bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract LB-269: Genome-wide expression profiling of highly degraded formalin-fixed paraffin-embedded tissue from non-small cell lung carcinoma
Authors: Su Li , Wu I-Chen , Wu Ming-Tsang , Chirieac Lucian R. , Wang Zhaoxi , Christiani David C.
Published: June 2012

Microarray-based genome-wide gene expression analysis on fresh frozen tissue is widely used in cancer studies. Compared to fresh frozen tissues, formalin-fixed paraffin-embedded (FFPE) tissues are more accessible in the clinical setting for genomic analysis, but its use has been hampered by technical difficulty. In this study, we investigated the potential use of the Whole-Genome DASL HT Assay (Illumina, San Diego, CA) for global expression profiling (covering >47,000 annotated transcripts) in 24 tumor/non-affected FFPE tissues obtained by biopsy from patients with non-small cell lung cancer (NSCLC). We obtained high-quality microarray data on 11 FFPE samples (46%). The FFPE samples had a relatively lower median call rate of 12.2% (range: 10–14.5%), as compared with those from fresh samples; ranging from 10% to 25%. Among genes differentially expressed between squamous carcinomas and adjacent non-affected lung tissue, we found that the RECK gene, encoding a tumor suppressor of reversion-inducing cysteine-rich protein with Kazal motifs, was decreased strongly in tumors (fold change: -2.7; p=0.018). This finding was consistent with previous reports that there was a significantly lower expression of RECK mRNA in NSCLC tissue in samples with promoter hypermethylation. During pathway-based analysis using GeneGo database, we found that differentially expressed genes were significantly enriched in several pathways, such as the RAS regulation pathways, epithelial-to-mesenchymal transition pathway, WNT signaling pathway, and signal transduction pathway of lung neoplasms. When comparing expression between adenocarcinoma and squamous NSCLC, the differentially expressed genes were clustered in keratin filaments pathway for cytoskeleton remodeling, WNT signaling pathway, and disease pathways related to bronchial neoplasms and NSCLC. The WNT/PCP signaling pathway has been implicated in human carcinogenesis. MAP3K7 is one of the key signaling molecules of non-canonical WNT pathway, which demonstrated high level expression in lung carcinoma but was not expressed in non-affected pulmonary tissues. Our study demonstrated that DASL expression profiling technology, genome-wide expression profiles can be successfully generated from FFPE lung tissues.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-269. doi:10.1158/1538-7445.AM2011-LB-269
Abstract LB-273: Preclinical assesment of a novel CDC7 inhibitor: Genomewide RNAi screening identifies unique synergetic and resistance genes
Authors: Liu-Sullivan Nancy , Bhinder Bhavneet , Shum David , Ramirez Christina , Radu Constantin , Djaballah Hakim , Frattini Mark G.
Published: June 2012

Despite extensive drug discovery efforts, drug-candidate failure and patients relapsing in the clinic remain as persistent problems. While insufficient drug-gene engagement leads to drug failure, de novo escape mutations give rise to patients relapsing, calling the need for systemic studies on how genes influence drug responsiveness. Towards this end, we have explored a functional short hairpin RNA (shRNA) based genomic screening platform aimed at interrogating drug-gene engagement and assessing its consequences on signaling pathways. We propose this concept as a novel way to evaluate drug candidates prior to clinical trials enabling liability assessment and predicting clinical outcome. We took advantage of the arrayed shRNA library produced in lentiviral particles and characterized by several obvious advantageous features including shRNA targeting one hairpin at a time and on the fly high content whole well microscopy imaging analysis. We carried out three parallel genomewide shRNA screens in the absence or presence of the novel CDC7 kinase inhibitor (MSK-777) at its IC20 and IC50 and have identified several gene candidates that influence MSK-777 sensitivity and resistance. These include synergizers that enhance MSK-777 sensitivity and rescuers that confer MSK-777 resistance. IPA analysis mapped clusters of these hits to multiple major pathways among them were the NF-kB pathway, the ubiquitin-proteasome pathway, DNA replication, and several epigenetic regulatory genes. We will present and discuss this concept together with the emerging pathways as a means to identify both key therapeutic targets and biomarkers of sensitivity and resistance. Thus, allowing for not only a broader applicability of assessing candidate genes that modulate specific drug agents, but also for the identification of a tailored and more efficacious therapeutic regimen to treat cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-273. doi:10.1158/1538-7445.AM2011-LB-273
Abstract LB-277: Dynamic functional analysis of the response of cancer cell lines to the drug UNBS1450
Authors: Bittner Michael L. , Smith Edward , Hua Jianping , Chao Sima , Cypert Milana , Gooden Gerald , Shack Sonsoles , Alla Lalitamba , Cerella Claudia , Diederich Marc , Weitman Steven
Published: June 2012

