Polyps

2021 ◽  
Vol 12 ◽  
Author(s):  
Yun Hao ◽  
Yan Zhao ◽  
Ping Wang ◽  
Kun Du ◽  
Ying Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Network Analysis ◽  
Chronic Rhinosinusitis ◽  
Nasal Polyps ◽  
Molecular Mechanisms ◽  
Sinus Surgery ◽  
Receptor Interaction ◽  
Integrated Analysis ◽  
Healthy Controls ◽  
Drug Candidates

Chronic rhinosinusitis with nasal polyps (CRSwNP) is a chronic sinonasal inflammatory disease with limited treatment options of corticosteroids, sinus surgery, or both. CRSwNP is frequently associated with allergic rhinitis and asthma, but the molecular mechanisms underlying CRSwNP inflammation are not completely understood. We obtained four gene expression profiles (GSE136825, GSE36830, GSE23552, and GSE72713) from four Gene Expression Omnibus (GEO), which collectively included 65 nasal polyp samples from CRSwNP patients and 54 nasal mucosal samples from healthy controls. Using an integrated analysis approach, we identified 76 co-differentially expressed genes (co-DEGs, including 45 upregulated and 31 downregulated) in CRSwNP patients compared with the healthy controls. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses identified the terms including immune effector process, leukocyte migration, regulation of the inflammatory response, Staphylococcus aureus infection, and cytokine-cytokine receptor interaction. protein-protein interaction (PPI) network analysis and real-time quantitative PCR (RT-qPCR) showed that 7 genes might be crucial in CRSwNP pathogenesis. Repurposing drug candidates (Alfadolone, Hydralazine, SC-560, Iopamidol, Iloprost, etc) for CRSwNP treatment were identified from the Connectivity Map (CMap) database. Our results suggest multiple molecular mechanisms, diagnostic biomarkers, potential therapeutic targets, and new repurposing drug candidates for CRSwNP treatment.

scholarly journals Identification of Key Genes and Pathways Associated with Mast Cells Resting in Meningioma

2020 ◽  
Author(s):  
Hui Xie ◽  
Xiao-hui Ding ◽  
Ce Yuan ◽  
Jin-jiang Li ◽  
Zhao-yang Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mast Cells ◽  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Immune Cell ◽  
Risk Model ◽  
Kegg Pathway ◽  
Expression Profiles ◽  
Receptor Interaction ◽  
Key Genes

Abstract Background: To identify candidate key genes and pathways related to mast cells resting in meningioma and the underlying molecular mechanisms of meningioma.Methods: Gene expression profiles of GSE43290 and GSE16581 datasets were obtained from the Gene Expression Omnibus (GEO) database. GO and KEGG pathway enrichments of DEGs were analyzed using the ClusterProfiler package in R. The protein-protein interaction network (PPI), and TF-miRNA- mRNA co-expression networks were constructed. Further, the difference in immune infiltration was investigated using the CIBERSORT algorithm.Results: A total of 1499 DEGs were identified between tumor and normal controls. The analysis of the immune cell infiltration landscape showed that the probability of distribution of memory B cells, regulatory T cells (Tregs), and resting mast cells in tumor samples were significantly higher than those in the controls. Moreover, through WGCNA analysis, the module related to mast cells resting contained 158 DEGs, and KEGG pathway analysis revealed that the DEGs were dominant in the TNF signaling pathway, cytokine-cytokine receptor interaction, and IL-17 signaling pathway. Survival analysis of hub genes related to mast cells resting showed that the risk model was constructed based on 9 key genes. The TF-miRNA- mRNA co-regulation network, including MYC-miR-145-5p, TNFAIP3-miR-29c-3p, and TNFAIP3-hsa-miR-335-3p, were obtained. Further, 36 nodes and 197 interactions in the PPI network were identified. Conclusions: The results of this study revealed candidate key genes, miRNAs, and pathways related to mast cells resting involved in meningioma development, providing potential therapeutic targets for meningioma treatment.

scholarly journals Analysis of Transcriptomic Changes in Bovine Endometrial Stromal Cells Treated With Lipopolysaccharide

