Genome-wide And MicroRNAs Expression Profiling Of Colonic Mucosa In Diarrhea-predominant Irritable Bowel Syndrome And Ulcerative Colitis

and Aims] Diarrhea-predominant irritable bowel syndrome (IBS-D) and ulcerative colitis (UC) are the diseases characterized with diarrhea symptom. Manifestation of mild UC or inactive UC is similar to that of IBS, but it is unclear whether there is relationship of pathogenesis between IBS-D and UC. We have found some differential expression genes in IBS-D based on the recent improvements in molecular level study, but the change of single gene expression cannot explain the complex pathophysiological processes. We have also found the differential expression proteins by proteomics, and several mRNA expressions are inconsistent with the protein expression which indicates there is a potential mechanism to regulate corresponding gene expression. With the determination of the human genome sequence, we have known that large amount of non-coding RNA are in the human genome sequence, such as microRNA(miRNA) which cannot be translated to proteins, but plays regulatory roles by repressing translation or cleaving RNA transcripts in the protein synthesis procedure. We supposed the negative regulation result in the inconsistent expression between the proteins and their mRNA, which lead to the reversibility of diseases in certain stages, and the manifestation become mild and dormant. We believed that it could promote the improvement and apply a new clue to the research of pathogenesis in IBS if we can find the coincident results between the miRNAs, target genes and protein expression in colonic mucosa in IBS. Rapid improvements in bio-chip technique and bioinformatic approaches make it possible to study the genome-wide and miRNAs expression profiling with high throughput and high efficiency. The aims of this study are to investigate the expression spectrum of genome-wide and miRNAs using the bio-chip technique, and clarify the differential expression genes and miRNAs in IBS-D and UC. The differential expression miRNAs and possible target genes are analyzed by bioinformatics approaches secondly. Finally, the differential expression genes of IBS-D are predicted the classification of biological functions in order to apply a new clue and evidences to the molecular mechanism and molecular diagnosis in IBS-D and UC.[Material and Methods] In our study,56 samples (IBS-D 20 cases, UC 20 cases and controls 16 cases) of colonic mucosa were performed for genome-wide scanning and 48 samples (IBS-D 16 cases, UC 17cases and controls 15 cases) for miRNAs expression profiling. Data of profiling were analyzed by bioinformatics approaches. Illumina custom model, Mann-Whitney and t test were used to achieved the differ score and p value in IBS-D compared with control and UC compared with control, respectively. MiRanda software was used to screening the target genes and miRNAs. The information of differential expression genes was searched in NCBI Gene, Gene Ontology and OMOM database to predict the possible classification in biological functions. Cluster analysis included pedigree clusters and SAM clusters. Molecular classification to the IBS-D and UC were analyzed by T-class based on miRNA profiling.[Results] 1. Genome-wide and microRNAs expression profiling of colonic mucosa in patients with diarrhea-predominant irritable bowel syndrome and ulcerative colitis were achieved successfully. One hundred and twenty-three genes and 61 miRNAs expression were significantly increased and 99 genes and 78 miRNAs were markedly decreased in colonic tissue of IBS-D. One thousand three hundred and one genes,33 miRNAs expression was increased in UC. On the contrary,1595 genes and 35 miRNAs expression was suppressed in UC. Five genes expression was increased and 17 genes expression was decreased consistently in both groups, and 15 genes expression was reversed. Twenty-one miRNAs were enhanced and 29 were attenuated identically between two groups.2. Differential expression genes and target miRNAs were determined in IBS-D and UC.3. Prediction to the possible classification in biological functions indicated the differential expression genes were related to the transcription regulation, energy metabolism and cytoskeleton.4. Potential molecular subtypes of IBS-D were found for the first time, one subtype was characterized by the increased expression of miR-634, miR-561 and miR-33, and another by the increased expression of miR-548, miR-489 and miR-513.5. Combined detection of 5 miRNAs including miR-100, miR-125a, miR-132, miR-25, and miR-30a-3p could differentiate IBS-D from UC accurately.[Conclusions] 1. Genome-wide and miRNAs expression profiling of colonic mucosa in patients with diarrhea-predominant irritable bowel syndrome and ulcerative colitis were achieved successfully, and differential expression genes and miRNAs were found.2. Differential expression genes and target miRNAs were determined in IBS-D and UC.3. Differential expression genes in IBS-D were mainly related to the transcription regulation, energy metabolism and cytoskeleton according to the biological functions prediction.4. Molecular subtypes of IBS-D were found for the first time.5. Molecular markers of IBS-D and UC were found firstly, which is possible to differentiate IBS-D from UC. The significance of our findings should be clarified in future.