bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3969: A novel statistical method for detecting association of copy number variations in genome-wide association studies of cancers
Authors: Shi Jianxin , Li Peng
Published: August 2012

Copy number variations (CNVs) are one of the major genetic resources in human populations. In large scale genome-wide association studies (GWAS), CNVs are usually detected from intensity data, quantified as Log R Ratio (LRR) and B-allele Frequency (BAF), generated by single nucleotide polymorphism (SNP) genotyping arrays. The standard approach for detecting CNV associations is based on two-step procedures: CNVs are first detected using intensity data and then association is tested based on the detected CNVs. Because the accuracy of CNV calling depends on the number of probes covered in the CNV region, short CNVs are generally detected with low sensitivity. Consequently, the statistical power of detecting short CNVs associated with diseases is low. We develop a novel method, variable thresholding exact statistic (VTES) implemented in a package SegCNV, for identifying genomic regions within which the frequency of CNVs is significantly higher in cases than in controls. VTES optimally summarizes the LRR and BAF of the probes to maximize the power. Extensive simulation studies demonstrated that VTES had a much better power for detecting rare, short CNVs associated with common diseases compared to standard two-step procedures, while maintaining correct type-I error rates. Particularly, the power of VTES is close to the ideal power when CNVs can be called perfectly. VTES is flexible to detect both recurrent CNVs and non-overlapping CNVs associated with diseases. VTES is computationally efficient and can analyze a GWAS of 2000 subjects within 20 hours using a single core. We applied VTES to a GWAS of testicular cancer and lung cancer, and identified regions that show strong evidences of CNV associations. We expect that VTES will prove useful for CNV association analysis in existing large scale GWAS of 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 3969. doi:1538-7445.AM2012-3969
Abstract 4251: Evaluating novel targeted therapeutic agents in T-cell acute lymphoblastic leukemia using a zebrafish xenotransplantation model
Authors: Corkery Dale , Balci Tugce B. , Berman Jason N. , Dellairee Graham
Published: August 2012

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy accounting for 25% of adult and 10-15% of pediatric ALL cases. The disease is characterized by infiltration of the bone marrow and peripheral blood with immature lymphoblasts bearing T-lineage markers. Although current multi-agent chemotherapy regimens have dramatically improved cancer outcomes, a significant proportion of T-ALL do not respond to therapy or relapse post therapy. Novel molecular-based treatment strategies are desperately needed to improve outcome and limit toxicity. Mutations that activate the NOTCH and PTEN/PI3K pathways are common in human T-ALL and may drive T-ALL cell proliferation. Gamma secretase inhibiting compounds that block NOTCH signaling have been effective against subtypes of T-ALL with NOTCH mutations but have had limited success in clinical trials due to severe gastrointestinal toxicity, and problems with drug resistance. Recently, inhibition of the PI3K pathway (including the downstream kinase AKT) have shown efficacy in vitro and in pre-clinical animal models. We have recently developed a novel human cancer xenotransplantation (XT) animal model using the zebrafish, which can be used for high throughput pre-clinical testing of human tumour-drug interactions for both leukemia and solid tumours (Corkery et al., 2011 Brit. J. Haemat.). Using the zebrafish XT model we are studying a number of compounds that specifically target the PI3K/AKT kinase pathway for ability to inhibit T-ALL cell proliferation in vivo. Preliminary proof-of-principal studies have shown that we can successfully engraft the PTEN-deficient T-ALL leukemia Jurkat cell line in zebrafish embryos. In agreement with published data, we have shown that treating Jurkat transplanted embryos with the mTOR inhibitor rapamycin inhibits in vivo proliferation of the human leukemia cells line by 60%, while, by contrast, the AKT inhibitor triciribine does not significantly inhibit proliferation. We have also successfully transplanted primary bone marrow from pediatric T-ALL patients which go on to engraft in the zebrafish embryos. The ability to screen novel compounds against a panel of primary patient samples could provide a more accurate means of predicting the efficacy of said compounds across heterogeneous patient populations. We are now employing the zebrafish XT model to study the effects of novel PI3K/AKT kinase inhibition on the proliferation of a panel of human T-ALL cell lines and primary patient samples as a means of rapidly selecting new drug candidates to move forward into the rodent model and Phase I clinical trials.

