bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2129A: Clinical implications of infrequent BRAF mutation in advanced stage low-grade ovarian serous carcinomas
Authors: Wong Kwong-Kwok , Tsang Yvonne TM , Deavers Michael T. , Mok Samuel C. , Gershenson David M.
Published: February 2011

Serous carcinoma is the most common histologic subtype of epithelial ovarian cancer. Recent evidence strongly suggests that a 2-tier system stratifying serous carcinoma into low-grade and high-grade categories is biologically and clinically relevant. Low-grade ovarian serous carcinomas are believed to arise via an adenoma-borderline-carcinoma sequence. We analyzed 91 ovarian tumor samples for mutations in BRAF, KRAS, and TP53. No TP53 mutations were detected in serous borderline tumors (n = 30) or low-grade serous carcinomas (n = 43), but 73% of high-grade serous carcinomas (n = 18) carried a TP53 mutation. BRAF and KRAS mutations together were detected in 47% of serous borderline tumors, but among the low-grade serous carcinomas, only 2% had a BRAF mutation and 19% had a KRAS mutation. The low frequency of BRAF mutations in advanced stage low-grade serous carcinomas suggests that low-grade serous carcinomas are likely derived from serous borderline tumors without BRAF mutations. This hypothesis is further supported by the fact that 2 of the patients with serous borderline tumors without BRAF or KRAS mutations developed recurrent low-grade serous carcinoma 17 and 60 months after the initial diagnosis of a serous borderline tumor. Moreover, it is interesting that 4 of the 8 patients with either BRAF or KRAS mutations have had no evidence of disease after optimal debulking surgery and standard platinum-taxane-based chemotherapy, while patients without mutations are either diseased or alive with recurrent disease. Thus, mutational analysis of BRAF may have prognostic utility in that a finding of a BRAF mutation may suggest a low risk of recurrent low-grade serous carcinoma.

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 2129A.
Abstract 213: Combinative treatment for prostate cancer by adenoviral-mediated gene therapy expressing a novel apoptosis gene and chemotherapy
Authors: Lu Yi , Beheshti Ben , Zhang Xiongwen
Published: February 2011

A novel gene, rat pHyde, and its human homologue, hpHyde, have been cloned from prostate cancer cells. Database search and FISH analysis consistently indicated that hpHyde gene localizes at human chromosome 2q14. Protein sequence analysis suggests that hpHyde may be a plasma membrane protein with calcium channel function. hpHyde is differentially expressed in various normal human tissues and organs, suggesting that hpHyde may play roles in development and differentiation. A recombinant adenovirus containing pHyde cDNA gene (AdRSVpHyde) showed significant growth inhibition on human prostate cancer cells, both in vitro and in vivo, through a caspase-3 dependent apoptosis induction. The anti-prostate cancer effects of pHyde in conjunction with chemotherapy agent were analyzed by in vitro and in vivo assays using AdRSVpHyde in combination with DNA damaging chemotherapeutic agent, cisplatin, and docetaxel, respectively. Growth suppression and induction of apoptosis were additively greater in DU145 human prostate cancer cells treated with AdRSVpHyde and cisplatin than either agent alone both in vitro and in vivo. Moreover, AdRSVpHyde and docetaxel also have a similar additively inhibitory effect on DU145 cell growth. Taken together, these results support the potential use of pHyde for prostate cancer gene therapy coupled with chemotherapy to improve therapeutic index. Our results also suggest that pHyde may play important physiological and pathological roles in normal prostate development and prostate carcinogenesis.

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 213.
Abstract 2131: Accurate quantitation of absolute allelic copy-numbers in primary solid tumor samples from SNP-array / WGS data reveals patterns of tumor progression
Authors: Carter Scott L. , Getz Gad , Meyerson Matthew L.
Published: February 2011

Genomic imbalances are a hallmark of cancer cells. Genomic regions recurrently gained or lost in many cancer samples often harbor oncogenes or tumor suppressors, making whole-genome characterization of copy-number a widely adopted strategy for the study of cancer

In practice, copy-number analysis is typically performed using techniques such as array-CGH, SNP-array, or whole genome sequencing (WGS) analysis. Because a fixed quantity of DNA is extracted from a tumor sample for each of these methods, the concentration of each genomic locus is dependant on both the fraction of tumor cells and the ploidy (DNA mass) of each tumor cell. Because these quantities are generally unknown, downstream analysis of copy-number changes has been limited to consideration of relative gains/losses.

Here we describe a recently developed computational method capable of accurately inferring the tumor purity, ploidy, and genome-wide absolute allelic copy-numbers from data obtained by either SNP-array (several platforms are supported), or WGS. Validation data comprised of tumor-normal cell-line mixing experiments verify the accuracy of the method.

