scholarly journals RNA-sequencing analysis of high glucose-treated monocytes reveals novel transcriptome signatures and associated epigenetic profiles

2013 ◽  
Vol 45 (7) ◽  
pp. 287-299 ◽  
Author(s):  
Feng Miao ◽  
Zhuo Chen ◽  
Lingxiao Zhang ◽  
Jinhui Wang ◽  
Harry Gao ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
High Glucose ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Blood Monocytes ◽  
Motif Analysis ◽  
Interferon Stimulated Genes ◽  
Normal Glucose ◽  
Upregulated Genes

We performed high throughput transcriptomic profiling with RNA sequencing (RNA-Seq) to uncover network responses in human THP-1 monocytes treated with high glucose (HG). Our data analyses revealed that interferon (IFN) signaling, pattern recognition receptors, and activated interferon regulatory factors (IRFs) were enriched among the HG-upregulated genes. Motif analysis identified an HG-responsive IRF-mediated network in which interferon-stimulated genes (ISGs) were enriched. Notably, this network showed strong overlap with a recently discovered IRF7-driven network relevant to Type 1 diabetes. We next examined if the HG-regulated genes possessed any characteristic chromatin features in the basal state by profiling 15 active and repressive chromatin marks under normal glucose conditions using chromatin immunoprecipitation linked to promoter microarrays. Composite profiles revealed higher histone H3 lysine-9-acetylation levels around the promoters of HG-upregulated genes compared with all RefSeq promoters. Interestingly, within the HG-upregulated genes, active chromatin marks were enriched not only at high CpG content promoters, but surprisingly also at low CpG content promoters. Similar results were obtained with peripheral blood monocytes exposed to HG. These new results reveal a novel mechanism by which HG can exercise IFN-α-like effects in monocytes by upregulating a set of ISGs poised for activation with multiple chromatin marks.

Identification of Differentially Expressed and Spliced Genes with RNA Sequencing Analysis of CLL Specimens

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 4582-4582
Author(s):  
Wei Liao ◽  
Gwen Jordaan ◽  
Artur Jaroszewicz ◽  
Matteo Pellegrini ◽  
Sanjai Sharma
Keyword(s):  
B Cells ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Fold Change ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Mrna Isoforms ◽  
Core Set

Abstract Abstract 4582 High throughput sequencing of cellular mRNA provides a comprehensive analysis of the transcriptome. Besides identifying differentially expressed genes in different cell types, it also provides information of mRNA isoforms and splicing alterations. We have analyzed two CLL specimens and a normal peripheral blood B cells mRNA by this approach and performed data analysis to identify differentially expressed and spliced genes. The result showed CLLs specimens express approximately 40% more transcripts compared to normal B cells. The FPKM data (fragment per kilobase of exon per million) revealed a higher transcript expression on chromosome 12 in CLL#1 indicating the presence of trisomy 12, which was confirmed by fluorescent in-situ hybridization assay. With a two-fold change in FPKM as a cutoff and a p value cutoff of 0.05 as compared to the normal B cell control, 415 genes and 174 genes in CLL#1 and 676 and 235 genes in CLL#2 were up and downregulated or differentially expressed. In these two CLL specimens, 45% to 75% of differentially expressed genes are common to both the CLL specimens indicating that genetically disparate CLL specimens have a high percentage of a core set of genes that are potentially important for CLL biology. Selected differentially expressed genes with increased expression (selectin P ligand, SELPLG, and adhesion molecule interacts with CXADR antigen 1, AMICA) and decreased (Fos, Jun, CD69 and Rhob) expression based on the FPKM from RNA-sequencing data were also analyzed in additional CLL specimens by real time PCR analysis. The expression data from RNA-seq closely matches the fold-change in expression as measured by RT-PCR analysis and confirms the validity of the RNA-seq analysis. Interestingly, Fos was identified as one of the most downregulated gene in CLL. Using the Cufflinks and Cuffdiff software, the splicing patterns of genes in CLL specimens and normal B cells were analyzed. Approximately, 1100 to 1250 genes in the two CLL specimens were significantly differentially spliced as compared to normal B cells. In this analysis as well, there is a core set of 800 common genes which are differentially spliced in the two CLL specimens. The RNA-sequencing analysis accurately identifies differentially expressed novel genes and splicing variations that will help us understand the biology of CLL. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Gene Profiling of Bone around Orthodontic Mini-Implants by RNA-Sequencing Analysis