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 4251. doi:1538-7445.AM2012-4251
Abstract 4253: In vivo activity of small molecule HIF2α inhibitors
Authors: Metelo Ana Marguerita , Xiang Li , Baker Rania , Burger Alexa , Peterson Randall , Iliopoulos Othon
Published: August 2012

Hypoxia-inducible factor (HIF) is a central regulator of the cellular response to hypoxia. Hypoxia promotes HIF activity by increasing its stability, transcriptional activity and translation. HIF target genes involved in several cellular processes including proliferation, angiogenesis, metabolism and promotion of the “stem-cell” phenotype. In normoxic conditions, HIF-α is recognized for degradation by the von Hippel-Lindau tumor suppressor protein (VHL). Loss-of-VHL function leads to constitutive expression of HIF regulatory subunits and consequent over-expression of HIF-target genes. We and others have shown that HIF2a is necessary and sufficient for the development of VHL-related renal cell carcinoma. We have developed small molecules that repress HIF-2α translation, in vitro, by enhancing the binding of Iron-Regulatory Protein 1 (IRP1) to the Iron-Responsive Element (IRE) within the 5′-UTR of HIF-2α mRNA (Zimmer M. et al. Molecular Cell 2008;32: 828-848). We showed that these small molecules down-regulate HIF2a expression in vitro, in all renal cell carcinoma cell lines. To validate these small molecules in vivo, we tested their efficacy on wild-type zebrafish embryos. Treatment of 3 days post fertilization zebrafish embryos with 100microM of the hypoxic mimetic DMOG or hypoxia dramatically upregulated the expression of HIF-target genes, such as Vascular Endothelial Growth Factor (Vegf), erythropoietin (Epo) and prolyl-hydroxylase 3 (Phd3). Pre-treatment of embryos with the small molecule HIF2a inhibitor 76 potently decreased the DMOG-induced upregulation of HIF target genes. The IC50 values of these small molecules were significantly less in vivo than in vitro. We are currently testing the efficacy of HIF2a inhibitors in rescuing the VHL zebrafish phenotype and prolonging survival of VHL mutant zebrafish embryos. In addition, data on the efficacy of these inhibitors on the growth of human renal cell carcinoma cells as tumors in the nude mouse xenograft assay will be presented.

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 4253. doi:1538-7445.AM2012-4253
Abstract 4260: Histone deacetylase 11 (HDAC11) as a novel therapeutic target in the regulation of myeloid-derived suppressor cell (MDSC)
Authors: Sahakian Eva , Powers John , Rock-Klotz Jennifer , Marsilio Adriani , Woan Karune , Merino Oscar , Gill Ajaypal , Deng Susan , Cheng Fengdong , Villagra Alejandro , Luekette Noreen , Seto Edward , Borrello Ivan , Sotomayor Eduardo , Pinilla Javier I.
Published: August 2012

The physiological role of this HDAC11, the newest member of the HDAC family was mainly unknown until the discovery by our group that HDAC11 regulates IL-10 gene expression in myeloid cells in-vitro. To better elucidate the role of HDAC11 in these cells, we have utilized HDAC11 promoter-driven eGFP reporter transgenic mice (TgHDAC11-eGFP) which allow us to “visualize” dynamic changes in HDAC11 gene expression /transcriptional activity in immune cells in vivo. Immature myeloid cells (IMCs) differentiate into macrophages, dendritic cells, and neutrophils and are also considered to be precursors of MDSCs in tumor-bearing hosts. Here, we show for the first time that HDAC11 plays an important role in this process. First, IMCs from the bone marrow and spleen of TgHDAC11-eGFP mice display high expression of eGFP indicative of HDAC11 transcriptional activation in these cells in the steady state. Subcutaneous injection of EL4 tumor cells into these mice resulted in expansion of MDSCs (identified by the expression of CD11b+/GR1+ [Ly6G and Ly6C] with variable expression of CD49d and CD115) in their lymphoid organs which was similar in extent to the expansion observed in tumor-bearing wild type (WT) mice. Of note, flow cytometric analysis revealed that expression of eGFP was significantly decreased in the myeloid compartment of tumor bearing TgHDAC11-eGFP mice, with greatest decrease in the Ly6Chigh population suggesting that the transition of IMC into MDSCs might require a decrease in HDAC11 expression. Reminiscent of our findings in the eGFP mice, studies in nontransgenic mice also demonstrated that tumor derived MDSCs display less HDAC11 mRNA expression compared to splenic MDSCs, with lowest expression of HDAC11 in the Ly6Chigh MDSCs. Additional support for the regulatory role of HDAC11 in MDSC expansion/function has been recently provided by our preliminary functional studies in TgHDAC11-eGFP mice which demonstrates that isolated GR1+/eGFP- cells demonstrate more suppressive phenotype than that of GR1+/eGFP+ cells, in the presence of tumor challenge. Taken together, these results suggest that HDAC11 plays a regulatory role in the expansion and function of MDSCs in vivo. A better understanding of this previously unknown role of HDAC11 in MDSC biology might lead to targeted epigenetic therapies to influence the suppressive abilities of these cells and augment the efficacy of immunotherapeutic approaches against malignancies.

