bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1979: Algebraic factorization of gene expression profiles reveals subtype-specific drug sensitivities among 54 breast cancer cell lines
Authors: Gibb William J. , Collisson Eric , Korkola James , Heiser Laura , Sadanandam Anguraj , Kuo Wen-Lin , Hu Zhi , Mao Jian-Hua , Wang Nicholas , Bayani Nora , Billig Jessica , Ziyad Safiyyah , Lewis Sophi , Feiler Heidi , Jakkula Lakshmi , Wolf Denise , Lenburg Marc , Spellman Paul , Gray Joe
Published: February 2011

Breast cancer is a heterogeneous disease, with reproducible and prognostically important subclasses. Breast cancer cell lines are widely used to study preclinical investigational agents, but the relationships, if any, between breast cancer subclass and drug response are not well understood. To help bridge this gap, we have profiled drug responses across a large panel of well-annotated breast cancer cell lines. In order to translate in vitro drug responses into clinically useful predictions, it is important that the cell line panel be organized into subtypes representative of the cancer subtype diversity found in the clinic. Recent studies have demonstrated that an algebraic clustering method known as “non-negative matrix factorization” (NMF) can be applied to gene expression profiles to resolve clinically meaningful cancer subtypes in greater detail than achievable using other clustering methods. To test whether NMF improves our ability to resolve drug sensitivities in breast cancer cell lines, we clustered pretreatment gene expression profiles of 54 breast cancer cell lines using two different methods: (1) NMF-based consensus clustering and (2) hierarchical consensus clustering. Using NMF-based consensus, we identified five robust subtypes (two Basal-A, one Basal-B and two Luminal classes). In contrast, using hierarchical consensus clustering, we could identify only three robust subtypes (one Basal-A, one Basal-B and one Luminal class). The drug response profiles were then segregated by subtype to determine whether either of the two clustering methods improves our ability to resolve drug sensitivities. Of the 67 drug compounds included in our study, the 5-subtype NMF-based classification scheme revealed three compounds (AG1024, CPT-11 and topotecan) exhibiting subtype-specific drug effects (p<0.1) that are undetectable using the 3-subtype hierarchical clustering. The statistical significance of drug sensitivity was gauged using the Kruskal-Wallis rank sum test, adjusted for false discovery rate Q=0.05. In conclusion, NMF consensus clustering can be used to detect drug response patterns that would otherwise go undetected.

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 1979.
Abstract 1983: TP53 mutations in hepatocellular carcinoma: Association with survival and stem cell-like gene expression traits
Authors: Woo Hyun Goo , Wang Xin Wei , Budhu Anuradha , Tang Zhao-You , Sun Zongtang , Harris Curtis C. , Thorgeirsson Snorri S.
Published: February 2011

PURPOSE

Mutations of TP53, a tumor suppressor gene, are associated with prognosis of many cancers. However, the prognostic value of TP53 mutations in hepatocellular carcinoma (HCC) is still unclear, largely because of the enormous heterogeneity in the geographic and etiological backgrounds of the HCC patients. Here, we analyzed the prognostic values of TP53 mutations. Gene expression profiling analysis was performed to evaluate the effect of TP53 mutations at the molecular level.

PATIENTS AND METHODS

TP53 mutations were investigated in a total of 409 HCC patients including Chinese (n=336) and Caucasian (n=73) patients using direct sequencing method.

RESULTS

A total of 125 TP53 mutations were found in Chinese HCC patients (37.2 %). HCC patients harboring TP53 mutations showed shorter overall survival compared to patients with wild-type TP53 (Hazard ratio [HR], 1.86; 95% confidence interval [CI], 1.37-2.52; P<0.001). The hotspot mutations at R249S and V157F were significantly associated with worse prognosis in both univariate (HR, 2.11; 95% CI, 1.51-2.94; P<0.001) and multivariate analyses (HR, 1.79; 95% CI, 1.29-2.51; P<0.001). In addition, gene expression profile analysis revealed the expression of stem cell-like traits in TP53 mutated tumors. This finding was validated in breast and lung cancers with TP53 mutations.

CONCLUSION

TP53 mutations, particularly hotspot mutations, are associated with poor prognosis in HCC. The acquisition of stem cell-like gene expression traits may contribute to the aggressive behavior of the TP53 mutated tumors.

