Colon cancer detection by measuring DNA of cells collected from rectum: A case-control study
Ontology highlight
ABSTRACT:
DISEASE(S): Colorectal Cancer
PROVIDER: 2426507 | ecrin-mdr-crc |
REPOSITORIES: ECRIN MDR
Similar Datasets
Project description:Study hypothesis: Cell exfoliation from the surface of colorectal tumours is much more intensive than from normal colorectal mucosa. The hypothesis is that exfoliated cells are transferred to the rectum within mucocellular layer separating colon mucosa from the gut contents, and accumulation of exfoliated cells in cancer patients is much greater comparing to healthy individuals. It is suggested that this phenomenon can be used for colorectal cancer early detection and screening.
Please note that another study closely related to this study has been registered with ISRCTN95403112 (http://www.controlled-trials.com/ISRCTN95403112)
Primary outcome(s): DNA yields from exfoliated materials (DNA scores) are assessed in terms of their predictive value in detecting the presence of serious colorectal conditions (colorectal cancer and inflammatory bowel disease)
| 2415258 | ecrin-mdr-crc
Project description:Comprehensive DNA methylation analysis using the clinical FFPE samples of the gastric cancer, gastric mucosa surrounding cancer, and biopsy gastric mucosa.
2023-10-31 | GSE199898 | GEO
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.
2011-05-04 | E-GEOD-27263 | biostudies-arrayexpress
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.
2011-05-04 | GSE27263 | GEO
Project description:The magnetic susceptibility (κ) of particulate matter (PM) is a useful tool in estimation concentration of iron-rich particles and provides useful information on the emission sources and pathways of spread of PM in the atmosphere. However, there is currently no established protocol for measuring the magnetic susceptibility of PM collected on filters used in standard monitoring of PM concentration. This paper presents a step-by-step process for collecting PM on filters in automatic samplers and measuring their κ. The procedure outlines requirements for data quality, measurement uncertainty, exposure time and conditions, and the amount of material collected on the filters. The study analyzed a 2-year dataset of magnetic susceptibility measurements by MFK-1 kappabridge (Agico, Czech Republic) for PM10 and PM2.5 collected at two locations, Warsaw and Cracow, in Poland using low-volume PM samplers. By strictly following the procedure for conditioning filters, measuring magnetic susceptibility and mass of PM, the study found that it is possible to obtain repeatable data with good measurement accuracy and acceptable errors. This makes magnetic susceptibility an additional reliable parameter for tracking of emission sources of iron-rich particles. Successful implementation of this magnetic method as a standard procedure for monitoring PM in addition to the PM mass collected on filters could be used to analyze sources of emission of Fe-particles and their contribution to the PM mass, especially in urban and industrial environments.
| S-EPMC10794260 | biostudies-literature
Project description:Microarray expression profiling of cervical exfoliated cells (10k genes) We used whole genome microarrays (25,353 unique genes) to compare the transcription profiles from seven samples of normal exfoliated cells and one cervical tissue.
2010-07-01 | E-GEOD-2711 | biostudies-arrayexpress
Project description:Microarray technology applied to miRNA profiling is a promising tool in many research fields. At present, only few studies have addressed intra- and inter-platform reproducibility by using tissues/cell-lines of different origin to maximize differences in miRNA content. Although the approach might provide an useful system to address technical issues since, for sure, a huge modulation can be evaluated, it does not reflect the common experimental practice in laboratory. As a matter of fact, from all these studies it is not know how concordant can be expected the results obtained by different platforms starting from biological meaningful specimens. We investigated the issue of inter-platform reproducibility using four miRNA microarray platforms and nine paired tumor/normal colon tissues. The tumor and the normal counter-part samples were prospectively collected from 9 patients who underwent surgical resection at the INT-MI. Neoplastic samples were obtained from the central area of the neoplasia, avoiding to select necrotic material or transition zones with healthy mucosa. Samples of colonic healthy mucosa were resected at least 20 centimeters far from the neoplasia and distant from the surgical resection margins. Tissue samples were stored in liquid nitrogen until RNA extraction. Total RNA was extracted from 10–20 mg of tumor samples and from 30–40 mg of normal samples. Nine paired tumor/normal colon tissues on Agilent human miRNA Microarray.
2012-11-26 | E-GEOD-33124 | biostudies-arrayexpress
Project description:Microarray technology applied to miRNA profiling is a promising tool in many research fields. At present, only few studies have addressed intra- and inter-platform reproducibility by using tissues/cell-lines of different origin to maximize differences in miRNA content. Although the approach might provide an useful system to address technical issues since, for sure, a huge modulation can be evaluated, it does not reflect the common experimental practice in laboratory. As a matter of fact, from all these studies it is not know how concordant can be expected the results obtained by different platforms starting from biological meaningful specimens. We investigated the issue of inter-platform reproducibility using four miRNA microarray platforms and nine paired tumor/normal colon tissues. The tumor and the normal counter-part samples were prospectively collected from 9 patients who underwent surgical resection at the INT-MI. Neoplastic samples were obtained from the central area of the neoplasia, avoiding to select necrotic material or transition zones with healthy mucosa. Samples of colonic healthy mucosa were resected at least 20 centimeters far from the neoplasia and distant from the surgical resection margins. Tissue samples were stored in liquid nitrogen until RNA extraction. Total RNA was extracted from 10–20 mg of tumor samples and from 30–40 mg of normal samples. Nine paired tumor/normal colon tissues on Miltenyi miRXplore Microarray.
2012-11-26 | E-GEOD-33123 | biostudies-arrayexpress
Project description:Microarray technology applied to miRNA profiling is a promising tool in many research fields. At present, only few studies have addressed intra- and inter-platform reproducibility by using tissues/cell-lines of different origin to maximize differences in miRNA content. Although the approach might provide an useful system to address technical issues since, for sure, a huge modulation can be evaluated, it does not reflect the common experimental practice in laboratory. As a matter of fact, from all these studies it is not know how concordant can be expected the results obtained by different platforms starting from biological meaningful specimens. We investigated the issue of inter-platform reproducibility using four miRNA microarray platforms and nine paired tumor/normal colon tissues. The tumor and the normal counter-part samples were prospectively collected from 9 patients who underwent surgical resection at the INT-MI. Neoplastic samples were obtained from the central area of the neoplasia, avoiding to select necrotic material or transition zones with healthy mucosa. Samples of colonic healthy mucosa were resected at least 20 centimeters far from the neoplasia and distant from the surgical resection margins. Tissue samples were stored in liquid nitrogen until RNA extraction. Total RNA was extracted from 10–20 mg of tumor samples and from 30–40 mg of normal samples. Nine paired tumor/normal colon tissues on Illumina Human_v2 microRNA expression Beadchips
2012-11-26 | E-GEOD-33125 | biostudies-arrayexpress
Project description:The relationship between DNA methylation changes in peripheral blood cells of CKD and ESKD patients and both DNA damage in renal constituent cells and fatty liver remains unclear. In this study, we analyzed DNA methylation changes in peripheral blood cells of CKD and ESKD patients and examined their associations with DNA damage levels in urinary exfoliated cells and HSI (Hepatic steatosis index).
2024-12-27 | GSE285416 | GEO