bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4925: The natural enzyme sequestration in signaling cascades provides inherent opportunities for off-target effects induced by kinase inhibitors
Authors: Wynn Michelle L. , Ventura Alejandra C. , Sepulchre Jacques-A. , Garcia Hector J. , Merajver Sofia D.
Published: August 2012

Off-target effects from targeted therapies are often attributed to cross-talk, which usually refers to inter-pathway molecular interactions that occur because of explicit regulatory feedback connections between two pathways. Recent experimental and theoretical studies have demonstrated, however, that covalently modified cascades naturally exhibit bidirectional signal propagation via a phenomenon termed retroactivity. This phenomenon arises due to enzyme sequestration where each cycle is coupled, not only to the next cycle, but also to the previous cycle. While retroactivity occurs naturally in covalently modified cascades, signaling pathways likely evolved to propagate information in a downstream manner. An important consequence of retroactivity, however, is that a downstream perturbation can induce an upstream response without the presence of regulatory feedback connections. We hypothesize that kinase inhibitors can produce off-target effects as a consequence of retroactivity alone via the following mechanism: a signal travels upstream from the site of a downstream perturbation through retroactivity and, upon reaching a shared upstream component, is delivered to an independent parallel pathway. To test the hypothesis we used a computational model to simulate the targeted inhibition of a specific kinase in a series signaling networks using physiologically and therapeutically relevant ranges for all parameters. Surprisingly, our results suggest that an off-target effect due to retroactive signaling is more likely when the first cycle in a non-inhibited cascade is “off” and not consuming large amounts of a shared up-stream activator. Our results also suggest that the kinetics governing covalently modified cycles in a cascade are more important for propagating an upstream off-target effect than the binding affinity of the drug to the targeted protein, which is a commonly optimized property in drug development. Finally, our results suggest that a single mutation has the capacity to produce a large spontaneous off-target effect without any direct regulatory connections between the targeted protein and the effected protein. Together, our results suggest that retroactivity may play an important role in the dysregulated signaling networks of cancer cells as well as the cellular response to targeted therapies. These findings have important implications for somatic evolution in cancer and the onset of therapeutic resistance, which has been widely reported for many targeted cancer therapeutics, including kinase inhibitors.

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 4925. doi:1538-7445.AM2012-4925
Abstract 4935: A quantitative model to study cell-type-specific transcriptional regulation between MCF-7 and LNCaP
Authors: Liu Yuwen , Zhou Jie , White Kevin P.
Published: August 2012

Transcriptional regulation lies at the heart of biological processes. To further understand the regulatory mechanism, we are studying the transcriptional networks of nuclear receptors in breast cancer cell line MCF-7 and prostate cancer cell line LNCaP. Based on whole-genome gene expression microarray data, we observed very different transcriptional programs induced by ligands of nuclear receptors between these two cell lines. In order to systematically explain cell-type-specific transcriptional regulation, we are trying to build a quantitative model to predict gene expression in different cellular contexts under different ligand stimulations. The model will be trained using data including genomic binding sites of nuclear receptors (ChIP-Seq), and time-series expression of nuclear receptors, cofactors and their target genes (Nanostring). The output of the model will be gene expression trajectories after ligand treatments in the two cell lines.

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 4935. doi:1538-7445.AM2012-4935
Abstract 4942: Can three-dimensional cell cultures be used to predict in vivo drug response and synergistic combinations
Authors: Brightman Frances A. , Fernandez Eric , Orrell David , Fell David , Chassagnole Christophe
Published: August 2012

The discovery of synergistic combinations of standard-of-care drugs or new chemical or biological entities shows much promise in the treatment of cancer, and there is much interest in this strategy. However, the increasing number of possible combinations makes the task of selecting the best regimens particularly difficult. As a response to this problem, we developed a computerized PK-PD model of a growing tumor, called the Virtual Tumor™. We demonstrated that this platform can successfully simulate the outcome of various drug combination schedules in xenografts, as well as predict optimal drug schedules and combinations. Although xenografts represent a convenient and relatively inexpensive approach to assessing the likely efficacy of proposed dosing regimens in vivo, the number of permutations that can be tested is still limited by practical considerations. We have therefore explored the use of three-dimensional tumor cell cultures (microtissues) as a more cost-effective alternative to xenografts for validating Virtual Tumor™ predictions. Using the Virtual Tumor™, we previously predicted that the efficacy of a gemcitabine-docetaxel combination could vary greatly depending on the scheduling of the drug administration, and verified these findings in vivo in MX-1 xenograft mouse model. We have now conducted a comparable study using MX-1 microtissues, in which the cultures were treated with these same two drugs in isolation or in combination, according to various regimens. Here we show how the microtissue Virtual Tumor™ model can be employed to simulate microtissue growth and response to drug treatment, and the capability of this model to predict drug synergy in vivo in xenografts. Furthermore, we discuss whether microtissues can be used as a surrogate for xenografts, in conjunction with the Virtual Tumor™, for designing new drug regimens, testing possible schedules for combinations of different drugs and prioritizing the most effective drug combinations.

