bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1960: Transgenic overexpression of Cdx1b in zebrafish induces metaplastic changes of gene expression in the squamous epithelium
Authors: Hu Bo , Liu Xiuping , Cole Gregory , Zhang Chengjin , Lee Ju-Ahng , Chen Xiaoxin (Luke)
Published: February 2011

Background and aims: Cdx2 has been suggested to play an important role in Barrett's esophagus (BE), or intestinal metaplasia (IM) in the esophagus. However, it is still unclear whether ectopic overexpression of Cdx2 may lead to IM in the esophagus in vivo. The aim of the present study was to investigate whether transgenic overexpression of Cdx1b, the functional equivalent of mammalian Cdx2 in zebrafish, may lead to IM of squamous epithelium in zebrafish.

Methods: We first characterized the histology of the upper gastrointestinal tract of zebrafish. A highly conserved promoter of zebrafish keratin 5 was cloned to drive transgenic expression of GFP. A transgenic zebrafish system was then developed by expressing Cdx1b gene under the control of zebrafish keratin 5 promoter (zK5p). Cdx1b expression in the squamous epithelium of transgenic zebrafish was analyzed by in situ hybridization, immunohistochemical staining and RT-PCR. Gene expression in the squamous epithelium of wild-type and transgenic zebrafish was analyzed by Affymetrix microarray and confirmed by in situ hybridization. Morphology, mucin expression, cell proliferation and apoptosis were analyzed by H&E staining, PAS Alcian blue staining, PCNA immunohistochemical staining and TUNEL assay as well.

Results: We found that zebrafish tongue was covered by a non-keratinized stratified squamous epithelium, which was similar to the oro-esophageal epithelium in humans. In situ hybridization showed that keratin 5, a marker of the basal cell layer of mammalian esophageal epithelium, was expressed in the squamous epithelium of zebrafish tongue. GFP expression in transgenic fish recapitulated endogenous zebrafish keratin 5 gene expression as shown by in situ hybridization. In Cdx1b transgenic zebrafish, Cdx1b was found to be overexpressed in the nuclei of squamous epithelial cells of the transgenic zebrafish. Cdx1b induced metaplastic changes in gene expression in the squamous epithelial cells, that is, up-regulation of intestinal differentiation markers and down-regulation of squamous differentiation markers. However, Cdx1b did not induce histological IM, or modulate cell proliferation and apoptosis in the squamous epithelium of transgenic zebrafish.

Conclusion: Transgenic overexpression of Cdx1b in the squamous epithelial cells induced metaplastic changes in gene expression, but failed to produce metaplastic changes in morphology. Cdx1b/Cdx2 may require cooperation of other genetic factors for induction of IM in squamous epithelium. In the present study, we first characterized the histology of the upper gastrointestinal tract of zebrafish.

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 1960.
Abstract 1966: In vivo detection of nucleotide lesions preceding mutation fixation
Authors: Mills Wilbur K. , Queimado Lurdes , Ramachandran Ilangovan , Friedberg Errol , Reis Antonio M. C.
Published: February 2011

Background and Purpose: Unrepaired DNA damage likely originates a large fraction of human cancer. However, a direct correlation between DNA damage and specific mutations is lacking. To identify in vivo nucleotide lesions that can act as the precursors of neoplastic mutations, we investigated the origin of specific tumor signature mutations previously reported on codon 122 of the p53 tumor suppressor gene (Trp53) in UVB radiation induced mouse skin tumors. Methods: The dorsal skin of wild-type (WT) and repair defective (Xpc−/− Trp53+/−) mice was shaved and exposed to a single dose of 4.8 kJ/m2 UVB radiation. Skin from unirradiated and irradiated animals was excised surgically at specific time points (0, 24 and 48 h after irradiation) and used for DNA extraction. A novel primer-anchored PCR based damage-detection methodology developed in our laboratory was used to identify and map DNA damage on the transcribed (TS) and non-transcribed strand (NTS) of the Trp53 gene. Results: Twenty-four and 48 h after UVB-radiation, significant levels of unrepaired nucleotide lesions persisted in genomic DNA of Xpc−/− Trp53+/− compared with WT mice. We observed that most of the damage blocked the primer-extension, yielding early stops. Additionally, most of the damage affecting Trp53 codon 122 in Xpc−/− Trp53+/− mice occurred in the NTS and strictly localized to 2 nucleotides. Importantly, a small percentage of the damage observed at these nucleotides allowed DNA polymerase bypass with misincorporation. Significantly, these lesions were detected precisely in the two nucleotides of Trp53 codon 122 that were found mutated in 64% of all tumors arising in this genotype. These results support the model that the tumor mutations at this site arise from error-prone bypass of long-lasting, unrepaired DNA lesions. Conclusions: We demonstrate a significant correlation between the persistence of precisely localized nucleotide lesions and the later establishment of tumor mutations at those specific nucleotides. Using a novel primer-anchored DNA damage methodology, we identified and mapped for the first time in vivo polymerase by-passable nucleotide lesions. Given the mutagenic potential of these lesions, the wide application of this novel technique for the identification of those lesions and the quantification of in vivo DNA damage might have major implications for early detection of cancer precursor lesions and evaluation of prevention strategies.

