scholarly journals Gene Expression Changes in Venous Segment of Overflow Arteriovenous Fistula

2013 ◽  
Vol 2013 ◽  
pp. 1-8
Author(s):  
Yasuhiro Hashimoto ◽  
Akiko Okamoto ◽  
Hisao Saitoh ◽  
Shingo Hatakeyama ◽  
Takahiro Yoneyama ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pathway Analysis ◽  
Hemodialysis Patients ◽  
Tissue Samples ◽  
Biological Insight ◽  
Av Fistulas ◽  
Upregulated Genes ◽  
Venous Segment ◽  
Insight Into ◽  
Venous Tissue

Aim. The objective of this study was to characterize coordinated molecular changes in the structure and composition of the walls of venous segments of arteriovenous (AV) fistulas evoked by overflow.Methods. Venous tissue samples were collected from 6 hemodialysis patients with AV fistulas exposed to overflow and from the normal cephalic veins of 4 other hemodialysis patients. Total RNA was extracted from the venous tissue samples, and gene expression between the 2 groups was compared using Whole Human Genome DNA microarray 44 K. Microarray data were analyzed by GeneSpring GX software and Ingenuity Pathway Analysis.Results. The cDNA microarray analysis identified 397 upregulated genes and 456 downregulated genes. Gene ontology analysis with GeneSpring GX software revealed that biological developmental processes and glycosaminoglycan binding were the most upregulated. In addition, most upregulation occurred extracellularly. In the pathway analysis, the TGF beta signaling pathway, cytokines and inflammatory response pathway, hypertrophy model, and the myometrial relaxation and contraction pathway were significantly upregulated compared with the control cephalic vein.Conclusion. Combining microarray results and pathway information available via the Internet provided biological insight into the structure and composition of the venous wall of overflow AV fistulas.

scholarly journals Bayesian Framework for Detecting Gene Expression Outliers in Individual Samples

2020 ◽  
pp. 160-170
Author(s):  
John Vivian ◽  
Jordan M. Eizenga ◽  
Holly C. Beale ◽  
Olena M. Vaske ◽  
Benedict Paten
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Rna Seq ◽  
Single Patient ◽  
Tissue Samples ◽  
Composite Tissue ◽  
Patient Sample ◽  
Statistical Framework ◽  
Therapeutic Leads ◽  
Upregulated Genes

PURPOSE Many antineoplastics are designed to target upregulated genes, but quantifying upregulation in a single patient sample requires an appropriate set of samples for comparison. In cancer, the most natural comparison set is unaffected samples from the matching tissue, but there are often too few available unaffected samples to overcome high intersample variance. Moreover, some cancer samples have misidentified tissues of origin or even composite-tissue phenotypes. Even if an appropriate comparison set can be identified, most differential expression tools are not designed to accommodate comparisons to a single patient sample. METHODS We propose a Bayesian statistical framework for gene expression outlier detection in single samples. Our method uses all available data to produce a consensus background distribution for each gene of interest without requiring the researcher to manually select a comparison set. The consensus distribution can then be used to quantify over- and underexpression. RESULTS We demonstrate this method on both simulated and real gene expression data. We show that it can robustly quantify overexpression, even when the set of comparison samples lacks ideally matched tissue samples. Furthermore, our results show that the method can identify appropriate comparison sets from samples of mixed lineage and rediscover numerous known gene-cancer expression patterns. CONCLUSION This exploratory method is suitable for identifying expression outliers from comparative RNA sequencing (RNA-seq) analysis for individual samples, and Treehouse, a pediatric precision medicine group that leverages RNA-seq to identify potential therapeutic leads for patients, plans to explore this method for processing its pediatric cohort.

scholarly journals HOXB9 Expression Correlates with Histological Grade and Prognosis in LSCC

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Chuanhui Sun ◽  
Changsong Han ◽  
Peng Wang ◽  
Yinji Jin ◽  
Yanan Sun ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hox Genes ◽  
Histological Grade ◽  
Clinicopathological Features ◽  
Tissue Samples ◽  
Hox Gene ◽  
Expression Levels ◽  
Qrt Pcr ◽  
Upregulated Genes ◽  
Gene Expression Levels

