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Series GSE83091 Query DataSets for GSE83091
Status Public on Jun 08, 2016
Title Acute Appendicitis: Transcript Profiling of blood identifies promising biomarkers and potential underlying processes
Organism Homo sapiens
Experiment type Expression profiling by array
Summary 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.
 
Overall design 40 samples were grouped into Discovery and Validation sets based on their clinical dx and analyzed for differential gene expression within groups by conditions
 
Contributor(s) Chawla LS, Toma IV, Davison D, Vaziri K, Lee J, Luca R, Seneff MG, Nyhan A, McCaffrey T
Citation(s) 27417541
Submission date Jun 07, 2016
Last update date Aug 13, 2018
Contact name Ian V Toma
E-mail itoma@gwu.edu
Phone 202-994-0292
Organization name The George Washington University
Department Medicine
Lab Genomic Medicine Division
Street address 2300 Eye Str., NW, Ross Hall, Rm. 443D
City Washington
State/province DC
ZIP/Postal code 20037
Country USA
 
Platforms (1)
GPL10558 Illumina HumanHT-12 V4.0 expression beadchip
Samples (40)
GSM2192918 PeripheralBlood_RNA_AppenDX_Project validation 073
GSM2192919 PeripheralBlood_RNA_AppenDX_Project validation 074
GSM2192920 PeripheralBlood_RNA_AppenDX_Project validation 076
Relations
BioProject PRJNA324717

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE83091_RAW.tar 90.1 Mb (http)(custom) TAR (of IDAT)
GSE83091_discovery_non-normalized.txt.gz 3.4 Mb (ftp)(http) TXT
GSE83091_discovery_normalized.txt.gz 5.0 Mb (ftp)(http) TXT
GSE83091_validation_non-normalized.txt.gz 3.1 Mb (ftp)(http) TXT
GSE83091_validation_normalized.txt.gz 4.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data provided as supplementary file
Processed data included within Sample table
Processed data is available on Series record
Raw data is available on Series record

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