scholarly journals RNA-Seq Analysis Identifies Differentially Expressed Genes in Subcutaneous Adipose Tissue in Qaidaford Cattle, Cattle-Yak, and Angus Cattle

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1077 ◽  
Author(s):  
Chengchuang Song ◽  
Yongzhen Huang ◽  
Zhaoxin Yang ◽  
Yulin Ma ◽  
Buren Chaogetu ◽  
...  
Keyword(s):  
Adipose Tissue ◽  
Meat Quality ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Cell Metabolism ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Control Group ◽  
Rna Seq ◽  
Angus Cattle

In the beef industry, fat tissue is closely related to meat quality. In this study, high-throughput RNA sequencing was utilized for adipose tissue transcriptome analysis between cattle-yak, Qaidamford cattle, and Angus cattle. The screening and identification of differentially expressed genes (DEGs) between different breeds of cattle would facilitate cattle breeding. Compared to Angus cattle adipose tissue, a total of 4167 DEGs were identified in cattle-yak adipose tissue and 3269 DEGs were identified in Qaidamford cattle adipose tissue. Considering cattle-yak as a control group, 154 DEGs were identified in Qaidamford cattle adipose tissue. GO analysis indicated the significant enrichment of some DEGs related to lipid metabolism. The KEGG pathway database was also used to map DEGs and revealed that most annotated genes were involved in ECM-receptor interaction and the PI3K-Akt signal pathway, which are closely related to cell metabolism. Eight selected DEGs related to adipose tissue development or metabolism were verified by RT-qPCR, indicating the reliability of the RNA-seq data. The results of this comparative transcriptome analysis of adipose tissue and screening DEGs suggest several candidates for further investigations of meat quality in different cattle breeds.

Expression profile analysis of Differentially Expressed Genes in Human Coronary Artery Endothelial Cells Induced by Serum from Kawasaki Disease: A preliminary study

2020 ◽  
Author(s):  
Xue Fan ◽  
Meng Li ◽  
Min Xiao ◽  
Cong Liu ◽  
Mingguo Xu
Keyword(s):  
Endothelial Cells ◽  
Coronary Artery ◽  
Kawasaki Disease ◽  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Healthy Children ◽  
Rna Seq ◽  
Human Coronary Artery

Abstract Background: Kawasaki disease (KD) leads to coronary artery damage and the etiology of KD is unknown. The present study was designed to explore the differentially expressed genes (DEGs) in KD serum-induced human coronary artery endothelial cells (HCAECs) by RNA-sequence (RNA-seq). Methods: HCAECs were stimulated with serum (15% (v/v)), which were collected from 20 healthy children and 20 KD patients, for 24 hours. DEGs were then detected and analyzed by RNA-seq and bioinformatics analysis. Results: The expression of SMAD1, SMAD6, CD34, CXCL1, PITX2, and APLN was validated by qPCR. 102 genes, 59 up-regulated and 43 down-regulated genes, were significantly differentially expressed in KD groups. GO enrichment analysis showed that DEGs were enriched in cellular response to cytokines, cytokine-mediated signaling pathway, and regulation of immune cells migration and chemotaxis. KEGG signaling pathway analysis showed that DEGs were mainly involved in cytokine−cytokine receptor interaction, chemokine signaling pathway, and TGF−β signaling pathway. Besides, the mRNA expression levels of SMAD1, SMAD6, CD34, CXCL1, and APLN in the KD group were significantly up-regulated compared with the normal group, whilePITX2 was significantly down-regulated. Conclusion: 102 DEGs in KD serum-induced HCAECs were identified, and six new targets were proposed as potential indicators of KD.

scholarly journals Transcriptome Analysis of Aedes aegypti Aag2 Cells in Response to Dengue Virus-2 Infection

2020 ◽  
Author(s):  
Man-jin Li ◽  
Ce-jie Lan ◽  
He-ting Gao ◽  
Dan Xing ◽  
Zhen-yu Gu ◽  
...  
Keyword(s):  
Aedes Aegypti ◽  
Dengue Virus ◽  
Cell Line ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Bioinformatics Analysis ◽  
Differentially Expressed ◽  
Control Group ◽  
Sequencing Data ◽  
Qrt Pcr