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 4942. doi:1538-7445.AM2012-4942
Abstract 4943: Genetically engineered osteoprotegerin for multiple myeloma osteolytic bone damage
Authors: Higgs Jerome T. , Jarboe John , Ponnazhagan Selverangan
Published: August 2012

Current treatments for osteolytic cancers include a combination of radiation, chemotherapy and cytotoxic products, but toxic side effects are still of major concern. Studies have shown that osteoclast activity is increased in patients with osteolytic cancers such as Multiple Myeloma (MM), through increased expression of Receptor Activator of Nuclear Factor Kappa B Ligand (RANKL) leading to RANKL/RANK signaling, resulting in osteoclast activation and ultimately bone resorption. Moreover, Osteoprotegerin (OPG) is drastically decreased in these patients who presents with bone lesion. Thus, the use of OPG as a therapeutic molecule would greatly decrease osteolytic damage and reduce morbidity. However, despite the of OPG potential in inhibiting the activation of bone resorbing osteoclast, OPG also binds to tumor related apoptosis-inducing ligand (TRAIL) making tumor cells resistant to apoptosis. TRAIL binds to the Death Receptor 4 and 5 (DR4, DR5) and initiate cell death of Transformed cells such as MM. The present study was designed to develop a novel therapeutic approach to the treatment of osteolytic bone damage by use of genetically altered OPG retaining RANKL binding but abolished of TRAIL binding. In order to eliminate TRAIL binding while maintaining RANKL binding, we created mutant OPG-Fc constructs by site directed mutagenesis based on interactive domain identification and by superimposing structural models of TRAIL, OPG and DR5. The mutant OPGs were produced in HEK 293 cells for characterization of potential mutants and their TRAIL binding ability. We conclude that using site-directed mutagenesis at the N-terminal of OPG effectively retains RANKL binding property but abolishes TRAIL binding property as determined by osteoclast and TRAIL assays respectively.

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 4943. doi:1538-7445.AM2012-4943
Abstract 4948: Uncovering microRNA and transcription factor-mediated regulatory network in glioblastoma
Authors: Zhao Zhongming , Sun Jingchun
Published: August 2012

Glioblastoma multiforme (GBM) is the most common and lethal brain tumor in humans. Recent studies revealed that patterns of microRNA (miRNA) expression in GBM tissue samples are different from that in normal brain tissues, suggesting that a number of miRNAs play critical roles in the pathogenesis of GBM. However, little is yet known about which miRNAs play central roles in the pathology of GBM and their regulatory mechanisms of action. In this study, we systematically explored the combinatory regulation of miRNAs and transcription factors (TFs) impacting GBM genes. We compiled GBM-related miRNAs, genes, and TFs and then identified 1,128 3-node feed-forward loops (FFLs) and 805 4-node FFLs with statistical significance. These FFLs were converged to construct a comprehensive GBM-specific miRNA-TF mediated regulatory network and, from which, an essential GBM-specific regulatory network. To further identify critical miRNA components in the GBM regulatory network, we specifically extracted a subnetwork for Notch signaling pathway. Our follow up network and functional association analyses revealed that six miRNAs (miR-124, miR-137, miR-219-5p, miR-34a, miR-9, and miR-92b) might play important roles in GBM, including some supported by previous studies. This study has generated the first comprehensive miRNA-TF regulatory network for GBM, providing a valuable resource for further understanding the complex regulatory mechanisms in GBM. Our findings of important miRNAs in the Notch signaling pathway, with partial verification by previous studies, demonstrates that our network-based approach is promising for identifying new and important miRNAs in GBM and, potentially, other cancers.

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 4948. doi:1538-7445.AM2012-4948
Abstract 4949: A dynamic TGFBR3-JUND expression circuit in single basal-like breast epithelial cells
Authors: Wang Chun-Chao , Jamal Leen , Bajikar Sameer S. , Atkins Kristen A. , Janes Kevin A.
Published: August 2012

Basal-like carcinoma is a subtype of breast cancer that is characterized by poor prognosis and high intratumor heterogeneity. In basal-like breast epithelia, we have identified two anticorrelated gene-expression programs that arise among single extracellular matrix (ECM)-attached cells during organotypic 3D culture. The first program contains multiple TGFβ-related genes including TGFBR3, and its heterogeneous induction is critical to suppress ductal branching. The second program contains JUND together with the basal-like marker, KRT5. Homogenizing JUND expression in single cells leads to 3D acini with bridged lumina that are similar to cribiform ductal carcinoma in situ. TGFBR3 and JUND together comprise a circuit that is interconnected via four negative-feedback loops. Computational modeling of the circuit predicts damped, antiphase oscillations upon stimulation with endogenous impulses of TGFβ-like ligand, and we directly observe these spontaneous responses in 3D culture by live-cell imaging. The TGFBR3-JUND circuit and its ECM-dependent regulation are remarkably conserved in early basal-like tumors that heterogeneously express KRT5, suggesting that asynchronous circuit dynamics are active in this patient subset. Preliminary studies suggested this intrinsic single-cell expression circuit might be regulated by a transcription factor, Nrf2, and a tumor suppressor, menin. Together, breast tumor heterogeneity need not stem from partial basal-like differentiation and could instead reflect dynamic toggling of individual cells between expression states.

