Project description:Targeted electrical energy externally applied to a complex wound, including pressure ulcers and venous leg has been shown to improve wound healing. However, how this repair process is stimulated is poorly understood. We examined by microarray analysis the effects of a class IIA medical device that delivers a specific sequence of electrical pulses (e-sequence) to the skin of healthy volunteers during a period of 48 hours.
Project description:AMD is a complex disorder related to environmental factors and genetic polymorphisms. We explored the interplay between the two factors by comparing the differences between HTRA1/ARMS2 high-risk and low-risk AMD alleles after exposure to smokers’ serum using iTRAQ-based proteomics. Primary human retinal pigment epithelial (hRPE) cells were obtained from donor eyes and screened for ARMS2/HTRA1 AMD risk genotypes, wild type allele as control. A gene ontology annotation analysis and KEGG metabolic pathway analysis were employed to obtain a global functional view of differentially expressed (DE) proteins. Significant DE proteins were screened and validated by real-time PCR, immunofluorescence and western blot. The relationship between HTRA1 and caveolin-1 protein was explored by HTRA1-overexpressing lentivirus-transduced ARPE-19 cells. A total of 400 DE proteins were detected for the high-risk allele after cigarette sera stimulation, which was much higher than the low-risk allele. The caveolin-1 protein was significantly up-regulated when HTRA1-overexpressing cells were exposed to smokers’ serum and the smoking effect was stronger than AMD high-risk allele. There were interplays between AMD high-risk allele and cigarette smoking. Smokers’ sera also accelerated the phagocytosis of hRPE cells. In addition, caveolin-1 may play an important role in the disease process, but its molecular mechanism requires further study.
Project description:Transplantation of amniotic membrane-expanded limbal epithelium (AMLE) in place of donor tissue grafts results in significantly improved outcomes for patients suffering from severe limbal stem cell deficiency; however the reasons for such superior results are unclear. The purpose of this study was to identify transcriptional gene profiles specific to AMLE and donor central corneal epithelium (CE), which may contribute to the divergent clinical outcomes observed following transplant. Limbal fibroblasts which underlie the epithelium and secrete extracellular matrix proteins following injury/surgery were also profiled. Using cell culture, immunofluorescence, microarray gene expression profiling and qRT-PCR validation; this study aims to identify enriched biological processes and pathways which characterise AMLE and CE tissues. We hope the study outcomes will shed light onto the factors which contribute to provide the improved clinical outcomes associated with AMLE transplantation. Gene expression profiling of three central corneal buttons, three amniotic membrane-expanded limbal epithelial cultures and three limbal fibroblast cultures
Project description:41 volunteers (male non-smokers) were exposed to formaldehyde (FA) vapors for 4 h per day over a period of 5 working days under strictly controlled conditions. For each exposure day, different exposure concentrations were used in a random order ranging from 0 up to 0.7 ppm. At concentrations of 0.3 ppm and 0.4 ppm, four peaks of 0.6 or 0.8 ppm for 15 min each were applied. During exposure, subjects had to perform bicycle exercises (about 80 W) four times for 15 min. Blood samples, exfoliated nasal mucosa cells and nasal biopsies were taken before the first and after the last exposure. Nasal epithelial cells were additionally sampled 1, 2 and 3 weeks after the end of the exposure period. The alkaline comet assay, the sister chromatid exchange (SCE) test and the cytokinesis-block micronucleus test (CBMNT) were performed with blood samples. The micronucleus test (MNT) was also performed with exfoliated nasal mucosa cells. The expression (mRNA level) of the GSH-dependent formaldehyde dehydrogenase (FDH, identical to alcohol dehydrogenase 5; ADH5; EC 1.2.1.46) was measured in blood samples by quantitative real-time RT-PCR with TaqMan probes. DNA microarray analyses using a full-genome human microarray were performed on blood samples and nasal biopsies of selected subgroups with the highest FA exposure at different days. None of the tests performed showed a biologically significant effect related to FA exposure. Under the experimental conditions of this study, inhalation of FA did not lead to genotoxic effects in peripheral blood cells and nasal mucosa and had no effect on the expression of the FDH gene. Inhalation of FA also did not cause biologically relevant alterations in the expression of genes in a microarray analysis with nasal biopsies and peripheral blood cells. Gene expression analysis of nasal biopsies and blood samples before and after inhalation of 0.7ppm formaldehyde (0 h, 24 h, or 72 h before sampling), and of blood cells before and after exposure to 200µM formaldehyde for 4 hours.
Project description:We explored the prognostic impact of the dynamic contrast enhanced MR imaging (DCE-MRI) parameter ABrix in cervical cancer combined with global gene expression data to reveal the underlying molecular phenotype of the parameter and construct a gene signature that reflected ABrix. Based on 78 cervical cancer patients subjected to curative chemoradiotherapy, we identified a prognostic ABrix parameter by pharmacokinetic analysis of DCE-MR images based on the Brix model, where tumors with low ABrix appeared to be most aggressive. Gene set enrichment analysis of 46 tumors with pairwise DCE-MRI and gene expression data showed a significant correlation between ABrix and the hypoxia gene sets, whereas gene sets related to proliferation, radioresistance, and wound healing were not significant. Hypoxia gene sets specific for cervical cancer created in cell culture experiments, including targets of the hypoxia inducible factor (HIF1M-NM-1) and the unfolded protein response (UPR), were the most significant. In the remaining 32 tumors, low ABrix was associated with upregulation of HIF1M-NM-1 protein expression, as assessed by immunohistochemistry, consistent with increased hypoxia. Based on the hypoxia gene sets, a signature of 31 genes that were upregulated in tumors with low ABrix was constructed. This DCE-MRI hypoxia gene signature showed prognostic impact in an independent validation cohort of 109 patients. Gene expression correlating with the DCE-MRI parameter ABrix were identified in 46 patients (DCE-MRI cohort) and used to find a hypoxia gene signature. The prognsotic impact of the gene signature was validated in an independent cohort of 109 patients (validation chort). Cell culture experiments were performed to generate cervical cancer specific gene lists associated with hypoxia (GSM897799 - GSM897804).
