bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 51: International Cancer Genome Consortium Data Portal – A ‘one-stop-shop’ for genomic, transcriptomic, and epigenomic data
Authors: Kasprzyk Arek 
Published: June 2012

Abstract
The International Cancer Genome Consortium (ICGC) (www.icgc.org) orchestrates a multi-national effort to catalogue genomic abnormalities in 50 different tumor types. For each type 500 pairs of matched tumor and normal tissues will be studied using multiple technologies including DNA sequencing, expression profiling, and epigenetic analysis. ICGC data will be linked to cancer etiology, drug response, and patient survival.
Each ICGC member institute generates its site-specific data independently and stores it in a local database. These databases are federated using BioMart technology (www.biomart.org) and made available to the public through the ICGC data portal (dcc.icgc.org). To the user, the multiple databases appear as a single integrated database.
The ICGC data portal provides a platform for scientists to search, download, and analyze a broad range of cancer data. In addition to the data generated by the ICGC members, the portal includes data from other projects such as The Cancer Genome Atlas (TCGA) and Tumor Sequencing Project (TSP). Currently, the portal contains data sets from 15 cancer types. Data sets are divided into two categories: open access and controlled access. Open access data sets are available to the entire research community and include somatic mutations (simple, copy number variations, and structural rearrangements), gene and miRNA expression, DNA methylation, and exon junctions. Controlled access data sets, such as germline mutations, are available to users who have been authorized according to ICGC policies.
The portal also includes annotation data from other publically available databases such as Ensembl, KEGG, Reactome, and the Pancreatic Expression Database. All data in the portal is exposed through a variety of user interfaces and can be processed using available analytical and visualization tools. For instance, users can perform gene- or pathway-centric analyses, such as compare mutation frequencies in specific genes or pathways, or compare mutation patterns between multiple tumor samples. Furthermore, by selecting diverse query and output criteria, users can retrieve data based on different molecular and clinical covariates.
The portal enables users to conveniently retrieve, characterize, and compare cancer data from different sources through a single point of access. As more ICGC data is added and portal's functionality is further enhanced, it is expected that it will become an increasingly important resource for cancer researchers with diverse user requirements.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 51. doi:10.1158/1538-7445.AM2011-51
Abstract 5105: Towards a multiparametric biomarker panel for pancreatic cancer detection
Authors: Makawita Shalini , Smith Chris , Batruch Ihor , Rueckert Felix , Diamandis Eleftherios P. 
Published: June 2012

Abstract
Pancreatic cancer is one of the most highly lethal of all solid malignancies for which serological biomarkers to aid in the detection and clinical management of patients are urgently needed. To date, the lack of a single highly specific and sensitive marker for pancreatic cancer detection has led to a growing consensus in the field towards the development of panels of biomarkers, where-by the combinatorial assessment of multiple biomarkers will likely result in increased sensitivity and specificity. In this respect, we previously characterized the conditioned media of six pancreatic cancer cell lines (MIA-PaCa2, BxPc3, PANC1, Su.86.86, CAPAN1, CFPAC1) and the normal human pancreatic ductal epithelial cell line HPDE, as well as six pancreatic juice samples from pancreatic ductal adenocarcinoma patients using strong cation exchange followed by reverse-phase coupled online to an LTQ-Orbitrap mass spectrometer. This resulted in the identification of 3810 non-redundant proteins in the cell lines and 648 proteins in the pancreatic juice. All proteins were identified with 2 or more peptides. Through subsequent bioinformatic analyses which included hierarchical clustering, label-free protein quantification between the cancer and normal cell lines, cellular localization, tissue specificity and integration of the proteomes from the multiple biological fluids, a list of candidate pancreatic cancer biomarkers was generated. Preliminary verification of selected candidates using enzyme-linked immunosorbent assays (ELISAs) in a screening set of plasma samples from pancreatic cancer patients and healthy age-sex matched controls (n=40) show five proteins (designated PANC1, PANC2, PANC3, PANC4 and PANC5) to be significantly increased in pancreatic cancer plasma (p=0.0011, p&lt;0.0001, p&lt;0.0001, p&lt;0.0001 and p=0.0098, respectively). Individually, these proteins did not exhibit improved area under the curve (AUC) in comparison to CA19.9 levels measured in the same samples; however the combination of the five proteins with CA19.9 showed improved AUC to CA19.9 alone (CA19.9 alone AUC = 0.97; all proteins with CA19.9 AUC = 1.0). These data suggest that this novel panel warrants further evaluation as a pancreatic cancer diagnostic tool.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5105. doi:10.1158/1538-7445.AM2011-5105
Abstract 5183: HOXB9 expression as a new metastatic biomarker for human breast cancer
Authors: Seki Hirohito , Hayashida Tetsu , Jinno Hiromitsu , Takahashi Maiko , Sakata Michio , Hirose Shigemichi , Mukai Makio , Kitagawa Yuko 
Published: June 2012

