bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5009: Identification of DNA methyltransferase target sites in cancer cells
Authors: Tiedemann Rochelle L. , Robertson Keith D. 
Published: August 2012

Abstract
Aberrant DNA methylation is commonly observed in cancer and is characterized by genome-wide hypomethylation and gene-specific hypermethylation, which is thought to contribute to genomic instability and tumor suppressor gene silencing, respectively. The DNA methyltransferases (DNMTs) are responsible for the establishment (DNMT3A, DNMT3B, DNMT3L) and maintenance (DNMT1) of DNA methylation patterns genome-wide. The mechanism by which DNA methylation patterns are altered in cancer is not well understood. Genome-wide unique and overlapping target sites for each of the DNMTs are also unknown both in normal and cancer states. Identification of DNMT target loci is essential in order to better understand how aberrant DNA methylation occurs in cancer. To study this process, DNMT mRNA levels were depleted both individually and in a combinatorial fashion via RNAi-based techniques in embryonic carcinoma cells. Following reduction in DNMT expression, the resulting DNA and RNA was analyzed for genome-wide DNA methylation and gene expression patterns, respectively. An affinity purification method, Methyl-Binding Domain (MBD)-seq, was used to capture and enrich methylated regions of the genome by utilizing the methyl-binding domain of MBD2b. The enriched methylated DNA was then used to construct an Illumina sequencing library. Global gene expression patterns were analyzed by microarray for each RNA sample. Next generation sequencing and microarray data were analyzed using several available algorithms (e.g. MACS) and high-throughput data software packages (e.g. Partek Genomics Suite) in order to construct and evaluate the DNA methylation profiles and subsequent gene expression changes that result from DNMT depletion. Our data show that distinct changes in DNA methylation profiles occur among the various DNMT knockdown samples that permit us to identify unique and cooperative target loci for each DNMT. Further elucidation of DNMT target sites holds great promise for enhancing our understanding of mechanisms that control aberrant DNA methylation that is observed in cancer as well as provide insight and rationale for targeting specific DNMTs in cancer therapies.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5009. doi:1538-7445.AM2012-5009
Abstract 5020: Genetic and epigenetic analysis of tumors in a zebrafish model of melanoma
Authors: Casa Angelo , Bourque Caitlin , Zack Yael , Houvras Yariv 
Published: August 2012

Abstract
The activating BRAF kinase mutation V600E occurs in ∼60% of human nevi and melanomas. A transgenic strain of zebrafish expressing BRAF-V600E under the control of the mitfa promoter on a p53 mutant background develops melanomas with 100% penetrance. Previously, we showed that a transposon-based vector, MiniCoopR, allows us to program melanocytes to express a candidate gene in a specialized zebrafish strain Tg(mitfa:BRAFV600E); mitfa-/-; p53-/-. This strain lacks melanocytes, but the lineage can be rescued by MiniCoopR injection at the 1-cell stage. This genetic system allows us to create cohorts of transgenic animals that express candidate genes and assay the effects on tumor development. Previous work identified two histone methyltransferases (HMTs), SETDB1 and SUV39H1, which cooperate with BRAF-V600E to accelerate the onset and severity of melanoma development. A number of HMTs display alterations in expression level or copy number in human cancers compared to normal tissues, and we tested a panel of methyltransferases using the MiniCoopR system. We hypothesize that HMTs promote tumorigenesis by altering the epigenetic program of melanocytes. In order to explore the effects on melanocyte specification and differentiation, we overexpressed and depleted candidate HMTs in zebrafish embryos and performed in situ hybridization for lineage-specific markers, such as crestin, sox10, mitfa, dct, and tyr. HMTs that exert specific developmental phenotypes were further characterized by performing chromatin immunoprecipitation (ChIP). Our goal is to correlate the processes affected in the developing embryo with the epigenetic program to elucidate the mechanism by which HMTs influence tumorigenesis. Additionally, we are developing a strain of zebrafish Tg(mitfa:BRAFV600E); mitfa-/-; alb-/-; p53-/-; Tg(mitfa:GFP) in which melanocytes rescued with MiniCoopR express GFP. These rescued melanocytes can be programmed to express candidate HMTs and allow us to visualize melanocyte and melanoma development in vivo. The work presented here will help correlate cancer phenotypes with specific chromatin-modifying enzymes that may be the basis for new drug development and biomarker discovery.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5020. doi:1538-7445.AM2012-5020
Abstract 5035: MicroRNA expression profiles classify renal cell carcinoma subtypes
Authors: Wach Sven , Theil Anne , Stoehr Christine , Hartmann Arndt , Ekici Arif B. , Taubert Helge , Wullich Bernd 
Published: August 2012

