Transcription profiling of mouse conventional and germ-free ileum, colon and rectum
ABSTRACT: Whole tissues corresponding to the ileum, colon and rectum were dissected from adult mice and used for RNA preparation. The aim of experiment was to study the impact of gut microbiota on gene expression in different gut regions. Experiment Overall Design: Three biological replicates were used for each condition. Each RNA preparation was independently hybridized to one chip.
Project description:Ochratoxin A gene expression profiling in liver and kidney, with time points of exposure from 7 days to 12 months Experiment Overall Design: three replicates for each timepoint measured, control and ochratoxin A treated for both liver and kidney. <br><br>Note that files GSM62732.CEL and GSM62733.CEL, and files GSM62730.CEL and GSM62739.CEL as downloaded from GEO contain identical data.
Project description:Colorectal cancer studies typically include both colon and rectum tumors as a common entity, though this assumption is controversial and only minor differences have been reported at the molecular and epidemiologic level. We conducted a molecular study based on gene expression data of tumors from colon and rectum to assess the degree of similarity between these cancer sites at transcriptomic level.A pooled analysis of 460 colon tumors and 100 rectum tumors from four data sets belonging to three independent studies was conducted. Microsatellite instable tumors were excluded as these are known to have a different expression profile and have a preferential proximal colon location. Expression differences were assessed with linear models, and significant genes were identified using adjustment for multiple comparisons.Minor differences at a gene expression level were found between tumors arising in the proximal colon, distal colon, or rectum. Only several HOX genes were found to be associated with tumor location. More differences were found between proximal and distal colon than between distal colon and rectum.Microsatellite stable colorectal cancers do not show major transcriptomic differences for tumors arising in the colon or rectum. The small but consistent differences observed are largely driven by the HOX genes. These results may have important implications in the design and interpretation of studies in colorectal cancer.
Project description:Squamous cell carcinoma (SCC) of the rectum is a rare clinical entity with an incidence rate of 0.1-0.25% per 1,000 cases. Though its etiology and pathogenesis remains unclear, it has been associated with chronic inflammation and infections. Herein, we report a case of an 82-year-old female who presented with a 2-month history of worsening abdominal pain, hematochezia, and bilateral inguinal lymphadenopathy with right-sided purulent discharge. Two years prior, she had had an unremarkable screening colonoscopy which met all quality indicators. Abdominal CT scan showed an irregular rectal mass with bulky pelvic and retroperitoneal adenopathy. Colonoscopy revealed one large circumferential nonobstructing lesion in the rectum. Endoscopic ultrasound confirmed its origin from the rectal wall with an enlarged perirectal lymph node. Cold biopsy followed by histopathology revealed SCC of the rectum.
Project description:Lower gastrointestinal (GI) bleed due to hemangioma in rectum is an uncommon problem. A 19-year-old female patient presented with history of recurrent episodes of lower GI bleeding 1-2 times/month for last 3 years. At the time of hospitalization her vital signs were normal and rectal examination revealed frank blood. Investigations revealed a hemoglobin level of 8.9 g/dL and normal coagulation parameters. Colonoscopy showed bluish reddish elevated nodular lesions limited to distal rectum. Magnetic resonance imaging and endoscopic ultrasound showed cavernous hemangioma.
Project description:Using isolation stress model, we showed that goblet cell-dependent mucosal barrier functions in the mouse rectum was more vulnerable to stress than the colon. We also found that isolation stress specifically stimulated IL-18 production only in the rectum. Furthermore, the crucial role of IL-18 in the stress response of the mouse rectum was confirmed using IL-18 knockout mice. Microarray analysis was used to assess the stress response and to identify responsible genes for the vulnerability of the mouse rectum to isolation stress. Experiment Overall Design: Total RNA was prepared from the colon and the rectum of wild-type and IL-18 knockout mice before isolation and 8 days after starting isolation. The one GSM sample of microarray analysis was made by pooling an equal amount of total RNA 5 mice of each group. Agilent whole mouse genome oligonucleotide microarray was used to measure gene expression in these samples according to the manufacture’s protocol.