The analysis of the dynamics of cellular responses to drugs is currently bounded by inherent limitations of the methods most often used to assess levels of promoter activity and protein abundance or activation. The sensitivity of these assays is limited by the averaging of analyte over many cells, which can produce an average that is not accurately descriptive of the wide range of activities of members of the population examined. The ability of these assays to indicate the trajectory of the various responses is limited by a very infrequent sampling rate, frequently 2–4 time points spread over many hours. These limits are further exacerbated by populations of treated cells' inhomogeneity in the timing of their own response to the drugs. To improve the determination of the functional dynamics of cells' responses to drugs, PBS-Bio has developed technology that allows gathering data from living cells using fluorescent reporter technology. This technology allows measurements to be made serially on single populations of cells at the individual cell level, providing both high sensitivity in terms of when even a small fraction of the cells exhibit significant shifts of a particular activity, the rate of shift of cells in the population to this different activity and the ability to temporally order the timing of events relative to each other. Experimentation on two cell lines, A549 and PC3, using a variety of drugs that affect different cellular processes and a set of fluorescent reporters that provide information on a variety of cellular processes it was possible to show that the modified cardenolide drug, UNBS1450 (Unibioscreen), provoked a very early reduction in the expression of the MCL1 and MYC genes, followed by induction of a strong apoptotic response in both cell lines. As loss of MCL1 provoked by other means has been shown to be sufficient to induce apoptosis in both these lines, a very strong case can be made for UNBS1450's ability to provoke Mcl1 protein reduction as the drug's mode of apoptotic induction. This finding would also implicate Mcl1 as a useful biomarker of the possible efficacy of UNBS1450.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-277. doi:10.1158/1538-7445.AM2011-LB-277
Abstract LB-69: Minnesota Ovarian Cancer Alliance
Authors: Gavin Kathleen A.
Published: June 2012

The Minnesota Ovarian Cancer Alliance (MOCA) is a nonprofit organization whose mission is to create awareness regarding early warning signs that may be indicative of ovarian cancer; to develop and promote resources for support, networking and education for women diagnosed with ovarian cancer and their families; to unite and educate individuals, the medical community and organizations to achieve earlier diagnosis, better treatment and a cure for ovarian cancer; and to advance ovarian cancer research toward earlier diagnosis, better treatment, and ultimately, a cure.

MOCA staff and members primarily serve as patient advocates and consumer reviewers to state and national gynecologic oncology research initiatives including the GOG, the Mayo Ovarian SPORE, the DOD, and others. MOCA funds ovarian cancer research, with the average grant award at around $70,000. To date, the organization has awarded $2.6 million to over 40 research projects in the last 10 years. MOCA also provides scholarships to support oncology nurses' attendance at national educational conferences.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-69. doi:10.1158/1538-7445.AM2011-LB-69
Abstract LB-71: Poke, Tweet, Share, Tag: A New Generation of Cancer Advocacy
Authors: Hammersmith Leslie
Published: June 2012

After a diagnosis of cancer, a whole new, lasting identity imprints itself on you, especially if you're still young. Cancer in young adults brings a set of unique issues, including dealing with a delayed diagnosis, having access to clinical trials, finding age-appropriate peer support, feelings of isolation, and finding some kind of balance between survivorship and feeling cured. Encouraging, supporting and educating a generation of young advocates and survivors requires the attention of the medical community and mentoring from experienced advocates. Building credibility within the scientific community is crucial to establishing the influence of a community of survivors typically underrepresented.

Significant challenges exist for the medical community to be effective disseminators of cancer research information to generations 40 years and under. It also takes time for the young advocate to understand the many facets of engagement as a patient advocate. This poster will describe the experiences of a young breast cancer survivor, diagnosed at age 36, as she discovers how becoming an advocate for young women dealing with breast cancer in her community connected her to the science, politics, and ethics of the medical community. Generational expectations combined with professional and cultural differences between the young patient and medical community lead her to find ways to help educate her medical providers, cancer clinics, and fellow patients. The disappointment of finding that many research studies have not considered the issues unique to breast cancer in younger women and the revelation that awareness of breast cancer in women under 40 is minimal inspired her to seek out ways to increase her understanding of the science and improve her understanding of how the medical teams work. This poster will also discuss other opportunities for young advocates to add value to the science of cancer research and its impact on the patient. These opportunities include volunteering as a Patient Advocate with NCCTG through her local Cancer Center, serving as the patient advocate who reviews all research protocols being considered for deployment in her area, seeking out valuable professional development opportunities such as programs through Research Advocacy Network's Research Advocate Institute, and establishing a local affiliate of Young Survival Coalition to link communities of survivors with national resources and education. Through pokes, tweets, tagging, and sharing, she uses media to connect the experience of the young survivor to the science of accelerating progress against cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-71. doi:10.1158/1538-7445.AM2011-LB-71
Abstract LB-72: Advocacy in Action: A Research Advocacy Program with a Multilateral Approach at the Vanderbilt-Ingram Cancer Center
Authors: Hanson Caroline
Published: June 2012