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 1983.
Abstract 1987: RNA-seq of the bronchial airway transcriptome identifies novel gene and microRNA expression changes associated with smoking and lung cancer
Authors: Beane Jennifer , Gerrein Joseph , Vick Jessica , Gindin Yevgeniy , Anderlind Christina , Levy Shawn , Massion Pierre , Schembri Frank , Lenburg Marc , Spira Avrum
Published: February 2011

Prior studies have shown that cigarette smoke creates a field of molecular injury in the airway epithelium. Using microarrays, our group has previously identified gene and microRNA expression differences in bronchial airway epithelial cells that are associated with smoking and lung cancer. We hypothesize that RNA-seq of the airway transcriptome will enhance our understanding of the response to tobacco smoke exposure and lung cancer pathogenesis by identifying mRNA splice variants, non-coding RNA, and novel RNA not interrogated by microarrays.

We profiled pooled bronchial airway epithelial cell brushings (n=3 patients/pool) obtained during bronchoscopy from healthy never and current smoker volunteers and smokers with and without lung cancer undergoing surgery for suspicion of lung cancer. The high MW fraction (>200 bp) was amplified using a combination of oligo d(T) and random hexamers (NuGEN, San Carlos, CA) followed by library preparation with Illumina's mRNA Seq Library Prep Kit and sequencing using Illumina's Genome Analyzer generating ∼27-30 million 36 bp reads/sample. The low MW fraction (15-40 bp) was processed using ABI's Small RNA Library Sequencing Kit and sequenced using ABI's SOLiD system generating ∼50-90 million 35 bp reads/sample. The high MW reads were aligned to rRNA (5-13%), the human genome (33-40%), and to computationally generated splice junctions (1%) using BowTie. Differential gene and isoform expression was evaluated using Cufflinks and the R package Genominator. Low MW reads were aligned using both RNA2MAP and Geospiza to a filter containing rRNA, tRNA, and repeats (4-14%), to miRBase (4-10%), and the human genome minus miRBase sequences (4-8%). Expression values were calculated for microRNAs. We compared Affymetrix Exon 1.0 ST, HGU133A2, and Invitrogen miRNA microarrays to RNA-seq and found strong correlation for genes/miRNAs interrogated by microarrays, with most smoking- and cancer related changes in transcript expression being identified by sequencing and not by arrays. Genes found differentially expressed only by sequencing were validated by RT-PCR. RNA-seq also reveals differentially expressed isoforms, potential novel miRNAs, and several isoforms of known miRNAs which are being further investigated.

RNA-seq provides a comprehensive and high-resolution view of the airway transcriptome and will provide insights into the molecular field of injury induced by smoking and the pathogenesis of smoking-related lung disease.

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 1987.
Abstract 2000: Biological function annotation of microarray data using correlated gene indices
Authors: Feng Bin , Sun Kathryn , Nicoletti Richard , Abraham James , Robinson Murray O.
Published: February 2011

Although whole-genome microarray analysis has become a routine tool in biomedical research, extracting meaningful information remains a challenge. We describe a method for assessing biological information in microarray data that relies on the observation that genes common to a biological function often exhibit correlated expression within a microarray dataset. This method comprises the identification of gene sets representing a biological process of interest, determining the subset of genes that exhibit significantly correlated/anti-correlated expression, followed by the quantitative cumulated expression of the set of correlated genes.

We applied the pathway index approach by using available gene lists, Pearson correlation, and mean of correlated gene expression values to estimate the pathway status. We then annotated a renal cancer dataset with pathway index scores of 183 canonical pathways, to identify hypoxia deregulation in Renal Cell Carcinoma samples. Using the pathway index approach, we also established a biological correlation between previously identified chromosomal instability signature and proliferation signature in human cancer, and revealed relationships between two distinct prognostic breast cancer signatures, Mammaprint, Oncotype DX, and basal subtypes within a breast tumor dataset. Our analysis indicated that both Mammaprint and Oncotype DX are good prognostic biomarkers and both biomarkers correlated with basal signature score. However, we also demonstrated that both Mammaprint and Oncotype Dx predicted patient outcome in non-basal type cohort respectively, which suggested that in addition to identify basal subtype as bad outcome group, both Mammaprint and Oncotype DX were good prognostic biomarkers in non-basal type cohort. We also applied this approach to analyze genes collinear along chromosome 7 to identify EGFR locus of chromosomal amplification using only transcriptome microarray data. Thus, gene index methodology provides a new tool to annotate microarray data with biological pathway information.

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 2000.
Abstract 2001: Non-negative matrix factorization (NMF) as a clinical classifier: An example with chemotherapy response in ovarian cancer
Authors: Christopher Szeto , Benz Stephen , Vaske Charles , Sanborn J. Zachary , Zhu Jing , Stuart Joshua , Haussler David
Published: February 2011

Large-scale whole-genome assays such as aCGH and expression profiling are providing an overabundance of data on disease states, yet much of the information is not relevant to driving the disease. There is a need for generating concise explanatory modules with powerful predictive results.

