Gene expression profile in porcine buccal pouch mucosal cells during long-term in vitro culture
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ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE112659 | GEO | 2018/04/05
REPOSITORIES: GEO
Similar Datasets
Project description:To examine the mechanism underlying chemoprevention and changes in gene expression pattern induced by chlorophyllin and ellagic acid during 7,12-dimethylbenz[a]anthracene (DMBA)-induced hamster buccal pouch (HBP) carcinogenesis
2011-06-02 | GSE29679 | GEO
Project description:To examine the mechanism underlying chemoprevention and changes in gene expression pattern induced by chlorophyllin and ellagic acid during 7,12-dimethylbenz[a]anthracene (DMBA)-induced hamster buccal pouch (HBP) carcinogenesis Two-condition experiment, Control vs. DMBA, Control vs. DMBA+chloophyllin, Control vs. DMBA+ellagic acid. Biological replicates: 2 control replicates, 2 DMBA replicates, 2 DMBA+chlorophyllin replicates, 2 DMBA+ellagic acid replicates.
2011-06-02 | E-GEOD-29679 | biostudies-arrayexpress
Project description:Gene expression profile in porcine buccal pouch mucosal cells during long-term in vitro culture
| PRJNA448669 | ENA
Project description:A total proctocolectomy with ileal pouch-anal anastomosis (IPAA) is considered the surgery of choice for definitive management of familial adenomatous polyposis (FAP) and selected patients with ulcerative colitis (UC). However, this surgical treatment often associates with a long-term complication, pouchitis, which occurs mostly in UC patients. To better define the molecular background of pouchitis, the microarray-based survey was performed using pouch mucosal samples collected from 28 and 8 patients operated for UC and FAP, respectively. A number of 4771 genes was significantly differentiating uninflamed from inflamed mucosal samples, and their functional features were represented mostly by alerted metabolic and cell proliferation pathways. In contrast, functional analyses of aberrantly expressed probe sets between UC and FAP samples, irrespectively of mucosal inflammation status, revealed multiple pathways and terms which were linked to changes in immune response. Noteworthy, the comparison of uninflamed UC and FAP samples distinguished a set of 26 altered mRNAs including inflammation-related transcript encoding a Charcot-Leyden crystal (CLC) protein. The most discrete changes in gene expression profiles differentiating uninflamed UC and FAP mucosal samples were attributed to a Gene Ontology category innate immune response. Our study confirmed alterations of the immune responses as dominant in UC pouchitis which were earlier found in the studies using analyses of singular molecular elements. This observation may be important when managing IPAA patients. Each sample represents three biopsies taken from single patient, from the same areas of the lower part of the pouch mucosa (above the rectal cuff) during endoscopic examination. 28 patients underwent surgery for UC and 8 patients for FAP.
2014-05-01 | E-GEOD-50788 | biostudies-arrayexpress
Project description:Mast cells (MCs) were implicated in tissue remodelling in hamster models of heart inflammatory diseases. Here we asked whether MCs promote inflammatory neovascularization in hamster cheek pouch (HCP) parasitized by Trypanosoma cruzi, the protozoan that causes Chagas disease. Intravital microscopy (IVM) performed 3 days after inoculation of Dm28c trypomastigote (GFP-TCTs) showed a subtle infiltration of rhodamine-labeled leukocytes. Interestingly, the baseline levels of FITC-dextran leakage (3 dpi) were consistently increased, raising the possibility that intracellular amastigotes may coopt the low-grade inflammation to facilitate the delivery of plasma-borne nutrients during the period in which host cells must metabolically sustain parasite division. Although proangiogenic indexes were only mildly stimulated at 3 dpi, we found a positive correlation with transcription of proinflammatory cytokines (pro-IL- and IFN-). Having established 3 dpi as a timepoint in which vascular remodeling was already measurable, we next compared the proteomic profiles of parasitized HCP with those of internal controls (PBS injected 3 days earlier in the contralateral pouch) we found 87 proteins upregulated, and 17 were downregulated in the parasitized HCP. Minor changes in protein expression were observed in response to PBS injection (2 upregulated and 12 downregulated proteins. Congruent with the increased density of MCs observed in parasitized HCP (histological analysis), the MC protease 1 (chymase) stood out as the most abundant sequence. Interestingly, toluidine blue staining appointed clusters of MCs degranulating at 3 dpi. Noteworthy, two plasma proteins (complement C3 and serum albumin) were also identified as major proteins, further suggesting that leaky capillaries irrigated the HCP at early stages (3 dpi) of infection . Detection of cytokines or classical proangiogenic factors was beyond the sensitivity of our methods.
