bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 5143: From sequencing data to mutation spectra: a high throughput analysis pipeline.
Authors: Jones David , Butler Adam P. , Teague Jon W. , Raine Keiran M. , Menzies Andrew , Marshall John , Hinton Jonathan , Dronov Serge , Stebbings Lucy , Jayakumar Alagu , Leroy Catherine , Zamora Jorge , Ramakrishna Manasa , Papaemmanuil Elli , Davies Helen , Cooke Susanna L. , Nik-Zainal Serena , McDermott Ultan , Stratton Michael R. , Campbell Peter
Published: August 2014

Advances in massively parallel sequencing technology have revolutionized the way we characterise cancer genomes and provided significant new insights to our understanding of the mechanisms that underpin oncogenesis. A diverse range of mutations types including single base-pair changes, insertions, deletions, copy number alterations and larger structural variations are common in cancer genomes.

To rapidly and accurately screen next generation sequencing data for these somatic mutations in cancer, the Cancer Genome Project (CGP) has developed a high throughput analysis pipeline utilising a suite of analysis software developed by the group. Built around a compute farm of ∼2,000 nodes and using a Lustre filesystem, raw data files (BAM etc.), analysis results files and version information are efficiently stored and tracked in our archive/storage system, FileTrk. Lane data is aligned using Burrows-Wheeler Aligner (BWA) and web interfaces have been developed to allow scientific staff to rapidly QC aligned lanes. Once QC'd and desired coverage is reached, lanes are merged into a single sample BAM file and the sample is then ready for analysis.

In house algorithms are used to detect point mutations (CaVEMan), structural variation breakpoints (Brass) and copy number changes (ASCAT and PICNIC), whilst Pindel is used to detect small insertions/deletions. Post-processing filters then remove false positives and the results are uploaded into a database. Mutations are annotated to the protein and RNA levels using standard nomenclature (Vagrent, in-house software). Downstream analysis software has been developed (CANDI, in-house software) which produces a range of plots to aid visualisation of mutation context and mutation spectra patterns in related cancer samples.

Current IT development is focussed on converting the pipeline to produce and store VCF output, incorporate further downstream analysis software and automate data export to COSMIC and the ICGC data portal.

Citation Format: David Jones, Adam P. Butler, Jon W. Teague, Keiran M. Raine, Andrew Menzies, John Marshall, Jonathan Hinton, Serge Dronov, Lucy Stebbings, Alagu Jayakumar, Catherine Leroy, Jorge Zamora, Manasa Ramakrishna, Elli Papaemmanuil, Helen Davies, Susanna L. Cooke, Serena Nik-Zainal, Ultan McDermott, Michael R. Stratton, Peter Campbell. From sequencing data to mutation spectra: a high throughput analysis pipeline. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5143. doi:10.1158/1538-7445.AM2013-5143
Abstract 5147: drugCARD: a database of anticancer treatment regimens and drug combinations.
Authors: Fernandez Eric , Pang Jianxiong , Snell Chris , Derow Cathy , Brightman Frances , Chassagnole Christophe , Jackson Robert
Published: August 2014

Physiomics and Pharmacometrics have collaborated to design a new database of anti-cancer drugs and therapeutic treatment information. The objective is to provide a database of anti-neoplastic agents, regimens and combinations for use by clinicians and researchers in oncology.

The drugCARD database, accessible through the web, offers data on more than 130 anti-cancer drugs (small molecules and biologics) used in research and in the clinic. It contains information on drug combinations as well as several hundreds of cancer chemotherapy regimens used routinely in the clinic. The data are classified according to tumour type, species and experimental system (in vitro or in vivo). This database will be regularly expanded and curated with the most current information.

Individual drug information contained within the database comprises pharmacokinetic profiles, mechanisms of action and resistance, dose-response effect, dosing limits, therapeutic index and immunosuppression data. Drug combinations are also referenced. The database covers synergy or antagonism, and includes the combination therapeutic index and cross-resistance information. Drug combinations where the level of synergy is dependent upon the drug schedule, drug sequence or administration timing are also referenced and thoroughly discussed. The user can browse and compare chemotherapeutic regimens, and analyse the overall drug dose over a course of treatment, by tumour type, in animal and clinical models. Moreover, the database enables users to design new combinations and regimens that obey dosing constraints (such as MLD and MTD), and can be used to determine drug candidates that could be combined with a new chemical or biological entity, given the respective mechanisms of action and other PK/PD data. Data can be exported for analysis in spreadsheets, modelling software or simulation packages. Advanced functions will include the ability to carry out statistical analysis on drug usage and dosing in various contexts. Finally, the database allows the expression and nomenclature of chemotherapy regimens to be standardized, which is of paramount importance in improving efficacy, as well as reducing medication errors (Kohler et al 1998).

