bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2168: Molecular pathway analysis of esophageal squamous cell differentiation versus carcinoma formation
Authors: Yan Wusheng , Zhu Liang , Shih Joanna , Rodriguez-Canales Jaime , Hipp Jason , Player Audrey , Hu Nan , Goldstein Alisa M. , Taylor Philip R. , Emmert-Buck Michael R. , Erickson Heidi S. 
Published: February 2011

Abstract
Esophageal squamous cell carcinoma (ESCC) is the predominant histological subtype of esophageal cancer and is characterized by high mortality. Our previous work analyzing candidate tumor associated genes in ESCC highlighted the important differences in mRNA expression between the normal esophageal and tumor epithelial compartments. However, to date there are limited studies examining expression changes that occur during esophageal squamous cell differentiation versus those associated with ESCC tumorigenesis.
To address this issue, we microdissected the basal cell layer and differentiated cell layer from normal epithelium and compared these expression profiles with matched tumor samples in twelve patients using gene expression microarrays (Hu133A 2.0, Affymetrix, Inc.) and qRT-PCR for selected miRNAs. Genes and pathways of interest were determined using class comparison and pathway analyses.
Pathway expression of BRCA1 in the DNA damage response pathway presented the most significant difference (P &lt;0.00001) in normal differentiated cells compared to tumor differentiated cells, but no difference was present between normal basal cells and tumor peripheral cells. PDGF signaling was significant only in the normal basal vs. tumor comparison. Taken together, BRCA1 and PDGF expression suggest oncogenetic process differences in esophageal epithelial compartments. Basal cells presented with CCND1 and CDKN2A high expression and p53 low expression, implying that basal cells gene expression is closer to a pattern of tumorigenesis than that of differentiated cells. A typical “stem cell” pattern of CD44high/CD24low expression in normal basal cells vs. normal differentiated cells and tumor vs. normal comparisons indicated that the basal cell compartment may house progenitor or stem-like cells and tumor cells expression is indicative of this stem-like origin. Converse to our expectations, tumor peripheral vs. tumor center comparison revealed that the ESCC tumor clusters were essentially homogenous on the transcriptomic level.
Overall, the preliminary results indicate that tumor profiles were closer to basal cells than differentiated cells, consistent with their rapid growth rate and less well differentiated morphology. Investigation of gene expression patterns in normal cell types and ESCC provides novel insight into the transcript profiles associated with normal development versus carcinogenesis.
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 2168.
Abstract 2169: Integrated proteomic and genomic profiling data from a tongue squamous cell carcinoma cell line separates normal and tumor tongue tissue
Authors: Ceder Rebecca , Staab Claudia A. , Roberg Karin , Jörnvall Hans , Höög Jan-Olov , Grafström Roland C. 
Published: February 2011

Abstract
In depth characterization of individual human tumor cell lines might serve to explore the concept of future personalized cancer management. To address this question, standardized serum-free cultures of normal oral keratinocytes (NOK) were compared relative to the tongue squamous cell carcinoma line LK0412 via multiple bioinformatics-based assessments of transcript and protein profiles. Two-dimensional polyacrylamide electrophoresis identified 27 differentially expressed abundant proteins in LK0412. Gene Ontology enrichment analysis indicated alterations of the regulation of cell death, protein metabolism, energy pathways and various binding activities. Based on the protein-enriched GO-categories, the web-based program AffyAnnotator conducted the selection of 119 differently expressed transcripts from the microarray data in LK0412 vs. NOK. Ingenuity Pathway Analysis of these pertubated transcripts then revealed associations to cancer, cellular assembly and organization as well as cellular movement, and moreover, identified an 11-gene profile composed of central regulators within the networks. Notably, the differently expressed proteins and transcripts, as well as the 11-gene profile, variably classified two independent public microarray data sets of totally 38 normal and 57 tumor tongue samples, including a power of 95% accuracy from the 11-gene profile. Additional evaluation of the derived signatures by so called “signature evaluation tool” (implementing the Golub's weighted voting algorithm), identified reduced gene number signatures that similarly discriminated the normal from the tongue tissues in both data sets up to an accuracy rate of 95%. The overall results suggest that combined bioinformatics processing of transcript and protein data might serve as a constructive strategy for identification of potential candidate biomarkers in individual tumor samples, that may then serve to aid in cancer management. Additionally, gene signature profiles, generated as described, may serve to improve current efforts to accurately classify normal and tumor tongue tissues.
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 2169.
Abstract 2173: Cytokeratin-19, a predictive marker and an early determinant of progenitor-derived hepatocellular carcinoma
Authors: Andersen Jesper B. , Loi Roberto , Perra Andrea , Factor Valentina M. , Ledda-Columbano Giovanna M. , Columbano Amedeo , Thorgeirsson Snorri S. 
Published: February 2011

