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MicroRNAs (miRNAs) have been identified in many organisms, and they are essential for gene expression regulation in many critical cellular processes. The expression levels of these genes and miRNAs are closely associated with the progression of diseases such as cancers. Furthermore, survival analysis is a significant indicator for evaluating the criticality of these cellular processes in cancer progression. We established a web tool, miRNA Target Viewer (miR-TV), which integrates 5p-arm and 3p-arm miRNA expression profiles, mRNA target gene expression levels in healthy and cancer populations, and clinical data of cancer patients and their survival information. The developed miR-TV obtained miRNA-seq, mRNA-seq and clinical data from the Cancer Genome Atlas and potential miRNA target gene predictions from miRDB, targetScan and miRanda. The data presentation was implemented using the D3 javascript toolkit. The D3 toolkit is frequently used to provide an easy-to-use interactive interface. Our miR-TV provides a user-friendly and interactive interface, which can be beneficial for biomedical researchers to freely interrogate miRNA expression information and their potential target genes. We believe that such a data visualization bioinformatics tool is excellent for obtaining information from massive biological data. Database URL: http://mirtv.ibms.sinica.edu.tw., (© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

MicroRNAs (miRNAs) play important roles in human cancers. In previous studies, we have demonstrated that both 5p-arm and 3p-arm of mature miRNAs could be expressed from the same precursor and we further interrogated the 5p-arm and 3p-arm miRNA expression with a comprehensive arm feature annotation list. To assist biologists to visualize the differential 5p-arm and 3p-arm miRNA expression patterns, we utilized a user-friendly mobile App to display. The Cancer Genome Atlas (TCGA) miRNA-Seq expression information. We have collected over 4,500 miRNA-Seq datasets from 15 TCGA cancer types and further processed them with the 5p-arm and 3p-arm annotation analysis pipeline. In order to be displayed with the RNA-Seq Viewer App, annotated 5p-arm and 3p-arm miRNA expression information and miRNA gene loci information were converted into SQLite tables. In this distinct application, for any given miRNA gene, 5p-arm miRNA is illustrated on the top of chromosome ideogram and 3p-arm miRNA is illustrated on the bottom of chromosome ideogram. Users can then easily interrogate the differentially 5p-arm/3p-arm expressed miRNAs with their mobile devices. This study demonstrates the feasibility and utility of RNA-Seq Viewer App in addition to mRNA-Seq data visualization., Competing Interests: The authors do not have a direct financial relation that might lead to conflict of interests for any of them.

E26 transformation-specific sequence (ETS)-2 is a transcriptional modulator located on chromosome 21, alterations in its expression have been implicated with a reduced incidence of solid tumors in Down syndrome patients. MicroRNAs (miRNAs) are thought to participate in diverse biological functions; however, the regulation of miRNAs is not well characterized. Recently, we reported that miR-196b is highly expressed in gastric cancers. Herein, we demonstrate that miR-196b expression was significantly repressed by ETS2 during gastric cancer oncogenesis. We demonstrate that knockdown of endogenous ETS2 expression increases miR-196b expression. A genomic region between -751 and -824 bp upstream of the miR-196b transcriptional start site was found to be critical for the repression activity. This putative regulatory promoter region contains three potential ETS2-binding motifs. Mutations within the ETS2 binding sites blocked the repression activity of ETS2. Furthermore, knockdown of ETS2 or overexpression of miR-196b significantly induced migration and invasion in gastric cancer cells. In addition, alterations in ETS2 and miR-196b expression in gastric cancer cell lines affected the expression of epithelial-mesenchymal transition-related genes. The levels of vimentin, matrix metalloproteinase (MMP)-2 and MMP9 were drastically induced, but levels of E-cadherin were decreased in shETS2- or miR-196b-transfected cells. Our data indicate that ETS2 plays a key role in controlling the expression of miR-196b, and miR-196b may mediate the tumor suppressor effects of ETS2. We demonstrated that miR-196b was transcriptionally regulated by ETS2 and there was an inverse expression profile between miR-196b and ETS2 in clinical samples. This finding could be beneficial for the development of effective cancer diagnostic and alternative therapeutic strategies.

Unlabelled: Biological functions of receptor tyrosine kinase-like orphan receptor 1 (ROR1) remain to be elucidated due to the lack of identified genuine ligands. Previously, transiently expressed ROR1 was unexpectedly found to exhibit nuclear localization, the functions of which are unknown., Materials and Methods: We constructed nuclear-homing peptidyl-prolyl cis-trans isomerases (FKBP) domain fusion ROR1-expressing cells and used a synthetic dimerizer to specifically activate FKBP-fused ROR1 proteins for subsequent functional characterization., Results: Activation of nuclear-homing ROR1 by treating cells with AP20187 dimerizer led to significant increase in actin stress fibers and increased cellular migration. Following gene expression microarray analysis, we demonstrated that activated ROR1 affects several genes involved in the regulation of the actin cytoskeleton (radixin (RDX), ezrin (EZR), son of sevenless homolog 2 (SOS2) and caldesmon 1 (CALD1))., Conclusion: Our data indicate that nuclear-localized ROR1 may play an important role in cell migration and cytoskeleton remodeling. This might explain the critical roles of ROR1 in neuron development.