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 4949. doi:1538-7445.AM2012-4949
Abstract 4953: Interaction of vitamin E compounds with docosahexaenoic acid on induction of apoptosis in human triple negative breast cancer cells
Authors: Xiong Ailian , Yu Weiping , Sanders Bob , Kline Kimberly
Published: August 2012

Successful treatment of triple negative (ER-, PR-, HER2-) breast cancers (TNBC) remains elusive because of the limitations of currently available chemotherapeutic agents for TNBC, drug resistance and drug toxicities. Docosahexaenoic acid (DHA), an n-3 polyunsaturated fatty acid, has been shown to exhibit anticancer actions both in vitro and in vivo in a variety of cancers, including human breast cancer. Here, we report that DHA induces apoptosis in TNBC cell lines, which is associated with cleavage of caspase-8 and -9. DHA induces endoplasmic reticulum (ER) stress evidenced by the increased levels of ER stress markers, GRP78, CHOP, and spliced XBP-1, and induced increased levels of death receptor DR5 protein expression. siRNAs to CHOP and DR5 blocked DHA-induced apoptosis and siRNA to CHOP blocked DHA-induced upregulation of DR5, indicating that DHA induces ER stress mediated death receptor dependent apoptosis in TNBC cells via CHOP. Furthermore, our data show that DHA mediated increases in levels of reactive oxygen species (ROS), apoptosis and ER stress can be blocked by antioxidants; N-Acetyl Cysteine (NAC) and alpha-tocopherol (αT) indicating that ROS plays a critical role in DHA-induced apoptosis and ER stress. In contrast to αT, gamma-tocotrienol (γT3), another form of vitamin E, cooperated with DHA to induce apoptosis and ER stress in TNBC cells. siRNAs to CHOP and DR5 blocked the combination effects mediated by DHA + γT3 on induction of apoptosis and ER stress. Taken together, our data, for the first time, demonstrate that DHA induces apoptosis in TNBC cells via activation of an ER stress mediated DR5 dependent pro-apoptotic pathway. Our data also show that different forms of vitamin E exhibit different combinational effects on DHA-induced apoptosis; namely, blockage by αT and enhancement by γT3. (Funding for these studies was provided by the Clayton Foundation for Research).

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 4953. doi:1538-7445.AM2012-4953
Abstract 4956: Regulation of anoikis by DBC1 (Deleted-In-Breast Cancer 1) through NF-kB
Authors: Park Sun , Riley Philip A. , Cieply Benjamin , Frisch Steven M.
Published: August 2012

Cancer cells that undergo epithelial-to-mesenchymal transition (EMT) evade anoikis, apoptosis induced by detachment from extracellular matrix. The mechanism of anoikis-resistance is an area of ongoing research. The gene Deleted in Breast Cancer 1, DBC1, is found in chromosomal region 8p21, which is deleted in some breast cancers, while several other cancers show DBC1 overexpression. DBC1 interacts with various proteins, such as SIRT1, ERα, RARα and SUV39H1 in a cancer context dependent manner. We found that depletion of DBC1 sensitized MCF10-A mammary epithelial cells to anoikis both in two-dimensional and three dimensional culture models. This effect was also observed in several breast cancer cell lines. Microarray analysis showed that DBC1 regulates the level of the c-FLIP in MCF10a cells, which was confirmed by RT-PCR. In addition, real time PCR studies showed that DBC1 induces other NF-kB transcription factor target genes such as Bcl2 and XIAP, some of which are known suppressors of anoikis. Luciferase assays demonstrated that DBC1 induces NF-kB transcriptional activity. NF-KB is a transcription factor that regulates genes involved in inflammatory response, cell survival and death. We found, through the use of the NF-kB inhibitors BAY 117082 and curcumin, that NF-kB suppressed anoikis. Conversely, SIRT1 –a deacetylase that inhibits NF-kB and that is itself inhibited by DBC1– promoted anoikis. The pathway in which DBC1 regulates anoikis through NF-κB will be further investigated in the future, with a view toward understanding the role of DBC1 in modulating the inflammatory signaling pathways that control anoikis.

