bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1922: miR-301 expression is deregulated in rhabdomyosarcoma
Authors: Rota Rossella , Gualtieri Alberto , Cossetti Cristina , Pomella Silvia , Adesso Laura , Locatelli Franco 
Published: July 2016

Abstract
Rhabdomyosarcoma (RMS) is an aggressive pediatric soft tissue sarcoma of myogenic derivation. Conversely to normal myoblasts, RMS cells are unable to differentiate, thus they proliferate indefinitely. MicroRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression by affecting both the stability and translation of mRNAs. They are fundamental regulators of myogenesis and their deregulation has been involved in the pathogenesis of RMS. We evaluate here the expression and regulation of miR-301, which has been related to tumorigenesis in other types of cancers. We report here that the expression of miR-301 is upregulated in primary samples of both the alveolar RMS, which bears the fusion protein PAX3-FOXO1 (P3F) (ARMS), and the fusion-negative embryonal RMS (ERMS) compared to normal muscle tissues. Similarly, it appears higher in RMS cell lines versus normal skeletal myoblasts. Using an inhibitor of miR-301 (CONTRAmiR) we demonstrate that this miRNA favors RMS cell mobility and down-regulates p21Cip1, PTEN and DICER1 levels. However, the inhibition of miR-301 with the CONTRAmiR does not reduce tumor cell proliferation suggesting that the regulation of cell cycle is not under the control of this miRNA in RMS. Interestingly, the expression of SKA2 (Spindle And Kinetochore Associated Complex Subunit 2), whose gene hosts miR-301, is also upregulated in our setting. Experiments are ongoing to determine whether miR-301 and SKA2 are associated with RMS pathogenesis and could be targets for an anti-RMS therapy.
This work was supported by the Associazione Italiana per la Ricerca sul Cancro (AIRC).
Citation Format: Rossella Rota, Alberto Gualtieri, Cristina Cossetti, Silvia Pomella, Laura Adesso, Franco Locatelli. miR-301 expression is deregulated in rhabdomyosarcoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1922.
Abstract 1924: miR-142-3p is a candidate mediator of chloride intracellular channel 4 (CLIC4) loss during squamous cancer progression
Authors: Carofino Brandi L. , Yuspa Stuart H. 
Published: July 2016

Abstract
Chloride intracellular channel 4 (CLIC4) is a broadly expressed protein that has been implicated in multiple cellular processes, including cellular differentiation and apoptosis. As a soluble factor, CLIC4 translocates to the nucleus following exposure to a variety of stimuli, including TGF-β, TNF-α, and etoposide. Nuclear CLIC4 potentiates TGF-β signaling by preventing the dephosphorylation of phospho-SMAD2 and 3 and promotes growth arrest. Although its primary function is as a tumor suppressor, CLIC4 expression is progressively diminished during cancer progression and CLIC4 protein is excluded from the nucleus of many human epithelial neoplasms and squamous cell carcinoma (SCC) cell lines. To date, no gene deletions or mutations have been identified to account for this phenomenon; thus, identifying the mechanism of CLIC4 loss is our primary focus. To determine if epigenetic gene silencing is responsible, we evaluated the methylation status of the CLIC4 promoter in a progression panel (normal, papilloma, SCC) of epithelial cell lines by performing bisulfite sequencing. No differential promoter methylation was found between the cell lines, suggesting that the regulation may be post-transcriptional or post-translational. Because microRNAs (miRNAs) are known to regulate gene expression by mediating the degradation or translational repression of target mRNAs, we performed a bioinformatic analysis of the CLIC4 3’ UTR, which revealed a large number of putative targeting miRNAs. One such miRNA, miR-142-3p, has been predicted to target CLIC4 by multiple algorithms and has been shown to interact with the CLIC4 3’ UTR by high-throughput sequencing and crosslinking immunoprecipitation. We confirmed the functional activity of miR-142-3p against the CLIC4 3’ UTR by using a 3’ UTR luciferase reporter assay and a miR-142-3p mimic. miR-142-3p is high in the tumor tissue and plasma of patients with head and neck SCC and is correlated with worse prognosis, where CLIC4 expression is known to be low. Thus, miR-142-3p may be responsible for mediating CLIC4 loss in squamous lesions and warrants further investigation.
Citation Format: Brandi L. Carofino, Stuart H. Yuspa. miR-142-3p is a candidate mediator of chloride intracellular channel 4 (CLIC4) loss during squamous cancer progression. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1924.
Abstract 1927: Myc-induced suppression of the RNA-binding protein ZAR2 in breast cancer cells
Authors: Misra Smita , Chaudhuri Gautam 
Published: July 2016

