bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract LB-457: Multiplexing protein and DNA biomarkers on a single analytical platform
Authors: Li Shuqiang , Campo Maria F. , Fernandez Cecilia A. , Shuber Anthony P. 
Published: August 2012

Abstract
We have recently developed a non-invasive assay that combines protein and DNA biomarkers for triaging bladder cancer patients and demonstrated that this multi-analyte approach improves clinical performance. This assay combines detection in urine of Matrix Metalloproteinase-2 (MMP-2) protein, hypermethylation of two DNA markers (Twist1 and Nid2) and mutation detection of the FGFR3 gene. To eliminate the need to perform separate analytical procedures for protein and DNA, and to decrease assay complexity and cost while increasing assay throughput, we are now developing a method for simultaneous detection of protein and DNA biomarkers on a qPCR platform. To this end, we have identified and characterized six DNA aptamers that specifically bind Matrix Metalloprteinase-2 (MMP-2). DNA aptamers are single stranded DNA oligos that can bind specifically to their target molecules, including proteins. Once bound to the protein, these aptamers can then be used as templates for quantitative PCR-mediated protein detection. We have developed qPCR assays for each of the six MMP-2-specific aptamers, and demonstrate detection limits for each aptamer as low as 5x102 copies. Kinetic and equilibrium analysis was used to determine the KD constant for the aptamers. High affinity interactions were observed for all aptamers, with two aptamers having the highest affinity and calculated KD values of 15 and 10nM. Using one of these aptamers, we bound MMP-2 protein to the aptamer in solution and then immunoprecipitated the protein/aptamer complexes using biotin-labeled MMP-2-specific antibodies. Immunoprecipitated complexes were then quantitated using the aptamer-specific qPCR assay. In this study, we show that by qPCR, we can efficiently detect 10-12 mol/L of MMP-2 using the aptamer as the detection molecule. This level of MMP-2 protein detection is equivalent to commercially available ELISA assays. To further improve performance and to take advantage of the known specificity of aptamers, we intend to develop a system that uses one aptamer for detection and a second biotin-labeled aptamer for immunoprecipitation. We subsequently demonstrate the ability to multiplex the aptamer qPCR assay with our qPCR assay for FGFR3 and intend to add the other DNA markers into this multiplex system in the future. This is the first demonstration of simultaneous detection of protein and DNA biomarkers using a single analytical platform.
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 LB-457. doi:1538-7445.AM2012-LB-457
Abstract LB-462: AGO2 PAR-CLIP suggests a shift in specific miRNA target spectra upon modulation of EWS-FLI1 in Ewing's sarcoma
Authors: Herrero-Martin David , Kauer Max , Sienski Grzegorz , Fourtouna Argyro , Kralovics Robert , Kovar Heinrich 
Published: August 2012

