Abstract
Peripheral blood is an attractive source for the discovery of disease biomarkers. Gene expression profiling of whole blood or its components has been widely conducted for various diseases. However, due to population heterogeneity and the dynamic nature of gene expression, certain biomarkers discovered from blood transcriptome studies could not be replicated in independent studies. In the meantime, it’s also important to know whether a reliable biomarker is shared by several diseases or specific to certain health conditions. We hypothesized that common mechanism of immune response in blood may be shared by different diseases. Under this hypothesis, we surveyed publicly available transcriptome data on infectious and autoimmune diseases derived from peripheral blood. We examined to which extent common gene dys-regulation existed in different diseases. We also investigated whether the commonly dys-regulated genes could serve as reliable biomarkers. First, we found that a limited number of genes are frequently dys-regulated in infectious and autoimmune diseases, from which we selected 10 genes co-dysregulated in viral infections and another set of 10 genes co-dysregulated in bacterial infections. In addition to its ability to distinguish viral infections from bacterial infections, these 20 genes could assist in disease classification and monitoring of treatment effect for several infectious and autoimmune diseases. In some cases, a single gene is sufficient to serve this purpose. It was interesting that dys-regulation of these 20 genes were also observed in other types of diseases including cancer and stroke where certain genes could also serve as biomarkers for diagnosis or prognosis. Furthermore, we demonstrated that this set of 20 genes could also be used in continuous monitoring of personal health. The rich information from these commonly dys-regulated genes may find its wide application in clinical practice and personal healthcare. More validation studies and in-depth investigations are warranted in the future.
Highlights
Peripheral blood as a minimally invasive source has been widely used in biomarker discovery for many diseases
The remaining 12 datasets[8, 19,20,21,22,23,24,25,26,27,28,29] were related to malaria, systemic lupus erythematosus (SLE), burn, injury, tuberculosis (TB), scleroderma, primary Sjogren’s Syndrome, rheumatoid arthritis (RA), sarcoidosis, common variable immune deficiency (CVID), Kawasaki disease (KD), systemic-onset juvenile idiopathic arthritis
We have demonstrated that a small set of 20 genes displayed frequent and significant dys-regulation in infectious and autoimmune diseases
Summary
Data collectionWe collected public datasets on blood transcriptome from Gene Expression Omnibus (GEO). We collected 20 datasets on infectious or autoimmune diseases for gene selection (Table A in S1 File). The frontline of immune response in peripheral blood blood transcriptome was chosen for each disease, preferably with sample size greater than 20 in both case and control groups. These included 4 datasets[13,14,15] for bacterial infections and 4 datasets[15,16,17,18] for viral infections. We collected 34 additional datasets on infectious or autoimmune diseases or cancer (Table E in S1 File). For datasets with similar experimental design, we generally selected the ones with larger sample size and higher quality (defined below)
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