2015 ◽  
Vol 2015 ◽  
pp. 1-14 ◽  
Author(s):  
Kyung-Yen Nahm ◽  
Jung Sun Heo ◽  
Jae-Hyung Lee ◽  
Dong-Yeol Lee ◽  
Kyu-Rhim Chung ◽  
...  
Keyword(s):  
Bone Formation ◽  
Rna Sequencing ◽  
Cell Fate ◽  
Reduction Process ◽  
Gene Profiling ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Mini Implants ◽  
Oxidation Reduction ◽  
The Times

This study aimed to evaluate the genes that were expressed in the healing bones around SLA-treated titanium orthodontic mini-implants in a beagle at early (1-week) and late (4-week) stages with RNA-sequencing (RNA-Seq). Samples from sites of surgical defects were used as controls. Total RNA was extracted from the tissue around the implants, and an RNA-Seq analysis was performed with Illumina TruSeq. In the 1-week group, genes in the gene ontology (GO) categories of cell growth and the extracellular matrix (ECM) were upregulated, while genes in the categories of the oxidation-reduction process, intermediate filaments, and structural molecule activity were downregulated. In the 4-week group, the genes upregulated included ECM binding, stem cell fate specification, and intramembranous ossification, while genes in the oxidation-reduction process category were downregulated. GO analysis revealed an upregulation of genes that were related to significant mechanisms, including those with roles in cell proliferation, the ECM, growth factors, and osteogenic-related pathways, which are associated with bone formation. From these results, implant-induced bone formation progressed considerably during the times examined in this study. The upregulation or downregulation of selected genes was confirmed with real-time reverse transcription polymerase chain reaction. The RNA-Seq strategy was useful for defining the biological responses to orthodontic mini-implants and identifying the specific genetic networks for targeted evaluations of successful peri-implant bone remodeling.

scholarly journals Deep RNA sequencing analysis of syncytialization-related genes during BeWo cell fusion

Reproduction ◽  
2017 ◽  
Vol 153 (1) ◽  
pp. 35-48 ◽  
Author(s):  
Ru Zheng ◽  
Yue Li ◽  
Huiying Sun ◽  
Xiaoyin Lu ◽  
Bao-Fa Sun ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Cell Fate ◽  
Cell Fusion ◽  
Mapk Pathway ◽  
Differentially Expressed ◽  
Cell Junction ◽  
Bewo Cell ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Bewo Cells

The syncytiotrophoblast (STB) plays a key role in maintaining the function of the placenta during human pregnancy. However, the molecular network that orchestrates STB development remains elusive. The aim of this study was to obtain broad and deep insight into human STB formation via transcriptomics. We adopted RNA sequencing (RNA-Seq) to investigate genes and isoforms involved in forskolin (FSK)-induced fusion of BeWo cells. BeWo cells were treated with 50 μM FSK or dimethyl sulfoxide (DMSO) as a vehicle control for 24 and 48 h, and the mRNAs at 0, 24 and 48 h were sequenced. We detected 28,633 expressed genes and identified 1902 differentially expressed genes (DEGs) after FSK treatment for 24 and 48 h. Among the 1902 DEGs, 461 were increased and 395 were decreased at 24 h, whereas 879 were upregulated and 763 were downregulated at 48 h. When the 856 DEGs identified at 24 h were traced individually at 48 h, they separated into 6 dynamic patterns via a K-means algorithm, and most were enriched in down–even and up–even patterns. Moreover, the gene ontology (GO) terms syncytium formation, cell junction assembly, cell fate commitment, calcium ion transport, regulation of epithelial cell differentiation and cell morphogenesis involved in differentiation were clustered, and the MAPK pathway was most significantly regulated. Analyses of alternative splicing isoforms detected 123,200 isoforms, of which 1376 were differentially expressed. The present deep analysis of the RNA-Seq data of BeWo cell fusion provides important clues for understanding the mechanisms underlying human STB formation.

scholarly journals Differentially Expressed Gene Profile of Acanthamoeba castellanii Induced by an Endosymbiont Legionella pneumophila

2021 ◽  
Vol 59 (1) ◽  
pp. 67-75
Author(s):  
Eun-Kyung Moon ◽  
So-Min Park ◽  
Ki-Back Chu ◽  
Fu-Shi Quan ◽  
Hyun-Hee Kong
Keyword(s):  
Rna Sequencing ◽  
Legionella Pneumophila ◽  
Differentially Expressed Gene ◽  
Acanthamoeba Castellanii ◽  
Opportunistic Pathogen ◽  
Sequencing Analysis ◽  
Sequencing Data ◽  
Oxidoreductase Activity ◽  
Transcriptional Changes ◽  
Upregulated Genes