Citation Format: Eric Fernandez, Jianxiong Pang, Chris Snell, Cathy Derow, Frances Brightman, Christophe Chassagnole, Robert Jackson. drugCARD: a database of anticancer treatment regimens and drug combinations. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5147. doi:10.1158/1538-7445.AM2013-5147
Abstract 5148: CanDrA: Cancer-specific driver missense mutation annotation with optimized features.
Authors: Mao Yong , Chen Han , Liang Han , Meric-Bernstam Funda , Mills Gordon , Chen Ken
Published: August 2014

Driver mutations are somatic mutations that provide growth advantage to tumor cells, while passenger mutations are those that are not functionally associated with oncogenesis. Distinguishing drivers from passengers is challenging because drivers occur much less frequently than passengers, they turn to have low prevalence, and their functions are multifactorial. Missense mutations are excellent candidates for driver identification, as they occur more frequently and are potentially easier to target than other types of mutations. Although several methods have been developed for predicting the functional impact of missense mutations, only a few are specifically designed for identifying driver mutations. As more mutations are being discovered, more accurate predictive models can be developed using machine learning approaches that systematically characterize the commonality and peculiarity of somatic mutations under specific cancer background. Here, we present such a Cancer Driver Annotation (CanDrA) tool that assesses the driver potential of missense somatic mutations based on a set of 95 structural and evolutionary features computed by over 10 functional prediction algorithms from SNVBOX, VEP, ANNOVAR and Mutation Assessor. Through feature optimization and supervised training, CanDrA outperforms existing tools in analysing the glioblastoma multiforme and the ovarian carcinoma data in The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia project.

Citation Format: Yong Mao, Han Chen, Han Liang, Funda Meric-Bernstam, Gordon Mills, Ken Chen. CanDrA: Cancer-specific driver missense mutation annotation with optimized features. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5148. doi:10.1158/1538-7445.AM2013-5148
Abstract 5149: Translating biospecimen science research results to improved biospecimen practices.
Authors: Moore Helen M. , Engel Kelly , Greytak Sarah , Bass B. Paige , Vaught Jim
Published: August 2014

Cancer tissues and blood are collected, processed and stored in different ways, across the country and across the world. Biospecimen Science is the study of how different methods of biospecimen collection, processing, and storage affect downstream analysis. The NCI Biospecimen Research Network (BRN) program sponsors, conducts, and collaborates on Biospecimen Science research to better understand how biospecimen pre-analytical factors influence the molecular integrity of biospecimens, and in turn, how such variation affects the reproducibility of research results. New data on how pre-analytical variation affects molecular integrity will support best practice Standard Operating Procedures for research and clinical trials biospecimens.

This presentation will focus on results from the first phase of the BRN program and current efforts to translate research results to evidence-based biospecimen practices. A summary of research results will be presented from several research studies which have performed systematic perturbations of blood and tissue collection and processing procedures, with subsequent molecular analysis. We will also present an overview of the Biospecimen Research Database (BRD; https://brd.nci.nih.gov), developed to improve access to the literature in Biospecimen Science. The BRD is a free and publicly accessible web-based database that currently contains over 1500 review and research articles covering a broad range of topics spanning the biospecimen lifecycle. Articles are meticulously categorized and annotated by a team of Ph.D. level scientists according to the type of biospecimen and technology platform used, the experimental variables investigated, and many other parameters. Progress will be described on a new approach to perform meta-analyses of the literature evidence related to different tissue preservation methodologies, such as freezing and temperature storage methods and formalin fixation and paraffin embedding. In addition, we will describe current progress on the development of evidence-based biospecimen practices based on BRN research results, literature evidence, and expert input.

Citation Format: Helen M. Moore, Kelly Engel, Sarah Greytak, B. Paige Bass, Jim Vaught. Translating biospecimen science research results to improved biospecimen practices. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5149. doi:10.1158/1538-7445.AM2013-5149
Abstract 515: Aurora-A is a determinant of tamoxifen resistance by phosphorylation and activation of ERα in breast cancer.
Authors: Zheng Xiangqian , Guo Jianping , Yang Hua , He Lili , Kanai Masayuki , Coppola Domenico , Gao Ming , Ren Xiubao , Cheng Jin Q.
Published: August 2014

Aurora-A kinase is frequently overexpressed/activated in various types of human malignancy including breast cancer. In this study, we demonstrated that Aurora-A induces estrogen receptor α (ERα) transactivation activity in the presence and absence of estrogen. Aurora-A also interacts with and phosphorylates ERα at serine-167 and -305 in vitro and in vivo. As a result, Aurora-A induces ERα transcriptional activity, enhances ERα binding to DNA and transcriptionally up-regulates its targeting genes such as CCDN1 in a phospho-ERα-Ser-167/305 dependent manners. Further, overexpression of Aurora-A decreases whereas depletion of Aurora-A enhances tamoxifen sensitivity in ERα-positive breast cancer cells. Significantly, Aurora-A inhibitor synergized with tamoxifen and overcame tamoxifen-resistance in vitro and in animal model. These data suggest that ERα is a bona fide substrate of Aurora-A and that Aurora-A plays a pivotal role in tamoxifen resistance. Thus, Aurora-A represents a critical therapeutic target in breast cancer endocrine-therapy.