Here we describe a semi-supervised machine-learning method for classifying -omics data with associated clinical features. Using NMF a matrix of -omics data is convoluted step-wise into two matrices; a table of k “metagenes” containing coefficients for membership of each gene, and a table of prediction strengths for each patient into each k-class. Where the class of a patient is known we initially set the prediction strength for that class high, otherwise the prediction strength for each class is set equally. As the NMF algorithm progresses, the class prediction can be swapped if this is supported by the -omics data. Initially the metagene coefficients are unknown and seeded randomly. As NMF does not converge onto a unique solution, multiple metagenes were learned starting at different random coefficients. These multiple models were cross-validated as predictors against held-out sets of patients using a correlation statistic different from the one used to train the model. Where a held-out patient correlates with none of the model's k-classes they are considered members of a novel class, and can be abstained from classification a priori.

We applied our method on the TCGA ovarian serous carcinoma. In this study aCGH and expression profiles were was taken before platinum treatment and the time to relapse recorded. These -omics measurements were then integrated into inferred pathway activities using a computational model of the central dogma (DIGMA). We predicted platinum sensitivity (no relapse or relapse after 12 mo) vs. platinum resistance (relapse within 3mo) on these inferred pathway activities. Consistently, the model with the highest predictive accuracy in a cross-validation setting correctly placed patients into the correct class >80% of the time. Using abstaining it is possible to achieve >90% correct prediction upon a subset of the patients. These results provide useful prognostic indicators as well as indicators for which events drive disease.

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 2001.
Abstract 2003: Detecting clonal relationships of multifocal tumors
Authors: Fox Aleah K. , Jensen Shane T. , Snijders Antoine M. , Schmidt Brian L. , Albertson Donna G. , Maley Carlo C.
Published: February 2011

Understanding the development and progression of tumors is fundamental for the improvement of patient treatment and care. Proliferative verrucous leukoplakia (PVL) is a recurrent, multifocal, precancerous lesion that often transforms into oral squamous cell carcinoma (SCC). Multifocal lesions may be separated in either space (synchronous) or time (metachronous). It is essential to determine the relationship between multifocal lesions in order to properly understand the progression of the disease and treat it accordingly. It has yet to be determined whether PVL lesions arise independently or are derived from a common ancestral clone of cells. We have developed a permutation algorithm to test the null hypothesis that the tumors from the same patient share no more genetic alterations than tumors originating from different patients. The alternative hypothesis is that tumors from the same patient, though separated by time and/or space, share a greater number of chromosomal abnormalities than would be expected by chance and so likely share a common premalignant ancestor cell. This will allow us to determine if the tumors arise as independent events or share some clonal relationship. Biopsy data from nine patients, each with multiple tumors, was used to run individual BAC arrays for each lesion. The breakpoints of genetic alterations were determined using Circular Binary Segmentation (CBS) and served as input for our permutation algorithm which counts the number of shared breakpoint positions between tumors. Though many regions in the genome may be prone to gain or loss in a tumor, the exact start and stop of a breakpoint likely defines a unique event such that two or more lesions sharing this alteration can be considered a signature of clonality. We found that five of the nine patients share a significant number of genetic aberrations between their SCC lesions, leading to the conclusion that in approximately half of patients, multifocal PVL tumors are clonally related. Our algorithm for identifying clonality between multiple samples from a patient could be used on a variety of platforms including high density SNP arrays, measuring loss of heterozygosity and copy number alterations, as well as high throughput sequencing. All that is required is multiple, spatially or temporally distinct samples from each patient and multiple 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 2003.
Abstract 2004: Search for biomarkers of oral lesion by laser microdissection and LC/MS/MS method
Authors: Yamamoto Gou , Hokazono Chie , Kawamoto Mao , Isobe Tomohide , Irie Tarou , Shintani Satoru , Tachikawa Tetsuhiko
Published: February 2011

When we perform profiling analysis using tissue of Homo sapiens, individual difference becomes one of large problems. We use a laser microdissection as one of the solutions for this problem and try profiling analysis from tissue section. This technique can collect the part where morphologic evidence varies from the same tissue section, and comparison in an equivalence case besides in same lesion become possible. In addition, a laser microdissection method is effective in hyperplasia, papilloma, border domain, complicated differentiation form, such as lesion difficult to obtain a cultured cell. In this study, we collected area of normal epithelium, epithelial dysplasia and squamous cell carcinoma from tissue section by using laser microdissection. Collected tissue was dissolved in lysis buffer and digested by trypsin to make samples. Each sample was analyzed and quantified by LC/MS/MS, then, obtained data was referred to the protein database (SWISS PROT). From this procedure, we found over 100 different types of protein in every area. In comparison with each protein profiling list, many already known marker of oral squamous cell carcinoma, such as keratin 17, keratin 13, lumican and CD98, was detected. Two new candidate markers of oral squamous cell carcinoma are discovered at present: one is keratin superfamily, and another is tumor related protein. About extracted new candidate markers, we perform real time PCR, immunohistochemistry and Western blot from tissue section for validation. In conclusion, Laser microdissection and LC/MS/MS were useful method to search for markers of oral squamous cell carcinoma, and detected candidate marker was thought to be effective for diagnosis.

