PVT1: a rising star among oncogenic long non-coding RNAs

It is becoming increasingly clear that short and long noncoding RNAs critically participate in the regulation of cell growth, differentiation, and (mis)function. However, while the functional characterization of short non-coding RNAs has been reaching maturity, there is still a paucity of well characterized long noncoding RNAs, even though large studies in recent years are rapidly increasing the number of annotated ones. The long noncoding RNA PVT1 is encoded by a gene that has been long known since it resides in the well-known cancer risk region 8q24. However, a couple of accidental concurrent conditions have slowed down the study of this gene, that is, a preconception on the primacy of the protein-coding over noncoding RNAs and the prevalent interest in its neighbor MYC oncogene. Recent studies have brought PVT1 under the spotlight suggesting interesting models of functioning, such as competing endogenous RNA activity and regulation of protein stability of important oncogenes, primarily of the MYC oncogene. Despite some advancements in modelling the PVT1 role in cancer, there are many questions that remain unanswered concerning the precise molecular mechanisms underlying its functioning

SWIM: A computational tool to unveiling crucial nodes in complex biological networks

SWItchMiner (SWIM) is a wizard-like software implementation of a procedure, previously described, able to extract information contained in complex networks. Specifically, SWIM allows unearthing the existence of a new class of hubs, called "fight-club hubs", characterized by a marked negative correlation with their first nearest neighbors. Among them, a special subset of genes, called "switch genes", appears to be characterized by an unusual pattern of intra- and inter-module connections that confers them a crucial topological role, interestingly mirrored by the evidence of their clinic-biological relevance. Here, we applied SWIM to a large panel of cancer datasets from The Cancer Genome Atlas, in order to highlight switch genes that could be critically associated with the drastic changes in the physiological state of cells or tissues induced by the cancer development. We discovered that switch genes are found in all cancers we studied and they encompass protein coding genes and non-coding RNAs, recovering many known key cancer players but also many new potential biomarkers not yet characterized in cancer context. Furthermore, SWIM is amenable to detect switch genes in different organisms and cell conditions, with the potential to uncover important players in biologically relevant scenarios, including but not limited to human cancer

Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer

Background: Non-coding RNAs (ncRNAs) are emerging as key regulators of many cellular processes in both physiological and pathological states. Moreover, the constant discovery of new non-coding RNA species suggests that the study of their complex functions is still in its very early stages. This variegated class of RNA species encompasses the well-known microRNAs (miRNAs) and the most recently acknowledged long non-coding RNAs (lncRNAs). Interestingly, in the last couple of years, a few studies have shown that some lncRNAs can act as miRNA sponges, i.e. as competing endogenous RNAs (ceRNAs), able to reduce the amount of miRNAs available to target messenger RNAs (mRNAs).Results: We propose a computational approach to explore the ability of lncRNAs to act as ceRNAs by protecting mRNAs from miRNA repression. A seed match analysis was performed to validate the underlying regression model. We built normal and cancer networks of miRNA-mediated sponge interactions (MMI-networks) using breast cancer expression data provided by The Cancer Genome Atlas.Conclusions: Our study highlights a marked rewiring in the ceRNA program between normal and pathological breast tissue, documented by its " on/off" switch from normal to cancer, and vice-versa. This mutually exclusive activation confers an interesting character to ceRNAs as potential oncosuppressive, or oncogenic, protagonists in cancer. At the heart of this phenomenon is the lncRNA PVT1, as illustrated by both the width of its antagonist mRNAs in normal-MMI-network, and the relevance of the latter in breast cancer. Interestingly, PVT1 revealed a net binding preference towards the mir-200 family as the bone of contention with its rival mRNAs. © 2014 Paci et al.; licensee BioMed Central Ltd

The oncogenic role of circPVT1 in head and neck squamous cell carcinoma is mediated through the mutant p53/YAP/TEAD transcription-competent complex

Background: Circular RNAs are a class of endogenous RNAs with various functions in eukaryotic cells. Worthy of note, circular RNAs play a critical role in cancer. Currently, nothing is known about their role in head and neck squamous cell carcinoma (HNSCC). The identification of circular RNAs in HNSCC might become useful for diagnostic and therapeutic strategies in HNSCC. Results: Using samples from 115 HNSCC patients, we find that circPVT1 is over-expressed in tumors compared to matched non-tumoral tissues, with particular enrichment in patients with TP53 mutations. circPVT1 up-and down-regulation determine, respectively, an increase and a reduction of the malignant phenotype in HNSCC cell lines. We show that circPVT1 expression is transcriptionally enhanced by the mut-p53/YAP/TEAD complex. circPVT1 acts as an oncogene modulating the expression of miR-497-5p and genes involved in the control of cell proliferation. Conclusions: This study shows the oncogenic role of circPVT1 in HNSCC, extending current knowledge about the role of circular RNAs in cancer

Política exterior argentina: estrategia marca país y nueva diplomacia pública, ¿instrumentos de reinserción internacional del gobierno de Néstor Kirchner?

El actual escenario internacional caracterizado por la denominada Sociedad Informacional, actúa como condicionante central en cualquier política y/o estrategia de inserción internacional que intente proyectarse. No obtante ello, parece posible, una percepción optimista plasmada en algunas estrategias de inserción internacional que pretenden transformar debilidades en fortalezas. En tal sentido, se formulan e implementan políticas exteriores en el marco de las denomidas “Estrategias Marca País”, que persiguen como meta crucial, promover el desarrollo nacional. El análisis de estas formulaciones, concretamente sobre la “Estrategia Marca País Argentina” emprendida por el actual gobierno, constituye el objetivo principal de este análisis.Ponencia virtualInstituto de Relaciones Internacionale

Política exterior argentina: estrategia marca país y nueva diplomacia pública, ¿instrumentos de reinserción internacional del gobierno de Néstor Kirchner?

