bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1129: FLCN-putative tumor suppressor
Authors: Seabra Laurence , Nahorski Michael , Rienmann Anne , Lu Xiaohong , Lim Derek , Maher Eamonn 
Published: February 2011

Abstract
Birt-Hogg-Dubé (BHD) is an autosomal dominantly inherited genodermatosis associated with the development of renal neoplasia, spontaneous pneumothorax and benign fibrofolliculomas. The BHD gene has been maps to chromosome 17p11.2 and encodes a protein called folliculin (FLCN). Although familial forms of renal cell carcinoma account for only about 3% of all cases, the elucidation of the molecular mechanisms of familial RCC syndromes has provided seminal insights into the pathogenesis of sporadic RCC. This is exemplified by the role of VHL tumor suppressor gene (TSG) inactivation in sporadic clear cell RCC. The FLCN TSG product has been linked to the mTOR/AMPK signaling pathways but the function of folliculin is much less well characterised than for other renal TSGs such as VHL. Among the multiple functions that have been associated with the VHL TSG product is a role in the regulation of apoptotic cell death. We have investigated whether folliculin also has a role in apoptosis. Comparison of isogenic FLCN null and replete cell lines demonstrated increased cell death in the latter. Flow cytometry revealed a 30 % shift in apoptotic index as determined by Annexin V vs PI staining which was demonstrated by a shift in the cell population towards an early apoptotic state. Expression of apoptosis-related proteins was investigated in FLCN null and replete cell lines using proteome array profiler. This demonstrated increased expression of SMAC, claspin HTRA2 and XIAP in FLCN replete cells. Further investigations to determine the precise role of folliculin in the regulation of apoptosis and the relationship between FLCN-induced apoptosis and p53 status are in progress.
Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1129.
Abstract 1143: Translational control analysis by translationally active RNA capture/microarray analysis (TrIP-Chip)
Authors: Kudo Kenji , Xi Yaguang , Wang Yuan , Song Bo , Chu Edward , Ju Jingyue , Russo James J. , Ju Jingfang 
Published: February 2011

Abstract
We have developed a new approach to systematically study post-transcriptional regulation in a small number of cells. Actively translating mRNAs are associated with polysomes and the newly synthesized peptide chains are closely associated with molecular chaperones such as hsp70s, which assist in the proper folding of nascent polypeptides into higher ordered structures. These chaperones provide an anchor with which to separate actively translating mRNAs associated with polysomes from free mRNAs. Affinity capture beads were developed to capture hsp70 chaperones associated with the polysome complexes. The isolated actively translating mRNAs were used for high throughput expression profiling analysis. Feasibility was demonstrated using an in vitro translation system with known translationally regulated mRNA transcript thymidylate synthase (TS). We further developed the approach using HCT-116 colon cancer cells with both TS and p53 as positive controls. The steady state levels of TS and p53 mRNAs were unaltered after 5-fluorouracil (5-FU) treatment as assessed by real time qRT-PCR analysis. In contrast, the protein expression and polysome-associated mRNA levels of both genes were increased. These differences in translational rate were revealed with our new approach from 500 cells. This technology has the potential to make investigation of translational control feasible with limited quantities of clinical specimens.
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 1143.
Abstract 1148: Array comparative genomic hybridization of diffuse intrinsic pontine glioma samples obtained from formalin fixed paraffin embedded autopsy specimens
Authors: Suuriniemi Miia , Warren Katherine , Killian Keith , Wang Yonghong , Quezado Martha , Walker Robert L. , Meltzer Paul S. 
Published: February 2011

