bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract LB-399: Genome-wide expression analysis of subtypes of non-small cell lung carcinoma in highly degraded formalin-fixed paraffin-embedded tissue
Authors: Su Li , Wang Zhaoxi , Wu Chen , Chirieac Lucian R. , Christiani David C.
Published: August 2012

Previous studies demonstrated that gene expression profiles from formalin-fixed paraffin-embedded (FFPE) tissues are largely comparable to fresh frozen matched tissue. This technology can assist in discovering biomarkers of lung cancer prognosis and progression by vastly increasing in the potential resources available for cancer research. In this study, we investigated the potential use of the Whole-Genome DASL HT Assay (Illumina, San Diego, CA) for global expression profiling in FFPE tissues obtained by surgical biopsy from patients with early stage non-small cell lung cancer (NSCLC). We obtained high-quality microarray data on 26 pairs of tumor/non-affected tissues, including 18 pairs of adenocarcinoma and 8 pairs of squamous carcinomas. Among genes differentially expressed between squamous carcinomas and adjacent non-affected lung tissue, we found that the AKR1C1 gene, encoding an aldo-keto reductases, was increased strongly in tumors (fold change: 3.0; p=0.02). This finding was consistent with previous reports that overexpression of AKR1C1 gene as an indicator of poor prognosis and chemoresistance in NSCLC. During pathway-based analysis using GeneGo database, we found that differentially expressed genes of adenocarcinoma were significantly enriched in the pathway of cytoskeleton remodeling_TGF, WNT and cytoskeletal remodeling; and differentially expressed genes of squamous carcinomas were significantly enriched in the pathway of Lung Neoplasms_Signal transduction. Our study demonstrates that with DASL expression profiling technology, genome-wide expression profiles can be successfully generated from FFPE lung tissues. Support: CA092824 and CA CA90578, and CA074386 from NCI

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-399. doi:1538-7445.AM2012-LB-399
Abstract LB-401: Functional impact bias reveals cancer drivers
Authors: Gonzalez-Perez Abel , Lopez-Bigas Nuria
Published: August 2012

Currently, one of the main challenges in cancer genomics is the identification of driver genes and pathways among all the altered genes in a cohort of tumors. Typically, tests of recurrence are applied to identify significantly mutated genes, which are candidates to cancer drivers. These methods assess the probability to observe by chance the number of somatic single nucleotide variants (SNVs) found across a number of tumor samples. Some known limitations of these methods include the difficulty in correctly assessing background mutation rate, as all parameters that affect it are not well-understood, and the fact that they usually fail to identify lowly recurrently mutated driver genes. In addition, methods that compute recurrence treat all observed somatic SNVs equally when clearly their impact on protein function varies widely. We have developed a method which can complement the analysis of recurrence of SNVs across several tumor samples to detect candidate driver genes by taking advantage of the information provided by the analysis of functional impact of SNVs and short frameshift indels. The method is based on the assumption that any bias towards the accumulation of variants with high functional impact (FM bias) is an indication of positive selection and can thus be used to detect candidate driver genes or gene modules. We have called it Oncodrive-fm. We have applied the Oncodrive-fm approach to two datasets of genes with variants in samples of different tumor types: Chronic Lymphocytic Leukemia (cll: from Spanish ICGC Group) and Glioblastoma datasets (gbm: from TCGA). Most of the genes detected by recurrence analysis (i.e MutSig) also show significant FM bias (eg. TP53, EGFR, PTEN in gbm and SF3B1 in cll), we call these clear drivers. However, Oncodrive-fm can also detect lowly recurrent likely driver genes that are overlooked by recurrence analysis (eg. IDH1, FGFR1 and FGFR3 in gbm and CDH9 and CHD2 in cll), and identify genes with high number of mutations that do not show FM bias, which we term as candidate false positives. The application of Oncodrive-fm to the analysis of pathways reveals several pathways with FM bias, such as MAPK and mTOR pathways in gbm and mRNA splicing pathway in cll. In summary we show that FM bias helps to uncover drivers and recommend its computation in conjunction with the analysis of recurrence in a cohort of tumor samples to identify candidate driver genes and gene modules. Oncodrive-fm method is available at http://bg.upf.edu/oncodrive.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-401. doi:1538-7445.AM2012-LB-401
Abstract LB-403: Recurrent fusion transcripts in breast cancer
Authors: Sadanandam Anguraj , Wullschleger Stephan , Spellman Paul , Hanahan Douglas , Gray Joe W.
Published: August 2012