Application of these methods to large tumor-cohorts allowed for systematic re-assessment of homozygous deletion and LOH in heavily contaminated samples. These results allow for the assessment of preferential allelic deletion or amplification in genomic regions of recurrent copy loss or gain, respectively.

Our data suggest that the distribution of tumor-ploidy is bi-modal for many common epithelial tumor types, with a hypo-diploid subset and a second subset of samples with ploidy ranging from three to five [haploid genomes]. The observed patterns of allelic copy-number are consistent with a model of tumor progression by which high-ploidy samples arose via whole-genome doubling from an intermediate hypo-diploid state. These analyses allow us to define characteristic “early” genomic events in several tumor types.

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 2131.
Abstract 2145: Identification of genomic alterations and integrated gene expression profiles for MSS colon tumors
Authors: Loo Lenora W.M , Tiirikainen Maarit , Cheng Iona , Okimoto Gordon , Lum-Jones Annette , Seifried Ann , Gallinger Steven , Thibodeau Steven N. , Casey Graham , Marchand Loic Le
Published: February 2011

Colon cancer is the result of a multi-step process involving the accumulation of genetic and epigenetic alterations leading to the transformation of normal colon epithelium to adenocarcinoma. Identification of characteristic genetic alterations is of critical importance to increase our understanding of the transformation process. We focused our analysis on the most common molecular sub-type of colon cancers, microsatellite stable (MSS) and CpG island methylator phenotype (CIMP)-negative, to identify characteristic copy number alteration (CNA) events and associated gene expression profiles using high-resolution genome-wide microarrays.

DNA and RNA were extracted from 41 fresh-frozen paired colon tumors and adjacent normal tissue collected by the Colon Cancer Family Registry. Genomic profiles, such as CNAs and loss of heterozygosity (LOH), were identified with the Affymetrix Genome-Wide Human SNP 6.0 array for both tumor and adjacent normal tissue. Gene expression profiles of tumors and adjacent normal tissue were identified with the Affymetrix GeneChip Human Exon 1.0 ST array. Partek Genomics Suite software was used for analysis and data integration.

We identified recurrent (>25%) CNAs in several chromosomal regions: gain in 1q, 7p, 7q, 8q, 13q, 20p, 20q, Xp, Xq and loss in 5q, 8p, 14q, 16p, 17p, 18p, and 18q. In addition, based on the allele information from the SNP arrays, we found a subset of these recurrent CNAs were associated with LOH. Preliminary results from the integration of CNA and gene expression data in tumors indicate that a subset of these recurrent CNAs is associated with the disruption of gene expression. For example, we observed recurrent copy number gain in 8q24.21, the genomic region containing the c-MYC gene, and associated up-regulation of c-MYC gene expression in tumors compared to adjacent normal tissue. In another example, recurrent copy number loss at 5q22.2 was associated with down-regulation of APC gene expression; loss of function of this tumor suppressor is associated with both hereditary and sporadic colon cancer.

This genome-wide characterization of both genomic alterations and gene expression may help identify key genes and pathways that are disrupted in this common molecular subtype of colon cancer. We will present detailed results from this integrated and comprehensive genetic profiling of MSS and CIMP-negative colon cancers.

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 2145.
Abstract 2147: Molecular allelokaryotyping to identify mechanism of development of Asian chronic lymphocytic leukemia
Authors: Kawamata Norihiko , Ogawa Seishi , Kato Motohiro , Raynauld Sophie , Saitoh Takayuki , Nakahashi Hirotaka , Karasawa Masamitsu , Koeffler H. Phillip
Published: February 2011

Chronic lymphocytic leukemia (CLL) is a common hematological malignancy in western countries. However, this disease is very rare in Asian countries. It is not clear whether the mechanisms of development of CLL in Caucasian and Asian are same. To answer this question, we compared genomic abnormalities in Asian and Caucasian CLL using single-nucleotide-polymorphism genomic microarray (SNP-chip). We analyzed 75 cases of Japanese CLL (Binet stage A: 51 cases, B: 8 cases, C: 16 cases, unknown: 3 cases) using 250-k GeneChip from Affymetrix. We compared these results to 56 cases of Caucasian CLL. Asian CLL had 4 common genomic abnormalities: deletion of 13q14.3 (36 cases, 49 %), trisomy 12 (23 cases, 30 %), abnormalities of 11q (9 cases, 13 %: 7 deletions and 2 uniparental disomy), and abnormalities of 17p (5 cases, 8 %: 4 deletions and 1 uniparental disomy). These 4 common genomic abnormalities were also identified in Caucasian CLL cases. Interestingly, in both racial groups, trisomy 12 and deletion of 13q14.3 were mutually exclusive (p = 0.01). Nevertheless, frequency of trisomy 12 was higher in Japanese CLL cases (23/75 cases, 30 %) than in Caucasian cases (4/56 cases; 7 %) while frequency of deletion of 13q14.3 was comparable in Japanese and Caucasian (49 % and 48 %, respectively). Frequency of deletion of 11q23.1 was similar in both racial groups. Notably, not only did all these cases involve deletion of ATM but always also deleted miR 34b and 34c. Furthermore, one case had a homozygous deletion of 11q22.3 involving caspase 1/4/5 and COP1. Interestingly, all except one CLL case with 11q abnormalities had either deletion or acquired uniparental disomy. Both Asian and Caucasian CLL had a commonly deleted region at 13q14.3 involving miR 15-a and 16-1. Interestingly, one case had two distinct deletions in this region; one involved miR 15-a and 16-1; the other involved Rb1. On close inspection, 36 % of cases with deletion of 13q, had a deletion of Rb1, suggesting that Rb1 might be another target of deletion of 13q. In summary, the new findings of this study are: 1) Genomic abnormalities in Asian and Caucasian CLL were comparable except for a higher frequency of trisomy 12 in Asian CLL; 2)Trisomy 12 and 13q deletions were mutually exclusive suggesting that either lesion can substitute for the other and may involve a common cellular pathway; 3)New CLL genomic abnormalities include deletion of miR 34b and 34c, caspase 1/4/5 and COP1 (11q), and Rb1 (13q).

