1,720,972 research outputs found
Splicing Dysregulation as Oncogenic Driver and Passenger Factor in Brain Tumors
Get PDFBrain tumors are a heterogeneous group of neoplasms ranging from almost benign to highly aggressive phenotypes. The malignancy of these tumors mostly relies on gene expression reprogramming, which is frequently accompanied by the aberrant regulation of RNA processing mechanisms. In brain tumors, defects in alternative splicing result either from the dysregulation of expression and activity of splicing factors, or from mutations in the genes encoding splicing machinery components. Aberrant splicing regulation can generate dysfunctional proteins that lead to modification of fundamental physiological cellular processes, thus contributing to the development or progression of brain tumors. Herein, we summarize the current knowledge on splicing abnormalities in brain tumors and how these alterations contribute to the disease by sustaining proliferative signaling, escaping growth suppressors, or establishing a tumor microenvironment that fosters angiogenesis and intercellular communications. Lastly, we review recent efforts aimed at developing novel splicing-targeted cancer therapies, which employ oligonucleotide-based approaches or chemical modulators of alternative splicing that elicit an impact on brain tumor biology
CDK12/13 promote splicing of proximal introns by enhancing the interaction between RNA polymerase II and the splicing factor SF3B1
Get PDFTranscription-associated cyclin-dependent kinases (CDKs) regulate the transcription cycle through sequential phosphorylation of RNA polymerase II (RNAPII). Herein, we report that dual inhibition of the highly homologous CDK12 and CDK13 impairs splicing of a subset of promoter-proximal introns characterized by weak 3 ' splice sites located at larger distance from the branchpoint. Nascent transcript analysis indicated that these introns are selectively retained upon pharmacological inhibition of CDK12/13 with respect to downstream introns of the same pre-mRNAs. Retention of these introns was also triggered by pladienolide B (PdB), an inhibitor of the U2 small nucelar ribonucleoprotein (snRNP) factor SF3B1 that recognizes the branchpoint. CDK12/13 activity promotes the interaction of SF3B1 with RNAPII phosphorylated on Ser2, and disruption of this interaction by treatment with the CDK12/13 inhibitor THZ531 impairs the association of SF3B1 with chromatin and its recruitment to the 3 ' splice site of these introns. Furthermore, by using suboptimal doses of THZ531 and PdB, we describe a synergic effect of these inhibitors on intron retention, cell cycle progression and cancer cell survival. These findings uncover a mechanism by which CDK12/13 couple RNA transcription and processing, and suggest that combined inhibition of these kinases and the spliceosome represents an exploitable anticancer approach
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
MYC up-regulation confers vulnerability to dual inhibition of CDK12 and CDK13 in high-risk Group 3 medulloblastoma
Get PDFBackgroundMedulloblastoma (MB) is the most common cerebellar malignancy during childhood. Among MB, MYC-amplified Group 3 tumors display the worst prognosis. MYC is an oncogenic transcription factor currently thought to be undruggable. Nevertheless, targeting MYC-dependent processes (i.e. transcription and RNA processing regulation) represents a promising approach.MethodsWe have tested the sensitivity of MYC-driven Group 3 MB cells to a pool of transcription and splicing inhibitors that display a wide spectrum of targets. Among them, we focus on THZ531, an inhibitor of the transcriptional cyclin-dependent kinases (CDK) 12 and 13. High-throughput RNA-sequencing analyses followed by bioinformatics and functional analyses were carried out to elucidate the molecular mechanism(s) underlying the susceptibility of Group 3 MB to CDK12/13 chemical inhibition. Data from International Cancer Genome Consortium (ICGC) and other public databases were mined to evaluate the functional relevance of the cellular pathway/s affected by the treatment with THZ531 in Group 3 MB patients.ResultsWe found that pharmacological inhibition of CDK12/13 is highly selective for MYC-high Group 3 MB cells with respect to MYC-low MB cells. We identified a subset of genes enriched in functional terms related to the DNA damage response (DDR) that are up-regulated in Group 3 MB and repressed by CDK12/13 inhibition. Accordingly, MYC- and CDK12/13-dependent