bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2198: Exome and transcriptome sequencing of human tumors and tumor-derived cell lines
Authors: Nickerson Michael L. , McGee Kate , Gold Bert , Lawley Cindy , Tran Bao , Stewart Claudia , Harkins Tim , Waldman Fred , Zbar Berton , Moore Lee , Dean Mike
Published: February 2011

Insight into the cancer genome has recently increased in an unprecedented way due to high throughput (HT) sequencing technology to examine the genome, exome, and transcriptome. We sought new genetic biomarkers for cancer by using HT sequencing to examine highly characterized primary sporadic tumors and tumor-derived cell lines. Several tumors/cell lines represented the most common subtype of kidney cancer, clear cell renal cell carcinoma, as well as NCI-60 panel cell lines from breast (MCF7) and prostate (PC3). Incorporation of NCI-60 panel cell lines was advantageous due to extensive prior characterization of these reagents, including gene expression, comparative genome hybridization, SNPs, and drug cytotoxicity. The study was performed using three major platforms (454, Illumina, ABI) to compare sequencing quality, cost, quantity, and computational amenability. Different methodologies were examined including exome, transcriptome, and whole genome sequencing. Alignment of sequence to a consensus genome (hg 18) allowed identification of novel and previously documented genomic variants. Various filters were implemented to sort the large number of variants detected, including dbSNP, personal genome variants, and 1000 genomes data. An average of 65 million 35-50 base pair sequences were generated from transcriptomes of two primary clear cell RCC tumors. Over 2 million 375 base pair sequences were generated from each of four cell line exomes. Differences were observed in extent and depth of coverage of a given target region by various experimental approaches. SNP array genotyping showed 1% discordance with sequencing. Previously characterized mutations were confirmed in HT sequences. We identified multiple regions of homozygosity at an unprecedented resolution. For example, in the clear cell renal cancer cell line, 786-0, a known mutation in VHL (311delG) was identified, and LOH at SNP positions across the entire length of chromosome 3 was confirmed.

Alignment to a reference genome (hg 18) permitted identification of 2583-5307 genomic sequence variants, including 92-297 novel non-synonymous variants in the exomes of each cell line. Variants include frameshift and nonsense mutations. Novel non-synonymous variants were identified in cancer-related genes and these are being examined in additional tumors. Potential functions of newly identified mutated genetic loci suggest perturbation of signaling pathways and are candidates for targeted therapy.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2198.
Abstract 2206: Distinct somatic mutation patterns in multiple human cancers and their subtypes
Authors: Kan Zhengyan , Stinson Jeremy , Bhatt Deeplai , Kaminker Joshua , Stern Howard , Faham Malek , Seshagiri Somasekar
Published: February 2011

We have systematic analyzed 4.5Mb of DNA representing 1507 genes in 450 human fresh frozen tumors covering four major human cancers and their subtypes for somatic mutations. For this analysis we used E. coli mismatch repair detection (MRD) for our primary mutation scans. All the identified variations were validated as somatic using nucleic acid mass spec and confirmed to be present in the original tumor and absent in the matched adjacent normal DNA. Of the all tumor samples analyzed ∼80% show somatic mutations in one or more genes studies. Of the genes analyzed we identified mutation in 842 genes. Applying statistical techniques and other measures we have identified 221 genes to be significantly mutated across all cancers studied. Further analysis of mutated genes by tumor types and subtypes revealed distinct patterns of significantly mutated genes. Besides the previously known mutated genes, we have identified several novel mutated genes with previously unknown role in cancers across the various cancer types studied. To further ascertain the relevance we have performed integrated analysis of mutation and copy number variations data from the samples studied and identified putative tumor supressors and oncogenes. Also, we have performed mutational analysis at the level of biological pathways and identified several mutated pathways.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2206.
Abstract 2209: Integrative analysis of DNA copy number and gene expression in metastatic tumor cells from oral squamous cell carcinoma for the identification of genes associated with survival
Authors: Xu Chang , Liu Yan , Wang Pei , Fan Wenhong , Rue Tessa C. , Upton Melissa P. , Houck John R. , Lohavanichbutr Pawadee , Doody David R. , Futran Neal D. , Zhao Lue P. , Schwartz Stephen M. , Chen Chu , Méndez Eduardo
Published: February 2011

