scholarly journals Bacillus subtilis Attenuates Hepatic and Intestinal Injuries and Modulates Gut Microbiota and Gene Expression Profiles in Mice Infected with Schistosoma japonicum

2021 ◽  
Vol 9 ◽  
Author(s):  
Datao Lin ◽  
Qiuyue Song ◽  
Yishu Zhang ◽  
Jiahua Liu ◽  
Fang Chen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Cell Differentiation ◽  
Gut Microbiota ◽  
Signaling Pathway ◽  
Schistosoma Japonicum ◽  
Expression Profiles ◽  
Parasitic Infection ◽  
Differentially Expressed ◽  
Rrna Gene

Parasitic infection can induce pathological injuries and impact the gut microbiota diversity and composition of the host. Bacillus subtilis is a nonpathogenic and noninvasive probiotic bacterium for humans and other animals, playing an important role in improving the host immune system’s ability to respond to intestinal and liver diseases and modulating gut microbiota. However, whether B. subtilis can impact biological functions in Schistosoma japonicum–infected mice is unclear. This study used oral administration (OA) of B. subtilis to treat mice infected with S. japonicum. We evaluated changes in the gut microbiota of infected mice using 16 S rRNA gene sequencing and differentially expressed gene profiles using transcriptome sequencing after OA B. subtilis. We found that OA B. subtilis significantly attenuated hepatic and intestinal pathological injuries in infected mice. The gut microbiota of mice were significantly altered after S. japonicum infection, while OA B. subtilis remodel the diversity and composition of gut microbiomes of infected mice. We found that the S. japonicum–infected mice with OA B. subtilis had an overabundance of the most prevalent bacterial genera, including Bacteroides, Enterococcus, Lactobacillus, Blautia, Lachnoclostridium, Ruminiclostridium, and Enterobacter. Transcriptomic analysis of intestinal tissues revealed that OA B. subtilis shaped the intestinal microenvironment of the host responding to S. japonicum infection. Differentially expressed genes were classified into KEGG pathways between S. japonicum–infected mice and those without included cell adhesion molecules, intestinal immune network for IgA production, hematopoietic cell lineage, Fc epsilon RI signaling pathway, Th1 and Th2 cell differentiation, Th17 cell differentiation, calcium signaling pathway, Fc gamma R-mediated phagocytosis, chemokine signaling pathway, phospholipase D signaling pathway, NF-kappa B signaling pathway, B cell receptor signaling pathway, pancreatic secretion, and phagosome. In conclusion, our findings showed that OA B. subtilis alleviates pathological injuries and regulates gene expression, implying that B. subtilis supplementation may be a potential therapeutic strategy for schistosomiasis. Our study may highlight the value of probiotics as a beneficial supplementary therapy during human schistosomiasis, but further studies are needed.

The MDS-Associated Gene DLK Modulates Gene Expression in Human Myeloid Cells by Altering the Activity of Multiple Transcription Factors.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3428-3428
Author(s):  
Liang Li ◽  
Rushabh Modi ◽  
Xiwei Wu ◽  
Stephen J. Forman ◽  
Ravi Bhatia
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Cell Differentiation ◽  
Linear Model ◽  
Expression Profiles ◽  
Myeloid Cells ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Differentiation And Proliferation ◽  
And Control

