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Definition of an ulcerative colitis preinflammatory state

ABSTRACT: The samples are a part of a study aiming at diagnosing ulcerative colitis from genome-wide gene expression analysis of the colonic mucosa. Colonic mucosal samples were collected as endoscopic pinch biopsies from ulcerative colitis patients and from control subjects. Samples with and without macroscopic signs of inflammation were collected from the patients. Keywords: Disease state analysis

ORGANISM(S): Homo sapiens

PROVIDER: GSE9452 | GEO | 2007/10/31

SECONDARY ACCESSION(S): PRJNA103213

REPOSITORIES: GEO

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Transcription profiling of human ulcerative colitis colonic mucosa to define an ulcerative colitis preinflammatory state

Project description:The samples are a part of a study aiming at diagnosing ulcerative colitis from genome-wide gene expression analysis of the colonic mucosa. Colonic mucosal samples were collected as endoscopic pinch biopsies from ulcerative colitis patients and from control subjects. Samples with and without macroscopic signs of inflammation were collected from the patients. Experiment Overall Design: The series contain eight UC samples with macroscopic signs of inflammation, 13 UC smaples without macroscopic signs of inflammation, five control subjects.

2008-06-20 | E-GEOD-9452 | biostudies-arrayexpress

Genome-wide gene expression differences between Crohn’s and ulcerative colitis from endoscopic pinch biopsies:

Project description:Ulcerative colitis (UC) and Crohn’s disease (CD) are inflammatory bowel diseases (IBD) with variable, overlapping clinical features and complex pathophysiologies. To identify pathogenic processes underlying these disease subtypes, using single endoscopic pinch biopsies to estabolish 36 expression profiles, we elucidated gene expression patterns of active and inactive areas of UC and CD, and compared these to infectious colitis and healthy controls. Keywords: RNA

2007-03-01 | GSE6731 | GEO

Transcription profiling of human colon biopsies obtained from patients with ulcerative colitis, Chrohn's disease vs. normal to identify pathogenic processes underlying these disease subtypes

Project description:Ulcerative colitis (UC) and Crohns disease (CD) are inflammatory bowel diseases (IBD) with variable, overlapping clinical features and complex pathophysiologies. To identify pathogenic processes underlying these disease subtypes, using single endoscopic pinch biopsies to estabolish 36 expression profiles, we elucidated gene expression patterns of active and inactive areas of UC and CD, and compared these to infectious colitis and healthy controls.To identify pathogenic processes underlying these disease subtypes, using single endoscopic pinch biopsies, we elucidated gene expression patterns of active and inactive areas of UC and CD, and compared these to infectious colitis and healthy controls. An unsupervised classification of a total of 36 samples yielded promising separation between IBD affected, unaffected, non-IBD colitis and normal controls, suggesting distinctive gene expression patterns for each sample type. The Significance Analysis of Microarays (SAM) software to select biologically significant changes in gene expression between groups. The criteria selected for SAM analysis are, a median false discovery rate (FDR) ? 0.00001%, fold change >2, and a Log2 mean expression index > 6.64.

2007-11-02 | E-GEOD-6731 | biostudies-arrayexpress

Expression data from intestinal mucosa of patients with UC

Project description:Ulcerative colitis (UC) is a chronic inflammatory disease of the colon with preiods of active disease followed by remission. We performed a whole-genome transcriptional analysis of colonic biopsies from patients with histologically active and inactive UC, as well as non-inflammatory controls. Ulcerative colitis patients and non-inflammatory controls were collected for RNA extraction and hybridization on Affymetrix microarrays. Inclusion criteria for UC patients were: age between 18 and 65, diagnosis of UC established at least 6 months before inclusion and exclusion of concomitant infection. Active disease was defined by endoscopic and histologic score: Mayo sub score >=2 and MATTS >=3 respectively . Inactive disease was also defined by endoscopic and histologic score: Mayo sub score =0 and MATTS <=2 respectively, and a remission state for a minimum of 5 month prior to biopsy collection, and remained inactive for at least 6 months after. Uninvolved mucosa from patients with active UC was defined as a colonic segment with completely normal endoscopic appearance, normal histology, and absence of any previous evidence of active disease. Finally, a total of 43 biopsies were analyzed: 13 healthy controls, 8 inactive UC, 7 non-involved active UC and 15 involved active UC.