Citation Format: Xiangqian Zheng, Jianping Guo, Hua Yang, Lili He, Masayuki Kanai, Domenico Coppola, Ming Gao, Xiubao Ren, Jin Q. Cheng. Aurora-A is a determinant of tamoxifen resistance by phosphorylation and activation of ERα in breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 515. doi:10.1158/1538-7445.AM2013-515
Abstract 5153: PAK2-mediated c-Jun phosphorylation at 5 threonine sites promotes cell transformation.
Authors: Li Tingting , Zhang Jishuai , Zhu Feng , Wen Weihong , Zykova Tatyana , Li Xiang , Liu Kangdong , Peng Cong , Ma Wei-Ya , Dong Zigang , Bode Ann M.
Published: August 2014

PAK2 plays an important role in cell proliferation, but the direct downstream proteins and precise regulatory mechanism involved in mediating PAK2’s role in proliferation are not yet clear. Here, we found that epidermal growth factor (EGF) induces phosphorylation of c-Jun by P21-activated kinase (PAK2). Knockdown of PAK2 in JB6 Cl41 (P+) cells had no effect on c-Jun phosphorylation at Ser63 or Ser73 but resulted in decreases in EGF-induced anchorage-independent cell transformation, proliferation and AP-1 activity. The oncoprotein c-Jun is one of the components of the activator protein-1 (AP-1) transcription factor complex. AP-1 activates a variety of tumor-related genes and promotes tumorigenesis and malignant transformation. Knockdown of PAK2 in SK-MEL-5 melanoma cells also decreased colony formation, proliferation and AP-1 activity. We found that PAK2 binds and phosphorylates c-Jun at five threonine sides (Thr2, Thr8, Thr89, Thr93 and Thr286) in vitro and in vivo. Mutation at all five sites decreased the transforming ability of JB6 cells. These results indicated that PAK2/c-Jun signaling plays an important role in tumorigenesis and provides an increased understanding of the signaling transduction mechanism of skin tumor cells and suggests that PAK2 might be a new chemopreventive or chemotherapeutic target.

Citation Format: Tingting Li, Jishuai Zhang, Feng Zhu, Weihong Wen, Tatyana Zykova, Xiang Li, Kangdong Liu, Cong Peng, Wei-Ya Ma, Zigang Dong, Ann M. Bode. PAK2-mediated c-Jun phosphorylation at 5 threonine sites promotes cell transformation. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5153. doi:10.1158/1538-7445.AM2013-5153
Abstract 5158: Generation of a fully human Gas6 neutralizing antibody with anti-tumor activity in vivo.
Authors: Moody Gordon E. , Belmontes Brian , King Chadwick , Liu Shuying , Masterman Stephanie , Murawsky Chris , Tsuruda Trace , Wang Wei , Radinsky Robert , Beltran Pedro J.
Published: August 2014

Growth arrest specific 6 (Gas6) is a vitamin-K dependent protein that is involved in the regulation of a wide array of cellular activities, including adhesion, migration, immune evasion, and apoptosis. Gas6 as well as its receptors Axl, Mer, and Tyro3 are highly expressed in multiple malignancies suggesting that signaling through this axis may be tumor promoting in human disease. A strategy was devised to generate fully human neutralizing antibodies against Gas6 using XenoMouse technology. Hybridoma supernatants were first screened for their ability to bind Gas6, then for their ability to inhibit Gas6 binding to the Axl receptor and block Gas6-induced Axl phosphorylation in human cells. Two purified antibodies isolated from the screened hybridomas, 1D9.1 and 1G9.1, maintained potency in all 3 assays and also inhibited Gas6-induced cellular migration and proliferation. In the scratch wound migration assay, the antibodies inhibited both basal and Gas6-induced wound closure to a greater extent than the soluble extracellular domain of the receptor Axl (Axl- Fc). In the proliferation assay, the antibody 1D9.1 completely inhibited Gas6-induced proliferation with a half maximal effective concentration (EC50) of 0.15nM. In vivo characterization of one of the antibodies, 1D9.1, was conducted using a pharmacodynamic (PD) assay that measured the ability of the antibody to inhibit Gas6-induced Akt activation in the mouse spleen. Treatment of mice with a single dose (100-1000 μg) of 1D9.1 led to greater than 90% inhibition of Gas6-induced phosphorylated Akt (pAkt) for up to 72 hours. Based on the target coverage observed in the PD assay, we tested the efficacy of 1D9.1 against Panc-1 human pancreatic adenocarcinoma xenografts implanted in athymic nu/nu female mice. At doses of 50 and 150 μg, twice weekly, the Gas6 neutralizing antibody 1D9.1 was able to inhibit 55% and 76% of tumor growth, respectively. (p<0.001 for both treatments vs. control Ig). When combined with gemcitabine, 1D9.1 was able to inhibit tumor growth to a greater extent than either agent alone (p<0.001 vs. either monotherapy). Together, the data suggest that Gas6 neutralization should be further explored as a potential strategy for the treatment of pancreatic cancer.

