bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2197: A robotic genome-scale shRNA screen identifies metabolic drug targets and a glioblastoma gene signature
Authors: Colombi Marco , Benjamin Don , Hall Michael N. , Thiemeyer Anke , Molle Klaus , Moroni Christoph 
Published: February 2011

Abstract
Proteins encoded by oncogenes represent suitable drug targets and several have been validated clinically. However, certain non-oncogenes, which are downstream effectors of oncogenes, may be similarly useful as potential targets of therapy. We have developed a high-throughput strategy using a shRNA genomic library and tumor cells addicted to the mTOR pathway to identify genes (oncogenes or non-oncogenes) which control the oncogenic phenotype. mTOR addicted cells were generated from IL-3 dependent cells following frame-shift mutagenesis and selection for IL-3 independence. mTOR addicted cells obtained from this selection carried frame-shift mutations in the PTEN gene. mTOR addiction was revealed by sensitivity to rapamycin and confirmed biochemically by examining phosphorylation of the mTOR targets S6K and PKB. Interestingly (and of importance to our shRNA-based screening strategy), addition of IL-3 rescued cells from mTOR addiction, as this growth factor antagonized the apoptotic effect of rapamycin. Using robotics (BioMek-NX) and a genomic retroviral shRNA library we evaluated 14’000 genes for a potential role in maintaining mTOR addicted growth. Our strategy was to screen cells in the presence and absence of IL-3 to identify shRNAs that antagonize growth of cells in the absence of IL-3. We identified around 300 genes required for mTOR addicted growth. This set of genes was enriched in highly significant manner for genes known to be involved in cancer, providing proof of concept for the strategy. Examples of identified genes include ras, raf, PKB and mTOR. Also, genes with no cancer link and genes with unknown function were identified. Use of Ingenuity software allowed to place many of the identified genes into functionally distinct groups or pathways. In addition numerous hits affecting metabolic functions, redox functions, and ROS generating systems were identified including the cytoplasmic NADPH complex and complex I-IV of the respiratory chain. Combining the genes et with an Affymetrix gene overexpression analysis in the same cells and analysing by Oncomine software, we identified a glioblastoma gene signature consisting of 13 genes (p-value 2.4E-5) containing 3 oncogenes and several signaling elements. Downregulation of several of these genes in human cancer lines induced apoptosis. Some of he genes identified represent novel potential drug targets.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2197.
Abstract 2213: Identification of novel cancer mutations in sarcomas
Authors: Abaan Ogan D. , Francis Princy , Pineda Marbin , Walker Robert L. , Bilke Sven , Davis Sean R. , Meltzer Paul S. 
Published: February 2011

Abstract
Understanding of how cancer initiates and progresses is the fundamental of cancer research. Identification of cancer mutations is of profound importance for both understanding of the disease and for developing novel therapies. To search novel cancer mutations, we have utilized a “targeted resequencing” approach to resequence coding exons from about 1300 genes in a panel of various sarcoma patient samples. We used the previously published method of “In-solution capture” to enrich for regions of interest and resequenced the enriched population on an Illumina GAII platform using single-ended or paired ended reads. The performance and depth of the enrichment and resequencing was adequate for variant calling. We obtained roughly 70% on genome reads and about 30% of the reads fall on target while about 40% of the reads fall on target±500bp. An in house variant calling script was used for SNP/variant calling. Each sample yielded multiple genes with novel variations some of which are either missense or nonsense and in a highly conserved residue that were also previously identified in other cancers as well. Preliminary results from samples resequenced so far demonstrate that these sarcoma samples have variations in a variety of genes with diverse functions, including but not limited to signaling pathway intermediates. In conclusion, our work will be important in cataloging novel cancer mutations in rare sarcomas, with potential implications for understanding their biology and the development of new therapies.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2213.
Abstract 2219: Identification of oncogenes in mutant Rpa1 associated tumorigenesis
Authors: Huang Bin , Zhang Weijia , Edelmann Winfried , Wang Yuxun 
Published: February 2011