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 4260. doi:1538-7445.AM2012-4260
Abstract 4262: NR2F1 and SOX9 mediate reprogramming of tumor cells into dormancy: Potential role in dormant bone marrow DTCs
Authors: Sosa Maria S. , Estrada Yeriel , Parikh Falguni , Bosch-Gutierrez Almudena , Ekpin Esther , George Ajish , Farias Eduardo F. , Aguirre-Ghiso Julio A.
Published: August 2012

Single disseminated tumor cells (DTCs) found in secondary organs (i.e. bone marrow BM, lung, liver) appear to activate a quiescence program and undergo a dormancy phase triggered by specific tissue microenvironment signals. The timing of this asymptomatic clinical phase may rely on specific signals that convert a previous non-permissive/non-proliferative environment into a permissive one, fueling metastasis development. The mechanisms underlying dormancy and means to maintain this state remain unknown. Here we show that the orphan nuclear receptor NR2F1/COUP-TF1 is silenced in breast and HNSCC tumors, cancer cell lines and MMTV-Neu and -Myc mouse tumor models. Surprisingly, retinoid signaling, stress signaling and microenvironmental cues from target organs (i.e. bone marrow) can induce re-expression of NR2F1 and dormancy of HNSCC cells. Forced NR2F1 re-expression resulted in induction of tumor cell quiescence in vivo and this effect depended on the expression of the transcription factor SOX9 and p27 induction. In contrast, RNAi-mediated silencing of NR2F1 or SOX9 interrupted the quiescence of dormant tumor cells. Further, quiescence induction was associated with p27, p15, p16 and HES-1. Mechanistic analysis revealed that NR2F1 is primarily nuclear and that its expression is activated by MKK6-p38α stress signaling and is negatively regulated by DNA promoter methylation. Lastly, we showed that atRA treatment followed 5-Aza-C treatment reprograms tumorigenic cells into dormancy in an NR2F1-dependent fashion. Our data suggest that re-expression of NR2F1 may promote reprogramming of aggressive tumor cells into dormancy identifying a new target for maintenance therapies for residual disease.

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 4262. doi:1538-7445.AM2012-4262
Abstract 4264: NFκB activation in mesenchymal stromal cells induced by leukemia-stroma interaction plays a central role in stroma-mediated chemo-resistance of leukemic cells
Authors: Jacamo Rodrigo O. , Chen Ye , Wang Zhiqiang , Ma Wencai , Zhang Min , Venkata Batulla L. , Schober Wendy D. , Davis Richard E. , Konopleva Marina , Andreeff Michael
Published: August 2012

Within the bone marrow (BM) microenvironment, BM mesenchymal stromal cells (BM-MSC) produce cytokines and chemokines and initiate cellular adhesion-mediated signals that tightly regulate normal and malignant hematopoietic cell development. This rich environment serves as a sanctuary for malignant hematopoietic cells, offering protection from chemotherapeutic agents and promoting residual disease with greater potential for developing acquired drug resistance. In this study we utilized gene expression profiling (GEP) as a genome-wide exploratory approach to characterize changes caused by the interaction between leukemic cells and BM-MSC, and how these changes can contribute to the observed microenvironment-mediated chemoresistance. Co-culture of REH, a pre-B-ALL cell line, with normal-donor BM-MSCs for 48 hours upregulated a variety of genes encoding cytokines and chemokines in BM-MSCs such as CXCR6, CCL5, CCL2, IL32, IL34, IL8, IL6, CXCL12, and the VLA4 ligand VCAM-1. These microarray-based GEP findings were confirmed by qRT-PCR. Gene Set Enrichment Analysis (GSEA) implicated activation of NFκB in BM-MSCs as a potential cause of these changes. Similar upregulation of NFκB target genes was found in MSC co-cultured with the AML cell line OCI-AML3, suggesting that NFκB activation is a common consequence of leukemia-stroma interation. Given known paracrine functions of NFκB-regulated target genes such as IL-8, we hypothesized that stromal NFκB activation contributes to stroma-mediated chemo-resistance of leukemic cells. Stable transduction of BM-MSC to overexpress a super-repressor form of IαBβ (IαBβ-SR), to block canonical-pathway NFκB activation in the stromal compartment, significantly reduced the stroma-mediated chemo-resistance to Vincristine (VCR) of REH cells. NFκB inhibition using a specific IKKα inhibitor (MLN120B), affecting both BM-MSC and tumor cells, highly increased the apoptotic effects in leukemia-stroma co-cultures of VCR in REH cells and NALM6, another pre-B-ALL cell line. Similar results were obtained with CDDO-Me, another NFκB inhibitor. Altogether these results indicate that the interaction of leukemic cells with BM stromal cells activates NFκB in the stromal compartment, with subsequent transcriptional upregulation of a number of cytokines and chemokines ultimately favoring the survival of leukemic cells. We propose that targeting NFκB may ameliorate stroma-mediated chemo-resistance and help in eliminating bone-marrow resident leukemic cells.

