Investigation of reaction of large intestine subcutaneous myofibroblasts to inflammatory cytokines.
Ontology highlight
ABSTRACT:
DISEASE(S): Ulcerative Colitis, Crohn’s Disease, Colorectal Cancer
PROVIDER: 2645606 | ecrin-mdr-crc |
REPOSITORIES: ECRIN MDR
Similar Datasets
Project description:Rat chondrocytes were divided into control group (RP), thrombin group (RPT), and thrombin plus inhibitor group (RPTi). The differential genes were identified by RNA-sequencing, and verified by western blot (WB), quantitative polymerase chain reaction (qPCR), cell immunofluorescence (IF), endoplasmic reticulum (ER) staining, functional enrichment analysis, and Gene Ontology (GO).
2023-02-10 | GSE196498 | GEO
Project description:A female patient with a partial trisomy 16q was described previously. Her clinical characteristics included obesity, severe anisomastia, moderate to severe mental retardation, dysmorphic facies, and contractions of the small joints. In this paper, we describe a more detailed analysis of the genetic anomaly in this patient. We were particularly interested in the involvement of the fat mass and obesity associated gene (FTO) in her duplication. Single nucleotide polymorphisms in FTO have recently been associated with obesity. We have precisely mapped the breakpoints of the duplication using high resolution oligonucleotide array comparative genome hybridization (CGH). We found that the duplication spans 11.45 Mb on 16q11.2 to 16q13 and it includes FTO. The increased copy number of FTO was confirmed with a qPCR on genomic DNA of the patient and healthy controls. We investigated the influence of the increased FTO copy number on FTO gene expression in immortalized lymphocytes from the using qPCR. We found no evidence of increased FTO expression in the patient. This observation could be explained by maternal imprinting. We found evidence supporting this hypothesis in a database of imprinted genes. In addition, our results generated new candidate genes for the mental retardation, dysmorphic facies, small joints contractions, small teeth, and anisomastia of the patient. We used a high density oligonucleotide microarray to delineate the borders of the duplication with high resolution. This analysis enabled us to confirm the inclusion of FTO in the duplication. This was confirmed with quantitative real-time PCR (qPCR) at the level of genomic DNA. To further investigate the role of FTO in the obese phenotype of the patient, we used qPCR to study the expression of FTO in immortalized lymphocytes of the patient. Remarkably, the increased FTO copy number in the patient’s genomic DNA did not give rise to an increased copy number of FTO mRNA molecules. We think this may be the result of maternal imprinting of the gene. The CGH results also allowed us to generate new hypotheses regarding the etiology of the other clinical problems of the patient. We propose candidate genes for her mental retardation, dysmorphic facies, joint contractures, small teeth, and anisomastia.
2010-09-10 | E-GEOD-12741 | biostudies-arrayexpress
Project description:Real-time quantitative PCR analysis of human epithelial cells The activity of Malva sylvestris extract and fractions infected by A. actinomycetemcomitans were investigated using an adapted dual chamber model, oral human epithelial cells were used in the co-culture model. One microgram of RNA was converted in cDNA using RT2 First Strand Kit. 84 genes were analyzed using inflammatory response & Autoimmunity Array RT2 profiler (Qiagen Sabiosciences, Valencia, CA, USA) with buffers supplied by the manufacturer qPCR gene expression profiling. Oral human epithelial cells were infected by A. Actinomycetemcomintans and treated with Malva sylvestris extract and fractions prior to gene expression analysis.
2015-08-27 | E-GEOD-72443 | biostudies-arrayexpress
Project description: Not available
| S-EPMC6908826 | biostudies-literature
Project description:Background: Systemic drug reaction (SDR) is a major safety concern of weekly rifapentine-based treatment (known as 3HP) for latent tuberculosis infection (LTBI). Understanding predictors of SDR and identifying risk subjects before treatment can improve public acceptance and cost-effective implement of LTBI program. Methods: We first prospectively recruited 187 subjects receiving 3HP and randomly selected a pilot cohort for generating whole-blood transcriptomic data. After integrating the hierarchical systems biology model (HiSBiM) and a therapy-biomarker pathway approach, candidate genes were obtained and evaluated by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Then, we developed interpretable machine learning models and established universal cut-off value (shapley additive explanations value) for each SDR prediction model. An independent cohort was used to evaluate the performance of these predictive models. Findings: Based on the transcriptomic profile of the pilot cohort, a total of 19 candidate genes were identified. Among them, six were sieved out by RT-qPCR results of a small number of samples from the training cohort. By applying the SHAP values of various combinations of the 6 gene expression signature, and the best model consisted of three genes, had an G-mean of 0.959, sensitivity of 0.972 and specificity of 0.947 for the joint of the two cohorts, and worked well across different subgroups.
2022-02-10 | GSE174552 | GEO
Project description:Interventions: Group 1: Quantitative Expression Analysis of the proteom and gene Expression of Primary Tumor, normal tissue, and metastases
Primary outcome(s): Disease associated Proteins and Genes
Study Design: Allocation: ; Masking: ; Control: ; Assignment: ; Study design purpose: basic science
| 2431957 | ecrin-mdr-crc
Project description:Interventions: None; molecular analysis
Primary outcome(s): - Less SMAD4 positive colorectal cancers in Statin users
Study Design: Non-randomized controlled trial, Open (masking not used), N/A , unknown, Parallel
| 15779 | ecrin-mdr-crc
Project description:Objective: Alcoholic hepatitis (AH) is characterized by the expansion of ductular reaction (DR) cells and expression of liver progenitor cell (LPC) markers. The aim of this study was to identify the gene expression profile and associated genes of DR cells and to evaluate its weight in alcoholic disease progression. Design: KRT7+, KRT7- and total liver fractions were laser microdissected from liver biopsies (n=6) of patients with AH and whole transcriptome was sequenced. Gene signature was assessed in transcriptomic data from 41 patients with alcoholic liver disease. Pro-inflammatory profile was evaluated in tissue and serum samples and in human LPC organoids. Results: Transcriptome analysis of KRT7+ DR cells uncovered intrinsic gene pathways of DR and allowed identifying genes associated with DR expressed in AH. In addition, DR gene signature and associated genes correlated with disease progression and poor outcome in AH patients. Importantly, DR presented a pro-inflammatory profile with expression of CXC and CCL chemokines and was associated with infiltrating neutrophils. Moreover, LPC markers correlated with liver expression and circulating levels of inflammatory mediators. In vitro, human LPC organoids mimicked ductular reaction gene expression profile and produced chemokines. Moreover, LPC promoted neutrophil migration and enhanced their inflammatory profile. Conclusions: Here we report for the first time the gene expression signature of DR in AH and its association with disease progression. Functional and experimental analysis demonstrates that DR cells have a pro-inflammatory profile, and suggest their involvement in neutrophil recruitment and liver inflammatory response.
2019-01-11 | GSE100901 | GEO
Project description: Not available
| S-EPMC8528003 | biostudies-literature
Project description:Whole genome bisulfite-seq on 8 week adult mouse large intestine For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
2021-11-04 | GSE188006 | GEO