To analyse the lymph node involvement pattern in large intestine cancer after surgery and correlate with different clinical and pathological parameters for better surgical outcomes.
Ontology highlight
ABSTRACT:
DISEASE(S): Malignant Neoplasm Of Colon, Unspecified
PROVIDER: 2596143 | ecrin-mdr-crc |
REPOSITORIES: ECRIN MDR
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Project description:Human mucosa was collected from two different individuals undergoing colectomy. After treatment with EDTA, colonic crypts were isolated and further dis-aggregated using Dispase. Next, cells were stained using antibodies directed against the extracellular domain of EpCAM, PTK7, CD11, CD31, and CD45. Cells were analyzed and sorted via flow cytometry (BD Aria). After excluding non-epithelial cells (Epcam. CD11, CD31, and CD45 negative), the EpCAM positive fraction was divided into fractions expressing either high, medium, low, or negative levels of PTK7. Sorted cells were transferred to Trizol for RNA extraction and RNA was purified using the Qiagen RNA Mini Kit. Colonic crypts were isolated from normal human mucosa derived from individuals undergoing colectomy. Single cell fractions from these crypts were sorted and isolated RNA processed and hybridized to Affymetrix PrimeView Arrays
2016-01-12 | E-GEOD-68340 | biostudies-arrayexpress
Project description:Tissue for normal colonic stem cell isolation was obtained via colectomy from a colorectal cancer patient. It was shown that the resected tissue and the in vitro-cultured organoids grown from tissue-derived adult stem cells do not harbor chromosomal alterations. For that purpose, genomic DNA from resected mucosa or genomic DNA from adult stem cell-derived organoids grown in a 3-dimensional culture system was compared to white blood cell genomic DNA obtained from the same individual. Furthermore, in vitro organoids which were cultured and serially passaged for several weeks did not acquire chromosomal alterations. Analysis of chromosomal stability of colonic tissue or in vitro-cultured organoids via comparison with blood cells derived from the same individual.
2011-11-22 | E-GEOD-31256 | biostudies-arrayexpress
Project description:Provides a set of enriched normal colon epithelial cells to use as a baseline for disease of the colon We present a dependable expression reference data set for non-neoplastic colonic epithelial cells. An enriched population of fresh colon epithelial cells were obtained from non-neoplastic, colectomy specimens and analyzed using Affymetrix GeneChip Exon 1.0 ST arrays. The findings from this study represent the first comprehensive expression profile for non-neoplastic colonic epithelial cells reported. For demonstration purposes, we have compared the data derived from these cells to a publically available set of tumor and normal matched colon data. This analysis allowed an assessment of global gene expression alterations and demonstrated that adjacent normal tissues, with a high degree of cellular heterogeneity, are not always representative of normal cells for comparison to tumors which arise from the colon epithelium. We also examined alternative splicing events in tumors compared to normal colon epithelial cells. Our analysis of splice variants on a genome-wide scale illustrate that this is a very labor intensive procedure, requiring vigilant examination of the data. It is projected that the contribution of this set of data derived from pure colonic epithelial cells will enhance studies in colon-related disease and offer a vital baseline for studies aimed at elucidating the mechanisms of alternative splicing.
2009-12-10 | GSE19163 | GEO
Project description:Background: Ulcerative colitis (UC) develops from chronic inflammation of the colon. Most patients respond favorably to medical management, however around 25% of UC patients will require surgery to treat their disease. While surgery is the only curative treatment for UC, it can carry its own risks, particularly when the surgery is emergent. Time from diagnosis to surgery varies dramatically amongst UC patients, thus a better understanding of how the colonic microenvironment relates to disease severity is needed to improve patient outcomes. Methods: We conducted RNA-seq on full-thickness sigmoid colonic tissues from 26 UC patients undergoing colectomy for their disease. Hierarchical clustering of the transcriptomes identified disease subsets. Subsets were characterized using differential gene expression analysis, cell type deconvolution, and network analysis. Results: We identified two distinct UC subsets in our cohort that were distinguished by 957 differentially expressed genes. Cluster 1 was enriched in genes associated with intestinal epithelial cell differentiation, while cluster 2 was enriched in genes associated with epithelial-to-mesenchymal transition and inflammatory responses. Cluster 1 was associated with an extended time from UC diagnosis to colectomy. Of cluster 1 genes, elevated MUC5B, MUC4, and MUC2 expression displayed the strongest correlation with increased time to surgery. Conclusion: Our transcriptome analysis indicates that UC can be subclassified into at least two distinct molecular signatures. We find that elevated mucin gene expression correlates with prolonged time to colectomy after diagnosis. These results identified MUC5B, MUC4, and MUC2 as potential prognostic indicators of disease severity, as reflected in time to surgery.