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 4264. doi:1538-7445.AM2012-4264
Abstract 4280: Genome-wide expression and methylation analysis in CD31+ cells from African American and Caucasian American benign and malignant prostate tissue
Authors: Luo Wei , Deeb Kristin K. , Liu Song , Ma Yingyu , Morrison Carl D. , Trump Donald L. , Johnson Candace S.
Published: August 2012

Prostate cancer exhibits striking racial disparity; African American (AA) men have a markedly higher risk of being diagnosed and of dying of prostate cancer compared to Caucasian American (CA) men. This disparity may be due to biologic differences associated with race or to sociologic factors, such as economic disparities or differences in access to care or interactions of all these factors. Differences in tumor gene expression and methylation might be associated with the poorer prognosis seen among AA men and may contribute to better understanding of these disparities and the delineation of new therapeutic targets. In order to study the effect of the tumor microenvironment on endothelial cells found in tissue from AA and CA patients with prostate cancer, we first established a method for the isolation of the endothelial cells from malignant and benign prostate tissue obtained at prostatectomy. We then conducted a pilot study of transcriptome and methylome analysis in 5 pairs of CD31+ endothelial cells isolated from paired samples of benign and malignant tissue from AA and CA patients with prostate cancer. We have identified 2,096 and 920 differentially expressed transcripts for the tumor versus normal in AA and CA group, respectively. However, only 140 transcripts are shared. Furthermore, a total of 2,248 transcripts show different level of expression change for tumor versus normal in samples with AA origin compared to samples with CA origin. Genome-wide DNA methylation profiling in the same endothelial samples have identified 18,093 differentially methylated loci in AA group, and 12,372 differentially methylated loci in CA group. Only a total of 1,324 loci are shared. Remarkably, there are a total of 20,164 loci with different level of methylation change for tumor versus normal in AA group compared to CA group. Integrative analysis of transcriptome and methylatome data showed that a large percentage of differentially expressed genes have loci whose methylation change is inversely correlated with gene expression change, and vice versa. Taken together, our pilot data, while preliminary, suggest the possibility that there is a potential racial difference in terms of differential expression and methylation between CA and AA endothelial cell populations. Future large studies are warranted to confirm our findings and further explore the role of race disparity in the delineation of novel therapeutic targets to be utilized clinically for prostate 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 4280. doi:1538-7445.AM2012-4280
Abstract 4283: Cross-species hybridization of microarrays for studying tumor transcriptome of brain metastasis
Authors: Park Eun Sung , Kim Sun-Jin , Kim Seung Wook , Yoon Se-Lyun , Leem Sun-Hee , Kim Sang-Bae , Kim Soo Mi , Park Yun-Yong , Cheong Jae-Ho , Woo Hyun Goo , Mills Gordon B. , Fidler Isaiah J. , Lee Ju-Seog
Published: August 2012

Although the importance of the cellular microenvironment (soil) during invasion and metastasis of cancer cells (seed) has been well-recognized, technical challenges have limited the ability to assess the influence of the microenvironment on cancer cells at the molecular level. Here, we show that an experimental strategy, competitive cross-species hybridization of microarray experiments, can characterize the influence of different microenvironments on cancer cells by independently extracting gene expression data of cancer and host cells when human cancer cells were xenografted into different organ sites of immunocompromised mice. Surprisingly, the analysis of gene expression data showed that the brain microenvironment induces complete reprogramming of metastasized cancer cells, resulting in a gain of neuronal cell characteristics and mimicking neurogenesis during development. We also show that epigenetic changes coincide with transcriptional reprogramming in cancer cells. These observations provide proof of principle for competitive cross-species hybridization of microarray experiments to characterize the effect of the microenvironment on tumor cell behavior

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 4283. doi:1538-7445.AM2012-4283
Abstract 4285: Visualizing cancer vaccine clearance in vivo using magnetic resonance imaging
Authors: Brewer Kim , Lake Kerry , Pelot Nicole , DeBay Drew , Penwell Andrea , Weir Genevieve , Bowen Chris , Karkada Mohan , Mansour Marc
Published: August 2012

Magnetic Resonance Imaging (MRI) is a powerful tool in the evaluation of immunotherapies, since it permits non-invasive longitudinal assessment of tumor growth, and as our group has previously demonstrated, it allows monitoring of immune response via volumetric changes in lymph nodes (LNs) adjacent to (inguinal LNs) or distant from (popliteal LNs) the site of vaccination. MRI also offers potential for visualizing the uptake behavior of vaccines such as DepoVaxTM, a novel liposome-in-oil-based vaccine platform developed by Immunovaccine Inc. In the context of cancer immunotherapy, this platform uses tumor-associated antigens (TAA), adjuvant and stimulator of T helper cells encapsulated in liposomes and suspended in oil. The oil substrate of the DepoVaxTM immunotherapy vaccine platform acts as an adjuvant that greatly increases the potency of the vaccines, eliciting a strong cytotoxic T-cell response, and also permits longitudinal visualization of the vaccine site with MRI. However, this does not reveal any information about the clearance time of the individual vaccine components, particularly the TAAs. By attaching superparamagnetic iron oxide (SPIO) to the TAA and then encapsulating it in liposomes, it is possible to visualize the biodistribution of the TAA over time using MRI and evaluate whether there is truly a slow clearance of the antigen from the depot site, facilitating a prolonged immune response. In this study, tumor-bearing mice challenged with C3 cells (HPV16 tumor model) were evaluated for the longitudinal clearance of the DepoVaxTM vaccine components using SPIO conjugated to the TAA or associated with the lipid component of the vaccine. The SPIO-conjugated antigen was also tested in a Montanide® oil emulsion vaccine as a control. Over the course of this study, we observed the vaccine being distributed to the surrounding tissue from the injection site, and the antigen was actively transported from the vaccine depot site. The iron-labeled antigen cleared slowly but consistently, decreasing by approximately 40% over 35 days. This study provides direct in vivo evidence that DepoVaxTM resides at the vaccine injection site for a prolonged period of time, increasing exposure to antigen in a controlled fashion, which is likely a key factor in the enhanced immune response elicited by this novel depot vaccine.