El actual escenario internacional caracterizado por la denominada Sociedad Informacional, actúa como condicionante central en cualquier política y/o estrategia de inserción internacional que intente proyectarse. No obtante ello, parece posible, una percepción optimista plasmada en algunas estrategias de inserción internacional que pretenden transformar debilidades en fortalezas. En tal sentido, se formulan e implementan políticas exteriores en el marco de las denomidas “Estrategias Marca País”, que persiguen como meta crucial, promover el desarrollo nacional. El análisis de estas formulaciones, concretamente sobre la “Estrategia Marca País Argentina” emprendida por el actual gobierno, constituye el objetivo principal de este análisis.Ponencia virtualInstituto de Relaciones Internacionale

Nucleophosmin and its AML-associated mutant regulate c-Myc turnover through Fbw7γ

Mutations leading to aberrant cytoplasmic localization of nucleophosmin (NPM) are the most frequent genetic alteration in acute myelogenous leukemia (AML). NPM binds the Arf tumor suppressor and protects it from degradation. The AML-associated NPM mutant (NPMmut) also binds p19Arf but is unable to protect it from degradation, which suggests that inactivation of p19Arf contributes to leukemogenesis in AMLs. We report here that NPM regulates turnover of the c-Myc oncoprotein by acting on the F-box protein Fbw7γ, a component of the E3 ligase complex involved in the ubiquitination and proteasome degradation of c-Myc. NPM was required for nucleolar localization and stabilization of Fbw7γ. As a consequence, c-Myc was stabilized in cells lacking NPM. Expression of NPMmut also led to c-Myc stabilization because of its ability to interact with Fbw7γ and delocalize it to the cytoplasm, where it is degraded. Because Fbw7 induces degradation of other growth-promoting proteins, the NPM–Fbw7 interaction emerges as a central tumor suppressor mechanism in human cancer

Plant and fungus transcriptomic data from grapevine berries undergoing artificially-induced noble rot caused by Botrytis cinerea

Noble rot is a latent infection of grape berries caused by the necrotrophic fungus Botrytis cinerea, which develops under specific climatic conditions. The infected berries undergo biochemical and metabolic changes, associated with a rapid withering, which altogether offer interesting organoleptic features to sweet white wines. In this paper, we provide RNAseq datasets (raw and normalized counts as well as differentially expressed genes lists) of the transcriptome profiles of both grapevine berries (Vitis vinifera cv. Garganega) and B. cinerea during the establishment of noble rot, artificially induced in controlled conditions. The sequencing data are available in the NCBI GEO database under accession number GSE116741. These data were exploited in a comprehensive meta-analysis of gene expression during noble rot infection, gray mold and post-harvest withering. This highlighted an important common transcriptional reprogramming in different botrytized grape berry varieties and led to the identification of key genes specifically modulated during noble rot infection, which are described in the article entitled \u201cSpecific molecular interactions between Vitis vinifera and Botrytis cinerea are required for noble rot development in grape berries\u201

Comprehensive RNA dataset of AGO2 associated RNAs in Jurkat cells following miR-21 over-expression

AbstractWe set out to identify miR-21 targets in Jurkat cells using a high-throughput biochemical approach (10.1016/j.biochi.2014.09.021 [1]). Using a specific monoclonal antibody raised against AGO2, RISC complexes were immunopurified in Jurkat cells over-expressing miR-21 following lentiviral trasduction as well as in Jurkat control cells lines. A parallel immunoprecipitation using isotype-matched rat IgG was performed as a control. AGO2 associated mRNAs were profiled by microarray (GEO: GSE37212). AGO2 bound miRNAs were profiled by RNA-seq

Cost-effectiveness of tenofovir in the treatment of patients with chronic hepatitis B: data from literature

Chronic hepatitis B (CHB) is a complex disease with significant social impact both on the patients' quality of life of and the economic resources involved. Its chronicity affects considerably not only the clinical management of the disease (for the need for drugs with proven long-term safety and low rate of resistance), but also the economic impact (for the high costs of treatment, the management of complications, and the constant monitoring of therapy).Since, as is well known, the main problem of modern health care systems is the general scarcity of available resources in the face of growing demand for health, the issue of economic evaluation of therapies for the treatment of chronic hepatitis B has been addressed in numerous national and international studies. In fact, clinicians find a strong support for the choice of the most suitable therapeutic pathway in the major scientific societies' guidelines (European Association for the Study of The Liver – EASL, American Association for the Study of Liver Diseases – AASLD, Associazione Italiana per lo Studio del Fegato – AISF), while the analysis of the economic implications is rather more difficult, even for the methodological differences and peculiarities of the different countries.The aim of this paper is to present a brief summary of some of the recently conducted cost-effectiveness analyses and extrapolate some data to support the economic evidence related to the treatment of CHB with nucleos(t)ide analogs. In particular, the article focuses on the comparison between entecavir (ETV) and tenofovir (TDF), the two oral antiviral therapies recommended for first-line treatment. In the selected studies, the comparison between the different treatment options was conducted in order to assess the incremental cost-effectiveness ratio (ICER) and the results were expressed in terms of QALYs (Quality Adjusted Life Years) gained.Despite the methodological differences among the selected studies, tenofovir is found to be, in the context of first-line oral antiviral therapies, the most cost-effective treatment for patients with chronic hepatitis B