2012-11-09 | E-GEOD-38713 | biostudies-arrayexpress

Ulcerative colitis gene expressions file

Project description:Ulcerative colitis related gene expressions analysis in colonic biopsy samples from control and ulcerative colitis patients

2019-07-10 | GSE134025 | GEO

Homo sapiens

Project description:Genome-wide gene expression differences between Crohn’s and ulcerative colitis from endoscopic pinch biopsies:

| PRJNA98959 | ENA

Dextran sodium sulfate treatment of wild type and Pirc rats alters colonic normal tissue gene expression

Project description:Dextran sodium sulfate (DSS) causes inflammation in the gut similar to ulcerative colitis in humans. Patients with ulcerative colitis have increased risk of developing colon cancer. We sought to determine which genes are altered in the normal colonic epithelium, and which changes depend on the Pirc mutation. 97 day old (ACIxF344)F1 wild type and Pirc male rats either untreated or given 4% DSS in the drinking water from 40-47 and 54-61 days of age, housed in 12 hour light:12 dark, ad lib feeding. Normal colonic tissue was collected from the distal colon at 97 days of age.

2014-01-14 | E-GEOD-54005 | biostudies-arrayexpress

Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease

Project description:This scRNA-seq dataset of five human subjects with ulcerative colitis (derived from colonic lamina propria samples), was analyzed and published as part of a larger manuscript (Mitsialis, V et al, "“Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease” in Gastroenterology), which reported immune signatures of blood and intestinal tissue differentiating ulcerative colitis from Crohn's disease from non-IBD human subjects using mass cytometry as well as scRNA-seq.

2020-05-09 | GSE150115 | GEO

Gene expression patterns of biopsies from a colonoscopy taken in 2009 of an ulcerative colitis patient infected with Trichuris trichiura

Project description:Helminth infection may have the potential to suppress intestinal inflammation in inflammatory bowel diseases. Ulcerative colitis is more common in developed countries than in developing countries endemic for helminth infections. There are animal models, as well as clinical trials, suggesting therapeutic effects of experimental helminth infection. Here, we provide a comprehensive molecular portrait of dynamic changes in the intestinal mucosa of an individual who infected himself with Trichuris trichiura to treat his symptoms of ulcerative colitis. Genes involved in carbohydrate and lipid metabolism were upregulated in helminth-colonized tissue, while tissues with active colitis showed upregulation of proinflammatory genes such as IL-17, IL13RA2, and CHI3L1. T. trichiura colonization of the intestine may reduce symptomatic colitis by promoting goblet cell hyperplasia and mucus production through TH2 cytokines and IL-22. By better understanding the physiological effects of helminth infection, new therapies for ulcerative colitis could be identified. This is the third (out of three) series of arrays from this patient from a colonoscopy in 2009 when the patient was in remission. We analyzed 12 HEEBO arrays on which were hybridized RNA amplified from pinch biopsies collected from different regions of the colon. 4 samples were from the ascending colon, which was colonized by worms at the time. 3 samples were from the transverse colon, which appeared normal at the time. 3 samples were from the recto-sigmoid colon, which had recovered from colitis at the time. 2 samples were from the terminal ileum, which was unaffected by worms or colitis.

2010-11-20 | E-GEOD-25277 | biostudies-arrayexpress

Gene expression patterns of biopsies from a colonoscopy taken in 2008 of an ulcerative colitis patient infected with Trichuris trichiura

Project description:Helminth infection may have the potential to suppress intestinal inflammation in inflammatory bowel diseases. Ulcerative colitis is more common in developed countries than in developing countries endemic for helminth infections. There are animal models, as well as clinical trials, suggesting therapeutic effects of experimental helminth infection. Here, we provide a comprehensive molecular portrait of dynamic changes in the intestinal mucosa of an individual who infected himself with Trichuris trichiura to treat his symptoms of ulcerative colitis. Genes involved in carbohydrate and lipid metabolism were upregulated in helminth-colonized tissue, while tissues with active colitis showed upregulation of proinflammatory genes such as IL-17, IL13RA2, and CHI3L1. T. trichiura colonization of the intestine may reduce symptomatic colitis by promoting goblet cell hyperplasia and mucus production through TH2 cytokines and IL-22. By better understanding the physiological effects of helminth infection, new therapies for ulcerative colitis could be identified. This is the second (out of three) series of arrays from this patient from a colonoscopy in 2008 when the patient was suffering from severe colitis but still had worms in the ascending colon. We analyzed 12 HEEBO arrays on which were hybridized RNA amplified from pinch biopsies collected from different regions of the colon. 4 samples were from the ascending colon, which was colonized by worms at the time. 4 samples were from the transverse colon, which was no longer colonized by worms at the time. 4 samples were from the recto-sigmoid colon, which was suffering from severe colitis at the time.

2010-11-20 | E-GEOD-25276 | biostudies-arrayexpress

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