To examine the impact of copy number aberrations (CNA) on gene expression in oral squamous cell carcinoma (OSCC) metastasis, we used Affymetrix 250K Nsp single nucleotide polymorphism arrays and U133 Plus 2.0 expression arrays, respectively, to interrogate the DNA and RNA from metastatic OSCC cells isolated using laser capture microdissection from lymph nodes of 20 patients. Overall, CNA accounted for expression changes in about 30% of the transcripts studied. With a false discovery rate < 1%, 530 transcripts (461 genes) were identified as to have significantly correlated CNA and expression. When tested using an independent dataset with expression profiles for 148 primary OSCC and 45 normal oral mucosa, the genes were enriched with candidates associated with OSCC (vs. normal oral mucosa) (n=174 transcripts differentially expressed) and OSCC-specific survival (n=32 transcripts associated), as compared to a random gene set of the same size (p < 0.001). We then fit two Cox models using the first two principal components derived from these two gene sets (‘174-transcript PCA’ or ‘32-transcript PCA’), and two other models that combined stage with either the 174- or the 32-transcript PCA score. The Area Under the Curve (AUC) for a model combining stage with 174-gene PCA was significantly higher than that for a model with stage alone (AUC=0.80 vs. 0.72, p = 0.042). Further investigation is warranted to confirm these findings and to examine the biologic role of these copy number-associated transcripts in OSCC metastasis and their potential as therapeutic targets.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2209.
Abstract 221: C6-ceramide sensitizes the aggressive L3-6 pancreatic cancer cell line to paclitaxel-mediated antitumor effects in vivo and in vitro
Authors: Cao Cong , Bowen Wayne , Wanebo Harold , Wan Yansheung , Ji Fran , Lu Su , Shrayer David
Published: February 2011

Key words: C6 Ceramide, Taxol, Gemcitabine, AMPK, AKT/mTOR, chemotherapy, pancreatic cancer

Background: Survival after therapy of pancreatic cancer is about <5% with a strong need for new chemotherapy enhancing strategies. Our previous in vivo studies have demonstrated that C6 Ceramide has synergistic anti tumor effects on agents (Taxol, Oxaliplatin, Gemcitabine) against the aggressive pancreatic cancer cell line L3.6 in scid mice. The molecular mechanisms of this synergistic effect are our current focus.

Methods: The synergistic effects of C6 ceramide on Paclitaxel and Gemcitabine were studied both in vivo (by monitoring survival, tumor size, tumor growth rate, in heterografted L3-6 pancreatic cancer cells in scid mice) and in vitro (by MTT assay and apoptosis assays-(Caspase dependent/independent), and Western blot assays of signal transduction pathways to determine molecular mechanisms involved in the C6 Ceramide synergistic effects.

Results: In vivo and in vitro data confirmed significant C6 Ceramide synergistic enhancement of Paclitaxel (P) and Gemcitabine (G) in the L3-6 model. Basic findings: Paclitaxel alone activates pro-survival pathway PI3K/AKT/mTOR in L3.6 cells. C6 ceramide induces pharmacological and genetic inhibition of the PI3K/AKT/mTOR pathway sensitizing L3.6 cells to Paclitaxel induced cell death and apoptosis. C6 Ceramide also dramatically enhanced Paclitaxel induced AMPK activation, a key energy switch enzyme that is responsible for cell apoptosis in stress. PI3K/AKT/mTOR inhibition and AMPK induction may be major mechanisms of C6 synergistic effect on paclitaxel induced cell death. We also found that C6 Ceramide also promotes Paclitaxel induced activation of the mitochondrial mediated apoptosis pathway sensitizing L3.6 to chemotherapeutic induced cell death.

Conclusion: Our data suggests that combining C6 Ceramide with traditional chemotherapy drugs illustrated by paclitaxel may have potential as a new biologic therapeutic intervention against pancreatic cancer and merits continued study.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 221.
Abstract 2210: Quantification of the relative amount of mouse and human DNA in cancer xenografts using species-specific gene length variations
Authors: Lin Ming-Tseh , Tseng Li-Hui , Kamiyama Hirohiko , Kamiyama Mihoko , Lim Phillip , Wheelan Sarah , Eshleman James
Published: February 2011

Human cancer cell lines and xenografts are valuable samples for whole-genome sequencing of human cancer. Tumors can be maintained by serial xenografting in athymic (nude) or severe combined immunodeficient (SCID) mice. Critical to next generation based sequencing is the relative proportions of human and mouse DNA. In the current study, we developed a molecular assay to quantify the relative contributions of human and mouse in mixed DNA samples. The assay was designed based on deletion/insertion variation between human and mouse genomes. The percentage of mouse DNA was calculated according to the relative peak heights of PCR products analyzed by capillary electrophoresis. Three markers from chromosomes 9 and 10 accurately predicted the mouse genome ratio and were combined into a multiplex PCR reaction. We used the assay to quantify the relative DNA amounts of 93 mouse xenografts used for a recently reported integrated genomic analysis of human pancreatic cancer. Of the 93 xenografts, the mean % of contaminating mouse DNA was 47%, ranging from 17% to 73%, with 43% of samples having greater than 50% mouse DNA. We then comprehensively compared the human and mouse genomes to identify 370 additional candidate gene loci demonstrating human-mouse length variation. With increasing use of whole genome sequencing of human cancers, this assay should be useful to monitor strategies to enrich human cancer cells from mixed human-mouse cell xenografts.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2210.
Abstract 2211: Array-comparative genomic hybridization identifies important recurrent copy number alterations in non-small cell lung cancer
Authors: Sriram Bajee K. , Larsen Jill E. , Francis Santiyagu M. Savarimuthu , Wright Casey M. , Clarke Belinda E. , Duhig Edwina E. , N Hayward K. , Bowman Rayleen V. , Yang Ian A. , Fong Kwun M.
Published: February 2011

