scholarly journals Characterization and Duodenal Transcriptome Analysis of Chinese Beef Cattle With Divergent Feed Efficiency Using RNA-Seq

2021 ◽  
Vol 12 ◽  
Author(s):  
Chaoyun Yang ◽  
Liyun Han ◽  
Peng Li ◽  
Yanling Ding ◽  
Yun Zhu ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Differentially Expressed Genes ◽  
Feed Intake ◽  
Feed Efficiency ◽  
Muscle Development ◽  
Dietary Factors ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Biological Regulation ◽  
Key Genes

Residual feed intake (RFI) is an important measure of feed efficiency for agricultural animals. Factors associated with cattle RFI include physiology, dietary factors, and the environment. However, a precise genetic mechanism underlying cattle RFI variations in duodenal tissue is currently unavailable. The present study aimed to identify the key genes and functional pathways contributing to variance in cattle RFI phenotypes using RNA sequencing (RNA-seq). Six bulls with extremely high or low RFIs were selected for detecting differentially expressed genes (DEGs) by RNA-seq, followed by conducting GO, KEGG enrichment, protein-protein interaction (PPI), and co-expression network (WGCNA, n = 10) analysis. A total of 380 differentially expressed genes was obtained from high and low RFI groups, including genes related to energy metabolism (ALDOA, HADHB, INPPL1), mitochondrial function (NDUFS1, RFN4, CUL1), and feed intake behavior (CCK). Two key sub-networks and 26 key genes were detected using GO analysis of DEGs and PPI analysis, such as TPM1 and TPM2, which are involved in mitochondrial pathways and protein synthesis. Through WGCNA, a gene network was built, and genes were sorted into 27 modules, among which the blue (r = 0.72, p = 0.03) and salmon modules (r = −0.87, p = 0.002) were most closely related with RFI. DEGs and genes from the main sub-networks and closely related modules were largely involved in metabolism; oxidative phosphorylation; glucagon, ribosome, and N-glycan biosynthesis, and the MAPK and PI3K-Akt signaling pathways. Through WGCNA, five key genes, including FN1 and TPM2, associated with the biological regulation of oxidative processes and skeletal muscle development were identified. Taken together, our data suggest that the duodenum has specific biological functions in regulating feed intake. Our findings provide broad-scale perspectives for identifying potential pathways and key genes involved in the regulation of feed efficiency in beef cattle.

scholarly journals Bioinformatics-based Screening of Key Genes for Saponin Metabolism in Quinoa

2021 ◽  
Author(s):  
Chengang Guo ◽  
Zhimin wei ◽  
Wei Lyu ◽  
Yanlou Geng
Keyword(s):  
Differentially Expressed Genes ◽  
Principal Component ◽  
Enrichment Analysis ◽  
Hierarchical Cluster ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Differential Analysis ◽  
Rna Seq ◽  
Protein Coding ◽  
Key Genes

Abstract Quinoa saponins have complex, diverse and evident physiologic activities. However, the key regulatory genes for quinoa saponin metabolism are not yet well studied. The purpose of this study was to explore genes closely related to quinoa saponin metabolism. In this study, the significantly differentially expressed genes in yellow quinoa were firstly screened based on RNA-seq technology. Then, the key genes for saponin metabolism were selected by gene set enrichment analysis (GSEA) and principal component analysis (PCA) statistical methods. Finally, the specificity of the key genes was verified by hierarchical clustering. The results of differential analysis showed that 1654 differentially expressed genes were achieved after pseudogenes deletion. Therein, there were 142 long non-coding genes and 1512 protein-coding genes. Based on GSEA analysis, 116 key candidate genes were found to be significantly correlated with quinoa saponin metabolism. Through PCA dimension reduction analysis, 57 key genes were finally obtained. Hierarchical cluster analysis further demonstrated that these key genes can clearly separate the four groups of samples. The present results could provide references for the breeding of sweet quinoa and would be helpful for the rational utilization of quinoa saponins.

scholarly journals Identification of Differentially Expressed Genes in Different Types of Broiler Skeletal Muscle Fibers Using the RNA-seq Technique

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Han Wang ◽  
Zhonghao Shen ◽  
Xiaolong Zhou ◽  
Songbai Yang ◽  
Feifei Yan ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Differentially Expressed Genes ◽  
Muscle Fiber ◽  
Muscle Development ◽  
Skeletal Muscle Fiber ◽  
Differentially Expressed ◽  
Muscle Fiber Types ◽  
Type I ◽  
Fiber Types ◽  
Rna Seq