Abstract Delta-Like 1 (DLK) is an EGF-like transmembrane protein, which is overexpressed in myelodysplastic syndrome (MDS) CD34+ cells. We have previously shown that ectopic DLK expression inhibits HL-60 cell differentiation and proliferation through intracellular domain interactions. To further investigate mechanisms underlying DLK effects on myeloid cell differentiation and proliferation, we compared gene expression profiles of DLK expressing and control HL-60 cells, with or without differentiating induction with ATRA, using Affymetrix HG-U133A arrays. Gene expression data was analyzed using affy and limma (linear model of microarray analysis) packages in the open-source BioConductor project (v 1.6). Raw data were processed using robust multi-chip average (RMA) algorithm, a linear model fit to each gene, and the following comparisons were made: (a) effects of DLK expression in unstimulated cells, (b) effects of DLK expression in ATRA exposed cells, (c) effects of ATRA induction on R1 cells, (d) effects of ATRA induction on DLK+ cells, and (e) differences in the response of DLK+ vs. control cells to ATRA. Adjusted P values and log odds of differential expression (B statistic, 50% probability when B=0) were calculated. B values > 0 were considered statistically significant. 523 genes were differentially expressed between unstimulated control and DLK+ cells, 343 genes were differentially expressed between control and DLK+ cells after ATRA stimulation, and 204 genes were common to the two sets. 802 genes were differentially expressed after ATRA stimulation in control cells, 742 genes in DLK+ cells, with 550 genes common to the two sets. 13 genes were differentially expressed when ATRA responses of control and DLK+ cells were compared. Gene ontology (GO) analyses indicated that "Biological processes" significantly affected by DLK overexpression included signal transduction, cell cycle, proliferation, cell death, protein metabolism and enzyme cascades, and "Molecular functions" most affected included nucleotide/DNA binding and protein kinase activity. These observations are consistent with observed cellular effects of DLK. Using MotifRegressor software, we performed promoter analysis correlating common transcription factor-binding motifs with expression profiles of genes differentially expressed between DLK+ and control cells. We identified the transcription factors (TF) PBX, GATA-1, c-Myc: Max, HIF-1, DEC1, Hand1, Lmo2, NKX25, GKLF and AP-1 as being potentially involved in DLK-mediated changes in gene expression. The observed patterns of differential gene expression were consistent with altered activities of these TF. Electrophoresis mobility shift assays (EMSA) indicated increased PBX and reduced HIF-1 and GATA-1 activities in DLK+ cells. Interestingly, Hand1, c-Myc: Max and Dec1 are basic Helix-loop-Helix (b-HLH) factors with E box binding sites, which are known to associate and form regulatory complexes with other TF. TF such as GATA-1, GLKF and Lmo2, also identified in our analysis, are known to be associated with such complexes. In conclusion, gene expression profiles of DLK expressing human myeloid cells are consistent with observed alterations in cell proliferation and differentiation. We have identified TF that may act individually and/or in concert to induce the observed changes in gene expression in DLK+ cells. Further evaluation of their role of these TF in mediating DLK effects and in abnormal hematopoietic cell growth in MDS is warranted.

Identification of DMSA-Coated Fe3O4 Nanoparticles Induced-Apoptosis Response Genes in Human Monocytes by cDNA Microarrays

2013 ◽  
Vol 749 ◽  
pp. 377-383 ◽  
Author(s):  
Ying Xun Liu ◽  
Jian Yuan Huang ◽  
Dong Liang Wang ◽  
Jin Ke Wang
Keyword(s):  
Gene Expression ◽  
Signaling Pathway ◽  
Cell Apoptosis ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Dependent Manner ◽  
Receptor Signaling ◽  
Apoptosis Pathway ◽  
Receptor Signaling Pathway

This study investigated the cell apoptosis and gene expression profiles of human THP-1 monocytes in order to identify the molecular mechanism of cell apoptosis induced by meso-2,-3-dimercaptosuccinnic acid-coated Fe3O4magnetic nanoparticles. Cell apoptosis was visualized with flow cytometry after treated by 50 and 100 μg/ml Fe3O4nanoparticles, and the gene expression profiles were detected with Affymetrix Human Genome U133 Plus 2.0 GeneChips® microarrays. The transmission electron microscopy obserbation revealed that THP-1 cells were effectively labeled by the Fe3O4nanoparticles. The internalized Fe3O4nanoparticles increased cell apoptosis in a dose-dependent manner, but not decreased cell viability significantly. The cDNA microarray results showed that hundreds of genes were significantly regulated at the concentration of 50 and 100 μg/ml, and the level of these genes exhibited a dose response, includingCD14,CD86,CFLAR,IL-1,NFKBIA,NLRC4,NAIPandAIP3. The Fe3O4nanoparticles treatments resulted in significantly altered in Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, and Cell apoptosis signaling pathway. Gene ontology analysis of these differentially expressed genes demonstrated that mainly up-regulated genes were related to cytokine production and cell apoptosis. These results showed that the Fe3O4nanoparticles induced THP-1 cells apoptosis and the level of lots of genes involved in extrinsic apoptosis pathway differentially expressed, which further revealed demonstrated the relation between Fe3O4MNPs treatment and cell apoptosis.