Comprehensive knowledge of the genomic aberrations involved in NSCLC may deliver improved therapies, diagnostic and prognostic biomarkers. Recurrent copy number alterations (CNA) found in the same locus across a set of tumour samples are assumed to be the site of “driver” cancer genes. We hypothesize that whole genome array comparative genomic hybridization (aCGH) will identify recurrent regions of gains and loss in NSCLC containing candidate “driver” genes. Methods: DNA from fresh-frozen tumor tissue of 133 NSCLCs were obtained from The Prince Charles Hospital lung tumour bank. aCGH was performed using Agilent CGH 44B microarrays (Agilent Technologies). Recurrent CNAs were identified using the Genomic Identification of Significant Targets in Cancer (GISTIC) algorithm, controlling for false discovery rates (q≤0.005). Focal (<50% of chromosome arm) regions of amplification and deletion were identified by applying GISTIC with thresholds of log2 0.848 and −0.747, respectively, corresponding to 3.6 copies and 1.2 copies with stromal contamination of 30%. Results: Regions of amplification occurred in 3q26.33, 5p15.33, 8p11.23, 11q13.3 and 19q13.2 and deletions occurred in 3p11.2, 4p15.1, 4q34.3, 5q14.1, 6q22.31, 8p23.1, 9p21.3, 10q23.31, 11q25, 13q14.3, 15q14, 16q23.3, 17p12, 18q22.3, 21q21.3 and 22q13.33. The most significant CNA regions were deletion in 9p21.3 (q=1.20E-40) and amplification in 3q26.33 (q=1.13E-10). These regions contain known tumor suppressor genes (TSGs) (CDKN2A in 9p21.3) and oncogenes (SOX2 in 3q23.33). Conclusion: We have identified regions with recurrent CNAs in NSCLC many of which harbor known oncogenes and TSGs. Further validation will be performed using public datasets and independent test cohorts. Supported by: NHMRC Medical Postgraduate Scholarship 569762.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2211.
Abstract 2215: Association between acquired uniparental disomy and homozygous mutations and HER2/neu, ER, and PR status in breast cancer: Meta-analysis
Authors: Tuna Musaffe , Foekens John A. , Amos Christopher I.
Published: February 2011

Mutations in genes that encode components of cellular signaling networks are a hallmark of cancer. However, sequencing the whole genome for each tumor sample is challenging. A novel form of abnormality called acquired uniparental disomy (aUPD) was recently found, which can pinpoint a region containing mutated genes predisposing to various cancers, therefore identifying a candidate region for subsequent next-generation. We conducted a large meta-analysis of genomic data from the Gene Expression Omnibus database to retrieve genome-wide regions of aUPD in breast tumor samples using approaches that can reliably detect aUPD. aUPD was identified in 40.57% of the samples. The most recurrent aUPD regions were located at chromosomes 17q, 3p, 13q, and 11q. These data suggest that multiple genes may be targeted for homozygous mutations. Then we found association between aUPD and homozygous point alterations by integrating our data with previously published mutation data on reference gene sequences in breast tumors. We also evaluated the data for any correlation between the most recurrent aUPD region at chromosome 17q and HER2/neu, ER, and PR status, and we found a statistically significant correlation between aUPD at chromosome 17q and HER2/neu-, ER- and PR-negative breast cancers. We conclude that aUPD is a common and nonrandom new molecular mechanism in breast tumorigenesis. Identifying UPD regions would be a more effective approach to take than randomly sequencing the genome for discovering novel candidate genes for mutation. An integrative view of aUPD and homozygous sequence alterations on a genome-wide scale should provide further valuable insights into breast tumorigenesis.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2215.
Abstract 222: Inhibition of cellular FLICE-inhibitory protein and induction of death receptor 5 expression is a major component of δ-tocotrienol-induced apoptosis in pancreatic cancer cells
Authors: Zhang Anying , Francois Rony A. , Hodul Pamela J. , Husain Kazim , Shivers Steven C. , Coppola Domenico , Sebti Said M. , Malafa Mokenge P.
Published: February 2011

Background: Previous pre-clinical studies have demonstrated that δ-tocotrienol, is the most bioactive natural vitamin E compound against pancreatic cancer. δ-Tocotrienol induces growth arrest and apoptosis in several human pancreatic cancer cell lines; however, the underlying mechanism remains unknown. In this study, we evaluated the role of the extrinsic and intrinsic apoptotic signaling pathways in δ-tocotrienol induced apoptosis and investigated the modulation of cellular FLICE-inhibitory protein (c-FLIP) and death receptor 5 (DR5) by δ-tocotrienol and the involvement of c-FLIP down-regulation and DR5 up-regulation in δ-tocotrienol-induced apoptosis.