Abstract
Our objective is to verify the hypothesis that c-Myc-regulated oncomiR miR-130a-5p suppresses the level of the RNA-binding tumor suppressor protein ZAR2 in the cMyc-high aggressive breast cancer cells. We experimentally validated the binding of miR130a-5p miRISC to ZAR2 mRNA in vivo and inhibition of the translation of this mRNA by this binding. We used three commercially available c-Myc-high ZAR2-low breast cancer cell lines BT549, MDA-MB-453 and MDA-MB-231 and two c-Myc-low ZAR2-high breast cancer cells MCF7 and HCC38 for our studies. We cloned the full length 3′-UTR (179 bp) of human ZAR2 mRNA immediately downstream of the firefly luciferase open reading frame sequence contained in the reporter plasmid. We also have created different mutants of the 3’-UTR, each having mutation in each of the putative miR130a-5p binding sites. We transiently transfected the recombinant plasmid and miR130a-5p miRNA mimic into breast cancer cells and assessed luciferase activity or fluorescence 24-48 hours after transfection. We also have transfected just the reporter construct into breast cancer cells which express the endogenous miR130a-5p miRNAs, along with vectors which express mutant versions of the miRNA binding sites. In this experimental system the wild-type reporters had less activity than their respective mutants. To evaluate the functional importance of miR130a-5p miRNA/ZAR2 mRNA pair, we transiently over-expressed a miR130a-5p miRNA mimic in the cMyc-low breast cancer breast cancer cells and subsequently analyzed the level of ZAR2 protein levels. Our data showed that ZAR2 protein levels are decreased by the mimic increasing the in vitro invasiveness of these cells. Our results thus reveal a novel mechanism for the induction of aggressiveness by cMyc in the breast cancer cells. This research is supported in part by DOD-CDMRP IDEA Expansion Grant# BC103645 and NIH/NCI grant 1R21CA181920-01 to GC and NIH grant 1U54RR026140 TO SM
Citation Format: Smita Misra, Gautam Chaudhuri. Myc-induced suppression of the RNA-binding protein ZAR2 in breast cancer cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1927.
Abstract 1929: The novel role of microRNA-128 in proneural to mesenchymal subtype transition in glioblastoma stem cells by targeting components of pro-oncogenic Polycomb Repressor Complex
Authors: Rooj Arun K. , Mineo Marco , Ricklefs Franz , Bronisz Agnieszka , Chiocca Ennio , Godlewski Jakub 
Published: July 2016