higher expression of DDR genes in Group 3 MB cells limits the toxic effects of endogenous DNA lesions in these cells. More importantly, chemical inhibition of CDK12/13 impaired the DDR and induced irreparable DNA damage exclusively in MYC-high Group 3 MB cells. The augmented sensitivity of MYC-high MB cells to CDK12/13 inhibition relies on the higher elongation rate of the RNA polymerase II in DDR genes. Lastly, combined treatments with THZ531 and DNA damage-inducing agents synergically suppressed viability of MYC-high Group 3 MB cells.ConclusionsOur study demonstrates that CDK12/13 activity represents an exploitable vulnerability in MYC-high Group 3 MB and may pave the ground for new therapeutic approaches for this high-risk brain tumor
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Functional role of the zinc finger factor ZNF281 in DNA damage response
No full textLa sopravvivenza degli organismi dipende dall'accurata trasmissione dell'informazione genetica durante i processi che portano alla divisione cellulare. Questa fedele trasmissione richiede non soloun'elevata precisione nella replicazione del DNA e nella perfetta segregazione cromosomica, ma anche la capacità di sopravvivere ai danni al DNA spontanei o indotti minimizzando il numero di mutazioni ereditabili dalle cellule figlie. Le cellule sono constantemente soggette agli effetti citotossici e mutageni degli agenti in grado di causare danno al DNA. Per rispondere e difendersi da questa minaccia, le cellule eucariotiche hanno evoluto dei processi che sono collettivamente catalogati come risposta al danno al DNA (DDR). La DDR è una complessa via di trasduzione del segnale che ha la capacità di riconoscere la presenza di danni al DNA e trasdurre questa informazione nella cellula al fine di attivare i processi di riparo. Infatti, le cellule possiedono diversi enzimi capaci di rimodellare e riparare il DNA, comunque la loro attività deve essere spazialmente e temporalmente regolata per ottimizzare il riparo del DNA e prevenire potenziali e deleterie alterazioni nella struttura del DNA. In questi ultimi anni considerevoli progressi sono stati fatti per delucidare le componenti e i processi che caratterizzano la DDR eucariotica. Nonostante questo, un punto centrale in questo campo di studio rimane l'identificazione dei geni e delle proteine che controllano l'espressione delle proteine coinvolte nella DDR. Di interesse è la recente scoperta di un numero crescente di fattori di trascrizione che in grado di regolare direttamente la riparazione del DNA e che fanno parte come componenti integrali del macchinario di riparo stesso con meccanismi indipendenti dalla loro abilità di promuovere e/o reprimere la trascrizione. Infatti, gli agenti di danno al DNA (radiazioni, chemioterapia, agenti genotossici) sono in grado di promuovere la traslocazione di alcuni fattori di trascrizione direttamente sulle lesioni al DNA, dove partecipano all'attivazione del riparo al DNA. ZNF281 è un fattore di trascrizione appartenente alla tipologia degli "zinc finger" coinvolto nel mantenimento della staminalità cellulare e nei processi di transizione epiteliale-mesenchimale (EMT). In questo studio vengono analizzati i ruoli di ZNF281 durante la DDR. Infatti, riportiamo che l'espressione di ZNF281 aumenta sia a livello di mRNA, che di proteina dopo stress genotossico indotto da agenti chimici che causano danno al DNA (etoposide, doxorubicina, camptotecina) in diversi sistemi quali le cellule tumorali, cellule di cheratinociti primari e nell’epidermide del Mus musculus. Il comet assay dimostra che il riparo al DNA è ritardato nelle cellule silenziate per l'espressione di ZNF281 e trattate con etoposide. Inoltre, l'analisi con RT profiler array ha dimostrato che l'espressione di dieci geni coinvolti nella risposta al danno al DNA è diminuita nelle cellule trattate con etoposide e silenziate per l'espressione di ZNF281. In linea con questa scoperta, XRCC2 e XRCC2, due geni che prendono parte rispettivamente ai processi di ricombinazione omologa (HR) e Non Homologous End Joining (NHEJ), sono trascrizionalmente attivati da ZNF281 attraverso un meccanismo dipendente dal legame al DNA come dimostrato da esperimenti di saggio della luciferasi e di immunoprecipitazione della cromatina (ChIP). Inoltre, ZNF281 è un co-fattore della proteina c-Myc per l'attivazione dell'espressione della nucleolina e della ciclina B1; mentre c-Myc, anche se in grado di legare promotori di XRCC2 e XRCC4, non è capace di promuovere la