Abstract
Background: There are several reports showing a HOX gene family, which plays the critical roles for the differentiation during the embryonic stage, is associated with the tumorigenicity. It was demonstrated that HOXB9 is overexpressed in 42% of breast cancers, specifically those with high histological grade, and it defined the functional consequences of elevated HOXB9 expression in breast cancer. Moreover, HOXB9 expression promotes increased neovascularization and tumor metastasis to the lung in mouse xenograft models (Hayashida et al., PNAS, 2010). The purpose of this research is to evaluate the correlation between HOXB9 expression and poor prognosis in breast cancer patients.
Patients and methods: A consecutive series of 141 patients with invasive ductal carcinoma who underwent surgical treatment at Keio University Hospital from January 2004 to January 2005 was involved. HOXB9 expression was analyzed immunohistochemically on formalin-fixed, paraffin-embedded tumor sections using rabbit anti-human HOXB9 polyclonal antibody.
Results: The age at the diagnosis ranged from 30 to 93 years (median age, 58 years), and median observation period was 62.2 months. Of 141 tumor specimens immunostained for HOXB9, 69 specimens (48.9%) were positive staining. Univariate logistic regression revealed ER negativity (p&lt;0.001), PR negativity (p&lt;0.001), HER2 positivity (p=0.031), high nuclear grade (p&lt;0.001) and large pathological tumor size (p=0.002) as significant variables associated with HOXB9 expression. The disease-free survival (DFS) at 5 year was significantly different between the HOXB9 positive group and HOXB9 negative group (HR=8.5, 95%CI 3.3-21.9, p=0.001). A Multivariate analysis indicated that HOXB9 expression was the independent prognostic factor for DFS (Table 1). Number of the patients with lung metastasis was significantly larger in HOXB9 positive patients. Conclusion: These data show that HOXB9 expression can be a new independent prognostic factor in breast cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5183. doi:10.1158/1538-7445.AM2011-5183
Abstract 5197: Identification of prognostic cancer stem cell marker profiles in aggressive metastatic colorectal cancer
Authors: Hessman Crystal , Anderson Eric , Wong Melissa 
Published: June 2012

Abstract
Background: Despite recent advances in screening and treatment, metastatic colorectal cancer (CRC) remains a leading cause of cancer-related death in the United States. A subset of patients with metastatic disease to the liver may achieve long-term survival with metastasectomy. However, the majority of patients with liver metastases have a median survival of approximately 2 years despite treatment. Several studies have proposed that cancer stem cells (CSC) may be linked to metastasis, treatment resistance and recurrence, but to date, no one has examined whether the expression of CSC markers can be prognostic indicators of recurrence and overall survival in metastatic CRC.
Methods: Formalin-fixed, paraffin-embedded metastatic CRC tissue samples were obtained from patients treated with metastasectomy of liver disease. Using standard immunohistochemical techniques, tissue samples were stained with antibodies to previously characterized CSC markers CD166, CD133, CD44 and CD26. Cellular expression patterns for solitary and multiple CSC markers were analyzed using an automated open source image quantification program (CellProfiler 2.0). Expression profiles were then correlated to patient outcomes (disease recurrence and overall survival).
Results: Variable expression of CSC markers was seen between long- and short-term survival as well as rate of recurrence. Patients with an increased overall survival showed a higher level of CD44 expression. Co-expression of CD44 and CD166 correlated to increased disease-free survival.
Conclusion: In this study, we identify a subset of CSC markers that correlates to disease behavior and tumor biology in metastatic CRC. Further delineation of CSC profiles may give valuable clues to therapeutic resistance as well as offer new therapeutic targets in the treatment of this disease.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5197. doi:10.1158/1538-7445.AM2011-5197
Abstract 521: Active sonic hedgehog signaling between androgen independent human prostate cancer cells and normal/benign but not cancer-associated prostate stromal cells
Authors: Shigemura Katsumi , Haung Wen-chin , Zhau Haiyen , Li Xiangyan , Yamashita Masuo , Gotoh Akinobu , Arakawa Soichi , Chung Leland , Fujisawa Masato 
Published: June 2012

