Gene Expression Profiling of Chronically Inflamed FFPE Placental Tissue
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE68474 | GEO | 2015/09/01
SECONDARY ACCESSION(S): PRJNA282815
REPOSITORIES: GEO
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Project description:The aim of this research was to explore gene expression changes in chronically inflammed placental tissue This study compared FFPE tissue with and without chronic placental inflammation, manifested as overlapping chronic chorioamnionitis, chronic villitis of unknown etiology, and chronic deciduitis. RNA expression profiling was conducted on formalin fixed, paraffin embedded placental tissue using Illumina microarrays. To further explore and validate gene expression findings, we conducted immunohistochemical assessment of protein level expression.
2015-09-01 | E-GEOD-68474 | biostudies-arrayexpress
Project description:The goal of this study was to compare the gene expression profiles of chronically inflamed human peri-implant and chronically inflamed human periodontal tissues in order to elucidate potential changes at the molecular level. Cells out of the pocket depth of the inflamed peri-implant and periodontal ligament as well as from the middle third of healthy periodontal ligament were applied. Genome-wide gene expression was compared with the help of microarray analysis, and the data were validated by real-time RT-PCR. The expression rates of 14,239 genes were investigated and 2,079 of them were found differentially expressed by at least two-fold; the expression rates of 1,093 genes were significantly up-regulated and the expression rates of 986 genes were significantly down-regulated in inflamed peri-implant cells compared to inflamed periodontal cells. We focused on genes coding for extracellular matrix components and those that degrade them. Only genes of non-fibril-forming collagens (types IV, VI, VII, and XVII) were increased in inflamed peri-implant tissue, whereas only the genes of two fibril-forming collagens (types III and XVII) were decreased, suggesting that peri-implant tissue re-models faster than periodontal tissue. Furthermore, cathepsin D and cathepsin S might participate to a greater extent in connective tissue destruction of peri-implant tissue. The present investigation demonstrated that, despite their clinical similarities, periimplantitis and periodontitis are two different diseases at the genetic level. Keywords: inflammation, peri-implant, periodontal ligament cells The peri-implant tissue was scraped of the implant and the periodontal tissue was scraped off the roots of the teeth. Both tissue probes were treated with the RNeasy mini Kit (Qiagen, Hilden, Germany) to isolate total RNA from chronically inflamed peri-implant and chronically inflamed PDL cells, according to the manufacturer’s instructions. Healthy PDL cells were taken from the middle third of the root clearly avoiding sampling the gingiva. The chronically inflamed peri-implant and periodontal cells were taken directly out of the depth of the pocket again avoiding the ingrown gingiva. Quality control and quantitation of total RNA samples were determined prior to the microarray experiments (Agilent 2100 Bioanalyzer, Agilent Technologies, Palo Alto, CA, USA). Equal amounts of total RNA were pooled into an inflamed peri-implant and an inflamed and healthy periodontal cell pool. To monitor the relative abundance of mRNA for full-length human genes, the Affymetrix GeneChip HG_U133A was used, representing 22,283 probe sets (14,239 unique human genes). Labelled cRNA, fragmented to an average size of 100–150 bases, was hybridized to the GeneChips. For each pool of cRNA, two GeneChips were hybridized. Chronically inflamed peri-implant as well as healthy and chronically inflamed periodontal tissue was collected from 48 patients at the Dental Medical School of the University of Goettingen (21 men, 27 women, aged between 18 and 72 years) from March 2005 to August 2006, as already described by Gersdorff et al. (2007). The peri-implant tissue probes were taken from endosteal implants (Astra Tech®, ITI Bonefit®, or Brånemark®) with chronic peri-implant lesions (Schwarz et al. 2007). The periodontal tissue probes were taken from teeth, either extracted for orthodontic reasons or due to carious lesions (healthy periodontium) or from teeth with generalized chronic periodontitis (Armitage 2004). Teeth with healthy PDL had no clinical signs of inflammation (no bleeding on probing), exhibited a probing depth of ?3,5 mm and had no radiographic detectable bone loss. In contrast, implants and teeth with generalized chronic inflammation exhibited obvious clinical signals of inflammation (bleeding on probing), exhibited a probing depth of >4 mm and had radiographic evidence of bone loss (1 to 7 mm). A detailed anamnesis of each patient was explored. All patients were without a medical history, i.e. heart diseases or diabetes, and were not on medication. In addition, the tissue samples used in our study were only taken from non-smokers. The explanted implants and extracted teeth were immediately frozen and stored at -80 °C. All patients who participated in the study were informed about the nature and aim of this project and gave their written informed consent. The study was approved according to the regulations of the Ethics Committee of the Medical Faculty of the University of Goettingen.