Abstract
Heterogeneous glioblastoma multiforme (GBM) was categorized based on transcriptional signatures into four subtypes (proneural (PN), neural, classical, and mesenchymal (MES)). In order to develop effective targeted therapeutic strategies, understanding the heterogeneous gene expression and molecular features of these subtypes is crucial. De-regulation of microRNA expression and activity has been shown to play an important role in tumor initiation and progression, including gliomagenesis. We have previously reported that expression of microRNA-128 (miR-128) is significantly down regulated in GBM and it diminishes self-renewal of GBM stem-like cells (GSCs) and sensitizes them to irradiation. Proneural-to-mesenchymal transition (PMT) manifested by concomitant up regulation of MES markers and down regulation of PN markers, is associated with increased malignancy, therapy-resistance and worse prognosis, but the underlying causes of PMT have not been convincingly characterized yet. In this study, we have demonstrated that miR-128 can regulate the PMT in GSC subsets. We showed that the expression of miR-128 in PN GSCs was significantly higher compared to MES subtype. As a tumor suppressive microRNA, miR-128 inhibited the MES GSC-specific high expression of Bmi1 and Suz12, two components of Polycomb Repressor Complexes (PRC) 1 and 2, respectively. In both GSC subtypes, miR-128 driven targeting of PRCs suppressed their epigenetic activity measured by ubiquitination of H2AK119 and tri-methylation of H3K27. Stable down regulation of miR-128 in PN GSCs significantly increased the expression of MES-specific gene signature (BCL2A1, CD44, WT-1, LYN, and MET) while its stable up regulation in MES GSCs resulted in the restoration of PN specific gene signature (CD133, SOX2, NES, OLIG2, and NOTCH1). We also showed that stable expression of miR-128 in GSCs could regulate the process of irradiation-induced PMT. Our in vivo studies showed the anti-tumorigenic role of miR-128 in both PN and MES GSC-derived intracranial tumor models. Taken together, we demonstrated that altering levels of miR-128 was sufficient to cause or reverse PMT, most likely by targeting the level/functions of PRCs and their target genes in GBM.
Citation Format: Arun K. Rooj, Marco Mineo, Franz Ricklefs, Agnieszka Bronisz, Ennio Chiocca, Jakub Godlewski. The novel role of microRNA-128 in proneural to mesenchymal subtype transition in glioblastoma stem cells by targeting components of pro-oncogenic Polycomb Repressor Complex. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1929.
Abstract 1932: The importance of RNA editing enzymes in glioblastoma
Authors: Gallo Angela 
Published: July 2016

Abstract
This study was supported by AIRC.
Glioblastoma (or grade IV astrocytomas) is a highly heterogeneous and deadly malignant brain tumor and one of the most incurable form of cancer in human that urgently needs new therapeutic targets. There is great interest in elucidating all the molecular basis and functional importance of genetics and epigenetic mechanisms occurring in glioblastoma. In our laboratory, we investigate whether essential post-transcriptional event (such as the A-to-I RNA editing) is a possible molecular mechanism involved in the appearance/progression of glioblastoma.
A-to-I RNA editing modifies the nucleotide sequence of RNA target molecules. The ADARs (Adenosine Deaminases that Act on RNA) are the enzymes responsible for this conversion acting on pre-mRNAs or non-coding RNAs (such as microRNA). Inosine, is recognized by the translation and splicing machineries, as Guanosine. Therefore, ADARs can play a direct and critical role in generating alternative protein isoforms (by codon changes and splicing pattern alterations) and modulating gene expression levels (by editing microRNAs and/or 3’-UTRs). In mammals, there are three different ADAR enzymes (ADAR1-3). The deregulation of ADAR2 activity has been connected with several neurological human diseases and Adar2 knockout animals show a lethal neurological phenotype. We demonstrated a direct correlation between a progressive decrease of ADAR2 editing activity and the increased grade of malignancy in paediatric astrocytomas (from grade I to grade IV). We show that the rescue of ADAR2 in glioblastoma cells is able to significantly inhibit in vivo glioblastoma tumor growth. Differently, when we decrease the expression of ADAR2 in malignant but not tumorigenic astrocytoma cell line (A172) we observed a boost of several cancers cell features such as cell proliferation, migration and colony formation.
By integrating deep-sequencing and array approaches with bioinformatics analyses and molecular studies, we observed that ADAR2 is essential to edit a small number of mature miRNAs and to significantly modulate the expression of about 90 miRNAs in glioblastoma cells that may contribute to cancer progression.
Our findings disclose an additional layer of complexity in miRNome regulation and provide information to better dissect the impact of ADAR2 editing enzyme in glioblastoma.
Citation Format: Angela Gallo. The importance of RNA editing enzymes in glioblastoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1932.
Abstract 1935: A role for microRNAs in the regulation of transcription factor ATF5
Authors: Gaither Kari A. , Liu David X. , Madarampalli Bhanupriya 
Published: July 2016