Abstract Background: Dengue virus (DENV) is a flavivirus transmitted by mosquitoes that is prevalent in tropical and subtropical countries and has four serotypes (DENV1-4). Aedes aegypti, as the main transmission vector of DENV, exhibits strong infectivity and transmission. With the aim of obtaining a better understanding of the Ae. aegypti-DENV interaction, the transcriptome changes in DENV-2-infected Aag2 cells were studied to describe the immune responses of mosquitoes using the Ae. aegypti Aag2 cell line as a model.Methods: RNAseq technology was used to sequence the transcripts of the Ae. aegypti Aag2 cell line before and after infection with DENV-2. A bioinformatics analysis was then performed to assess the biological functions of the differentially expressed genes, and the sequencing data were verified by quantitative reverse transcription-polymerase chain reaction (qRT-PCR).Results: The transcriptome analysis generated 8866 unigenes that were found in both groups, 225 unigenes that were only found in the infection group, and 683 unigenes that only existed in the control group. A total of 1199 differentially expressed genes, including 1014 upregulated and 185 downregulated genes, were identified. The bioinformatics analysis showed that the differentially expressed genes were mainly involved in the longevity regulating pathway, circadian rhythm, DNA replication, and peroxisome, purine, pyrimidine, and drug metabolism. The qRT-PCR verification results showed the same trend, which confirmed that the expression of the differentially expressed genes had changed and that the transcriptome sequencing data were reliable.Conclusions: This study investigated the changes in the transcriptome levels in the DENV-2-infected Ae. aegypti Aag2 cell line, which provides a faster and effective method for discovering genes related to Ae. aegypti pathogen susceptibility. The findings provide basic data and directions for further research on the complex mechanism underlying host-pathogen interactions.

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 Study on the Effect of Macrophages on Vascular Endothelium in Mice With Different TCM Syndromes of Dyslipidemia and its Biological Basis Based on RNA-Seq Technology

2021 ◽  
Vol 12 ◽  
Author(s):  
Jing Chen ◽  
Chao Ye ◽  
Zheng Yang ◽  
Tieshan Wang ◽  
Bing Xu ◽  
...  
Keyword(s):  
Quality Assessment ◽  
Differentially Expressed Genes ◽  
Normal Control ◽  
Normal Control Group ◽  
Differentially Expressed ◽  
Control Group ◽  
Biological Processes ◽  
Rna Seq ◽  
Pathogenic Factors ◽  
Protective Processes

Background: “Treating the same disease with different methods” is a Traditional Chinese medicine (TCM) therapeutic concept suggesting that, while patients may be diagnosed with the same disease, they may also have different syndromes that require distinct drug administrations.Objective: This study aimed to identify the differentially expressed genes and related biological processes in dyslipidemia in relation to phlegm–dampness retention (PDR) syndrome and spleen and kidney Yang deficiency (SKYD) syndrome using transcriptomic analysis.Methods: Ten ApoE−/− mice were used for the establishment of dyslipidemic disease–syndrome models via multifactor-hybrid modeling, with five in the PDR group and five in the SKYD group. Additionally, five C57BL/6J mice were employed as a normal control group. Test model-quality aortic endothelial macrophages in mice were screened using flow cytometry. Transcriptomic analysis was performed for macrophages using RNA-Seq.Results: A quality assessment of the disease–syndrome model showed that levels of lipids significantly increased in the PDR and SKYD groups, compared to the normal control group, p < 0.05. Applying, in addition, hematoxylin and eosin staining of aorta, the disease model was also successfully established. A quality assessment of the syndrome models showed that mice in the PDR group presented with typical manifestations of PDR syndrome, and mice in the SKYD group had related manifestations of SKYD syndrome, indicating that the syndrome models were successfully constructed as well. After comparing the differentially expressed gene expressions in macrophages of the dyslipidemic mice with different syndromes, 4,142 genes were identified with statistical significance, p < 0.05. Gene ontology analysis for the differentially expressed genes showed that the biological process of difference between the PDR group and the SKYD group included both adverse and protective processes.Conclusion: The differentially expressed genes between PDR syndrome and SKYD syndrome indicate different biological mechanisms between the onsets of the two syndromes. They have distinctive biological processes, including adverse and protective processes that correspond to the invasion of pathogenic factors into the body and the fight of healthy Qi against pathogenic factors, respectively, according to TCM theory. Our results provide biological evidence for the TCM principle of “treating the same disease with different treatments.”

scholarly journals Transcriptome Analysis of Orbital Adipose Tissue in Active Thyroid Eye Disease Using Next Generation RNA Sequencing Technology

2018 ◽  
Vol 12 (1) ◽  
pp. 41-52 ◽  
Author(s):  
Bradford W. Lee ◽  
Virender B. Kumar ◽  
Pooja Biswas ◽  
Audrey C. Ko ◽  
Ramzi M. Alameddine ◽  
...  
Keyword(s):  
Adipose Tissue ◽  
Differential Expression ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Thyroid Eye Disease ◽  
Differentially Expressed ◽  
Eye Disease ◽  
Healthy Controls ◽  
Rna Seq ◽  
Next Generation

