bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1097: Knockdown of splicing factor ESRP1 affects multiple splicing factors
Authors: Gökmen-Polar Yesim , Neelamraju Yaseswini , Gu Xiaoping , Nallamothu Gouthami , Janga Sarath C. , Badve Sunil 
Published: August 2015

Abstract
Introduction: Tissue-specific alternative splicing (AS) is an important mechanism for regulating gene expression. Epithelial Splicing Regulatory Proteins 1 and 2 (ESRP1 and ESRP2), two RNA-binding proteins (RBPs) that promote splicing, are potential candidates that contribute to breast cancer recurrence and resistance to therapies. In our prior studies, we have shown that ESRPs are associated with endocrine resistance. In this study, we seek to investigate the impact of the ESRP1 knockdown in endocrine resistant breast cancer cells. Methods: Expression of ESRP1 was analyzed in endocrine resistant-LCC2 and LCC9 cells. Knockdown of ESRP1 expression in LCC2 and LCC9 cells was achieved using lenti-viral based shRNA approach (Mission TRC human shRNA constructs, Sigma). We next performed paired-end RNA-sequencing of LCC2 and LCC9 cells transfected with control and two clones representative of shRNA knockdown (Illumina HiSeq platform, SeqWright Genomic Services) according to the manufacturer's instructions. After processing and quality check of raw FASTQ data (Illumina CASAVA, FASTQ and FASTX toolkits), reads were aligned, and quantified using bioinformatics software tools (Tophat/Cufflinks and Sailfish). Results: Expression of ESRP1 is significantly elevated in ERα-positive endocrine -resistant cells (LCC2 and LCC9 cells). ESRP1 knockdown was confirmed using qRT-PCR analysis in LCC2 cell lines (clone1 - 80% reduction and clone 3- 95% reduction) and in LCC9 cells (clone 2- 90% reduction and clone 3- 50% reduction). RNA-seq analysis identified 5153 differentially regulated genes between ESRP1 knockdown and control LCC2 cell lines. Of the 5153 genes, 1117 and 2109 genes were unique to clone 1 and clone 3, respectively, while 1927 genes were common in both clones. Targeted RNA-seq analysis also revealed that ESRP1 regulates the expression of several genes including other splicing factors. Furthermore, a functional enrichment analysis of these genes revealed a possible role of altering important pathways such as cell-cell adhesion and cell signaling. Additionally, it was observed that neither ESR1 nor any of its downstream genes were affected by the knockdown of ESRP1. This data was similar to that obtained in knockdown of LCC9 cells. Conclusions: ESRP1 regulates splicing of multiple genes in ER+ breast cancer. The process is independent of ER pathway. Targeting splicing could be a novel modality for treating endocrine therapy resistant breast cancer.
Citation Format: Yesim Gökmen-Polar, Yaseswini Neelamraju, Xiaoping Gu, Gouthami Nallamothu, Sarath C. Janga, Sunil Badve. Knockdown of splicing factor ESRP1 affects multiple splicing factors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1097. doi:10.1158/1538-7445.AM2015-1097
Abstract 110: The role of the p53 target Wig-1 in senescence and cancer
Authors: Jerhammar Fredrik , Bersani Cinzia , Djureinovic Dijana , Micke Patrick , Wiman Klas G. 
Published: August 2015