Breast cancer is the second leading cause of cancer deaths among women in the United States. Genome wide analyses in primary breast tumors and ∼50 breast cancer cell lines using gene expression profiling revealed subsets defined as luminal, basal-like, ERBB2 and claudin-low. The general hypothesis is that recurrent fusion transcripts exist and play a central role in the pathophysiology and clinical outcome of breast cancer. We identified recurrent fusion transcripts specific to breast cancer cell lines by performing Solexa based paired-end sequencing of whole-transcriptome (RNAseq) using 9 basal, 9 luminals, 4 ERBB2 and 1 claudin-low breast cancer cell lines. In addition, we cross-compared the predicted fusion transcripts with that of copy number and gene expression changes in the respective cell lines and performed gene ontology (GO) based enrichment analysis using the genes that were involved in the fusion. The sequencing of 19 breast cancer cell lines resulted in a range of ∼15 million to ∼45 million paired-end reads of 76 bp per cell line and out of which 93% to 98.6% had quality reads. On average, we predicted ∼14 fusion genes per cell lines (331 fusion genes in total) that are expressed atleast in one cell line. Interestingly, basal breast cancer cell lines on average have more number of fusion transcripts (∼13 per cell line and 115 in total) whereas luminal cell lines have only ∼9 predicted fusion transcripts per cell line (84 in total). Among the 418 unique genes that were involved in fusion processes, 20% of the genes occurred atleast twice and GO enrichment analysis show similar terms to be significantly enriched. Intriguingly, we identified 24 different recurrent fusion transcripts in total. In summary, the data demonstrates that there is more number of predicted fusion transcripts in breast cancer than initially thought. Also, the data suggest that genes with similar functions or processes fuse together. Currently studies are in progress to test if recurrent gene fusions may have a functional role, which may assist in the design of appropriate strategies to target recurrent events, and may be associated with poor outcome of basal breast cancers. Overall, this may improve the prognosis of breast cancer patients.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-403. doi:1538-7445.AM2012-LB-403
Abstract LB-411: RNA sequencing reveals CUX1 to be a conserved tumor suppressor in acute myeloid leukemia associated with loss or deletion of chromosome 7
Authors: McNerney Megan E. , Brown Christopher D. , Wang Xiaoyue , Karmakar Subhradip , Bandlamudi Chaitanya , Yu Shan , Anastasi John , Le Beau Michelle M. , White Kevin
Published: August 2012

Loss of chromosome 7 and del(7q) [-7/del(7q)] are recurring cytogenetic abnormalities in acute myeloid leukemia (AML), occurring in 9% of de novo AML and 50% of therapy-related myeloid neoplasms (t-MN). Abnormalities of chromosome 7 carry an adverse prognosis. Despite intensive analysis by many laboratories, and the identification of multiple minimally deleted regions on 7q, the putative tumor suppressor(s) on chromosome 7 is currently unknown. We performed transcriptome sequencing on 22 samples and SNP array analysis on 35 samples from patients with myeloid neoplasms, half of which contain -7/del(7q). Copy number analysis identified a 2.17 Mb commonly deleted segment on chromosome band 7q22.1 containing CUX1, a gene encoding a homeodomain-containing transcription factor normally expressed highly in hematopoietic stem cells. CUX1 was found to be disrupted in a translocation resulting in a chimeric RNA fusion transcript in one patient. We found the CUX1 transcript and protein to be expressed at haploinsufficent levels in -7/del(7q) leukemias. To test the tumor suppressor activity of CUX1, the drosophila homologue, CUT, was knocked-down in Drosophila melanogaster hemocytes, which led to significantly increased numbers of hemocytes and melanotic tumor formation. Restoration of CUX1 expression in a human AML cell line with -7 decreased proliferation. These data indicate that CUX1 is a conserved, haploinsufficient, tumor suppressor that promotes leukemogenesis in -7/del(7q) AML.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-411. doi:1538-7445.AM2012-LB-411
Abstract LB-416: Genetic analysis of pediatric brainstem glioma using protein analysis of cerebrospinal fluid
Authors: Saratsis Amanda M. , Nazarian Javad
Published: August 2012

