Project description:To investigate the gene expression profile of inflamed and non-inflamed mucosa in patients with Crohn's disease. To investigate TCR repertoires in the intestinal mucosa, the expression profile of the TCR repertoire gene was analyzed.
Project description:A small percentage of ulcerative colitis patients may experience disease progression into colitis-associated colorectal cancer (CA-CRC). In the clinic, it is challenging to identify these patients. Consequently, all UC patients are followed closely by e.g. annual colonoscopy from eight years of the UC diagnosis. Although, the progression may still be difficult to discover as the neoplastic mucosa may appear with a flat structure. The need for biomarkers that early in the UC disease course can predict the predisposition to progress into CA-CRC is therefore highly wanted in the clinic. The objective of this gene expression analysis was to identify a set of genes with differential expression in inflamed mucosa of progressed UC patients compared to inflamed mucosa of non-progressed UC patients. The gene expression was examined using Agilent SurePrint G3 human gene expression 60K microarray.
Project description:Differential gene expression in inflamed mucosa of progressed UC patients compared to inflamed mucosa of non-progressed UC patients
Project description:The Illumina Infinium EPIC Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 867,000 CpGs in ileal fibroblast samples. Samples included 5 control samples and 13 Crohn’s disease samples. The Crohn’s disease samples can be further subdivided into inflamed (2), non-inflamed (7) and stenotic (4) samples. This experiment together was performed in conjunction with a gene expression experiment (GSE99816). Use Supplemental Table 2 of the manuscript to quickly find the samples that were present in both experiments.
Project description:The Illumina NextSeq500 was used to sequence the gene expression profiles of 21 ileal fibroblast samples. Samples included 6 control samples and 15 Crohn’s disease samples. The Crohn’s disease samples can be further subdivided into inflamed (4), non-inflamed (6) and stenotic (5) samples. This experiment together was performed in conjunction with a DNA methylation experiment (GSE99788). Use Supplemental Table 2 of the manuscript to quickly find the samples that were present in both experiments.
Project description:Studying differences in responders and non-responders to therapy in inflammatory bowel disease (IBD) patients (crohn's disease and ulcerative colitis)
Project description:Histology in the mesentery pointed to altered blood vessels. This experiment was designed to define the differences in gene expression in vessels from Crohn's disease versus controls. Crohn's disease was separately evaluated in inflamed (central disease) areas and in adjacent noninflamed areas. Laser capture microdissection was carried out on Carnoy's fixed mesenteric samples, comparing normal arteries or veins with Crohn's inflamed or nonifnlamed arteries or veins.
Project description:In Crohn's disease, creeping fat is the characteristic expansion of mesenteric adipose tissue wrapping around the inflamed intestine. Through a comparative transcriptomic analysis of creeping fat and normal-looking mesenteric adipose tissues from patients with Crohn's disease and non-Crohn's disease, we found that a dynamic transcriptional and cell compositional change occurs during the progression from non-Crohn's disease to Crohn's disease, and finally to creeping fat.