Citation Format: Gordon E. Moody, Brian Belmontes, Chadwick King, Shuying Liu, Stephanie Masterman, Chris Murawsky, Trace Tsuruda, Wei Wang, Robert Radinsky, Pedro J. Beltran. Generation of a fully human Gas6 neutralizing antibody with anti-tumor activity in vivo. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5158. doi:10.1158/1538-7445.AM2013-5158
Abstract 516: VDR overexpression restores tamoxifen responsiveness.
Authors: Louie Maggie C. , Laim Johnny
Published: August 2014

Breast cancer is classified as either Estrogen Receptor (ER) positive or ER negative, depending on the presence or absence of the ERα. Approximately, 70% of breast cancers express ERα, with tamoxifen being the most commonly used treatment. However, prolonged treatment often results in the development of acquired resistance, which has presented a major challenge in development of more effective therapeutics for breast cancer. While many studies have focused on understanding the mechanisms behind the development of tamoxifen resistance, few have been successfully implemented into clinical practice. To mimic acquired resistance, we have established a tamoxifen-resistant cell line by treating MCF-7 cells with tamoxifen over prolong period of time in order to select for the resistant phenotype. Our lab has preliminary data that suggest that the Vitamin D receptor (VDR) is downregulated in tamoxifen-resistant breast cancer cells (MCF-7TamR) when compared to the parental MCF-7 cells. The role of VDR in tamoxifen resistance is unclear; however our preliminary data suggest that tamoxifen resistant cells transfected with a VDR overexpression plasmid displayed decrease cell proliferation when treated with tamoxifen in comparison to cells transfected with an empty vector, suggesting that restoring VDR expression may restore tamoxifen responsiveness. Data from this study will give us a better understanding about the role of VDR in the development of acquired resistance.

Citation Format: Maggie C. Louie, Johnny Laim. VDR overexpression restores tamoxifen responsiveness. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 516. doi:10.1158/1538-7445.AM2013-516
Abstract 517: Ectopic expression of an obscurin signaling cassette decreases migration and invasion of metastatic breast cancer cells.
Authors: Perry Nicole A. , Kontrogianni-Konstantopoulos Aikaterini
Published: August 2014

The obscurins (∼70-820 kDa) are a family of proteins expressed from the 150 kb OBSCN gene, located on human chromosome 1. Sequencing analysis of breast and colorectal cancers, as well as melanoma and glioblastoma, revealed that obscurins are mutated at a substantial frequency and these mutations may be driving tumor formation. Our work has recently demonstrated that obscurins are present in normal breast, skin, and colon cells, but absent in their cancerous counterparts. Downregulation of obscurins’ expression is sufficient to allow non-tumorigenic breast epithelial cells to evade apoptosis induced by etoposide. Furthermore, absence of obscurins allows increased migration and invasion of breast epithelial cells. Remarkably though, we observed that ectopic expression of a fragment of obscurin composed of tandem src homology 3-Rho guanine exchange factor-pleckstrin homology (SH3-RhoGEF-PH) motifs was sufficient to decrease monolayer migration and invasion of metastatic breast cancer MDA-MB-231 cells, which are naturally deficient in obscurins, by >20% and >70%, respectively. Based on our observations that 1) absence of obscurins allows increased migration and invasion of breast cells, and 2) expression of an obscurin cassette mitigates this migratory and invasive behavior of metastatic breast cancer cells, we postulate that obscurins may act as metastasis suppressors in breast epithelium. We have therefore begun to investigate how the tripartite obscurin fragment, SH3-RhoGEF-PH, can influence the behavior of the cytoskeleton and therefore affect migration and invasion. We have found that the RhoGEF domain directly induces guanine nucleotide exchange in RhoA, but not Rac1 or Cdc42. This activity may be allosterically regulated by the adjacent SH3 domain, which interacts with the RhoGEF domain in a yeast two-hybrid assay. Furthermore, the PH domain binds to 3’-phosphorylated inositol lipid headgroups, providing a mechanism for the obscurins to respond to signals generated at the plasma membrane. Together, this evidence suggests that the tripartite signaling cassette can recapitulate the full-length obscurins’ metastasis-suppressing activity, and may merit development as a therapy for advanced breast cancer.

Citation Format: Nicole A. Perry, Aikaterini Kontrogianni-Konstantopoulos. Ectopic expression of an obscurin signaling cassette decreases migration and invasion of metastatic breast cancer cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 517. doi:10.1158/1538-7445.AM2013-517
Abstract 5173: The circadian factor period 2 modulates p53 stability and function in downstream signaling.
Authors: Finkielstein Carla V. , Gotoh Tetsuya , Vila-Caballer Marian , santos carlo , liu jingjing , yang jianhua
Published: August 2014

The human Period 2 (hPer2) factor is a transcriptional regulator placed at the core of the circadian clock mechanism responsible for generating the negative feedback loop that sustains the clock. Its relevance to human diseases is underlined by alterations in its function that impacts many biochemical and physiological processes and, when absent, results in the development of various cancers. The tumor suppressor role of Per2 is speculated to involve transcriptional activation of p53, altered expression of cell cycle components, and regulation of the DNA-damage response pathway. However, it is entirely unclear how Per2 operates mechanistically. First, we identified hPer2 binds the C-terminus half of human p53 (hp53) and forms a stable trimeric complex with hp53’s negative regulator, the oncogenic protein Mdm2. Second, we determined that hPer2 binding to hp53 prevents Mdm2 from ubiquitinating and targeting hp53 by the proteasome. Accordingly, downregulation of hPer2 expression directly impacts hp53 levels whereas its overexpression influences both hp53 protein stability and transcription. Furthermore, we spatially define the distribution of the trimeric complex and determine the site for processing to be located in the nucleus. Third, we establish that hp53-mediated gene transcription is influenced by the presence of hPer2. Target genes such as 14-3-3σ, hp21WAF1/CIP1, and gadd45α show a synergistic increase in expression when hPer2 and hp53 are co-expressed in a hp53-deficient background. This result is the direct consequence of hPer2 dissociation of hp53 as result of checkpoint activation as shown by studies performed using a constitutively bound form of the hPer2/hp53 complex. Overall, our findings directly place hPer2 at the heart of the hp53-mediated response by modulating its stability and controlling its function.