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 4285. doi:1538-7445.AM2012-4285
Abstract 4291: Near-infrared optical imaging visualizes tumor cell death induced by adoptive transferred T cells
Authors: Sato Noriko , Aras Omer , Choyke Peter
Published: August 2012

Cytotoxic functions of CD8 T cells change as the cells differentiate and are under the control of various positive and negative regulators. The number of cytotoxic T cells found in the tumor site does not necessarily correlate with the growth or reduction of the tumor. Monitoring the functionality of T cells is desired. In order to visualize tumor killing effects of adoptive transferred cytotoxic T cells, near-infrared optical imaging was employed using a probe against phosphatidylserine exposed on the tumor cells attacked by the T cells. CD8 T cells specific for ovalbumin (OVA) were isolated from OT-1 T cell receptor transgenic mice and were stimulated with an OVA peptide (257-264, SIINFEKL) followed by an antigen free culture. T cells were transferred to the recipient mice bearing intramuscular OVA-positive thymoma (EG.7) and the parental OVA-negative thymoma (EL4) in the thigh. One day later, a near-infrared optical probe with a phosphatidylserine binding motif, PSVue 794 (Em 810 nm, 3 mg/kg), was intravenously injected and optical images were acquired up to 5 days after the injection. Some mice also received an injection of fluorescein (FITC)- or Alexa 488-labeled annexin V 12hr after the PSVue 794 injection. Flow cytometry analysis showed a double staining of apoptotic tumor cells with PSVue 794 and annexin V, confirming the binding ability of PSVue 794 to the cells undergoing apoptosis. Whole-body optical images demonstrated an accumulation of PSVue 794 in the OVA expressing EG.7 tumor, the target of OT-1 CD8 T cells, at 24hr and later, but not in the control EL4 tumor. Analysis of tumor sections revealed co-localization of PSVue 794 and annexin V, with a migration of OT-1 T cells to the site. Collectively, a near-infrared optical probe targeting phosphatidylserine enabled visualization of tumor cell death induced by adoptively transferred cytotoxic T cells in an immunotherapy model. Monitoring functionality and therapeutic effects of T cells or natural killer cells transferred in therapies would provide crucial information for the improvements of therapeutic strategies.

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 4291. doi:1538-7445.AM2012-4291
Abstract 4293: In vivo imaging and tracking of a PARP inhibitor at single-cell resolution
Authors: Yang Katherine , Thurber Greg , Reiner Thomas , Kohler Rainer , Weissleder Ralph
Published: August 2012

PARP is an enzyme involved in sensing single-stranded DNA breaks and plays a critical role in the organization of DNA damage repair. Several PARP inhibitors have been developed for clinical use, particularly in breast and ovarian cancers with BRCA mutations. Despite the scientific rationale and promising early clinical results with PARP inhibitors, more advanced clinical trials in breast cancer have been disappointing. One of the questions arising from these trials is to better understand why the PARP inhibitors failed. We used a window-chamber system in mice to image the distribution and function of model PARP inhibitors such as AZD2281-Bodipy. Specifically, we measured the kinetics of vascular, cellular, and subcellular uptake and distribution of AZD2281-Bodipy in breast (MDA-MB-231, MDA-MB-436) and ovarian (OVCAR429, A2780) tumors over time. Additionally, using the fluorescently-labeled inhibitor, we were able to examine the heterogeneity of AZD2281 localization in single cancer cells in vivo. Our data provide the first example of single-cell distribution of fluorescent small molecule inhibitors. When coupled with reporter cell lines (e.g. for apoptosis, DNA damage, autophagy, and senescence), this approach will be a powerful tool to understand drug action in vivo.