Abstract
We have recently optimized the method of formalin fixed paraffin embedded (FFPE) tissue processing for high resolution array comparative genomic hybridization (aCGH). This will facilitate the copy number assessment of number archival clinical surgical pathology specimens as well as biopsies with debated utility. Molecular characterization of archival specimens can potentially clarify the biology of diseases with unclear etiology and poor prognosis such as diffuse intrinsic pontine glioma (DIPG). In the case of DIPG, which is seldom biopsied, at present autopsy samples provide the only practical approach to studying this disorder. Here we performed aCGH on FFPE autopsy specimens obtained from children with DIPG.
DNA was extracted from FFPE blocks obtained from autopsy on 14 pediatric DIPG patients using a modified Qiagen DNeasy kit. Non-enzymatic Universal Linkage System (ULS) chemical labeling was used to directly couple fluorescent dyes with the sample and reference DNAs (1ug each), which were then hybridized to 105k oligonucleotide CGH microarrays (Agilent). Arrays were scanned and data analyzed in Nexus Copy Number software.
Twenty-one samples from 14 subjects were available for the study from which CGH was successfully performed on 18 samples representing 12 patients. All samples demonstrated DNA aberrations. Frequent DNA copy number changes included gain of 1q, 7p, and loss of 10q. High copy number amplification of known oncogenes was observed, including PDGFRA, EGFR, CCND1, and MYCN. Homozygous deletions of known tumor suppressor genes included PTEN and CDKN2A.
Our tissue processing method demonstrates the feasibility of successfully using DNA derived from FFPE autopsy material for aCGH. The pediatric DIPG sample set was highly informative with the majority of specimens showing at least 1 abnormality related to a known cancer gene. Significant heterogeneity among DIPG patients as well as aberrations in candidate drug targets (KIT and EGFR) were observed.
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 1148.
Abstract 1149: Genetic analysis of single cells
Authors: Fan Jian-Bing , Chen Jing , April Craig , Klotzle Brandy , Royce Thomas , Cann Gordon , Talasaz AmirAli H. , Islam Saiful , Kjallquist Una , Linnarsson Sten 
Published: February 2011

Abstract
We are developing highly sensitive and quantitative genomic technologies for genetic and expression analysis of single cells or trace amount of DNA/RNA materials, using microarray and next-generation sequencing platforms. We have tested various Multiple Displacement Amplification (MDA)-based protocols under a variety of reaction conditions. With our current protocol and a 300K-SNP chip readout, we were able to obtain 88.3% and 93.9% call rate, and 97.4% and 99.9% call accuracy with direct cell lysis from 1 cell and 5 cells, respectively. We are also developing RNA amplification methods for high-throughput expression profiling of single cells. With our current protocol, we were able to generate reproducible expression profiles, R2 = 0.73 and 0.77, using 10 pg and 50 pg total RNA input, respectively. In addition, the profiles correlated well with those obtained with standard 100 ng total RNA input, R2 = 0.61 and 0.77, respectively. Our data show that sequencing of single-cell transcriptomes can clearly distinguish embryonic stem cells from embryonic fibroblasts and tumor cells. We are currently using these technologies to study medical specimens such as circulating tumor cells and cancer stem cells.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1149.
Abstract 1151: HER2- and EGFR-specific Affiprobes - Novel recombinant optical probes for cell imaging
Authors: Lyakhov Ilya , Kuban Monika , Zielinski Rafal , Kramer-Marek Gabriela , Capala Jacek 
Published: February 2011

Abstract
The human epidermal growth factor receptors EGFR (Her1, ErbB1) and HER2 (HER2/neu, ErbB2, or c-erb-b2) are members of EGFR (ErbB) family of cell-surface receptors/tyrosine kinases: EGFR, HER2, HER3, and HER4. There are several identified ligands for these receptors (except HER2), including EGF and TGF-alpha, that induce receptor dimerization followed by tyrosine autophosphorylation, which leads to cell proliferation. EGFR and HER2 are found overexpressed in a number of cancer types, such as breast, ovarian, salivary gland, stomach, kidney, colon, prostate, and non-small cell lung cancer. Research has shown that EGFR- or HER2-positive cancers represent a more aggressive disease with greater likelihood of recurrence, poorer prognosis, and decreased survival rate compared to EGFR- or HER2-negative cancers. The details of HER2 proto-oncogenic function, its internalization mechanism, and subcellular trafficking are not fully understood, partially because the availability of imaging reagents and tools for detection of EGFR and HER2 is still restricted to medium/low affinity antibody conjugated to small-molecule dyes. We have created photo-stable and relatively simple-to-prepare imaging probes for in vitro staining of EGFR and HER2. These new reagents, called Affiprobes, consist of the targeting moiety, a HER2- or EGFR-specific Affibody® molecule, and a fluorescent detection moiety mCherry (Red), or EGFP (Green). These fluorescent proteins were chosen due to their high stability and solubility and low toxicity for eukaryotic cells. Furthermore, HER2 and EGFR receptors can be detected simultaneously using corresponding optical filter sets. Our flow cytometry and confocal microscopy experiments demonstrated high specificity and signal/background ratio for the Affiprobes. This type of optical probe can be easily extended to targeting other cell-surface antigens/receptors using different Affibody® molecules and fluorescent proteins.
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 1151.
Abstract 1155: Quantification of circulating tumor cells in peripheral blood using EGFR-targeting gold nanoparticles
Authors: Wang Xu , Qian Ximei , Beitler Jonathan J. , Chen Zhuo Georgia , Nie Shuming , Shin Dong M. 
Published: February 2011