Citation Format: Carla V. Finkielstein, Tetsuya Gotoh, Marian Vila-Caballer, carlo santos, jingjing liu, jianhua yang. The circadian factor period 2 modulates p53 stability and function in downstream signaling. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5173. doi:10.1158/1538-7445.AM2013-5173

Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.
Abstract 5178: Smad7 is integrated mediator for the proteolysis of Myc.
Authors: Kang Jin-Muk , Hyun Ja-Shil , Lee Bona , Kim Ja-Kyung , Lee Ji-Hee , Kim Seong-Jin , Kim Tae-Aug
Published: August 2014

Myc, a pleiotropic transcription factor, plays a prominent role in human cancer progression. The regulation of Myc stability, therefore, is critical to understand the molecular mechanism of tumorigenesis in various cancers. Myc stability is tightly regulated by the activity of ubiqutin ligases, Skp2 and Fbw7. However, a key mediator of this process has not been addressed yet. Here, we have identified Smad7 as an intermediary regulating Myc stability by recruiting F-box protein, Skp2. Microarray analysis using the cell lines stably expressed Smad7, indicates that Smad7 markedly inhibits transcription of, c-myc-target genes including Id1, Id2, and Id3 without affecting c-myc gene expression. The expression of Myc protein, however, is down-regulated by induction of Smad7 in vitro, and in vivo, Smad7 transgene inducible system in primary epidermal keratinocyte. Conversely, the loss of Smad7 is implicated in the increase of endogenous Myc and Id2 expression, indicating that Smad7 is involved in post-translational regulation of Myc. Indeed, Smad7 ubiquitylates Myc through Smad7 PY motif, showing that mutation or deletion on PY motif diminishes the ubiquitylation of Myc. Treatment of proteasome inhibitor abates Smad7-mediated Myc degradation in HaCaT cell line that conditionally express level of human c-myc. Mapping of Smad7 interactions with Myc and Skp2 indicates that c-terminus, MH2 domain, of Smad7 binds to 3LRR/7LRR domain (aa142-390) of Skp2, and also interacts with Fbw7. Furthermore, intermediate domain (aa 162-236) of Myc has been identified to interact with c-terminus of Smad7. In the presence of Skp2 and Fbw7, Smad7 facilitated the degradation of Myc, thus impairing Myc stability. Smad7 also markedly represses Myc-mediated transcriptional activity and its target gene expression. These findings provide a new insight of Smad7 functions as a key mediator for the proteolysis of Myc proto-oncoprotein.

Citation Format: Jin-Muk Kang, Ja-Shil Hyun, Bona Lee, Ja-Kyung Kim, Ji-Hee Lee, Seong-Jin Kim, Tae-Aug Kim. Smad7 is integrated mediator for the proteolysis of Myc. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5178. doi:10.1158/1538-7445.AM2013-5178
Abstract 5186: PPME1 is a potential novel molecular target in gastric and lung cancer.
Authors: Li Jing , Han Sufang , Qian Ziliang , Su Xinying , Fan Shuqiong , Fu Jiangang , Liu Charles , Yin Lucy , Gao Zeren , Zhu Guanshan , Zhang Jingchuan , Yu De-Hua , Ji Qunsheng
Published: August 2014

Protein phosphatase 2A (PP2A) is a human tumor suppressor, and it accounts for the majority of serine/threonine phosphatase activity which is tightly regulated via the methylation of carboxy-terminal of PP2A. Methylation at the carboxyterminal Leu 309 residue by S-adenosylmethionine-dependent leucine carboxyl methytransferase-1 (LCMT1) leads to the activation of PP2A, whilst demethylation of Leu 309 by specific protein phosphatase methylesterase-1 (PPME1) suppresses the PP2A activity. Recent evidence showed that PPME1 is up-regulated in glioblastoma patients and associated with a poor prognosis. In this study we profiled 131 Chinese gastric cancer (GC) samples and 124 Chinese non-small cell lung carcinoma (NSCLC) samples by Affy and aCGH to identify potential drug targets, and found PPME1 gene amplification in 3.8% of the GC samples and 3.1% of the NSCLC samples. The PPME1amplification correlated with its mRNA expression. In addition, we confirmed that PPME1 protein expressions were also elevated in the PPME1-amplified tumor samples indicated by immunohistochemistry as compared with corresponding adjacent non-tumor samples. To further investigate the role of PPME1 amplification in tumor growth, we utilized siRNA-mediated gene silencing approaches to specifically knock down PPME1 expression in the PPME1 amplified human cancer cell lines SNU668 (GC) and Oka-C1 (NSCLC). We found that suppression of the PPME1 expression resulted in significant inhibition of cell proliferation and induction of cell death in those cells. In contrast, little effects were observed on the cell growth and survival of non PPME1-amplified human cancer cells, MKN1 (GC) and HCC95 (NSCLC). Moreover, we showed that the PPME-1 knock-down also resulted in a decrease of PP2A demethylation at Leu309, which correlated with down-regulation of phosphorylation of MAPK and AKT in the cells. Taken together, our data indicate that PPME-1 could be an attractive therapeutic target for subsets of gastric and lung cancers.