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 1966.
Abstract 1967: UvrABC excision of interstrand crosslink mitomycin C-DNA lesion induces double-stranded DNA breaks
Authors: Weng Mao Wen , Zheng Yi , Jasti Vijay P. , Champeil Elise , Tomasz Maria , Wang Yin sheng , Basu Ashis K. , Tang Moon Shong
Published: February 2011

Mitomycin C (MC) forms at least nine different covalent DNA adducts including an N2-2’-deoxyguanosine monoadduct (MC-mono-dG) and inter- and intrastrand bis-adducts with 2’-deoxyguanosine (dG) in vivo. Inter-strand cross-linked (ICL) dG-MC-dG-DNA adducts can prevent strand separation, and therefore, the MC antitumor activity is most likely derived from formation of ICL-MC adducts. In Escherichia coli cells, UvrABC, the nucleotide excision repair (NER) enzyme complex can repair ICL psoralen lesions that cause DNA bending. The mechanism and the consequence of NER of ICL dG-MC-dG lesions that do not induce DNA bending remain unclear. In order to compare the NER of MC-mono-dG with an ICL dG-MC-dG adduct, we constructed DNA fragments containing the adducts in the same DNA sequence context. We determined that UvrABC incises only at the strand containing MC-mono-dG adduct. In contrast, UvrABC makes three types of incisions on a site specific ICL dG-MC-dG adduct: type 1 (40 %), a single 5’ incision on one strand and 3’ incision on the other; type 2 (21 %), dual incisions on one strand and a single incision on the other strand; and type 3 (39%), dual incisions on both strand of both 5’ and 3’ sides of the ICL dG-MC-dG adduct. These three types of incisions occur with similar kinetics. An important consequence of these incisions is formation of DNA double-stranded breaks (DSB). Contrary to conventional model, we also found that UvrA, UvrA+UvrB and UvrA+UvrB+UvrC bind to MC-modified DNA specifically and form complexes that include UvrA. No UvrB- and UvrB+UvrCDNA complexes were observed. Our findings challenge the current UvrABC incision model of ICLs. We propose that NER of ICL dG-MC-dG adduct produces DSB, a lethal event that contributes to MC antitumor activity, and causes a non-homologous end-to-end joining that leads to DNA translocation and deletion mutations.

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 1967.
Abstract 197: The KRAB-containing zinc finger protein ZNF545 is a functional tumor suppressor exerting proapoptotic and antiproliferation abilities with frequent epigenetic inactivation in multiple carcinomas
Authors: Cheng Yingduan , Liang Pei , Geng Hua , Cheng Suk Hang , Ng Margaret H L , Chan Anthony T c , Tao Qian
Published: February 2011

Epigenetic silencing of tumor suppressor gene is frequently involved in tumor development. Some zinc finger proteins (ZFPs) involved in tumorigenesis are down-regulated through CpG methylation in multiple carcinomas. Here, through genome wide-screening, we identified a novel KRAB domain-containing zinc finger protein (KRAB-ZFP), ZNF545, downregulated in multiple tumor cell lines including nasopharyngeal, esophageal, colon, stomach, liver, kidney, breast, cervix, and prostate carcinomas, in contrast to its broad expression in normal tissues. The promoter of ZNF545 contains a typical CpG island and is frequently methylated in multiple carcinoma cell lines. Transcriptional silencing of ZNF545 could be reversed by pharmacologic demethylation or genetic demethylation, indicating a direct epigenetic silencing mechanism. ZNF545 was also frequently methylated in primary tumors of NPC and ESCC, but less frequently in normal epithelial tissues and paired surgical marginal normal tissues. ZNF545 was found to be a transcriptional repressor when fused to Gal4-binding domain, as determined by the luciferase assay. Ectopic expression of ZNF545 in silenced cancer cell lines significantly inhibited their colony formation, proliferation and induced apoptosis, indicating that ZNF545 can function as a tumor suppressor. ZNF545 also can inhibit the activity of NF-KappaB and AP-1, which play an important role in tumorigenesis. We further found that ZNF545 was located in the nucleus and sequestered in the nucleolus in some cells. ZNF545 could co-localize with KAP1 and heterochromatin protein, so we proposed that ZNF545 could inhibit tumorigenesis, at least partially through downregulating the transcription of target genes, or regulating nucleolus function such as ribosome biogenesis. The tumor specific-silencing of ZNF545 could serve as an epigenetic biomarker for common 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 197.
Abstract 1980: Transcriptional profiling in peripheral blood mononuclear cells of patients with pancreatic cancer identifies several genes with potential diagnostic and prognostic implications
Authors: Baine Micahel , Chakraborty Subhankar , Smith Lynette , Mallya Kavita , Sasson Aaron , Batra Surinder
Published: February 2011