Abstract: Diffuse intrinsic pontine glioma (DIPG) is a leading cause of brain tumor death in children due to lack of effective therapy. Genetic analysis of DIPG has been limited due to the lack of readily available tumor tissue for molecular study. Molecular analysis of cerebrospinal fluid (CSF) could provide information on chromosomal abnormalities in DIPG. Methods: CSF samples from normal and brainstem glioma patients were analyzed by MS/MS label-free proteomic analysis using LTQ-Orbitrap-XL. Proteins were identified using the Sequest algorithm in the Bioworks browser against the Uniprot database and quantitated using ProteoIQ software. Relative protein expression was used to extrapolate potential regions of chromosomal amplification and deletion. Results: Quantitative proteomic analysis revealed 309 proteins detected in DIPG CSF specimens but absent in controls 76% of which correlated to regions of known genomic amplification in pediatric brainstem glioma. Specifically, 1q and 17q were chromosomal regions that showed the greatest amplification as judges by high expression in DIPGs CSF Specimens Moreover, 46 proteins were detected in all controls but absent in DIPG CSF specimens. Of these, 58% mapped to known genomic deletion sites, with X, 5p and 17p the most common abnormal regions. These findings correlate with existing data in the literature on genetic abnormalities of brainstem glioma. Conclusions: Cerebrospinal fluid from children with DIPG and other craniospinal tumors are more readily available than biopsies tumor specimen. Proteomic analysis can reveal potential regions of genomic change that correlates with existing data in the literature and can provide insight to pathways of brainstem gliomagenesis. Further analysis of CSF and validation of observed dysregulation is warranted.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-416. doi:1538-7445.AM2012-LB-416
Abstract LB-417: Identification of calreticulin as an invasion-associated protein in ovarian cancer by proteomic approach.
Authors: Chiang Fan-Ying , Shih Ho-Jun , Chow Lu-Ping , Torng Pao-Ling , Lin Chin-Tarng
Published: August 2012

Ovarian cancer is the most lethal gynecological cancer among women worldwide. The majority of malignant ovarian tumors are epithelial ovarian cancer and metastasis has occurred in most patients at the time of diagnosis with worse outcome. In our previous study, we have established an ovarian endometrioid carcinoma cell line OVTW59. The original lines were designated as P0, and the highly invasive subline P4 was isolated from 4 rounds of invasion selection. By cDNA microarray analysis and further functional analysis, we have reported insulin-like growth factor binding protein-3 (IGFBP-3) as an invasion suppressor gene that correlated with poor patient survival outcome. In this study, we compared the protein profiles between OVTW59 P0 and P4 using 2D-electrophoresis to select metastasis-associated proteins. The potential candidates were subsequently analyzed by LC-MS/MS. We identified 49 positive invasion-associated proteins and 20 negative invasion-associated proteins. Gene-Ontology analysis showed that more than 50% of these proteins were invasion-related proteins. We then built up a potential network involving these differentially expressed proteins by Ingenuity Pathway Analysis. From these data, we selected Calreticulin for further analysis. Calreticulin has been reported in associated with cell adhesion, apoptosis, wound healing, removal of cancer cells, and autoimmune. By q-RT-PCR, Western blot and scratch test, we found Calreticulin positively associated with cancer invasion in our in-vitro system. In addition, higher Calreticulin expression was found in SCID mice with higher metastasitc capability. Clinically, immunohistochemical staining in 58 cases of ovarian endometiroid cancer will be performed. The result will be further correlated with patient outcome. In this study, we found Calreticulin a novel invasion-associated protein in ovarian endometrioid cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-417. doi:1538-7445.AM2012-LB-417
Abstract LB-7: Protein crosstalk in tumor microenvironment: direct identification of intercellular protein transfer in retinoblastoma after topotecan or radiation treatment
Authors: Lee Susan , Fanter Robert , Harutyunyan Narine , Murphree A Linn
Published: August 2012

Current work on the tumor microenvironment has shown that crosstalk between cancer and normal cells can be of significant importance. Here we show direct intercellular communication between different cancer cell populations can provide insights into the tumor microenvironment and the bystander effect. Retinoblastoma is the primary intraocular cancer in childhood and resistance to current treatments such as chemotherapy or radiation often results in enucleation. We seek to improve retinoblastoma treatments by elucidating the diversity of and communication between retinoblastoma tumors. Here we provide the first direct evidence of intercellular protein transfer between retinoblastoma cells after topotecan or radiation treatment using stable isotope labeling and tandem mass spectrometry-based protein identification. Retinoblastoma Y79 cells were grown in media containing 13C, 15N lysine and arginine analogues (Y79S) so that all the proteins had full incorporation of these stable isotopes. The Y79S cells were untreated, treated with 0.02 micromolar topotecan, or treated with 4 Gy of radiation before being co-cultured with either Y79 or CHLA215 retinoblastoma cells for 48 hr. Protein populations within each cell type and the concentrated media were identified using mass spectrometry-based sequencing. Direct intercellular transfer was monitored using the unique 13C, 15N protein tags. Changes in the tumor microenvironment and the protein communication between retinoblastoma cells with chemotherapy and radiation treatment were monitored using a transwell co-culture system. As expected, irradiation resulted in a significant decrease in Y79S cell number and viability. Additionally, irradiated Y79S cells caused a significant decrease in the viability of the non-irradiated Y79 bystander cells. Studies of the proteins directly transferred from Y79S to the other retinoblastoma cells identified heat shock protein 90 (HSP90) in both the topotecan and radiation studies. Significantly, time point data provided insights into the protein transfer dynamics. We show significant protein transfer by 24 hours with a decrease in isotopically labeled proteins by 48 hours. We are currently working on elucidating the functional roles of HSP90 and the other proteins transferred during chemotherapy and radiation treatment. In summary, we have shown the first evidence for direct protein crosstalk between retinoblastoma cell populations in response to chemotherapy and radiation. We anticipate that this work will lead to greater insights into how tumor heterogeneity contributes to treatment response.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-7. doi:1538-7445.AM2012-LB-7
Abstract LB-72: A20 ubiquitin ligase-mediated RIP1 polyubiquitin chains inhibits TRAIL-induced apoptosis in glioblastoma
Authors: Bellail Anita C. , Olson Jeffrey J. , Yang Xiaolu , Chen Zhijian J. , Hao Chunhai
Published: August 2012

The tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) apoptotic pathway has emerged as a cancer therapeutic target; however, clinical trials have proven that the vast majority of human cancers are resistant to TRAIL apoptotic pathway-targeted therapies. We show here that A20-mediated ubiquitination inhibits caspase-8 cleavage and TRAIL-induced apoptosis in glioblastoma through two signaling complexes. A20 is highly expressed in glioblastomas and, together with the death receptor 5 (DR5) and receptor-interacting protein 1 (RIP1), forms a DR5-associated plasma membrane bound signaling complex that we named the preligand assembly complex (PLAC) under physiologic conditions. TRAIL treatment leads to the recruitment of caspase-8 to the PLAC for the assembly of a death-inducing signaling complex (DISC). In the DISC, the C-terminal Zinc finger domain of the A20 ubiquitin ligase mediates RIP1 ubiquitination through lysine (K)-63-linked polyubiquitin chains, which bind to the protease domain of caspase-8 and inhibits its dimerization, cleavage and the initiation of TRAIL-induced apoptosis in glioblastoma-derived cell lines and tumor-initiating cells. These results identify A20 ubiquitin ligase as a therapeutic target whose inhibition can overcome TRAIL resistance in glioblastoma and thus have an impact on ongoing clinical trials of TRAIL apoptotic pathway-targeted combination cancer therapies (the manuscript was published online first in Cancer Discovery).

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-72. doi:1538-7445.AM2012-LB-72
Abstract LB-76: Mibefradil, a novel therapy for glioblastoma: An interlaced therapy approach
Authors: Keir Stephen T. , Gray Lloyd , Friedman Henry S.
Published: August 2012

INTRODUCTION: Finding new ways to improve the efficacy and/or overcome resistance to conventional chemotherapy for brain tumor patients is an ongoing research paradigm. Interlaced TherapyTM is a synergistic cancer therapy involving sequential administration of a T-type calcium channel blocker and a cytotoxic agent. For the purpose of this study, mibefradil dihyrdochloride (MBFD), a T-type calcium channel blocker was interlaced with the standard of care treatment - temozolomide (TMZ) for GBM. Different dosing strategies were tested to maximize efficacy of combination. METHODS: Intracranial (ic) adult brain tumor xenografts (D-270 MG) were grown in athymic BALB/c mice. Three days after ic implantation groups of 10 mice were randomly treated with either drug vehicle/control, MBFD alone PO, TMZ alone IP, or the interlaced therapy of agents. Tumor responses for ic xenografts were assessed by difference in median survival. Two sets of studies were conducted to determine most efficacious delivery of combination: 1) Extended treatment regimen with TMZ, and 2) Time optimization of interlaced approach. RESULTS: The interlaced therapy of MBFD and TMZ demonstrated statistically significant (p<0.001) increases in median survival of 142%, 168%, 174%, and 163% vs. control animals when TMZ is delivered on a regimen of 3, 5, 10, and 15 days respectively. More importantly, interlaced therapy produced significant (p<0.026) increases in survival of 48%, 65%, 68% and 61% at 3, 5, 10, and 15 day dosing regimens vs. TMZ alone. When the TMZ dosing regimen was held constant (5 days) and delivered 0.5, 12, 24, 36 and 48 hours after MBFD, the combination produced statistically significant (p<0.001) increases in median survival of 168%, 158%, 105%, 84% and 74% respectively vs. control animals. More importantly, interlaced therapy produced significant (p<0.042) increases in survival of 65%, 58% and 26% respectively at 0.5, 12 and 24 hour time points vs. TMZ alone. CONCLUSION: Our results establish the therapeutic efficacy of the delivery of MBFD and TMZ via Interlaced TherapyTM against D-270 MG xenografts grown intracranially. Furthermore, this study clearly demonstrates that the synchronization of MBFD with TMZ can be optimized. As such, the blockade of T type calcium channels may well be a target that produces clinically effective, safe synchronization that can be used in conjunction with conventional chemotherapy to render it more effective. The results from this study will be used to help guide clinicians as they move forward with clinical trial design to produce the most efficacious combination of MBFD + TMZ using Interlaced TherapyTM.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-76. doi:1538-7445.AM2012-LB-76
Abstract LB-78: Synergistic effect of combination of MEK and phosphatidylinositol 3-kinase inhibitor on cell death in human prostate cancer DU145 cells
Authors: Kim Yunlim , Hwang Jung Jin , Park Hongzoo , Lee Gil Nam , You Dalsan , Jeong In Gab , Kim Choung-Soo
Published: August 2012