scholarly journals Potential genes and pathways associated with heterotopic ossification derived from analyses of gene expression profiles

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Zhanyu Yang ◽  
Delong Liu ◽  
Rui Guan ◽  
Xin Li ◽  
Yiwei Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Kinase ◽  
Heterotopic Ossification ◽  
Signaling Pathway ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Heterotopic Bone ◽  
Hub Genes ◽  
Ppi Networks

Abstract Background Heterotopic ossification (HO) represents pathological lesions that refer to the development of heterotopic bone in extraskeletal tissues around joints. This study investigates the genetic characteristics of bone marrow mesenchymal stem cells (BMSCs) from HO tissues and explores the potential pathways involved in this ailment. Methods Gene expression profiles (GSE94683) were obtained from the Gene Expression Omnibus (GEO), including 9 normal specimens and 7 HO specimens, and differentially expressed genes (DEGs) were identified. Then, protein–protein interaction (PPI) networks and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed for further analysis. Results In total, 275 DEGs were differentially expressed, of which 153 were upregulated and 122 were downregulated. In the biological process (BP) category, the majority of DEGs, including EFNB3, UNC5C, TMEFF2, PTH2, KIT, FGF13, and WISP3, were intensively enriched in aspects of cell signal transmission, including axon guidance, negative regulation of cell migration, peptidyl-tyrosine phosphorylation, and cell-cell signaling. Moreover, KEGG analysis indicated that the majority of DEGs, including EFNB3, UNC5C, FGF13, MAPK10, DDIT3, KIT, COL4A4, and DKK2, were primarily involved in the mitogen-activated protein kinase (MAPK) signaling pathway, Ras signaling pathway, phosphatidylinositol-3-kinase/protein kinase B (PI3K/Akt) signaling pathway, and Wnt signaling pathway. Ten hub genes were identified, including CX3CL1, CXCL1, ADAMTS3, ADAMTS16, ADAMTSL2, ADAMTSL3, ADAMTSL5, PENK, GPR18, and CALB2. Conclusions This study presented novel insight into the pathogenesis of HO. Ten hub genes and most of the DEGs intensively involved in enrichment analyses may be new candidate targets for the prevention and treatment of HO in the future.

Global Gene Expression Revealed a Set of Genes Involved in the Modification of Cells during Erythropoiesis.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 4074-4074
Author(s):  
Anderson F. Cunha ◽  
Ana F. Brugnerotto ◽  
Adriana S.S. Duarte ◽  
Gustavo G.L. Costa ◽  
Sara T.O. Saad ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Differentiation ◽  
Blood Cell ◽  
Red Blood Cell ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Erythroid Differentiation ◽  
Global Gene Expression ◽  
Differentially Expressed ◽  
Globin Genes