Citation Format: Jing Li, Sufang Han, Ziliang Qian, Xinying Su, Shuqiong Fan, Jiangang Fu, Charles Liu, Lucy Yin, Zeren Gao, Guanshan Zhu, Jingchuan Zhang, De-Hua Yu, Qunsheng Ji. PPME1 is a potential novel molecular target in gastric and lung cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5186. doi:10.1158/1538-7445.AM2013-5186
Abstract 5197: RIN1 suppresses apoptosis in melanoma cells and is a potential therapeutic target.
Authors: Ting Pamela Y. , Colicelli John
Published: August 2014

The RAS effector RIN1 is frequently overexpressed in melanoma tumor samples. This aberrant overexpression is associated with tumor thickness, lymph node metastasis and poor prognosis. RIN1 is a multifunctional protein that has been shown to regulate growth factor receptor signaling and endocytosis, as well as the activity of the non-receptor tyrosine kinase ABL, which functions in actin remodeling and the DNA damage response.

Here, we identify RIN1 as a suppressor of apoptosis in melanoma. shRNA-mediated knockdown of RIN1 in the melanoma cell line A375 suppressed proliferation and induced apoptosis. We found RIN1 to be commonly overexpressed in melanomas, with elevated levels of the protein detected in 10 of 13 melanoma cell lines tested in comparison with human neonatal melanocytes. Additionally, depletion of RIN1 in several primary cell types does not affect cell viability. This supports the hypothesis that some melanoma cells are addicted to RIN1 and suggests its potential as a therapeutic target.

To examine the role of RIN1 in melanoma cell survival, point mutations were made to disrupt several known functions. These include receptor tyrosine kinase binding, ABL binding, Rab5 GEF activity and RAS association. The mutants have been stably transduced into melanoma cells under the control of a tetracycline-responsive promoter and they will be used to elucidate the contribution of different RIN1-dependent pathways to oncogenic activity. Overall, our goal is to determine the molecular mechanisms governing oncogenic addiction to RIN1 as well as points of vulnerability that could be therapeutically targeted.

Citation Format: Pamela Y. Ting, John Colicelli. RIN1 suppresses apoptosis in melanoma cells and is a potential therapeutic target. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5197. doi:10.1158/1538-7445.AM2013-5197
Abstract 5200: Genome-wide integrative analysis for the determination of the consequence of AT-rich interacting domain 2 (ARID2) depletion in hepatocellular carcinoma.
Authors: Furuta Mayuko , Nguyen Ha H. , Fujimoto Akihiro , Shiraishi Yuichi , Miyano Satoru , Tsunoda Tatsuhiko , Nakagawa Hidewaki
Published: August 2014

Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. We previously reported the genomic aberrations obtained by the whole genome sequencing of 27 HCCs derived from Japanese patients (Nature Genetics 44, 760, 2012). The statistical and functional analyses yielded frequently and recurrently mutated genes involved in chromatin regulation, including ARID1A, ARID1B, ARID2, MLL and MLL3. Among the chromatin regulators mutated in HCCs, we here focused on ARID2, a component of Polybromo-associated BRG1-associated factor (PBAF) complex, which is one of the SNI/SNF chromatin remodeling complex involved in ligand-dependent transcriptional activation by nuclear receptors. Most of the somatic mutations in ARID2 detected in HCCs by our sequencing studies indicated its loss-of-function, suggesting their role as a tumor-suppressor. Although its somatic mutation in HCC and other types of cancer have been recently reported, its detailed function and role in tumorigenesis is poorly understood. To determine its role in hepatocarcionogenesis, we first analyzed their activity on cell growth using HCC cell lines. Knockdown (KD) of ARID2 in ARID2-intact HCC cell lines, JHH4 and JHH5, promoted cell growth, while overexpression of ARID2 in ARID2-null HuH28 suppressed cell growth compared with controls. These findings are consistent with its role as a tumor-suppressor in HCC. We also performed RNA-Seq using the ARID2-KD RNA samples from ARID2-intact cell lines to predict its down-stream target genes, which might be affected by ARID2 depletion in HCCs. Pathway analysis of genes up- or down-regulated by ARID2-KD revealed that a large number of cancer-related genes showed their expression changes. In addition, some cytokines and kinases involved in carcinogenesis significantly appeared to be activated on the basis of down-stream target gene expression profile. These results indicate that somatic loss-of-function mutations in a component of chromatin regulator such as ARID2 could lead the genome-wide gene expression change appeared in HCCs.