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 2004.
Abstract 2007: Concurrent gene promoter hypermethylation and allele loss occurs infrequently in head and neck squamous cell carcinomas
Authors: Poage Graham M. , Christensen Brock C. , Houseman E. Andres , McClean Michael D. , Wiencke John K. , Posner Marshall R. , Clark John R. , Nelson Heather H. , Marsit Carmen J. , Kelsey Karl T.
Published: February 2011

Malignancies arise as a result of environmental insults that cause an accumulation of molecular changes in the genomes and epigenomes of the affected somatic cells. Numerous models have been described that outline the set of consequential alterations for different tumor types throughout carcinogenesis. The implication of Knudson's two-hit hypothesis for inactivation of tumor suppressor genes, with regards to the emerging field of integrative genomics, is that this gene silencing can be achieved through deletion of one allele and hypermethylation of the other. We aimed to characterize this process in the upper airway epithelium through an array-based molecular investigation of 19 head and neck squamous cell carcinomas (HNSCCs). We utilized a genome-wide integrated approach, combining data from DNA methylation arrays (>1400 loci) with SNP-based resequencing (>500K loci) copy number data, and a novel analytical approach involving model-based clustering methods. We found that while methylation and gene copy number were well-correlated for a number of loci, few tumor suppressors exhibited concomitant silencing alterations. In fact, of the commonly altered genes in this disease only CDKN2A possessed both hypermethylation and allele loss, and only at one locus for a minority of tumors (3/18). Three tumors also lacked one copy of the maintenance methyltransferase gene, DNMT1, and these samples had a lower average methylation across all loci measured than those with a normal copy number (P<0.0001) at this site. Our results suggest that coordination of molecular mechanisms rarely occurs at single genes; however they may be linked through global regulatory processes affecting the patterns of coordinated alterations in order to control carcinogenic gene pathways. A thorough understanding of these alteration patterns and integration of such molecular processes are critical for the identification of cellular targets/biomarkers in HNSCC and for rational therapeutic administration.

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 2007.
Abstract 2010: A Network Phenotyping Strategy (NPS) for HCC identifies distinct coherent survival groupings from observed clinical traits
Authors: Pancoska Petr , Carr Brian I. , Branch Robert A.
Published: February 2011

Background: HCC is a complex disease with tumor growth replacing adjacent liver. Our initial hypothesis was that tumor traits and loss of liver function are independent processes. We examined this, seeking evidence of coherent discrete structure with respect to survival. Methods: NPS was used to analyze 970 patients with biopsy-proven, non-surgical HCC, all followed prospectively until death. We assumed stochasticity with respect to timing of diagnosis and ambiguity of each variable with respect to survival and used a combination of k-partite graph-based analysis with statistical processing of pairwise dependencies of clinical data ordered by survival, each characterized by the mean of clinical parameters of the 100 patients with the closest survival, for 678 survivals. Results: NPS clearly identified heterogeneity, with 3 distinctive phenotypes based on coherence of multiple variables. Each had different survival ranges with trends of collinear relationships between bilirubin, AFP, alkaline phosphatase, SGOT and GGTP. In patients >70 years, the larger the tumor the higher the biochemical values, with the trends decreasing with longer survival. Above 80 years, bilirubin and AFP were normal, with long survival, 330-1250 days. There were 2 groups of younger patients (<55 years). One, with 30-45 days survival, had a similar profile to the older group. In the other, with 90-330 days survival, the profile was for multiple small tumors to trend with biochemical values. A striking finding was the close correlation in trends for AFP against bilirubin, alkaline phosphatase, GGTP or SGOT values, suggesting that liver damage parameters and tumor parameters were not independent factors, but might be inter-twined, especially in older patients. Conclusions: This NPS analysis does not support the hypothesis that tumor growth and cirrhotic damage are independent, but are intertwined processes. Furthermore, we have evidence based on coherence between variables that the growth rates for unifocal tumors of equivalent size are faster in the young than in the elderly. NPS provides useful insights to design future genomic studies to compare different phenotypes and understand the different pathophysiological processes involved.