Methods: We examined δ-tocotrienol induced apoptosis in human pancreatic cancer cell lines in vitro and in vivo. We used western blot and immunohistochemistry to determine the expression of DR4, DR5, Caspase 8, Caspase 9, Caspase 3, C-FLIPs and PARP. The effect of combination treatment with TRAIL and δ-tocotrienol was also determined. We examined the cellular effects of DR5 knockdown using small interfering RNA oligonucleotides, and c-FLIP overexpression using cDNA, on δ-tocotrienol-induced apoptosis using various assays.

Results: Delta-tocotrienol activated caspase-8 and its downstream caspases but not caspase-9, whereas caspase-8 specific inhibitor abrogated δ-tocotrienol-induced apoptosis indicating that δ-tocotrienol induces caspase-8-dependent apoptosis. c-FLIP was rapidly down-regulated by δ-tocotrienol in all of the tested cell lines. δ-Tocotrienol up-regulated DR4 and DR5 significantly and enhanced tumor necrosis factor-related apoptosis-inducing ligand-induced apoptosis. Enforced expression of ectopic c-FLIP, and DR5 knockdown partially abolished δ-tocotrienol-induced apoptosis. δ-Tocotrienol inhibition of pancreatic tumor growth in SCID mice was associated with significant induction of apoptosis, activation of caspase 8, and down-regulation of c-FLIP expression.

Conclusion: We conclude that DR5 up-regulation and c-FLIP down-regulation contributes to δ-tocotrienol-induced apoptosis in pancreatic cancer cells.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 222.
Abstract 2226: International Cancer Genome Consortium (ICGC)
Authors: Jennings Jennifer L. , Hudson Thomas J.
Published: February 2011

The International Cancer Genome Consortium (ICGC) is one of most ambitious biomedical research efforts since the Human Genome Project. The ICGC is coordinating an international-scale research effort to obtain a comprehensive description of genomic, transcriptomic and epigenomic changes in the major forms of cancer. This information will lead to better ways of diagnosing, treating and preventing cancer.

The ICGC was launched in April 2008, with the announcement of the proposed strategies and policies to the international scientific community to enable funding agencies and research groups to plan their participation within the ICGC. As of December 2009, the ICGC has received commitments from funding organizations in Asia, Australia, Europe and North America for the following cancer genome projects: breast cancer, Her2+ (France); breast cancer, multiple subtypes (United Kingdom); chronic lymphocytic leukemia (Spain); gastric adenocarcinoma (China), hepatocellular carcinoma, alcohol and associated etiologies (France); pediatric brain cancers - medulloblastoma and pilocytic astrocytoma (Germany); hepatocellular carcinoma, viral etiologies (Japan); oral cavity cancer (India), and pancreatic adenocarcinoma (Australia and Canada). Furthermore, the latest call for proposals published in the Health Theme of the European Union's 7th Research Framework Programme includes a research topic to support European participation in the ICGC. The ICGC projects will complement a large US-based pilot project called The Cancer Genome Atlas, which oversees projects related to glioblastoma multiforme, squamous carcinoma and serous adenocarcinoma. Over time, additional nations and organizations

Each project is expected to involve specimens from approximately 500 patients. Over the next ten years, the ICGC expects to produce comprehensive catalogues of the full range of genetic mutations involved in 50 types of cancer, with key factors being the ability to detect all mutated cancer genes, data at the level of individual DNA bases, application of common standards for pathology and technology and comparison data from matched, non-tumour tissue.

The ICGC's informed consent and ethical oversight policies state that cancer patients enrolled in an ICGC-related study should be informed that their participation is voluntary, that their clinical care will not be affected by their participation and that data obtained from analyses using their samples will be made available to the international research community.

ICGC projects will use common standards of data collection and analysis. The ICGC will make its data rapidly and freely available to the global research community.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2226.
Abstract 223: Apoptotic activity of Polygonum cuspidatum in KB human oral cancer cells through the downregulation of specificity protein 1
Authors: Shin Ji-Ae , Shim Jung-Hyun , Jeon Jae-Gyu , Cho Sung-Dae
Published: February 2011

Polygonum cuspidatum (Polygonaceae) has traditionally been used in folk medicine to improve oral public health. However, there are no reports related to its potential of controlling oral cancer. In this study, we evaluated the anti-tumorigenic effects and mechanisms of methanol extract and its fractions separated from Polygonum cuspidatum root in KB human oral cancer cells. The methanol extract of Polygonum cuspidatum (MEPC) inhibited the proliferation of KB cells in a dose- and time-dependent manner by inducing caspase-dependent apoptosis. Protein and mRNA expression levels and the transactivation of Specificity protein 1 (Sp1) were markedly decreased in KB cells treated with MEPC. Ethyl acetate fraction (EA) from MEPC was more potent than aqueous fraction (AQ) from MEPC to induce apoptosis. F2, F3 and F4 from EA differentially inhibited the growth of KB cells and it depends on the amount of Emodin in F2, F3 and F4. Moreover, Emodin inhibited KB cell growth and induced caspse-dependent apoptosis. Thus, the results from this study strongly suggest that MEPC, its fraction and Emodin may be potential bioactive materials to cause apoptosis mechanism via the down-regulation of Sp1 in KB human oral cancer cells.