Abstract
The wild type p53-induced gene 1, Wig-1 (also known as Zmat3 or PAG608) binds to AU-rich elements in mRNAs and thereby regulates important tumor associated factors including p53, FAS, and N-Myc.
Focusing on normal human diploid fibroblasts (HDF), we are now exploring the role of Wig-1 in senescence. SiRNA-mediated Wig-1 depletion increases senescence markers such as Beta-galactosidase staining, H3K9me3, H4K20me3, and p21. Also, Wig-1 is spontaneously downregulated in cells undergoing replicative senescence.
The trimethylation of lysine 9 on histone 3 (H3K9me3) is an established marker of cellular senescence and increases upon siRNA-mediated Wig-1 knockdown in HDF cells. It is also increased in late passage (senescent) fibroblasts that express low Wig-1 levels.
Our RNA-immunoprecipitation sequencing (RIP-seq) data of tumor cells shows that Wig-1 binds histone-modifying enzymes SUV39H2 (which trimethylates H3K9), and subunits of PP1 (protein phosphatase 1, which dephosphorylates H3T10). These mRNAs have AU-rich elements in the 3´UTR. Importantly, we have observed that both SUV39H2 and its corresponding methylation (H3K9me3) is increased upon Wig-1 silencing.
In a cohort of 350 lung cancer patients, we found Wig-1 gene amplification in a large portion of squamous cell carcinomas, whereas in lung adenocarcinomas the Wig-1 gene was unchanged. Interestingly, strong Wig-1 staining in this cohort correlates to worse prognosis.
We think Wig-1 attenuates senescence via downregulating important senescence markers in both tumor and normal cells. Evidence point to Wig-1 playing an inhibitory role on the mRNAs of histone modifying enzymes, thereby acting on well established senescence markers of gene expression and chromatin regulation.
Citation Format: Fredrik Jerhammar, Cinzia Bersani, Dijana Djureinovic, Patrick Micke, Klas G. Wiman. The role of the p53 target Wig-1 in senescence and cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 110. doi:10.1158/1538-7445.AM2015-110
Abstract 1115: Targeted RNA sequencing improves transcript analysis in cancer samples
Authors: Lin Ling , Abo Ryan , Dolcen Deniz , Paquette Rachel , Laing Angelica , de Waal Luc , Thorner Aaron , Ducar Matthew , Ziaugra Liuda , Wollison Bruce , Breneiser Marc , Hahn William , Meyerson Matthew , Van Hummelen Paul , MacConaill Laura 
Published: August 2015

Abstract
RNA sequencing (RNA-seq) is a transcriptome profiling technology that provides multiple levels of insight into the genome. In addition to expression levels (transcript abundance), it generates endpoints such as alternative splicing, somatic mutations and rearrangements, which may have functional consequences in cancer. Although somatic mutations are generally identified by DNA sequencing, RNA-seq has the advantage of detecting allele-specific expression affecting a variant allele, as well as functional chimeric transcripts that result from structural rearrangements. Compared to microarray technologies, RNA-seq can provide additional information about novel transcripts. Due to the complexity of the human transcriptome and the variability of gene abundance, the cost of whole transcriptome sequencing to achieve sufficient coverage to detect these types of alterations remains high. To explore the feasibility of a more cost-effective method, we compared the performance of three different RNA-seq methods: whole-transcriptome-, exome-, and targeted RNA-seq, using RNA derived from cancer cell lines and Formaldehyde Fixed-Paraffin Embedded (FFPE) samples. For whole-transcriptome preparation, we used the Illumina TruSeq Stranded mRNA and total RNA kits for cell line and FFPE samples, respectively. Exome-RNAseq was performed using the Illumina Access kit. The libraries from whole-transcriptome RNAseq were subjected to hybridization capture using OncoPanel-an Agilent SureSelect baitset of 500 cancer-related genes. Compared to whole-transcriptome, exome- and targeted-RNA-seq demonstrated (1) higher coding exon coverage and multiplexing capability; (2) reduced rRNA composition to 1%; (3) comparable gene abundance information and (4) over 90% of reads aligned to coding exon regions in FFPE samples, compare to ∼30% when using whole transcriptome method. In conclusion, we demonstrated that exome- and targeted RNA-seq provide a cost-effective way to analyze a subset of the transcriptome. Furthermore, targeted RNA-seq can be highly multiplexed and is therefore amenable for large-scale tumor profiling in clinical or research settings.
Citation Format: Ling Lin, Ryan Abo, Deniz Dolcen, Rachel Paquette, Angelica Laing, Luc de Waal, Aaron Thorner, Matthew Ducar, Liuda Ziaugra, Bruce Wollison, Marc Breneiser, William Hahn, Matthew Meyerson, Paul Van Hummelen, Laura MacConaill. Targeted RNA sequencing improves transcript analysis in cancer samples. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1115. doi:10.1158/1538-7445.AM2015-1115
Abstract 1140: PI3K/Akt inhibition decreases oxygen consumption In tumor cells by phosphorylating and inactivating pyruvate dehydrogenase PDH E1α subunit
Authors: Cerniglia George John , Day Souvik , Gallagher-Colombo Shannon M. , Daurio Natalie , Tuttle Stephen , Busch Theresa M. , Busch Theresa M. , Lin Alexander , Esipova Tatiana V. , Vinogradov Sergei A. , Koumenis Constantinos , Maity Amit 
Published: August 2015