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 4956. doi:1538-7445.AM2012-4956
Abstract 4959: Osteoprotegerin mediates resistance to TRAIL-induced apoptosis in pancreatic ductal adenocarcinoma
Authors: Kanzaki Hirotaka , Otaki Akashi , Greene Mark I. , Murali Ramachandran
Published: August 2012

[Purpose] Tumor Necrosis Factor (TNF)-Related Apoptosis-Inducing Ligand (TRAIL) has been shown to have great potential for the treatment of most human tumor cells without harming normal cells. However, some cancers show resistance to TRAIL induced apoptosis. The poor prognosis of both pancreatic ductal adenocarcinoma (PDAC) is likely due to the absence of valid approaches for early detection, the frequency of its metastases at the time of diagnosis, frequent recurrence after surgery, and poor responsiveness to chemotherapy. PDAC is also known as the most common resistant cells to TRAIL. Since osteoprotegerin (OPG) is known as a decoy receptor that binds to TRAIL and inhibits TRAIL-induced apoptosis, we hypothesized that OPG might play a role in mediating resistance to apoptosis in PDAC cells. [Methods and Results] To investigate the expression of OPG in PDAC cells, RT-PCR, Western blot and ELISA were performed. From the results, we found significant expression of OPG in both cell and cell culture medium. To investigate the apoptotic activity of TRAIL, we performed cell viability assay and apoptosis assay with or without siRNA against OPG. We found that PDAC cells showed significantly resistance to TRAIL induced apoptosis and knocking down of OPG sensitized TRAIL induced apoptosis in PDAC cells. [Conclusion] This study demonstrated that OPG played a role in resistance to TRAIL-induced apoptosis in PDAC cells. Expression of OPG might provide PDAC cells with an essential growth advantage through resistance to TRAIL-induced apoptosis. Inhibition of OPG expression and blocking OPG function might be a new therapeutic approach for the treatment of pancreatic cancer patients.

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 4959. doi:1538-7445.AM2012-4959
Abstract 4969: Impact of proteasome inhibition of caspase-8 regulation in cancer
Authors: Fiandalo Michael , Schwarze Steven , Kyprianou Natasha
Published: August 2012

Dissection of the extrinsic and intrinsic pathways of apoptosis has lead to the development of new anti-cancer therapeutic strategies. Strategies involve combination of a chemotherapeutic agent with a death inducing ligand, such as TNF-alpha Related Apoptosis Inducing Ligand (TRAIL) to induce apoptosis in cancer cells that are resistant to apoptosis. We recently demonstrated that proteasome inhibition sensitizes TRAIL resistant prostate cancer to TRAIL mediated apoptosis using both in-vitro and in-vivo models, by stabilizing the active p18 subunit of initiator caspase-8. Based on this data indicating a potential relationship between caspase-8 and the proteasome, we hypothesize that caspase-8 ubiquitination and targeting to the 26S proteasome regulates the extrinsic pathway of cancer cell apoptosis. This study pursues the impact of proteasome inhibition on caspase-8 stability, trafficking and activity following death receptor activation. The contribution of caspase-8 polyubiquitination in regulating the extrinsic pathway of apoptosis is determined, using subcellular fractionation, caspase-8 and polyubiquitin immunoprecipitation (IP), and fluorescent microscopy techniques in diverse experimental cell models. The cell lines analyzed include the TRAIL resistant LNCaP prostate cancer cell line and caspase-8 deficient neuroblastoma (NB7) cell line, engineered to re-express and test the wild-type and non-cleavable mutant forms of caspase-8. Our findings indicate that the non-cleavable forms of caspase-8 are capable of inducing apoptosis comparably to wild-type caspase-8 upon treatment with proteasome inhibitor and TRAIL. Moreover we provide evidence that caspase-8 polyubiquitination occurs following caspase-8 processing into its active subunits, processed caspase-8 accumulates at the DISC, and ultimately cycles into the cytosol for proteasomal degradation. This study identifies caspase-8 processing as a significant regulatory mechanism in apoptosis outcomes in cancer cells, but not required for caspase-8 activation. Together these data provide a better understanding of caspase-8 regulation that can be used as a platform for identifying new molecular targets such as E3 ligases responsible for caspase-8 regulation. Further defining caspase-8 regulation can lead to strategies that enhance efficacy of current therapies or lead to development of new more specific caspase-8 driven anti-cancer approaches. Funding provided by DOD GRANT USAMRMC PC073314

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 4969. doi:1538-7445.AM2012-4969
Abstract 4971: The oncometabolite (R)-2-hydroxyglutarate modulates stress-induced caspase activity in glioma cells
Authors: Gilbert Misty , Liu Yinxing , Morris Andrew , Sunkara Manjula , Kyprinaou Natasha , Horbinski Craig
Published: August 2012