The research advocacy program at Vanderbilt Ingram Cancer Center (VICC) is paving the way as a model for nationally-recognized research advocacy programs. As survivors and caregivers that come from a variety of backgrounds and perspectives, research advocates at VICC are well-equipped to collaborate substantially in the development, oversight and dissemination of cancer research. Our approach is to provide VICC researchers with the “patient perspective”_to help guide and refine research at our institution so it is meaningful and relevant to patients/participants and to improve the credibility of cancer research and clinical trials in the community. This multilateral approach does not discriminate cancer as limited to one organ site or one demographic. Research advocates at VICC participate in a wide variety of advocacy activities. Opportunities to provide the “patient perspective” include attendance at research seminars, research project meetings, conferences and advocate meetings. Advocates also develop and deliver research advocacy presentations and participate/collaborate with other VICC and community programs, as well as the National Cancer Institute to facilitate academic/advocacy partnerships. To help guide research at VICC to ensure it is meaningful and relevant to patient/participants, advocates review and provide input on research development, design, clinical trials and informed consent. Advocates also develop patient oriented resources and tools for clinical trials, as well as serve as grant reviewers. To improve the credibility of cancer research and clinical trials in our community, advocates collaborate with local, regional and national organizations to facilitate advocacy participation and develop educational programs for the community to promote awareness of cancer research in clinical trials. One example is a novel educational outreach program entitled, “Mythbusters: Cancer Research in Jeopardy,” that aims to dispel common myths associated with cancer research and clinical trials. The research advocacy program at VICC uses a strategy to educate the community using an interactive program significantly increases knowledge. This interactive approach, as well as more traditional methods, allows our research advocates to take an active role in the direction of cancer research and treatment, and to tackle the important task of bridging the gaps between cancer researchers, survivors, caregivers and the community.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-72. doi:10.1158/1538-7445.AM2011-LB-72
Abstract SY16-03: Dose matters and angiogenesis
Authors: Hodivala-Dilke Kairbaan M.
Published: June 2012

Focal adhesion kinase (FAK) is a cytoplasmic tyrosine kinase that plays a fundamental role in integrin and growth factor mediated signaling and is an important player in cell migration and proliferation, processes vital for angiogenesis. However, the role of FAK in adult pathological angiogenesis is unknown. We have generated endothelial-specific tamoxifen-inducible FAK knockout mice by crossing FAK-floxed (FAKfl/fl) mice with the Pdgfb-iCreER mice. Tamoxifen-treatment of Pdgfb-iCreER;FAKfl/fl mice results in FAK deletion in adult endothelial cells (EC) without any adverse effects. Importantly however, endothelial FAK-deletion in adult mice inhibited tumor growth and reduced tumor angiogenesis. Furthermore, in in vivo angiogenic assays FAK-deletion impairs vascular endothelial growth factor (VEGF)-induced neovascularization. In addition, in vitro deletion of FAK in ECs resulted in reduced VEGF-stimulated AKT phosphorylation, and correlating reduced cellular proliferation and increased cell death. Our data suggest that FAK is required for adult pathological angiogenesis and validates FAK as a possible target for antiangiogenic therapies. In a follow up study we are testing the effects of reduced, as apposed to null, levels of FAK on tumor angiogenesis and will be reporting on that at the meeting.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr SY16-03. doi:10.1158/1538-7445.AM2011-SY16-03
Abstract SY29-02: Pathway analysis of cancer GWAS data using ALIGATOR
Authors: Holmans Peter
Published: June 2012

Although genome-wide studies of complex traits have had some success, there have as yet been relatively few robustly replicated associations, and the effect sizes associated with individual genes tend to be small. One explanation for the small effect sizes observed in complex traits is allelic heterogeneity – that is, affected individuals may possess disease susceptibility alleles in different genes. If the susceptibility genes act together in a biological pathway, then a joint analysis of the set of genes in that pathway may increase power to detect association, and improve reproducibility across studies.