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 4293. doi:1538-7445.AM2012-4293
Abstract 4310: TWIST1, a B-RAF effector, promotes invasion and is a novel regulator of MMP-1 in human melanoma cells
Authors: Weiss Michele B. , Abel Ethan V. , Mayberry Melanie M. , Aplin Andrew E.
Published: August 2012

Metastatic melanoma is the deadliest form of skin cancer due to its highly aggressive and chemotherapy-resistant nature. Therefore, determining the factors impacting melanoma advancement toward metastasis is an important and clinically-relevant task. Importantly, RAF/MEK/ERK signaling is hyperactive in the great majority of melanoma cells and is a driver of melanoma growth and invasion. In addition, the TWIST1 protein is up-regulated in melanoma and its expression correlates strongly with poor clinical prognosis. However, the mechanism underlying TWIST1 up-regulation, as well as the role of high TWIST1 expression in traits associated with the progression of melanoma, has yet to be uncovered. In this study, we report that disruption of RAF/MEK/ERK signaling strongly represses TWIST1 at the mRNA and protein level. We further show that TWIST1 protein levels are especially high in B-RAF mutant cells as well as in vertical growth phase melanoma cells, which are those that first begin to invade downward into the deeper dermal layers eventually leading to metastasis. To that effect, depletion of TWIST1 in several invasive melanoma cell lines significantly reduces Matrigel invasion. The inverse phenotype is apparent when TWIST1 is overexpressed in low TWIST1-expressing, non-invasive melanoma cell lines. Additionally, we tested the effect of altered Twist expression in three-dimensional collagen spheroid outgrowth assays, which mimic both tumor architecture and the in vivo collagen-rich dermal layer. We observe significant reduction in spheroid outgrowth when invasive cell lines are depleted for TWIST1 as well as increases in outgrowth when non-invasive cells overexpress TWIST1. Alterations to spheroid outgrowth were not as a result of apoptotic changes or proliferative rate. Importantly, we have found matrix metalloproteinase-1 (MMP-1) to be a downstream effector of TWIST1. Furthermore, TWIST1 acts as a mediator between activated B-RAF signaling and MMP-1 in a dose-dependent and direct manner at the level of transcription. Our findings uncover the novel interplay between B-RAF, TWIST1, and MMP-1 which is likely important in the progression of melanoma towards metastasis.

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 4310. doi:1538-7445.AM2012-4310
Abstract 4314: Dynamin 2 mediates PDGFRα-SHP-2-promoted glioblastoma growth and invasion
Authors: Feng Haizhong , Guo Ping , Liu Kun-wei , Cheng Shi-Yuan , Zhang Peng , Hu Bo , Cheng Tao , McNiven Mark A. , Johnson Gibbes R.
Published: August 2012

Dynamin 2 (Dyn2), a large GTPase, is involved in receptor tyrosine kinase (RTK)-promoted cell migration. However, molecular mechanisms by which Dyn2 regulates RTK-induced cell migration have not been established. Recently we reported that SHP-2 and PI3K mediate PDGFR[[Unsupported Character - Symbol Font α]]-promoted glioma tumor growth and invasion. Here, we show that Dyn2 is an effector downstream of the PDGFR[[Unsupported Character - Symbol Font α]]-PI3K/SHP-2 signaling in glioma cells. Depletion of endogenous Dyn2 by shRNAs inhibited PDGFR[[Unsupported Character - Symbol Font α]]-stimulated phosphorylation of Akt, Erk1/2, Rac1 and Cdc42 activities, glioma cell migration and survival in vitro, tumor growth and invasion in the brains of mice. Dyn2 binds to SHP-2, PI3K and co-localizes with PDGFR[[Unsupported Character - Symbol Font α]] at the invasive fronts in PDGF-A-stimulated glioma cells. Inhibition of SHP-2 by siRNA knockdown abrogated Dyn2 association with activated PDGFR[[Unsupported Character - Symbol Font α]] and PDGFR[[Unsupported Character - Symbol Font α]] activation of Rac1 and Cdc42, glioma cell migration, thereby establishing a link between SHP-2 interaction with Dyn2 and the PDGFR[[Unsupported Character - Symbol Font α]] signaling. Furthermore, a dominant negative SHP-2 C459S mutant inhibited PDGF-A-stimulated glioma cell migration, phosphorylation of Dyn2 and concomitantly blocked PDGFR[[Unsupported Character - Symbol Font α]]-induced Src activation. Inhibition of Src by Src inhibitors attenuated PDGF-A-stimulated phosphorylation of Akt and Dyn2 and glioma cell migration. Additionally, mutations of binding sites to PI3K, SHP-2 or Src of PDGFR[[Unsupported Character - Symbol Font α]] impaired PDGFR[[Unsupported Character - Symbol Font α]]-stimulated phosphorylation of Akt and Dyn2, and Dyn2 association with activated PDGFR[[Unsupported Character - Symbol Font α]]. Taken together, this study identifies Dyn2 as an effector that mediates PDGFR[[Unsupported Character - Symbol Font α]]-SHP-2-induced glioma tumor growth and invasion, suggesting that targeting the PDGFR[[Unsupported Character - Symbol Font α]]-SHP-2-Dyn2 pathway may be beneficial to patients with malignant glioblastomas.