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 2010.
Abstract 2012: Off-target drug effects due to retroactivity in signaling pathways
Authors: Wynn Michelle , Ventura Alejandra , Garcia Hector , Merajver Sofia
Published: February 2011

A majority of targeted cancer therapeutics involve the specific inhibition of a molecular target in a signal transduction pathway. It is well known that targeted therapies, such as kinase inhibitors, may have effects on pathways other than those specifically targeted, whether by non-specific interactions or by indirect pathway cross-talk effects. The simplest view of signal transduction entails a cascade of molecular events initiated by the recognition of a stimulus and culminating in the chemical alteration of an effector molecule. We have recently shown that cascades can exhibit bidirectional signal propagation without the addition of regulatory feedback connections via a phenomenon termed retroactivity. Thus, retroactivity represents another potential source of off-target effects in signaling cascades.

We have extended our previous work to a computational model which allows us to characterize the significance of the upstream off-target effect via retroactivity with a series of simple signaling networks using physiologically relevant parameters values. We aim to understand the dynamics of cancer signaling by integrating systems biology based models of signaling dynamics into our experimental investigations of breast cancer with the intent of both directing experiments and making predictions. One of the signaling networks we studied takes the form of two independent signaling cascades which have no regulatory feedback connections but are activated by the same upstream kinase. Our results suggest that under physiologically relevant conditions the application of an inhibitor near the bottom of one cascade can produce a significant change in concentration of a protein in the other cascade, even without a regulatory feedback connection between the two cascades. Developing a deeper understanding of bidirectional signal propagation in signal transduction pathways will be vitally important in the effort to develop safer and more effective targeted cancer therapies. Our modeling results challenge the notion that information in cascades only flows in the cell surface-to-nucleus direction and suggests that a perturbation applied within a cascade can produce both an upstream and a downstream effect. The notion of an upstream off-target effect is completely novel and may have significant implications if the perturbation takes the form of an inhibitory therapeutic drug.

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 2012.
Abstract 2013: Integrative genomic studies pertaining to cigarette smoke and human lung carcinogenesis
Authors: Yang Maocheng , Xi Sichuan , Liu Fang , Rao Mahadev , Schrump David S.
Published: February 2011

Lung cancer is a major cause of cancer deaths worldwide. Whereas the vast majority of these neoplasms are directly attributable to cigarette abuse, the molecular mechanisms contributing to tobacco- associated pulmonary carcinogenesis are not well understood. In the present study, we utilized microarray techniques and systems biology analysis to investigate global mRNA and microRNA (miRNA) expression profiles during lung cancer progression using an in-vitro model. Four sets of cell lines were chosen to examine miRNA/mRNA signatures during lung cancer progression, including primary normal human bronchial epithelia (NHBE) as well as small airway epithelial cells (SAEC), immortalized human bronchial epithelial cells (HBEC), a lung cancer line (H1975) derived from a non-smoker, and three lung cancer lines (H1299, Calu-6 and A549) derived from smokers. Cells were cultured in normal media (NM) with or without cigarette smoke condensate (CSC), the DNA demethylating agent, 5 aza-2’ deoxycytidine (DAC), and the histone deacetylase inhibitor Depsipeptide (DP) to examine how cigarette smoke and epigenetic events may affect global mRNA and miRNA expression during pulmonary carcinogenesis. Based on global mRNA/miRNA expression clustering, primary respiratory epithelial cells, immortalized HBEC, and smoker as well as non-smoker derived lung cancer lines were readily distinguished from one another. Each cell group exhibited its own special set of miRNAs /mRNAs, which were over or under-expressed relative to primary cells. Comparison of miRNA profiles in CSC-treated vs untreated NHBE, SAEC, HBEC, A549 and Calu-6 cells revealed that cigarette smoke induces over-expression of miR-21 and miR-31. MiR-21 and miR-31 were also significantly over-expressed in smoker-derived A549 and Calu-6 lung cancer cells relative to non-smoker-derived H1975. In addition, differential gene expression profiles were observed in smoker-derived vs non-smoker derived lung cancer cells. A group of miRNAs/ mRNA were preferentially modulated by sequential DAC/DP treatment in these cultured cells. Further analysis of differentially expressed miRNAs/mRNAs observed in this model system may provide new insight regarding molecular mechanisms associated with pulmonary carcinogenesis, and reveal novel biomarkers for lung cancer diagnosis and prognosis.

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 2013.
Abstract 2015: Patient-specific pathway analysis using DIGMA identifies key activities in multiple cancers
Authors: Benz Stephen , Vaske Charles , Sanborn J. Zachary , Stuart Joshua , Haussler David
Published: February 2011

Cancer is a disease of genomic perturbations that lead to dysregulation of multiple pathways within the cellular system. While common pathways are believed to be shared within specific cancer types, the mechanisms of why particular patients respond differently to treatment is not fully understood. Current -omics studies such as The Cancer Genome Atlas (TCGA) and Stand Up To Cancer (SU2C) have attempted to address this issue by using large-scale whole-genome measurements of mRNA expression, DNA copy number, and epigenetic features. Typical analysis of these measurements relies on integrating data from multiple samples to distinguish signal from noise. However, few analytical methods allow for sample-specific differences to identify features and pathways that are significant for prognosis and clinical treatment classifications.