Abstract
BACKGROUND: Sonic hedgehog (Shh) signaling plays a pivotal role in stromal-epithelial interaction during normal development but its role in tumor-stromal interaction during carcinogenic progression is less well defined. Since hormone refractory prostate cancer with bone metastasis is difficult to treat, it is crucial to investigate how androgen independent (AI) human prostate cancer cells communicate with their associated stroma.
METHODS: Shh and its downstream target transcription factor, Gli1 mRNA, was assessed in vitro by RT-PCR and real time quantitative RT-PCR in co-culture, as cell recombinants under Shh-enriched conditions using AI human C4-2 prostate cancer, and prostate stromal fibroblasts established from normal/benign (NPF) or cancer-associated (CPF) specimens, or human bone marrow stromal (HS27A) cells. In vivo investigation was performed by monitoring serum PSA and immunohistochemical stainings by mouse models bearing chimeric tumors consisting of C4-2 and prostate stromal fibroblast cells.
RESULTS: We found that 1) Shh has minimal growth-stimulating effects on prostate cancer or prostate stromal fibroblasts; 2) active Shh signaling was found between AI human prostate cancer and prostate stroma; and 3) osteonectin (ON) is a Gli-1 target gene in benign/normal but not cancer-associated stromal fibrobasts. ON upregulation was observed in co-cultured human prostate stromal cells when in contact with prostate stromal cells.
CONCLUSIONS: Based on co-culture and chimeric tumor models, active Shh-mediated signaling was demonstrated between AI human prostate cancer and prostate stroma in a paracrine- and tumor progression-dependent manner. Our study suggests drugs like cyclopamine that interferes with Shh signaling could be beneficial in preventing AI progression of human prostate cancer.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 521. doi:10.1158/1538-7445.AM2011-521
Abstract 5242: Obtaining a transcriptomic profile of a single prostate cancer cell
Authors: Morrissey Colm , Coleman Ilsa , Chen Shu , Coleman Roger , Gulati Roman , Lakely Bryce , Brown Lisha G. , Kinnunen Martin , Corey Eva , Etzioni Ruth , Lange Paul H. , Nelson Peter S. , Vessella Robert L. 
Published: June 2012