Abstract
Background: Renal cell carcinoma (RCC) accounts for about 2-4% of all human malignancies. Hereby, the entity of papillary RCC (pRCC) is the second most common entity with about 10-15% of all RCC. According to histomorphological characteristics pRCCs can be further subdivided in two distinct subtypes. Type 2 pRCCs are correlated with a worse clinical outcome than type 1 pRCCs. In order to characterize these RCC subtypes we studied microRNA (miRNA) expression profiles of primary pRCCs type 1 and 2 as well as clear cell RCC (ccRCC). Material and Methods: We performed comparative miRNA expression profiling using Affymetrix miRNA microarrays. Ten to fifteen samples were analyzed for each subtype containing matched pairs of microdissected malignant and nonmalignant tissue. Hierarchical clustering was used to identify characteristic miRNA expression signatures. The expression of selected miRNAs was validated using quantitative PCR. Results: Hierarchical clustering was not able to identify miRNA expression signatures characteristic for all RCC subtypes, highlighting the heterogeneity among RCC tumors. But when stratified according to histological subtypes, tumor and nonmalignant tissue samples could be separated from each other. Interestingly, pRCC tumors of type 1 and 2 displayed a characteristic miRNA expression profile making it possible to separate these two tumor subtypes. A differential expression of miRNAs miR-200c, mir-143, miR-145, miR-210 and miR-10b could be confirmed by qRT-PCR in a cohort of pRCC samples (p&lt;0.05; paired t-test). Applying a binary logistic regression model, a combination of only three of these miRNA miRNAs was sufficient to correctly determine the subtype of all pRCC tumor samples. Conclusion: Our findings demonstrate that miRNA expression in RCC is heterogeneous but there are characteristic miRNA expression profiles within RCC subtypes. In pRCC, specific miRNAs may reflect a molecular correlate to the histological differences between the two subtypes, which in turn are correlated to the clinical outcome.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5035. doi:1538-7445.AM2012-5035
Abstract 5040: Aberrant DNA methylation of microRNAs in hepatocellular carcinoma
Authors: Shen Jing , Wang Shuang , Zhang Yu-Jing , Kappil Maya , Wu Hui-Chen , Kibriya Muhammad G. , Wang Qiao , Jasmine Farzana , Ahsan Habib , Lee Po-Huang , Yu Ming-Whei , Chen Chien-Jen , Santella Regina M. 
Published: August 2012

Abstract
microRNAs (miRNAs) are a class of small non-coding RNAs involved in post-translational gene silencing by accelerating the degradation of mRNA and translational inhibition. miRNAs may regulate more than 60% of protein-coding genes’ translation. Previous studies have found that down-regulation of miRNAs is one of the most common features observed in solid tumors, including hepatocellular cancer (HCC). In the current study, we employed a genome-wide approach to test the hypothesis that methylation alteration in miRNA genes is an important mechanism causing deregulated miRNA expression in HCC. We analyzed tumor and adjacent non-tumor tissues from 62 Taiwanese HCC cases using the HumanMethylation27 DNA Analysis BeadChips that include 255 CpG sites relevant to 64 miRNA genes. A volcano plot was used to display mean DNA methylation differences of all CpG sites. The hierarchical clustering for the significant CpG sites was performed to differentiate tumor and non-tumor tissues. After Bonferroni adjustment, a total of 54 CpG sites (27 relevant genes) significantly differed in methylation levels, with 53 CpG sites significantly hypermethylated in tumor compared to non-tumor tissues. Among the significant CpG sites, 15 sites have more than 2 fold tumor/non-tumor differences, 17 sites have a difference between tumor and non-tumor tissues of &gt;10%, and 10 sites have both features. PANTHER ontology analysis suggested several enriched biological pathways for these miRNAs, including Wnt signaling, Ras, oxidative stress response, glutamine/glutamate conversion and mannose metabolism. The miRNAs methylation profiles were also compared by viral status (HBV/HCV) and AFB1 exposures. No statistically significant miRNA was identified. Analysis of a panel of candidate miRNAs (miR-196, miR-10a, miR-10b and miR-170) is ongoing in the same HCC tissues to evaluate whether the aberrant DNA methylation significantly correlates with expression.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5040. doi:1538-7445.AM2012-5040
Abstract 5184: Expression profiling of ECM proteins in advanced carcinoma of uterine cervix
Authors: Khan Rehan , Sharma Manoj , Sharma Alpana 
Published: August 2012