We developed a pathway inference method called DIGMA (Directed and Integrated Graphical Modeling of Activities) to identify patient- and sample-specific pathway activities. DIGMA is capable of inferring individual gene and protein level measurements within pathways as well as overall pathway alterations specific to an individual tumor. DIGMA models each gene's “Central Dogma” within an overall pathway structure using probabilistic graphical models (PGMs). Individual -omic measurements are attached to their represented protein within the network and proteins are connected using interactions defined in curated pathway models. This representation is flexible enough to support any number of -omics measurements, which can be connected to the protein and pathway in biologically meaningful ways.

Applying our method to TCGA ovarian serous carcinoma and glioblastoma multiforme samples identified pathways both significantly activated across a large majority of the cohort as well as pathways useful for classification of samples that responded well to treatment. We used random simulations to measure the significance of the pathway activities and establish a false discovery rate. These results suggest the ability to identify critical intervention points for therapeutics at a sample-specific level.

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 2015.
Abstract 2019: Molecular pathways involved in docetaxel (D)-resistance hormone-independent prostate cancer (HIPC) cells
Authors: Marín-Aguilera Mercedes , Codony-Servat Jordi , Kalko Susana G. , Gascón Pere , Mellado Begoña
Published: February 2011

Background: D-based chemotherapy is the standard therapy of metastatic HIPC. However, only approximately 50% of patients respond to this treatment and most of them eventually develop resistance to the therapy. The molecular events that lead to D-resistance in HIPC are not well established.

Objectives: To determine the main molecular pathways responsible for D-resistance in two different HIPC cells lines.

Methodology: DU-145 and PC3 cell lines were converted to D-resistant cells (DU-145R and PC3R, respectively) by means of exposing parental cells to increasing doses of D. Affymetrix U133 Plus 2.0 whole genome arrays were used to compare global gene expression between these four cell lines. Genes, pathways and networks, commonly deregulated in both DU-145R and PC3R cells respect their parental cell lines, were analyzed in detail. Changes in expression of a subset of genes were confirmed by real-time RT-PCR.

Results: Differential expression of 321 genes (P<0.05 Bonferroni corrected and logFC>1.2) was found to be common in DU-145R and PC3R cells. Pathway and network analysis showed that these genes were particularly involved in cellular growth and proliferation, gene expression, cellular movement, cellular development, cell death and cell cycle. Other related functions are infection mechanism, cellular assembly and organization, tissue morphology, antigen presentation and cell-mediated immune response. RT-PCR confirmed differential expression in genes related with epithelial-mesenquimal transition (e-CADHERIN, α-CATENIN, VIMENTIN, SNAIL and TWIST), NFkB related genes (IL-6, IL-8, c-REL, P50 and P65) and ErbB signalling pathway family genes (EGFR and HER3).

Conclusions: These data reveals a set of gene networks involved in HIPC D-resistance. Key genes from these networks should be investigated further as new targets for potential therapeutic 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 2019.
Abstract 2022: The WAVE3-dependent cancer cell invasion is regulated by miR-31 during cancer progression and metastasis
Authors: Sossey-Alaoui Khalid
Published: February 2011

MicroRNAs are small non-coding RNAs that are directly involved in the regulation of gene expression by either translational repression or degradation of target mRNAs. Because of the high level of conservation of the target motifs, known as seed sequences, within the 3′-untranslated regions (UTR), a single microRNA can regulate numerous target genes simultaneously, providing a mechanism for this class of RNAs to serve as master regulators of gene expression. Loss of expression of miR-31 has recently been suggested to be associated with cancer progression and metastasis (1). Our previous studies reported a very significant correlation between the expression levels of WAVE3, an actin cytoskeleton remodeling protein, and advanced stages of breast cancer, clearly supporting the function of WAVE3 as a metastasis promoter protein (2). Here we show that the activity of WAVE3 to promote cancer cell invasion is regulated by miR-31 microRNA. We also show a clear inverse correlation between expression levels of WAVE3 and miR-31in invasive versus non-invasive cancer cells. miR-31 directly targets the 3’-UTR of the WAVE3 mRNA and inhibits its expression in the invasive cancer cells. The miR-31-mediated down-regulation of WAVE3 results in a significant reduction in the invasive phenotype of cancer cells, which is specific to the loss of WAVE3 expression since re-expression of a miR-31-resistant form of WAVE3 reverses miR-31-mediated inhibition of cancer cell invasion. We finally report a correlation between the expression levels of WAVE3 and miR-31 in non-invasive vs highly invasive primary human breast cancer tumors. In conclusion, a novel mechanism for the regulation of WAVE3 expression in cancer cells has been identified, which controls the invasive properties of cancer cells. The present study also identifies a critical role for WAVE3, downstream of miR-31, in at least one of the multiple steps that govern the invasion-metastasis cascade.