Abstract
There have been considerable advances in the detection, isolation and characterization of circulating tumor cells (CTC) and disseminated tumor cells (DTC) in prostate cancer (PCa) patients. However, the ability to interrogate these cells is restricted by the small number detected and isolated (typically &lt;10), and current technologies available to characterize individual cells. We set out to determine the limit of commercially available technologies to obtain a transcriptomic profile of a single PCa cell.
To do this we isolated clonally selected Aphidicolin synchronized C4-2B PCa cells. Ten sets of C4-2B cells were isolated individually or in pools of 5 or 10 cells. All thirty samples were amplified using WT-Ovation™ One-Direct (NuGEN), hybridized on a 44K Whole Human Gene Expression Microarray (Agilent Technologies) normalized for batch effects, and normalized within and between arrays. The amplified material was also assessed by realtime-PCR.
Using a high stringency cut off (mean signal intensity of 300) on the oligonucleotide arrays 22,365 probes were Cy3 positive for 10 cells, 19,393 for 5 cells and 15,441 for 1 cell. Furthermore, using the same high stringency cut off, the sensitivity and specificity between 1 and 10 cells was 0.640 and 0.946 respectively, and between 1 and 5 cells was 0.713 and 0.932, demonstrating a very low false positive rate. Ten-thousand randomly selected pairs of commonly expressed genes had a Pearson correlation coefficient of 0.862 and 0.908 for 1 vs. 10 cells and 1 vs. 5 cells respectively, indicating that the vast majority of detected probes maintained consistent relative abundance. The cycle threshold values for single cell samples by realtime-PCR were well within the detectable range for abundant transcripts (e.g. AR and KLK3). However, other transcripts (e.g. FKBP5 and TMPRSS2) were not detected in the single cell samples and had limited detection in 5 cell samples when compared to 10 cell samples.
These data suggest that currently commercially available technologies allow for the detection of a limited but significant number of genes from a single PCa cell. We are using the methodology described herein, to determine the heterogeneity of single DTC isolated from the bone marrow of patients with PCa.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5242. doi:10.1158/1538-7445.AM2011-5242
Abstract 5245: Apoptotic Circulating Tumor Cells (CTCs) in early and metastatic breast cancer patients
Authors: Kallergi Galatea , Konstantinidis Georgios , Papadaki Maria , Agelaki Sophia , Mavroudis Dimitris , Stournaras Christos , Georgoulias Vassilis 
Published: June 2012

Abstract
Introduction: Metastasis has been associated with the presence of circulating (CTCs) and disseminated (DTCs) tumor cells in peripheral blood and bone marrow of breast cancer patients, respectively. Recent studies have confirmed that the detection of CTCs and DTCs represents a strong and independent prognostic factor for decreased disease-free and overall survival. However, it is not clear so far whether all CTCs are capable to generate metastasis or some of them are destined to die. The aim of the present study was to analyze the presence of apoptotic CTCs in patients with early and metastatic breast cancer. Methods: Double staining immunofluorescent (IF) expreriments were performed in peripheral blood mononuclear cells (PBMC) cytospins of patients with early (n=23) and metastatic breast cancer (n=29), prior to the initiation of adjuvant and first-line chemotherapy, respectively. Pancytokeratin A45-B/B3 antibody (as a marker of CK-positive cells) was coupled with either M30 (marker of apoptotic cells) or Ki67 (marker of proliferating cells) antibodies. Apoptotic CTCs were also evaluated using a polycaspase detection kit. Results: Significantly lower proportions of apoptotic CTCs were detected in metastatic compared to early breast cancer patients using the polycaspase kit (10.6% vs 32.8%, p=0.008). These results were confirmed with M30 staining (36.0% vs 59.3%, in early and metastatic disease, respectively, p=0.048). The median percentage of apoptotic CTCs per patient was also lower in advanced compared to early disease patients (0% vs 40% with the polycaspase kit and 15% vs 69% with M30 staining). Ki67 positive CTCs were identified in 56% of metastatic patients, while 36% of their CTCs were double positive (CK+Ki67+). Conclusions: Apoptotic CTCs are more common in early compared to metastatic breast cancer, probably related to the disease progression. The presence of apoptotic CTCs in breast cancer patients may provide useful prognostic information and could be used to monitor the effectiveness of therapy.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5245. doi:10.1158/1538-7445.AM2011-5245
Abstract 5271: p16-LUC: an in vivo reporter allele for de novo tumor formation and therapeutic response
Authors: Burd Christin E. , Clark Kelly , Sharpless Norman E. 
Published: June 2012