Abstract
Background Carcinoma of uterine cervix accounts for most common malignancy in Indian women. Migration is one of the important processes fundamental to cell invasion and dissemination. Role of extracellular matrix (ECM) proteins is also very important in this crucial process and cannot be ignored. ECM proteins are involved in cell migration, tissue remodeling, angiogenesis and cell adhesion. Fibulin-1 is cysteine-rich, calcium-binding extracellular matrix and plasma protein that has been implicated as playing a role in tumour progression by modulating cell morphology, growth, adhesion, and motility. Increased plasminogen activator (PA) secretion has been observed in malignant cells and tissue and PA is thought to be involved in the processes of tumorigenesis, cancer invasion and metastasis. Laminins are important for proliferation, differentiation, growth, migration & angiogenesis. Besides the structural function of nidogens, it has long been suggested that nidogens play a role in cell attachment and tumor angiogenesis. Objectives This study was aimed to investigate the expression and significance of ECM proteins (Fibulin-1, uPA, Laminin and Nidogen) in advanced carcinoma of uterine cervix. Material & Methods 40 patients of cancer cervix stage IIIb were included in this study. Circulatory levels of Fibulin-1, Laminin and Nidogen were measured using high sensitivity ELISA kits. uPA activity was measured by activity assay kit. The levels of biochemical markers were compared with 20 healthy females, taken as control. mRNA levels of these molecules were further assessed by Real Time RT-PCR. Data was analyzed statistically. Results Statistical significant (p &lt; 0.001) increase was observed in Fibulin-1, uPA and Laminin levels and found to be significantly correlated with each other whereas Nidogen evels were insignificantly increased as compared to controls. Increased mRNA expression for all these molecules has also been observed in the isolated PBMC by qRT-PCR except nidogen (statistically insignificant increase). Conclusion The elevated serum/plasma levels and increased quantitative expression of these ECM proteins suggests their involvement in the pathogenesis of the disease. This study suggests that rise in ECM proteins might contribute to the complicated and unregulated process of metastasis in cancer of cervix. The association of extracellular matrix proteins and the prognosis of the disease may lead to have a better approach in treating the cervical cancer patients with a combination therapy.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5184. doi:1538-7445.AM2012-5184
Abstract 5188: Altering cell attachment to growth substrate up-regulates growth differentiation factor 15 (GDF15) expression
Authors: Yong Koh Meng Aw , Zeng Yu , Vindivich Donald , Getzenberg Robert 
Published: August 2012

Abstract
Cell attachment to the extracellular environment is critical in determining cell fate. When normal cells lose attachment, they undergo anoikis. Cancer cells develop resistance to anoikis which results in metastasis. While there are many known genes alterations that can alter cell adhesion, less is known about how such a loss of cell adhesion may influence gene expression. We believe that a change in cell adhesion could trigger changes to gene expression, and the resulting changes play an important role in prostate cancer metastasis. Using prostate cancer cell lines, we examined gene expression changes in cancer cells brought about by loss of attachment to their growth substrate through chemical and physical means and how these changes play a role in prostate cancer. Microarray analysis was performed on LNCaP cells treated with latrunculin B, an actin cytoskeleton disrupting agent for 8 hours. Using quantitative real time PCR and immunoblot analysis, a member of the tumor growth factor beta superfamily, GDF15 was found to be consistently up-regulated when the cells were treated with either latrunculin B or other drugs that disrupt the actin cytoskeleton. These findings were observed not only in LNCaP but in PC3 and DU145 as well. GDF15 expression was rapidly increased in these three cell lines when cells were prevented from attaching to tissue culture plastic and the levels of GDF15 expression could be maintained as long as the cells were not allowed to re-attach. This up-regulation was reversed when cells were allowed to re-attach to growth substrate, or by regaining cell shape when the drugs were removed. GDF15 has been shown to be associated with metastatic prostate cancer as well as contributing to disease associated cachexia. In our study, we demonstrated that loss of cell adhesion was sufficient to increase GDF15 expression in a rapid and sustainable manner. This finding is novel and different from other reports that increased GDF15 led to altered cell shape and adhesion. We believe that our findings may provide a picture of the initial stages in metastasis when a cancer cell loses adhesion to the extracellular environment. Furthermore, our results reinforce the potential utility of GDF15 as a prognostic marker in prostate cancer, as well as the intricate relationship between the cell and the physical environment in cancer.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5188. doi:1538-7445.AM2012-5188
Abstract 5192: Platelet derived growth factor receptors differentially inform intertumoral and intratumoral heterogeneity
Authors: Kim Youngmi , Kim Eunhee , Guryanova Olga , Hitomi Masahiro , Sloan Andrew E. , Hjelmeland Anita B. , Rich Jeremy N. 
Published: August 2012