Abstract
Genetic instability is a hallmark of human cancers. However, the precise molecular mechanism and its role in cancer remain elusive. We have demonstrated that a missense mutation in Rpa1 causes defective DNA repair, genetic instability and predisposes mice to cancer, thereby providing one of the first evidence showing a replication associated protein is essential in maintaining genome stability and suppressing tumorigenesis. In humans, loss of the chromosomal locus containing RPA1 and genetic polymorphisms in RPA1 have been found in a wide range of cancers. Hence, a better understanding about the role of Rpa1 mutation in genetic instability and cancer should have critical clinical implications. The studies from our lab and others established the association between mutant Rpa1 and tumors. However, it remains unknown which target is most related to cancer development associated with mutant Rpa1. To search for the candidate target genes, we applied whole genome array comparative genomic hybridization (aCGH) in the tumors developed in Rpa1 mutant mice. This genome-wide chromosome copy number analysis uncovered multiple chromosomal aberrations involving multiple genetic loci along the chromosomes in Rpa1 mutant tumor cells. Moreover, chromosomal profiling analysis revealed unique pattern of chromosomal changes in Rpa1 mutant lymphomas, which is distinct from lymphomas developed in other knockout mouse models carrying mutations in different tumor suppressors. Furthermore, we analyzed all the currently known tumor related genes and found 10 oncogenes to be involved in the chromosomal gains in Rpa1 mutant tumors including c-Myc on chromosome 15 which appears to be the most recurrent. We confirmed overexpression of c-Myc in Rpa1 mutant tumors while the other candidate oncogenes showed variable expression among different tumors. These results strongly suggest an important role of c-Myc in mutant Rpa1 mediated tumorigenesis.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2219.
Abstract 2222: Mutational and copy number analysis of the PI3K/Akt/mTOR pathway in oral cavity squamous cell carcinoma
Authors: Morris Luc GT , Ganly Ian , Heguy Adriana , Chan Timothy A. 
Published: February 2011

Abstract
The phosphatidylinositol 3-kinase signaling (PI3K) pathway is integral to cell growth, proliferation and survival, and is upregulated in multiple human cancers. Several oncogenes and tumor suppressors within this pathway are altered by mutation, amplification or deletion, and are currently being investigated as therapeutic targets. The pattern of dysregulation in this pathway differs among various cancers, and has not been comprehensively characterized in oral squamous cell carcinoma.
After institutional review board approval, fresh frozen tumor and matched normal tissues were obtained from 32 patients treated for oral cavity squamous cell carcinoma, and genomic DNA was extracted. Using high-throughput Sanger sequencing, the 23 component genes of the PI3K/Akt/mTOR pathway were comprehensively sequenced. Putative mutations identified by mutation detection software were validated on a second PCR and sequencing procedure. Array CGH was performed on the Agilent 1M microarray, and data analysis performed using the RAE method.
Component genes within the PI3K/Akt/mTOR pathway were comprehensively sequenced, including AKT1, AKT2, AKT3, AKTS1, AXL, AGAP2, MTOR, GBL, GOLPH3, RAPTOR, MUC1, PDPK1, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PTEN, RHEB, RICTOR, TSC1 and TSC2. Activating mutations were identified in PIK3CA in 2 of 32 (6.3%) specimens. No other genes harbored somatic mutations. DNA copy number gains and losses are described in detail.
In the first comprehensive mutational and copy number analysis of 23 component genes of the PI3K/Akt/mTOR pathway in cancer, we report a low prevalence of somatic mutations, and a higher frequency of copy number alteration in oral cancer specimens. In contrast to colorectal, breast, ovarian, brain and bladder cancers, mutation is not the primary source of activation of this pathway in oral cancers.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2222.
Abstract 2223: Screening for oncoviruses using next-generation sequencing
Authors: El-Dinali Mohamed , Braegelmann Johannes , Salgia Ravi , Seiwert Tanguy 
Published: February 2011

Abstract
Introduction: During the last decades numerous viruses have been found to play a causative role in cancer. Besides well established connections like HPV in cancers of the uterine cervix or EBV in nasopharyngeal carcinoma recent advances in next-generation sequencing technologies have led to the discovery of new tumor viruses e.g. a previously unknown Polyoma-virus subtype linked to Merkel-cell carcinoma of the skin.
Method: To gain insight into the mechanisms leading to tumor formation we sequenced the transcriptome from an HPV16 positive cell line using short-read Illumina RNA-Seq and established a computational pipeline to screen the short reads for viral sequences based on freely available alignment tools.
Results: Due to the large amount of data and in order to narrow down the search space and reduce the chance for false positives the first screening step consists in a subtraction of sequences that align to the human reference genome reducing the amount of reads by ∼70%. To find both known viruses and yet unknown strains/subtypes we apply a two-fold approach:
1. A rapid search for known viruses is done using a short-read alignment tool with a set of stringent parameters to map non-human reads to an index of the viral genbank and subsequent quantification of the hits.
2. Since slight differences between read and index sequence will cause the rapid search to not call a match we implemented a more lenient approach using standalone BLAST.
Applying approach 1) to the control cell line we clearly identified HPV16 as being present. To test the possibility of finding a potentially unknown virus we deleted HPV16 from both the rapid approach and the index which caused the first algorithm to no longer identify the virus. Running the BLAST basec approach 2) resulted in multiple hits the most prominent being alignments to HPV subtypes 35 and 58, thus indicating the successful identification of related strains.
Conclusion: We demonstrated the feasibility of our dual viral screening approach in an in-silico experiment using an HPV16 positive control. Our approach appears to be able to identify novel related viruses. In the future this will allow screening of patient samples and viral screening was added to our data pipeline.
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 2223.
Abstract 2236: Nuclear roundness variance predicts prostate cancer progression, metastasis and death: A prospective evaluation with up to 25 years of follow-up after radical prostatectomy
Authors: Veltri Robert W. , Isharwal Sumit , Miller Craig , Epstein Jonathan I. , Partin Alan W. 
Published: February 2011