The statistical issues involved in pathway analyses of genome-wide association data will be discussed, including the selection of pathways to be analysed, multiple testing correction for multiple nonindependent pathways, allowing for variable gene size and correlated observations within and between genes. Often, individual genotype data is not available, so the performance of methods that use summary data, such as ALIGATOR (Holmans et al. 2009) is of interest. As a practical illustration of the utility of pathway analysis methods, ALIGATOR results from genome-wide association studies of a number of publicly available cancer datasets, including breast, prostate, and lung cancer, will be presented. These will be used to identify pathways common across different cancers, and those that differentiate between them.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr SY29-02. doi:10.1158/1538-7445.AM2011-SY29-02
Abstract SY30-01: Metastasis mediated by lysyl oxidases
Authors: Erler Janine T.
Published: June 2012

Metastasis is responsible for over 90% of cancer patient deaths. Understanding the molecular processes that enable tumor cells to metastasize is key to understanding how best to prevent and treat metastases in cancer patients. Metastasis is a complex, multistep process driven by the tumor microenvironment. Two potent driving forces are hypoxia (low oxygen) and increased matrix stiffness. These are common features of aggressive solid tumors, and are clinically associated with metastasis and decreased survival of cancer patients. Both hypoxia and stiffness have been shown to greatly enhance the invasive and metastatic potential of cancer cells. We have identified two key mediator molecules, lysyl oxidase (LOX) and lysyl oxidase-like 2 (LOXL2). These are hypoxia-induced secreted enzymes that increase matrix stiffness through mediating the crosslinking of collagens and elastin in the extracellular matrix. We have investigated their role in metastasis using a variety of in vitro and in vivo models.

We showed that LOX expression is clinically correlated with hypoxia, metastasis and poor patient survival. Furthermore, inhibition of LOX through genetic, chemical or antibody means significantly reduces invasion and metastasis in several in vivo models of solid tumor metastasis. LOX enhances invasion through increasing matrix stiffness, thereby activating integrins, Src and FAK. LOX additionally enhances formation of distant metastases by playing a role in formation of premetastatic niches through recruitment of CD11b+ cells, which greatly enable metastatic colonization.

We have also investigated the role of LOXL2 in breast cancer metastasis and normal mammary tissue function. Like LOX, LOXL2 is clinically correlated with metastasis and poor patient survival. LOXL2 enhances invasion through regulation of matrix remodeling. Inhibition of LOXL2 through genetic, chemical or antibody means prevents invasion and metastatic dissemination in vivo. We further show that LOXL2 activity is highest during normal mammary gland involution, consistent with its role in matrix remodeling.

These findings provide insight into metastasis mediated by the tumor microenvironment and demonstrate preclinical effectiveness of anti-LOX/LOXL2 therapy, which may have important clinical implications.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr SY30-01. doi:10.1158/1538-7445.AM2011-SY30-01
Abstract A25: CK 5/6 and EMT-markers as poor prognostic factors in breast cancer patients
Authors: Ahrends Tomasz , Markiewicz Aleksandra , Nowialis Paweł , ska Barbara Seroczy , Skokowski Jarosław , Szade Jolanta , kiewicz Marzena Wełnikca-Ja , aczek Anna
Published: June 2012

Introduction: Cytokeratins 5/6 are expressed in basal layer of breast epithelium and are considered as markers of poor prognosis in breast cancer patients. It was also shown that tumors expressing basal markers often present phenotypical changes connected with epithelial-to-mesenchymal transition (EMT), like vimentin expression and E-cadherin loss. The aim of this study was to evaluate the expression of master regulators of EMT - TWIST, SNAIL and SLUG in breast cancer samples and correlate it with expression of CK 5/6 and markers of EMT - E-cadherin and vimentin.

Materials and Methods: Fresh-frozen and FFPE tumor samples from 136 consecutive, stage l-III breast cancer patients were examined. Expression of TWIST, SNAIL and SLUG in frozen tissues was measured by RT-qPCR method using ΔΔCt approach. Expression of CK 5/6, E-cadherin and vimentin was analyzed in FFPE material with a use of immunohistochemical staining of tissue microarrays (TMA-IHC). Based on the median gene expression level or intensity of the IHC staining samples were classified as positive or negative for a particular marker. Results were correlated with clinicopathological data of the patients and their outcome.

Results: CK 5/6 staining was positive in 19 (11.3%) of the samples and correlated positively with presence of EMT phenotype (0.00027, χ2 test), with 58% and 19.5% of EMT-positive samples in CK5/6 positive and negative subgroup, respectively. Moreover, elevated expression of SNAIL mRNA was detected more often in CK 5/6 positive than in negative samples (89% vs. 51 %, p=0.032, Fisher's exact test). Elevated expression of TWIST (p=0.05, Fisher's exact test) and SNAIL (p=0.003, Fisher's exact test) genes was found in tumors with EMT phenotype. No correlation was found between TWIST, SNAIL, SLUG protein levels as well as SLUG gene expression and EMT phenotype. Expression of CK 5/6 was associated with decreased DFS (p = 0.00044, log-rank test) and OS (p = 0.00001, log-rank test), while occurrence of EMT phenotype with worse OS (p=0.01, log-rank test)