Abstract
Background: The prognostic significance of circulating tumor cells (CTCs) in patients with squamous cell carcinoma of the head and neck (HNSCC) is of great clinical interest. HNSCCs are overwhelmingly EGFR positive. Objective: Our goal was to pilot nanotechnology to identify CTCs in human xenograft mouse model as a prelude to clinical use. Methods: Surface-enhanced Raman Scattering (SERS)-gold nanocrystals (60 nm) were prepared by spectral encoding with a Raman reporter molecule and then stabilized and protected by low molecular weight polyethylene glycols (PEGs). Heterofunctional PEG was covalently conjugated to epidermal growth factor (EGF) peptide, a ligand that binds to EGFR with high specificity and affinity. To identify CTC in normal mouse blood, varying quantities of Tu212 cells were added into mice blood samples, then our nanoparticle was added to the sample and the presence of Tu212 cells were detected in vitro using laser excitation of the Raman reporters. Different types of cancer cells with variable EGFR expression were also examined in blood to confirm the specificity of the EGF-targeted SERS nanoparticles. Normal mouse blood served as the experimental control to account for non-specific binding. Results: The cellular uptake of the EGFR-targeting nanoparticle in high EGFR expression Tu212 cells was about 10-fold higher than that in low EGFR expression H460 cells in vitro, suggesting a specific EGFR targeting of the gold nanoparticle. Tu212 cells could be selectively labeled and quantified (5.6 × 104 nanoparticles/cell) at a concentration of approximately 10 cells per ml of normal mouse blood. Comparing the labeling of Tu212 cells by our nanoparticles with H460 cells in the mouse blood samples showed that the signal intensity in Tu212 cells was about 9-fold higher than that in H460 cells ((3750 ± 230 vs. 350 ± 120, respectively, p &lt;0.05). These results indicated high sensitivity and specificity of using SERS-gold nanoparticles for detection of CTCs. Conclusion: We have demonstrated the ability to use targeted surface-enhanced Raman gold nanoparticles to quantify CTCs with EGFR expression (This research was supported by the National Cancer Institute award 5 P50 CA128613 and U54CA119338-04).
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 1155.
Abstract 1157: Ubiquitin-proteolytic control of HOX homeodomain proteins in normal and malignant hematopoiesis
Authors: Zhou Pengbo , Lee Jennifer , Zhang Jianxuan , Liu Liren , Shieh Jae-Hung , Moore Malcolm A. S. 
Published: February 2011