Abstract
The PI3K/mTOR pathway plays a central role in coupling metabolic processes to the cellular proliferative state. Pharmacologic inhibitors of the PI3K/mTOR pathway or genetic inhibition of Akt/PI3K decreased the oxygen consumption rate (OCR) in transformed cell lines in vitro by 30-40%. Pharmacologic inhibition of this pathway increased phosphorylation of the E1α subunit of the pyruvate dehydrogenase (PDH) complex on Ser293, an inhibitory modification of this critical gatekeeper of mitochondrial respiration. Expressing wild type PTEN in a doxycycline-inducible manner in a glioblastoma cell line with mutant PTEN led to an increase in PDH E1α phosphorylation and a decrease in OCR. The decrease in OCR with PI3K/Akt/mTOR inhibition was recapitulated by knocking down PDH E1α expression using siRNA. Pre-treatment with dichloroacetate (DCA), a known inhibitor of the pyruvate dehydrogenase kinases (PDKs) that phosphorylate PDH E1α, prevented the upregulation in PDH E1α phosphorylation, induced by inhibition of the pathway and also blunted the decrease in OCR. Likewise, introduction of exogenous PDH-E1α that contains serine to alanine mutations, which can no longer be regulated by phosphorylation, also blunted the decrease in OCR seen with PI3K/mTOR inhibition. Our findings highlight an association between the PI3K/mTOR pathway and tumor cell oxygen consumption that is regulated in part by PDH phosphorylation. These results have important implications for understanding the effects PI3K pathway activation in tumor metabolism and also in designing cancer therapy trials that use inhibitors of this pathway.
Citation Format: George John Cerniglia, Souvik Day, Shannon M. Gallagher-Colombo, Natalie Daurio, Stephen Tuttle, Theresa M. Busch, Theresa M. Busch, Alexander Lin, Tatiana V. Esipova, Sergei A. Vinogradov, Constantinos Koumenis, Amit Maity. PI3K/Akt inhibition decreases oxygen consumption In tumor cells by phosphorylating and inactivating pyruvate dehydrogenase PDH E1α subunit. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1140. doi:10.1158/1538-7445.AM2015-1140
Abstract 1141: LPA stimulates glycolytic shift of ovarian cancer cells via gip2 oncogenes
Authors: Ha Ji Hee , Radhakrishnan Rangasudhagar , Dhanasekaran Danny 
Published: August 2015

Abstract
Ovarian cancer patients show increased levels of lysophosphatidic acid (LPA) in their serum and ascitic fluid. Our previous studies have established a critical role for LPA in inducing proliferation as well as migration of ovarian cancer cells. In the present study, we focused on identifying novel therapeutic targets in the oncogenic signaling pathway regulated by LPA. Using a commercial pathway reporter array of 45 transcription factors, we found that hypoxia-induced factor-1 alpha (HIF-1 alpha) was the most activated transcription factor induced by LPA. Both stable as well as transient silencing of Galphai2, a downstream signaling mediator for LPA, abrogates LPA induced increase in HIF-1 alpha expression. In addition, our results indicate that LPA stimulated an increase in the expression of Hexokinase-2 (HK2) and Glucose transporter 1 (GLUT1), which are targets of HIF-1 alpha, are also mediated via Galphai2 signaling pathway. To determine the outcome LPA induced increase in HK2 and GLUT1 on glycolytic rates, we measured the extracellular acidification rate (ECAR) in ovarian cancer cells following treatment with LPA, using an XFe analyzer. In both SKOV3-ip and OVCA429 cells, LPA increased ECAR in a dose-dependent manner. Silencing Galphai2 as well as HIF-1 alpha in ovarian cancer cells reduced ECAR indicative of reduced glycolytic rate. The current study, points to the identification of LPA(R)-Galphai2-HIF-1 alpha-GLUT1 signaling axis as potential metabolism-targets in ovarian cancer treatment.
Citation Format: Ji Hee Ha, Rangasudhagar Radhakrishnan, Danny Dhanasekaran. LPA stimulates glycolytic shift of ovarian cancer cells via gip2 oncogenes. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1141. doi:10.1158/1538-7445.AM2015-1141
Abstract 1144: Antioxidant enzyme-mediated survival of ECM-detached breast cancer cells requires AMPK activation
Authors: Durbin Sienna M. , Versagli Calli , Pape Daniel , Schafer Zachary 
Published: August 2015