Although chemotherapy has been used in castration-resistant prostate cancers (CRPCs) for a number of years, only limited improvement in survival is observed. Therefore, novel targeted therapeutic approaches must be developed for the treatment of CRPC. Currently, a wide range of small-molecular kinase inhibitors have been developed that target signaling pathways for survival, and inhibitors for MEK and PI3 kinase are currently being evaluated in clinical trials. To evaluate whether the combination treatment with MEK and PI3 kinase inhibitors is synergistic in prostate cancers, we used AZD6244 and a compound of GlaxoSmithkline (Smithkline) that inhibit MEK and PI3 kinase respectively. The combination of AZD6244-Smithkline showed synergistic anti-proliferative effect on growth of prostate cancer cells compared with the single treatment. In addition, a combination treatment induced apoptotic cell death, cleavage of caspase-9, caspase-3, and PARP synergistically. A significant increase in apoptosis was detected by annexin V-PI staining in DU145 cells after combined treatment compared with the single treatment. This study suggests that the combination with AZD6244 and Smithkline has a significant synergistic effect on cell growth in CRPC DU145 cells via apoptotic pathway.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-78. doi:1538-7445.AM2012-LB-78
Abstract LB-83: Reduced expression of DRAM2 in tumor cells interferes with both apoptosis and autophagy
Authors: Park Junsoo , Lee Eun-Ju , Jang Ik-Soon
Published: August 2012

Although the role of autophagy in tumorigenesis remains controversial, recent reports support the notion that inhibition of autophagy promotes tumor formation. Damage-regulated autophagy regulator (DRAM) has been identified as an effector molecule that is critical for p53-mediated apoptosis, and we investigated whether there might be other DRAM-like molecules linking autophagy and apoptosis. In this study, we cloned a novel DRAM-homologous protein, DRAM2, and showed that the expression of DRAM2 is down-regulated in ovarian tumors. DRAM2 is mainly localized in the lysosome, and co-localizes with DRAM. While expression of DRAM or DRAM2 individually did not induce cell death, co-expression of DRAM2 with DRAM significantly induced cell death, while the silencing of endogenous DRAM2 attenuated cell death. In addition, overexpression of DRAM2 induces cytoplasmic GFP-LC3 punctuates, and increases the level of endogenous LC3-II. Moreover, the silencing of endogenous DRAM2 interferes with starvation-induced autophagy. Thus, we propose that DRAM2 as well as DRAM is involved in both apoptosis and autophagy.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-83. doi:1538-7445.AM2012-LB-83
Abstract LB-96: Exploring personalized pathways enriched with putative cancer genes identified by next generation sequencing
Authors: Jia Peilin , Zhao Zhongming
Published: August 2012

Keywords: pathway enrichment test; pathway crosstalk; co-mutation; lung adenocarcinomas; glioblastoma; gene length; cancer mutation genes Contact information of the corresponding author: Zhongming Zhao, Ph.D. Department of Biomedical Informatics Vanderbilt University School of Medicine 2525 West End Avenue, Suite 600 Nashville, TN 37203, USA Phone: (615) 343-9158 FAX: (615) 936-8545 Email: zhongming.zhao@vanderbilt.edu List of abbreviations: GBM, Glioblastoma multiforme; NGS, next generation sequencing. Financial support: None. Abstract Pathway analysis of a set of genes represents an important area in large-scale omic data analysis. However, the application of traditional pathway enrichment methods to next-generation sequencing (NGS) data is prone to several potential biases including genomic/genetic factors (e.g., the particular disease and gene length) and environmental factors (e.g., personal life-style and frequency and dosage of exposure to mutagens). We proposed a novel method for the pathway analysis of NGS mutation data by explicitly taking into account the gene-wise mutation rate. We estimated the gene-wise mutation rate based on the individual-specific background mutation rate, which makes different samples comparable, along with the gene length, which makes different genes comparable. The mutation rate was then utilized as the weight for each gene in our weighted resampling strategy, which builds the null distribution for each pathway while matching the gene length patterns. The empirical P value obtained then provides an adjusted statistical evaluation. We demonstrated our weighted resampling method to a lung adenocarcinomas dataset and a glioblastoma (GBM) dataset, and compared it to other widely applied methods. By explicitly adjusting gene-length, the weighted resampling method effectively reject many marginally significant pathways detected by standard methods, including several long gene based, cancer unrelated pathways. We further demonstrated that by reducing such biases, pathway crosstalk for each individual and pathway co-mutation map across multiple individuals can be objectively explored and evaluated. This method performs pathway analysis in a sample-centered fashion, providing an alternative way for accurate analysis of cancer personalized genomic data.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-96. doi:1538-7445.AM2012-LB-96
Abstract LB-97: Optimizing SELEX with high-throughput sequencing
Authors: White Brian S. , Ozer Abdullah , Lis John T. , Shalloway David
Published: August 2012