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 2147.
Abstract 2157: Is CDK6 the target of amplification at 7q21 in esophageal adenocarcinoma
Authors: Ismail Amin , Zhou Zhongren , Toia Liana , Reveiller Marie , Bandla Santhoshi , Pennathur Arjun , Luketich James , Godfrey Tony
Published: February 2011

Introduction: The cyclin-dependent kinase 6 (CDK6) is a positive regulator of the cell cycle. It binds to D-type cyclins and phosphorylates the pRb tumor suppressor proteins allowing progression through the G1-phase of the cell cycle. Amplification of the 7q21 chromosomal region has been reported in esophageal adenocarcinoma (EAC) and it has been proposed that CDK6 is the key gene targeted by this event. However, overexpression of CDK6 in vitro suppresses proliferation of breast cancer cells and causes nuclear accumulation of pRb2 tumor suppressor protein. Thus, it remains unclear whether amplification and overexpression of CDK6 is truly driving the 7q21 amplicon in EAC.

Methods: For DNA copy number analysis we analyzed genomic DNA from 83 EAC tumors using Affymetrix 6.0 SNP arrays. Protein expression was analyzed in tissue microarrays comprised of 116 independent EAC samples and pre-EAC lesions (15 high grade dysplasia (HGD), 18 low grade dysplasia (LGD), and 283 cases of columnar cell change (CCM)) using a monoclonal antibody against CDK6. CDK6 was overexpressed by stable transfection of OE19, OE33 and Flo1A esophageal cancer cells using CDK6 cDNA under the control of the pCMV promoter.

Results: The microarray DNA copy number analysis showed amplification of the 7q21 region in at least 25% of cases. The minimal amplicon contained CDK6 along with 4 other genes. Immunohistochemistry showed both cytoplasmic and nuclear CDK6 staining in EAC (36, 31.3%), HGD (6, 40.0%), LGD (5, 27.7%), and the CCM (29, 10.2%).

Overexpression of CDK6 in EAC cell lines caused either suppression of proliferation and anchorage independence (OE19 cells) or had no effect on proliferation (OE33 and Flo1A cells). The suppression of proliferation in OE19/CDK6 cells is dependent on the kinase activity of CDK6 as OE19 cells overexpressing a kinase-deficient form of CDK6 proliferate normally. As previously reported in breast cancer cells, pRb2 (p130) tumor suppressor protein is upregulated in OE19/CDK6 cells. The upregulation of pRb2, however, does not seem to account for the hypo-proliferative effect of OE19/CDK6 cells as it is also upregulated in normally proliferative cells that overexpress the kinase-negative form of CDK6.

Conclusion: Although CDK6 is amplified and overexpressed in EAC and its preneoplastic lesions, it does not seem to account for the tumorigenic importance of the 7q21 amplicon. CDK6 overexpression in vitro does not show any mitogenic phenotype in EAC tumor cells. The presence of other genes within the minimal amplicon raises the possibility that one or more of them might drive such a potential.