Abstract
Normal epithelial cells require attachment to the extracellular matrix (ECM) for proper maintenance of metabolic function and survival. However, it has recently become clear that cancer cells must alter their metabolism during times of ECM-detachment in a fashion that promotes their survival. We have discovered that breast cancer cells utilize the activity of antioxidant enzymes to eliminate the detachment-induced elevation in reactive oxygen species (ROS). This decrease in ROS relieves the inhibitory effects that ROS have on fatty acid oxidation (FAO) which in turn facilitates ATP production during times of energy deprivation. Interestingly, this critical role of antioxidant enzymes is not evident in ECM-attached cells suggesting that targeting antioxidant enzymes may be an effective strategy to eliminate ECM-detached cells. Furthermore, our studies have revealed that the molecular mechanisms controlling the regulation of FAO by antioxidant enzymes involve modulation of AMPK protein levels. Thus, our data reveal that antioxidant enzymes and AMPK signaling may be attractive targets for the design of novel therapeutics aimed at eliminating ECM-detached cancer cells.
Citation Format: Sienna M. Durbin, Calli Versagli, Daniel Pape, Zachary Schafer. Antioxidant enzyme-mediated survival of ECM-detached breast cancer cells requires AMPK activation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1144. doi:10.1158/1538-7445.AM2015-1144
Abstract 115: SMYD2-mediated methylation regulates PTEN activity
Authors: Nakakido Makoto , Nakamura Yusuke , Hamamoto Ryuji 
Published: August 2015

Abstract
PTEN is a well characterized tumor suppressor protein. PTEN counteract PI3K-AKT pathway, which is one of the key signaling pathway for human tumorigenesis, through its lipid phosphatase activity. Whereas PTEN is known to be modified with various kinds of post-translational modifications such as phosphorylation, acetylation, and ubiquitination, methylation has not been reported to date. In this study, we elucidated SMYD2 (SET and MYND domain containing 2), a protein methyltransferase related to human tumorigenesis, methylated PTEN at lysine 313 in C2 domain. SMYD2 knockdown caused downregulation of PI3K-AKT pathway and led to cell growth suppression, suggesting that SMYD2-mediated PTEN methylation would negatively regulate PTEN activity. Given the critical role of PTEN as a tumor suppressor, our finding would not only contribute to further understanding of the mechanism of SMYD2 depending human tumorigenesis, but also may lead to a novel anti-cancer therapeutic strategy.
Citation Format: Makoto Nakakido, Yusuke Nakamura, Ryuji Hamamoto. SMYD2-mediated methylation regulates PTEN activity. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 115. doi:10.1158/1538-7445.AM2015-115
Abstract 1152: The regulatory effect of fructose-bisphosphate aldolase C in oral squamous cell carcinoma progression
Authors: Li Yueju , Huang Tse-Hung , Lin Been-Ren , Chang Cheng-Chi 
Published: August 2015

Abstract
In previous studies, glycolysis machinery has been identified as a regulating pathway in cancer cell. However, the role of glycolysis in oral squamous cell carcinoma (OSCC) progression is still largely unknown. Fructose-bisphosphate aldolase C (ALDOC), one of the key enzymes in glycolysis, expresses in OSCC patients and cell lines and detects by real-time quantitative RT-PCR. The functions of ALDOC were determined by gain and loss function approaches and the orthotopic animal model was performed. ALDOC mRNA and protein expression was significantly decreased in advanced migratory cell and negatively correlated with lymph node metastasis and advanced tumor TNM stage in OSCC patients. In conclusion, ALDOC plays as an OSCC prognosis marker clinically, and functions to suppress OSCC cell migration and invasion. ALDOC could be a potential therapeutic target to block OSCC progression.
Citation Format: Yueju Li, Tse-Hung Huang, Been-Ren Lin, Cheng-Chi Chang. The regulatory effect of fructose-bisphosphate aldolase C in oral squamous cell carcinoma progression. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1152. doi:10.1158/1538-7445.AM2015-1152
Abstract 1157: Potential mechanism for mitochondrial uncoupling protein 2 promotes skin carcinogenesis
Authors: Zhang Chunjing , Zhao Yunfeng 
Published: August 2015