Conclusions: CK 5/6 was found to be a marker of poor prognosis in terms of DFS and OS in the whole studied group of patients. EMT phenotype and SNAIL gene overexpression were more frequent in CK 5/6-positive tumors, which suggests a link between basal phenotype of the tumors and their predisposition to undergo EMT process. As EMT is thought to confer aggressive behavior of the tumor, this correlation might explain the observed negative impact of CK5/6 positive tumors on patients' survival.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr A25.
Abstract A50: Loss of pVHL inactivates p53 by permission of interaction between p14/ARF and progerin
Authors: Lee Su-Jin , Jung Youn-Sang , Lee Sun-Hye , Chung Ji-Yun , Park Bum-Joon
Published: June 2012

Renal cell carcinoma (RCC) is a common primary renal malignancy in adults. The typical feature is the nuclear irregularity which is a basis for grading. Moreover, resistance to chemotherapy and irradiation (IR) is also one of the characters of RCC. p53 inactivation without genetic mutation and pVHL mutation in early stage are shown in RCC. However, it is still remained the question about the mechanism of the nuclear deformation and chemotherapy resistance. Here we proposed that the effect of progerin on RCC. Progerin elevated in RCC and the elimination of progerin could ameliorate the nuclear morphology. Moreover, knockdown of progerin could recover DNA damage sensitivity and p53 activation in RCC. Loss of pVHL induces elevated progerin expression, which inhibit p14/ARF by direct interaction to suppress p53 activity. Moreover, forced enhancement of progerin is found in human leukemia sample. In this study, we provide that the novel mechanism for p53 suppression in RCC and the importance of progerin in cancer progression.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr A50.
Abstract A58: Wnt signaling pathway components are associated with telomerase activity in breast cancer
Authors: Listerman Imke , Gazzaniga Francesca S. , Heiser Laura M. , Lukas Jason J. , Goldstein Ted , Haussler David , Gray Joe W. , Blackburn Elizabeth H.
Published: June 2012

Telomerase is a ribonucleoprotein complex that adds TTAGGG repeats to telomeres in a highly regulated fashion. Telomerase activity is absent in normal somatic cells, thus limiting their number of cell divisions due to telomere shortening. In contrast, the large majority of tumor cells upregulate telomerase activity, consistent with their ability to maintain stable telomere lengths and to divide indefinitely. Telomerase activity is detectable in over 90% of breast tumors, and it is well established that telomerase overexpression is an important step in the progression of normal epithelium to invasive breast cancer. In addition to telomerase upregulation, deregulation of various signaling pathways promotes tumor progression and metastasis. To better understand in which cellular pathway telomerase and telomeres are involved, we comprehensively quantified telomerase activity and telomere length in a panel of 52 extensively characterized breast cancer cell lines and correlated these metrics with the expression profiles of the cell lines. Across the entire panel of breast cancer cell lines, expression of 530 genes was significantly correlated with telomerase activity (FDR-corrected p-val < 0.2), while expression of 585 genes was significantly correlated with telomere length. Secondary G0-term analysis revealed that telomere length was significantly associated with genes involved in Alzheimer's disease, apoptosis regulation and negative regulation of transcription. Genes significantly correlated with telomerase activity were associated with apoptosis regulation, DNA repair, nucleotide metabolism and Wnt signaling. Several Wnt target genes, including MYC, KLF5, and FGF18 were also correlated with telomerase activity. We also used the network analysis tool PARADIGM (1) to identify cellular pathways associated with telomerase activity and telomere length. Notably, Wnt signaling components were significantly correlated with telomerase activity. Given the recent evidence that the telomerase component TERT can act as a transcriptional modulator of the Wnt/beta-catenin signaling pathway (2), we are currently testing how Wnt signaling is altered due to telomerase perturbation in breast cancer cells.

(1) Vaske, C. J. et al. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics 2010; 26:i237–245

(2) Park, J. I. et al. Telomerase modulates Wnt signaling by association with target gene chromatin. Nature 2009; 460:66–72

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr A58.
Abstract A61: 14-3-3gamma transforming ability is determined by a motif outside the conserved phosphoamio-acid binding domain
Authors: Radhakrishnan Vijayababu M. , Putnam Charles W. , Martinez Jesse D.
Published: June 2012