Background: Pancreatic cancer is one of the most lethal human malignancies, being the fourth most common cause of cancer-related mortality in the Western world and fifth most common worldwide. Despite advancements in understanding the pathogenesis of this malignancy, no reliable screening test currently exists for pancreatic cancer. As a result, the majority of patients present with advanced stage disease contributing to a poor prognosis. Owing to their accessibility, peripheral blood mononuclear cells (PBMCs) are a rich source of potential biomarkers for diagnosis and predicting patient outcome. The question of whether the gene expression profile in PBMCs of pancreatic cancer patients could be useful for its detection has not been examined. Hence, we tested the hypothesis that global gene expression profiling of PBMCs from pancreatic cancer patients could be useful to identify genes potentially useful as specific, early, surrogate biomarkers in the diagnosis of lethal pancreatic cancer.

Experimental design: We evaluated the transcriptional profile in PBMCs of 35 patients with pancreatic adenocarcinoma and compared it to that of 33 healthy controls using a Phalanx whole genome microarray containing probes for 39,200 genes. The Universal human reference was used as the reference against which all samples were normalized. We further validated the results of the microarray by quantitative real time PCR using SYBR green based chemistry. The normalization of the data was performed using the BRB Array tool software (http://linus.nci.nih.gov/BRB-ArrayTools.html)

Results: After normalization and filtering the genes (criteria: false discovery rate <10%, confidence level 90%), 21,671 genes remained for analysis. 530 genes were found to be differentially expressed in pancreatic cancer patients (p<0.05). 78 of these genes had at least a 1.5 fold change (up or down-regulation) in expression compared to that in the control PBMCs. The expression of two significantly upregulated genes (GAPDH, ASGR2) and four significantly down-regulated genes (DYRK2, MS4A1, EDG1, GRAMD1C) were validated via quantitative PCR. There was an 83% correlation between the microarray and qPCR results for these genes.

Conclusion: The present study represents the first example of gene expression profiling in the PBMCs of pancreatic cancer patients with the aim of identifying patterns of gene expression for diagnostic and prognostic purposes.

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 1980.
Abstract 199: HPV-16 E6 silencing of p16INK4a in human cervical cancer cells
Authors: Yeung Chi Lam Au , Tsang Tsun Yee , Co Ngai Na , Yau Pak Lun , Kwok Tim Tak
Published: February 2011

Aberrant promoter methylation and silencing of tumor suppressor genes such as p16INK4a were reported in association with cervical carcinogenesis. Persistent infection with high-risk human papillomavirus (HPVs), such as HPV-16, contributes significantly towards the cervical cancer development. One of the HPV-16 early proteins E6 is considered to function as an oncoprotein. In the present study, the role of HPV-16 E6 in the regulation of p16INK4a silencing was investigated.

Knockdown of E6 in HPV-16 positive human cervical carcinoma SiHa cells by the technique of small interfering RNA (siRNA) led to an increase in p16INK4a mRNA expression as assessed by quantitative RT-PCR analysis. Addition of DNA demethylating agent, 5-aza-2’-deoxyctidine, also had similar effect. Moreover, by methylation-specific PCR analysis, hypo-methylation of p16INK4a promoter was detected in HPV-16 E6 knockdown SiHa cells. The results indicated that HPV-16 E6 may regulate the expression of p16INK4a through promoter methylation. By Western blot analysis, the expression of DNA methyltransferase DNMT1 was repressed in HPV-16 E6 knockdown SiHa cells while it was induced in HPV-16 E6 over-expressed cells. In addition, decrease in p16INK4a mRNA expression and hyper-methylation of its promoter were observed in SiHa cells upon DNMT1 cDNA transfection.

To sum up, HPV-16 E6 silencing of p16INK4a may be through the upregulation of DNMT1 which in turn induces the hyper-methylation of p16INK4a promoter and thus suppresses p16INK4a expression. This pathway may be one of the possible mechanisms for the oncogenic function of HPV-16 E6 in human cervical cancer development.

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 199.
Abstract 1991: Integrated analysis of copy number alteration and RNA expression profile in pediatric diffuse intrinsic pontine glioma
Authors: Zarghooni Maryam , Bartels Ute , Bouffet Eric , Hawkins Cynthia
Published: February 2011

DIPG is one of the most devastating of pediatric malignancies and one for which no effective therapy exists. A major contributor to the failure of therapeutic trials is the assumption that biologic properties of childhood brainstem tumors are identical to adult high-grade gliomas. A better understanding of the biology of DIPG itself is needed in order to develop agents targeted more specifically to these children's disease. Here we address this lack of knowledge by performing the first high-resolution, DNA- and RNA-microarray analysis of pediatric DIPG.