This paper was supported by the Korea Research Foundation Grant funded by the Korean Government (MOEHRD, Basic Research Promotion Fund, KRF-2008-331-E00260) and Bio R&D program through the Korea Science and Engineering Foundation funded by the Ministry of Education, Science and Technology (M10870050003-08N7005-00311).

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 223.
Abstract 2231: Detection of circulating tumor cells in peripheral blood of patients with renal cell carcinoma correlates with prognosis
Authors: Goebel Steffen , Bluemke Karen , Bilkenroth Udo , Meye Axel , Fuessel Susanne , Lautenschlaeger Christine , Melchior Andres , Heynemann Hans , Fornara Paolo , Taubert Helge
Published: February 2011

Purpose. The aim of this study was to evaluate the clinical relevance of the presence of disseminated tumor cells in peripheral blood [so called circulating tumor cells (CTCs)] for renal cell carcinoma (RCC) patients.

Methods. 233 peripheral blood samples from 154 RCC patients were investigated for the presence of disseminated tumor cells (DTCs) by autoMACS technique and immunocytochemical (ICC) staining of cytokeratin. The frequency of CTCs was analyzed statistically for correlation with relevant clinical data.

Results. Two kinds of tumor cells were detected: those with expression of cytokeratin 8/18 (CK+), but also cells without a detectable CK+ expression, which we called large blue stained (Bl+) cells with a tumor-like morphology. After following the CD45 autoMACS depletion protocol, we identified CTCs in 96 out of 233 peripheral blood samples (41%), which originated from 81 out of 154 (53%) RCC patients. A significant correlation between the detection of CTCs and positive lymph node status (p<0.001; chi2-test) and the presence of synchronous metastases at the time of primary tumor resection (p=0.014; chi2-test) was found. In a multivariate Cox's regression hazard model, presence of CK+ CTCs was significantly correlated with poor overall survival for RCC patients (RR=2.3; P=0.048).

Conclusions. The presence of CTCs correlated to lymph node status and presence of synchronous metastases in RCC. It is important to evaluate CK+ and Bl+ tumor cells together to determine the role of CTCs in tumor behavior and disease progression. Detection of CK+ CTCs in peripheral blood is a significant and independent prognostic factor for RCC.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2231.
Abstract 2235: Immunohistochemical analysis of RUNX2 in human colon cancer
Authors: Sase Tomohiko , Suzuki Takashi , Miura Kou , Onodera Yoshiaki , Sato Ryuichirou , Karasawa Hideaki , Yamamura Akihiro , Kimura Syunichi , Egawa Shinichi , Shibata Chikashi , Sasaki Iwao , Sasano Hironobu
Published: February 2011

[Background] Runt-related transcription factor (RUNX) family comes to attract attention in a field of differentiation and carcinogenesis. However, the RUNX2 expression in human colon cancer has not been fully analyzed. Therefore, we immunohistochemically analyzed the RUNX2 expression in human colon cancer. [Method] Primary colon cancer specimens were obtained from 158 colon cancer patients. All patients had undergone operations at Tohoku University Hospital, from 1994 to 2000. The formalin-fixed paraffin-embedded tissue sections were used for immunohistochemical analysis. [Result] RUNX2 was detected exclusively in nuclear of cancer cells, and 66.5% of cancer tissues were positive for RUNX2 (105/158 cases). Statistical analysis demonstrated that positive RUNX2 status was significantly associated with poor survival (Log-lank test: P=0.0178). In addition, RUNX2-positve patients had higher incidence of lymph node and liver metastasis compared to RUNX2-negative patients (P=0.0147 and 0.0038, respectively) [Discussion] RUNX2 may therefore play an important role in metastatic ability of human colon cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2235.
Abstract 2237: Expression of the trefoil protein TFF3 in human breast cancers
Authors: Ahmed Ahmed Roshdi Hamed , May Felicity EB , Tilby Michael J.
Published: February 2011

Expression of the trefoil protein TFF3 in human breast cancers

The purpose of this study is to investigate expression of the trefoil factor family protein, TFF3 in a large series of human breast cancers. Trefoil factors are small secreted proteins that are expressed in mucus secreting epithelia. They are involved in mucosal protection in part by stimulation of cell motility. It has been proposed that the motogenic actions of trefoil proteins may facilitate tumor cell invasion and metastasis. Expression of TFF3 mRNA is regulated by estrogen in human breast cancer cell lines and strong association between estrogen receptor and TFF3 mRNA expression has been demonstrated in breast tumors by expression microarray analyses.