Point mutations in isocitrate dehydrogenase 1 and 2 (IDH1/2) are present in the majority of WHO grade II and III gliomas, as well as secondary grade IV glioblastomas. These are gain-of-function mutations resulting in the neoenzymatic conversion of alpha-ketoglutarate into R-2-hydroxyglutarate (2HG), which is present in high concentrations (10-30 mM) in mutated gliomas. The mutation appears to be a favorable prognostic marker, suggesting better response to stressors like adjuvant radiation and chemotherapy; however, its effects on cell signaling and glioma cell death are not fully understood. In this study we investigated the impact of 2HG in glioma cell survival pathways. A single pulse of 2HG (30mM) increased phosphorylated Erk (p-Erk 1/2), but not pAkt, in the PTEN-intact glioma cell lines LN18 and LN229. Both p-Erk 1/2 and pAkt were unchanged in the PTEN-deficient cell lines U87 and U138. A single 2HG pulse, followed by prolonged withholding of medium changes, also enhanced caspase 3/7 activity in LN18 cells and LN229 cells, whereas it actually suppressed caspase 3/7 activity in U87 and U138 cells. Pretreatment with the MEK inhibitor UO126 prior to the 2HG pulse suppressed caspase 3/7 activity in LN18 cells, but not in LN229 cells. In U87 cells, the 2HG-induced suppression of caspase 3/7 activity was reversed by UO126, while no change was observed in U138 cells. These data indicate that 2HG can modulate stress-induced cell death in a MAPK/ERK-dependent manner, but that such modulation may vary greatly depending on the occurrence of other genetic aberrations in gliomas. Ongoing studies are pursuing potential mechanisms via which 2HG exerts such functionally divergent effects, aiming to develop better adjuvant therapeutic approaches for IDH-mutant gliomas.

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 4971. doi:1538-7445.AM2012-4971
Abstract 5046: miR-199a/125b inhibits tumor growth
Authors: Jiang Bing-Hua , He Jun , Xu Qing , Peiper Stephen , Liu Ling-Zhi
Published: August 2012

Many human cancers of epithelial origin are associated with overexpression of epidermal growth factor receptor (EGFR) family. In particular, ERBB2 and ERBB3 overexpression are linked with cancer development and poor prognosis. Except ERBB2/ERBB3 gene amplification, other mechanism(s) of ERBB2 and ERBB3 overexpression remains elusive. Recent studies show that aberrant expressions of miRNAs are associated with cancer development. To identify specific miRNAs for regulating ERBB2 and ERBB3 expression, we find that miR-199a and miR-125b directly target ERBB2 and ERBB3, and are downregulated in ovarian tissues and cancer cells. Elevated reactive oxygen species (ROS) have been observed in tumor growth and drug resistance. Interestingly we show that increased ROS downregulate miR-199a and miR-125b for inducing ERBB2 and ERBB3 expression. ERBB2 and ERBB3 in turn activate AKT/P70S6K1/HIF signaling leading to tumor growth and angiogenesis. This study provides a novel mechanism of ERBB2 and ERBB3 regulation by miR-199a and miR-125b and new concept of ROS for inducing ERBB2 and ERBB3 in tumor growth and angiogenesis; and establishes a rationale for using miR-199a and miR-125b mimics and ROS scavengers as new therapeutic agents in the future.

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 5046. doi:1538-7445.AM2012-5046
Abstract 5048: Global microRNA expression array analysis and potential application in discovery of promising drugs for hematologic cancer
Authors: Shivapurkar Narayan M.
Published: August 2012

Hematologic cancers, the third most common cause of cancer deaths, will kill ∼50,000 Americans this year. Early diagnosis and innovative treatment has been proposed to result in cure. Bendamustine (BM) is a synthetic drug which is highly effective in broad range of hematologic cancers. The efficacy of the drug is attributed to the ability of the drug to induce apoptosis as well as to inhibit cell cycle. It was highly effective in patients whose disease is refractory to other established drugs. Gambogic acid (GA) is the major active component of gambose, the resin secreted from Garcinia hanburryi which also has strong ability to induce apoptosis as well as inhibit cell cycle. microRNAs (miRNAs) are master regulators of the gene expression. Neither BM nor GA had been previously reported for their effect on miRNA expression profiles in hematologic or other cancers. We have set up an innovative global miRNA expression analysis array. Using this miRNA expression array, we analysed global expression in leukemia cells in culture treated with or without treatment of MB or GA. Our data showed comparable inhibition of cell cycle and induction of apoptosis by both GA and BM at a dose of GA several folds lower than that of BM. Our data, based on miRNA expression analysis using genome-wide miRNA expression array showed five common miRNAs, found differentially expressed (more than 3 times up or down regulated compared to untreated group with p<0.05) in both GA and BM treated groups. The data is particularly interesting, since these miRNAs have been reported to target and thus modulate expression of proteins of apoptotic pathway and senescence pathway. Out data suggest that drugs that induce apoptosis as well as inhibit cell cycle may have great therapeutic potential in hematologic cancers. Based on our data it appears that the drugs with anticancer properties may affect a common set or sets of miRNAs. To our knowledge, this constitutes the first report describing effect of both BM and GA on miRNA expression profile, not in just hematologic cancer but any cancer. Our study provides strong evidence to suggest that specific miRNA expression signature/s of hematologic cancer cells in culture following drug treatment should be further explored to screen promising drugs with higher anticancer properties.