Nine DIPGs were prospectively collected at post-mortem following consent for research purposes. Four pre-treatment surgical samples were also retrieved from our pathology archives. All samples were hybridized to Affymetrix SNP-arrays (250k or 6.0). Nine samples were also hybridized to the HumanRef-8 v3.0 (DASL) or HumanWG-6 v3.0 expression beadchip from Illumina. Data were analyzed using the Copy Number Analysis Tool (Affymetrix) and Partek Genomics Suite using HMM and segmentation algorithm for copy number and clustering algorithm for gene expression.

DASL and Whole genome beadchip from Illumina have 18,404 probes in common. Those common probes were selected in the two data sets and the gene intensities related to those probes were pulled out for each sample separately. The differentially expressed genes were then identified using one-way ANOVA. For each sample, a gene list was created containing genes having a fold change between 2 and −2. The intersection of the seven gene lists was found using a Venn diagram. In total 234 genes were found that are differentially expressed in all seven samples.

The gene expression and gene copy number data were then integrated. In total 5 genes show correlation between copy number and gene expression in all seven samples.

Among the 234 differentially expressed genes, Ingenuity pathway analysis identified 63 genes associated with different aspect of cancer including proliferation, metastasis, polyploidization, neoplasia, adhesion, migration, survival, acidification, attachment, cell cycle progression, differentiation, growth and invasion.

Our data provides the first, comprehensive, genomic analysis of pediatric DIPG. A thorough understanding of the genetic abnormalities in DIPG is a crucial first step in the development of targeted therapies for this devastating group of tumors. This is of particular importance for DIPG given the lack of efficacy of current treatment regimens and the dismal prognosis for these 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 1991.
Abstract 1999: Aberrant expression of HOX transcript in ovarian carcinoma
Authors: Thompson Kevin J. , Southern G. Kirk , Bahrani-Mostafavi Zahra , Mostafavi M. Taghi , Tait David L.
Published: February 2011

Ovarian cancer is a complex disease phenotype that is challenging to diagnose, primarily because patients tend to remain non-symptomatic until after metastasis has initiated. For those individuals identified early in the disease progression the survival rate is promising, but for the majority, diagnosed late, the 5-year survival rate is dismal. Our eventual goal is to identify a panel of circulating markers that distinguish early onset of the disease. In particular, we have examined the homeobox (HOX) transcript family of genes, known to be involved in cancer progression. These genes are intrinsic cellular factors regulating positional development during embryogenesis and bone formation, and are documented upstream regulators of 16 signaling pathways.

Methods: The tissue-specific gene expression from 35 human ovarian tissue samples, using Affymetrix GeneFocusTM microarrays was examined. The microarray analysis was performed on tissues from 8 normal ovaries, 12 benign and 15 malignant epithelial tumors. Microarray output was processed with a stringent data cleansing pipeline to ensure the investigated genes can be unambiguously interpreted.

Results: ANOVA analysis reveals a significant alteration in the HOX expression profiles between ovarian tumorous and non-tumorous tissues. While several members of the homeobox gene family are reported to be differentially expressed, we observed a significant shift from healthy HOXC6 expression to an aberrant HOXB2 expression. Whereas non-tumorous tissue demonstrated elevated levels of HOXC6 mRNA transcript, the malignant tissues demonstrated elevated levels of HOXB2 transcript. A possible consequence of the aberrant HOX expression levels is to increase the production and hence the paracrine signaling of osteopontin (SPP1), which is reported to be negatively regulated by a SMAD-HOX interaction. Osteopontin has been correlated to cancer progression, metastasis, and patient survival. We observed a significant correlation between elevated SPP1 expression and the observed HOX disregulation.

Conclusion: We demonstrated a correlation between malignant associated SPP1 upregulation and aberrant HOX transcript regulation. These alterations in transcript and protein levels are significant to the epithelial microenvironment. These results have been validated by qRT-PCR and IHC and confirmed with additional patient specimens. The correlation between these two events needs to be further investigated as to their significance in the progression of the disease and as potential candidate biomarkers for ovarian 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 1999.
Abstract 2: Naked CanScript, an 18-base pair sequence, has tumor cell-specific promoter activity in vivo: Implications for targeted gene therapy
Authors: Sawicki Janet A. , Huang Yu-Hung , Cozzitorto Joseph , Langer Robert , Anderson Daniel G. , Brody Jonathan R.
Published: February 2011