Abstract Erythroid differentiation is a dynamic and complex process in which a pluripotent stem cell undergoes a series of developmental changes that commit it to a specific lineage. These alterations involve changes in gene expression profiles. Extensive studies have led to a considerable understanding of the cellular and molecular control of hemoglobin production during red blood cell differentiation, however, a complete understanding of human erythropoiesis will require a robust description of the entire transcriptome of these cells during differentiation. From a global point of view of cell metabolic regulation, where genomic information could be complemented with gene expression, the use of methods that enable quantification of the entire transcriptome of the red blood cell during differentiation is of great importance. In this study, the gene expression profiles during differentiation of Human erythroid cells of a normal blood donor in a two-phase liquid culture (Fibach & Rachmilewitz, 1993) were evaluated using Serial analysis of gene expression (SAGE). Global gene expression was evaluated in cells collected immediately before the addition of erythropoeitin (0 hour) and 192 and 336 hours after the addition of this hormone. We generated a total of 30512 tags at 0h, 30117 tags at 192h and 30189 tags at 336h, representing 12026, 11709 and 11337 unique tags, respectively. In the 0h library, a high expression of ferritin genes and CD74 antigen gene was observed. As expected, the expression of globin genes started during intermediate stages of differentiation (predominantly basophilic erythroblasts) and were the most expressed genes at the end of the culture (predominantly orthocromatic erythroblasts). Ribosomal genes were the most expressed genes at 192 hours, indicating an increase in protein synthesis. To identify the genes that were differentially expressed between the libraries, a P value < 0.01 and fold ≥ 5 were considered as statistically significant. In the comparison of the 0h and 192h libraries, 179 differentially expressed transcripts were identified. From these genes, in addition to the globin genes, we found an up-regulation of several genes related to protein binding (LXN, GSTM3, and TRIP6), transcription factor (GATA-1), hydrolase activity (TPSAB1), ion transport (SLC12A9) and regulation of apoptosis (PRDX2). Comparing the 192h and 336h libraries, 103 differentially expressed transcripts were identified. The up-regulated genes were generally related to hemoglobin synthesis, such as ALAS2, involved in the biosynthesis of the heme group or related to intracellular transport such as MSCP and NUDT4 and cell differentiation such as GDF15. The transcription of some of these genes, such as SLC12A9, TRB3, EYA3 and TWIST2 are described for the first time during erythroid differentiation. The results indicated that the global aspects of the transcriptome were similar during differentiation for the majority of the genes and that probably a relative small set of genes is involved in the modification of erythroid cells during differentiation. The results of this study amplify the previous published data (Komor et al, 2005) and may contribute to the comprehension of erythroid differentiation and identification of new target genes involved in some erythroid diseases.

Potential Genes and Pathways Associated with Heterotopic Ossification, Derived from Analyses of Gene Expression Profiles

2021 ◽  
Author(s):  
Zhanyu Yang ◽  
Delong Liu ◽  
Rui Guan ◽  
Xin Li ◽  
Yiwei Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Kinase ◽  
Heterotopic Ossification ◽  
Signaling Pathway ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Heterotopic Bone ◽  
Hub Genes ◽  
Ppi Networks

Abstract Background: Heterotopic ossification (HO) represents pathological lesions, referred to the development of heterotopic bone in extraskeletal tissues around joints. This study will investigate the genetic characteristics of bone marrow mesenchymal stem cells (BMSCs) from HO tissues and explore the potential pathways involved. Methods: The gene expression profiles (GSE94683) was obtained from the Gene Expression Omnibus (GEO), including 9 normal specimens and 7 HO specimens, and differentially expressed genes (DEGs) were identified. Then, the protein‑protein interaction (PPI) networks, Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analysis were performed for further analysis. Results: Totally 275 DEGs were differentially expressed, of which 153 were upregulated and 122 were downregulated. In the biological process (BP), the majority of DEGs, including EFNB3, UNC5C, TMEFF2, PTH2, KIT, FGF13 and WISP3, were intensively enriched in cell signal transmission items, including axon guidance, negative regulation of cell migration, peptidyl-tyrosine phosphorylation and cell-cell signaling. Moreover, KEGG analysis indicated that the majority of DEGs, including EFNB3, UNC5C, FGF13, MAPK10, DDIT3, KIT, COL4A4 and DKK2, primarily involved in mitogen-activated protein kinase (MAPK) signaling pathway, Ras signaling pathway, phosphatidylinositol-3-kinase/protein kinase B (PI3K/Akt) signaling pathway and Wnt signaling pathway. 10 hub genes were identified, including CX3CL1, CXCL1, ADAMTS3, ADAMTS16, ADAMTSL2, ADAMTSL3, ADAMTSL5, PENK, GPR18, CALB2.Conclusions: This study presents a novel insight into the pathogenesis of HO. 10 hub genes and most of the DEGs intensively involved in enrichment analyses may be the new candidate targets for the prevention and treatment of HO in the future.