Abstract
The chimeric oncoprotein EWS-FLI1 is the driving pathogenic force in Ewing's sarcoma family tumors (ESFT). As an aberrant ETS transcription factor it directly deregulates a multitude of genes related to proliferation control and differentiation. Recently, we reported on the EWS-FLI1 microRNA (miRNA) signature based on knockdown experiments in ESFT cell lines and on differential expression in primary tumors versus mesenchymal stem cells. In order to define the mRNA targets of EWS-FLI1 regulated miRNAs, we now performed pull-down experiments of AGO2 complexes after photoactivated ribonucleoside-enhanced cross-linking followed by NGS sequencing of associated mRNAs (PAR-CLIP). We obtained 92 Mio high quality reads of which 63 Mio were aligned to the reference genome. The genomic localization of these sequences demonstrated the specific enrichment of 3'UTRs (&gt;17 fold). Among obtained reads, T to C conversions were highly enriched consistent with crosslinking via 4-thiouridine to AGO2 containing complexes. PAR-CLIP results indicate AGO2 binding next to miRNA seed sequences for 4695 and 5160 genes associated with 1876 and 1860 miRNAs in the presence and absence of EWS-FLI1, respectively. Strikingly, for individual miRNAs the mRNA target spectra drastically changed upon EWS-FLI1 knockdown. For instance, for the two top EWS-FLI1 signature miRNAs hsa-mir-145 and hsa-mir 424 a shift from genes involved in cell death and differentiation to protein activator activity, and from protein degradation and cell cycle control to protein kinases and protein phosphorylation was observed, respectively. Of note, a target shift was also observed for miRNAs that did not change in response to EWS-FLI1 knockdown. In addition for many specifc targets no correlation was observed between mRNA abundancy and the level of association with AGO2 as reflected by read counts. These data suggest that EWS-FLI1 perturbs post-translational gene regulation by changing access of the RISC complex to its target mRNAs. Supported by EC-FP7 grant 259348 “ASSET”.
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 LB-462. doi:1538-7445.AM2012-LB-462
Abstract LB-467: miR-135b and miR-210 induce invasion and distant metastasis by targeting SIAH1 and SETD2 in colorectal cancer
Authors: Mudduluru Giridhar , Lunavat Taral R. , Scharp Maike , Muppala Santoshi , Patil Nitin , Leupold Jörg H. , Abba Mohammed , Allgayer Heike 
Published: August 2012

Abstract
The metastatic spread of tumor cells is ultimately responsible for the vast majority of cancer related mortality. In the attainment of a metastatic phenotype, several intricately interwoven processes are involved that lead to uncontrolled proliferation, loss of intracellular adhesions, extracellular matrix degradation, intravasation and dissemination into distant organs. Therefore, an improved understanding of molecular mechanisms which regulate metastatic transformation and progression of the cancer cells is of paramount importance. In this present study we performed miRNA-microarray analysis of six patient samples comprising normal, primary tumor and distant metastasis tissues, where we found miR-135b, miR-210, miR-378, miR-19a to be significantly up-regulated in both tumor and metastasized tissues as compared to the respective normal equivalents. We validated miR-135b and -210 in a series of 30 colorectal patients, in which we were able to demonstrate an increased expression in tumor as compared to normal tissues (p=0.008 and p=0.03, respectively). Forced in vitro expression of these miRNAs resulted in increased migration and invasion of Rko, SW480 and SW620 colorectal cancer (CRC) cell lines. Additionally, these cells manifested a gain of mesenchymal marker (N-cadherin) and a loss of epithelial marker (E-cadherin) expression at the protein level. Furthermore, of the several predicted targets identified, through luciferase, RT-PCR and Western blot analysis we found SIAH1 and SETD2 to be regulated by miR-135b and -210, respectively. Furthermore, in vivo, chorioallantoic membrane (CAM) metastasis assays revealed that miR-135b and miR-210 significantly induce distant metastasis to the lungs and liver (p=0.05). Our preliminary findings suggest that miR-135b and 210 play important roles in inducing tumor progression and may be useful as potential targets for mitigating metastatic spread
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 LB-467. doi:1538-7445.AM2012-LB-467
Abstract LB-469: An Epstein-Barr virus-encoded microRNA miR-BART5 upregulates human cellular microRNA miR-146a and downregulates IRAK1/NFκB in stomach cancer cells
Authors: Kim Dong Ha , Rho jin Kyung , Woo Jun Hee , Lee Byung Lan , Kim Chul Woo , Kim Woo Ho , Chang Mee Soo 
Published: August 2012