A tissue microarray was constructed from 300 primary breast tumors and 76 metastatic deposits of breast tumors from patients who presented in the northern region of England between 2002 and 2003. TFF3 expression was evaluated by immunohistochemistry with an antibody raised against correctly-folded human TFF3 protein. Each sample was analyzed in duplicate. The intensity of the immunoreactions in 1,000 tumor cells was evaluated as: absent, weak, moderate or strong. The association of TFF3 expression with various clinico-pathological features and with estrogen receptor protein expression was tested statistically with SPSS software (p<0.01).

Clear TFF3 expression is demonstrated in normal and malignant breast epithelial cells. There is no expression in stromal, endothelial or immune cells. Expression of TFF3 varied enormously between tumor samples. TFF3 expression is highest in mucinous and tubular breast adenocarcinomas. TFF3 is expressed at higher levels in lobular than in ductal breast cancers. TFF3 expression is associated strongly with estrogen receptor expression. There is a negative association between TFF3 expression and tumor grade. There is however a positive association between TFF3 expression and presence of vascular invasion and TFF3 expression is higher in metastatic breast tumor cells than in primary breast tumor cells.

This is the first report of TFF3 protein expression in a large series of human breast tumors. The strong association between TFF3 and estrogen receptor suggests that TFF3 expression is dependent on estrogen in a significant proportion of breast tumors. The high expression of TFF3 in breast tumors with vascular invasion and in metastatic breast tumor cells supports the hypothesis that TFF3 predisposes towards breast cancer cell invasion.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2237.
Abstract 2238: A novel prognostic marker in patients with squamous cell carcinoma of the tongue: high endothelial venules
Authors: Lee Ser Yee , Ooi Aik Seng , Qian Chao-Nan , Hwang Siok Gek , Teh Bin Tean , Soo Khee-Chee
Published: February 2011

AIMS: To evaluate tumor-induced vascularization in regional lymph nodes (LN) of patients with tongue carcinoma by studying the morphological and functional alterations of high endothelial venules (HEV) and its correlation to clinico-pathological features.

BACKGROUND: Squamous cell carcinoma (SCC) of the tongue is one of the most prevalent tumors of the head and neck region. The extent of LN metastasis is a major determinant for the staging and the most reliable adverse prognostic factor. Primary tumors can induce lymphatics and vasculature reorganizations within sentinel LN before the arrival of cancer cells and these key blood vessels are identified as HEV. The morphological altera[[Unsupported Character - Codename ­]]tion of HEV in the presence of a cancer, coupled with the increased proliferation rate of the endothelial cells, results in a functional shift of HEV from immune response mediator to blood-flow carrier.

METHODS: This study is based on 65 consecutive patients with tongue SCC who underwent primary surgical treatment at Singapore General Hospital from January 2001 to December 2005. The patients were categorized into 2 groups (Cases and Controls) based on the presence of malignancy in their cervical lymph nodes. A review of the patients’ pathological and clinical data was performed from a prospective database. Immunohistochemical staining of the tissue blocks for HEV and high-power-field image analysis were performed and analyzed with correlation to the patients’ clinico-pathological features.

RESULTS: The total number of HEVs is significantly associated to disease-free interval when controlling for the group (p=0.022) as well as combining both groups as one cohort (p=0.023). There also a similar association comparing the HEV parameters to overall survival.

CONCLUSION: Our results suggest that the HEV possibly plays a key role in the pathogenesis of lymphatic and subsequent distant metastases. Confirmation of this hypothesis would offer a novel therapeutic approach to preventing metastasis by blocking the remodeling processes of HEV in LN.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2238.
Abstract 2248: The Y-box-binding protein 1 is associated with breast cancer progression and metastasis
Authors: Yu Yingnan , Yip George Wai-Cheong , Tan Puay-Hoon , Matsumoto Ken , Tsujimoto Masafumi , Bay Boon-Huat
Published: February 2011

The Y-box-binding protein 1 (YB-1) which belongs to the RNA- and DNA-binding protein family with a conserved cold-shock domain, is known to regulate transcription and translation. Extensive studies carried out on the multi-functional YB-1 protein have implicated its role in tumor growth and drug resistance. However, the association between YB-1 and breast cancer metastasis has not been fully investigated. To determine if YB-1 expression is correlated with breast cancer progression, we evaluated protein expression analysis in breast cancer tissue microarrays from the Singapore General Hospital by immunohistochemistry using an N-terminal YB-1 antibody and gene expression analysis in a TissueScan breast cancer tissue qPCR array (a rapid-scan cDNA panel of 48 breast cancer tissues representing breast cancer in different tumor stages) by real time RT-PCR. Next, we down-regulated the expression of the YB-1 protein in MDA-MB-231 breast cancer cells by si-RNA mediated silencing of the YB-1 gene and performed migration assays (using polycarbonate membranes of transwells separating the upper and lower chambers in 24-well plates) and invasion assays (using Matrigel-coated transwell chambers). The results show that 88.7% of breast cancer tissues were positively immunostained for the YB-1 protein and a higher YB-1 expression level was associated with axillary lymph node spread. YB-1 gene expression level in the breast cancer tissues was also higher in the advance stages of breast cancer as compared to the early stage of the tumor. In the in vitro experiments, the silencing efficiency of the YB-1 siRNA was around 90% and significant down-regulation of the YB-1 protein was verified by Western blot analysis and immunostaining of the MDA-MB-231 cells. Furthermore, siYB-1 mediated knockdown of YB-1 expression significantly reduced the migration ability and invasive potential of MDA-MB-231 cells as compared to the control group. Collectively, the data obtained from breast cancer tissues and in vitro experiments has provided evidence that YB-1 expression is associated with aggressive behavior in breast cancer. It would seem that YB-1 is a potential biomarker of metastasis in breast cancer and a promising molecular target in breast cancer therapy.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2248.
Abstract 2249: Slug Expression is predictive marker of lymph node metastasis and prognosis in colorectal carcinoma
Authors: Toiyama Yuji , Yasuda Hiromi , Saigusa Susumu , Inoue Yasuhiro , Miki Chikao , Hori Hiroki , Kusunoki Masato
Published: February 2011

