Developing gene signature against Mycobacterium bovis infection in Cattle
Ontology highlight
ABSTRACT:
ORGANISM(S): Bubalus bubalis
SUBMITTER: SANJEEV SHUKLA
PROVIDER: E-GEOD-74050 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Background: Mycobacterium avium subspecies paratuberculosis (MPTb) is the causative agent of Johne’s disease, an intestinal disease of ruminants with major economic consequences. MPTb bacilli are phagocytosed by host macrophages upon exposure where they persist, resulting in lengthy subclinical phases of infection that can lead to immunopathology and disease dissemination. Consequently, analysis of the macrophage transcriptome in response to MPTb infection can provide valuable insights into the molecular mechanisms that underlie Johne’s disease. Here, we investigate pan-genomic gene expression in bovine monocyte-derived macrophages (MDM) purified from seven age-matched non-related females, in response to in vitro infection with MPTb (multiplicity of infection 2:1) at intervals of 2 hours, 6 hours and 24 hours post-infection. Results: Differentially expressed genes were identified by comparing the transcriptomes of the infected MDM to the control MDM at each time point (adjusted P-value threshold ≤ 0.10). 1,050 differentially expressed unique genes were identified 2 hours post-infection, with 974 and 84 differentially expressed unique genes detected 6 hours and 24 hours post-infection, respectively. Furthermore, in the infected MDM the number of upregulated genes exceeded the number of downregulated genes at each time point, with the fold-change in expression for the upregulated genes markedly higher than that for the downregulated genes. Conclusions: Inspection and systems analysis of the differentially expressed genes revealed changes in the expression profiles of genes involved in the inflammatory response, cell signalling pathways and apoptosis. The transcriptional changes associated with cellular signalling and the inflammatory response may reflect different immuno-modulatory mechanisms that underlie host-pathogen interactions during infection. Affymetrix GeneChip® Bovine Genome Arrays were used to examine gene expression of bovine monocyte-derived macrophages (MDM) after in vitro challenge with Mycobacterium avium subspecies paratuberculosis across a time series of 2 hr, 6 hr and 24 hr post-challenge. A 0 hr control treatment was also generated and seven different age-matched female Holstein-Friesian cattle were used for each time-point/treatment combination for a total of 49 microarrays, one of which was excluded from analysis since it did not pass quality control.
2012-01-31 | E-GEOD-35185 | biostudies-arrayexpress
Project description:Mycobacterium bovis is an intracellular pathogen that causes tuberculosis in cattle. Following infection, the pathogen resides and persists inside host macrophages by subverting host immune responses via a diverse range of mechanisms. Here, a high-density bovine microarray platform was used to examine the bovine monocyte-derived macrophage transcriptome response to M. bovis infection relative to infection with the attenuated vaccine strain, M. bovis Bacille CalmetteM-bM-^@M-^SGuM-CM-)rin. Differentially expressed genes were identified (adjusted P-value M-bM-^IM-$ 0.01) and interaction networks generated across an infection time course of 2, 6 and 24 h. The largest number of biological interactions was observed in the 24 h network, which exhibited small-worldscale-free network properties. The 24 h network featured a small number of key hub and bottleneck gene nodes, including IKBKE, MYC, NFKB1 and EGR1 that differentiated the macrophage response to virulent and attenuated M. bovis strains, possibly via the modulation of host cell death mechanisms. These hub and bottleneck genes represent possible targets for immunomodulation of host macrophages by virulent mycobacterial species that enable their survival within a hostile environment. Affymetrix GeneChipM-BM-. Bovine Genome Arrays were used to examine gene expression from a paired comparison of bovine monocyte-derived macrophages (MDM) after in vitro challenge with Mycobacterium bovis versus M. bovis BCG across a time series of 2 hr, 6 hr and 24 hr post-challenge.