Abstract
Epstein-Barr virus (EBV) contributes to the development of the specific subsets of stomach cancer, nasopharyngeal cancer and malignant lymphoma etc. MicroRNAs (miRNAs) have been implicated in the regulation of various pathobiological processes in cancer. Recently, EBV-encoded viral miRNAs have been disclosed, whereas the functions of which remain largely unknown. A notable example of this is the human miRNA, which is targeted by viral miRNA. In this study, we investigated EBV-encoded viral miRNA miR-BART5/human cellular target interaction. The EBV miR-BART5 in EBV-infected stomach cancer cell line SNU719 was highly expressed comparing with that in EBV-infected lymphoma cell lines, Raji and Jijoye. In addition, EBV-infected stomach cancer cell revealed high level of human cellular miR-146a comparing with EBV-negative stomach cancer cells SNU601 and SNU216. Either miR-BART5 inhibitor product (anti-miR-BART5) or miR-BART5 precursor product (pre-miR-BART5) was transfected into EBV-infected stomach cancer cell, or EBV-negative stomach cancer cell, respectively. As a result, the expression of human cellular miR-146a was decreased in EBV-infected stomach cancer cell transfected with anti-miR-BART5 comparing with that in its original cell, while miR-146a was increased in EBV-negative stomach cancer cell transfected with pre-miR-BART5. As a predicted target of miR-146a, based on predicted base pairing using miRBase online program, we focused on interleukin-1 receptor-associated kinase 1 (IRAK1). Once EBV-negative stomach cancer cell was transfected with pre-miR-BART5, IRAK1 protein level was reduced by 50%, and nuclear factor-kappaB (NF-κB) (p65) was decreased. To check miR-BART5 influences on cellular biologic properties, when pre-miR-BARF5 was transfected into EBV-negative stomach cancer cell, invasion capacity of cancer cell was suppressed with a statistical significance. In conclusion, miR-BART5 could inhibit invasion of stomach cancer cell, which is in part due to the upregulation of miR-146a and downregulation of IRAK-1/ NF-κB signal pathway, offering clinicopathologic entity with a better prognosis to EBV-infected stomach 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 LB-469. doi:1538-7445.AM2012-LB-469
Abstract LB-47: The Prostate Net: We Inform To Fight
Authors: Arias Janet 
Published: August 2012

Abstract
The Prostate Net (TPN) is a non-profit patient education and advocacy organization dedicated to serving Prostate Cancer patients and their caregivers. Using the experience gained as a marketing professional and as a 16-year Prostate cancer survivor, TPN founder and president Virgil Simons has built an international organization that uses websites, 800 numbers, email and personal team counselors, newsletters and public forums to address disease risk awareness and early intervention. TPN's core objectives are to (1) Educate consumers most at-risk for a diagnosis of prostate cancer; (2) Inform the community on co-morbid diseases and conditions of negative impact; (3) Motivate consumers to make informed choices about healthcare and lifestyle management; (4) Lay the foundation for on-going healthcare information dissemination and interaction between the community and medical centers; and (5) Create an interactive network to maximize broad scale, mass communications of actionable health messages.
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 LB-47. doi:1538-7445.AM2012-LB-47
Abstract LB-473: The HDAC inhibitor entinostat targets erbB2/erbB3 receptors via functional cooperation of miR-125a, miR-125b, and miR-205 in breast cancer cells
Authors: Wang Shuiliang , Huang Jingcao , Lee Choon-Kee , Liu Bolin 
Published: August 2012