Abstract
The HOX homeodomain proteins are key regulators of hematopoiesis. HOX genes are expressed in primitive hematopoietic cells, and their prompt downregulation is associated with hematopoietic differentiation and maturation. Although transcriptional inactivation of HOX genes during hematopoietic differentiation has been established, little is known about the biochemical mechanisms underlying the subsequent removal of HOX proteins. We have previously shown that the CUL4A ubiquitin ligase controls the stability of HOXA9 by promoting its ubiquitination and proteasome-dependent degradation. Interfering with CUL4A biosynthesis resulted in alterations of the abundance of HOXA9, mirrored by impairment of the myeloid progenitor cells to undergo proper terminal differentiation into granulocytes. Here we show that other HOX family members are also subjected to CUL4A-mediated ubiquitination and destruction, and defined the degradation signal (degron) for these HOX proteins. A degradation-resistant recombinant HOX protein was engineered and affinity-purified, and when directly transduced into G-CSF-mobilized CD34+ adult hematopoietic cells, demonstrated significant enhancement of promoting ex vivo expansion of these primitive hematopoietic progenitors. These results revealed a novel regulatory mechanism of hematopoiesis by ubiquitin-dependent proteolysis, and opened up new avenues for ex vivo expansion of hematopoietic stem cells for therapeutic use.
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 1157.
Abstract 116: A novel methodology for analyzing post-processed LC/MS metabolomics data
Authors: Mak Tytus , Tyburski John B. , Kalinich John F. , Fornace Albert J. 
Published: February 2011

Abstract
Metabolomics, the global study of small molecule complements, shows great promise as a tool for the discovery of biomarkers of mutagen exposure and early tumorigenesis. With the ever increasing pool of quantitative data yielded from metabolomic research, methods and tools with which to analyze and extract meaningful conclusions from these data are becoming more and more crucial. Methods currently in wide use are limited in either the scope and depth of analysis or are not specifically tailored to metabolomic datasets. In light of this, a new methodology has been developed and presented here that is specifically tailored to characteristics unique to post-processed LC/MS metabolomic data acquired from biofluid samples. For this study, twenty-four-hour urine samples were collected from male rats before and after whole body exposures to doses of gamma radiation ranging from 0.5 to 10 Gy (n = 20 per dose). Urine metabolomics data were acquired by Ultra-Performance Liquid Chromatography coupled to time-of-flight mass spectrometry, operated in both positive and negative electrospray ionization modes, and pre-processed using MarkerLynx software (Waters, Inc.). Relative abundances of urinary ions were normalized to corresponding creatinine relative abundances to reduce the probability of confounding by variation in renal function. These data were then used to develop our methodology, which can be used as a visualization tool effective in qualitatively illustrating an overall metabolome response to radiation exposure. This is achieved by creating 3D plots, on which each plotted point represents a metabolite, specified by its mass/charge (X axis) and retention time (Y axis), with its pre- to post-exposure change in regulation (Z axis) colorized with regard to the magnitude of change. In addition, numerous data filters and data augmentation schemes, such as noise filters, were developed in order to yield results that were more quantitatively robust, from which stronger conclusions can be drawn about the experiment, such as identifying specific metabolites of interest. With the development of this methodology, the repertoire of analytical tools available to metabolomics researchers will be enhanced, facilitating more rapid and meaningful biomarker discovery.
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 116.
Abstract 1160: Whole genome amplification and high-throughput sequencing of formalin-fixed paraffin-embedded colorectal cancer
Authors: Myllykangas Samuel , Buenrostro Jason , Bell John , Ji Hanlee P. 
Published: February 2011

Abstract
Formalin-fixed paraffin-embedded (FFPE) tumors represent a valuable resource for translational cancer genomic research. However, genetic analysis of the FFPE material is challenging, as archived tissues are often small biopsies and the fixation process damages DNA. In researching a solution to this, we have evaluated the performance of different whole genome amplification methods for obtaining DNA samples from archived tumors and their use as a template in high-throughput sequencing.
Two whole genome amplification methods were applied using 20 μm sections of FFPE colorectal cancer tissue and normal human genome DNA samples. Genomic DNA was amplified using Multiple Displacement Amplification (MDA) method and a modified version of Degenerate Oligonucleotide PCR (DOP) assay. Non-amplified human genomic DNA was used as a reference when genomic coverage, linearity and uniformity of the amplified products were assessed. Paired-end sequencing libraries were prepared from the DOP amplified templates while the MDA samples underwent single read library preparation. Sequencing was performed using an Illumina Genome Analyzer II.
2.5 million 54-mer reads mapping to the human genome were generated for each sample. Whole genome amplification was shown to produce artifacts when compared to non-amplified genomic DNA sequences. The modified DOP method preferentially amplified non-repetitive sequences in the human genome. Using the MDA-based method, genomic sequence coverage was generally more even between regions of repetitive and non-repetitive DNA. However, spread of the sequence read counts was greater in the MDA method and MDA amplification offered less dynamic range to identify copy number aberrations. Using whole genome amplification methods with the FFPE colorectal tumor sample we were able to generate 130 Mb of genomic sequence data and identify DNA copy number gains in chromosomes 13 and 20q.
Whole genome amplification and high-throughput sequencing can be used to generate sequence data from minute amounts of FFPE material and identify DNA copy number aberrations in the archived tumors. Nonetheless, whole genome amplification produces artifacts by introducing bias towards specific regions of the genome, generating artificial and random DNA fragment assemblies (MDA) and introducing universal primer sequence in the ends of the amplified DNA fragments (DOP).
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 1160.
Abstract 1168: Urothelial cell carcinomas harbor very frequent mutations in FGFR3-PI3K-AKT pathway and highest prevalence of mutations is related to low-grade tumors
Authors: Hernandez Silvia , Agell Laia , Muga Silvia De , Juanpere Nuria , Lopez Laura , Murillo Raquel , Lorenzo Marta , Serrano Sergio , Bellmunt Joaquim , Lloreta Josep 
Published: February 2011