Abstract
Growth factor-mediated proliferation and self-renewal maintains tissue specific stem cells and is frequently dysregulated in cancers. Platelet-derived growth factor ligands and receptors (PDGFRs) are commonly overexpressed in gliomas and initiate tumors in genetically engineered models. PDGFRα alterations inform intertumoral heterogeneity towards a proneural glioma subgroup. We interrogated the role of PDGFRs in intratumoral heterogeneity with regards to differences in tumor cells. We found that PDGFRα is expressed only in a subset of gliomas while PDGFRβ is more commonly expressed in tumors but largely restricted to self-renewing tumorigenic glioma stem cells (GSCs). Targeting PDGFRβ genetically or with specific inhibitors attenuated GSC self-renewal, survival, tumor growth, and invasion. PDGFRβ targeting was associated with decreased activation of the cancer stem cell signaling node STAT3, and STAT3 activity rescued loss of PDGFRβ expression. These results demonstrate that a growth factor receptor family can differentially function to promote tumor heterogeneity. Our results may explain mixed clinical responses of anti-PDGFR based approaches, and suggest the need for integration of models of cancer as an organ system into development of cancer therapies.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5192. doi:1538-7445.AM2012-5192
Abstract 5197: Quantitative phosphorproteomics identified GPER-initiated PKA signal transduction event in breast cancer stem cell
Authors: Lai Alan Chuan-Ying , Wang Yi-Ting , Lin Ruey-Jen , Wu Hsin-Yi , Chang Wen-Wei , Chang Wen-Ying , Chen Yu-Ju , Yu Alice L. 
Published: August 2012

Abstract
Human breast cancer stem cells (BCSC) identified recently have the ability to initiate neoplastic growth with differentiation and display higher resistance to chemotherapy and radiotherapy. The allure of targeting this specific group of cells to reduce mortality of disease has attracted research efforts toward BCSC. Although some unique properties of BCSC have been deciphered, the molecular mechanisms are still poorly understood. Here, we applied in-house developed techniques to quantitatively compare the phosphoproteomic profiles between BCSC and non-cancer stem cells (nonCSC) derived from a xenograft of human breast cancer. For quantitative analysis, we utilized a SEMI-strategy for multiplexed label-free quantitation combining pH/acid-controlled IMAC chromatography and LC-MS/MS for relative quantitation of site-specific phosphorylation. This strategy effectively increases the phosphopeptide quantitation coverage. The differentially expressed phosphoproteins were mapped to multiple signaling pathways including NOTCH, CDK/ERK and JAK-STAT pathways, which potentially orchestrate the self renewal and stemness of BCSC. We also demonstrated ∼2 fold greater expression of GPER in BCSC than non-BCSC population, and GPER signaling could induce PKA-mediated phosphorylation of BAD in BCSC. Silencing of GPER via RNAi or mutation of phosphorylation sites of BAD led to reduced proliferation to 40.8 and 53.2 % of control, respectively, and the RNAi silencing of GPER decreased the mammosphere formation of BCSC to 43.5 % of control. These findings implies the importance of GPER and its downstream PKA pathway to the maintenance of stemness characteristics of BCSC.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5197. doi:1538-7445.AM2012-5197
Abstract 5201: Suppression of WNT1 expression inhibits the maintenance and expansion of cancer stem cells in a mouse model of breast cancer
Authors: Kim Ran-Ju , Choi A-Ram , Roh Kyung-Jin , Kim Soo-Rim , Park Ju-Hyun , Lee Su-Youn , Park Se-Jin , Nam Jeong-Seok 
Published: August 2012

Abstract
Cancer relapse is the most common cause of mortality in breast cancer patients. The cancer stem cell (CSC) hypothesis proposes that CSCs are the root of cancer. CSC-targeted therapies may prevent cancer relapse and provide more effective treatment. It has been known that stem cells can be enriched in non-adherent sphere culture. To identify molecular targets in breast CSC, we compared transcription levels of stem cell-related genes between tumorspheres established from Balb/c mice-derived 4T1 mammary carcinoma and mammospheres from the mammary glands of Balb/c mice. The most differentially expressed gene was found to be Wingless-type MMTV integration site family, member 1 (WNT1). To determine whether WNT1 has any relevance in breast carcinoma, we analyzed the expression of WNT1 in the human matched normal breast and breast cancer samples. Immunofluorescent staining showed that WNT1 expression was elevated ∼17-63-fold in cancerous tissues compared with non-cancerous tissues from the same breast cancer patients. Functionally, knockdown of WNT1 in 4T1 cells reduced the Aldefluorpos cell compartment enriched in CSCs and suppressed the properties of CSCs, including anti-apoptosis, sphere-forming ability, and tumor initiation ability in vivo. Collectively, these results show that WNT1 expression gives rise to properties of CSC in breast cancer. Therefore, the targeting of WNT1-associated signaling may provide an effective therapeutic approach in the treatment of advanced breast cancer.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5201. doi:1538-7445.AM2012-5201