2020 ◽  
Vol 7 ◽  
Author(s):  
Xuefen Ding ◽  
Haimiao Lv ◽  
Lixin Deng ◽  
Wenju Hu ◽  
Zhan Peng ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Stromal Cells ◽  
Cell Activation ◽  
Molecular Mechanisms ◽  
Interleukin 1 ◽  
Interleukin 12 ◽  
Receptor Interaction ◽  
Control Group ◽  
Toll Like Receptor ◽  
Endometrial Stromal Cells

Endometritis adversely affects the ability of cattle to reproduce and significantly reduces milk production. The is mainly composed of epithelial and stromal cells, and they produce the first immune response to invading pathogens. However, most of the epithelial cells are disrupted, and stromal cells are exposed to an inflammatory environment when endometritis occurs, especially postpartum. Many bacteria and toxins start attacking stromal cell due to loss of epithelium, which stimulates Toll-like receptor (TLRs) on stromal cells and causes upregulated expression of cytokines. Understanding the genome-wide characterization of bovine endometritis will be beneficial for prevention and treatment of endometritis. In this study, whole-transcriptomic gene changes in bovine endometrial stromal cells (BESCs) treated with LPS were compared with those treated with PBS (control group) and were analyzed by RNA sequencing. Compared with the control group, a total of 366 differentially expressed genes (DEGs) were identified in the LPS-induced group (234 upregulated and 132 downregulated genes), with an adjusted P &lt; 0.05 by DESeq. Gene Ontology (GO) enrichment analysis revealed that DEGs were most enriched in 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 the TNF signaling pathway, Toll-like receptor signaling pathway, cytokine–cytokine receptor interaction, NF-κB signaling pathway, and chemokine signaling pathway. The results of this study unraveled BESCs affected with LPS transcriptome profile alterations, which may have a significant effect on treatment inflammation by comprehending molecular mechanisms and authenticating unique genes related to endometritis.

Validation of novel hub genes and molecular mechanisms in acute lung injury using an integrative bioinformatics approach

2021 ◽  
Author(s):  
Qingchun Liang ◽  
Qin Zhou ◽  
Jinhe Li ◽  
Zhugui Chen ◽  
Zhihao Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Lung Injury ◽  
Lung Injury ◽  
Molecular Mechanisms ◽  
Molecular Biomarkers ◽  
Functional Enrichment ◽  
Lung Injury Score ◽  
Control Group ◽  
High Morbidity ◽  
Hub Genes

Abstract Acute lung injury (ALI) is an inflammatory pulmonary disease that can easily develop into serious acute respiratory distress syndrome, which has high morbidity and mortality. However, the molecular mechanism of ALI remains unclear, and few molecular biomarkers for diagnosis and treatment have been identified. In this study, we aimed to identify novel molecular biomarkers using a bioinformatics approach. Gene expression data were obtained from the Gene Expression Omnibus database, co-expressed differentially expressed genes (CoDEGs) were identified using R software, and further functional enrichment analyses were conducted using the online tool Database for Annotation, Visualization, and Integrated Discovery. A protein–protein interaction network was established using the STRING database and Cytoscape software. Lipopolysaccharide (LPS)-induced ALI mouse model was constructed and verified. The hub genes were screened and validated in vivo. The transcription factors (TFs) and miRNAs associated with the hub genes were predicted using the NetworkAnalyst database. In total, 71 CoDEGs were screened and found to be mainly involved in the cytokine–cytokine receptor interactions, and the tumor necrosis factor and malaria signaling pathways. Animal experiments showed that the lung injury score, bronchoalveolar lavage fluid protein concentration, and wet-to-dry weight ratio were higher in the LPS group than those in the control group. Real-time polymerase chain reaction analysis indicated that most of the hub genes such as colony-stimulating factor 2 (Csf2) were overexpressed in the LPS group. A total of 20 TFs including nuclear respiratory factor 1 (NRF1) and two miRNAs were predicted to be regulators of the hub genes. In summary, Csf2 may serve as a novel diagnostic and therapeutic target for ALI. NRF1 and mmu-mir-122-5p may be key regulators in the development of ALI.

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