The 14-3-3 proteins are a set of seven highly conserved scaffolding proteins that have been implicated as having a role in human tumorigenesis. However, despite the striking similarity of amino acid sequences and structures of the eukaryotic 14-3-3 family of proteins, there is increasing evidence that the seven human isoforms manifest disparate functions. For instance 14-3-3gamma functions as an oncogene and 14-3-3sigma acts as a tumor suppressor. To gain insight into how specific functions are manifested we constructed chimeric proteins by swaping various regions between gamma and sigma. Chimeric proteins were then utilized in NIH3T3 cell transformation assays. We found that transforming ability was associated with a small variable 40 amino acid region in the N-terminus of the gamma protein and that the transforming ability of gamma was dominant to the tumor suppressor activity of sigma. Importantly, the transforming motif was located outside the conserved 14-3-3 phosphoamino acid binding motif. Hence, transforming ability of 14-3-3 proteins is determined by a variable region that does not involve the phosphoamino acid binding site.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr A61.
Abstract B10: Germline copy number variation in Li-Fraumeni syndrome patients with TP53 mutations
Authors: Silva Amanda G.S. , Achatz Maria Isabel W. , Brentani Ricardo , Krepischi Ana Cristina V. , Rosenberg Carla
Published: June 2012

Li-Fraumeni syndrome (LFS) is an autosomal dominantly inherited disorder characterized by a remarkably increased risk of early-onset and multiple cancers, including breast, brain tumors and other neoplasms in individuals carrying germline TP53 mutations. The specific presence of constitutional copy number variation of large DNA segments (CNV) in LFS individuals may either represent a cancer susceptibility factor or result from a genetic instability. We used a 180K oligoarray platform from Agilent to estimate the CNV frequencies in 21 unrelated Li-Fraumeni patients carrying TP53 mutations. We compared the resulting frequencies between these individuals (n=21) to a population based control group (n=100), and defined as “rare genomic alterations” those located in coding regions and covered by ≤3 individual CNVs described in DGV (Database of Genomic Variants). Similar frequencies of CNVs were found in both patients and control groups with an average of 7–8 CNVs per genome. Rare CNVs were significantly more frequent among cancer patients (average of 0.8 per individual) than among controls (average of 0.3 per individual) (p<0.0001). Some of the genes encompassed by the rare germline CNVs from Li-Fraumeni patients have been previously reported to be altered in tumors, but are here described for the first time as altered in germline.

Funding by Fapesp and CNPq.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr B10.
Abstract B16: Tumor suppressive functions by ATF2/7 transcription factors in a cMyc-driven B-cell lymphoma model
Authors: Walczvnski Jacek , Jones Nic , Breitwieser Wolfgang
Published: June 2012

ATF2 and the highly homologous ATF7 are members of the AP-1 transcription factor family which regulate expression of genes involved in development and stress response. In cancer, ATF2 has been reported to function both as a tumor suppressor and tumor promoter. The aim of the project was to investigate the possible roles of ATF2/7 in cMyc-driven B-cell lymphoma development and to characterize their interaction with the cMyc oncogene. Previously, cMyc, which is frequently deregulated in Burkitt's lymphoma (Rabbitts et al, 1984), was shown to prolong the half-life and induce phosphorylation of ATF2 (Miethe et al, 2001). In addition, the MAP kinase JNK and its substrate ATF2 are frequently found upregulated in B-cell lymphomas (Kersten et al, 2004; Gururajan et al, 2005).

We established a mouse B-cell lymphoma model by crossing B-cell specific knockouts of Atf2/7 (Atf2ΔBC, Atf7−/−) with Eμ-Myc transgenic animals. Eμ-Myc mice express the cMyc proto-oncogene driven by the immunoglobulin heavy chain enhancer (Eμ) and develop B-cell lymphomas with high frequency. We compared timing of tumor onset between Eμ-myc, Atf2ΔBC, Atf7−/− Eμ-myc, Atf2ΔBC/+, Atf7−/−, and Eμ-myc, Atf7−/−. In addition, we derived cell lines fom Eμ-Myc-driven lymphomas and characterized growth, apoptosis, and drug sensitivity in the presence or absence of functional Atf2/7.

Atf2 and its phosphorylated (activated) form were found to be upregulated in cells obtained from tumor samples from Eμ-Myc mice in comparison to normal B lymphocytes. Analysis of tumor-free survival showed that Eμ-myc, AtfΔBC, Atf7−/− develop B-cell lymphomas at significantly faster rates than controls. In vitro deletion of Atf2 in cell lines derived from cMyc-driven lymphomas resulted in a marked reduction in the basal levels of apoptosis. Furthermore, Atf2/7-deficient Eμ-myc tumor cells were significantly more resistant to genotoxic stress (e.g., doxorubicin) induced apoptosis. Gene expression analysis identified proapoptotic members of the Bcl-2 family as possible transcriptional targets of Atf2.