Project description:This SuperSeries is composed of the following subset Series:; GSE12585: Expression data from healthy smokers; GSE12586: Alterations of gene expression in human peripheral lymphocytes after exposure to cigarette smoke condensate in vitro Experiment Overall Design: Refer to individual Series
Project description:Infiltration of human myometrium and cervix with leukocytes and formation of a pro-inflammatory environment within the uterus has been associated with the initiation of both term and preterm parturition. The mechanism regulating the onset of this pro-inflammatory cascade is not fully elucidated. We demonstrate that prokineticin 1 (PROK1) is up-regulated in human myometrium and placenta during labour. Gene array analysis identified 65 genes up-regulated by PROK1 in human myometrium, mainly cytokines and chemokines including: Interleukin-1beta (IL1B), chemokine C-C motif ligand 3 (CCL3) and Colony Stimulating Factor 3 (CSF3). We additionally demonstrate that PROK1 increases expression of chemokines C-C motif ligand 20 (CCL20), Interleukin-6 (IL-6), Interleukin-8 (IL-8), prostaglandin synthase 2 (PTGS2) and prostaglandin E2 and F2? secretion. We propose that PROK1 is a novel inflammatory mediator that can contribute to onset of human parturition at term and partially mediate premature onset of inflammatory pathways during bacterial infection. Total RNA was extracted from human term non-labour myometrium explants treated with prokineticin for 6 and 24 hours compared to vehicle-treated explants. Six biological replicates were analyzed for each treatment and time point. Two of the 6-hour vehicle samples failed a quality-control analysis and were substituted with a 4-hour vehicle treatment from the same tissue sample in each case.
Project description:We aimed to investigate the transcriptional program associated with pimonidazole staining in prostate cancer. A pimonidazole gene signature was identified that showed positive correlation to Ki67 labeling index, indicating increased proliferation in pimonidazole positive tumors. A positive correlation to clinical tumor stage and presence of lymph node metastasis was also found, consistent with associations between pimonidazole staining and clinico-pathological parameters. Moreover, the gene signature was associated with high Gleason score in a validation cohort of 59 patients and showed prognostic impact independent of Gleason score and other clinical markers in a watchful waiting validation cohort of 281 patients. Our work reveals the molecular basis of an aggressive prostate cancer phenotype reflected by pimonidazole staining, and suggests that genes involved in proliferation, DNA repair and hypoxia response contribute to this phenotype. We combined pimonidazole immunohistochemistry data and expression profiles to identify transcriptional program activated in pimonidazole positive tumors. Whole-genome gene expression profiles were determined in tumor biopsies from an investigation cohort of 46 patients, where 39 patients had received pimonidazole prior to surgery. Gene ontology analysis of 1046 genes upregulated in pimonidazole positive tumors, as defined by a staining fraction above 10%, showed significant enrichment of the biologic processes cell cycle, translation and cellular response to stress. Gene set analysis based on this result identified gene expressions in proliferation, DNA repair and hypoxia response as major parts of the transcriptional program associated with pimonidazole staining. Gene expression data of four prostate cancer cell lines were used to generate hypoxia response gene sets for this analysis. A signature of the 32 most essential genes in the program was constructed and shown to be associated with prostate cancer aggressiveness in two independent validation cohorts.
Project description:We report the establishment of a stable 3D in vitro organoid culture procedure from human fallopian tube samples and confirming experimentally the existence of adult stem cells in this epithelial tissue. Long term growth and the differentiation of the organoids depend on the interplay between the paracrine signaling pathways Wnt, NOTCH and BMP, since R spondin 1 and Wnt3a are required for preservation of stemness in concert with continuous suppression of TGF-beta activity. Microarray analysis revealed that inhibition of NOTCH signaling by the gamma-secretase inhibitor DBZ leads to down-regulation of a gene cluster associated with pluripotency, as the adult stem cell signature is significantly enriched in the list of downregulated targets. Microarray experiments were performed as dual-color hybridizations on Agilent human whole genome catalog 44K arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.
Project description:Transcriptional analysis of ovine skin response to infection with the parasitic mite Psoroptes ovis using the Agilent ovine transcriptome microarray platform. The results of statistical analysis (differential gene expression across the time course of infection was determined using a one way-analysis of variance (ANOVA) with a Student-Newman-Keuls (SNK) post-hoc test in Genespring GX 11.0 (Agilent Technologies, UK) comparing each of the 5 time points, non-infected and 1, 3, 6 and 24 hours post infection. Multiple test correction was performed using the Benjamini & Hochberg False Discovery Rate (FDR) procedure with an FDR corrected p-value cut-off set at 0.05) and fold change analysis (Fold change analysis was performed on the one-way anova dataset, probes with a fold change greater than 2 between any of the conditions were carried forward) are in archive E-TABM-1012.additional.zip. Quality control: Six biological replicates (sheep, n=6), multiple biopsies pooled from each animal at each time point of infection. Pooled samples from each sheep at each time point hybridised in single-dye (Cy3) format to Agilent ovine arrays. Positive and negative control probes utilised to assess array QC and real time qRT-PCR validation of selected array probes