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 2157.
Abstract 2162: Gene expression profile for predicting survival in ovarian cancer across two independent datasets
Authors: Yoshihara Kosuke , Tajima Atsushi , Yahata Tetsuro , Kodama Shoji , Fujiwara Hiroyuki , Suzuki Mitsuaki , Onishi Yoshitaka , Hatae Masayuki , Sueyoshi Kazunobu , Fujiwara Hisaya , Kudo Yoshiki , Kotera Kohei , Masuzaki Hideaki , Tashiro Hironori , Katabuchi Hidetaka , Inoue Ituro , Tanaka Kenichi
Published: February 2011

Advanced-stage ovarian cancer patients are generally treated with platinum/taxane-based chemotherapy after primary debulking surgery. However, there is a wide range of outcomes for individual patients. Therefore, the clinicopathological factors alone are insufficient for predicting prognosis. To identify a progression-free survival (PFS) related profile for predicting survival, advanced-stage serous ovarian cancer tissues from 110 patients who underwent primary surgery and platinum/taxane-based chemotherapy were profiled using oligonucleotide microarrays. We first selected 88 PFS-related genes by a univariate Cox model (p < 0.01). To avoid overfitting our dataset, we then adjusted regression coefficients of the genes by ridge regression Cox model using 10-fold cross-validation. The prognostic index for each patient based on the 88-gene expression profile with the estimated coefficients was significantly correlated with PFS time as a continuous variable. In multivariate analysis, the prognostic index was independently associated with PFS time compared to other clinical factors [hazard ratio (HR), 4.84; 95% confidence interval (CI), 3.50-6.55; p < 0.001]. This prognostic ability was validated using an external validation dataset (n = 87) and proven by multivariate analysis (HR, 1.25; 95% CI, 1.08-1.45; p = 0.0032). The correlation between the prognostic index and overall survival time was confirmed in the two independent datasets. Furthermore, biological characterization of 88 PFS-related genes mainly highlighted several oncogenic signaling pathways. This PFS-related profile is the first step toward clinical practice for optimizing clinical management for advanced-stage serous ovarian cancer patients.

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 2162.
Abstract 2166: Identification of novel epigenetically silenced genes by a global reactivation screen of prostate cancer
Authors: Ibragimova Ilsiya , de Cáceres Inmaculada Ibáñez , Hoffman Amanda M. , Al-Saleem Tahseen , Hudes Gary R. , Ochs Michael F. , Cairns Paul
Published: February 2011

The epigenetic alteration of aberrant DNA methylation of CpG island in the promoter region is a common mechanism of inactivation of tumor suppressor genes in cancer cells and a number of other cancer genes have been identified as hypermethylated with associated loss of expression in prostate cancer. By definition, a candidate gene approach has resulted in the examination of only a limited number of genes for epigenetic alteration. Many other tumor suppressor and cancer genes important in prostate tumorigenesis likely remain to be identified. A global approach to the identification of epigenetically silenced genes in prostate tumor cells could provide methylation signatures for early detection and for prognostic and predictive classification studies, identify novel targets for therapy, and lead to further elucidation of the biology of this disease.

One global approach to the identification of epigenetically silenced genes in tumor cells is based on the reversal of epigenetic silencing by drugs such as 5-aza-2 deoxycytidine resulting in re-expression analyzed by well-annotated gene expression arrays. This approach can preferentially identify re-expression of epigenetically silenced genes over methylated CpG islands that do not affect transcription. A proportion of the reexpressed genes will have been silenced by promoter hypermethylation in the untreated tumor cell lines.

In this study we performed a demethylating drug-based global epigenetic reactivation screen with an expression microarray on 4 well-established prostate cancer cell lines (LNCaP, DU-145, PC-3 and MDA2b) to identify new methylated genes in prostate cancer. A total of 2998 genes were found to have at least 2-fold upregulation of expression after drug treatment in one or more of four prostate tumor cell lines. Using qMSP and bisulfite sequencing, we studied the first 45 upregulated genes that were prioritized by examination of expression status in the normal cell counterpart compared to the tumor cell and the presence and location of a CpG island in the promoter region. Validation studies revealed several novel genes hypermethylated in primary prostate tumors compared to normal prostate that may have utility in methylation-based detection of prostate cancer tests.

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 2166.
Abstract 2178: Serial analysis of gene expression (SAGE) of esophageal squamous cell carcinoma: ADAMTS-16 is up-regulated in esophageal squamous carcinoma
Authors: Sakamoto Naoya , Oue Naohide , Noguchi Tsuyoshi , Sentani Kazuhiro , Anami Katsuhiro , Sanada Yuichi , Yoshida Kazuhiro , Yasui Wataru
Published: February 2011

