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Updated: Sep 16, 2025
Perturbations of Circulating miRNAs in Irritable Bowel Syndrome Detected Using a Multiplexed High-throughput Gene Expression Platform
Published on: November 30, 2016
Biomarker discovery for non-invasive diagnosis of inflammatory bowel disease using blood transcriptomics
Mohammad Hossein Derakhshan Nazari1, Mahsa Ghorbaninejad1, Shabnam Shahrokh2
1Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
Introduction:
Colonoscopy remains the gold standard for diagnosing inflammatory bowel disease (IBD) even though it is an invasive and costly procedure. To enable non-invasive diagnosis, we aimed to identify blood-based transcriptomic biomarkers that specifically distinguish IBD from healthy and inflammatory controls.
Methods:
Public microarray and RNA-seq datasets from whole blood of IBD, rheumatoid arthritis (RA), and control subjects were analyzed. RA was included as a positive control for systemic inflammation to filter out non-IBD-specific gene signatures. Differentially expressed genes (DEGs) were identified, followed by immune cell deconvolution (CIBERSORTx), pathway and network analysis, and diagnostic model construction using LASSO and SVM. A real-life cohort (36 IBD patients, 30 controls) was recruited for qRT-PCR validation.
Results:
IBD blood transcriptomes exhibited altered immune profiles, including increased M0 macrophages, Tregs, and CD4 naïve T cells, and decreased memory B and activated NK cells. After excluding RA-overlapping DEGs, 25 IBD-specific DEGs with |log2FC| > 0.5 were prioritized. LASSO and SVM identified a three-mRNA panel-IL4R, EIF5A, and SLC9A8-which achieved 84% diagnostic accuracy in the discovery cohort and 99% accuracy in the real-life cohort. Network analysis highlighted NDUFB2 as a key downregulated hub gene linked to mitochondrial complex I dysfunction and oxidative phosphorylation disruption. Elevated oxidative stress in IBD was confirmed by increased Total Oxidant Status (TOS) levels in patient plasma.
Discussion:
Our findings support the use of peripheral blood transcriptomics for IBD diagnosis and demonstrate that a focused three-gene panel can achieve high diagnostic accuracy. The inclusion of RA as an inflammatory control enabled the identification of IBD-specific markers, minimizing confounding from general immune activation. These results provide a practical foundation for developing non-invasive diagnostic tools for clinical use.
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