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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome analysis of patients with recurrent aphthous stomatitis suggests novel therapeutic targets

ABSTRACT: Gene expression patterns in tissue from control individuals is similar to non-ulcerated tissue from afflicted individuals, whereas marked differences were observed in ulcerated materials. Gene expression differences in ulcerated tissues provide clues to potential treatment options. Comparison of gene expression between normal tissue from control individuals and ulcer and non-ulcer tissue from afflicted individuals.

ORGANISM(S): Homo sapiens

SUBMITTER: M Cecilia Lopez

PROVIDER: E-GEOD-37265 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptome analysis of patients with recurrent aphthous stomatitis suggests novel therapeutic targets

Project description:Gene expression patterns in tissue from control individuals is similar to non-ulcerated tissue from afflicted individuals, whereas marked differences were observed in ulcerated materials. Gene expression differences in ulcerated tissues provide clues to potential treatment options.

2013-01-01 | GSE37265 | GEO

Transplantation of gastric organoid-derived spasmolytic polypeptide/TFF2-expressing metaplasia (SPEM) cell lineage promotes ulcer repair in the aged stomach

Project description:Background & Aims: Spasmolytic polypeptide/TFF2-expressing metaplasia (SPEM) is known to emerge following parietal cell loss and during Helicobacter pylori infection, however its role in gastric ulcer repair is unknown. Therefore, we sought to investigate if SPEM plays a role in epithelial regeneration. Methods: Acetic acid ulcers were induced in young (2-3 months) C57BL/6 mice to determine the quality of ulcer repair. Gastric tissue was collected and analyzed to determine the expression of SPEM within the regenerating epithelium. As a comparison to native tissue the expression of SPEM was also identified within cultured gastric mouse-derived organoids. Results: Wound healing in the mice coincided with the emergence of SPEM expressing CD44v within the ulcerated region. The emergence of SPEM was also observed in cultured gastric organoids. Conclusions: These data demonstrate the SPEM may play a role in epithelial regeneration. Conclusions: These data demonstrate the SPEM may play a role in epithelial regeneration. 4 samples were used for ulcerated and uninjured tissue. 1 sample was used for intact tissue and organoid-derived RNA. The 'Ulcerated' samples represent C57BL/6 mice with ulcers and the 'Uninjured' samples represent the healthy controls (for "ulcerated" samples). The "Intact stomach tissue" and "Gastric organoids" samples are other types of samples that compared separately. "Gastric organoids" in this comparison are derived from "Intact stomach tissue".

2015-09-23 | E-GEOD-73336 | biostudies-arrayexpress

Characterization of transcriptomic profile of ulcerated and intact stomach epithelium

Project description:Purpose: To explore the processes and mechanisms that are up/downregulated following ulceration of the stomach, in order to identify key mechanisms underlying ulcer healing. Methods: mRNA profiles of paired ulcerated and intact tissues were obtained from 4-month-old C57BL6 mice, in triplicate, 30 days after ulcer generation through 99% acetic acid. With a workflow involving alignment, quantification, and statistical analysis in GeneSpring NGS, data were analyzed at the gene level using a paired t-test. Results: Approximately 30million mRNA reads per sample aligned to over 34,000 known transcripts (UCSC mm10 genome). Paired t-tests that compared within-mouse ulcerated to intact tissue, identified 1165 transcripts with a p-value < 0.05 and fold change > 1.5. Conclusion: Among significantly dysregulated transcripts in ulcerated tissues, we observe a significant enrichment of genes related to stem-ness, tissue repair, and cancer-related processes

2017-01-01 | GSE76565 | GEO

Transplantation of gastric organoid-derived spasmolytic polypeptide/TFF2-expressing metaplasia (SPEM) cell lineage promotes ulcer repair in the aged stomach

2015-09-23 | GSE73336 | GEO

mRNA expression in ulcerated primary cutaneous melanoma (validation cohort)

Project description:mRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from ulcerated primary cutaneous melanoma compared to non-ulcerated primary cutaneous melanoma

2022-08-13 | GSE211093 | GEO

mRNA expression in ulcerated primary cutaneous melanoma

Project description:mRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from ulcerated primary cutaneous melanoma compared to non-ulcerated primary cutaneous melanoma

2022-08-13 | GSE211091 | GEO

microRNA expression in ulcerated primary cutaneous melanoma

Project description:microRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from ulcerated primary cutaneous melanoma compared to non-ulcerated primary cutaneous melanoma

2022-08-13 | GSE211090 | GEO

microRNA expression in ulcerated primary cutaneous melanoma (validation cohort)

Project description:microRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from ulcerated primary cutaneous melanoma (n=6) compared to non-ulcerated primary cutaneous melanoma (n=6)

2022-08-13 | GSE211092 | GEO

Comparative genomic hybridization of single colony purified H. pylori adhesin phenotyped isolates obtained from 25 cases and 71 controls in a Swedish case-control study of gastric cancer

Project description:Helicobacter pylori enhances the risk for ulcer disease and gastric cancer, yet only a minority of H. pylori-colonized individuals develop disease. We examined the ability of two H. pylori isolates to induce differential host responses in vivo or in vitro, and then used an H. pylori whole genome microarray to identify bacterial determinants related to pathogenesis. Gastric ulcer strain B128 induced more severe gastritis, proliferation, and apoptosis in gerbil mucosa than did duodenal ulcer strain G1.1, and gastric ulceration and atrophy occurred only in B128+ gerbils. In vitro, gerbil-passaged B128 derivatives significantly increased IL-8 secretion and apoptosis compared with G1.1 strains. DNA hybridization to the microarray identified several strain-specific differences in gene composition including a large deletion of the cag pathogenicity island in strain G1.1. Partial and complete disruption of the cag island in strain B128 attenuated induction of IL-8 in vitro and significantly decreased gastric inflammation in vivo. These results indicate that the ability of H. pylori to regulate epithelial cell responses related to inflammation depends on the presence of an intact cag pathogenicity island. Use of an H pylori whole genome microarray is an effective method to identify differences in gene content between H. pylori strains that induce distinct pathological outcomes in a rodent model of H. pylori infection.

2005-06-30 | E-SMDB-1587 | biostudies-arrayexpress

H. pylori strain comparisons

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