Esophageal squamous cell carcinoma (ESCC) is one of the most common malignancies worldwide. To identify potential targets for diagnosis and therapeutics of ESCC, we performed Serial Analysis of Gene Expression (SAGE) on the ESCC sample. We generated the SAGE library from one ESCC sample and obtained a total of 14,430 tags, including 5,765 that were unique. By comparing SAGE tags from ESCC samples with those from normal human squamous esophagus (Gene Expression Omnibus accession number, GSM52501), we found several genes and tags that were differentially expressed between ESCC and normal squamous esophagus. Among these, we focused on the ADAM metallopeptidase with thrombospondin type 1 motif, 16 (ADAMTS16) gene. ADAMTS has been described as part of a family of zinc dependent proteases (metzincin family), which play important roles in a variety of normal and pathological conditions including arthritis and cancer. Although ADAMTS16 is expressed in some organs, the relationship with cancers, including ESCC, has not been studied. Quantitative reverse transcription-polymerase chain reaction analysis showed a high level of ADAMTS16 expression in 8 out of 20 ESCC samples (40%) but not in 15 kinds of normal tissues. We also investigated the mRNA expression levels of SCCA1, which encodes SCC antigen. High levels of SCCA1 mRNA expression were found in 4 of 20 cases (20%). We then investigated the relation of ADAMTS16 expression to clinicopathologic characters and found that ADAMTS16 overexpression correlated with the advanced T grade (p = 0.0215). Western blot analysis revealed that ADAMTS16 protein expression was detected in all 4 ESCC cases, whereas in 1 of the 4 corresponding non-neoplastic mucosa. Furthermore, ADAMTS16 protein was detected in culture media from the TE5 ESCC cell line which expressed significant level of ADAMTS16 mRNA, indicated that ADAMTS16 is surely secreted. To evaluate the biological significance of ADAMTS16 in ESCC, we performed MTT assay and transwell invasion assay. These examination revealed that knockdown of ADAMTS16 by siRNA in TE5 cells inhibited both cell growth and invasion ability. These results suggest that ADAMTS16 has a high potential as a serum tumor marker and therapeutic target for ESCC.

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 2178.
Abstract 2179: Computational pharmacogenomics analysis of human cancer cell lines
Authors: Edelman Elena
Published: February 2011

Purpose:

The goal of this study is to use cell-based drug screening and genome-wide molecular information to identify fundamental genomic alterations useful for clinical applications.

Experimental Approach:

Molecular data has been collected in the form of high-throughput microarray-based assays measuring gene expression and copy number changes for 294 cell lines, as well as cell-based drug sensitivity measures for 110 drugs. A computational analysis approach is taken to integrate information from the large cancer cell line datasets to discover predictive biomarkers that can be used to better guide targeted cancer drugs. Cancer genes and gene networks that are vital in a cancer cell's sensitivity or resistance to these drugs are identified by first locating genomic regions of recurrent amplification and deletion across the entire cell line panel. These regions are further analyzed for copy number associations with marked drug sensitivity or resistance. Those regions with copy number differences between drug sensitive and resistant cell lines are then examined on the gene expression level for cancer gene deregulation.

Results:

156 chromosomal regions of recurrent copy number alteration are identified across the cell line panel. 15 compounds are associated with differential copy number between sensitive and resistant cell lines in one or more of these regions for a total of 77 significant drug-region associations. Out of these 77 associations, 13 of the regions also include genes which are differentially expressed between the sensitive and resistant cell lines.

Conclusions:

Genes that are deleted in drug sensitive or drug resistant cell lines can act as biomarkers for drug sensitivity or resistance respectively. Similarly, genes amplified in drug sensitive cell lines can act as biomarkers for drug sensitivity. Genes amplified in drug resistant cell lines provide hypotheses for combination therapy, as we believe that the amplification that is seen only in the drug resistant cell lines is a driving factor causing the resistance to that drug. Using the drug along with pharmacological inhibition or experimental knockdown of the gene commonly amplified in the resistant cell lines is hypothesized to alter the cell lines from a drug resistant to a drug sensitive state. Novel combination therapies for use in given drug resistant cell lines harboring specific amplifications are currently being validated.

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 2179.
Abstract 218: Ginsenoside Rh2 induced bcl2 family proteins mediated apoptosis in vitro and xenograft in vivo
Authors: Choi Sunga , Oh Jun-Young , Song Jung-A , Kim Soo-Jin
Published: February 2011