In this study, we show a novel tumor suppressive role of ATF2 in cMyc-induced lymphomagenesis and suggest the potential functions of ATF2 in regulating programmed cell death. The results also imply that the evaluation of levels of activated ATF2 in clinical samples of B-cell lymphoma may give an indication of their sensitivity to chemotherapeutic agents.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr B16.
Abstract B42: Structure-activity study of tubulin precipitation by thiol-reactive compounds
Authors: Mi Lixin , Chung Fung-Lung
Published: June 2012

Tubulin, a major constituent of microtubules, has been established as an important chemotherapeutic target. Its expression is tightly regulated at the transcriptional level and not affected by tubulin targeting agents including taxanes and vinca alkaloids. Recently, we reported that benzyl isothiocyanate (BITC) and phenethyl isothiocyanate (PEITC), two isothiocyanates (ITCs) derived from cruciferous vegetables, induce rapid and significant precipitation and degradation of both α- and β-, but not γ-, tubulin at 10 μM through covalent binding to cysteine residues. In contrast, sulforaphane and erucin, two hydrophilic ITCs, and N-methylphenethylamine, an analog of PEITC without electrophilic functional group, show no activity as well as little downstream effects such as cell cycle arrest at mitosis and apoptosis induction at the same concentration. Because ITC are electrophiles, these findings suggest that thiol-reactivity may be the triggering event, the structure of compounds is associated with its activity, and tubulin precipitation and degradation are biologically important. In this study, we report that other thiol-reactive compounds, such as N-benzylmaleimide, phenylarsine oxide, and phenylmercuric chloride, also induce significant tubulin precipitation. They were much more potent than their hydrophilic counterparts, such as N-maleoyl-beta-alanine, arsenic oxide, and mercury chloride. These results shed lights onto structure-activity relationships. More importantly, their potencies of precipitating tubulin correlate well with not only their affinity to tubulin cysteines but also induction of G2/M phase arrest and apoptosis in human lung cancer cells A549. The results support the notion that cysteine modification is an upstream event for tubulin instability and cytotoxicity. The study presents critical knowledge on the rational design and screening of thiol-reactive compounds targeting the stability of tubulin.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr B42.
Abstract B53: Evaluation of HIF-1α mRNA inhibitor as antimultiple myeloma agent
Authors: Borsi Enrica , Perrone Giulia , Terragna Carolina , Durante Sandra , Martello Marina , Baccarani Michele , Cavo Michele
Published: June 2012

Hypoxia-inducible factor-1 alpha (HIF-1α) is a transcription factor that plays a critical role in survival and angiogenesis. In solid tumors, elevated expression of HIF-1α, in response to hypoxia or activation of growth factor pathways, is associated with tumor proliferation, metastasis, and drug resistance and correlated with poor prognosis. In contrast to solid tumours, the role of HIF-1α in hematological malignancies is not completely known. In particular in multiple myeloma (MM) HIF-1α has been suggested to be constitutively expressed and HIF-1α knockdown cell lines have shown higher sensitivity to standard chemotherapy, suggesting a role in the pathophysiology of MM. In the present study, we explored the effect of EZN2968, an antisense oligonucleotide against HIF-1α, as a molecular target in MM.

We showed that the expression of HIF-1α in several MM cell lines is detectable in either normoxia or hypoxia conditions and is increased in the presence of growth stimuli (IL-6 and stroma cells). In vitro, EZN2968 induced selective and stable down-modulation of HIF-1α mRNA and protein expression, either in normoxia or hypoxia conditions. Immunofluorescence analysis confirmed the reduction of the protein after 24 hours of treatment, as well as a lower expression of VEGF.

Clinically achievable doses of EZN2968 induced cell cycle arrest and cell death (10% to 60% of apoptotic cells compared to the controls after 24 to 96 hours, respectively) in MM cell lines. The activation of the apoptotic pathway was confirmed by western blot analysis at different time points. Moreover we observed an irreversible commitment to cell death after 48 hours of exposure. To evaluate the effect of microenvironment, MM cells treated with EZN2968 were exposed to IL-6 and stroma cells for additional 24 hours. EZN2968 overcame the proliferative effect induced by cytokines. EZN2968 showed moderate increase in efficacy in combination with conventional agents such as Melphalan, and immunomodulatory agents (Thalidomide and Lenalidomide).

No significant effect on cell viability was observed on peripheral blood mononuclear cells and CD34+ cells from healthy donors treated with increasing doses of EZN2968.

Evaluation of gene expression profiling modulation induced by EZN 2968 is ongoing.

