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ABSTRACT:
PROVIDER: PRJNA1120246 | ENA |
REPOSITORIES: ENA
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Project description:Clinical strain from a perianal abscess
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Project description:The CA-MRSA- or MSSA-infected pus samples of breast abscess were collected for the followed dual-omics studies. For label-free analysis, five CAMRSA and five MSSA samples were used, followed by PRM validation of candidate biomarkers.
2024-01-26 | PXD046678 | Pride
Project description:Carbapenem-resistant Enterobacteriaceae perianal abscess as a secondary bacterial infection in a critically-ill COVID-19 patient
| PRJDB11627 | ENA
Project description:Perianal Fistulizing Crohn’s Disease (perianal-CD) is a debilitating form of CD typically associated with prolonged periods of morbidity. Leveraging single-cell RNA sequencing, rectal mucosal tissue was sequenced from individuals following anti-TNF biologic therapy having either active perianal-CD and inflamed rectal mucosa or healed perianal-CD but non-inflamed mucosa. Single cell transcriptomic profiles of the inflamed and non-inflamed tissue were contrasted to test for specific cellular subsets of rectal epithelial and immune cell compartments associated with inflamed perianal disease. We identified eight broad classes of epithelial, six of immune, and a small population of stromal cells in the rectal mucosa. There was an increase in colonocytes in the non-inflamed tissue compared to the inflamed tissue, and an increase of naïve b cells and plasma cells associated with inflamed tissue. The cell type proportions of immune cells, highlighted patient heterogeneity of cell type abundance and potential dysregulation of both the immune and epithelial compartment. We also note enrichment of IgG plasma cells in inflamed tissue of two donors and expansion of IgA plasma cells of non-inflamed tissue in two donors. Differential gene expression analysis of goblet cells revealed enrichment of inflammatory pathways, such as IL6 and interferon gamma signaling, in inflamed tissue. These inflammatory pathways might affect tight junctions between epithelial cells leading to increased permeability and potentially affect fistula formation. Our findings suggest dysregulation of crypt maturation during persistent inflammation and over-abundance of goblet cells and colonocyte precursors in inflamed tissue of perianal-CD.
2023-02-20 | GSE225199 | GEO
Project description:Background and aims: Perianal fistulizing Crohn’s disease (CD) is severe and often more difficult to treat than luminal CD. Current therapeutics focusing solely on the immune system neither target epithelial and mesenchymal compartments nor consider genetic/epigenetic mechanisms, potentially missing causative aspects of the disease. Thus, the mucosal cells and organoids from a cohort of perianal fistulizing CD patients and controls with diverse genetic backgrounds were experimentally examined. Results: Overall, 140,503 mucosa and 77,044 organoid cells were sequenced. Inflamed perianal CD showed changes across the mucosal compartments (epithelium, immune, stromal), the most dramatic taking place in the epithelium. Epithelial changes occurring in the rectum of perianal CD patients associated with inflammation, gender, and ancestry, and were accompanied by a reduction in differentiated lineages. Organoids from the patient cohort retained both the gender- and ancestral-specific gene expression but did not overwhelmingly reflect their disease status. Organoids lacked bona fide differentiated lineages, but secretory pathways were promoted through PGE2-PTGER4 signaling and HDAC function. Conclusion: Epigenetic modifications are disrupted in the epithelium during inflammation and perianal fistulizing CD that affect the differentiation capacity of those cells, limiting their production/function and thus diminishing the ability of the patients’ mucosal tissue to heal. These epigenetic modifications appear to be modulated by crosstalk between the epithelial and mesenchymal cells, and thus might be leveraged therapeutically.
2024-11-22 | GSE256497 | GEO