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 5048. doi:1538-7445.AM2012-5048
Abstract 507: Nitrogen oxides-derived immunotherapy: Revealing cryptic melanoma-specific immune targets
Authors: Zhu Weidong , Eng Ashley C. , Olson Samuel Y. , Márquez-Garbán Diana C. , Garbán Hermes J.
Published: August 2012

Nitrogen oxides (NOx) can exert their relevant biological functions through two reversible molecular modifications: a) direct interaction with metals (nitrosation), and b) by interacting with thiols (s-nitrosylation); or irreversible modifications of aromatic amino acid residues such as tyrosine or phenylalanine (nitration). Any of these modifications have been demonstrated to affect the biological fate of the modified molecule or alter their functions. We have previously shown that these NOx-derived changes will trigger a myriad of modifications at the genetic, epigenetic and post-translational level in tumor cells resulting in a robust and effective therapeutic immune response against cancer cells. However, the molecular mechanisms and immune-related tumor targets remain elusive. Thus, we hypothesize that NOx-derived protein modifications (i.e., Tyrosine nitration) will differentially prime the immune system with otherwise subdominant antigens (cryptic) making them immune visible and triggering an effective anti-tumor immune response. We have tested this hypothesis using the well-characterized B16-C57BL/6 syngeneic and poorly immunogenic melanoma mouse model. NOx-modified and non-modified B16-F0 melanoma cell lysates were used to immunize naïve C57BL/6. Post-immunized sera was screened against SDS-PAGE resolved untreated B16-F0 lysates and human protein library micro array for differential recognition of immune cross-reactive of novel mouse and human melanoma targets by the mouse IgG fraction. Our results demonstrated the highly significant (p <0.0001) IgG-associated immune recognition of five cross-reactive novel melanoma targets (in relative affinity decreasing order): 1) Golgi reassembly stacking protein 1 (GORASP1), 2) ArfGAP w/GTPase domain-ankyrin repeat and PH domain 1 (AGAP1), 3) Microtubule-associated protein tau (MAPT), 4) Mitochondrial ribosomal protein L46 (MRPL46), and 5) Protocadherin beta 6 (PCDHB6). Currently, we are evaluating the significance and functional activity of the identified targets and their isolated/purified specific immune effector (IgG) counterparts. In addition, we are characterizing the potential molecular and immunological mechanisms that might lead to the use of these novel melanoma-specific immune targets as diagnostic/prognostic and/or immunotherapeutic tools.

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 507. doi:1538-7445.AM2012-507
Abstract 5076: Integrative genomic and transcriptomic analysis of metaplastic carcinomas of the breast
Authors: Mackay Alan G. , Natrajan Rachael , Maher Christopher , Lambros Maryou , Weigelt Britta , Nava-Rodrigues Daniel , Wilkerson Paul , CampionFlora Adriana , Kozarewa Iwanka , Fenwick Kerry , Campbell James , Chen Lina , Lord Christopher J. , Gauthier Arnaud , Pawar Vidya , Mariani Odette , Vincent-Salomon Anne , Reis-Filho Jorge
Published: August 2012

Background Metaplastic breast carcinomas (MBCs) are characterised by neoplastic cells that display differentiation towards squamous epithelium or mesenchymal elements. These tumours are of triple-negative phenotype and have an aggressive clinical behaviour. The aims of this study were to characterise a series of MBCs at the genomic and transcriptomic level to identify potential drivers of this breast cancer special type. Design Twenty-five frozen MBCs and two MBC cell lines (HCC1569 and Hs578T) were subjected to genotyping (Affymetrix SNP6), 32K BAC microarray comparative genomic hybridisation (aCGH), microarray gene expression profiling (Illumina HT12) and massively parallel mRNA-sequencing (RNA-seq, Illumina GAII). Novel chimaeric transcripts were identified using Chimerascan v0.4.3. 10 cases with available germline DNA were subjected to targeted exomic sequencing (Illumina HiSeq). Somatic variants were called using the Genome Analysis Toolkit (GATK) using best practice guidelines. Fusion genes and mutations were validated using (RT)-PCR and Sanger sequencing, respectively. Results MBCs displayed a complex pattern of gene copy number aberrations, with multiple copy number gains and losses throughout the genome. Recurrent amplifications/ high-level gains at 3q25.2-q27.1, 8p11.21-q24.3 and 12p13.33 and recurrent homozygous deletions on 9p21.3 (CDKN2A/2B) and 10q23.31 (PTEN) were found. Unsupervised clustering of gene expression showed that MBCs associated with chondroid differentiation separated into a distinct cluster, whereas MBC's with spindle and epithelial morphology did not cluster apart. Integration of SNP6 copy number and gene expression data identified 198 genes overexpressed when amplified. RNA-seq revealed 1025 unique nominated fusion gene events (43-119 per tumour), including 254 fusions predicted to be in-frame. These included a promoter swap involving TBXLR1 fused to PIK3CA and a recurrent promoter swap involving NF1 that was also seen in the MBC cell line Hs578T. Targeted exome sequencing identified 402 somatic coding variants (12-96 per tumour), including recurrent mutations in TP53 (5/10) and genes involved in PI3K signaling. Conclusion Our results demonstrate that MBCs have complex genomes and are heterogeneous at both the genomic and transcriptomic levels. TP53, CDKN2A/2B and PTEN mutations and/ or homozygous deletions, and activation of the PI3K pathway are recurrent events in these tumours.