Project description:Using isolation stress model, we showed that goblet cell-dependent mucosal barrier functions in the mouse rectum was more vulnerable to stress than the colon. We also found that isolation stress specifically stimulated IL-18 production only in the rectum. Furthermore, the crucial role of IL-18 in the stress response of the mouse rectum was confirmed using IL-18 knockout mice. Microarray analysis was used to assess the stress response and to identify responsible genes for the vulnerability of the mouse rectum to isolation stress. Overall design: Total RNA was prepared from the colon and the rectum of wild-type and IL-18 knockout mice before isolation and 8 days after starting isolation. The one GSM sample of microarray analysis was made by pooling an equal amount of total RNA 5 mice of each group. Agilent whole mouse genome oligonucleotide microarray was used to measure gene expression in these samples according to the manufacture’s protocol.
Project description:We have demonstrated that the colon and rectum are transcriptionally distinct in mice and that the colon can be differentiated from rectum based on microarray profiles. This transition occurs over the first weeks of life, indicating environmental exposure is an important mediator. Colon and rectum RNA from E18 to 8 week old C57BL/6J mice along with 8 week old gnotobiotic C57BL/6J mice were evaluated with microarray technology. For each array analysis a pool of RNA(2-8) from individual colons or rectums were co-hybridized with a reference pool of 4 RNA samples from mouse small intestine, rectum and colon (SIRC)) to Agilent Mouse Whole Genome 4x44k microarrays and scanned on an Agilent microarray scanner. Files were extracted using Agilent Feature Extraction version 9.5.
Project description:Gastrointestinal stromal tumors (GISTs) of the colon and rectum are the most common mesenchymal tumors of the gastrointestinal tract. GISTs of the colon and rectum constitute ~5% of all cases. Although colorectal GISTs can be small and found incidentally, the majority appear to be high risk and carry a significant likelihood of recurrent and metastatic disease. Surgery remains the mainstay of treatment for primary disease. There is now considerable interest in GISTs because they can be treated effectively with targeted molecular therapies, specifically tyrosine kinase inhibitors (TKIs), such as imatinib mesylate and sunitinib malate. GISTs are best treated by a multidisciplinary team comprised of the surgeon, medical oncologist, pathologist, and radiologist in the initial evaluation, management, and in continued follow-up. Increasing the number of resectable cases through pharmacologic debulking, optimizing the timing of surgery and organ preservation, reducing recurrence and surgical morbidity, prolonging survival, and possibly enhancing response to imatinib through surgical cytoreduction are all potential benefits of multidisciplinary management.
Project description:Normal human colorectal mucosa was sampled at points along the colon. Keywords: normal human tissue Overall design: Normal human colorectal mucosa, cecum, ascending, transverse, sigmoid and rectum
Project description:Autonomic and somatic components participate in the defecation process in mammals, combining signals from the brainstem and forebrain. The innervation pattern involved in micturition in rats has been well studied, while defecation has been less studied. The aim of the present study was to identify the most important sensory and motor nerves of the anal canal and rectum involved in defecation. The amplitudes of evoked potential of the anal canal and rectum were higher when L6 and S1 ventral rootlets were stimulated, compared with the other segments (ANOVA and Tukey's post hoc test, all P?<?0.05). The S1 segment was more strongly cholera toxin subunit B conjugated to horseradish peroxidase (CB-HRP) positive compared with the other segments (ANOVA and Tukey's post hoc test, P?<?0.05). Ventral spinal rootlets of L6 and S1 mainly contributed to the pressure change in the anal canal and rectum when the ventral spinal rootlets from L5 to S3 were stimulated electrically. In conclusion, many afferent and efferent nerves innervate the anal canal and rectum and are involved in defecation, but the S1 nerve rootlet could be the most efficient one. These results could provide a basis for defecation reconstruction, especially for patients with spinal cord injuries.