The difference in muscle fiber types is very important to the muscle development and meat quality of broilers. At present, the molecular regulation mechanisms of skeletal muscle fiber-type transformation in broilers are still unclear. In this study, differentially expressed genes between breast and leg muscles in broilers were analyzed using RNA-seq. A total of 767 DEGs were identified. Compared with leg muscle, there were 429 upregulated genes and 338 downregulated genes in breast muscle. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in cellular processes, single organism processes, cells, and cellular components, as well as binding and catalytic activity. KEGG analysis shows that a total of 230 DEGs were mapped to 126 KEGG pathways and significantly enriched in the four pathways of glycolysis/gluconeogenesis, starch and sucrose metabolism, insulin signalling pathways, and the biosynthesis of amino acids. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) was used to verify the differential expression of 7 selected DEGs, and the results were consistent with RNA-seq data. In addition, the expression profile of MyHC isoforms in chicken skeletal muscle cells showed that with the extension of differentiation time, the expression of fast fiber subunits (types IIA and IIB) gradually increased, while slow muscle fiber subunits (type I) showed a downward trend after 4 days of differentiation. The differential genes screened in this study will provide some new ideas for further understanding the molecular mechanism of skeletal muscle fiber transformation in broilers.

scholarly journals Effect of hyperoside on cervical cancer cells and transcriptome analysis of differentially expressed genes

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Weikang Guo ◽  
Hui Yu ◽  
Lu Zhang ◽  
Xiuwei Chen ◽  
Yunduo Liu ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Cell Proliferation ◽  
Differentially Expressed Genes ◽  
Interaction Network ◽  
Differentially Expressed ◽  
Control Group ◽  
Rna Seq ◽  
Network Construction ◽  
Target Network ◽  
Key Genes

Abstract Background Hyperoside (Hy) is a plant-derived quercetin 3-d-galactoside that exhibits inhibitory activities on various tumor types. The objective of the current study was to explore Hy effects on cervical cancer cell proliferation, and to perform a transcriptome analysis of differentially expressed genes. Methods Cervical cancer HeLa and C-33A cells were cultured and the effect of Hy treatment was determined using the Cell Counting Kit-8 (CCK-8) assay. After calculating the IC50 of Hy in HeLa and C-33A cells, the more sensitive to Hy treatment cell type was selected for RNA-Seq. Differentially expressed genes (DEGs) were identified by comparing gene expression between the Hy and control groups. Candidate genes were determined through DEG analysis, protein interaction network (PPI) construction, PPI module analysis, transcription factor (TF) prediction, TF-target network construction, and survival analysis. Finally, the key candidate genes were verified by RT-qPCR and western blot. Results Hy inhibited HeLa and C33A cell proliferation in a dose- and time-dependent manner, as determined by the CCK-8 assay. Treatment of C-33A cells with 2 mM Hy was selected for the subsequent experiments. Compared with the control group, 754 upregulated and 509 downregulated genes were identified after RNA-Seq. After functional enrichment, 74 gene ontology biological processes and 43 Kyoto Encyclopedia of Genes and Genomes pathways were obtained. According to the protein interaction network (PPI), PPI module analysis, TF-target network construction, and survival analysis, the key genes MYC, CNKN1A, PAX2, TFRC, ACOX2, UNC5B, APBA1, PRKACA, PEAR1, COL12A1, CACNA1G, PEAR1, and CCNA2 were detected. RT-qPCR was performed on the key genes, and Western blot was used to verify C-MYC and TFRC. C-MYC and TFRC expressions were lower and higher than the corresponding values in the control group, respectively, in accordance with the results from the RNA-Seq analysis. Conclusion Hy inhibited HeLa and C-33A cell proliferation through C-MYC gene expression reduction in C-33A cells and TFRC regulation. The results of the current study provide a theoretical basis for Hy treatment of cervical cancer.

scholarly journals Effect of Gender and Residual Feed Intake Phenotype on the Transcriptome of Liver and Skeletal Muscle Tissue in Purebred Simmental Beef Cattle

2020 ◽  
Author(s):  
Clare McKenna ◽  
Kate Keogh ◽  
Richard K. Porter ◽  
Sinead M. Waters ◽  
Paul Cormican ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Differentially Expressed Genes ◽  
Feed Intake ◽  
Feed Efficiency ◽  
Cell Signalling ◽  
Residual Feed Intake ◽  
Differentially Expressed ◽  
Physiological Age ◽  
Hepatic Tissue ◽  
Molecular Control