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 5076. doi:1538-7445.AM2012-5076
Abstract 508: Correlation of antibody and T-cell responses against XAGE-1b in NSCLC patients
Authors: Ohue Yoshihiro , Eikawa Shingo , Mizote Yu , Matsumoto Hirofumi , Isobe Midori , Fukuda Minoru , Uenaka Akiko , Nakayama Eiichi , Oka Mikio
Published: August 2012

BACKGROUND: XAGE-1b is a cancer/testis antigen identified in lung cancer using autologous patient serum by SEREX. The expression of XAGE-1b is observed frequently in lung adenocarcinoma and rarely in some other tumors. Recently, we showed spontaneous T-cell response against XAGE-1b in XAGE-1b-antibody positive non-small cell lung cancer (NSCLC) patients. In this study, we analyzed the frequency of XAGE-1b-reactive CD4 and CD8 T-cells in NSCLC patients showing high, intermediate and low antibody responses. MATERIALS AND METHODS: Sera and PBMCs were obtained from NSCLC patients who visited Kawasaki Medical School Hospital between 2009 and 2011. Antibody response was determined for XAGE-1b protein by ELISA using O.D. values at 1:900 serum dilution and classified as high ≥ 3.0, 3.0 > intermediate ≥ 1.0 and 1.0 > low. CD4 and CD8 T-cell responses against XAGE-1b were examined by IFN-γ ELISA using 12- or 16-mer XAGE-1b-overlapping peptides (OLPs) spanning the entire XAGE-1b protein in antibody-positive patients. Cytotoxicity was analyzed determining GAPDH release by aCellaTox kit. RESULTS: The number of XAGE-1b-antibody positives was 29 (9.0%) of 323 NSCLC patients. Within those, the patients showing high, intermediate and low antibody response was 6, 11 and 12, respectively. The frequency of XAGE-1b-reactive CD4 T-cells in patients showing high, intermediate and low antibody response was 5.5 ±2.1 x 10-5, 1.5 ±0.7 x 10-5 and < 1.1 x 10-5, respectively. The frequency of XAGE-1b reactive CD8 T-cells was 6.9 ±1.6 x 10-6, 4.6 ±1.6 x 10-6 and < 1.1 x 10-6, respectively. The ratio of the CD8 T-cells recognizing XAGE-1b-expressing tumor to the XAGE-1b-peptide reactive CD8 T-cells in patients showing high and intermediate antibody responses was 60.0% and 14.3%, respectively. CONCLUSION: Our findings indicate correlation of antibody response to CD4 and CD8 T-cell responses against XAGE-1b in NSCLC patients.

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 508. doi:1538-7445.AM2012-508
Abstract 5085: TopModel: An online resource for predictive models in cancer
Authors: Szeto Christopher W. , Sokolov Artem , Benz Stephen , Stuart Joshua , Haussler David
Published: August 2012

One goal of characterizing the genome-wide landscape of cancer cells is to identify predictive signatures of onset, progression, and treatment outcomes. Many computational approaches have been developed to discover gene signatures with a range of success. The challenge still remains to identify the best approach that, when trained on one cohort, remains accurate in predicting outcomes on an unseen cohort. Thus far, no clear themes have emerged that might provide clues about which method works for a particular task. We have built a system called TopModel that facilitates the identification of top-performing machine-learning algorithms for a series of cancer-genomics challenges. The four components of the system include: 1) a benchmark that includes several cancer genomics datasets with outcome variables as targets to predict; 2) a database of results derived from the application of thousands of machine-learning and feature selection combinations; 3) a web interface that allows bioinformaticians to evaluate their own prediction results; and 4) a web interface that allows a biomedical researcher to upload data on a sample or set of samples in order to receive a report on the signatures predicted to exist in the sample(s). The cancer benchmark component provides a common ground for the development and evaluation of prediction methods for variables such as cancer subtype, drug response, survival, and others. Several datasets have been loaded including predicting survival in the TCGA cohorts, and the hundreds of drug sensitivities in several cancer cell line cohorts. We demonstrate the utility of the resource by comparing state-of-the art feature selection methods to a new approach that uses locality on a genetic interaction network. We evaluate the performance in terms of how well the features generalize across datasets as a trade-off to the accuracy of prediction. In addition to identifying high-value genome features, we explore the robustness of the cancer state in the absence of these features. We simulate gene knock outs by disconnecting these features in our pathway models, inferring the pathway interaction network in the absence of these features, and then reassessing using the top-performing predictive models of 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 5085. doi:1538-7445.AM2012-5085
Abstract 509: Immunoglobulin reactivity analysis of chronic lymphocytic leukemia patients unveils Lymphocyte Cytosolic Protein 1 (LCP1) as a novel CLL exosome antigen
Authors: Dubovsky Jason A. , Andritsos Leslie A. , Blum William , Johnson Amy , Muthusamy Natarajan , Byrd John C.
Published: August 2012