Natural products have received increasing attention in recent years for the discovery of novel cancer preventive and therapeutic agents. The root of Panax ginseng has been used for thousands of years in Korean medicine practice for treatment of diverse ailments. More recent studies have indicated that ginsenoside saponins, a constituents of Panax ginseng can induce retardation of growth and cell death of cancer in culture and in vivo. In this study, we used two human breast cancer cells, MCF7 (wild type p53, ER responsive), MDA-MB-231 (mutated p53, ER-independent) and xenograft nude mouse model to investigate further insights into the mechanism of Ginsenoside Rh2-induced cell death. It was observed that Rh2 treatment significantly decreases viability at 40 to 60 μM concentrations as judged by trypan blue dye exclusion assay in both two cell lines. Rh2 treatment also increased in a concentration- and time-dependent cell death in cytoplasmic histone-associated DNA fragmentation assay. Bcl-2 family proteins have emerged as critical regulators of apoptosis by functioning either as promoters (e.g., Bax and Bak) or inhibitors (e.g., Bcl-2 and Bcl-xL) of the cell death process. Rh2-induced apoptosis was correlated with induction of Bax and Bak and a decrease in Bcl-xL and Bcl-2 protein levels in both two cell lines. Transient transfection of MCF7 cells with Bak- and Bax-targeted siRNAs conferred partial yet significant protection against ginsenoside Rh2-induced apoptosis. The increased expression level of Bax was associated with initiation of intrinsic apoptotic pathway. The pathway initiated translocation of Bax from cytosol following release of mitochondrial cytochrome c dependent on ginsenoside Rh2 treatment time. To test whether Rh2-mediated inhibition of MDA-MB-231 xenograft growth in vivo at the 2mg dose was due to increased apoptosis, tumor tissues from control and Rh2-treated mice were examined for histologic evidence of apoptosis. The tumors from Rh2-treated mice exhibited markedly higher count of apoptotic bodies and reduced proliferation index. The tumor section also exhibited the changed protein level compared with control one in specific for Bax or Bcl-2 immunohistochemistry. It was consistent in RT-PCR using appropriate Bcl2- family gene primers. In conclusion, our data suggests Rh2-mediated suppression of MDA-MB-231 xenograft growth in vivo and MF7 cells in vitro highly correlates with increased apoptosis. The results of the present study show that the ability of Rh2 to inhibit cell growth or cause apoptotic cell death in two human breast cancer cells is not influenced by either p53 functional status or ER responsiveness.

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 218.
Abstract 2185: Identification of novel compounds that preferentially kill repair deficient cells using high-throughput screening
Authors: Peterson-Roth Elizabeth , Abriola Laura , Merkel Jane , Glazer Peter
Published: February 2011

Loss of functional DNA repair pathways is a common occurrence in cancer cells and discovery of novel drugs that selectively kill repair deficient tumors cells could identify new cancer therapies. In this work we describe the use of high-throughput screening to determine chemicals that sensitize cells deficient in the fanconi anemia protein, FANCD2. Cell growth of human fibroblasts proficient (PD20+D2) and deficient (PD20) for FANCD2 were screened using two libraries containing over 1000 bioactive compounds and kinase inhibitors. The cells were treated with compounds continuously for 3 days and cell growth was assessed using a luciferase-based assay measuring ATP levels. The initial screen identified numerous compounds inducing differential survival in cells with and without FANCD2 and follow-up testing will be required to confirm these potential hits. However, it is promising that, in addition to novel compounds, several crosslinking agents, including mitomycinC, which are known to sensitize fanconi anemia cells to cell death are among the positive hits. Our results validate chemical screening as a tool to discover potential new cancer therapies targeting repair deficient cells lines. In addition, other than their role in crosslink repair, there is still not much known about the fanconi anemia protein family and the discovery of novel compounds involved in FANCD2 dependent cell survival could lead to the discovery of new functions of this protein family.

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 2185.
Abstract 2188: A high throughput RNAi screen for regulators of thioredoxin in pancreatic cancer cells identifies components of TGFβ-signaling as inducers of thioredoxin expression
Authors: Grandjean Geoffrey , Bartholomeusz Geoffrey , Kingston John , Powis Garth
Published: February 2011

Thioredoxin (Txn), thioredoxin reductase (TxnR) and NADPH comprise a thioredoxin system which exists in nearly all living cells functioning in multi-facetted processes in mammalian cells. These include thiol-dependent thiol-disulfide exchange reactions crucial to control the redox homeostasis, cellular growth, defense against oxidative stress and control of apoptosis. Thioredoxin expression has been observed to be elevated in some types of human cancer and has been shown to confer resistance to chemotherapy or radiation-induced apoptosis. It has also been shown that elevated levels of thioredoxin contribute to the carcinogenic process and invasive phenotype of cancer. Identifying key inducers of thioredoxin expression in cancer cells will permit us to specifically target these components with the goal of improving the clinical outcome of treatment of patients with thioredoxin overexpressing cancers. Here, we describe a functional genomic screen designed to identify inducers of thioredoxin expression in which a library of 7040 small interfering RNAs (targeting human kinome and druggable genes) was screened for their ability to block the expression of endogenous thioredoxin in the pancreatic cancer cell line, MiaPaCa2. The primary screen identified numerous potential inducers of thioredoxin expression and, through the use of extensive validation of all these potential hits, yielded 21 high confidence genes that have not previously been associated with the induction of thioredoxin expression. Six of these target genes were associated with TGFβ signaling and selected for this study. Downregulation of these genes strongly inhibited the expression of endogenous thioredoxin in the MiaPaCa pancreatic cancer and other cancer cell lines. Moreover, treating MiaPaCa2 cells with TGF-β1 induced the expression of thioredoxin. TGF-β1-induced expression of thioredoxin is mediated through SMAD2, SNL2, ITGAV, ITGb3 and SP1 thus showing that our study uncovers new aspects of thioredoxin regulation. Collectively, these observations offer several insights on how thioredoxin mediates tumor growth and demonstrates the utility of large-scale RNAi screens in mammalian 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 2188.
Abstract 2191: Development of a phylogenetic tree model to investigate the role of genetic mutations in a single endometrial tumor
Authors: Dai Donghai , Beck Brandon B. , Zhang Guoyi , Luo Wentao , Wu Fan , Kingsmore Stephen F.
Published: February 2011

