Single-molecule modeling of mRNA degradation by miRNA: Lessons from data

[The role of miRNA in the pathogenesis of diseases associated with functional dysregulation of the lacrimal gland]

At this time, the mechanism causing lacrimal gland dysfunction is not understood completely. In diseases associated with lacrimal gland involvement (Sjogren's syndrome, sarcoidosis, IgG4-associated disease, etc.) patients have been observed to experience elevated cellular apoptosis, active production of autoantibodies to glandular tissue, increased level of pro-inflammatory cytokines, functional disruption of signaling molecules leading to changes in tear production. Difficulties in differential diagnosis of lacrimal gland dysfunction in above-listed diseases are associated, on the one hand, with similarity of the clinical picture of ophthalmological manifestations, and on the other hand - with complicated morphological interpretation of changes in the glandular tissues. In this view, miRNA is a promising diagnostic and prognostic marker that would help with differential diagnosis as well as with choosing the treatment tactics. Methods of molecular profiling and identification of "molecular phenotypes" of lacrimal gland and ocular surface damage will allow the use of miRNA as biomarkers and prognostic factors for personalized treatment.

Identification of 5 microRNA biomarkers associated with the prognosis of uveal melanoma

To uncover the role of microRNAs in the occurrence and development of uveal melanoma (UM), we used R language packages in this study to analyze the correlations between the expression of microRNA isoforms, their target genes, and the clinical data for UM patients retrieved from The Cancer Genome Atlas (TCGA). We used Weighted Correlation Network Analysis (WGCNA) to divide the expression profiles of different microRNAs into 10 modules, among which blue and yellow modules were associated with UM survival. Hsa-miR-513a-5p, miR-506-3p, miR-508-3p, miR-140-3p, and miR-103a-2-5p were further identified as the top 5 node microRNAs based on the risk scores in both modules using least absolute shrinkage and selection operator (LASSO) Cox regression analysis. After combining these 5 microRNAs into an integrated risk signature, the prognostic performance of the risk signature was evaluated by area under the receiver operating characteristic (AUROC) curve, and their association with UM clinical characteristics was further analyzed using multiple Cox regression. Our results showed that this risk signature was sensitivity and specificity, and could serve as an independent prognostic factor. In addition, Spearman correlation analysis showed that expression of almost all target mRNAs were significantly positively or negatively correlated with the associated microRNAs. The gene ontology (GO), pathways, and disease enrichment analyses also showed that these 5 microRNAs were closely related to the incidence and progression of tumor, indicating their potential for predicting the outcome of UM.

Degradation Parameters from Pulse-Chase Experiments

Pulse-chase experiments are often used to study the degradation of macromolecules such as proteins or mRNA. Considerations for the choice of pulse length include the toxicity of the pulse to the cell and maximization of labeling. In the general case of non-exponential decay, varying the length of the pulse results in decay patterns that look different. Analysis of these patterns without consideration to pulse length would yield incorrect degradation parameters. Here we propose a method that constructively includes pulse length in the analysis of decay patterns and extracts the parameters of the underlying degradation process. We also show how to extract decay parameters reliably from measurements taken during the pulse phase.

Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics

This Preface introduces the content of the BioMed Central journal Supplements related to BITS2014 meeting, held in Rome, Italy, from the 26th to the 28th of February, 2014.