Abstract
Mitochondrial uncoupling has recently been proposed as a novel survival mechanism for cancer cells, However, there is no direct evidence supporting that uncoupling proteins promote carcinogenesis. Herein, we examined whether mitochondrial uncoupling affects mouse skin carcinogenesis using uncoupling protein 2 (UCP2) homozygous knockout mice, and explored the mechanisms of tumor promotion by mitochondrial uncoupling by overexpressing UCP2 in JB6 P+ cells, which are the only characterized skin cell model to study tumor promotion. The vivo results indicate that the rates of oxygen consumption were only decreased in the carcinogen-treated UCP2 knockout mice whereas glycolysis was only increased in the carcinogen-treated wild-type mice. The levels of metabolites pyruvate, malate and succinate showed different trends after carcinogen treatments between the wild-type and UCP2 knockout mice. In addition, UCP2 knockout decreases 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase (PFKFB2, especially on the regulation of the key enzyme in glycolysis), CyclinB1 and the oncoprotein Fra-1 expression during skin carcinogenesis. The vitro results indicate that overexpression of UCP2 enhanced colony formation in response to tumor promoter treatment. In addition, overexpression of UCP2 induced the upregulation of Fra-1 and PFKFB2 expression. Although UCP2 overexpression could suppress apoptosis in vitro, But UCP2 Knockout did not cause increase in apoptosis. This study provides the first in vivo evidence using UCP2 mice supporting that UCP2 promotes carcinogenesis. Although the current data are unable to answer the question of how UCP2 knockout suppresses skin cancer formation, an interesting and important finding is the adverse changes of the three metabolites and especially on the regulation of the key enzyme in glycolysis pathway during carcinogenesis, which provides a clue for future studies. Together with early studies showing that UCP2 is overexpressed in a number of human cancers and knockout of UCP2 significantly reduced the formation of both benign (papilloma) and malignant (squamous cell carcinoma) tumors in mice, UCP2 could be a potential target for cancer prevention and/or therapy.
Citation Format: Chunjing Zhang, Yunfeng Zhao. Potential mechanism for mitochondrial uncoupling protein 2 promotes skin carcinogenesis. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1157. doi:10.1158/1538-7445.AM2015-1157
Abstract 116: Targeting EZH2 catalytic independent functions in breast cancer
Authors: Lim Keng Gat 
Published: August 2015

Abstract
Advances in drug discovery have enabled the development of catalytic inhibitors or inhibitors that disrupt protein-protein interactions. One validated drug target is the polycomb repressive complex 2 (PRC2), which promotes cancer development and reduces patient survival in multiple cancers. The core of PRC2 consists of Enhancer of Zeste Homolog 2 (EZH2) and Embryonic Ectoderm Development (EED). Currently, inhibitors targeting the catalytic site of EZH2 were efficacious in inhibiting a subset of blood cancers. In addition, a recently developed peptidomimetic inhibitor that disrupts the EED-EZH2 interaction also inhibits PRC2 activity and decreases proliferation of solid tumors. In this study, we investigated the effects of EZH2 protein depletion versus EZH2 catalytic inhibition with two small molecule inhibitors, GSK126 (an EZH2 catalytic inhibitor) and DZNep (a histone methylation inhibitor that depletes EZH2). We found that catalytic inhibition of EZH2 was insufficient to block cancer cell proliferation whereas depletion of EZH2 was effective at killing cancer cells. This study suggests that depleting EZH2 to inhibit both catalytic dependent and independent functions could be useful in the treatment of solid tumors such as breast cancer.
Citation Format: Keng Gat Lim. Targeting EZH2 catalytic independent functions in breast cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 116. doi:10.1158/1538-7445.AM2015-116