Abstract
Breast cancer is highly heterogeneous and has been classified into five distinct subtypes, among which erbB2-overexpressing (erbB2+) and basal breast cancers have the least favorable prognosis and express erbB receptors that are excellent targets for anti-cancer therapies. We previously reported that the class I HDAC inhibitor, entinostat (also known as MS-275, SNDX-275, Syndax Pharmaceuticals, Inc., Waltham, MA) selectively inhibited proliferation and induced apoptosis in erbB2+ breast cancer cells. Entinostat preferably targeted erbB2 and erbB3 receptors rather than the epidermal growth factor receptor (EGFR). Here, we study the molecular mechanism through which entinostat downregulates erbB2/erbB3 and promotes the breast cancer cells undergoing apoptosis. We showed that entinostat dramatically reduced the protein levels of erbB2/erbB3, whereas it had no significant effect on their mRNA expression in MDA-MB-453 and BT474 breast cancer cells. In addition, entinostat specifically decreased the endogenous, but not the exogenous erbB2/erbB3, suggesting that it did not promote erbB2/erbB3 protein degradation. Therefore, we hypothesizes that entinostat reduces erbB2/erbB3 receptors through transcription-independent mechanism; it may inhibit erbB2/erbB3 protein translation via induction of specific miRNA. Quantitative real-time (qRT) PCR revealed that entinostat significantly upregulated the expression of three erbB2/erbB3-targeting miRNAs, miR-125a, miR-125b, and miR-205 in erbB2+ breast cancer cells. Specific miRNA inhibitors were used to determine whether these miRNAs played a causal role in entinostat-induced downregulation of erbB2/erbB3 and apoptosis. While inhibition of any one of the three miRNAs failed to block entinostat action, simultaneous inhibition of any two of them significantly abrogated entinostat-induced erbB2/erbB3 reduction and apoptosis. Collectively, these data demonstrate that entinostat targets erbB2/erbB3 receptors via functional cooperation of miR-125a, miR-125b, and miR-205. Our findings suggest that miRNA-mediated epigenetic regulation may represent a novel strategy targeting erbB2/erbB3 to treat the aggressive erbB2+ breast cancer. The combinations of entinostat and erbB2-targeted therapy may be more efficacious for breast cancer patients whose tumors overexpress erbB2. This hypothesis will be directly tested by a recently initiated clinical study determining the activity of entinostat in combination with lapatinib in breast cancer patients that are erbB2+ and progressed on trastuzumab.
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 LB-473. doi:1538-7445.AM2012-LB-473
Abstract LB-48: The survivorship and advocacy task force model at Breast Cancer Connections
Authors: Brain Susie 
Published: August 2012

Abstract
This poster demonstrates that an advocacy program can facilitate effective collaboration between a non-profit cancer support organization and the cancer research community. The evolution and scaling of the Survivorship and Advocacy Task Force Model is illustrated so that it can be replicated by other non-profit disease support organizations. Breast Cancer Connections (BCC), is a non-profit breast cancer resource center serving people touched by breast cancer in the San Francisco Bay Area and globally via the Internet and the telephone Helpline. BCC provides personalized information, support, and connections to other local and national resources in an atmosphere of warmth, sensitivity, and understanding. BCC was founded in 1993, by a surgeon and her patient who saw a need to augment what was being offered through the medical model. With more than 35 programs and services, all offered at no charge, BCC remains a vital and unique resource. Prompted by the requirement for patient advocate and survivor involvement in the research grant application process (California Breast Cancer Research Program, DoD, Susan G. Komen for the Cure) as well as by the increasing needs of breast cancer survivors, BCC formed the Survivorship and Advocacy Task Force (SATF) in 2008. The dual purpose of the SATF is to provide input and review to researchers applying for research grants and to assist BCC in developing services and programs that will improve the lives of breast cancer survivors. Task Force members who participate in reviewing research grants must be active research advocates and have formal training in the language and concepts of breast cancer research (such as Project LEAD Institute) or a Ph.D. in a discipline relevant to breast cancer research.The poster author chairs the BCC's SATF with five active members. The Task Force's efforts include meeting the PI to hear about the research, providing input to the PI on the research from the patient/survivor perspective, reviewing the grant proposal, refining the language of the lay abstract, writing a letter of support to accompany the grant proposal, and participating in the research if the research application is accepted. Current collaborators include breast cancer researchers from Stanford University, Palo Alto Medical Foundation, and University of California, San Francisco. As funding agencies increase their requirements for advocate involvement and as awareness of the importance of survivorship continues to grow, requests for SATF participation continues to increase.
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 LB-48. doi:1538-7445.AM2012-LB-48
Abstract LB-484: Molecular regulation of HIF-1α by CDK1 and the cell cycle
Authors: Warfel Noel A. , El-Deiry Wafik S. 
Published: August 2012