Modern genome sequencing technology has identified thousands of mutations in human tumors, but analysis of the role of genetic mutations in tumor development, utilizing prevalence information from many tumors, has yet to define in patients the functional contribution of genetic mutations, individually and collectively. To understand the genetic basis of human endometrial cancer, the fourth most common cancer in women, transcriptome sequencing was performed on an endometrial tumor paired with normal cervical tissue, and 26 non-synonymous somatic mutations were confirmed in the tumor genome DNA. A phylogenetic tree illustrating the mutational timeline was developed based upon the distribution of 26 mutations in 30 randomly-selected laser-captured single cells from the tumor sections. Five ubiquitous mutations were identified that are presumed to occur in the cancer founder cell of the tumor, which may collectively play critical roles in endometrial oncogenesis. However, further testing in 10 additional endometrial tumors failed to show overlapping mutations, indicating the lack of a single common oncogenic pathway for these endometrial tumors.

Furthermore, we developed a mathematical and phylogenetic calculation of the cell population produced by a mutated ancestor cell, which quantifies the role of tumor-specific individual genetic mutations in cancer cell proliferation in a single resected patient tumor, without relying on prevalence information from other patients. This novel approach will be further tested in a larger sample set to determine whether multiple genetic mutations’ quantitative contributions can be used to predict patient outcomes.Functional contribution of individual mutationsmutant genesgenetic timeoffspring (million cells)ScoreC10orf26, GMPPA CREBL1 PPP2R2D SLCO2A13010000.997DDEF1 LOC728069298330.025LDLRAP1 PLEC129167−0.06MYST1286670.025GORASP2 ILKAP, LOC72942328100−0.07INCENP, ME22867−0.09PDZD8274000.011AP1G227267−0.01POLE4, SDC2263000.025PIF1, XYL226100−0.04TOR3A251670.01LOC642934251330CCDC50, CIZ12467−0.01LOC645634241000.014

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 2191.
Abstract 2192: Functional genomic screen to identify candidates capable of modulating invasive properties of HNSCC
Authors: Lepikhova Tatiana N. , Imai Misa , Peitsaro Nina , Klefstrom Juha , Monni Outi M.
Published: February 2011

Head and neck squamous cell carcinomas (HNSCC) contain a heterogeneous population of cancer cells some of which is explained by ongoing mutations that occur due to genetic instability and environmental factors. Not all of the cancer cells have a similar ability to drive tumor formation. To identify genes capable of modulating invasive properties in head and neck squamous cell carcinoma (HNSCC), we have compared copy number profiles (244K aCGH) of 12 primary and metastatic cancer cell lines obtained from patients with HNSCC of tongue and larynx. A specific pattern of copy number gains and losses was present in each cell line studied. Majority of the changes occurred in both the primary tumor and corresponding metastasis, but some amplifications, such as 10q21.1., 11q22, and 17p12 occurred more frequently in metastatic cancers. To determine whether any genes located at the amplicons input to metastatic potential of HNSCC we are performing a systematic loss-of-function survey. First, we examined the cell growth and invasive properties of primary and metastatic cell lines in vitro and in vivo. We then set up a genetic screen using highly metastatic cell lines in in vitro invasion assay system. pLKO1 shRNA library targeting genes located at identified amplified regions in invasive cells were transduced into the selected cell lines and transduced cell lines were subjected to transwell invasion assay. Several genes targeted for amplification and capable of modulating invasive properties of HNSCC in vitro have been selected for further validation in vivo.

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 2192.
Abstract 2197: A robotic genome-scale shRNA screen identifies metabolic drug targets and a glioblastoma gene signature
Authors: Colombi Marco , Benjamin Don , Hall Michael N. , Thiemeyer Anke , Molle Klaus , Moroni Christoph
Published: February 2011