The MSLN gene encodes mesothelin and is highly active in several human malignancies including ovarian, pancreatic, bronchial, gastroesophageal, cervical, endometrial, and biliary carcinomas. The high cancer cell-specific activity of MSLN is attributable to an 18-bp upstream enhancer, CanScript, which selectively elevates transcription upon binding of TEF-1, a transcription enhancer factor, to a MCAT motif. It has previously been shown that three concatemerized copies of CanScript produce a 30-fold enhancement over a SV40 minimal promoter in MSLN-expressing cancer cells (Cancer Res. 2007 Oct 1;67(19):9055-65). To determine whether incorporation of CanScript into gene constructs may have application in enhancing activity of promoters used in cancer-targeting gene therapy strategies, we generated several luciferase reporter gene constructs having different cell type-specific promoters (MSLN, HE-4, PSA) and different copy numbers of CanScript (1X, 2X, 3X, 6X). We transfected multiple cell lines, including MSLN+ (ovarian and pancreatic) and MSLN− (liver, lung, and prostate) tumor cells, with these DNA constructs, and measured luciferase activity 48 hrs later. To replicate an in vivo therapeutic setting, we used nanoparticles to deliver the constructs to the peritoneal space of healthy and ovarian-tumor bearing mice, and measured gene expression in tumors and multiple organs by optical imaging. Surprisingly, we determined that an 18-bp CanScript sequence activates gene expression in a cell-specific manner in the absence of any other promoter sequence, and that amplification of CanScript in combination with either the MSLN or HE4 promoter sequences, i.e., two gene promoters that are highly active in ovarian cancer cells, significantly enhances their activity proportional to the number of copies of CanScript, in MSLN+ cells, including MSLN+ HE4− pancreatic cells, but has little effect in MSLN− cells. These results support the use of CanScript when increased, specific gene expression is desired to improve therapeutic efficacy in tumor cells in which MSLN is highly active.

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 2.
Abstract 2002: Cell reprogramming by hypoxia
Authors: Luigi Varesio , Fardin Paolo , Versteeg Rogier , Blengio Fabiola , Barla Annalisa , Bosco Maria Carla
Published: February 2011

Background

Low oxygen tension (hypoxia) is an important determinant in tumor progression. In this study we assess the prognostic value of an in vitro derived hypoxia gene signature in neuroblastoma patients.

Material and Methods l1-l2 regularization framework has been applied on gene expression profiles of 11 neuroblastoma cell lines to define the neuroblastoma hypoxia signature. We applied k-means clustering on the expression level of the signature 62 probesets to segregate 88 neuroblastoma patients and subgroups obtained by common risk factors stratification. We analyzed the classes by Kaplan-Meier curves and log-rank test for overall survival (OS) and event-free survival (EFS). Multivariate Cox analysis was performed to define the predictive power of the signature.

Results

The neuroblastoma hypoxia signature distinguished two groups of neuroblastoma patients classifying them as poor prognosis (21 patients), those having OS rate of 25.5% and EFS rate of 27.7%, and as good prognosis (67 patients), those having OS rate of 73.2% and EFS rate of 67.7%. The poor prognosis patients show an over-expression of the hypoxia probesets. Multivariate Cox analysis revealed that the neuroblastoma hypoxia signature is a significant independent predictor after controlling for commonly used risk factors. When applied to MYCN not amplified patients, the hypoxia signature was capable to stratify patients with OS rate of 24.2% and EFS rate of 27.3% for the patients with poor prognosis, compared with OS rate of 81.4% and EFS rate of 74.8% for the patients with good prognosis.

Conclusions

We demonstrate that the NB-hypo signature is a significant prognostic factor capable of stratify neuroblastoma patients. Furthermore, we obtained the proof of principle that the approach of hypoxia genes selection from in vitro controlled tumor cell lines, is a feasible method to identify specific contribution of the microenvironment to the tumors’ biology.

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 2002.
Abstract 2006: Mathematical and computational models for cellular space in cancer growth
Authors: Olsen Megan , Sitaraman Ramesh , Siegelmann-Danieli Nava , Siegelmann Hava
Published: February 2011

This study investigates the dependency of tumor cell growth on specific spatial regulations for both normal and tumor cells. In general it is known that cellular growth is affected by contact inhibition, but many models fail to include this aspect explicitly. Our work studies the extent to which spatial constraints and interactions between normal and tumor cells affect tumor growth.

We model spatial constraints via a set of differential equations, modified from the classic logistic equation. These equations represent the hallmarks of cancer, with the addition of spatial rules based on the ratio of living tumor to normal cells in the tissue. Four different sets of equations are analyzed and compared, each representing a different potential scenario of how tumor and normal cells differ in their views of space. Most computational models of cancer do not investigate the interactions between normal cells and tumor cells, and our approach demonstrates that these interactions are crucial for modeling and understanding cancer growth.

Our results provide a delineation of when tumor growth will take over an area versus when it will be slowed or stopped for each type of spatial constraint. Our results indicate that different combinations of spatial regulations cause different outcomes in tumor growth. They also demonstrate that cells following the same set of rules for proliferation, death, and mutation meet different outcomes given a change in spatial constraints. Thus, an accurate modeling of spatial interactions between two cellular populations is crucial to adequately examine tumor cells. Our results suggest that a treatment assuming one set of rules will fail if another set of rules is in place. Further, if we learn to modify these spatial rules in a tissue then tumor growth could be decreased. Our work also implies that to be able to use computational models for evaluating options for treatment proper spatial rules must be taken into account in the model.