Purpose: Slug is a member of the snail family of transcription factors, plays a crucial role in the regulation of epithelisal-mesenchymal transition(EMT) by suppressing several epithelial markers. In this study, we investigated the clinical significance of Slug expression in colorectal cancer and identified the function of Slug gene in vitro.

Methods: Slug gene expression in surgically resected colorectal carcinoma of 184 patients were quantified by real-time quantative reverse transcription-PCR to assess the association between Slug expression and clinicopathologic factors and survival. To identify the function of Slug RNA interference (RNAi) was used to inactivate this gene in the colon cancer cell line SW480. Immunohistochemical analysis was performed to characterize the pattern of Slug expression in colorectal cancer.

Results: Slug expression in cancer tissue was significantly higher than that in normal tissue and significantly higher in patients with invasive tumor stage, lymphatic invasion, lymph node involvement, liver metastasis and advanced TNM stage. Increased Slug expression demonstrated a significantly associated with poor prognosis and independent prognostic factor not only in all colorectal cancer patients but also in patients with curative intent. Furthermore, increased Slug expression was an independent marker for predicting lymph node metastasis. Function of Slug gene investigated by RNAi have ability of cell proliferation and invasive ability to basal membrane in cancer cell line and this protein was mainly expressed in the invasive front of the tumor.

Conclusions: Slug is up-regulated in human colon cancer and seems to play a role in cancer invasion from primary lesion. Our present data might be suggested that quantification of slug gene in colorectal cancer could be useful marker to identify the patients with lymph node positive or with poor prognosis in curative intent.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2249.
Abstract 2251: Functional significance of prostate derived ETs factor in detection of highgrade prostate cancer
Authors: Koul Sweaty , Kumar Binod , Maroni Paul D. , Meacham randall B. , Koul Hari K.
Published: February 2011

INTRODUCTION AND OBJECTIVES: Conventional therapies produce a high rate of cure for patients with localized prostate cancer, but there is, at present, no effective treatment for intervention in metastatic prostate cancer. These facts underline the need to develop new approaches for early diagnosis of aggressive prostate cancer patients, and mechanism based anti-metastasis therapies that will improve the outlook for hormone-refractory prostate cancer. In this study we evaluated role of prostate-derived Ets factor (PDEF) in prostate cancer.

METHODS: PDEF and MMP9 expression was assayed by Immuno-histochemical methods in Prostate Cancer tissue microarrays. PDEF expression in cell lines was investigated using Western Blot analysis. We constructed cells with stable expression of PDEF using a retroviral vector or knocked down PDEF in cells using PDEF specific SiRNA. Cell migration, invasion and clonogenic activity were monitored using scratch assays, Matrigel invasion assays and growth in soft agar respectively.

RESULTS: We observed decrease of PDEF expression in prostate cancer cell lines correlated with increased aggressive phenotype, and complete loss of PDEF protein in metastatic prostate cancer cell lines. Loss of PDEF expression was confirmed in high Gleason Grade prostate cancer samples by immunohistochemical methods. Our results also demonstrated that PDEF down regulated MMP-9 promoter activity, suppressed MMP9 mRNA expression, and resulted in loss of MMP9 activity in prostate cancer cells. These results suggested that loss of PDEF might be associated with increased MMP9 expression and activity in aggressive prostate cancer. To confirm results we investigated MMP9 expression in clinical samples of prostate cancer. Results of these studies show increased MMP9 expression correlated with advanced Gleason grade. Taken together our results demonstrate that decreased PDEF expression and increased MMP-9 expression during the transition to aggressive prostate cancer.