Objective: This study utilized Next Generation Sequencing (NGS) to identify differentially expressed transcripts in orbital adipose tissue from patients with active Thyroid Eye Disease (TED) versus healthy controls. Method: This prospective, case-control study enrolled three patients with severe, active thyroid eye disease undergoing orbital decompression, and three healthy controls undergoing routine eyelid surgery with removal of orbital fat. RNA Sequencing (RNA-Seq) was performed on freshly obtained orbital adipose tissue from study patients to analyze the transcriptome. Bioinformatics analysis was performed to determine pathways and processes enriched for the differential expression profile. Quantitative Reverse Transcriptase-Polymerase Chain Reaction (qRT-PCR) was performed to validate the differential expression of selected genes identified by RNA-Seq. Results: RNA-Seq identified 328 differentially expressed genes associated with active thyroid eye disease, many of which were responsible for mediating inflammation, cytokine signaling, adipogenesis, IGF-1 signaling, and glycosaminoglycan binding. The IL-5 and chemokine signaling pathways were highly enriched, and very-low-density-lipoprotein receptor activity and statin medications were implicated as having a potential role in TED. Conclusion: This study is the first to use RNA-Seq technology to elucidate differential gene expression associated with active, severe TED. This study suggests a transcriptional basis for the role of statins in modulating differentially expressed genes that mediate the pathogenesis of thyroid eye disease. Furthermore, the identification of genes with altered levels of expression in active, severe TED may inform the molecular pathways central to this clinical phenotype and guide the development of novel therapeutic agents.

scholarly journals Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Lyudmila V. Dergunova ◽  
Ivan B. Filippenkov ◽  
Vasily V. Stavchansky ◽  
Alina E. Denisova ◽  
Vadim V. Yuzhakov ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Rat Model ◽  
Transcriptome Analysis ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Genome Wide

scholarly journals Dorsal Striatum Transcriptome Profile Profound Shift in Repeated Aggression Mouse Model Converged to Networks of 12 Transcription Factors after Fighting Deprivation

Genes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 21
Author(s):  
Vladimir Babenko ◽  
Olga Redina ◽  
Dmitry Smagin ◽  
Irina Kovalenko ◽  
Anna Galyamina ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Expression Profile ◽  
Transcriptional Repression ◽  
Gene Networks ◽  
Dorsal Striatum ◽  
Differentially Expressed ◽  
Control Group ◽  
Rna Seq ◽  
Withdrawal Effect ◽  
Transcriptome Expression

Both aggressive and aggression-deprived (AD) species represent pathologic cases intensely addressed in psychiatry and substance abuse disciplines. Previously, we reported that AD mice displayed a higher aggressive behavior score than the aggressive group, implying the manifestation of a withdrawal effect. We employed an animal model of chronic social conflicts, curated in our lab for more than 30 years. In the study, we pursued the task of evaluating key events in the dorsal striatum transcriptome of aggression experienced mice and AD species compared to controls using RNA-Seq profiling. Aggressive species were subjected to repeated social conflict encounters (fights) with regular positive (winners) experience in the course of 20 consecutive days (A20 group). This led to a profoundly shifted transcriptome expression profile relative to the control group, outlined by more than 1000 differentially expressed genes (DEGs). RNA-Seq cluster analysis revealed that elevated cyclic AMP (cAMP) signaling cascade and associated genes comprising 170 differentially expressed genes (DEGs) in aggressive (A20) species were accompanied by a downturn in the majority of other metabolic/signaling gene networks (839 DEGs) via the activation of transcriptional repressor DEGs. Fourteen days of a consecutive fighting deprivation period (AD group) featured the basic restoration of the normal (control) transcriptome expression profile yielding only 62 DEGs against the control. Notably, we observed a network of 12 coordinated DEG Transcription Factor (TF) activators from 62 DEGs in total that were distinctly altered in AD compared to control group, underlining the distinct transcription programs featuring AD group, partly retained from the aggressive encounters and not restored to normal in 14 days. We found circadian clock TFs among them, reported previously as a withdrawal effect factor. We conclude that the aggressive phenotype selection with positive reward effect (winning) manifests an addiction model featuring a distinct opioid-related withdrawal effect in AD group. Along with reporting profound transcriptome alteration in A20 group and gaining some insight on its specifics, we outline specific TF activator gene networks associated with transcriptional repression in affected species compared to controls, outlining Nr1d1 as a primary candidate, thus offering putative therapeutic targets in opioid-induced withdrawal treatment.

scholarly journals Complement C3a Not C4a Activates Osteoclasts By Regulating the PI3K/PDK1/SGK3 Pathway in Patients with Multiple Myeloma

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 4416-4416
Author(s):  
Rong Fu ◽  
Fengjuan Jiang ◽  
Hui Liu ◽  
Zhaoyun Liu ◽  
Siyang Yan ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Bone Disease ◽  
Cathepsin K ◽  
Differentially Expressed ◽  
Control Group ◽  
Rna Seq ◽  
Relative Expression ◽  
Absorption Area ◽  
Osteoclast Resorption