The purpose of this study was to investigate the HOX gene expression profile in laryngeal squamous cell carcinoma (LSCC) and assess whether some genes are associated with the clinicopathological features and prognosis in LSCC patients. The HOX gene levels were tested by microarray and validated by qRT-PCR in paired cancerous and adjacent noncancerous LSCC tissue samples. The microarray testing data of 39 HOX genes revealed 15 HOX genes that were at least 2-fold upregulated and 2 that were downregulated. After qRT-PCR evaluation, the three most upregulated genes (HOXB9, HOXB13, and HOXD13) were selected for tissue microarray (TMA) analysis. The correlations between the HOXB9, HOXB13, and HOXD13 expression levels and both clinicopathological features and prognosis were analyzed. Three HOX gene expression levels were markedly increased in LSCC tissues compared with adjacent noncancerous tissues (P<0.001). HOXB9 was found to correlate with histological grade (P<0.01) and prognosis (P<0.01) in LSCC. In conclusion, this study revealed that HOXB9, HOXB13, and HOXD13 were upregulated and may play important roles in LSCC. Moreover, HOXB9 may serve as a novel marker of poor prognosis and a potential therapeutic target in LSCC patients.

scholarly journals Screening differentially expressed genes of pancreatic cancer between Mongolian and Han people using bioinformatics technology

2019 ◽  
Author(s):  
Jiasheng Xu ◽  
Kaili Liao ◽  
ZHONGHUA FU ◽  
ZHENFANG XIONG
Keyword(s):  
Gene Expression ◽  
Pancreatic Cancer ◽  
Gene Ontology ◽  
Differentially Expressed Genes ◽  
Pathway Analysis ◽  
Differentially Expressed ◽  
Cancer Tissue ◽  
Pancreatic Cancer Tissue ◽  
Tissue Samples ◽  
Multiple Difference

Abstract Objective To screen and analyze differentially expressed genes in pancreatic carcinoma tissues taken from Mongolian and Han patients by Affymetrix Genechip. Methods: Pancreatic ductal cell carcinoma tissues were collected from the Mongolian and Han patients undergoing resection in the Second Affiliated Hospital of Nanchang University during March 2015 to May 2018 and the total RNA was extracted. Differentially expressed genes were selected from the total RNA qualified by Nanodrop 2000 and Agilent 2100 using Affymetrix and a cartogram was drawn; The gene ontology (GO) analysis and Pathway analysis were used for the collection and analysis of biological information of these differentially expressed genes. Finally, some differentially expressed genes were verified by real-time PCR. Results Through the microarray analysis of gene expression, 970 differentially expressed genes were detected by comparing pancreatic cancer tissue samples between Mongolian and Han patients. A total of 257 genes were significantly up-regulated in pancreatic cancer tissue samples in Mongolian patients;while a total of 713 genes were down-regulated. In the Gene Ontology database, 815 differentially expressed genes were identified with clear GO classification, and CPB1 gene had the highest multiple of differential expression (difference multiple: 31.76). The Pathway analysis detected 28 signaling pathways that included these differentially expressed genes, involving a total of 178 genes. Among these pathways, the enrichment of differentially expressed genes in the FAK signaling pathway was the highest and COL11A1 gene had the highest multiple difference (multiple difference: 5.02). The expressions of differentially expressed genes CPB1, COL11A1、ITGA4、BIRC3、PAK4、CPA1、CLPS、PIK3CG and HLA-DPA1 determined by real-time PCR were consistent with the results of gene chip analysis. Conclusions The results of microarray analysis of gene expression profiles showed that there are a large number of differentially expressed genes in pancreatic cancer tissue samples compared between Mongolian and Han populations. These genes are closely related to the proliferation, differentiation, invasion and metastasis and multi-drug resistance of pancreatic cancer and are involved in the regulation of multiple important signaling pathways in organisms.