2014-08-01 | E-GEOD-59774 | biostudies-arrayexpress
Project description:Background: Mycobacterium bovis, the causative agent of bovine tuberculosis, is a major cause of mortality in global cattle populations. Macrophages are among the first cells types to encounter M. bovis following exposure and the response elicited by these cells is pivotal in determining the outcome of infection. Here, a functional genomics approach was undertaken to investigate global gene expression profiles in bovine monocyte-derived macrophages (MDM) purified from seven age-matched non-related females, in response to in vitro challenge with M. bovis (multiplicity of infection 2:1). Total cellular RNA was extracted from non-challenged control and M. bovis-challenged MDM for all animals at intervals of 2 hours, 6 hours and 24 hours post-challenge and prepared for global gene expression analysis using the Affymetrix® GeneChip® Bovine Genome Array. Results: Comparison of M. bovis-challenged MDM gene expression profiles with the non-challenged MDM controls at each time point identified 3,529 differentially expressed genes after 2 hours post-challenge, with 5,211 and 6,150 differentially expressed genes detected at the 6 hour and 24 hour time points, respectively (adjusted P-value threshold ≤ 0.05). Notably, the number of downregulated genes exceeded the number of upregulated genes in the M. bovis-challenged MDM across all time points; however, the fold-change in expression for the upregulated genes was markedly larger than that for the downregulated genes. Systems analysis revealed enrichment for genes involved in: (1) the inflammatory response; (2) cell signalling pathways, including Toll-like receptors and intracellular pathogen recognition receptors (PRRs)-receptors; and (3) apoptosis. Conclusions: The increased number of downregulated genes is consistent with previous studies showing that M. bovis infection is associated with the repression of host gene expression. The results also support important roles for MYD88-independent signalling and intracellular PRRs in mediating the host response to M. bovis, which to our knowledge have not been reported previously. Affymetrix GeneChip® Bovine Genome Arrays were used to examine gene expression of bovine monocyte-derived macrophages (MDM) after in vitro challenge with Mycobacterium bovis across a time series of 2 hr, 6 hr and 24 hr post-challenge. A 0 hr control treatment was also generated and seven different age-matched female Holstein-Friesian cattle were used for each time-point/treatment combination for a total of 49 microarrays.
2011-12-31 | E-GEOD-33309 | biostudies-arrayexpress
Project description:Whole genome expression of bone marrow deived hepatocytes after 1 and 5 months of transplantation are compared with that of primary hepatocytes and Lin- BM cells Agilent one-color experiment,Organism:Mouse, Agilent Whole Genome Mouse 8x60k (AMADID: 028005 & 026986) , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)
2016-07-01 | E-GEOD-73543 | biostudies-arrayexpress
Project description:The aim of the study was to determine biological relevance of differentially expressed genes in Lactobacillus plantarum C2 during fermentation of plant substrates. Whole-transcriptome analysis based on customized microarray profiles has been used to determine altered transcription patterns in L. plantarum C2. L. plantarum C2 was grown (24 h at 30°C) and stored ( 21 days at 4°C) in carrot or pineapple juices to mimic the chemical composition of the respective raw matrices. De Man, Rogosa and Sharpe broth was used as the control medium for optimal growth. Samples were analyzed at the late exponential phase of growth and after storage
2015-04-24 | E-GEOD-68188 | biostudies-arrayexpress
Project description:Transcriptional profiling of Candida cells comparing the control vs Ses treated cells Organism : Candida albicans, Agilent custom C.albicans Gene Expression 8x15k Array (AMADID: 026377) designed by Genotypic Technology Private Limited
2016-07-18 | E-GEOD-83080 | biostudies-arrayexpress
Project description:BACKGROUND: This study was conducted to analyse M. leprae gene expression profiles in biopsy of leprosy patient and in environmental soil samples. Investigation was carried out to find out the expression profile for the minimal gene set necessary for growth of environmental M. leprae and its genes potentially require for infection and pathogenesis of leprosy. METHOD: RNA was extracted from human biopsy and environmental soil samples and total RNA obtained by subtractive hybridization of rRNA, was reverse transcribed and amplified using random primers. The whole genome was tiled at 10bp to obtain probes having 60 mer oligonucleotides in sense orientation. 179963 probes were designed in both sense and antisense orientation. Blast was performed against the mRNA sequence databases to check the specificity of the probes. Finally, 359926 probes were designed and 56579 specific probes were replicated to fill the remaining spots. RESULTS: Up regulation of several functional genes of M. leprae genome were observed from soil samples responsible for metabolism of Carbon compounds [9], Amino acids and amines [4] , Fatty acids synthesis [21], Lipid Biosynthesis [33], Phosphorous compounds [2]. Up regulation of genes were observed from soil samples in energy metabolism function such as Glycolysis [6], Pyruvate dehydrogenase [1], TCA cycle [12], Glyoxylate bypass [12]. In up regulation of respiration function [11] genes were observed and some of genes responsible for miscellaneous oxidoreductases and oxygenases [22] function, ATP-proton motive force [4] were also observed. Up regulation of genes for cell envelope function [65], conserved membrane proteins [107], cell processes [62], central intermediary metabolism [79], polyamine synthesis[38], biosynthesis of cofactors, prosthetic groups and carriers [36], broad regulatory functions [35], macromolecule metabolism[103], degradation of macromolecules [25], miscellaneous transferases [36], conserved hypothetical [204] and unknowns [101] were observed. Significant up regulation of Virulence genes [9], PE and PPE families [3] were also observed from soil samples. CONCLUSION: Transcriptome analysis indicated that up regulation of essential genes of M. leprae transcripts in environmental samples as compared to M. leprae from human biopsy samples which strongly suggested that several M. leprae genes are expressed more in environment for its survival and may act as source of infection. RNA was extracted from human biopsy and environmental soil samples and total RNA obtained by subtractive hybridization of rRNA, was reverse transcribed and amplified using random primers. The whole genome was tiled at 10bp to obtain probes having 60 mer oligonucleotides in sense orientation. 179963 probes were designed in both sense and antisense orientation. Blast was performed against the mRNA sequence databases to check the specificity of the probes. Finally, 359926 probes were designed and 56579 specific probes were replicated to fill the remaining spots.