Abstract Background: The selection of cattle with enhanced feed efficiency is of paramount importance with regard to reducing feed costs in the beef industry. However the role, if any, of gender to the underlying molecular control of feed efficiency in cattle is not currently known. Global transcriptome profiling was undertaken on liver and skeletal muscle biopsies from Simmental heifers and bulls divergent in residual feed intake (RFI) feed efficiency phenotype, in order to identify differentially expressed genes that may be associated with this trait. Results: We identified 5 genes (p<0.001; false discovery rate (FDR) <0.1) to be differentially expressed in skeletal muscle between high and low RFI heifers with all 5 transcripts being up-regulated in the low RFI phenotype. Among these differentially expressed genes, all transcripts were involved in oxidative phosphorylation and mitochondrial homeostasis. A total of 11 genes (p<0.001;FDR <0.1) were differentially expressed in hepatic tissue between high and low RFI bulls with 8 transcripts being up-regulated and 3 being down-regulated in the low RFI phenotype. These differentially expressed genes were related to oxidative response, protein mediation and cell signalling. No genes were identified as differentially expressed in both heifer liver and bull muscle analyses. Conclusions: Results from this study show a clear effect of gender to the underlying molecular control of RFI in cattle, which may be attributable to differences in the physiological age between heifers and bulls. Despite this we have highlighted a number of genes that may hold potential as molecular biomarkers for RFI cattle.

scholarly journals RAPID COMMUNICATION: Residual feed intake in beef cattle is associated with differences in protein turnover and nutrient transporters in ruminal epithelium

2019 ◽  
Vol 97 (5) ◽  
pp. 2181-2187
Author(s):  
Ahmed A Elolimy ◽  
Emad Abdel-Hamied ◽  
Liangyu Hu ◽  
Joshua C McCann ◽  
Daniel W Shike ◽  
...  
Keyword(s):  
Amino Acid ◽  
Beef Cattle ◽  
Protein Degradation ◽  
Insulin Signaling ◽  
Feed Intake ◽  
Feed Efficiency ◽  
Protein Turnover ◽  
Residual Feed Intake ◽  
Ubiquitin Proteasome ◽  
Ruminal Epithelium

Abstract Residual feed intake (RFI) is a widely used measure of feed efficiency in cattle. Although the precise biologic mechanisms associated with improved feed efficiency are not well-known, most-efficient steers (i.e., with low RFI coefficient) downregulate abundance of proteins controlling protein degradation in skeletal muscle. Whether cellular mechanisms controlling protein turnover in ruminal tissue differ by RFI classification is unknown. The aim was to investigate associations between RFI and signaling through the mechanistic target of rapamycin (MTOR) and ubiquitin-proteasome pathways in ruminal epithelium. One hundred and forty-nine Red Angus cattle were allocated to 3 contemporary groups according to sex and herd origin. Animals were offered a finishing diet for 70 d to calculate the RFI coefficient for each. Within each group, the 2 most-efficient (n = 6) and least-efficient animals (n = 6) were selected. Compared with least-efficient animals, the most-efficient animals consumed less feed (P &lt; 0.05; 18.36 vs. 23.39 kg/d DMI). At day 70, plasma samples were collected for insulin concentration analysis. Ruminal epithelium was collected immediately after slaughter to determine abundance and phosphorylation status of 29 proteins associated with MTOR, ubiquitin-proteasome, insulin signaling, and glucose and amino acid transport. Among the proteins involved in cellular protein synthesis, most-efficient animals had lower (P ≤ 0.05) abundance of MTOR, p-MTOR, RPS6KB1, EIF2A, EEF2K, AKT1, and RPS6KB1, whereas MAPK3 tended (P = 0.07) to be lower. In contrast, abundance of p-EEF2K, p-EEF2K:EEF2K, and p-EIF2A:EIF2A in most-efficient animals was greater (P ≤ 0.05). Among proteins catalyzing steps required for protein degradation, the abundance of UBA1, NEDD4, and STUB1 was lower (P ≤ 0.05) and MDM2 tended (P = 0.06) to be lower in most-efficient cattle. Plasma insulin and ruminal epithelium insulin signaling proteins did not differ (P &gt; 0.05) between RFI groups. However, abundance of the insulin-responsive glucose transporter SLC2A4 and the amino acid transporters SLC1A3 and SLC1A5 also was lower (P ≤ 0.05) in most-efficient cattle. Overall, the data indicate that differences in signaling mechanisms controlling protein turnover and nutrient transport in ruminal epithelium are components of feed efficiency in beef cattle.

scholarly journals AB0005 IDENTIFICATION OF KEY GENES AND PATHWAYS FOR PSORIASIS BASED ON GEO DATABASES BY BIOINFORMATICS ANALYSIS