scholarly journals Microbial Metabolic Genes Crucial for S. aureus Biofilms: An Insight From Re-analysis of Publicly Available Microarray Datasets

2021 ◽  
Vol 11 ◽  
Author(s):  
Rania Nassar ◽  
Mahmood Hachim ◽  
Mohannad Nassar ◽  
Eleftherios G. Kaklamanos ◽  
Mohamed Jamal ◽  
...  
Keyword(s):  
Gene Expression ◽  
Maturation Stage ◽  
Metabolic Genes ◽  
Human Infections ◽  
Microarray Datasets ◽  
Phenotypic Shift ◽  
Hospital Acquired ◽  
Protected Mode ◽  
Upregulated Genes ◽  
Insight Into

Bacterial biofilms are microbial lifestyles found in all environments. Up to 80% of human infections and 60–70% of hospital-acquired infections have a biofilm origin, with Staphylococcus aureus one of the leading causes of these infections. Microorganisms in biofilms exhibit significant antimicrobial resistance which poses important treatment challenges, hence the urgent need to identify novel antibiofilm strategies. Microbes form biofilms in response to various factors, and once these 3-dimentional structures form they are highly recalcitrant to removal. The switch from planktonic lifestyle to the biofilm protected mode of growth results in a phenotypic shift in the behavior of the microorganisms in terms of growth rate and gene expression. Given these changes, investigation of microbial gene expression and their modulation at different stages of biofilm maturation is needed to provide vital insight into the behavior of biofilm cells. In this study, we analyzed publicly available transcriptomic dataset of S. aureus biofilms at different stages of maturation to identify consistently upregulated genes irrespective of the biofilm maturation stage. Our reanalysis identified a total of 6 differentially expressed genes upregulated in both 48 and 144-h old S. aureus biofilms. Functional analysis revealed that these genes encode for proteins which play a role in key microbial metabolic pathways. However, these genes, as yet, are unrelated or fully studied in the context of biofilm. Moreover, the findings of this in silico work, suggest that these genes may represent potential novel targets for the development of more effective antibiofilm strategies against S. aureus biofilm-associated infections.

Gene-expression profile and postpartum transition of bovine endometrial side population cells†

2021 ◽  
Author(s):  
Ryoki Tatebayashi ◽  
Sho Nakamura ◽  
Shiori Minabe ◽  
Tadashi Furusawa ◽  
Ryoya Abe ◽  
...  
Keyword(s):  
Gene Expression ◽  
Progenitor Cells ◽  
Pathway Analysis ◽  
Kegg Pathway ◽  
Side Population ◽  
Gene Set Enrichment Analysis ◽  
Stem Cell Marker ◽  
Endometrial Cells ◽  
Kegg Pathway Analysis ◽  
Upregulated Genes

Abstract The mechanism of bovine endometrial regeneration after parturition remains unclear. Here, we hypothesized that bovine endometrial stem/progenitor cells participate in the postpartum regeneration of the endometrium. Flow cytometry analysis identified the presence of side population (SP) cells among endometrial stromal cells. Endometrial SP cells were shown to differentiate into osteoblasts and adipocytes. RNA-seq data showed that the gene expression pattern was different between bovine endometrial SP cells and main population cells. Gene Set Enrichment Analysis identified the enrichment of stemness genes in SP cells. Significantly (false discovery rate &lt; 0.01) upregulated genes in SP cells contained several stem cell marker genes. Gene ontology (GO) analysis of the upregulated genes in SP cells showed enrichment of terms related to RNA metabolic process and transcription. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of upregulated genes in SP cells revealed enrichment of signaling pathways associated with maintenance and differentiation of stem/progenitor cells. The terms involved in TCA cycles were enriched in GO and KEGG pathway analysis of downregulated genes in SP cells. These results support the assumption that bovine endometrial SP cells exhibit characteristics of somatic stem/progenitor cells. The ratio of SP cells to endometrial cells was lowest on days 9–11 after parturition, which gradually increased thereafter. SP cells were shown to differentiate into epithelial cells. Collectively, these results suggest that bovine endometrial SP cells were temporarily reduced immediately after calving possibly due to their differentiation to provide new endometrial cells.