Abstract
Introduction and Objective: Nuclear structure is often altered in cancer due to spatial rearrangements of chromatin organization via activation of oncogenes and other chromatin remodeling genes. Therefore, we evaluated the prognostic value of nuclear roundness variance (NRV) for prostate cancer (PCa) progression, metastasis and PCa-specific death-free survivals in a cohort of 116 men after radical prostatectomy (RP).
Methods: For each patient, ∼150 intact nuclei from the primary tumor were captured using the DynaCELL Motility Morphometry Measurement workstation (JAW Associates, Inc., Annapolis, MD) at a magnification of 1250X in 1992-93. Next, nuclear roundness variance (NRV) was calculated for each of the 116 cases using the this unique shape factor from ∼150 nuclei captured. The resulting variance values were multiplied by 10,000 to determine the NRV factor for each case. NRV data was merged with clinical, pathologic and follow-up data for all patients in 2009. Cox proportional hazards regression was used to identify significant prognostic factors for prediction of progression, metastasis and PCa-specific death free survivals.
Results: Median follow-up time after RP for all patients was 19.0 years (range: 1-25 years, mean: 17.43 years), with approximately 92% (107/116), 71% (82/116) and 47% (55/116) patients having ≥10 years, 15 years and 20 years of follow-up respectively. NRV was the most significant parameter for prediction of all three outcomes and its concordance-index (C-Index) increased from progression (0.7080) to metastasis (0.7332) to PCa-specific death (0.8090) free survival predictions. Of note, NRV C-Index was significantly higher compared to Gleason Score C-Index for metastasis (0.7332 vs. 0.6046; p = 0.027) and PCa-specific death (0.8090 vs. 0.6336; p = 0.004) free survival predictions. However the difference between NRV and Gleason Score C-Indexes was not statistically significant for progression free survival prediction (0.7080 vs. 0.6463; p = 0.106).
Conclusions: Variance of nuclear roundness (a measure of tumor heterogeneity) is a valuable nuclear structural feature to assess an aggressive phenotype of prostate cancer.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2236.
Abstract 2240: Clinical significance of CEA, PRL3 and EZH2 transcripts expressed in lymph nodes of colorectal cancer patients
Authors: Lagarde Alain E. , Wood Caroline , Guindi Maha , Stern Hartley S. 
Published: February 2011

Abstract
Objective: The role of micrometastases detected immunologically and molecularly in lymph nodes of colorectal cancer patients remains elusive. We investigated the prognostic significance of CEA, PRL3 and EZH2 expressed in lymph nodes of 42 pathologically node-negative (pN0) colorectal patients and 13 stage III/IV patients as controls. Seventeen pN0 patients (40%) received adjuvant therapy after curative surgery.
Experimental design: CEA, PRL3 and EZH2 transcripts were amplified by reverse transcription PCR in nearly 600 paraffin embedded lymph nodes. On average 9.7 ± 5.7 nodes were harvested per case. After 55 months median follow-up, gene expression was correlated with recurrence-free (RFS), overall (OS) and disease-free survival (DFS), using Kaplan-Meier analysis and log-rank test for comparison.
Results: The proportion of cases demonstrating CEA+, PRL3+ and EZH2+lymph node expression increased from stage I to III/IV and reached 71%, 76% and 26% respectively in the pN0 group. EZH2 had no significant prognostic value among pN0 patients. Disease progressed more rapidly (50% DFS at 30 versus 53 months) in EZH2+ than EZH2- node-positive patients. CEA+ was associated with ∼18% lower RFS/OS, and 8% lower DFS than CEA- among therapeutically-untreated patients, those with colon and with stage II tumors. pN0 patients with PRL3+ nodes had better outcomes than PRL3- cases (DFS, P= 0.059), namely in the colorectal (OS, P= 0.056; DFS, P= 0.12), colon (DFS, P= 0.056) and stage II tumor in the non-adjuvant settings (DFS, P= 0.0047).
Conclusions: Lymph node expression of the PRL3 phosphatase gene predicted more favorable outcomes for pN0 colorectal cancer patients. The role of CEA as an adverse predictor of survival was confirmed albeit less significant than previously reported. Neither CEA nor PRL3 nodal expression was predictive of rectal cancer recurrence.
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 2240.
Abstract 2243: Prognostic significance of nuclear Sox4 expression in cutaneous melanoma and its role in cell migration
Authors: Shourkaei Seyed Mehdi Jafarnejad , Wani Aijaz Ahmed , Martinka Magdalena , Li Gang 
Published: February 2011

