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

Targeting Glioma Stem Cells by Functional Inhibition of a Prosurvival OncomiR-138 in Malignant Gliomas

SummaryMalignant gliomas are the most aggressive forms of brain tumors, associated with high rates of morbidity and mortality. Recurrence and tumorigenesis are attributed to a subpopulation of tumor-initiating glioma stem cells (GSCs) that are intrinsically resistant to therapy. Initiation and progression of gliomas have been linked to alterations in microRNA expression. Here, we report the identification of microRNA-138 (miR-138) as a molecular signature of GSCs and demonstrate a vital role for miR-138 in promoting growth and survival of bona fide tumor-initiating cells with self-renewal potential. Sequence-specific functional inhibition of miR-138 prevents tumorsphere formation in vitro and impedes tumorigenesis in vivo. We delineate the components of the miR-138 regulatory network by loss-of-function analysis to identify specific regulators of apoptosis. Finally, the higher expression of miR-138 in GSCs compared to non-neoplastic tissue and association with tumor recurrence and survival highlights the clinical significance of miR-138 as a prognostic biomarker and a therapeutic target for treatment of malignant gliomas

Reply to “Letter to the Editor”

Dear Editor, We thank Rentoft and colleagues for commenting on our paper “Transcriptional profiling of oral squamous cell carcinoma using formalin-fixed paraffin-embedded samples”, and agreeing that formalin-fixed paraffin embedded (FFPE) tissue specimens can be used for gene expression studies using microarrays, to identify genes that are significantly involved in oral carcinogenesis. The similarities and high concordance between the study by Rentoft et al. [1] and ours [2] is comforting and clearly supports the use of FFPE tissues in such experiments. More importantly, these studies act as independent validation for one another and strongly suggests that genes that were found to be up- or down-regulated in oral squamous cell carcinoma (OSCC) do indeed play a role in these cancers and therefore warrant further investigation to determine their utility as biomarkers and therapeutic targets for OSCC. We wanted to point out however, that the similarities between these 2 studies are not completely unexpected despite previous reports highlighting that the concordance between microarray studies are hard to achieve [3]. The main disparities between datasets from microarray experiments have been attributed to the use of different microarray platforms and the heterogeneity of the tissue specimens that were used [4], [5]. Indeed, many microarray studies reported for the head and neck, used tissues from several distinct areas which have been reported to be genetically heterogeneous, and associated with different aetiologies [6], [7]. Given that both our studies used the DASL assay and tissues from the oral cavity (albeit from different sites-explained further below) the consistency of the genes that were identified should not come as a complete surprise. However, it is still intriguing that the similarities between these two studies were so close despite previous reports indicating that there are distinct differences between oral cancers associated with different aetiology [8], [9], and reports describing the distinct genetic differences between subsites of the oral cavity [10], [11], [12]. Our previous study describing the differences in gene-expression patterns between oral cancers associated with betel quid chewing and smoking demonstrated that despite the differences seen, genetic changes common to all the cancers were also observed suggesting that there are core events and pathways that are important regardless of the aetiology or site of the cancer [8]. Consistently, upon close examination of the genes that are most differentially expressed between our study and that of Rentoft et al. [1] 5 of the top 10 over-lapping genes most differentially expressed were matrix metalloproteinases, whilst other genes include IL-8, CXCL-9 and BCL2A1, genes that were consistently up-regulated in many other microarray studies of the head and neck independent of the subsites of cancer [8], [12], [13], [14]. An unprecedented large overlap of genes between our study [2] and that of Rentoft and colleagues [1] may also be due to the smaller number of genes on the arrays that were used in these studies (502 genes), and that these genes were pre-selected based on their involvement in cancer development, whereas the majority of previous studies used platforms consisting of larger arrays and hence could capture much more of the heterogeneity typically observed in cancers. More recently, Illumina launched its whole genome DASL assay and it would be interesting to see if the similarities between buccal and tongue cancers still prevails. In conclusion, increasing number studies including the 2 compared here, strongly supports the use of FFPE tissues for gene expression studies using microarrays. The development of new technologies and statistical methods that addresses the challenges associated with using FFPE tissues, combined with the clinical information available with these specimens, will indeed facilitate the identification and discovery of clinically relevant gene signatures and biomarkers and therapeutic targets to improve the management of cancers in general

NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential

Summary: Waddington’s epigenetic landscape is a powerful metaphor for cellular dynamics driven by gene regulatory networks (GRNs). Its quantitative modeling and visualization, however, remains a challenge, especially when there are more than two genes in the network. A software tool for Waddington’s landscape has not been available in the literature. We present NetLand, an open-source software tool for modeling and simulating the kinetic dynamics of GRNs, and visualizing the corresponding Waddington’s epigenetic landscape in three dimensions without restriction on the number of genes in a GRN. With an interactive and graphical user interface, NetLand can facilitate the knowledge discovery and experimental design in the study of cell fate regulation (e.g. stem cell differentiation and reprogramming). Availability and Implementation: NetLand can run under operating systems including Windows, Linux and OS X. The executive files and source code of NetLand as well as a user manual, example models etc. can be downloaded from http://netland-ntu.github.io/NetLand/.Published versio

Sensitivity of dopaminergic neuron differentiation from stem cells to chronic low-dose methylmercury exposure

Perinatal exposure to low doses of methylmercury (MeHg) can cause adult neurological symptoms. Rather than leading to a net cell loss, the toxicant is assumed to alter the differentiation and neuronal functions such as catecholaminergic transmission. We used neuronally differentiating murine embryonic stem cells (mESC) to explore such subtle toxicity. The mixed neuronal cultures that formed within 20 days contained a small subpopulation of tyrosine hydroxylase (TH)–positive neurons with specific dopaminergic functions such as dopamine transport (DAT) activity. The last 6 days of differentiation were associated with the functional maturation of already preformed neuronal precursors. Exposure to MeHg during this period downregulated several neuronal transcripts, without affecting housekeeping genes or causing measurable cell loss. Profiling of mRNAs relevant for neurotransmitter systems showed that dopamine receptors were coordinately downregulated, whereas known counterregulatory systems such as galanin receptor 2 were upregulated. The chronic (6 days) exposure to MeHg, but not shorter incubation periods, attenuated the expression levels of endogenous neurotrophic factors required for the maturation of TH cells. Accordingly, the size of this cell population was diminished, and DAT activity as its signature function was lost. When mixed lineage kinase activity was blocked during MeHg exposure, DAT activity was restored, and the reduction of TH levels was prevented. Thus, transcriptional profiling in differentiating mESC identified a subpopulation of neurons affected by MeHg, and a pharmacological intervention was identified that specifically protected these cells