In conclusion, we recognize that the influence of contact inhibition on different populations of cells can drive one cancer to take over the system, while it can significantly slow the growth of another. Such spatial constraints are extremely crucial to modeling and understanding cancer growth and in evaluating options for 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 2006.
Abstract 2009: A new repressive network module in Ewing's Sarcoma
Authors: Kauer Maximilian O. , Jug Gunhild , Niedan Stephan , Walker Robert L. , Meltzer Paul S. , Kovar Heinrich
Published: February 2011

The EWS-FLI1 chimeric transcription factor characteristic of Ewing's sarcoma family tumors (ESFT) constitutes the prototype of an aberrant ETS transcription factor causally involved in oncogenesis. However, the mechanisms of transcriptional regulation leading to ETS driven tumorigensis are poorly understood. Previously, we have successfully established and tested a research plan that proceeds from genomics data production, via bioinformatic generation of specific hypotheses to functional elucidation of EWS-FLI1 associated transcription network modules. In-silico analysis of time-resolved expression data revealed enrichment of ETS binding motifs in early EWS-FLI1 activated target genes, while EWS-FLI1 repressed genes showed most prominently enrichment of recognition motifs for forkhead box (FOX) proteins. Other motifs significantly co-occurring in the same promoter with FOX motifs were mainly containing homeobox domains (POU, SOX, NKX, CDP, TGIF). Concentrating on the EWS-FLI1 repressed transcriptional network most FOX proteins (FOXO1, FOXO3, FOXD1 and FOXN3) in the data set were found to be EWS-FLI1 repressed. Promoters of two of these genes, FOXO1 and FOXO3, were directly bound by EWS-FLI1 in a ChIP-seq experiment, and were also expressed at lower levels in ESFT than in mesenchymal progenitor cells which constitute a likely cell of origin for ESFT. Furthermore, bioinformatic analysis showed that FOX motifs were significantly co-enriched with ETS motifs in promoters of the same gene for ∼4% of all genes. Thus, we hypothesize that EWS-FLI1 exerts a major part of its repressive effect via inhibition of FOX proteins and may also directly (co-)repress a subset of these genes. In depth dissection of this newly identified repressive module of the EWS-FLI1 transcription network is performed by ectopic expression, RNA interference (RNAi) and reporter gene technologies combined with mutation analysis, and chromatin immunoprecipitation and protein co-immunoprecipitation.

This study was funded by: “European Embryonal Tumor Pipeline” 6th framework program of the European Commission, (STREP “E.E.T. Pipeline” contract LSHC-CT-2006-037260), and by funds from the Austrian Research Fund FWF.

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 2009.
Abstract 2014: An estrogen receptor - centered network for probing anti-estrogen drug resistance with siRNA screening technology
Authors: Nasto Rochelle E. , Serebriiskii Ilya , Jablonski Sandra A. , Johnson Michael D. , Clarke Robert , Weiner Louis M. , Golemis Erica A.
Published: February 2011

De novo and acquired drug resistance pose significant problems for the effective treatment of estrogen-receptor (ER) positive breast cancers. We hypothesized that changes in the action of proteins interacting with core components of the estrogen response machinery may be responsible for such resistance, and that inhibition of these proteins may modulate response to hormonal therapies. To test this idea, we created a 631 gene network using ERα (ESR1), ERβ (ESR2), estrogen related receptors α (ESRRA) and γ (ESRRG), and aromatase as seed genes. The addition of genes to the network was selectively based on connectedness to the 5 seed genes. We used a set of bioinformatic resources including protein-protein interactions (PPIs), protein complexes, canonical pathways and estrogen responsive genes, to generate candidates for insertion into this network.

An siRNA library has been developed from these 631 genes, for use in screening of breast cancer cell lines. Our primary goal is to identify networks of candidate genes involved in resistance to estrogen pathway-targeted drugs, corresponding to genes that reduce cell viability specifically in the presence of the hormonal therapies fulvestrant and tamoxifen. We have used MCF7/LCC1 cells (tamoxifen sensitive/fulvestrant sensitive), MCF7/LCC2 (tamoxifen resistant/fulvestrant sensitive) and MCF7/LCC9 (tamoxifen resistant/ fulvestrant resistant) cell lines as syngeneic models with varying drug resistance profiles for these experiments. In addition, we are identifying genes that differentially affect the intrinsic viability of these cell lines, and thus should illuminate the mechanism of their resistance to hormonal therapies. Our goal is to elucidate a network of regulators of anti-estrogen resistance.