Abstract
ATF5 is a widely expressed transcription factor that modulates survival, proliferation, and differentiation and plays a role in homeostasis and cellular stress response. In unstressed conditions, ATF5 has a short half-life and is rapidly degraded due to post-translational modifications. Conversely, ATF5 is upregulated in cells under cellular stress. Furthermore, we have found that ATF5 is elevated in transformed C6 glioma and MCF7 breast cancer compared to nontransformed cells and is a survival factor for both transformed cell lines. Although it is known that ATF5 mRNA can be stabilized at the 5’ untranslated region (UTR) and protected from degradation via interactions with other proteins, regulation of ATF5 expression is not fully understood. We hypothesize that microRNA (miRNA) play a role in regulating the expression of ATF5 at the 3’ UTR. MiRNAs are endogenous small non-coding RNAs 20-25 nucleotides in length that contribute to regulation of gene expression at the translational level. Herein, we sought to identify the presence of specific miRNA and their levels and ability to downregulate ATF5 during cellular stress and other physiological conditions in vitro. To date, no studies have examined the regulation of ATF5 by miRNA. Binding sites of miRNA are typically found in the UTRs of target mRNAs. We used TargetScan, miRanda, and other in silico modeling programs to identify miRNAs that were predicted to bind to the 3’ UTR of ATF5 and selected miRNAs 129-5p, 433-3p, and 520b as initial candidates for their potential in regulation of ATF5. Here, we have employed multiple strategies to investigate a potential role of miRNAs in the regulation of ATF5. Luciferase reporter assays were used as an initial method of validation for the miRNA candidates. Subsequently, transfections were carried out with precursor microRNA and expression levels of ATF5 were measured under varying physiological conditions via Western blot analysis. Additionally, immunoprecipitations were carried out with ATF5 3’ UTR mRNA and HeLa cell lysate to assess the presence of miRNAs and quantify the amount of specific miRNA bound to the 3’ UTR under varying physiological conditions via qPCR analysis. Preliminary data show that miRNA are bound to the 3’ UTR of ATF5 and that miRNAs 129-5p, 433-3p, and 520b help to regulate the expression of ATF5 under varying stress conditions and at steady state. Better understanding of the regulation of ATF5 could have implications in a broad range of human malignancies, including glioma and potentially several other types of cancer.
Citation Format: Kari A. Gaither, David X. Liu, Bhanupriya Madarampalli. A role for microRNAs in the regulation of transcription factor ATF5. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1935.
Abstract 1949: MicroRNA-137 is a putative predictive biomarker and can inhibit cell proliferation and induce apoptosis in colorectal cancer
Authors: HUANG. YU-CHUAN 
Published: July 2016

Abstract
MicroRNA-137 (miR-137) is a potential tumor suppressor in many kinds of cancers, including colorectal cancer (CRC). However, the role of miR-137 in CRC remains unclear. Our study showed that miR-137 is silenced in human colorectal cancer tissues and colon polyps. The methylation of miR-137 promoter is determined by methylation-specific PCR (MSP) and quantified by pyrosequencing analysis. By bioinformatics analysis and Q-PCR assay, we confirmed that miR-137 can target COX2, CDC42, CDK6, and Aurora-A. The negative expression of miR-137 and Aurora-A is confirmed in human colorectal cancer tissues and colon polyps, as well as colon polyps from the AOM/DSS-treated mouse model. Enforcing expression of miR-137 in colorectal cancer cells resulted in G2/M arrest, reduced cell proliferation, and finally led to apoptosis. Those effects can be rescued by overexpressed Aurora-A. By xenograft animal model, the growth of tumors was attenuated in miR-137-overexpressing colorectal cancer cells, in which the tissues show an increased Annexin V signal. Additionally, the AOM/DSS-induced colorectal adenocarcinoma can be restored by demethylation drug treatment. Taken together, our study suggests that epigenetic silence of miR-137 may contribute to early CRC formation through inhibiting the expression of Aurora-A, and loss of miR-137 expression in colon polyps may serve as a potential biomarker to predict the tendency towards to CRC formation. The investigation of the regulatory mechanism of miR-137 in CRC progression may shed new light on early prognosis or cancer therapy for CRC in the future.
Citation Format: YU-CHUAN HUANG. MicroRNA-137 is a putative predictive biomarker and can inhibit cell proliferation and induce apoptosis in colorectal cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1949.
Abstract 195: Defining the role of PAK7 variants in melanoma
Authors: LaPak Kyle M. , Gross Michael A. , Vroom Denny C. , Lesinski Greg B. , Carson William E. , Burd Christin E. 
Published: July 2016