2022-04-04 | PXD026905 | Pride
Project description:A total proctocolectomy with ileal pouch-anal anastomosis (IPAA) is considered the surgery of choice for definitive management of familial adenomatous polyposis (FAP) and selected patients with ulcerative colitis (UC). However, this surgical treatment often associates with a long-term complication, pouchitis, which occurs mostly in UC patients. To better define the molecular background of pouchitis, the microarray-based survey was performed using pouch mucosal samples collected from 28 and 8 patients operated for UC and FAP, respectively. A number of 4771 genes was significantly differentiating uninflamed from inflamed mucosal samples, and their functional features were represented mostly by alerted metabolic and cell proliferation pathways. In contrast, functional analyses of aberrantly expressed probe sets between UC and FAP samples, irrespectively of mucosal inflammation status, revealed multiple pathways and terms which were linked to changes in immune response. Noteworthy, the comparison of uninflamed UC and FAP samples distinguished a set of 26 altered mRNAs including inflammation-related transcript encoding a Charcot-Leyden crystal (CLC) protein. The most discrete changes in gene expression profiles differentiating uninflamed UC and FAP mucosal samples were attributed to a Gene Ontology category innate immune response. Our study confirmed alterations of the immune responses as dominant in UC pouchitis which were earlier found in the studies using analyses of singular molecular elements. This observation may be important when managing IPAA patients.
2014-05-01 | GSE50788 | GEO
Project description:Normal and two transformed buccal keratinocyte lines were cultured under a standardized condition to explore mechanisms of carcinogenesis and tumor marker expression at transcript and protein level. An approach combining three bioinformatic programs allowed coupling of abundant proteins and large-scale transcript data to low-abundance transcriptional regulators. The analysis identified previously proposed, and suggested novel, protein biomarkers, Gene Ontology categories and molecular networks including functionally impaired key regulator genes for buccal/oral carcinoma. Experiment Overall Design: Analysis of differential expression in two transformed buccal keratinocyte lines (SVpgC2a and SqCC/Y1) relative to normal buccal keratinocytes. Both normal and transformed cells were cultured under a standardized serum-free condition. Experiment Overall Design: Two replicates for all cell types were included.
2008-06-15 | E-GEOD-7862 | biostudies-arrayexpress
Project description:Normal and two transformed buccal keratinocyte lines were cultured under a standardized condition to explore mechanisms of carcinogenesis and tumor marker expression at transcript and protein level. An approach combining three bioinformatic programs allowed coupling of abundant proteins and large-scale transcript data to low-abundance transcriptional regulators. The analysis identified previously proposed, and suggested novel, protein biomarkers, Gene Ontology categories and molecular networks including functionally impaired key regulator genes for buccal/oral carcinoma. Keywords: Cell type comparison
2007-08-21 | GSE7862 | GEO
Project description:Pouchitis is a common complication for ulcerative colitis (UC) patients with ileal pouch-anal anastomosis (IPAA) surgery. Similarly to IBD, both innate host factors such as genetics, and environmental stimuli including the tissue-associated microbiome have been implicated in the pathogenesis. In this study, we make use of the IPAA model of inflammatory bowel disease (IBD) to carry out a study associating mucosal host gene expression with the microbiome and corresponding clinical outcomes.
2015-01-27 | GSE65270 | GEO
Project description:UC pouchitis is a potential model of UC. We prospectively examined the pouch transcriptomes of UC and familial adenomatous polyposis (FAP) IPAA patients to unveil molecular mechanisms of UC pouchitis susceptibility. Methods: Total RNA was isolated using the AllPrep DNA/RNA Mini Kit (QIAGEN, Cat No. 8020). RNA quality was evaluated using Bioanalyzer (Agilent, Santa Clara, CA). All RNA samples displayed RNA Integrity Number (RIN) >7. RNAseq including cDNA library preparation was processed at the Genomics Core Facility of University of Chicago (https://fgf.uchicago.edu/). Total RNA in the amount of 100-500μg per sample was depleted of ribosomal RNA using the Ribo-Zero kit (Epicentre, Madison, WI). The directional (first strand) cDNA libraries were prepared following the guide of TruSeq Stranded Total RNA Sample Preparation kit. Results: Unlike FAP patients, UC subjects exhibited a large set of differentially expressed genes (DEGs) between pouch and pre-pouch mucosa as early as 4 months after pouch functionalization. Functional pathway analysis of DEGs in UC pouch revealed: (1) Gain of colon-associated gene expressions and loss of ileum associated gene expressions, (2) enhanced state of immune/inflammatory response, and (3) suppressed xenobiotic, lipid, and bile acid metabolic pathways. These changes were corroborated upon reanalysis of a published larger cross-sectional study of UC and FAP patients. Moreover, >70% of DEGs mapped to published IBD and normal colonic microarray datasets displayed directional changes consistent with active UC, but not Crohn's disease. Conclusions: UC patients exhibit a unique transcriptomic response to ileal pouch creation that can be observed well before disease. The transcriptome alterations provide insights into pouchitis
2016-05-11 | GSE81266 | GEO