Objective: Myeloma bone disease (MBD) is the most common complication of multiple myeloma (MM). We found that the serum levels of C3/C4 in MM patients were significantly positive correlated with the severity of bone disease in our previously study. Thus, we conduct detailed studies to explore the effect and potential mechanism of C3a/C4a on osteoclasts in patients with MM. Methods: By adding C3a/C4a to culture system of osteoclasts induced from mononuclear cells in vitro, and the expression of related gene, number and function of osteoclasts were detected. RNA-Seq analysis was used to detect the differentially expressed genes on osteoclasts between the complement group and control group, and the possible signal pathways were analyzed. Quantitative real-time PCR (qRT-PCR), Western blot and pathway inhibitors were used for further validation. R esults: In vitro, the osteoclasts area per view induced by C3a 1μg/ml (52.794±13.027 %) and 10μg/ml (51.797±12.464 %) was significantly increased than control group (0μg/ml) (33.668±8.427 %) (P<0.001; P<0.001), the mRNA relative expression of osteoclasts related genes OSCAR/TRAP/RANKL/Cathepsin K induced by C3a 1μg/ml (median 5.041; 3.726; 1.638; 4.752) and 10μg/ml (median 5.140; 3.702; 2.250; 5.172) was significantly increased than control group (0μg/ml) (median 3.137; 2.004; 0.573; 2.257) (1μg/ml P=0.001; P=0.003; P<0.001; P=0.008; 1μg/ml P<0.001; P=0.019; P<0.001; P=0.002), and the absorption area of osteoclast resorption pit per view induced by C3a 1μg/ml (51.464±11.983 %) and 10μg/ml (50.219±12.067 %) was also significantly increased than control group (0μg/ml) (33.845±8.331 %) (P<0.001; P<0.001) in NDMM patients. There was no difference among the osteoclasts area, relative expression of osteoclasts related genes and absorption area of osteoclast resorption pit between C4a (1μg/ml and 10μg/ml) group and control group (0μg/ml). RNA-Seq was performed on total RNA of osteoclasts induced by C3a in 1μg/ml group and 0μg/ml group of 4 patients with NDMM. There were 184 differentially expressed genes that were detected by RNA-Seq analysis. KEGG Pathway enrichment bubble chart shows C3a may through Phosphoinositide 3-kinase (PI3K) signaling pathways (including PI3K-Akt pathway and AKT-independent signaling pathway) promotes the proliferation of osteoclast. Upregulated differentially expressed genes in this pathway among at least 3 patients with sequencing were validated by qRT-PCR and Western Blot. It was found that the relative expression level of Phosphoinositide dependent kinase-1 (PDK1) / Serum and glucocorticoid inducible protein kinases (SGK3) genes (median 2.078; 4.428) in C3a group (1μg/ml) was significantly higher than control group (0μg/ml) (median 1.336; 1.714) (P<0.001; P=0.001). The relative grayscale levels of PDK1/ P-SGK3 protein (1.785±0.323; 2.190±0.274) in C3a group (1μg/ml) was significantly stronger than control group (0μg/ml) (0.8653±0.588; 0.176±0.152) (P=0.034; P<0.001). Under the action of C3a in patients with NDMM, osteoclasts area per view in SGK inhibitor (EMD638683) 1μM group (39.244±9.089 %) and 10μM group (39.299±9.587 %) significantly reduced than control group (0μM) (54.884±12.837 %) (P<0.001; P<0.001), the relative expression of osteoclast related genes OSCAR/RANKL/TRAP/Cathepsin K in EMD638683 1μM group (median 0.869; 1.097; 0.902; 1.328) and 10μM group (median 0.703; 1.391; 0.843; 1.418) significantly decreased than control group (0μM) (median 2.270; 3.024; 2.208; 3.237) (1μM P=0.015; P=0.002; P=0.003; P=0.015; 10μM P=0.012; P=0.006; P<0.001; P=0.017), and the absorption area per view of osteoclast resorption pit in EMD638683 1μM (35.383±7.794 %) group and 10μM group (32.886±8.993 %) significantly reduced than control group (0μM) (49.358±11.856 %) (P < 0.001; P < 0.001). Conclusions:ComplementC3a activates osteoclasts by regulating the PI3K/PDK1/SGK3 pathway in patients with MM, thus leading to the occurrence of bone diseases. SGK inhibitor has a significant inhibitory effect on osteoclasts in patients with MM. This study provide important evidences for the search for new therapeutic targets and strategies for myeloma bone disease patients. Disclosures No relevant conflicts of interest to declare.

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