Large-Scale microRNA Expression Profiling Identifies Putative Retinal miRNA-mRNA Signaling Pathways Underlying Form-Deprivation Myopia in Mice

Development of myopia is associated with large-scale changes in ocular tissue gene expression. Although differential expression of coding genes underlying development of myopia has been a subject of intense investigation, the role of non-coding genes such as microRNAs in the development of myopia is largely unknown. In this study, we explored myopia-associated miRNA expression profiles in the retina and sclera of C57Bl/6J mice with experimentally induced myopia using microarray technology. We found a total of 53 differentially expressed miRNAs in the retina and no differences in miRNA expression in the sclera of C57BL/6J mice after 10 days of visual form deprivation, which induced -6.93 ± 2.44 D (p < 0.000001, n = 12) of myopia. We also identified their putative mRNA targets among mRNAs found to be differentially expressed in myopic retina and potential signaling pathways involved in the development of form-deprivation myopia using miRNA-mRNA interaction network analysis. Analysis of myopia-associated signaling pathways revealed that myopic response to visual form deprivation in the retina is regulated by a small number of highly integrated signaling pathways. Our findings highlighted that changes in microRNA expression are involved in the regulation of refractive eye development and predicted how they may be involved in the development of myopia by regulating retinal gene expression

Licensed human natural killer cells aid dendritic cell maturation via TNFSF14/LIGHT

Interactions between natural killer (NK) cells and dendritic cells (DC) aid DC maturation and promote T cell responses. Here, we have analysed the response of human NK cells to tumor cells and we identify a pathway by which NK-DC interactions occur. Gene expression profiling of tumor-responsive NK cells identified the very rapid induction of TNFSF14 (also known as LIGHT), a cytokine implicated in the enhancement of anti-tumor responses. TNFSF14 protein expression was induced by three primary mechanisms of NK cell activation, namely via the engagement of CD16, by the synergistic activity of multiple target cell-sensing NK cell activation receptors and by the cytokines IL-2 and IL-15. For anti-tumor responses, TNFSF14 was preferentially produced by the licensed NK cell population, defined by the expression of inhibitory receptors specific for self-MHC class I molecules. In contrast, IL-2 and IL-15 treatment induced TNFSF14 production by both licensed and unlicensed NK cells, reflecting the ability of pro-inflammatory conditions to override the licensing mechanism. Importantly, both tumor and cytokine activated NK cells induced DC maturation in a TNFSF14-dependent manner. The coupling of TNFSF14 production to tumor-sensing NK cell activation receptors links the tumor immune surveillance function of NK cells to DC maturation and adaptive immunity. Furthermore, regulation by NK cell licensing helps to safeguard against TNFSF14 production in response to healthy tissues

Discovering putative protein targets of small molecules : a study of the p53 activator Nutlin

Small molecule drugs bind to a pocket in disease causing target proteins based on complementarity in shape and physicochemical properties. There is a likelihood that other proteins could have binding sites that are structurally similar to the target protein. Binding to these other proteins could alter their activities leading to off target effects of the drug. One such small molecule drug Nutlin binds the protein MDM2, which is upregulated in several types of cancer and is a negative regulator of the tumor suppressor protein p53. To investigate the off target effects of Nutlin, we present here a shape-based data mining effort. We extracted the binding pocket of Nutlin from the crystal structure of Nutlin bound MDM2. We next mined the protein structural database (PDB) for putative binding pockets in other human protein structures that were similar in shape to the Nutlin pocket in MDM2 using our topology-independent structural superimposition tool CLICK. We detected 49 proteins which have binding pockets that were structurally similar to the Nutlin binding site of MDM2. All of the potential complexes were evaluated using molecular mechanics and AutoDock Vina docking scores. Further, molecular dynamics simulations were carried out on four of the predicted Nutlin-protein complexes. The binding of Nutlin to one of these proteins, gamma glutamyl hydrolase, was also experimentally validated by a thermal shift assay. These findings provide a platform for identifying potential off-target effects of existing/new drugs and also opens the possibilities for repurposing drugs/ligands.Agency for Science, Technology and Research (A*STAR)Economic Development Board (EDB)Accepted versionFunding was provided by Biomedical Research Council (A*STAR), Singapore. M.S.M. would also like to acknowledge Wellcome Trust-DBT India alliance for a senior fellowship. N.S. would like to acknowledge a CSIR-SPMF fellowship for funding. M.N.N. would like to acknowledge the Biomedical Research Council (BMRC)-Economic Development Board (EDB) Industry Alignment Fund (IAF311017G and H18/01/ a0/B14), A*STAR, Singapore for funding

Overlap between miRNAs differentially expressed in the myopic retina and miRNAs differentially expressed in the retina versus sclera.

<p>Venn diagram shows overlap between 53 miRNAs, which were differentially expressed in the myopic retina, 136 miRNAs, which were up-regulated in the retina versus sclera, and 109 miRNAs, which were up-regulated in the sclera versus retina. Eighteen differential miRNAs were equally expressed in both retina and sclera, 20 differential miRNAs were up-regulated in the retina versus sclera and 15 differential miRNAs were down-regulated in the retina versus sclera.</p

Overlap between miRNA-regulated signaling pathways affected in myopic retina.

<p>Diagram depicts miRNA contributions to the 9 miRNA-mRNA signaling cascades associated with form-deprivation myopia in mice.</p

MiRNAs and their target mRNAs differentially expressed in myopic retina versus control retina.

<p>MiRNAs and their target mRNAs differentially expressed in myopic retina versus control retina.</p