scholarly journals Lung tissue gene-expression signature for the ageing lung in COPD

Thorax ◽  
2017 ◽  
Vol 73 (7) ◽  
pp. 609-617 ◽  
Author(s):  
Maaike de Vries ◽  
Alen Faiz ◽  
Roy R Woldhuis ◽  
Dirkje S Postma ◽  
Tristan V de Jong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pathway Analysis ◽  
Lung Tissue ◽  
Interaction Analysis ◽  
Current Knowledge ◽  
Calcium Signalling ◽  
Gene Expression Signature ◽  
Differentially Expressed ◽  
Tissue Samples ◽  
Expression Signature

IntroductionCOPD is a chronic, progressive, inflammatory disease of the lungs and the third leading cause of death worldwide. The current knowledge of the pathophysiology of COPD is limited and novel insights in underlying disease mechanisms are urgently needed. Since there are clear parallels between ageing and COPD, we investigated genes underlying lung ageing in general and abnormal lung ageing in COPD.MethodsWhole genome mRNA profiling was performed on lung tissue samples (n=1197) and differential gene expression with increasing age was analysed using an adjusted linear regression model. Subsequent pathway analysis was performed using GeneNetwork and the gene-expression signature was compared with lung ageing in the Genotype-Tissue Expression (GTEx) project. In a subset of patients with COPD (n=311) and non-COPD controls (n=270), we performed an interaction analysis between age and COPD to identify genes differentially expressed with age in COPD compared with controls, followed by gene set enrichment pathway analysis.ResultsWe identified a strong gene-expression signature for lung ageing with 3509 differentially expressed genes, of which 33.5% were found nominal significant in the GTEx project. Interestingly, we found EDA2R as a strong candidate gene for lung ageing. The age*COPD interaction analysis revealed 69 genes significantly differentially expressed with age between COPD and controls.ConclusionsOur study indicates that processes related to lung development, cell-cell contacts, calcium signalling and immune responses are involved in lung ageing in general. Pathways related to extracellular matrix, mammalian target of rapamycin signalling, splicing of introns and exons and the ribosome complex are proposed to be involved in abnormal lung ageing in COPD.

scholarly journals Identification of Potential Biomarkers for Thyroid Cancer Using Bioinformatics Strategy: A Study Based on GEO Datasets

2020 ◽  
Vol 2020 ◽  
pp. 1-21 ◽  
Author(s):  
Yujie Shen ◽  
Shikun Dong ◽  
Jinhui Liu ◽  
Liqing Zhang ◽  
Jiacheng Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Thyroid Cancer ◽  
Small Molecules ◽  
Signaling Pathway ◽  
Pathway Analysis ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Receptor Interaction ◽  
Tissue Samples ◽  
Key Genes

Background. The molecular mechanisms and genetic markers of thyroid cancer are unclear. In this study, we used bioinformatics to screen for key genes and pathways associated with thyroid cancer development and to reveal its potential molecular mechanisms. Methods. The GSE3467, GSE3678, GSE33630, and GSE53157 expression profiles downloaded from the Gene Expression Omnibus database (GEO) contained a total of 164 tissue samples (64 normal thyroid tissue samples and 100 thyroid cancer samples). The four datasets were integrated and analyzed by the RobustRankAggreg (RRA) method to obtain differentially expressed genes (DEGs). Using these DEGs, we performed gene ontology (GO) functional annotation, pathway analysis, protein-protein interaction (PPI) analysis and survival analysis. Then, CMap was used to identify the candidate small molecules that might reverse thyroid cancer gene expression. Results. By integrating the four datasets, 330 DEGs, including 154 upregulated and 176 downregulated genes, were identified. GO analysis showed that the upregulated genes were mainly involved in extracellular region, extracellular exosome, and heparin binding. The downregulated genes were mainly concentrated in thyroid hormone generation and proteinaceous extracellular matrix. Pathway analysis showed that the upregulated DEGs were mainly attached to ECM-receptor interaction, p53 signaling pathway, and TGF-beta signaling pathway. Downregulation of DEGs was mainly involved in tyrosine metabolism, mineral absorption, and thyroxine biosynthesis. Among the top 30 hub genes obtained in PPI network, the expression levels of FN1, NMU, CHRDL1, GNAI1, ITGA2, GNA14 and AVPR1A were associated with the prognosis of thyroid cancer. Finally, four small molecules that could reverse the gene expression induced by thyroid cancer, namely ikarugamycin, adrenosterone, hexamethonium bromide and clofazimine, were obtained in the CMap database. Conclusion. The identification of the key genes and pathways enhances the understanding of the molecular mechanisms for thyroid cancer. In addition, these key genes may be potential therapeutic targets and biomarkers for the treatment of thyroid cancer.