scholarly journals Comprehensive Comparison of Amnion Stromal Cells and Chorion Stromal Cells by RNA-Seq

2021 ◽  
Vol 22 (4) ◽  
pp. 1901
Author(s):  
Brielle Jones ◽  
Chaoyang Li ◽  
Min Sung Park ◽  
Anne Lerch ◽  
Vimal Jacob ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stromal Cells ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Principal Component ◽  
Differentially Expressed ◽  
Inflammatory Factor ◽  
Next Generation Sequencing Technology ◽  
Angiogenic Potential ◽  
Anti Inflammatory

Mesenchymal stromal cells derived from the fetal placenta, composed of an amnion membrane, chorion membrane, and umbilical cord, have emerged as promising sources for regenerative medicine. Here, we used next-generation sequencing technology to comprehensively compare amniotic stromal cells (ASCs) with chorionic stromal cells (CSCs) at the molecular and signaling levels. Principal component analysis showed a clear dichotomy of gene expression profiles between ASCs and CSCs. Unsupervised hierarchical clustering confirmed that the biological repeats of ASCs and CSCs were able to respectively group together. Supervised analysis identified differentially expressed genes, such as LMO3, HOXA11, and HOXA13, and differentially expressed isoforms, such as CXCL6 and HGF. Gene Ontology (GO) analysis showed that the GO terms of the extracellular matrix, angiogenesis, and cell adhesion were significantly enriched in CSCs. We further explored the factors associated with inflammation and angiogenesis using a multiplex assay. In comparison with ASCs, CSCs secreted higher levels of angiogenic factors, including angiogenin, VEGFA, HGF, and bFGF. The results of a tube formation assay proved that CSCs exhibited a strong angiogenic function. However, ASCs secreted two-fold more of an anti-inflammatory factor, TSG-6, than CSCs. In conclusion, our study demonstrated the differential gene expression patterns between ASCs and CSCs. CSCs have superior angiogenic potential, whereas ASCs exhibit increased anti-inflammatory properties.

4 Molecularly guided multiplexed digital spatial analysis reveals differential gene expression profiles in the WNT-β-catenin pathway between melanoma and prostate tumors

2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A4-A4
Author(s):  
Anushka Dikshit ◽  
Dan Zollinger ◽  
Karen Nguyen ◽  
Jill McKay-Fleisch ◽  
Kit Fuhrman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Single Molecule ◽  
Spatial Information ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Fluorescence Assay ◽  
Differentially Expressed ◽  
Tumor Type ◽  
Prostate Tumors