Abstract
Sry-related high-mobility group (Sox) family of genes is consisted of transcription factors involved in various physiological processes including embryonic development, cell fate decision and differentiation. Deregulated expression of Sox4 has been reported in several human cancer types so far; nevertheless the expression and possible role of Sox4 in human melanoma cancer progression is yet to be identified. To investigate the putative role of Sox4 in the development of melanoma and its correlation with patient survival, we examined the expression of Sox4 protein in different stages of melanocytic lesions and its role in melanoma cancer cells proliferation and migration. Using tissue microarray and immunohistochemistry, we evaluated Sox4 protein expression in 43 dysplastic nevi, 89 primary melanomas, and 48 metastatic melanomas. We observed a marked reduction in nuclear Sox4 expression in malignant melanomas compared with dysplastic nevi (Kruskal-Wallis test; p &lt; 0.05) and primary melanomas (Kruskal-Wallis test; p &lt; 0.01). Moreover, the reduced nuclear Sox4 expression was significantly correlated with a poorer disease-specific 5-year survival of patients with primary and metastatic melanoma (Kaplan-Meier test; P = 0.039). Multivariate Cox regression analysis revealed that reduced nuclear Sox4 expression is an independent prognostic factor to predict patient outcome (p = 0.049). We also knocked down the expression of Sox4 in MMRU human melanoma cell line by siRNA and the migratory ability of the cells as well as their proliferation rate were analyzed following Sox4 silencing. Strikingly, the wound healing assay revealed an augmented migration ability of MMRU cells upon siRNA mediated knockdown of Sox4. However, the absence of Sox4 did not affect the rate of melanoma cancer cells proliferation. Our results suggest that Sox4 may be a suitable marker for the prognosis of the melanoma cancer outcome and a potential therapeutic target for human melanoma.
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 2243.
Abstract 2244: Internalization of basigin-2, a poor prognosis marker, by a monoclonal antibody
Authors: Lappi Douglas A. , Ancheta Leonardo , Nowak Romana A. 
Published: February 2011

Abstract
Basigin-2 (EMMPRIN, CD147) is widely expressed on the surface of numerous tumor types and is associated with poor prognosis. Basigin is an integral membrane glycoprotein also expressed on numerous normal cell types. Several functions have been described for basigin-2 within both normal and malignant tissues. The best characterized is its ability to induce the expression of matrix metalloproteinases in stromal cells. As such, it is suggested to play a role in tumor metastasis. Because of its association with poor prognosis and possible role in metastasis, we examined the ability of basigin-2 to be targeted on the cell surface and internalized as a possible gateway for entry into tumor cells, or for down-regulation for inhibition of metastasis. Belton et al. have documented internalization of basigin-2 by a recombinant soluble protein corresponding to the extracellular domain (ECD) of basigin-2 (J Biol Chem, 2008, 283:17805).
We have extended this investigation to examine antibody-mediated endocytosis. A monoclonal antibody to the basigin ECD (also reported in Belton et al.) has been used in an internalization assay using biotinylated antibody mixed with streptavidinylated-saporin (the ribosome-inactivating protein). This complex will eliminate cells only if there is antibody-mediated endocytosis, since saporin has no mechanism of cell entry. HeLa cells, which are known to express basigin-2, were challenged and a potent cytotoxicity was observed: the ED50 of the biotinylated antibody-streptavidin-saporin complex is 370 pM. This is evidence that the antibody internalizes in HeLa cells. Similar data were observed with ovarian carcinoma cells (OVCAR3, SKOV3). Non-tumor cells with low expression have low sensitivity to the complex and there was a correlation between basigin-2 expression on the cell surface and cytotoxicity.
We conclude that basigin-2 internalizes in response to antibody binding. Further work is necessary to determine if this can be used for introduction of molecules into basigin-2-expressing cells or if down-regulation would have an effect on metastasis promoted by this poor prognosis molecule.
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 2244.