Abstract
The hypoxia-inducible factor 1 (HIF-1) transcription factor is a critical mediator of the cellular response to oxygen deprivation. HIF-1α is frequently overexpressed in human cancers due to intratumoral hypoxia as well as genetic alterations that promote HIF-1α synthesis or inhibit its degradation (i.e. gain of function mutations in oncogenic pathways, such as RAS and PI3K, or loss of function mutations to the tumor suppressor, VHL, respectively). Under hypoxic conditions, HIF-1α is stabilized and translocates to the nucleus where it activates the transcription of genes that promote angiogenesis, cell proliferation/survival, and metastasis, among other processes. While the role of HIF-1 in the regulation of the cell cycle has been well studied, the effect of the cell cycle stage on HIF-1 expression and activity remains unknown. To address this question, HCT116 colon cancer cells were synchronized in G1, S, or G2/M-phase and exposed them to hypoxia (0.2% O2). Interestingly, HIF-1α expression was nearly abolished upon G2/M-phase arrest, and a significant increase was observed following arrest in S-phase. Therefore, cell cycle position influences the expression of HIF-1α, independent of oxygen concentration. Previous data in our lab indicates that knockdown of CDK1 decreased HIF-1α expression under hypoxic conditions. To further characterize this effect, we demonstrate that acute inhibition of CDK1 kinase activity with small molecules significantly decreases the stability of HIF-1α at the protein level, without affecting HIF-1α mRNA levels. Furthermore, cycloheximide chase experiments reveled that HIF-1α protein levels decreased at a significantly faster rate in the presence of a CDK1 inhibitor, R0-3306, (t1/2 = 38.2 ± 6.1 min) compared to controls (t1/2 = 54.6 ± 3.2 min). These results indicate that the half-life of HIF-1α is significantly decreased upon inhibition of CDK1. Taken together, these data indicate that CDK1 activity regulates the stability of HIF-1α, and suggests that CDK1 activity stabilizes HIF-1α through a post-translational modification that promotes its stability. Thus, we have discovered that CDK1 and the cell cycle position regulate the expression of HIF-1α. There is a subset of tumors that express HIF-1α under normoxic conditions, driving tumor progression and therapeutic resistance. Therefore the identification of alternative mechanisms that regulate HIF-1α expression would be extremely valuable in the clinical setting, as well as to aid the basic understanding of the role of HIF-1 in tumorigenesis.
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 LB-484. doi:1538-7445.AM2012-LB-484
Abstract LB-485: Estrogen receptor alpha activation is mediated by both the MAPK and PI3K phosphorylation pathway in hypoxia
Authors: Park Joon Woo , Lee Youngjoo 
Published: August 2012

Abstract
The estrogen receptor (ER) plays an important role in breast cancer development and progression. Hypoxia was shown to modulate the level of ERa expression and induce ligand-independent transcriptional activation of ERa, which may be intimately associated with the biology of breast carcinomas. Given that phosphorylation affects the transcriptional activity and stabilization of ERa, we examined the changes in phosphorylation of ERa under hypoxic conditions. Hypoxia induced phosphorylation of ERa at serine residues 118 and 167 in the absence of estrogen. Phosphorylation-defective ERa mutants with serine-to-alanine replacements at residues 118 and 167 had impaired hypoxia-induced ERa activation, showing that serine residues 118 and 167 are involved in hypoxia-induced ERa activation. The hypoxia-induced ERa-mediated transcriptional response was dependent on both the ERK1/2 MAPK and PI3K pathways, but not the p38 pathway, as assessed using chemical inhibitors. These data show that ERa phosphorylation via both the MAPK and PI3K pathways is one mechanism leading to ERa activation under hypoxia.
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 LB-485. doi:1538-7445.AM2012-LB-485