References:

1-Valastyan et al., A pleiotropically acting microRNA, miR-31, inhibits breast cancer metastasis. Cell 137:1032-1046. 2009.

2-Sossey-Alaoui et al., Down-regulation of WAVE3, a metastasis promoter gene, inhibits invasion and metastasis of breast cancer cells. Am J Pathol. 170:2112-2121. 2007.

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 2022.
Abstract 2024: Over-expression of miR-106b in metastatic hepatocellular carcinoma using an orthotopic metastasis animal model
Authors: Yau Wing Lung , Pang Roberta Wen Chi , Lee Terence Kin Wah , Wo Jana Yim Hung , Poon Ronnie Tung Ping
Published: February 2011

Hepatocellular carcinoma (HCC) is one the most fatal cancers worldwide. Early diagnosis is crucial for curing the disease. However, patients are often diagnosis at late-stage with distant metastasis, and the prognosis of metastatic HCC is poor. Molecular pathological studies confirm that gene expression alteration plays a critical role in disease progression. Recently it has been discovered that microRNA (miRNA) can alter the gene expression at post-transcription level. This study aimed to elucidate the role of miRNA in development of metastatic HCC using an orthotopic animal model and the molecular pathway involved.

Orthotopic metastasis animal model was established by implanting HCC cell lines onto the liver of the SCID mice. Tumor growth was monitored by in vivo imaging system. Primary tumor and lung metastasis were observed after 12 weeks of inoculation. Tumor were then excised and established into primary tumor cell lines (PT) and lung metastatic cell lines (LM). Functional studies comparing the PT and LM cell lines derived from HCC cell line PLC demonstrated higher cell invasion and migration ability in the metastatic cell line compared with the primary tumor cell line. In addition, the LM cell line possessed more stress fiber than the PT cell line. The PLC-derived cell lines and another metastatic HCC cell line, MHCC97H-derived cell lines were subjected to the miRNA microarray analysis. Fifteen human miRNAs were found to be differentially expressed in the LM cell lines when compared to the PT cell lines. miR-106b was one of the miRNAs which was over-expressed in LM cell lines. We further confirmed our findings in HCC clinical sample and found that miR-106b was over-expressed in HCC tumor compared with the adjacent non-tumor tissue, and its expression was significantly associated with the tumor grade (p=0.018). MicroRNA knock-down study was performed by using the miR-106b LNA knock-down probe. The miR-106b knock-down reverted the cell migration phenotype, and fluorescent staining of stress fiber formation showed that the miR-106b knock-down cells have less stress fiber formation than the parental cell lines and the scramble control. We further studied the expression of E-cadherin in PLC-PT, PLC-LM, the scramble control and the miR-106b knock-down cell lines. Our result demonstrated that miR-106b expression inversely correlated with E-cadherin level. Since decrease of E-cadherin expression is the hallmark for epithelia-mesenchymal transition (EMT), further studies will focus on the role of miR-106b in EMT of HCC 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 2024.
Abstract 2028: miR-433 attenuates the spindle assembly checkpoint (SAC) response to paclitaxel
Authors: Furlong Fiona M. , Prencipe Maria , McGoldrick Alo , McGettigan Paul , Carney Desmond , Doyle Emma , Kay Elaine , McCann Amanda
Published: February 2011

Paclitaxel is a microtubule inhibitory chemotherapeutic drug which is increasingly used for the treatment of solid tumours. In vitro studies have demonstrated that attenuating the spindle assemble checkpoint (SAC) alters the post-mitotic responses to paclitaxel. Furthermore, the aberrant expression of a number of the SAC proteins, MAD2, BUBR1, and Aurora A kinase, are associated with poor patient prognosis. We have identified a microRNA, miR-433, that regulates the expression of MAD2. Over-expression of miR-433 in HeLa cells induced downregulation of MAD2 mRNA and protein expression. We have also shown that HeLa cells over-expressing miR-433 and treated with paclitaxel are no longer capable of cyclin B stabilisation and thus have lost the ability to activate the SAC in response to paclitaxel. In addition, cell viability assays showed that HeLa cells over-expressing miR-433 and treated with paclitaxel have an attenuated response to pacilitaxel compared to microRNA scrambled controls. We have characterised the levels of miR-433, MAD2 gene expression and MAD2 protein levels in a cohort of ovarian cancer cell lines. Cell viability assays on this cohort revealed that responsiveness to paclitaxel is associated with high MAD2 protein expression and low miR-433 expression. We hypothesise that the expression of miR-433 when deregulated in cancer leads to altered MAD2 expression and a compromised SAC, a key feature underlying drug resistance to paclitaxel.