2020-04-18 | GSE130038 | GEO
Project description:To investigate the pathogenesis of slow transit constipation (STC), we have employed microarray-based miRNA analysis as a discovery platform to identify miRNAs potentially related with STC pathogenesis.Full-thickness specimens were obtained from colons of STC patients undergoing total colectomy and ileorectal anastomosis or subtotal colectomy with antiperistaltic cecoproctostomy. And patients undergoing radical surgery for non-obstructing colon cancer (left colon cancer) as control. These patients were not constipated and had no colonic dilatation. The control specimens were obtained at least 5 cm from the resection margin in tumor free areas. Expression of five miRNAs (miRNA-128, miRNA-129-3p, miRNA-20b,miRNA-27b and miRNA-30b) from this signature was identified by arbitrarily setting the threshold at a fold change of 1.3 or above combined with p < 0.05 in the same RNA samples. Expression of miRNAs in the colon may be involved in STC pathogenesis. The samples were obtained and washed with cold PBS, transported in liquid nitrogen and immediately stored in liquid nitrogen after removal. Total RNA was isolated from frozen histologic specimens using a mirVana™ RNA isolation Kit.
2014-05-27 | E-GEOD-57969 | biostudies-arrayexpress
Project description:To investigate the pathogenesis of slow transit constipation (STC), we have employed microarray-based miRNA analysis as a discovery platform to identify miRNAs potentially related with STC pathogenesis.Full-thickness specimens were obtained from colons of STC patients undergoing total colectomy and ileorectal anastomosis or subtotal colectomy with antiperistaltic cecoproctostomy. And patients undergoing radical surgery for non-obstructing colon cancer (left colon cancer) as control. These patients were not constipated and had no colonic dilatation. The control specimens were obtained at least 5 cm from the resection margin in tumor free areas. Expression of five miRNAs (miRNA-128, miRNA-129-3p, miRNA-20b,miRNA-27b and miRNA-30b) from this signature was identified by arbitrarily setting the threshold at a fold change of 1.3 or above combined with p < 0.05 in the same RNA samples. Expression of miRNAs in the colon may be involved in STC pathogenesis.
2014-05-27 | GSE57969 | GEO
Project description:To further understand different gene expression of miR-31 knockout mouse colon and normal colon, we have employed colonic epithelium microarray expression profiling as a discovery platform to identify different genes with miR-31 knockout mouse colon and normal colon.comparision with normal colonic epithelium,upgene is 285 and downgene is 178 in knockout group.
2019-07-16 | GSE123556 | GEO
Project description:Tissue for normal colonic stem cell isolation was obtained via colectomy from a colorectal cancer patient. It was shown that the resected tissue and the in vitro-cultured organoids grown from tissue-derived adult stem cells do not harbor chromosomal alterations. For that purpose, genomic DNA from resected mucosa or genomic DNA from adult stem cell-derived organoids grown in a 3-dimensional culture system was compared to white blood cell genomic DNA obtained from the same individual. Furthermore, in vitro organoids which were cultured and serially passaged for several weeks did not acquire chromosomal alterations.
2011-11-22 | GSE31256 | GEO
Project description:Human mucosa was collected from two different individuals undergoing colectomy. After treatment with EDTA, colonic crypts were isolated and further dis-aggregated using Dispase. Next, cells were stained using antibodies directed against the extracellular domain of EpCAM, PTK7, CD11, CD31, and CD45. Cells were analyzed and sorted via flow cytometry (BD Aria). After excluding non-epithelial cells (Epcam. CD11, CD31, and CD45 negative), the EpCAM positive fraction was divided into fractions expressing either high, medium, low, or negative levels of PTK7. Sorted cells were transferred to Trizol for RNA extraction and RNA was purified using the Qiagen RNA Mini Kit.
2016-01-12 | GSE68340 | GEO
Project description:We use ChIP-seq to understand the genomic binding sites of SATB2 in colonic epithelium and to study the shifting of CDX2 and HNF4A's genomic binding sites after SATB2 loss in colonic epithelium.
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