Abstract
More than 90% of bladder cancers are urothelial cell carcinomas. Superficial/papillary and invasive tumors progress via different molecular pathways. FGFR3 and PI3KCA mutations are more commonly found in superficial/papillary tumors. The PI3K-AKT pathway emerges as an alternative pathogenic mechanism linked to bladder cancer.
We have analyzed the prevalence of mutations in FGFR3, PI3KCA, KRAS, BRAF and AKT1 genes in a set of 61 bladder tumors classified as TaG1 (n=10), TaG2 (n=19), TaG3 (n=8), T1G2 (n= 3), T1G3 (n= 11), T2G2 (n=1) and T2G3 (n=10). We focused on analyzing the hot spot mutation codons and surrounding regions. Mutation analysis of DNA from paraffin-embedded tumors was performed by direct sequencing of PCR products. Thirty-six (60%) tumors presented mutations, 22 cases with only one mutated gene, whereas 14 of 61 cases had mutations in two genes. The most frequently mutated gene was FGFR3 in 25 tumors, followed by PI3KCA in 16 tumors. The distribution and combinations of mutations was: FGFR3 (n= 16), PI3KCA (n= 3), AKT1 (n= 2), KRAS (n= 1), FGFR3-PI3KCA (n= 9), FGFR3-AKT1 (n= 1), and PI3KCA-KRAS (n= 4). No tumor showed BRAF mutations. According to tumor stage, 26 of 37 (70%) Ta tumors, 3 of 13 (23%) T1 tumors and 7 of 11 (63%) of T2 tumors harbored mutations. On the other hand, according to tumor grade, the distribution of mutations was: grade 1, 9 of 11 (82%); grade 2, 15 of 22 (68%); and grade 3, 12 of 28 (43%), with an overall rate of 27 mutations in 50 high grade tumors (54%). In grade 1, 100% of mutations were found in FGFR3 and/or PI3KCA, with FGFR3 mutations in 9 of 10 tumors. In grade 2, 11 of 15 mutated tumors (73%) showed alterations in FGFR3 and/or PI3KCA, and 4 tumors displayed mutations in AKT1 and KRAS (3 of them in combination with FGFR3 or PI3KCA). In grade 3, 8 of 12 mutated tumors (66%) showed mutations in FGFR3 and/or PI3KCA, and 4 tumors harbored mutations in AKT1 and KRAS (2 of them in combination with PI3KCA). Mutations in AKT1 and KRAS were found in grade 2 and 3, but not in grade 1 tumors. Percentage of mutations in the FGFR3-PI3K-AKT1 pathway is inversely proportional to grade, and it is more often associated with low grade tumors. Mutations in FGFR3 are often found alone in bladder tumors, whereas PI3KCA mutations are more frequent in combination with other mutated genes, such as FGFR3 or KRAS. FGFR3 and KRAS mutations seem to be mutually exclusive, but not PI3KCA and KRAS, nor FGFR3 and AKT1 mutations.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1168.