BackgroundThe canonical WNT-β-catenin signaling pathway is vital for development and tissue homeostasis but becomes strongly tumorigenic when dysregulated. and alter the transcriptional signature of a cell to promote malignant transformation. However, thorough characterization of these transcriptomic signatures has been challenging because traditional methods lack either spatial information, multiplexing, or sensitivity/specificity. To overcome these challenges, we developed a novel workflow combining the single molecule and single cell visualization capabilities of the RNAscope in situ hybridization (ISH) assay with the highly multiplexed spatial profiling capabilities of the GeoMx™ Digital Spatial Profiler (DSP) RNA assays. Using these methods, we sought to spatially profile and compare gene expression signatures of tumor niches with high and low CTNNB1 expression.MethodsAfter screening 120 tumor cores from multiple tumors for CTNNB1 expression by the RNAscope assay, we identified melanoma as the tumor type with the highest CTNNB1 expression while prostate tumors had the lowest expression. Using the RNAscope Multiplex Fluorescence assay we selected regions of high CTNNB1 expression within 3 melanoma tumors as well as regions with low CTNNB1 expression within 3 prostate tumors. These selected regions of interest (ROIs) were then transcriptionally profiled using the GeoMx DSP RNA assay for a set of 78 genes relevant in immuno-oncology. Target genes that were differentially expressed were further visualized and spatially assessed using the RNAscope Multiplex Fluorescence assay to confirm GeoMx DSP data with single cell resolution.ResultsThe GeoMx DSP analysis comparing the melanoma and prostate tumors revealed that they had significantly different gene expression profiles and many of these genes showed concordance with CTNNB1 expression. Furthermore, immunoregulatory targets such as ICOSLG, CTLA4, PDCD1 and ARG1, also demonstrated significant correlation with CTNNB1 expression. On validating selected targets using the RNAscope assay, we could distinctly visualize that they were not only highly expressed in melanoma compared to the prostate tumor, but their expression levels changed proportionally to that of CTNNB1 within the same tumors suggesting that these differentially expressed genes may be regulated by the WNT-β-catenin pathway.ConclusionsIn summary, by combining the RNAscope ISH assay and the GeoMx DSP RNA assay into one joint workflow we transcriptionally profiled regions of high and low CTNNB1 expression within melanoma and prostate tumors and identified genes potentially regulated by the WNT- β-catenin pathway. This novel workflow can be fully automated and is well suited for interrogating the tumor and stroma and their interactions.GeoMx Assays are for RESEARCH ONLY, not for diagnostics.

scholarly journals Microarray analysis identification of key pathways and interaction network of differential gene expressions during osteogenic differentiation

2020 ◽  
Vol 14 (1) ◽  
Author(s):  
Fatemeh Khodabandehloo ◽  
Sara Taleahmad ◽  
Reza Aflatoonian ◽  
Farzad Rajaei ◽  
Zahra Zandieh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Signaling Pathway ◽  
Expression Profiles ◽  
Wnt Signaling Pathway ◽  
Hub Genes ◽  
Gene Expressions ◽  
Cell Based Therapy ◽  
Wnt Pathways ◽  
Key Pathways

Abstract Background Adult bone marrow-derived mesenchymal stem cells (BM-MSCs) are multipotent stem cells that can differentiate into three lineages. They are suitable sources for cell-based therapy and regenerative medicine applications. This study aims to evaluate the hub genes and key pathways of differentially expressed genes (DEGs) related to osteogenesis by bioinformatics analysis in three different days. The DEGs were derived from the three different days compared with day 0. Results Gene expression profiles of GSE37558 were obtained from the Gene Expression Omnibus (GEO) database. A total of 4076 DEGs were acquired on days 8, 12, and 25. Gene ontology (GO) enrichment analysis showed that the non-canonical Wnt signaling pathway and lipopolysaccharide (LPS)-mediated signaling pathway were commonly upregulated DEGs for all 3 days. KEGG pathway analysis indicated that the PI3K-Akt and focal adhesion were also commonly upregulated DEGs for all 3 days. Ten hub genes were identified by CytoHubba on days 8, 12, and 25. Then, we focused on the association of these hub genes with the Wnt pathways that had been enriched from the protein-protein interaction (PPI) by the Cytoscape plugin MCODE. Conclusions These findings suggested further insights into the roles of the PI3K/AKT and Wnt pathways and their association with osteogenesis. In addition, the stem cell microenvironment via growth factors, extracellular matrix (ECM), IGF1, IGF2, LPS, and Wnt most likely affect osteogenesis by PI3K/AKT.