SELEX (systematic evolution of ligands by exponential enrichment) identifies oligonucleotide “aptamers” that bind their protein targets with high affinity and specificity. Beyond inhibiting all protein function, aptamers can target specific functional regions (e.g., phosphorylation sites and catalytic domains) leaving other function intact. This selective inhibition is a valuable tool for dissection of signal transduction pathways, such as the growing list implicated in cancer by sequencing efforts interrogating tumor genomes. New technological innovations in aptamer discovery aim to keep pace with this need by improving the efficiency of the traditional SELEX enrichment process wherein oligonucleotides are iteratively bound to target, eluted, and amplified to purify an initial random library to a few high-affinity aptamers. Principal among these advances is the adoption of high-throughput sequencing (HTS-SELEX) to detect enrichment of candidate aptamers within the evolving pool. The improved sensitivity of high-throughput sequencing over the traditional use of cloning and sequencing reduces the number of rounds required to reach detectable enrichment. As with traditional SELEX, enrichment and hence number of rounds and overall efficiency are dependent on the free target and oligonucleotide pool concentrations. Though early theoretical approaches have addressed these issues for traditional SELEX, realizing the potential efficiency gains of the new HTS-SELEX approach requires an analysis and resulting protocol tailored to it specifically. Here we provide such an analysis and also re-examine earlier theoretical approaches to traditional SELEX. We show that HTS-SELEX motivates an optimization condition different from that of traditional SELEX and consider the role of stochastic fluctuations in the relatively low multiplicities of the enriched species resulting from the earlier enrichment detection of HTS-SELEX. Unlike previous approaches seeking to maximize some measure of per-round enrichment, this analysis is a global optimization of the entire SELEX process. It results in a specific recommendation for free target concentration, constant across rounds and simply related to the desired affinity, and for corresponding total ligand concentration. Applying the global analysis to an optimization condition appropriate for traditional SELEX again yields recommendations that are provably optimal and that differ from those previously published.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-97. doi:1538-7445.AM2012-LB-97
Abstract LB-98: Transcriptomic and genomic landscape of ovarian cancer stem cells
Authors: Zehir Ahmet , Ertem Server A. , Moore Malcolm A.S.
Published: August 2012

Ovarian cancer (OvCa) is the fifth leading cause of death among woman in USA. OvCa remains a fatal disease because of the lack of accurate early diagnostic methods as well as the heterogeneous nature of the disease itself. The cancer stem cell (CSC) hypothesis states the existence of a sub-population of cells in tumors that has the ability to self-renew as well as generating a fully differentiated tumor tissue. CSCs are also postulated to be resistant to conventional therapies, which might explain the recurrent nature of many cancers. We have recently identified a novel cellular structure in the ascites of NOD/SCID mice engrafted intraperitoneally with an OvCa cell line, consisting of free-floating chains of 4-72 cells with an extensive pericellular glycocalyx. We termed these structures “catenae” (Latin for “chains”). Catena develop by symmetric self-renewal and each cell retain tumor initiating function when transplanted in NOD/SCID IL2Rγ null mice. To elucidate the transcriptomic terrain and analyze expression of known and novel biomarkers, we performed RNA sequencing of catena using the SOLiD platform. We obtained more than 110 Million single reads of which ∼ 60% mapped uniquely to the human genome. Using this powerful technology, we detected expression of 15494 genes with RPKM values higher than 0.3 for which there are 42931 alternatively spliced transcripts. Roughly 3.5% of these alternative-splicing events seem to be novel. By using the aligned reads we detected 14361 single nucleotide polymorphisms (SNPs) which, after filtering, lead to 199 genes with novel SNPs. We also used the cancer genome atlas (TCGA) public database to determine whether any of these SNPs might be responsible for fast recurrence of ovarian cancer or shorter life span of patients. Furthermore, we detected novel fusion genes, which might lead to molecular classifications in ovarian CSCs. Once validated, these SNPs and fusion genes might prove to be pharmaceutical targets for eradication of ovarian cancer or improving patients’ lives.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-98. doi:1538-7445.AM2012-LB-98
Abstract PL01-01: The genetic basis for cancer therapeutics
Authors: Sellers William R.
Published: August 2012