2009-08-30 | E-GEOD-8908 | biostudies-arrayexpress
Project description:the goal of this study is to use high-throughput RNA-Sequencing technology to identify genes that are differentially expressed in iron deficient (ID) placentas compared to iron adequate (IA) placentas. A secondary aim is to explore whether iron deficiency has differential impact on male compared with female placental transcriptome.
2020-09-23 | GSE157667 | GEO
Project description:Hemoglobin Bart’s hydrops fetalis syndrome (BHFS) is the most severe form of α-thalassemia. Histological alternations can be observed in placenta, but placental transcriptome profile and circular RNAs have not been study in this disease. The aim of this study was to define the placental transcriptional changes and find relevant circular RNAs in BHFS. We performed high-throughput RNA sequencing to detect placental samples from fetuses affected by BHFS (n=5) and normal fetuses (NF, n=5). Our results showed 152 differentially expressed genes (DEGs), 112 circRNAs, and 45 microRNAs that were differentially expressed. DEGs were found to be involved in Gene Ontology terms related to gas transport, cell adhesion, oxidative stress, organ development, hemopoiesis, etc. Our study characterized the placental transcriptome of BHFS.
2023-09-26 | GSE184925 | GEO
Project description:Interventions: Group 1: The EC@T-project consists of three substudies: two qualitative and one quantitative study. In all three studies there will be two sample groups, providers and chronically ill patients (see fulfilling one of the diagnoses). First, within the qualitative study we will interview the attitudes of patients and providers and we are planning to generate items for the EC@T questionnaire. Then all participants will fill out the questionnaire.
Primary outcome of the project is to develop the EC@T questionnaire based on interview data and analysis of literature. aim: measurement of attitudes towards eCommunication of providers and chronically ill patients.
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| 2430027 | ecrin-mdr-crc
Project description:The aim of this microarray experiment was to compare the overall transcriptomic profile of human placenta derived trophoblast organoid cultures with its tissue of origin, human placental villi. As the placental villi contains both trophoblast and stromal populations, we have included placenta derived stromal cultures in this comparison.
2018-11-28 | E-MTAB-6683 | biostudies-arrayexpress
Project description: Not available
| S-EPMC2200913 | biostudies-literature
Project description:In this study, we screened human placental samples for allele-specific methylation and subsequently novel imprinted genes associated with these regions. We used reduced representation bisulfite sequencing to identify partially methylated CpG islands (CGIs) in the human placental genome. We were able to delineate potential candidates for allele-specific methylation based on the calculation of a concordance statistic. Amongst the 28 regions chosen for validation based on high levels of expression, two regions were shown to exhibit allele-specific expression. Single base-resolution methylation analysis in the placental genome and RNA-Seq
2013-10-09 | E-GEOD-40955 | biostudies-arrayexpress
Project description:Microarray analysis of differentially expressed genes from rats undergoing placental ischemia versus health controls Placental ischemia is believed to be an important contributor to human preeclampsia, though the targets induced by the ischemia remain unclear. Chorionic placental tissues from 6 control and 6 placental ischemic reduced uterine perfusion pressure (RUPP) rats were analyzed for gene expression by microarray.
2013-09-05 | E-GEOD-50596 | biostudies-arrayexpress
Project description:Hemoglobin Bart’s hydrops fetalis syndrome (BHFS) is the most severe form of α-thalassemia. Histological alternations can be observed in placenta, but placental transcriptome profile and circular RNAs have not been study in this disease. The aim of this study was to define the placental transcriptional changes and find relevant circular RNAs in BHFS. We performed high-throughput RNA sequencing to detect placental samples from fetuses affected by BHFS (n=5) and normal fetuses (NF, n=5). Our results showed 152 differentially expressed genes (DEGs), 112 circRNAs, and 45 microRNAs that were differentially expressed. DEGs were found to be involved in Gene Ontology terms related to gas transport, cell adhesion, oxidative stress, organ development, hemopoiesis, etc. Our study characterized the placental transcriptome of BHFS.
2023-09-26 | GSE184915 | GEO