Chronic lymphocytic leukemia (CLL) is incurable accumulation of malignant clonal B lymphocytes in the blood, bone marrow, lymph nodes, and spleen. A hallmark of CLL is profound immunosupression mediated by a litany of costimulatory, cytokine, and exosome signals within the microenvironment. One of the most promising recent advances in this disease has been the development of membrane targeted immunotherapeutics such as the monoclonal antibodies rituximab and alemtuzumab. However, a shortfall of most current and experimental immunotherapeutics is the reliance upon cluster of differentiation (CD) antigens that are also common to a variety of healthy tissues. Moreover, the non-obligate nature of many CD markers renders them susceptible to shedding and down- modulation in resistant CLL cases. In recent studies, we and others have identified endogenous adaptive immune responses against known CLL specific antigens such as ROR1. Curiously, this effect appears biased to tumor relevant antigens with defined malignant signaling. Using retrospective antigen identifications as proof of principle, we sought to further investigate humoral reactivity against autologous CLL membrane associated antigens to identify novel targets for immunotherapy. Mass spectroscopic analysis of CLL membrane antigens targeted by patient derived serum IgG repeatedly identified LCP1 as a lymphocyte specific target. Confirmation by immunoblot and ELISA revealed that CLL patients maintain elevated LCP1 IgG response despite an inability to respond to common vaccine antigens such as tetanus toxin, suggesting continued antigenic stimulation. Flow cytometry, RT-PCR, immunoblot, and confocal microscopic analyses revealed few differences in LCP1 protein levels, glyocoslyation, transcripts, and localization between healthy and malignant B lymphocytes. Given the potential for CLL exosomes to provide a vehicle for continued antigenic stimulation as well as a target for future therapeutics we investigated their LCP1 content. We found that LCP1 is an integral component of CLL exosomes and that production of LCP1-laden exosomes is increased upon CLL stimulation. Ongoing studies aimed at addressing the potential role of exosomal LCP1 in CLL will be discussed. Supported in part by NIH and D. Warren Brown Foundation

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 509. doi:1538-7445.AM2012-509
Abstract 5094: Genome-wide molecular profiles of undifferentiated pleomorphic sarcoma and leiomyosarcomas
Authors: Silveira Sara Martoreli , Villaces Rolando Andre Rios , Cunha Isabela Werneck , Lopes Ademar , Rogatto Silvia Regina
Published: August 2012

Malignant soft-tissue sarcomas are a heterogeneous group of mesenchymal cancers accounting for 1% of all malignant tumors in adult. These tumors are classified according their differentiation status. Undifferentiated high-grade spindle/pleomorphic sarcoma (UPS) presents a clinically aggressive behavior with frequent development of distant metastases and recurrence after surgery. The genome profile of 20 UPS and 17 leiomyossarcomas (LMS) was evaluated by array CGH and correlated with the clinical course and histopathological findings. Array CGH was done using the Human 44K Agilent oligoarrays according to manufacturer's instructions. Data were extracted using the Feature Extraction software, version 10.7, and analyzed by Nexus Software v 6.0 (BioDiscovery), with a FASST2 (Fast Adaptive States Segmentation Technique 2) algorithm. DNA copy number alterations were compared with a reference dataset of healthy Brazilian individuals and with Database of Genomic Variants. DNA from UPS presented 1406 CNAs and from LMS showed 625 CNAs. However, the genomic profile revealed striking similarities between both tumors that were indistinguishable by unsupervised hierarchical cluster analysis. In UPS samples, genomic gains were mainly found on chromosomes 1 and 7 (79 and 65 events, respectively), while recurrent losses encompassing chromosomes 1 and 12 (49 and 43 events, respectively). Recurrent gains on chromosomes 5 and 17 (28 and 30 events, respectively) and losses on chromosomes 2 and 10 (29 and 28 events, respectively) were frequently found in LMS. Gains on 2q11.1-q11.2 (P=0.031) and losses on 21p11.1 (P=0.001) were significantly detected in patients with UPS alive with the disease and alive without the disease, respectively. In LMS, gains in 1q and 11q (P=0.02 and P=0.043), as well as losses in 17q25 (P=0.05) were associated with tumor recurrence. Non-supervised hierarchical clustering revealed three groups. Cluster 2 was characterized by retroperitoneal tumors (P=0.04) and cluster 3 included both, LMS and UPS, from extremities (P=0.032). None exclusive alteration was verified for cluster 1. In addition, losses on 3p12.1-p11.2 found in UPS and gains on 1q21.3 and 11q13.2-q13.3 in LMS were associated significantly with reduced patient survival (P<0.05). These data suggest a very complex interplay between UPS and LMS, providing new hints about the pathobiology of these tumors.

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 5094. doi:1538-7445.AM2012-5094