Ontology highlight
ABSTRACT:
PROVIDER: PRJNA869932 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21081600_1.fastq.gz | Fastqsanger.gz | |||
| SRR21081600_2.fastq.gz | Fastqsanger.gz | |||
| SRR21081601_1.fastq.gz | Fastqsanger.gz | |||
| SRR21081601_2.fastq.gz | Fastqsanger.gz | |||
| SRR21081602_1.fastq.gz | Fastqsanger.gz |
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Project description:Background: The diagnosis of acute appendicitis can be surprisingly difficult without computed tomography, which carries significant radiation exposure. Genome-wide expression profiling was applied to whole blood RNA of acute appendicitis patients versus patients with other abdominal disorders, in order to identify biomarkers of appendicitis. From a large cohort of emergency patients, a discovery set of patients with surgically confirmed appendicitis, or abdominal pain from other causes, was identified. RNA from whole blood was profiled by microarrays, and RNA levels were filtered by a combined fold-change (>2) and p value (<0.05). A separate set of patients, including patients with respiratory infections, was used to validate a partial least squares discriminant (PLSD) prediction model. Results: Transcript profiling identified 37 differentially expressed genes (DEG) in appendicitis versus abdominal pain patients. The DEG list contained 3 major ontologies: infection-related, inflammation-related, and ribosomal processing. Appendicitis patients had lower level of neutrophil defensin mRNA (DEFA1,3), but higher levels of alkaline phosphatase (ALPL) and interleukin-8 receptor-ß (IL8RB), which was confirmed in a larger cohort of 60 patients using droplet digital PCR (ddPCR). Conclusions: Patients with acute appendicitis have detectable changes in the mRNA expression levels of factors related to neutrophil inate defense systems. The low defensin mRNA levels suggest that appendicitis patient's immune cells are not directly activated by pathogens, but are primed by diffusible factors in the microenvironment of the infection. The detected biomarkers are consistent with prior evidence that biofilm-forming bacteria in the appendix may be an important factor in appendicitis.
2016-06-08 | GSE83091 | GEO
Project description:Gene expression profiling of pediatric patients with simple appendicitis (SA) compared to perforated appendicitis (PA) and non-appendicitis abdominal pain (NAAP).
2024-02-20 | GSE225466 | GEO
Project description:Appendicitis is the most common condition necessitating emergency abdominal surgery. While most cases are localized, 20% are complicated and result in appendix perforation. The management of non-complicated appendicitis varies across different medical centers, encompassing both surgical and non-surgical options, whereas complicated appendicitis is predominantly managed surgically. Differentiating them poses a clinical challenge, especially in pediatric patients, crucial for guiding appropriate treatment strategies. Therefore, there is an unmet need for biomarkers to distinguish the two entities. Here we examined the utility of epigenetic liquid biopsies in appendicitis. We used DNA methylation markers specific to immune and gastrointestinal epithelial cells to assess the tissue origins of plasma cell-free DNA (cfDNA) in patients with appendicitis. Appendix epithelium cfDNA was not detected in plasma samples from children with appendicitis relative to patients with abdominal pain and controls. In contrast, neutrophil and regulatory T-cell cfDNA were elevated in appendicitis enhancing the specificity and sensitivity of appendicitis diagnosis beyond the information provided by neutrophil counts. Notably, eosinophil cfDNA was most significantly elevated in children with perforated compared with non-perforated appendicitis. This finding was cross-validated using a machine-learning approach. In conclusion, eosinophil cfDNA can serve as a non-invasive biomarker for diagnosing perforated appendicitis.
2025-04-30 | GSE275452 | GEO
Project description:Acute appendicitis manifests in two microbiome state types, with oral pathogens driving severity
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Project description:Appendiceal neoplasms include a heterogeneous group of epithelial and non-epithelial tumors with varying malignant potential. Despite the rise in incidence of appendiceal neoplasms in recent years, limited progress has been made in the understanding, management and therapeutic treatment. To comprehensively characterize the cell types and molecular mechanisms driving cellular remodeling in epithelial appendiceal neoplasms, we performed an integrated scRNA-seq study. We analyzed 126,998 cells from 16 appendix samples (11 peritoneal metastases samples, 5 healthy controls) and identified 33 distinct cell types/cell states with seven being cancer-specific. Highlights of our study include the characterization of tumor cells across the histologic spectrum, the identification of a novel cancer-associated-fibroblast (CAF) subtypes (fiCAFs) and the identification of pathologic-specific cellular crosstalks between tumor cells and the tumor microenvironment (TME). Together, our study provides a high-resolution insight into the complexity and heterogeneity of epithelial appendiceal neoplasms and a valuable resource for therapeutic strategies.
2023-10-04 | GSE244031 | GEO
Project description:Gene expression was evaluated in 9 appendix samples removed from patients who went to the operating room with the diagnosis of acute appendicitis and 4 samples removed for non-inflammatory reasons. A circumferential piece of tissue was obtained at the distal aspect of each specimen. The tissue was flash frozen at -80 degrees for later processing. Frozen specimens were homogenized into TriReagent and RNA was isolated according to the manufacturerâs instruction. RNA was processed and hybridized to Affymetrix microarray. Experiment Overall Design: 9 patients and 4 controls
2008-06-16 | E-GEOD-9579 | biostudies-arrayexpress
Project description:Gene expression was evaluated in 9 appendix samples removed from patients who went to the operating room with the diagnosis of acute appendicitis and 4 samples removed for non-inflammatory reasons. A circumferential piece of tissue was obtained at the distal aspect of each specimen. The tissue was flash frozen at -80 degrees for later processing. Frozen specimens were homogenized into TriReagent and RNA was isolated according to the manufacturer's instruction. RNA was processed and hybridized to Affymetrix microarray. Keywords: Disease state analysis
2008-04-22 | GSE9579 | GEO