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 4314. doi:1538-7445.AM2012-4314
Abstract 4320: Overexpression of Homeobox A5 decreases the invasive and migration capabilities of lung cancer cells
Authors: Liu Ya-Jung , Yu Sung-Liang , Chen Jeremy J. W. , Wang Chi-Chung
Published: August 2012

Homeobox genes are a family of regulatory genes containing a common homeobox and act as transcription factors. Many cancers exhibit unusual alteration and expression in homeobox genes, including leukemia, colon, skin, prostate, breast, and ovary cancers. Recent studies indicated that homeobox A5 (HOXA5) may behave as a tumor suppressor gene in breast cells. However, the real roles of HOXA5 in lung cancer remains to be further clarified. In this study, we investigated the effect of HOXA5 on the invasive ability of more invasive CL1-5 cells transfected with HOXA5 constitutively expressed system. The results revealed that the excessive expression of HOXA5 can inhibit tumor cell invasion and migration capabilities. In addition, the HOXA5 specific siRNA could restore these effects. The results of metastatic analysis in SCID mice also demonstrated that HOXA5-overexpressed transfectants could decrease in vivo tumor nodule numbers. Furthermore, the HOXA5 mRNA expression was measured by real time RT-PCR in NSCLC surgical specimens and correlated with the patients’ clinical outcome. The HOXA5 downstream genes and HOXA5-regulated pathways were identified by using Affymetrix microarray and CRSD bioinformatics platform built in-house. Our studies herein provide a new insight into how HOXA5 may contribute to tumor metastasis inhibition in lung 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 4320. doi:1538-7445.AM2012-4320
Abstract 4332: Proprotein convertases as target for therapy of pediatric sarcomas
Authors: Bernasconi Michele , D'Alessandro Valentina , Bornhauser Beat C. , Niggli Felix , Schaefer Beat W.
Published: August 2012

One of the biggest challenges of treating children with cancer is achieving complete remission, while ensuring that they will be able to lead normal, productive life in adulthood. To improve therapies for embryonal pediatric tumors such as rhabdomyosarcoma (RMS) the most common soft tissue sarcoma in children, we have selected by in vivo phage display for peptides that bind to RMS with high specificity. We have shown that coupling of Doxorubicin to RMS-P3, a RMS targeting peptide, considerably increases its therapeutic impact in a mouse model for RMS. We have identified proprotein convertases (PC), a family of ten serine proteases which convert inactive proprotein into their active form, as targets RMS binding peptides. Now we aimed at elucidating the contribution to RMS growth in vivo of the two proprotein convertases, furin and PC7, which are highly expressed in RMS tumors. To this end, we have generated a panel of RMS cell lines overexpressing furin, overexpressing a specific intrinsic PC inhibitor called α1-PDX, as well as cell lines were expression of furin or PC7 has been stably blocked by shRNA. These cells have been tested for their growth, migration and invasion potential in vitro as well as for their growth in vivo as subcutaneous xenografts. Histological analysis of tumor sections, in particular of microvessel density and angiogenesis has been performed to reveal if PC activity correlates with RMS progression. Our results confirm a strong correlation between PCs activity and RMS growth in vivo and suggest furin and PC7 as viable targets for therapeutic intervention and warrant further studies in the development of novel therapeutic approaches based both on specific inhibition of PCs protease activity and on targeted drug delivery by PCs targeting peptides.

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 4332. doi:1538-7445.AM2012-4332
Abstract 4334: Expression of PID1 correlates with PFS in pediatric medulloblastomas and negatively impacts growth of medulloblastoma, glioblastoma and AT/RT brain tumor cell lines
Authors: Erdreich-Epstein Anat , Ren Xiuhai , Zhou Hong , Schur Matthew , Ji Lingyun , Sposto Richard , Asgharzadeh Shahab
Published: August 2012

PID1, discovered in 2006, encodes an adapter protein that contains a phosphotyrosine binding (PTB) domain. Overexpression of PID1 can have inhibitory or proliferative effect, depending on the cell line. In adipocytes and myocytes PID1 inhibits insulin-induced signaling via a yet-unknown mechanism. To date, there are no reports on PID1 effects in cancer. Using quantitative real time RT-PCR of PID1 expression in 78 pediatric medulloblastoma tumors at diagnosis we found that higher PID1 expression correlated with longer progression-free survival (PFS) in multivariate analysis. Similar correlation was found for PID1 variant 1 and variant 2. Interestingly, PID1 was higher in desmoplastic medulloblastomas, which carry better prognosis vs. anaplastic medulloblastomas, which have poorer prognosis. Query of the REMBRANDT database showed that higher PID1 expression was highly correlated with longer overall survival (OS) in gliomas. REMBRANDT also showed that PID1 expression in GBMs (n=228) was 0.47 of the PID1 expression in non-tumor brain (n=28) (p<0.001) and similarly, was lower in GBMs compared to astrocytoma II/III or oligodendroglioma. TCGA similarly showed that PID1 expression in GBM was 0.40 of its expression in non-tumor brain. In tissue culture we found that transient transfection of PID1-tGFP, but not tGFP, inhibited colony formation in GBM (U251, LN229), medulloblastoma (D283MED) and ATRT (CHLA-06-ATRT) cell lines. PID1 expression decreased proliferation (BrdU, 7AAD), increased sub-G0/G1, increased apoptosis (AnnexinV), and increased mitochondrial depolarization (JC1 probe) of GBM, medulloblastoma and/or ATRT cell lines, supporting an inhibitory function for PID1 in these tumors. Studies are currently ongoing into the molecular mechanism that mediates these effects. In summary, our data demonstrate correlation between high PID1 expression and better patient outcome in two different brain tumors: medulloblastomas and gliomas, and inhibitory effect of PID1 in three types of brain tumor cell lines: medulloblastomas, gliomas, and ATRT. This suggests that PID1 may have a functional role in the biology, and possibly in response to therapy, of these three brain tumor types.