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 2014.
Abstract 2020: MiR-210 modulates the hypoxic response in endothelial and ovarian cancer cells
Authors: Subramanian Indira V. , Ghosh Goutam , Joshi Hemant , Zheng Yan , Benyumov Alexey , Ramakrishnan Sundaram
Published: February 2011

Tumor growth and progression is intricately linked to hypoxia induced adaptive changes. Hypoxia is known to alter chemosensitivity, upregulation of putative cancer initiating stem cells and the microenvironment. The multitude of these changes is brought about by differential gene expression. Hypoxia inducible transcription factor-1 alpha (HIF-α) is a key transducer of altered gene expression under low oxygen or ischemia. In addition to the transcriptional activation of multiple genes, hypoxia also alters miRNA levels in tumor and vascular endothelial cells. miRNAs are small noncoding RNAs ∼22 nucleotides in length representing 1%-2% of the eukaryotic transcriptome. We used microarrays to determine relative changes in 467 miRNAs in endothelial and MA148 ovarian cancer cells exposed to hypoxia. One of the miRNAs, miR-210 was significantly up-regulated under hypoxia by microarray analysis (2-fold, P <0.01). miR-210 expression changes were validated by RT-qPCR. Exogenous over expression of miR-210 in endothelial cells increased their proliferative capacity and induced angiogenesis. These effects were reversed by morpholino antagomiR specific for miR-210. In-vivo studies using transgenic zebrafish showed that miR-210 can increase angiogenesis which could be readily reversed by morpholino antagomiR. These studied together showed that miR-210 plays an important role in angiognenesis. We then over-expressed miR-210 in ovarian cancer cells. While in vitro growth rate was not altered, over expression of miR-210 changed the kinetics of tumor growth. Taken together, these data implicate an important role for mir-210 in hypoxia induced adaptive changes in tumor microenvironment.

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 2020.
Abstract 2027: Proteomic analysis identifies pathways regulated by miR-34a
Authors: Chen Qing-Rong , Yu Li-Rong , Cheuk Adam , Song Young , Wei Jun , Chung Joon-Yong , Hewitt Stephen , Veenstra Timothy D. , Khan Javed
Published: February 2011

MicroRNA 34a (miR-34a) is an important tumor suppressor gene and has been identified as a miRNA component of the p53 network. To better understand the biological pathways involved in miR-34a action, we performed parallel global protein and mRNA expression profiling on miR-34a treated neuroblastoma cells (IMR32 cells) using isotope-coded affinity tags (ICAT) and Affymetrix U133plus2 microarray respectively. Global profile suggests a mild overall mRNA expression changes in miR-34a treated cells, but systematic protein level changes have been detected. A total of 1495 proteins represented by 2 or more peptides were identified from the quantitative ICAT analysis, of which 143 and 192 proteins are significantly up- or down-regulated in miR-34a treated cells. Several of these down-regulated proteins contain seed sequences for miR-34a. Pathway analysis of the differentially expressed proteins shows the enrichment of apoptosis and cell death in up-regulated proteins, and DNA replication and cell cycle processes in the down-regulated proteins in miR-34a treated cells. Biological network analysis of direct interaction between differentially expressed proteins suggests that YY1 as well as its downstream proteins are significantly inhibited by miR-34a. Western blotting confirmed the suppression of YY1 protein expression by miR-34a. MiR-34a might target YY1 through miR-34a-binding site in the 3’ UTR of YY1. YY1 is a ubiquitous transcription factor and it is a negative regulator of p53. YY1 has been associated with cell proliferation, anti-apoptosis, tumorigenesis and metastatic potential. Therefore the elucidation of the role of YY1 may shed important light on tumor suppressive function of miRNA-34a.

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 2027.
Abstract 2030: Wnt/beta-catenin signaling acts as a master regulator of microRNA-181 expression in hepatocellular carcinoma
Authors: Ji Junfang , Yamashita Taro , Liu Hongjun , Finkel Toren , Wang Xin Wei
Published: February 2011

Hepatocellular carcinoma (HCC) is a malignant cancer with the observable heterogeneity and microRNAs (miRNAs) are functional associated with the tumorignesis of HCC. We recently identified that a group of HCC cells isolated with epithelial cell adhesion molecular (EpCAM) antibody are hepatic cancer stem cells (CSCs). In EpCAM+ hepatic CSCs, all miR-181 family members are highly expressed and Wnt/beta-catenin signaling is activated. Here, we investigated whether Wnt/beta-catenin signaling could regulate miR-181s expression in HCC. We first detected the association of beta-catenin and miR-181s expression in vitro and in vivo, and found that they were positively correlated. Further, the expression of miR-181s was induced following the activation of Wnt/beta-catenin signaling by the employment of Wnt10B conditioned media, LiCl, and transfection of beta-catenin and Tcf4. Meanwhile, the level of miR-181s was decreased after the inactivation of Wnt/beta-catenin signaling with induction of adenomatosis polyposis coli and transfection of beta-catenin siRNA. Moreover, we found Tcf4 associated with the promoter region of miR-181a-2 and miR-181b-2, in which there existed 7 classic Tcf4 binding elements. Taken together, our data indicate that miR-181s could be activated by Wnt/beta-catenin signaling and the transcript of miR-181a-2 and miR-181b-2 is a novel target of Tcf4/beta-catenin complex in HCC.