Cancer is a disease driven by the acquisition and clonal selection of gain- and loss-of-function genetic alterations. While a fuller understanding of the pattern, specificity and biological consequences of such genetic events remains for us to elucidate, it is now clear that therapeutics directed against the genetic underpinnings of cancer have had a marked clinical impact. The growing list of therapeutics with efficacy in defined genetic settings includes imatinib in BCR-ABL driven CML, trastuzumab in HER2+ breast cancer, and erlotinib and gefitinib in EGFR mutated lung cancer among others. Indeed, the efficacy of small molecule inhibitors of KIT, PDGFR, HER2, EGFR, BRAF and ALK in a diversity of malignances including GIST, lung cancer and melanoma support the notion that a new generation of efficacious drugs is emerging. Nonetheless, we can articulate 5 key road-blocks to the more rapid and widespread application of the “genetic paradigm” including 1) an incomplete understanding of the genetic alterations characteristic of human cancer; 2) the difficulty in developing therapeutics that reverse the activity of non-kinase oncogenes (e.g. RAS and MYC) or reverse the consequences of tumor suppressor mutations (e.g. p53, RB1); 3) the development of resistance to genetic targeted therapy; 4) the need to identify highly active novel combination therapy regimens and 5) the lack of a robust pre-clinical translational infrastructure allowing for the more accurate prediction of human clinical trial results. This lecture will discuss strategic approaches to these 5 problems in the context of novel emerging therapeutics.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr PL01-01. doi:1538-7445.AM2012-PL01-01
Abstract SY03-01: Revealing new metabolic networks in cancer
Authors: Gottlieb Eyal
Published: August 2012

The extent to which metabolism plays a role in tumorigenesis cannot be overstated and drugs that selectively target these processes are likely to at least delay, if not halt tumour progression. Our work utilizes analytical chemistry and system biology approaches to study metabolic transformation. We investigated cells deficient in the mitochondrial tumour suppressor fumarate hydratase (FH) and using extensive metabolomics data we applied a computer model, generated to study their unique metabolome. We identified several important metabolic pathways which are specific and crucial for the survival of cancer cells deficient in FH. These include the heme biosynthesis and degradation pathway as well as mechanisms of alleviating the tricarboxylic acid (TCA) cycle carbon stress. These technologies are not only important for understanding the basic biochemistry of cancer cells but they can inform us on future clinical management of cancer and may lead to new therapeutic approaches to target cancer-specific metabolic pathways.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr SY03-01. doi:1538-7445.AM2012-SY03-01
Abstract SY06-01: Intracellular antibody therapy: Specific delivery of synthetic antibodies to cytoplasmic targets in cancer cells
Authors: Kossiakoff Anthony A.
Published: August 2012

Synthetic Antigen Binders (sABs) are a new class of antibody-based reagents engineered using novel phage display libraries and selection strategies. These attributes provide for the ability to generate sABs that are customized to: 1) target specific regions on the surface of the protein, 2) recognize specific conformational or oligomeric states, 3) induce conformational changes, and 4) capture and stabilize multi-protein complexes. As such, they have the potential to outperform traditional monoclonal antibodies as therapeutic modalities for biomedical applications. However, a critical limitation is that antibodies can only be directed at extracellular targets because they cannot penetrate the cell membrane. This eliminates a rich set of potential cytoplasmic targets that function as crucial components of signaling pathways or structural networks. To overcome this limitation we have developed receptor-mediated delivery systems that have proven effective in internalizing a novel class of synthetic antigen binders in their fully functional form. Further, this delivery system inherently seeks out certain types of cancer cells, while being inert towards cells on normal tissue.

As a demonstration of the power of the approach, we have generated a set of sABs that have been tailored to induce conformational changes in F-actin filaments that substantially alter actin cytoskeletal structure by mechanisms involving depolymerizing, severing, bundling and capping of actin filaments. We introduce these sABs into cancer cells using receptor-mediated delivery and show the properties selected for in the in vitro phage display sorting are exactly recapitulated in the live cells. The effects of actin filament bundling are shown to be particularly detrimental to the cancer cells suggesting that sABs performing this function may be useful therapeutic agents. This approach is being expanded to make agents that target nuclear components to alter cell function at the DNA level.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr SY06-01. doi:1538-7445.AM2012-SY06-01
Abstract SY07-01: Functions of ubiquitin and SUMO in DNA damage bypass
Authors: Ulrich Helle D.
Published: August 2012

Ubiquitin and SUMO are members of a conserved family of proteins that exert their functions by being covalently attached to intracellular substrate proteins. Ubiquitin is best known for targeting its substrates to the 26S proteasome, but it mediates many non-proteolytic functions, mainly by modulating protein-protein interactions. Similarly, SUMO controls a variety of biological processes by changing the properties of its substrates. Both ubiquitin and SUMO play a prominent role in the maintenance of genome stability, and our lab is interested in elucidating the mechanisms by which the two modifiers affect DNA replication, repair and mutagenesis.