Legionella pneumophila is an opportunistic pathogen that survives and proliferates within protists such as Acanthamoeba spp. in environment. However, intracellular pathogenic endosymbiosis and its implications within Acanthamoeba spp. remain poorly understood. In this study, RNA sequencing analysis was used to investigate transcriptional changes in A. castellanii in response to L. pneumophila infection. Based on RNA sequencing data, we identified 1,211 upregulated genes and 1,131 downregulated genes in A. castellanii infected with L. pneumophila for 12 hr. After 24 hr, 1,321 upregulated genes and 1,379 downregulated genes were identified. Gene ontology (GO) analysis revealed that L. pneumophila endosymbiosis enhanced hydrolase activity, catalytic activity, and DNA binding while reducing oxidoreductase activity in the molecular function (MF) domain. In particular, multiple genes associated with the GO term ‘integral component of membrane’ were downregulated during endosymbiosis. The endosymbiont also induced differential expression of various methyltransferases and acetyltransferases in A. castellanii. Findings herein are may significantly contribute to understanding endosymbiosis of L. pneumophila within A. castellanii.

scholarly journals RNA-sequencing analysis of the effect of luteolin on methamphetamine-induced hepatotoxicity in rats: a preliminary study

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8529
Author(s):  
Dong Qu ◽  
Kaikai Zhang ◽  
Lijian Chen ◽  
Qi Wang ◽  
Huijun Wang
Keyword(s):  
Fatty Acid ◽  
Rna Sequencing ◽  
Biochemical Analysis ◽  
Fatty Acid Synthase ◽  
Sequencing Analysis ◽  
Protective Effects ◽  
Rna Seq ◽  
Oral Gavage ◽  
Fatty Acid Binding ◽  
Preliminary Study

In this study, RNA-sequencing (RNA-seq) was utilized to investigate the effects of luteolin on hepatotoxicity caused by methamphetamine (METH). The rats in METH group were administrated with METH (15 mg/kg, two times per day) via intraperitoneal (i.p.) injections for four consecutive days. The rats in luteolin + METH group were firstly administrated with luteolin (100 mg/kg, once a day) by oral gavage for 3 days before METH treatment. Lueolin attenuated the hepatotoxicity induced by METH via histopathological and biochemical analysis. The results of RNA-seq showed that luteolin could regulate 497 differentially expressed genes (DEGs), and the selected DEGs were mainly enriched in eight pathways, according to KEGG analysis. Furthermore, qRT-PCR was utilized to verify the results of RNA-seq. Six genes were selected as follows: liver enriched antimicrobial peptide 2 (Leap2), fatty acid synthase (Fasn), fatty acid binding protein 5 (Fabp5), patatin like phospholipase domain containing 3 (Pnpla3), myelin basic protein (Mbp) and calmodulin 3 (Calm3). Though because of the design flaws, the luteolin group has not been included, this study demonstrated that luteolin might exert hepato-protective effects from METH via modulation of oxidative phosphorylation, cytochrome P450 and certain signaling pathways.

Abstract WP261: Sex Differences in Circulating Leukocyte Subtype and Activation Following Ischemic Stroke

Stroke ◽  
2016 ◽  
Vol 47 (suppl_1) ◽  
Author(s):  
Meaghan Roy-O'Reilly ◽  
Hetal Mistry ◽  
Madeline Levy ◽  
Louise McCullough
Keyword(s):  
Flow Cytometry ◽  
Immune Response ◽  
Sex Differences ◽  
Ischemic Stroke ◽  
Rna Sequencing ◽  
Sequencing Analysis ◽  
Stroke Patients ◽  
Female Patients ◽  
Post Stroke ◽  
Upregulated Genes