Abstract
Background: Human hepatocellular carcinoma (HCC) is a heterogeneous disease of distinct clinical subgroups. A principal source of tumor heterogeneity may be cell type of origin which in liver includes hepatocyte and/or adult stem/progenitor cells. Objective: To address this issue, we investigated the molecular mechanisms underlying the fate of the enzyme-altered preneoplastic lesions in the resistant hepatocyte (RH) model. Methods: Sixty samples classified as focal lesions, adenoma, early and advanced HCCs were micro-dissected after morphological and immunohistochemical evaluation and subjected to global gene expression profiling. Results: The analysis of progression of the persistent GSTP+ focal lesions to fully developed HCC showed that about 50% of persistent nodules and all HCCs expressed CK19 whereas 14% of remodeling nodules were CK19+. Unsupervised hierarchical clustering of the expression profiles also grouped the samples according to CK19 expression. Further, supervised analysis using the differentially expressed genes in each cluster combined with the gene connectivity tools identified 1308 unique genes and a predominance of the AP-1/JUN network in the CK19+ lesions. In contrast, the CK19-negative cluster exhibited only limited molecular changes (156 differentially expressed genes vs. normal liver) consistent with remodeling towards differentiated phenotype. Finally, comparative functional genomics revealed a stringent clustering of CK19+ early lesions and advanced HCCs with human HCCs characterized by poor prognosis. Furthermore, the CK19 associated gene expression signature accurately predicted the patient survival (P&lt;0.009) and tumor recurrence (P&lt;0.006). Conclusion: Our data establish CK19 as a prognostic marker of early neoplastic lesions and strongly suggest the progenitor derivation of HCC in the rat RH model. The capacity of the CK19 associated gene signature to stratify HCC patients according to clinical prognosis indicates the usefulness of the RH model for studies of stem/progenitor-derived HCC.
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 2173.
Abstract 2177: Long-term storage in TRIzol has little effect on microarray-based gene expression profiling in primary myeloma or acute myeloid leukemia cells
Authors: Wang Michael , Wang Zhi-Qiang , Sun Luhong , Ma Wencai , Graber David , Matthews Jairo , Champlin Richard , Yi Qing , Orlowski Robert Z. , Kwak Larry , Weber Donna M. , Thomas Sheeba K. , Shah Jatin , Kornblau Steven , Davis Richard E. 
Published: February 2011