Abstract
The p16INK4a tumor suppressor is upregulated and serves to limit proliferation in response to cellular stressors and oncogenic events. Induction of p16INK4a is highly dynamic during tumorigenesis and aging, ranging from undetectable in unstressed cells to &gt;105 mRNA copies per cell when maximally activated. This property, along with the well established activation of p16INK4a in response to a variety of oncogenic stressors, led to the hypothesis that p16INK4a could be an excellent marker of tumorigenesis and aging. Toward that end, we developed a novel knock-in mouse model, p16-LUC, wherein the endogenous p16INK4a promoter drives single-copy expression of firefly luciferase. Using homologous recombination in ES cells, the open reading frame of firefly luciferase was inserted in-frame at the transcriptional start site of p16INK4a, preserving the structure and regulation of other genes (p19ARF and p15INK4b) encoded by the Cdkn2a/b locus. Murine embryo fibroblasts (MEFs) derived from p16-LUC animals demonstrate marked (&gt;105) upregulation of luciferase activity with culture, paralleling that observed for the endogenous allele. Such induction can also be monitored dynamically in vivo following treatment with DNA damaging stressors such as ionizing radiation. To test the ability of this allele to serve as a biomarker of oncogenic stress, we crossed the p16-LUC mouse to numerous genetically engineered mouse models (GEMMs) of human cancer. In these mice, potent induction of luciferase activity was apparent in tumors driven by a wide variety of oncogenes. Moreover, weeks before visual or palpable tumors could be detected, p16-LUC expression localized to future tumor sites. Treatment of these mice with a wide range of chemotherapeutic compounds also revealed novel insights into therapeutic efficacy and potential toxicities. Overall, the p16-LUC model has potential to advance the study of de novo tumor formation, therapeutic efficacy and toxicology by providing a reagent to conduct long-term, in vivo studies of GEMMs and potential anti-cancer compounds.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5271. doi:10.1158/1538-7445.AM2011-5271
Abstract 5292: Tumor accumulation and biodistribution of a thermally responsive cell cycle inhibitory polypeptide in vivo
Authors: Robinson Leslie , Perkins Eddie , McNally Lacey , Raucher Drazen 
Published: June 2012

Abstract
Elastin-like Polypeptide (ELP) is a macromolecular carrier for various therapeutic peptides that has the ability to penetrate tumor vasculature which is mediated by a cell-penetrating peptide. ELP is a biopolymer consisting of pentapeptide repeats in the motif Val-Pro-Gly-Xaa-Gly where Xaa is any amino acid except proline. The polymer is soluble at normal physiological temperature but aggregates above 41° C. Peptides without carriers have very short half-lives, so ELP not only allows for longer circulation time, but its thermal properties allow the peptide to accumulate inside the tumor when heated. Bac7-ELP1-p21 is an ELP conjugate that uses Bac7 to penetrate the nucleus and p21 to inhibit the cell cycle at G1/S. This construct can be actively targeted to the tumor site using focused infrared light that heats the tumor to 41-42° C.
In this study, tumor accumulation and biodistribution of fluorescently labeled Bac7-ELP1-p21 was monitored in a mouse subcutaneous xenograft model of S2013 pancreatic cancer by whole animal imaging using the IVIS® system. Luciferase transfected S2013 pancreatic cells were used to establish the tumor, allowing monitoring tumor growth by quantifying luciferase signal over a period of time. The animals were intravenously injected with Alexa750 labeled Bac7-ELP1-p21. Animals were imaged for fluorescence signal at 1, 2, 3, 4, 6, 8, 24, 48, and 72h after treatment to monitor the level of protein with respect to time. This allowed for the detection and quantification of the protein level throughout the whole body. Tumor uptake of intravenously administered Bac7-ELP1-p21 was examined in both heated and unheated tumors. Using both luminescence and fluorescence data, protein levels inside the tumor were compared to the whole body. Bac7-ELP1-p21 accumulates 3-fold more inside the heated tumor than the unheated tumor, and it is still present inside the tumor 72h after treatment. Fusing a therapeutic peptide to macromolecular carriers results in its improved pharmacokinetics and accumulation of the peptide preferentially in the tumor tissue due to passive targeting. Furthermore, this passive targeting is further improved due to externally induced hyperthermia. This approach will allow us to use lower concentrations of drug systemically and therefore reduce side effects in normal tissues.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5292. doi:10.1158/1538-7445.AM2011-5292