2016-06-01 | E-GEOD-68192 | biostudies-arrayexpress
Project description:Punch biopsies of patients enrolled in phase II clinical trial study was obtained at various time points. Skin biopsies from 16 responders and 8 non responders and partial responders, chosen after the completion of clinical trial, was evaluated before Itolizumab treatment (Day 1) and at Day 57. Responders had a PASI improvement >75% while non responders had a PASI improvement <60%. The gene expression values at Day 57 were normalised with values obtained at Day 1 of the respective patient sample. The genes with a minimum fold change of 1.8 spontaneously clustered into predominantly responders and non responders. Agilent Custom Human Gene Expression 8X15k (AMADID: 16332) designed by Genotypic Technology Private Limited .
2016-09-01 | E-GEOD-72246 | biostudies-arrayexpress
Project description:Background: MycobacteriumM-BM- bovis, the causative agent of bovine tuberculosis, is an intracellular pathogen that can persist inside host macrophages during infection via a diverse range of mechanisms that subvert the host immune response. In the current study, we have analysed and compared the transcriptomes of M.M-BM- bovis-infected monocyte-derived macrophages (MDM) purified from six Holstein-Friesian females with the transcriptomes of non-infected control MDM from the same animals over a 24 h period using strand-specific RNA sequencing (RNA-seq). In addition, we compare gene expression profiles generated using RNA-seq with those previously generated by us using the high-density AffymetrixM-BM-. GeneChipM-BM-. Bovine Genome Array platform from the same MDM-extracted RNA. Results: A mean of 7.2 million reads from each MDM sample mapped uniquely and unambiguously to single BosM-BM- taurus reference genome locations. Analysis of these mapped reads showed 2,584 genes (1,392 upregulated; 1,192 downregulated) and 757 putative natural antisense transcripts (558 upregulated; 119 downregulated) that were differentially expressed based on sense and antisense strand data, respectively (adjusted P-value M-bM-^IM-$ 0.05). Of the differentially expressed genes, 694 were common to both the sense and antisense data sets, with the direction of expression (i.e. up- or downregulation) positively correlated for 693 genes and negatively correlated for the remaining gene. Gene ontology analysis of the differentially expressed genes revealed an enrichment of immune, apoptotic and cell signalling genes. Notably, the number of differentially expressed genes identified from RNA-seq sense strand analysis was greater than the number of differentially expressed genes detected from microarray analysis (2,584 genes versus 2,015 genes). Furthermore, our data reveal a greater dynamic range in the detection and quantification of gene transcripts for RNA-seq compared to microarray technology.M-BM- Conclusions: This study highlights the value of RNA-seq in identifying novel immunomodulatory mechanisms that underlie host-mycobacterial pathogen interactions during infection, including possible complex post-transcriptional regulation of host gene expression involving antisense RNA. Description of the transcriptomic host response after infection of bovine monocyte-derived macrophages with Mycobacterium bovis
2013-03-26 | E-GEOD-45439 | biostudies-arrayexpress
Project description:The aim of this study was to investigate the effect of T0901317 LXR agonist on Retinoic Acid Receptor (RAR) family gene expression. T0901317 alone increase RARalpha gene expression in monocytes and the effects of the co treatment of the cells with T0901317 and a specific RARalpha agonist (AM580) were further studied. For this monocytes were treated for 24h with DMSO or T0901317 to induce RARalpha expression and in a second step cells were treated or not with AM580 for another 24h period. Gene expression was analysed for all the treatments (T0901317, AM580 or T0901317+AM580) and we focussed on genes which expression was synergitically induced by the co treatment as compared to the cells treated either by T0901317 or AM580. Monocytes were obtained from 2 healthy donors with inform consent. Cells were treated in vitro with the vehicle (DMSO 0,1%) or 10µM of the LXR agonist T0901317 for 24 hours. Then after cells were treated for another 24 hour period with or without 100nM of the RARalpha specific agonist AM580.
2010-04-08 | E-GEOD-13407 | biostudies-arrayexpress