CONCLUSIONS: These studies demonstrate for the first time negative regulation of MMP9 expression by PDEF, that PDEF expression was lost in aggressive prostate cancer and was inversely associated with MMP-9 expression in clinical samples of prostate cancer. Based on these exciting results we propose that loss of PDEF along with increased MMP9 expression should serve as novel markers for early detection of aggressive prostate cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2251.
Abstract 2256: Identifying the molecular signature of melanoma metastasis via a personalized quantitative proteomics approach
Authors: Eissa Azza , Cho Chan-Kyung J. , Diamandis Eleftherios P.D.
Published: February 2011

Melanoma metastasis is the primary cause of skin cancer deaths. Unfortunately, the biology of melanoma metastasis remains elusive, although several pathways, including epithelial-to-mesenchymal transition (EMT), have been suggested as underlying mechanisms of tumor progression and immunosuppression. No reliable single or multiple prognostic markers currently exist in the clinic to predict chances of melanoma metastasis, resistance to therapy, and recurrence after treatment. Microarrays have been the primary means for large-scale expression analyses of genes implicated in cancer progression. However, recent advents in high throughput mass spectrometry allow for investigating cancer development directly at the protein level. In this study, we applied a quantitative proteomics technique, Stable Isotope Labeling with Amino acids in Cell culture (SILAC), to compare the proteomes of primary and metastatic cancer cells derived from the same melanoma patient. We hypothesized that quantitative proteomic profiling of primary and metastatic cell lines from the same patient will: 1) reflect differences in their metastatic potential by identifying differentially expressed proteins and pathways, 2) uncover new protein candidates involved in cancer progression-related processes, such as EMT, and 3) yield promising prognostic biomarkers and therapuetic targets. A “bottom-up” proteomics approach and a two-dimensional (strong cation exchange followed by reversed-phase) LC-MS/MS strategy on an LTQ-Orbitrap were utilized to perform 3 different pair-wise comparisons of the expressions of extracellular and membrane-bound proteins in the conditioned media of melanoma cell lines from 3 different patients (3 primary cells labelled with ‘light’ arginine and lysine and their corresponding ‘heavy’- labelled metastatic counterparts). We identified over 1000 proteins from each pair of primary and metastatic cell conditioned media, several of which were previously reported as either up-regulated or down-regulated in melanoma, confirming the validity of our approach. In addition, we identified candidate proteins that have not been correlated previously with melanoma metastasis. Candidate proteins were selected based on the quantification ratio (>2-fold change) between the two conditions and the consistency among triplicates within each condition. Many of the identified proteins may shed light on the molecular mechanisms underlying melanoma metastasis and may open novel areas for further research geared towards finding effective personalized prognostic and therapeutic approaches to manage this devastating cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2256.
Abstract 2260: Modulation of P-glycoprotein expression by a novel nutrient mixture in multidrug-resistant human uterine sarcoma cell line MES-SA/Dx5 but not in drug-sensitive MES-SA cell line
Authors: Roomi M. Waheed , Roomi Nusrath W. , Rath Matthias , Niedzwiecki Aleksandra
Published: February 2011

Introduction: We have characterized a nutrient mixture containing lysine, proline, ascorbic acid and green tea extract as a novel antineoplastic agent with a broad spectrum of antitumor activity against a number of cancer cell lines.

Objective: We investigated the effect of NM on modulation of P-glycoprotein (Pgp) in the drug-resistant human uterine sarcoma cell line MES-SA/Dx5 and compared it with the effect on drug-sensitive cell line MES-SA. In addition we also studied the effect of NM on MMP expression and Rhodamine-123 accumulation and efflux.

Material and Methods: Human drug insensitive uterine sarcoma cell line MES-SA/Dx5 and drug sensitive cell line MES-SA (ATCC) were grown in RPMI 1640 medium supplemented with fetal bovine serum and antibiotics. At near confluence, the cells were tested with NM at 0, 50, 100, 250, 500 and 1000 mcg/ml, in triplicate at each dose. Cell proliferation was evaluated by MTT assay, MMPs by gelatinase zymography, and Pgp expression by Western blot and immunodetection using FITC-conjugated antibody and rhodamine-123 (Rh-123) accumulation and efflux assays.

Results: NM exhibited antiproliferative effect on MES-SA/Dx5, by 20% at 50 and 100 mcg/ml and by 40% at 25, 500 and 1000 mcg/ml, whereas in MES-SA cell line, NM showed dose-response toxicity of 40% at 50 and 30% at 1000 mcg/ml. In both cell lines, zymography demonstrated a band corresponding to MMP-2 in normal cells and MMP-9 with PMA treatment. Both MMPs showed dose-response inhibition by NM. NM treatment also showed diminished dose-dependent Pgp expression by MES-SA/Dx5 cell line by Western blot and by immunodetection, whereas MES-SA did not exhibit Pgp by Western blot or by immunostaining. NM enhanced the accumulation and efflux of Pgp substrate Rh-123 in MES-SA/Dx5 uterine sarcoma cell line but not in the drug-sensitive cell line MES-SA.

Conclusions: In summary, this study demonstrated that Pgp is modulated by NM, which may be an attractive potential agent for therapeutic use in cancer treatment

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2260.