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 1037.2-1038
Author(s):  
X. Sun ◽  
S. X. Zhang ◽  
S. Song ◽  
T. Kong ◽  
C. Zheng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signaling Pathways ◽  
Differentially Expressed Genes ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Shanxi Province ◽  
Receptor Interaction ◽  
Term Therapy ◽  
Pathway Enrichment Analysis ◽  
Key Genes

Background:Psoriasis is an immune-mediated, genetic disease manifesting in the skin or joints or both, and also has a strong genetic predisposition and autoimmune pathogenic traits1. The hallmark of psoriasis is sustained inflammation that leads to uncontrolled keratinocyte proliferation and dysfunctional differentiation. And it’s also a chronic relapsing disease, which often necessitates a long-term therapy2.Objectives:To investigate the molecular mechanisms of psoriasis and find the potential gene targets for diagnosis and treating psoriasis.Methods:Total 334 gene expression data of patients with psoriasis research (GSE13355 GSE14905 and GSE30999) were obtained from the Gene Expression Omnibus database. After data preprocessing and screening of differentially expressed genes (DEGs) by R software. Online toll Metascape3 was used to analyze Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs. Interactions of proteins encoded by DEGs were discovered by Protein-protein interaction network (PPI) using STRING online software. Cytoscape software was utilized to visualize PPI and the degree of each DEGs was obtained by analyzing the topological structure of the PPI network.Results:A total of 611 DEGs were found to be differentially expressed in psoriasis. GO analysis revealed that up-regulated DEGs were mostly associated with defense and response to external stimulus while down-regulated DEGs were mostly associated with metabolism and synthesis of lipids. KEGG enrichment analysis suggested they were mainly enriched in IL-17 signaling, Toll-like receptor signaling and PPAR signaling pathways, Cytokine-cytokine receptor interaction and lipid metabolism. In addition, top 9 key genes (CXCL10, OASL, IFIT1, IFIT3, RSAD2, MX1, OAS1, IFI44 and OAS2) were identified through Cytoscape.Conclusion:DEGs of psoriasis may play an essential role in disease development and may be potential pathogeneses of psoriasis.References:[1]Boehncke WH, Schon MP. Psoriasis. Lancet 2015;386(9997):983-94. doi: 10.1016/S0140-6736(14)61909-7 [published Online First: 2015/05/31].[2]Zhang YJ, Sun YZ, Gao XH, et al. Integrated bioinformatic analysis of differentially expressed genes and signaling pathways in plaque psoriasis. Mol Med Rep 2019;20(1):225-35. doi: 10.3892/mmr.2019.10241 [published Online First: 2019/05/23].[3]Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 2019;10(1):1523. doi: 10.1038/s41467-019-09234-6 [published Online First: 2019/04/05].Acknowledgements:This project was supported by National Science Foundation of China (82001740), Open Fund from the Key Laboratory of Cellular Physiology (Shanxi Medical University) (KLCP2019) and Innovation Plan for Postgraduate Education in Shanxi Province (2020BY078).Disclosure of Interests:None declared

scholarly journals Transcriptome Analysis of Differentially Expressed mRNA Related to Pigeon Muscle Development

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2311
Author(s):  
Hao Ding ◽  
Yueyue Lin ◽  
Tao Zhang ◽  
Lan Chen ◽  
Genxi Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Differentially Expressed Genes ◽  
Growth And Development ◽  
Muscle Development ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Growth Stages ◽  
Gene Expression And Regulation

The mechanisms behind the gene expression and regulation that modulate the development and growth of pigeon skeletal muscle remain largely unknown. In this study, we performed gene expression analysis on skeletal muscle samples at different developmental and growth stages using RNA sequencing (RNA−Seq). The differentially expressed genes (DEGs) were identified using edgeR software. Weighted gene co−expression network analysis (WGCNA) was used to identify the gene modules related to the growth and development of pigeon skeletal muscle based on DEGs. A total of 11,311 DEGs were identified. WGCNA aggregated 11,311 DEGs into 12 modules. Black and brown modules were significantly correlated with the 1st and 10th day of skeletal muscle growth, while turquoise and cyan modules were significantly correlated with the 8th and 13th days of skeletal muscle embryonic development. Four mRNA−mRNA regulatory networks corresponding to the four significant modules were constructed and visualised using Cytoscape software. Twenty candidate mRNAs were identified based on their connectivity degrees in the networks, including Abca8b, TCONS−00004461, VWF, OGDH, TGIF1, DKK3, Gfpt1 and RFC5, etc. A KEGG pathway enrichment analysis showed that many pathways were related to the growth and development of pigeon skeletal muscle, including PI3K/AKT/mTOR, AMPK, FAK, and thyroid hormone pathways. Five differentially expressed genes (LAST2, MYPN, DKK3, B4GALT6 and OGDH) in the network were selected, and their expression patterns were quantified by qRT−PCR. The results were consistent with our sequencing results. These findings could enhance our understanding of the gene expression and regulation in the development and growth of pigeon muscle.