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 2030.
Abstract 2037: Anti-miRNA-21 confers radiosensitivity through inhibition of PI3K/AKT pathway and enhancing autophagy
Authors: Gwak Ho-Shin , Kim Tae Hoon , Lee Seung Hoon , Yoo Heon , Park Jong Bae
Published: February 2011

Radiation is a core part of therapy for malignant glioma, which has been given after debulking surgery and prolonged patient's survival. However, the mass of glioma hardly shows response to radiation and frequently become radioresistant after the initial radiation. Among onco-microRNAs, microRNA-21 regulates expression of various molecules involved in anti-apoptosis, invasion, and metastasis in cancer. Yet, there has been known to the relationship between microRNA-21 and radioresistance of glioma. In this study, we investigate the effect of anti-mir-21 on radiosensitivity in glioblastoma and cervical cancer cell lines. Induction of mature microRNA-21 was confirmed by Nothern blotting after irradiation and the transfection of anti-mir-21 resulted in radiosenstivity on colony forming assay. The radiosensitive is thought to be the results of impairment of DNA repair in irradiated cancer cells, which is proved by γ-H2AX staining. In contrast to control group, a significant percentage of anti-mir-21 transfected cells retain DNA foci at 24 hours after irradiation. The suppression of radiation-activated PI3K/Akt pathway is proved on Western blot and thought to be one of the mechanisms for anti-mir-21 induced radiosensitization. Cell cycle analysis shows significant increase of G2/M phase arrest in anti-mir-21 treated cells compared to the control while subG1 population representing apoptotic cells reveals no significant difference between two groups. To investigate further the responsible cell death mechanism other than apoptosis, we measured the degree of autophagy in irradiated cells by both counting acid vesicular organelles using flow cytometry and Western blotting for LC-3 band. The autophagy is significantly increased in anti-mir-21 treated cells after radiation compared to mock treated cells.

We suggest that microRNA-21 is a pivotal regulator of mechanisms to evade radiation-induced cell death in cancer cell.

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 2037.
Abstract 2039: Hyaluronan-CD44 interaction with PKCε promotes oncogenic signaling by the stem cell marker, Nanog and the production of microRNA-21 leading to downregulation of the tumor suppressor protein, PDCD4, anti-apoptosis and chemotherapy resistance in breast tumor cells
Authors: Bourguignon Lilly Y. W , Spevak Christina C. , Wong Gabriel
Published: February 2011

Multidrug resistance and disease relapse is a challenging clinical problem in the treatment of breast cancer. In this study we investigated the hyaluronan (HA)-induced interaction between CD44 (a primary HA receptor) and protein kinase Cε (PKCε) which regulates a number of human breast tumor cell functions. Our results indicate that HA binding to CD44 promotes PKCε activation which, in turn, increases the phosphorylation of the stem cell marker, Nanog, in the breast tumor cell line, MCF-7. Phosphorylated Nanog is then translocated from the cytosol to the nucleus and becomes associated with RNase III DROSHA and the RNA helicase, p68. This process leads to microRNA-21 (miR-21) production, and a tumor suppressor protein [e.g., the Program Cell Death 4 (PDCD4)] reduction. All of these events contribute to upregulation of inhibitors of apoptosis proteins (IAPs, e.g., XIAP and survivin) and the multidrug resistant protein (MDR1)/P-glycoprotein (P-gp) resulting in anti-apoptosis and chemotherapy resistance.

Transfection of MCF-7 cells with PKCε or Nanog-specific small interfering RNAs (siRNAs) effectively blocks HA-mediated PKCε/Nanog signaling events, abrogates miR-21 production and increases PDCD4 expression/eIF4A binding. Subsequently, this PKCε/Nanog signaling inhibition causes IAP/MDR1 (P-gp) downregulation, apoptosis and chemosensitivity. To further evaluate the role of miR-21 in oncogenesis and chemoresistance, MCF-7 cells were also transfected with a specific anti-miR-21 inhibitor in order to silence miR-21 expression and inhibit its target functions. Our results indicate that anti-miR-21 inhibitor not only enhances PDCD4 expression/eIF4A binding, but also blocks HA/CD44-mediated tumor cell behaviors [e.g., IAP/MDR1 (P-gp) upregulation, anti-apoptosis and chemotherapy resistance] in MCF-7 cells. Taken together, these findings suggest that the HA-induced CD44 interaction with PKCε plays a pivotal role in Nanog signaling and miR-21 production leading to the tumor suppressor protein (PDCD4) downregulation, anti-apoptosis/survival and chemoresistance. Thus, this newly-discovered HA/CD44 signaling pathway should provide important drug targets for sensitizing tumor cell apoptosis and overcoming chemotherapy resistance in breast cancer cells.

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 2039.