Background and Purpose: Females exhibit a more robust immune response in many disease models, yet sex differences in the inflammatory response to ischemia remain largely unexplored. We conducted flow cytometry and RNA sequencing of blood from ischemic stroke patients, with follow-up studies in mice. Hypothesis: We assessed the hypothesis that there are sex differences in the acute immune response to ischemic stroke. Methods: Patient samples were drawn at 24 hours post-stroke for flow cytometry (n=6) and RNA sequencing Analysis (n=40). For murine studies, male and ovariectomized (OVX) female animals (n=14) were subjected to 90-minute middle cerebral artery occlusion or sham surgery and sacrificed at 24 hours. Murine blood was stained for leukocyte markers and CD62L (L-selectin). Results were analyzed by student T-test and two-way ANOVA. Results: RNA sequencing revealed that 24 hours after ischemic stroke, female patients had 79 significantly upregulated genes, compared to male patients with 6 significantly upregulated genes. Human flow cytometry revealed that male stroke patients had a significantly higher percentage of monocytes (p=.026), while females had a greater percentage of CD8+ T-cells (p=.023). Murine flow cytometry showed a post-stroke increase in peripheral myeloid cells at 24 hours in male mice only (p=.0046), whereas female mice had a higher CD8/CD4 T cell ratio (p=.0027). Neutrophils from male sham animals displayed greater L-selectin positivity, with stroke-induced shedding of L-selectin seen only in males (sex/stroke p=.0266). Male monocytes and lymphocytes also displayed higher L-selectin positivity (p=.0079, p=.0004). Conclusion: These results suggest that the immune response to ischemic stroke is different in male and female patients, a phenomenon that can be recapitulated in a mouse model of experimental stroke. Female immune cells exhibit a higher level of baseline activation (reduced L-selectin expression) and post-stroke activity, which may enable a quicker and more robust response to immune challenges. Understanding sex differences in the acute immune response is crucial to developing future immunomodulatory drugs for the safe and effective treatment of ischemic stroke in both sexes.

scholarly journals Effect of chronic uremia on the transcriptional profile of the calcified aorta analyzed by RNA sequencing

2016 ◽  
Vol 310 (6) ◽  
pp. F477-F491 ◽  
Author(s):  
Jakob L. Rukov ◽  
Eva Gravesen ◽  
Maria L. Mace ◽  
Jacob Hofman-Bang ◽  
Jeppe Vinther ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Vascular Tissue ◽  
Rat Aorta ◽  
Transcriptional Profile ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Chronic Uremia ◽  
Upregulated Genes ◽  
Calcified Aorta ◽  
First Time

The development of vascular calcification (VC) in chronic uremia (CU) is a tightly regulated process controlled by factors promoting and inhibiting mineralization. Next-generation high-throughput RNA sequencing (RNA-seq) is a powerful and sensitive tool for quantitative gene expression profiling and the detection of differentially expressed genes. In the present study, we, for the first time, used RNA-seq to examine rat aorta transcriptomes from CU rats compared with control rats. Severe VC was induced in CU rats, which lead to extensive changes in the transcriptional profile. Among the 10,153 genes with an expression level of >1 reads/kilobase transcript/million mapped reads, 2,663 genes were differentially expressed with 47% upregulated genes and 53% downregulated genes in uremic rats. Significantly deregulated genes were enriched for ontologies related to the extracellular matrix, response to wounding, organic substance, and ossification. The individually affected genes were of relevance to osteogenic transformation, tissue calcification, and Wnt modulation. Downregulation of the Klotho gene in uremia is believed to be involved in the development of VC, but it is debated whether the effect is caused by circulating Klotho only or if Klotho is produced locally in the vasculature. We found that Klotho was neither expressed in the normal aorta nor calcified aorta by RNA-seq. In conclusion, we demonstrated extensive changes in the transcriptional profile of the uremic calcified aorta, which were consistent with a shift in phenotype from vascular tissue toward an osteochondrocytic transcriptome profile. Moreover, neither the normal vasculature nor calcified vasculature in CU expresses Klotho.

scholarly journals how_are_we_stranded_here: Quick determination of RNA-Seq strandedness

2021 ◽  
Author(s):  
Beth Signal ◽  
Tim Kahlke
Keyword(s):  
Quality Control ◽  
Rna Sequencing ◽  
Published Data ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Sequencing Data ◽  
Sequence Quality ◽  
Quick Determination

ABSTRACTQuality control checks are the first step in RNA-Sequencing analysis, which enable the identification of common issues that occur in the sequenced reads. Checks for sequence quality, contamination, and complexity are commonplace, and allow users to implement steps downstream which can account for these issues. Strand-specificity of reads is frequently overlooked and is often unavailable even in published data, yet when unknown or incorrectly specified can have detrimental effects on the reproducibility and accuracy of downstream analyses. We present how_are_we_stranded_here, a Python library that helps to quickly infer strandedness of paired-end RNA-Sequencing data.

scholarly journals PSII-11 RNA sequencing analysis reveals differentially expressed genes and novel upstream transcriptional regulators in porcine longissimus dorsi muscle affected by dietary lysine restriction

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 233-233
Author(s):  
Ying Wang ◽  
Huaijun Zhou ◽  
Shengfa F Liao
Keyword(s):  
Protein Synthesis ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Muscle Protein ◽  
Transcriptional Regulators ◽  
Growing Pigs ◽  
Differentially Expressed ◽  
Longissimus Dorsi ◽  
Sequencing Analysis ◽  
Rna Seq