Our data suggest that HIF-1α inhibitor is an attractive therapeutic target for MM patients and provide the rationale for clinical evaluation of HIF inhibitor in combination with currently used MM agents.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr B53.
Abstract B58: Differential mechanisms control steady state expression of breast cancer antiestrogen resistance 3 (BCAR3) in non-invasive and invasive breast cancer cell lines
Authors: Guerrero Michael , Bouton Amy H.
Published: June 2012

The overexpression of breast cancer antiestrogen resistance 3 (BCAR3) has been shown to reduce the antagonistic effects of tamoxifen and fulvestrant in estrogen receptor positive (ER+) breast cancer cell lines. BCAR3 also has a role in the regulation of the migratory and invasive potential of both ER+ and ER- breast cancer cells. A tight correlation between BCAR3 expression and breast cancer cell phenotype exists such that non-invasive, early stage cells express very low levels whereas more invasive, mesenchymal-like cells express very high levels of BCAR3. Because of this correlation, it is important to understand the temporal and spatial regulation of BCAR3. In this study, we set out to define potential mechanisms that regulate BCAR3 expression to better understand, predict, and reverse the consequences of elevated expression. In MCF7 and T47D cells (non-invasive, early stage ER+), high plating density coincident with abundant cell-cell junctions resulted in low levels of both BCAR3 mRNA and protein. Conversely, BCAR3 expression was found to be elevated under conditions in which cell-cell junctions were reduced (low density plating). In the more invasive BT549 and MDA-MB-231 cell lines, BCAR3 mRNA and protein expression was found to be dependent upon the stable expression of its binding partner p130Cas (Cas). Interestingly, we previously showed that BCAR3 expression positively correlates with the tyrosine phosphorylation state of Cas, activation of the tyrosine kinase c-Src, and the physical interaction between Cas and c-Src. We are currently investigating whether cell-cell junction formation and differential expression alters the subcellular localization of BCAR3. Taken together, we propose a role for BCAR3 in driving the transition from localized disease to a more invasive and aggressive breast tumor phenotype.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr B58.
Abstract B61: HEF1-dependent Aurora A kinase phosphorylation activates HDAC6
Authors: Kozyreva Varvara K. , McLaughlin Sarah L. , Kelley Laura , Pugacheva Elena N.
Published: June 2012

Histone deacetylase 6 (HDAC6) is known to be important participant of many tumorgenesis processes including cytoskeleton rearrangement, cell migration and invasion. Activation of HDAC6 promotes cell motility and proteolytic degradation of the extracellular matrix which thereby facilitates invasion and metastasis of cancer cells. But precise mechanisms of HDAC6 regulation are still unknown. Human enhancer of filamentation 1 (HEF1/Cas-L/Nedd9) is scaffolding protein implicated in essential normal cell functions like cell division as well as pathologic conditions such as in cancer progression. It has been shown that HEF1 is over-expressed in multiple tumor types and is well known marker of malignancy. HEF1 possesses a key role in cancer development by acting as a signaling hub to coordinate tumor associated signaling. Among numerous targets which are regulated by HEF1 one of the most important is Aurora A kinase (AurA). It is known that up-regulation of AurA launches a cascade of reactions promoting oncogenic cell transformation. In our experiments, we demonstrated that HEF1 knockdown leads to impairment of cell capability to invade into extracellular matrix. We hypothesize that invasion deficiency in HEF1 depleted cells is directly linked to inability of AurA to phosphorylate/activate HDAC6. We have shown previously that depletion of HEF1 decreases AurA activity and demonstrated that HDAC6 is a substrate of AurA kinase. In this work we have determined AurA phosphorylation sites in HDAC6 using site-directed mutagenesis and in vitro kinase assay with wild-type HDAC6 and HDAC6 phospho-mutants. We revealed that AurA phosphorylates HDAC6 at Ser479/Thr481. We will test the effect of this AurA phosphorylation event on HDAC6 activation. Biological effect of such regulation will be explored in breast cancer cell lines. Our observation allows us to establish a mechanistic pathway that describes the convergent roles of HDAC6, AurA and HEF1 in tumor progression.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr B61.
Abstract C10: Complete genome sequencing of complex tumors and matched normals results in sensitive detection of somatic events
Authors: Jacobs Sharoni , Baccash Jonathon , Ghosh Srinka , Nilsen Geoff , Pant Krishna
Published: June 2012

For a comprehensive understanding of the tumor genome, it is important to identify all somatic event types: point mutations, small insertions and deletions, copy number aberrations, translocations, inversions, gene fusions, and more. Complete genome sequencing and analysis of paired tumor and normal samples yields a comprehensive view of the mutational landscape in the tumor. An integrated pipeline for the sequencing, computational analysis and annotation of complete human cancer genomes has been developed. Sequencing is performed on Complete Genomics DNA nanoarrays using a nonsequential, unchained read technology to generate 70base-pair paired end reads. Assembly, mapping, and variation calling are performed using methods that have recently been optimized for more sensitive detection of variants of low allelic fraction, as would occur in heterogeneous and/or aneuploid tumor genomes. Algorithmic enhancements designed to accommodate non-diploid genomes result in increased call rates and higher accuracy. Higher coverage levels also help to reduce error rates and improve the sensitivity of somatic variation detection. Approaches adopted to ensure a highly accurate and sensitive representation of tumor genomes will be presented.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr C10.