An important focus of our research is the investigation of DNA damage tolerance, a highly conserved mechanism that protects cells from the harmful effects of genotoxic agents by allowing the replication machinery to pass over DNA lesions. Although beneficial in terms of promoting cell survival, bypass of DNA damage can result in unwanted mutations that may ultimately lead to genetic instability and cancer. The activity of lesion bypass is carefully controlled through posttranslational modifications of PCNA, an essential processivity factor for DNA polymerases, by monoubiquitin, polyubiquitin chains and SUMO. Here I will discuss the effects of these modifications on the replication of damaged DNA, the interplay between the different conjugation systems and the mechanisms by which the relevant modifying enzymes are activated in response to the appropriate cellular signals.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr SY07-01. doi:1538-7445.AM2012-SY07-01
Abstract SY35-03: Gene expression and epigenetic programs in leukemia stem cell development
Authors: Armstrong Scott A.
Published: August 2012

Acute myelogenous leukemia stem cells (LSC) are the subset of leukemia cells capable of extensive self-renewal and maintenance of leukemia. We are interested in the mechanisms of leukemia development as they relate to activation and maintenance of gene expression programs by epigenetic pathways responsible for deregulated self-renewal in leukemia. We have demonstrated that oncogenic fusion proteins can activate a self-renewal associated gene expression program when expressed in myeloid progenitor cells that normally have limited self-renewal capabilities. Detailed characterization of LSC from multiple different mouse leukemias has shown that LSC are most similar to differentiating myeloid cells that express a limited hematopoietic stem cell (HSC) associated signature. Detailed analysis of the gene expression data from normal HSC and progenitors as compared to LSC identified the Wnt/β-catenin pathway as potentially important for acute myeloid leukemia LSC, and we have subsequently validated this pathway as critical using conditional mouse models. We are continuing to assess the gene expression programs subverted during the transition from normal HSC and progenitor cells to LSC and are comparing these data to genome wide epigenomic analyses to determine which specific epigenetic programs are required for leukemia stem cell maintenance. Identification of epigenetic pathways required to maintain leukemia self-renewal should provide new targets for novel therapeutic approaches.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr SY35-03. doi:1538-7445.AM2012-SY35-03
Abstract SY38-03: Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukemia
Authors: Huntly Brian
Published: August 2012

Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukemia Recurrent chromosomal translocations involving the mixed lineage leukemia (MLL) gene initiate aggressive forms of leukemia, which are often refractory to conventional therapies. Many MLL-fusion partners are members of the super elongation complex (SEC), a critical regulator of transcriptional elongation, suggesting that aberrant control of this process plays an important role in leukemia induction. Here we will describe a global proteomic strategy to demonstrate that MLL-fusions, as part of SEC and the polymerase associated factor (PAFc) complex are associated with the BET family of acetyl-lysine recognising, chromatin “adaptor” proteins. These data provided the basis for therapeutic intervention in MLL-fusion leukemia, via the displacement of the BET family of proteins from chromatin. We will show that a novel small molecule inhibitor of the BET family GSK1210151A (I-BET151) has profound efficacy against human and murine MLL-fusion leukemic cell lines, through the induction of early cell cycle arrest and apoptosis. I-BET151 treatment in two human leukemia cell lines with different MLL-fusions alters the expression of a common set of genes whose function may account for these phenotypic changes. The mode of action of I-BET151 is, at least in part, due to the inhibition of transcription at key genes (BCL2, C-MYC and CDK6) through the displacement of BRD3/4, PAFc and SEC components from chromatin. In vivo studies will demonstrate that I-BET151 has significant therapeutic value, providing survival benefit in two distinct mouse models of murine MLL-AF9 and human MLL-AF4 leukemia. In addition, the efficacy of I-BET151 against human leukemia stem cells (LSC) will be shown, providing further evidence of its potent therapeutic potential. These findings establish the displacement of BET proteins from chromatin as a promising epigenetic therapy for these aggressive leukemias.

To extend the applications of our work, we will also present preliminary data to demonstrate that inhibition of BET proteins has therapeutic promise in a larger number of AML subtypes. We will speculate on potential mechanisms for this, the investigation of which is ongoing. Finally, we will discuss extension of the paradigm of BET inhibition to the numerous other epigenetic “readers” implicated in the induction and progression of cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr SY38-03. doi:1538-7445.AM2012-SY38-03