Abstract The objective of this research was to investigate the effects of dietary lysine restriction on the global gene expression of skeletal muscle in growing pigs. Twelve crossbred (Yorkshire × Landrace) barrows (initial BW 22.6 ± 2.04 kg) were randomly assigned to two dietary treatments (Diet I: a lysine-deficient diet; Diet II: a lysine-adequate diet) according to a completely randomized experiment design (n = 6). After feeding for 8 weeks, muscle samples were collected from longissimus dorsi of individual pigs (approximately 2 g/each). The total RNA isolated was used to prepare cDNA library for RNA sequencing (RNA-Seq) analysis. The RNA-Seq data was then analyzed using the CLC Genomics Workbench to identify differentially expressed genes (DEGs). Sixty-nine genes were found differentially expressed (Benjamin-Hochberg corrected P < 0.05) in Diet I vs. Diet II pigs, of which 29 genes were down-regulated (Log₂ fold change (FC) < - 0.58) and 40 genes were up-regulated (Log₂ FC > 0.58). Gene ontology (GO) analysis of these DEGs for functional annotation using DAVID found a total of 36 GO terms. The significantly enriched terms (Benjamin-Hochberg corrected P < 0.05) are associated with biological processes that include acute-phase response, platelet activation, and protein polymerization, and Molecular Functions that include serine-type endopeptidase inhibitor activity, small molecule binding, heme binding, and oxidoreductase activity. In addition, Ingenuity Pathway Analysis predicted some upstream transcriptional regulators that regulate several sets of DEGs. For example, lysine restriction may lead inhibition of insulin, EIF2AK4 (an eIF2α activator), and MYC (a transcript elongation factor), which are associated with the regulation of protein synthesis. It may also lead activation of STAT3 and HNF1A, which regulate cell movement and fatty acid metabolism, respectively. In summary, these novel results showed that dietary lysine restriction may compromise pig muscle protein synthesis through the aforementioned transcriptional regulators and their affected genes.

scholarly journals RNA-sequencing analysis of differential gene expression associated with arterial stiffness

Vascular ◽  
2020 ◽  
Vol 28 (5) ◽  
pp. 655-663 ◽  
Author(s):  
Jeongok G Logan ◽  
Sijung Yun ◽  
Yongde Bao ◽  
Emily Farber ◽  
Charles R Farber
Keyword(s):  
Gene Expression ◽  
Cardiovascular Disease ◽  
Arterial Stiffness ◽  
Real Time ◽  
Rna Sequencing ◽  
Real Time Pcr ◽  
Disease Risk ◽  
Expression Profiles ◽  
Sequencing Analysis ◽  
Rna Seq

Objectives Arterial stiffness is recognized as an important predictor of cardiovascular disease morbidity and mortality, independent of traditional cardiovascular disease risk factors. Given that arterial tissue is not easily accessible, most gene expression studies on arterial stiffness have been conducted on animals or on patients who have undergone by-pass surgeries. In order to obtain a deeper understanding of early changes of arterial stiffness, this study compared transcriptome profiles between healthy adults with higher and lower arterial stiffness. Methods The sample included 20 healthy female adults without cardiovascular disease. Arterial stiffness was measured by carotid-femoral pulse wave velocity, the “gold-standard” measure of central arterial stiffness. Peripheral blood samples collected to PAXgene™ RNA tubes were used for RNA sequencing (RNA-seq). The potential confounding effects of age, body mass index, and mean arterial pressure were controlled for in RNA-seq analysis. To validate RNA-seq results, quantitative real-time PCR (qRT-PCR) was performed for six selected genes. Results The findings demonstrated that genes including CAPN9, IL32, ERAP2, RAB6B, MYBPH, and miRNA626 were down-regulated, and that MOCS1 gene was up-regulated among the people with higher arterial stiffness. Real-time PCR showed that the changes of CAPN9, IL32, ERAP2, and RAB6B were in concordance with RNA-seq data, and confirmed the validity of the gene expression profiles obtained by RNA-seq analysis. Conclusions Previous studies have suggested the potential roles of CAPN9, IL32, and ERAP2 in structural changes of the arterial wall through up-regulation of metalloproteinases. However, the current study showed that CAPN9, IL32, and ERAP2 were down-regulated in the individuals with higher arterial stiffness, compared with those with lower arterial stiffness. The unexpected directions of expression of these genes may indicate an effort to maintain vascular homeostasis during increased arterial stiffness among healthy individuals. Further studies are guaranteed to investigate the roles of CAPN9, IL32, and ERAP2 in regulating arterial stiffness in people with and without cardiovascular disease.

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