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 2028.
Abstract 203: The histone deacetylase inhibitor LBH589 sensitizes pancreatic cancer cells to TRAIL-induced apoptosis through induction of c-FLIP degradation
Authors: Kauh John , Fan Songqing , Yang Lily , Khuri Fadlo R. , Sun Shi-Yong
Published: February 2011

Great efforts have been made to develop novel and efficacious therapeutics against pancreatic cancer to improve the treatment outcomes. Tumor-necrosis factor-related apoptosis-inducing ligand (TRAIL) is such a therapeutic cytokine with selective killing effect toward malignant cells. However, some human pancreatic cancers are intrinsically resistant to TRAIL-mediated apoptosis or therapy. We are interested in overcoming TRAIL-resistance. In this study, we have shown that the histone deacetylase inhibitor LBH589 can cooperate with TRAIL to augment apoptosis even in TRAIL-resistant cells. LBH589 decreased c-FLIP levels in every tested cell line and survivin levels in some of the tested cell lines with minimal modulatory effects on the expression of death receptor 5 and XIAP. Enforced expression of ectopic c-FLIP, but not survivin, abolished the cooperative induction of apoptosis by the combination of LBH589 and TRAIL, indicating that c-FLIP downregulation plays a critical role in LBH sensitization of pancreatic cancer cells to TRAIL. Moreover, we found that LBH589 decreased c-FLIP stability and the presence of the proteasome inhibitor MG132 prevented c-FLIP from reduction by LBH589. Correspondingly, we detected increased levels of ubiqutinated c-FLIP in LBH589-treated cells. These data thus indicate that LBH589 promotes ubiqutin/proteasome-mediated degradation of c-FLIP, leading to downregulation of c-FLIP. Collectively, LBH589 induces c-FLIP degradation and accordingly sensitizes pancreatic cancer cells to TRAIL-induced apoptosis, highlighting a novel therapeutic regimen against pancreatic cancer. (This study was supported by the Georgia Cancer Coalition Distinguished Cancer Scholar award. F. R. K. and S-Y. S. are Georgia Cancer Coalition Distinguished Cancer Scholars)

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 203.
Abstract 2031: Regulation of glucocorticoid receptor in multiple myeloma by microRNA
Authors: Tessel Michael , Krett Nancy L. , Rosen Steven T. , Gunaratne Preethi
Published: February 2011

Resistance to glucocorticoid-based therapies affects the treatment options of many diseases including Multiple Myeloma (MM). Glucocorticoids (GCs) are the most successful treatment for MM, causing apoptosis in the malignant cells. Unfortunately, patients ultimately become resistant to this therapy and despite the application of novel therapeutics, this disease is ultimately fatal. Expression of glucocorticoid receptor (GR) is required for response to therapy and patients who express higher levels of GR have improved survival. To examine the regulation of GR, our lab has previously established tissue culture cell lines from a myeloma patient who had been treated with GCs and become resistant to that treatment. From the initial patient isolate, we established a cell line that is sensitive to GCs (MM.1S) and two phenotypes of GC resistance (MM.1Re and MM.1RL). We hypothesize that miRNA expression in the GC resistant cells cause a decrease in GR expression. To test this hypothesis, we transfected both GC-sensitive and -resistant MM cells with a luciferase reporter construct containing the GR 3′UTR. We measured a decrease in luciferase activity in the GC resistant cells indicating that miRNAs are most likely involved in GR regulation. To identify which miRNAs may be responsible for this regulation, we used deep sequencing miRNAome analysis of the MM.1S, MM.1Re and MM.1RL cell lines. miRNAs more highly expressed in the GC-resistant cells and containing seed sequences which could target the GR 3′UTR were considered candidates. Expression of the candidate miRNAs was validated by Taqman qRT-PCR. GR regulation by candidate miRNAs was tested by transfection of MM.1S cells with miRNA mimics and the luciferase reporter expressing the GR 3′UTR. When exogenously expressed with the luciferase reporter, miR-130b is able to significantly decrease luciferase activity compared to controls as well as reducing the endogenous GR protein expression. In addition, miR-130b over expression partially blocks GC induced cell death, suggesting a role for this miRNA in the regulation of GR and in GC resistance in MM.

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 2031.