miR-20b, miR-98, miR-125b-1*, and let-7e* as new potential diagnostic biomarkers in ulcerative colitis

Abstract

Author contributions: Coskun M and Bjerrum JT performed the experiments and data analysis, wrote the manuscript, and wrote the final revision of the article; Troelsen JT provided with analytical tools, intellectual input and advice; Olsen J provided with reagents and human tissue; Seidelin JB and Nielsen OH contributed to the conceptual design, drafting of the manuscript and revising it critically for important intellectual content; all authors approved the final submitted manuscript. Abstract AIM: To use microarray-based miRNA profiling of colonic mucosal biopsies from patients with ulcerative colitis (UC), Crohn's disease (CD), and controls in order to identify new potential miRNA biomarkers in inflammatory bowel disease. METHODS:Colonic mucosal pinch biopsies from the descending part were obtained endoscopically from patients with active UC or CD, quiescent UC or CD, as well as healthy controls. Total RNA was isolated and miRNA expression assessed using the miRNA microarray Geniom Biochip miRNA Homo sapiens (Febit GmbH, Heidelberg, Germany). Data analysis was carried out by principal component analysis and projection to latent structure-discriminant analysis using the SIM-CA-P+12 software package (Umetrics, Umea, Sweden). The microarray data were subsequently validated by quantitative real-time polymerase chain reaction (qPCR) performed on colonic tissue samples from active UC patients (n = 20), patients with quiescent UC (n = 19), and healthy controls (n = 20). The qPCR results were analyzed with Mann-Whitney U test. In silico prediction analysis were performed to identify potential miRNA target genes and the predicted miRNA targets were then compared with all UC associated susceptibility genes reported in the literature. RESULTS:The colonic mucosal miRNA transcriptome differs significantly between UC and controls, UC and CD, as well as between UC patients with mucosal inflammation and those without. However, no clear differences in the transcriptome of patients with CD and controls were found. The miRNAs with the strongest differential power were identified (miR-20b, miR-99a, miR-203, miR-26b, and miR-98) and found to be upregulated more than a 10-fold in active UC as compared to quiescent UC, CD, and controls. Two miRNAs, miR-125b-1* and let-7e*, were up-regulated more than 5-fold in quiescent UC compared to active UC, CD, and controls. Four of the seven miRNAs (miR-20b, miR-98, miR-125b-1*, and let-7e*) were validated by qPCR and found to be specifically upregulated in patients with UC. Using in silico analysis we found several predicted pro-inflammatory target genes involved in various pathways, such as mitogen-activated protein kinase and cytokine signaling, which are both key signaling pathways in UC.

Transcriptome and Multivariable Data Analysis of Corynebacterium glutamicum under Different Dissolved Oxygen Conditions in Bioreactors

“…MVDA effectively addresses complex information using advanced statistical algorithms and has been applied in the biopharmaceutical industry, including fermentation critical process data analysis, NIR spectral data analysis, and biomarker identification [40, 41]. We used MVDA to analyze the RPKM data to identify “biomarkers” of different DO conditions.…”

Biomarkers of Inflammatory Bowel Disease

“…Differentially expressed miRNAs were also observed in biopsies from the sigmoid colon of active UC patients, and quantitative PCR analysis confirmed the presence of two deregulated (both upregulated) miRNAs: miR-21 and miR-155 (92). A recent study comparing colonic mucosa biopsies from active UC or CD patients, quiescent UC or CD patients, and healthy controls, identified miR-20b, miR-99a, miR-203, miR-26b, and miR-98 as being upregulated in active UC compared to quiescent UC, CD, and controls (93). Two miRNAs, miR-125b-1* and let-7e*, were upregulated in quiescent UC compared to active UC, CD, and controls (93).…”

“…A recent study comparing colonic mucosa biopsies from active UC or CD patients, quiescent UC or CD patients, and healthy controls, identified miR-20b, miR-99a, miR-203, miR-26b, and miR-98 as being upregulated in active UC compared to quiescent UC, CD, and controls (93). Two miRNAs, miR-125b-1* and let-7e*, were upregulated in quiescent UC compared to active UC, CD, and controls (93). In the same year (2013), another paper showed that four miRNAs (miR-18a*, miR-629*, let-7b and miR-140-3p) were higher and three miRNAs were lower (miR-422a, miR-885-5p and miR-328) in the mucosa of active CD patients compared to quiescent CD patients, and two miRNAs were higher (miR-650 and miR-548a-3p) and three miRNAs were lower (miR-630, miR-489 and miR-196b) in the mucosa of active UC patients compared to quiescent UC patients (94).…”

miRNAs as new molecular insights into inflammatory bowel disease: Crucial regulators in autoimmunity and inflammation

“…Furthermore, they found that miR192 participated in the regulation of chemokine production in colonic epithelial cells. Since 2008, some new research in active UC and healthy controls has confirmed the upregulation of miR-21 [25,118] , miR 29a [119] , and miR126 [120] , and identified additional upregulated miRNAs, including miR7, miR29b, miR126*, miR1273p, miR135b, miR223 and miR 3243p [119] , miR31 [119,121] , miR150 [26] , miR155 [118] , miR146a, miR206, and miR424 [121] , and miR 20b and miR125b1* [122] . In contrast, miR1885p, miR215, miR320a, miR346 [119] , and miR200b [123] were downregulated in colon tissues from active UC patients compared with healthy controls.…”