MicroRNAs (miRNAs) are small noncoding RNAs that play fundamental roles in diverse biological and pathological processes by targeting the expression of specific genes. Here, we identified 38 methylation-associated miRNAs, the expression of which could be epigenetically restored by cotreatment with 5-aza-2'-deoxycytidine and trichostatin A. Among these 38 miRNAs, we further analyzed miR-34b, miR-127-3p, miR-129-3p and miR-409 because CpG islands are predicted adjacent to them. The methylation-silenced expression of these miRNAs could be reactivated in gastric cancer cells by treatment with demethylating drugs in a time-dependent manner. Analysis of the methylation status of these miRNAs showed that the upstream CpG-rich regions of mir-34b and mir-129-2 are frequently methylated in gastric cancer tissues compared to adjacent normal tissues, and their methylation status correlated inversely with their expression patterns. The expression of miR-34b and miR-129-3p was downregulated by DNA hypermethylation in primary gastric cancers, and the low expression was associated with poor clinicopathological features. In summary, our study shows that tumor-specific methylation silences miR-34b and miR-129 in gastric cancer cells., (Copyright © 2011 UICC.)

Many of the known microRNAs (miRNAs) are encoded by polycistronic transcripts and are thought to be co-expressed. In this study, we discovered that the expression of a large miRNA cluster (C19MC) on human chromosome 19 is upregulated by the demethylating agent, 5-aza-2'-deoxycytidine (5-Aza-dC), in AGS gastric cancer cells. We found that C19MC was rarely expressed in most cells, but its expression was restored through DNA demethylation. We confirmed that this miRNA cluster was mainly expressed in the placenta, as previously reported. Furthermore, its expression pattern was highly correlated with the methylation state of a distal CpG-rich region located about 17.6 kb upstream of the miRNA cluster. Using combined bisulfite restriction analysis (COBRA) and bisulfite-sequencing techniques, we determined that this CpG-rich region is hypermethylated in the AGS and HeLa cells, but hypomethylated in the placenta tissue. In conclusion, we demonstrated that the expression pattern of the C19MC was activated in human cancer cells through demethylation of a CpG-rich region.

Protein phosphorylation is an important regulatory mechanism involved in signal transduction and cancers. In comparison to the extensive tyrosine-kinase oncogenesis research, there are only relatively few studies of protein tyrosine-phosphatase expression in cancers. The expression profile for tyrosine-phosphatases was investigated in gastric cancers using RT-PCR and molecular cloning. The present study showed a general PTP expression profile in gastric cancer tissues, with the identification of 22 distinct tyrosine-phosphatases. Following the examination of five PTPs (PTPRA, PTPRB, PTPRD, PTPRG and PTPRZ) using immunohistochemistry, strong association was observed between PTPRA/PTPRZ expression and gastric cancer progression including lymphovascular invasion and liver/peritoneal dissemination.

We have adopted a special experimental strategy to identify early responsive genes during 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced macrophage-like differentiation of human myeloid leukemia cells (HL-60). This was performed in cells that were synchronized by nocodazole and treated with TPA in the presence of a protein synthesis inhibitor, cycloheximide, to prevent activation of secondary targets and therefore increase the probability of early transcripts in total RNA pool. The expression alteration was analyzed by microarray and the selection criteria of candidate genes were adjusted by real-time PCR validation to increase its reliability. Finally, 56 genes were identified as early TPA-responsive genes in this multiscreening step approach. Furthermore, upregulation of three candidate genes (NFIL3, SKIL, and JMJD3) was shown to be dosage and time dependent with TPA treatment and was found to be directly regulated by TPA through PKC-dependent signaling. These results revealed that our screenings provide a useful and efficient approach to identify early TPA-responsive genes and these genes might involve the regulation of TPA-induced differentiation program of HL-60 cells as primary

Alterations of protein tyrosine kinase and tyrosine phosphatase are often associated with uncontrolled cell growth and cellular transformation. Because of the large number of tyrosine kinase/phosphatase genes in such gene family, it is essential to use an efficient and simple approach to obtain comprehensive protein tyrosine kinase and protein tyrosine phosphatase expression profiles. Knowledge of such an overall expression pattern of tyrosine kinases/phosphatases in a given cancer cell represents the first step in understanding key components involved in the sequential events of tumor progression. In this article, we described a novel approach by using degenerate PCR primers according to the consensus catalytic motifs in order to amplify protein tyrosin kinase/phosphatase molecules from cancer cells by reverse-transcription polymerase-chain-reaction. An improved profiling approach (RAGE) was also described by utilizing restriction enzyme digestion and electrophoresis for quick and efficient kinase/phosphatase profiling.