scholarly journals PSVII-2 Differentially expressed genes and their biological function in skeletal muscle of calves born from cows with or without protein supplementation during mid-gestation

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 165-166
Author(s):  
Elisa B Carvalho ◽  
Letícia P Sanglard ◽  
Karolina B Nascimento ◽  
Javier M Meneses ◽  
Daniel R Casagrande ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Differentially Expressed Genes ◽  
Muscle Development ◽  
Negative Binomial ◽  
Muscle Protein ◽  
Basal Diet ◽  
Protein Supplementation ◽  
Differentially Expressed ◽  
Control Group ◽  
Q Value

Abstract Gestating cows have an increased nutrient demand to meet the needs of developing the fetus and the mid-gestation is a critical period for the fetal skeletal muscle development. The aim of this study was to evaluate the skeletal muscle transcriptome in the progeny as a function of the maternal protein nutrition during mid-gestation. Eleven Tabapuã cows and their male calves were used in this study. In the first third of gestation (0 to 100 days of gestation; dg), all cows were kept on pasture. From 100 to 200 dg, the control group (CTRL; 7 animals) received a basal diet achieving 5.5% crude protein (CP), whereas the supplemented group (SUPPL; 4 animals) received a basal diet plus protein supplementation (40% CP). After 200 dg, all animals received the same diet. Weaning was performed at 205 ± 7.5 days of age and animals were kept on pasture until reaching 240 days of age, when they were transferred to a feedlot. Muscle samples were collected at 260 days of age and RNA was extracted for RNA-seq analysis. Gene expression data was analyzed with a negative binomial model to identify (q-value ≤ 0.05) differentially expressed genes (DEG) between treatments. A total of 716 DEG were identified (289 DEG up-regulated and 427 down-regulated in SUPPL group; q-value ≤ 0.05). From the 10 most significant down-regulated DEG in the SUPPL group, two genes associated with apoptotic process were identified: MAPK8IP1 and GRINA, with log2 Fold-Changes (log2FC) of 1.04 and 0.49, respectively. From the 10 most significant up-regulated DEG in the SUPPL group, mTOR was identified, with log2FC=0.31. This is a well-known gene involved in muscle protein synthesis. In conclusion, maternal protein supplementation during mid-gestation affects the expression of genes related to energy metabolism and muscle development, which can lead to long-term impacts on production efficiency.

scholarly journals Key Genes and Prognostic Analysis in HER2+ Breast Cancer

2021 ◽  
Vol 20 ◽  
pp. 153303382098329
Author(s):  
Yujie Weng ◽  
Wei Liang ◽  
Yucheng Ji ◽  
Zhongxian Li ◽  
Rong Jia ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Protein Interaction ◽  
Differentially Expressed ◽  
Protein Kinase Activity ◽  
Protein Protein Interaction ◽  
Risk Of Death ◽  
Her2 Breast Cancer ◽  
Key Genes

Human epidermal growth factor 2 (HER2)+ breast cancer is considered the most dangerous type of breast cancers. Herein, we used bioinformatics methods to identify potential key genes in HER2+ breast cancer to enable its diagnosis, treatment, and prognosis prediction. Datasets of HER2+ breast cancer and normal tissue samples retrieved from Gene Expression Omnibus and The Cancer Genome Atlas databases were subjected to analysis for differentially expressed genes using R software. The identified differentially expressed genes were subjected to gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses followed by construction of protein-protein interaction networks using the STRING database to identify key genes. The genes were further validated via survival and differential gene expression analyses. We identified 97 upregulated and 106 downregulated genes that were primarily associated with processes such as mitosis, protein kinase activity, cell cycle, and the p53 signaling pathway. Visualization of the protein-protein interaction network identified 10 key genes ( CCNA2, CDK1, CDC20, CCNB1, DLGAP5, AURKA, BUB1B, RRM2, TPX2, and MAD2L1), all of which were upregulated. Survival analysis using PROGgeneV2 showed that CDC20, CCNA2, DLGAP5, RRM2, and TPX2 are prognosis-related key genes in HER2+ breast cancer. A nomogram showed that high expression of RRM2, DLGAP5, and TPX2 was positively associated with the risk of death. TPX2, which has not previously been reported in HER2+ breast cancer, was associated with breast cancer development, progression, and prognosis and is therefore a potential key gene. It is hoped that this study can provide a new method for the diagnosis and treatment of HER2 + breast cancer.

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