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 4334. doi:1538-7445.AM2012-4334
Abstract 4335: The genomic landscape of childhood pre-B acute lymphoblastic leukemia
Authors: Spinella Jean-François , Saillour Virginie , Richer Chantal , Ouimet Manon , Cassart Pauline , Healy Jasmine , Bareke Eric , Larivière Mathieu , St-Onge Pascal , Busche Stephan , Ge Bing , Montpetit Alexandre , Pastinen Tomi , Sinnett Daniel
Published: August 2012

Precursor B-cell acute lymphoblastic leukemia (pre-B ALL) is the most frequent pediatric cancer. Increased understanding of the pathobiology of B-cell ALL has led to risk-targeted treatment regimens and increased survival rates. However, the underlying causes of this pediatric cancer are still unclear. We are using next-generation sequencing technology to better understand the genomic landscape of pre-B ALL and to build a catalogue of variations involved in pediatric ALL onset and/or progression. Using a unique “quartet” design that involves matched tumor (at diagnosis) and normal (remission) samples, as well as DNA from both parents, we will be able to identify somatic mutations driving the leukemic process. Here, we report the deep-sequencing of the whole exomes, and the partial miRNomes, of over 60 childhood B-cell ALL quartets. Using ABI SOLiD technology, we captured over 4.0 Gb of sequence on average per sample with a mean coverage of 40X. Genome-wide genotyping (Illumina's Omni 2.5 array) was also for quality control and structural variant identification. For each individual, approximately 97% of the targeted region was covered α1X and 80% of the targeted bases passed our thresholds for variant calling (≥ 5X coverage, MQV ≤ 20). According to these criteria, about 25,000 SNPs were found per individual. Using this quartet design we were able to incorporate parental sequence information to reduce sequencing errors and facilitate the identification of true variants within a given family, and of leukemia-specific variants within the ALL cohort. We investigated the somatic mutation profiles of the ALL genomes and identified both recurrent and private leukemia-specific mutations, and highlighted genes/pathways with an increased burden of somatic loss of function variants. Our goal now is to validate potential driver mutations that could play a direct role in leukemogenesis through functional assessment. Ultimately, this work will provide invaluable insights to understand the genetic mechanisms underlying pediatric ALL which could lead to the development of powerful clinical tools to improve detection, diagnosis and treatment of this childhood 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 4335. doi:1538-7445.AM2012-4335
Abstract 4345: Inadequate repair of ionizing radiation damage: A consequence of the invasive tumor phenotype
Authors: Pond Erika D. , Sroka Thomas C. , Gard Jaime MC , Pawar Sangita C. , Nagle Raymond B. , Cress Anne E.
Published: August 2012

A major characteristic of the transition of prostatic intraepithelial neoplasia (PIN) to invasive prostate cancer is the progressive loss of laminin 322 in the basal lamina and loss of A6B4 integrin, a laminin 322 adhesion receptor in the basal cells. Previous work from our group reported that the loss of interaction with laminin 322 decreased the ability of normal prostate cells to respond to DNA damage. The defect was manifested as an alteration of an ionizing radiation (IR) induced G2 progression block. In this study, the goal was to determine if an invasive phenotype of human tumor cells, expressing A6B1 integrin, a laminin 511 adhesion receptor, influenced a DNA damage response (DDR) to IR. DU145 tumor cells were grown on laminin 511 and DDR was determined under conditions of stimulated invasion via HGF. The DDR endpoint chosen was the production, resolution and persistence of nuclear H2AX phosphorylation foci as an indicator of damage, repair and inadequate repair, respectively. Similar to a recent report, we observed a fast and transient phosphorylation of H2AX in response to IR within the basal cells of the normal human prostate epithelium that was both dose and time dependent. Utilizing tissue culture conditions, we determined that under optimal growth conditions on laminin 511 there was a dose and time response of H2AX phosphorylation in response to IR treatment. Under conditions of HGF stimulation, the persistence of H2AX foci 24 hours after IR was two to four fold higher as compared to unstimulated cells. The amplified persistence of H2AX foci was observed at 1, 2, 4, 6 and 8 Gy at both 24 and 36 hours after IR treatment. Current studies are determining if the inadequate repair response to IR under conditions of stimulated invasion results in an increased tumor cell killing or an increased genomic instability of surviving tumor cells. (Supported in part by NIH Cancer Center Core Grant CA 23074 and DOD grant W81XWH-10-1-0496)

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 4345. doi:1538-7445.AM2012-4345