Citation Format: Mayuko Furuta, Ha H. Nguyen, Akihiro Fujimoto, Yuichi Shiraishi, Satoru Miyano, Tatsuhiko Tsunoda, Hidewaki Nakagawa. Genome-wide integrative analysis for the determination of the consequence of AT-rich interacting domain 2 (ARID2) depletion in hepatocellular carcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5200. doi:10.1158/1538-7445.AM2013-5200
Abstract 5205: Galectin-3 and AP-1 mediate transcriptional effect of Arylsulfatase B (N-acetylgalactosamine-4-sulfatase) on versican in prostatic cells.
Authors: Bhattacharyya Sumit , Feferman Leonid , Tobacman Joanne Kramer
Published: August 2014

N-acetylgalactosamine-4-sulfatase (Arylsulfatase B; ARSB) modifies the glycosaminoglycans (GAGs) chondroitin-4-sulfate (C4S) and dermatan sulfate by removing 4-sulfate groups from the non-reducing end and thereby regulating GAG degradation. Previous studies demonstrated that ARSB was reduced in malignant human colonic, mammary, and prostatic tissue and suggested that ARSB acts as a tumor suppressor. In this report, ARSB was silenced by siRNA in the WPMY-1 human prostate stromal myofibroblast cell line (ATCC), and effects on C4S, total sulfated glycosaminoglycans (GAGs), ErbB2, total EGFR, phospho-ERK, versican, and AP-1 were determined. Total sulfated GAGs were measured by Blyscan assay (Biocolor), and C4S was determined by Blyscan assay following immunoprecipitation by C4S antibody. Phospho(T202/Y204 for ERK1 or T185/Y187 for ERK2)-ERK, ErbB2, and total EGFR were measured by ELISA. Versican, an extracellular matrix chondroitin sulfate proteoglycan with EGF-like repeats at its C-terminus, was measured by ELISA and QPCR. ARSB and galectin-3 were silenced by siRNA (Qiagen). ARSB activity declined from 140.4 ± 8.4 to 21.4 ± 0.9 nmol/mg protein/hr following silencing. Total sulfated GAGs increased from 17.9 ± 0.7 μg/mg protein in control cells to 28.6 ± 1.4 μg/mg protein following ARSB silencing, and C4S increased from 7.4 ± 0.6 μg/mg protein to 15.5 ± 0.8 μg/mg protein following ARSB silencing. Total EGFR increased to 2.65 times baseline, and ErbB2 increased to over six-fold times baseline. Phospho-ERK increased to more than three times baseline, from 5.0 ± 0.5 ng/mg protein to 15.2 ± 0.8 ng/mg protein following silencing. Versican protein increased from 122.1 ± 5.3 ng/mg protein in control to 295.2 ± 11.2 ng/mg protein and mRNA increased more than two-fold. ARSB-silencing induced increases in versican mRNA and in activation of c-Jun and c-Fos, and these increases were inhibited when galectin-3 was also silenced. [All findings are highly significant (p<0.001, one-way ANOVA with Tukey-Kramer post-test)]. Previously, we have shown reduced binding of galectin-3 to C4S following ARSB silencing. Since there is an AP-1 binding site in the versican promoter, study data demonstrate that transcriptional effects of ARSB silencing on versican are mediated by galectin-3 and AP-1. The profound effects of ARSB silencing on versican and phospho-ERK in the prostatic myofibroblasts provide further evidence that ARSB acts as a tumor suppressor.

Citation Format: Sumit Bhattacharyya, Leonid Feferman, Joanne Kramer Tobacman. Galectin-3 and AP-1 mediate transcriptional effect of Arylsulfatase B (N-acetylgalactosamine-4-sulfatase) on versican in prostatic cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5205. doi:10.1158/1538-7445.AM2013-5205
Abstract 5206: Role of CtBP1 as a transcriptional corepressor in prostate cancer.
Authors: Chakravarthi Balabhadrapatruni V. S. K. , Pathi Satya , Zheng Heng , Siddiqui Javed , Kunju Lakshmi P. , Palanisamy Nallasivam , Varambally Sooryanarayana
Published: August 2014

Background: C-terminal Binding Protein 1 (CtBP1), a transcriptional co-repressor that regulates the expression of tumor suppressors and genes involved in cell death, is known to play a critical role in multiple cancers. Earlier, we showed that CtBP1 is overexpressed in metastatic prostate cancer. Furthermore, our studies indicated a role for CtBP1 in conferring radiation resistance to prostate cancer cell lines. We also demonstrated the functional role of CtBP1 in regulating prostate cancer cell growth in vitro and tumor growth and metastasis in vivo.

Methods and Results: Our gene expression profiling and bioinformatics analysis found that multiple potential tumor suppressors are reactivated upon CtBP1 knockdown in multiple prostate cancer cell lines. We next validated these targets of CtBP1-mediated repression by qRTPCR and western blotting using CtBP1 stable knockdown prostate cancer cell lines, and in normal prostate epithelial PrEC cells overexpressing CtBP1. Our studies confirmed that CtBP1 targets multiple genes including SP8 transcription factor and kallikrein-related peptidase 10 (KLK10) among others. Knockdown of the reactivated gene led to a reversion of these cells to a more aggressive phenotype. Furthermore, our studies confirmed that the CtBP1 target genes are down-regulated in metastatic prostate cancer.