Nanoparticle-plasma Membrane Interactions: Thermodynamics, Toxicity and Cellular Response

2020 ◽  
Vol 27 (20) ◽  
pp. 3330-3345
Author(s):  
Ana G. Rodríguez-Hernández ◽  
Rafael Vazquez-Duhalt ◽  
Alejandro Huerta-Saquero
Keyword(s):  
Gene Expression ◽  
Immune Responses ◽  
Cellular Response ◽  
Cellular Level ◽  
Membrane Interactions ◽  
Daily Lives ◽  
Cellular Physiology ◽  
Associated Proteins ◽  
First Contact ◽  
Insight Into

Nanomaterials have become part of our daily lives, particularly nanoparticles contained in food, water, cosmetics, additives and textiles. Nanoparticles interact with organisms at the cellular level. The cell membrane is the first protective barrier against the potential toxic effect of nanoparticles. This first contact, including the interaction between the cell membranes -and associated proteins- and the nanoparticles is critically reviewed here. Nanoparticles, depending on their toxicity, can cause cellular physiology alterations, such as a disruption in cell signaling or changes in gene expression and they can trigger immune responses and even apoptosis. Additionally, the fundamental thermodynamics behind the nanoparticle-membrane and nanoparticle-proteins-membrane interactions are discussed. The analysis is intended to increase our insight into the mechanisms involved in these interactions. Finally, consequences are reviewed and discussed.

scholarly journals Gene Expression and Carcass Traits Are Different between Different Quality Grade Groups in Red-Faced Hereford Steers

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1910
Author(s):  
Bailey Engle ◽  
Molly Masters ◽  
Jane Ann Boles ◽  
Jennifer Thomson
Keyword(s):  
Gene Expression ◽  
Transcriptome Profiling ◽  
Fat Deposition ◽  
Lower Shear ◽  
The Us ◽  
Quality Grade ◽  
Longissimus Lumborum ◽  
Muscle Biochemistry ◽  
Marbling Deposition ◽  
Insight Into

Fat deposition is important to carcass value and some palatability characteristics. Carcasses with higher USDA quality grades produce more value for producers and processors in the US system and are more likely to have greater eating satisfaction. Using genomics to identify genes impacting marbling deposition provides insight into muscle biochemistry that may lead to ways to better predict fat deposition, especially marbling and thus quality grade. Hereford steers (16) were managed the same from birth through harvest after 270 days on feed. Samples were obtained for tenderness and transcriptome profiling. As expected, steaks from Choice carcasses had a lower shear force value than steaks from Select carcasses; however, steaks from Standard carcasses were not different from steaks from Choice carcasses. A significant number of differentially expressed (DE) genes was observed in the longissimus lumborum between Choice and Standard carcass RNA pools (1257 genes, p < 0.05), but not many DE genes were observed between Choice and Select RNA pools. Exploratory analysis of global muscle tissue transcriptome from Standard and Choice carcasses provided insight into muscle biochemistry, specifically the upregulation of extracellular matrix development and focal adhesion pathways and the downregulation of RNA processing and metabolism in Choice versus Standard. Additional research is needed to explore the function and timing of gene expression changes.

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