Abstract
Melanoma mortality is directly linked to its profoundly metastatic nature and inherent resistance to conventional chemotherapy. For this reason, increased understanding of the molecular mechanisms driving melanoma progression is of utmost importance. The p21-activated serine/threonine kinases (PAKs) are frequently mutated or overexpressed in cancer and have recently been implicated in tumor metastasis, proliferation, and apoptotic resistance. This observation has inspired drug discovery efforts to limit PAK activity; yet, mechanistic understanding of how PAKs (especially Type II PAKs) contribute to tumor initiation and progression is still evolving. PAK7, a type II PAK, is mutated in 16-18% of all melanomas. Melanoma-associated PAK7 mutations occur throughout the gene and have unknown biochemical and physiological consequences. The objective of this study was to determine how tumor-associated PAK7 variants mechanistically contribute to melanoma initiation and progression. First, we characterized PAK7 protein expression in a panel of 39 melanoma cell lines and primary melanocyte cultures. PAK7 levels were similar in both tumorigenic and non-tumorigenic cells and failed to correlate with the status of common melanoma driver mutations (e.g. NRASQ61, BRAFV600). In an array of 101 human tumor biopsies, PAK7 expression did not significantly change with advancing melanoma stage; however, PAK7 levels were higher in regional lymph node biopsies when compared to primary skin lesions. Since mutation is the predominant mechanism affecting PAK7 in melanoma, we investigated the biochemical and physiological consequences of common PAK7 variants. 11 distinct PAK7 mutations were stably expressed at low levels in VMM39 (melanoma) and NCI-H441 (lung) cells. Using these clones, changes in the phosphorylation of downstream PAK7 targets associated with cellular migration (p120), proliferation (CRAF), and apoptotic resistance (BAD, MDM2) were examined. In addition, we defined phenotypic alterations in cellular morphology, proliferation, migration, and apoptotic resistance associated with the expression of each mutant. These data allowed us to classify PAK7 variants of unknown significance into groups associated with specific cellular outcomes. To our knowledge, this is the first study to functionally characterize a wide variety of melanoma-associated PAK7 mutations and represents a critical first step in understanding how this kinase contributes to tumor initiation and progression.
Citation Format: Kyle M. LaPak, Michael A. Gross, Denny C. Vroom, Greg B. Lesinski, William E. Carson. Defining the role of PAK7 variants in melanoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 195.
Abstract 1958: Developing an online tool to validate survival-associated miRNAs utilizing expression data from 2,061 breast cancer patients
Authors: Győrffy Balázs , Lánczky András , Bottai Giulia , Nagy Ádám , Szabó András , Santarpia Libero 
Published: July 2016

Abstract
Background. MicroRNAs (miRNAs) are small non-coding RNAs capable of simultaneously regulating multiple gene networks, and affecting breast cancer patients’ outcome. Here we present the development of an online tool for the real-time meta-analysis of published miRNA datasets to identify novel prognostic biomarkers in breast cancer.
Methods. First, a comprehensive database was set up by searching GEO, TCGA, and PubMed repositories to identify datasets with published miRNA expression and clinical data. Due to platform differences, each dataset was processed separately. Kaplan-Meier and Cox regression analyses were performed to investigate the prognostic value of a set of dysregulated miRNAs in breast cancer. The complete analysis tool can be accessed online at: www.kmplot.com/mirna.
Results. Overall, 2,061 samples from four independent datasets were integrated into the tool including the expression signature of 1,302 distinct miRNAs. In addition to overall survival data, ER status (n = 2,039), histological grade (n = 1,396) and lymph node status (n = 1,933) are also available. By using our online tool, we demonstrated the prognostic value of some of the previous reported miRNAs implicated in breast cancer. For instance, miR-29c, miR-34c, miR-101, miR-125, and miR-190b, showed a consistent prognostic value in at least three out of four breast cancer datasets.
Discussion. In summary, we established the first online integrated platform for the rapid identification of the prognostic value of miRNAs in breast cancer.
Citation Format: Balázs Győrffy, András Lánczky, Giulia Bottai, Ádám Nagy, András Szabó, Libero Santarpia. Developing an online tool to validate survival-associated miRNAs utilizing expression data from 2,061 breast cancer patients. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1958.