scholarly journals HIV-1 Infection Transcriptomics: Meta-Analysis of CD4+ T Cells Gene Expression Profiles

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 244 ◽  
Author(s):  
Antonio Victor Campos Coelho ◽  
Rossella Gratton ◽  
João Paulo Britto de Melo ◽  
José Leandro Andrade-Santos ◽  
Rafael Lima Guimarães ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Differentially Expressed Genes ◽  
Cd4 T Cells ◽  
Expression Profiles ◽  
Meta Analysis ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Infected Cells ◽  
Hiv 1

HIV-1 infection elicits a complex dynamic of the expression various host genes. High throughput sequencing added an expressive amount of information regarding HIV-1 infections and pathogenesis. RNA sequencing (RNA-Seq) is currently the tool of choice to investigate gene expression in a several range of experimental setting. This study aims at performing a meta-analysis of RNA-Seq expression profiles in samples of HIV-1 infected CD4+ T cells compared to uninfected cells to assess consistently differentially expressed genes in the context of HIV-1 infection. We selected two studies (22 samples: 15 experimentally infected and 7 mock-infected). We found 208 differentially expressed genes in infected cells when compared to uninfected/mock-infected cells. This result had moderate overlap when compared to previous studies of HIV-1 infection transcriptomics, but we identified 64 genes already known to interact with HIV-1 according to the HIV-1 Human Interaction Database. A gene ontology (GO) analysis revealed enrichment of several pathways involved in immune response, cell adhesion, cell migration, inflammation, apoptosis, Wnt, Notch and ERK/MAPK signaling.

Regional variations in ABC transporter expression along the mouse intestinal tract

2004 ◽  
Vol 17 (1) ◽  
pp. 11-20 ◽  
Author(s):  
David M. Mutch ◽  
Pascale Anderle ◽  
Muriel Fiaux ◽  
Robert Mansourian ◽  
Karine Vidal ◽  
...  
Keyword(s):  
Gene Expression ◽  
Abc Transporter ◽  
Expression Profile ◽  
Abc Transporters ◽  
Intestinal Tract ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Assessment Model ◽  
Differentially Expressed ◽  
Distal Intestine

The ATP-binding cassette (ABC) family of proteins comprise a group of membrane transporters involved in the transport of a wide variety of compounds, such as xenobiotics, vitamins, lipids, amino acids, and carbohydrates. Determining their regional expression patterns along the intestinal tract will further characterize their transport functions in the gut. The mRNA expression levels of murine ABC transporters in the duodenum, jejunum, ileum, and colon were examined using the Affymetrix MuU74v2 GeneChip set. Eight ABC transporters (Abcb2, Abcb3, Abcb9, Abcc3, Abcc6, Abcd1, Abcg5, and Abcg8) displayed significant differential gene expression along the intestinal tract, as determined by two statistical models (a global error assessment model and a classic ANOVA, both with a P < 0.01). Concordance with semiquantitative real-time PCR was high. Analyzing the promoters of the differentially expressed ABC transporters did not identify common transcriptional motifs between family members or with other genes; however, the expression profile for Abcb9 was highly correlated with fibulin-1, and both genes share a common complex promoter model involving the NFκB, zinc binding protein factor (ZBPF), GC-box factors SP1/GC (SP1F), and early growth response factor (EGRF) transcription binding motifs. The cellular location of another of the differentially expressed ABC transporters, Abcc3, was examined by immunohistochemistry. Staining revealed that the protein is consistently expressed in the basolateral compartment of enterocytes along the anterior-posterior axis of the intestine. Furthermore, the intensity of the staining pattern is concordant with the expression profile. This agrees with previous findings in which the mRNA, protein, and transport function of Abcc3 were increased in the rat distal intestine. These data reveal regional differences in gene expression profiles along the intestinal tract and demonstrate that a complete understanding of intestinal ABC transporter function can only be achieved by examining the physiologically distinct regions of the gut.

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