Proteins encoded by oncogenes represent suitable drug targets and several have been validated clinically. However, certain non-oncogenes, which are downstream effectors of oncogenes, may be similarly useful as potential targets of therapy. We have developed a high-throughput strategy using a shRNA genomic library and tumor cells addicted to the mTOR pathway to identify genes (oncogenes or non-oncogenes) which control the oncogenic phenotype. mTOR addicted cells were generated from IL-3 dependent cells following frame-shift mutagenesis and selection for IL-3 independence. mTOR addicted cells obtained from this selection carried frame-shift mutations in the PTEN gene. mTOR addiction was revealed by sensitivity to rapamycin and confirmed biochemically by examining phosphorylation of the mTOR targets S6K and PKB. Interestingly (and of importance to our shRNA-based screening strategy), addition of IL-3 rescued cells from mTOR addiction, as this growth factor antagonized the apoptotic effect of rapamycin. Using robotics (BioMek-NX) and a genomic retroviral shRNA library we evaluated 14’000 genes for a potential role in maintaining mTOR addicted growth. Our strategy was to screen cells in the presence and absence of IL-3 to identify shRNAs that antagonize growth of cells in the absence of IL-3. We identified around 300 genes required for mTOR addicted growth. This set of genes was enriched in highly significant manner for genes known to be involved in cancer, providing proof of concept for the strategy. Examples of identified genes include ras, raf, PKB and mTOR. Also, genes with no cancer link and genes with unknown function were identified. Use of Ingenuity software allowed to place many of the identified genes into functionally distinct groups or pathways. In addition numerous hits affecting metabolic functions, redox functions, and ROS generating systems were identified including the cytoplasmic NADPH complex and complex I-IV of the respiratory chain. Combining the genes et with an Affymetrix gene overexpression analysis in the same cells and analysing by Oncomine software, we identified a glioblastoma gene signature consisting of 13 genes (p-value 2.4E-5) containing 3 oncogenes and several signaling elements. Downregulation of several of these genes in human cancer lines induced apoptosis. Some of he genes identified represent novel potential drug 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 2197.
Abstract 2213: Identification of novel cancer mutations in sarcomas
Authors: Abaan Ogan D. , Francis Princy , Pineda Marbin , Walker Robert L. , Bilke Sven , Davis Sean R. , Meltzer Paul S.
Published: February 2011

Understanding of how cancer initiates and progresses is the fundamental of cancer research. Identification of cancer mutations is of profound importance for both understanding of the disease and for developing novel therapies. To search novel cancer mutations, we have utilized a “targeted resequencing” approach to resequence coding exons from about 1300 genes in a panel of various sarcoma patient samples. We used the previously published method of “In-solution capture” to enrich for regions of interest and resequenced the enriched population on an Illumina GAII platform using single-ended or paired ended reads. The performance and depth of the enrichment and resequencing was adequate for variant calling. We obtained roughly 70% on genome reads and about 30% of the reads fall on target while about 40% of the reads fall on target±500bp. An in house variant calling script was used for SNP/variant calling. Each sample yielded multiple genes with novel variations some of which are either missense or nonsense and in a highly conserved residue that were also previously identified in other cancers as well. Preliminary results from samples resequenced so far demonstrate that these sarcoma samples have variations in a variety of genes with diverse functions, including but not limited to signaling pathway intermediates. In conclusion, our work will be important in cataloging novel cancer mutations in rare sarcomas, with potential implications for understanding their biology and the development of new therapies.

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 2213.
Abstract 2219: Identification of oncogenes in mutant Rpa1 associated tumorigenesis
Authors: Huang Bin , Zhang Weijia , Edelmann Winfried , Wang Yuxun
Published: February 2011

Genetic instability is a hallmark of human cancers. However, the precise molecular mechanism and its role in cancer remain elusive. We have demonstrated that a missense mutation in Rpa1 causes defective DNA repair, genetic instability and predisposes mice to cancer, thereby providing one of the first evidence showing a replication associated protein is essential in maintaining genome stability and suppressing tumorigenesis. In humans, loss of the chromosomal locus containing RPA1 and genetic polymorphisms in RPA1 have been found in a wide range of cancers. Hence, a better understanding about the role of Rpa1 mutation in genetic instability and cancer should have critical clinical implications. The studies from our lab and others established the association between mutant Rpa1 and tumors. However, it remains unknown which target is most related to cancer development associated with mutant Rpa1. To search for the candidate target genes, we applied whole genome array comparative genomic hybridization (aCGH) in the tumors developed in Rpa1 mutant mice. This genome-wide chromosome copy number analysis uncovered multiple chromosomal aberrations involving multiple genetic loci along the chromosomes in Rpa1 mutant tumor cells. Moreover, chromosomal profiling analysis revealed unique pattern of chromosomal changes in Rpa1 mutant lymphomas, which is distinct from lymphomas developed in other knockout mouse models carrying mutations in different tumor suppressors. Furthermore, we analyzed all the currently known tumor related genes and found 10 oncogenes to be involved in the chromosomal gains in Rpa1 mutant tumors including c-Myc on chromosome 15 which appears to be the most recurrent. We confirmed overexpression of c-Myc in Rpa1 mutant tumors while the other candidate oncogenes showed variable expression among different tumors. These results strongly suggest an important role of c-Myc in mutant Rpa1 mediated 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 2219.