Conclusion: Taken together, our studies demonstrated that dysregulated expression of CtBP1 plays an important role in prostate cancer progression by down-regulating the expression of multiple potential tumor suppressor genes. Thus, targeting CtBP1 in aggressive prostate cancer may have clinical significance.

Citation Format: Balabhadrapatruni V. S. K. Chakravarthi, Satya Pathi, Heng Zheng, Javed Siddiqui, Lakshmi P. Kunju, Nallasivam Palanisamy, Sooryanarayana Varambally. Role of CtBP1 as a transcriptional corepressor in prostate cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5206. doi:10.1158/1538-7445.AM2013-5206
Abstract 5210: KPT-330, a selective small molecule inhibitor of nuclear export, is active in bone and soft tissue sarcoma.
Authors: Nair Jayasree S. , Tap William , Vasudeva Shyamprasad Deraje , Sicklick Jason K. , Kauffman Michael , Shacham Sharon , Schwartz Gary K.
Published: August 2014

KPT-330 is a small molecule Selective Inhibitor of Nuclear Export (SINE) that irreversibly block the major nuclear export protein CRM1 (exportin 1, XPO1). The Chromosome Region Maintenance 1 (CRM1) protein is responsible for the nuclear export of snRNAs and of proteins bearing a leucine-rich nuclear export signal (NES). This class of drugs is expected to induce forced nuclear accumulation of tumor suppressor proteins (TSPs) and is believed to initiate a ‘genome survey’ leading to the death of cancer cells with normal cells undergoing transient, reversible cell cycle arrest. Our effort was to investigate the effects of KPT-330 in sarcomas and the mechanism by which it exerts the effect of tumor suppression. Our data clearly shows KPT-330 as active against a broad panel of human bone and soft tissue sarcoma cell lines at low nanomolar concentrations. The effect was mainly due to the induction of apoptosis. Target specificity of the drug was confirmed by the decrease in CRM1 protein level. An induction of p53 and p21 protein levels was observed. However, the effect of apoptosis or inhibition in proliferation seems to be independent of p53 status of the cell line. The effect of KPT-330 was further tested in xenograft models using malignant peripheral nerve sheath (MPNST) and de-differentiated liposarcoma (LS141) cell lines. Tumor suppression was observed in both the sarcoma models and its target specificity was confirmed in the xenografts. KPT-330 may represent a new drug for the treatment of bone and soft tissue sarcoma.

Citation Format: Jayasree S. Nair, William Tap, Shyamprasad Deraje Vasudeva, Jason K. Sicklick, Michael Kauffman, Sharon Shacham, Gary K. Schwartz. KPT-330, a selective small molecule inhibitor of nuclear export, is active in bone and soft tissue sarcoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5210. doi:10.1158/1538-7445.AM2013-5210
Abstract 5217: Integrative sequencing reveals novel alterations in untreated and castration resistant prostate cancer.
Authors: Annala Matti J. , Waltering Kati K. , Ylipää Antti , Kartasalo Kimmo , Tuppurainen Kirsi , Karakurt Serdar , Latonen Leena , Saramäki Outi , Leppänen Simo-Pekka , Seppälä Janne , Rauhala Hanna E. , Tammela Teuvo LJ , Yli-Harja Olli , Zhang Wei , Visakorpi Tapio , Nykter Matti
Published: August 2014

Prostate cancer is the third most common source of male cancer deaths in developed countries. The standard of care for aggressive prostate cancer is androgen ablation, which prolongs survival until the tumor acquires a castration resistant phenotype. The molecular pathology underlying prostate cancer progression is not yet fully understood. We used integrative high throughput sequencing to study cancer-associated alterations in 53 prostate cancer related neoplasia at the DNA, RNA and epigenetic levels. The cohort included both hormone-naive and castration resistant prostate cancers, along with two neuroendocrine prostate cancers. We identified two new fusion genes, one of which associated with neuronal differentiation and castration resistance. We also identified a number of novel prostate cancer associated transcripts, including transcripts specific to castration resistant tumors. Based on ChIP-seq data from prostate cancer cell lines, many of the novel transcripts were regulated by known oncogenes such as ERG and AR. Methylation sequencing revealed a near-identical pattern of promoter hypermethylation in both hormone-naive and castration resistant tumors. Enrichment of hypermethylation was observed at EZH2 binding sites, supporting the role of EZH2 in the recruitment of DNA methyltransferase in prostate cancer. Promoter hypermethylation suppressed the expression of hundreds of genes, but a subset of genes characterized by promoter H3K27 trimethylation responded to hypermethylation with increased expression.

Citation Format: Matti J. Annala, Kati K. Waltering, Antti Ylipää, Kimmo Kartasalo, Kirsi Tuppurainen, Serdar Karakurt, Leena Latonen, Outi Saramäki, Simo-Pekka Leppänen, Janne Seppälä, Hanna E. Rauhala, Teuvo LJ Tammela, Olli Yli-Harja, Wei Zhang, Tapio Visakorpi, Matti Nykter. Integrative sequencing reveals novel alterations in untreated and castration resistant prostate cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5217. doi:10.1158/1538-7445.AM2013-5217