trascrizione o di modificare l'attività di ZNF281 sui promotori di questi due geni. L'analisi bioinformatica di una coorte di 1971 pazienti affetti da cancro alla mammella rivela una correlazione statisticamente significativa tra l'espressione di ZNF281 e di XRCC2. Inoltre l'analisi proteomica e il proximity ligation assay (PLA) dimostrano che ZNF281 interagisce con DNA-PK, un'importante proteina del processo di DDR, suggerendo per ZNF281, un ruolo indipendente dalla trascrizione. In sintesi, i risultati discussi in questo lavoro, evidenziano per la prima volta il coinvolgimento di ZNF281 nella risposta cellulare a stress genotossici attraverso un controllo esercitato sull'espressione di geni che agiscono in differenti meccanismi di riparo al danno e attraverso la sua interazione con DNA-PK.The survival of organisms depends on the accurate transmission of genetic information from one cell to its daughters. Such faithful transmission requires not only extreme accuracy in replication of DNA and precision in chromosome distribution, but also the ability to survive spontaneous and induced DNA damage while minimizing the number of heritable mutations. Therefore, cells are constantly under threat from the cytotoxic and mutagenic effects of DNA damaging agents. To respond to these threats, eukaryotes have evolved the DNA damage response (DDR). The DDR is a complex array of different mechanisms that have the ability to sense DNA damage and transduce this information to the cell in order to modulate cellular responses to DNA damage. Cells possess several enzymatic tools capable of remodeling and repairing DNA; however, their activities must be tightly regulated in a temporal, spatial, and DNA lesion-appropriate fashion to optimize repair and prevent unnecessary and potentially deleterious alterations in the structure of DNA during normal cellular processes. During the past several years, considerable progress has been made in elucidating the components and the processes of the eukaryotic DDR. A central issue in this field, which remains to be understood in greater detail, is the identification of the controllers of the expression of DDR proteins. Interestingly, in recent years an increasing number of studies have revealed that several TFs regulate DNA repair directly and can function as integral components of the repair machinery itself in a transcription independent fashion. In fact, DNA damage-inducing insults (irradiation, chemotherapy drugs) promote translocation of some TFs directly to DNA lesions, where they actively facilitate DNA repair. ZNF281 is a zinc finger transcription factor involved in the control of cellular stemness and Epithelial Mesenchymal Transition (EMT). In this study we analyze the roles of ZNF281 during DDR. We report that ZNF281 expression increased after genotoxic stress caused by DNA damaging drugs (Etoposide, Doxorubicin, Camptothecin) in cancer cell lines, normal keratinocytes and in mouse skin in vivo. Comet assays demonstrated that DNA repair was delayed in cells silenced for the expression of ZNF281 and treated with Etoposide. Furthermore, RT profiler array analysis demonstrated that the expression of ten DDR genes was down-regulated in cells treated with Etoposide and silenced for ZNF281. In line with these findings, XRCC2 and XRCC4, two genes that take part in Homologous Recombination (HR) and Non Homologous End Joining (NHEJ) respectively, were transcriptionally activated by ZNF281 through a DNA binding-dependent mechanism as demonstrated by luciferase assays and Chromatin crosslinking ImmunoPrecipitation (ChIP) experiments. In addition, ZNF281 works as a c-Myc co-factor to stimulate the expression of nucleolin and cyclin B1; instead c-Myc, which also binds to the promoters of XRCC2 and XRCC4, was unable to promote their transcription or to modify ZNF281 activity. Bioinformatic analysis of 1971 breast cancer patients disclosed a significant correlation between the expression of ZNF281 and XRCC2. Moreover proteomic analysis and Proximity Ligation Assay (PLA) demonstrated that ZNF281 interacts with DNA-PK, an important protein of DDR, suggesting a transcription-independent role of ZNF281 in DDR. Our data highlight, for the first time, the involvement of ZNF281 in the cellular response to genotoxic stress through the control exercised on the expression of genes that act in different repair mechanisms and through interaction with with corecomponents of DNA repair pathways
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