Abstract
We used paired samples to address whether long-term storage of cells in TRIzol has a significant effect on microarray-based gene expression profiling (GEP). The TRIzol reagent is widely used for the preservation and isolation of RNA, but there is suspicion that prolonged storage of tissues prior to RNA isolation, even at −80 C., can cause chemical modification (depurination) of RNA. This could result in early termination during reverse transcription (RT) of mRNA molecules, potentially affecting GEP more strongly for transcripts with probes located farther from the 3’ end. The Myeloma and Leukemia Tissue Banks at M. D. Anderson Cancer Center routinely collect and store primary tumor samples for research under informed consent. From these banks we selected primary tumor samples of multiple myeloma (MM; CD138+) and acute myeloid leukemia (AML; Ficoll-purified, CD3- and CD19-depleted), for which paired aliquots had been stored frozen in TRIzol (“Tri”) or cryopreservation medium (RPMI + 20% FCS + 10% DMSO, “Cryo”) since the time of initial isolation (range, 2-9 years). Cryo aliquots were quickly thawed, washed, and placed in TRIzol, then total RNA was isolated from all aliquots as per the TRIzol manufacturer's instructions. RNA quality was assessed with a Bioanalyzer 2100 (Agilent); the RNA integrity number (RIN) was &gt; 9 for 12/12 AML Tri, 6/12 AML Cryo, 6/6 MM Tri, and 3/6 MM Cryo samples. RNA from 12 sample pairs (6 AML, 6 MM, all with RIN &gt; 7) was further purified with Qiagen RNAeasy columns, and the Illumina® TotalPrep RNA Amplification Kit (Ambion) was used to generate amplified, biotinylated cRNA after RT by the Eberwine procedure. Bioanalyzer-generated histograms of cRNA were similar for all sample aliquots, suggesting no early termination of RT due to TRIzol. GEP was performed with cRNA on Illumina HT-12 BeadArrays. Analysis of “probe-level” data with GenomeStudio software (Illumina), after median normalization, showed excellent concordance between sample Tri/Cryo pairs for all but probes with low intensities (&lt;50). For the 48795 probes on the arrays, no more than 320 gave DiffScores &lt; −13 or &gt; 13 for any sample pair, and most pairs had &lt;50 probes that differed. After exclusion of low-intensity values, hierarchical clustering associated all Tri aliquots with their corresponding Cryo aliquot. We conclude that long-term TRIzol storage has little effect on microarray-based GEP, and preserves RNA quality better than does cryopreservation.
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 2177.
Abstract 2181: Rapid screening of molecular targets using RT-PCR for solid tumor profiling
Authors: Pouliot Kimberly L. , Cadet Rudolph , Watkins Brynmor , Sonis Stephen T. , Fey Edward 
Published: February 2011

Abstract
Purpose: The identification of molecular targets will be an essential step in developing mechanistically-based approaches to cancer treatment, as well as for determining tumor response and/or resistance to therapy. Not only will identification of these targets in solid tumors, but in the subsequent metastasis as well. The purpose of this study was to evaluate the utility of a large-scale tumor bank, using both xenograft and orthotopic models, as a source of material for quantification of gene expression as a tumor profiling and screening tool.
Experimental Design: Solid tumors representing nine different indications were grown as a xenograft in nude mice. The panel of cell lines included: epidermoid carcinoma (A-431), lung carcinoma (A549, NCI-H460, small cell lung carcinoma: NCI-H82, NCI-H69), pancreatic carcinoma (AsPC-1, BxPC-3 and PANC-1), prostate carcinoma (Du145), breast carcinoma (MDA-MB-231, MDA-MB-435, MCF-7), colon carcincoma (HCT-15, HCT-116 and HT-29), ovarian carcinoma (OVCAR-3 and SK-OV-3) and glioma (U87-MG and U118-MG). In addition, five cell lines representing three indications were grown orthotopically (A549, NCI-H460, MDA-MB-231, MCF-7 and HT-29) in the lung, breast or colon, respectively. When subcutaneously implanted tumors reached a volume of 1500-2000mm3 samples were harvested by aseptic technique. Orthotopically implanted tumors were excised after 25 to 45 days post-implantation and tissues harvested. Animals with mammary fat pad tumors, also had lymph nodes and lungs removed. RNA was purified under sterile conditions. Expression of Akt, phosphoinositide-3 kinase (PI3K), epidermal growth factor receptor (EGFR), p53 and BCL-2 was determined using RT-PCR (Applied BioSystems TaqMan System).
Results: Differential expression of target genes within solid tumors was determined using RT-PCR. An emphasis on gene expression in orthotopic and metastatic models will be discussed.
Conclusion: Unlike semi-quantitiative methods such as immunohistochemistry (IHC) or Western Blotting, RT-PCR is ideal as screening tool as it is rapid, robust, quantitative and only requires a small amount of starting material. We describe a rapid screening method of gene expression in both xenograft and orthotopic models.
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 2181.
Abstract 2187: Optimization free oncogene mutation screening work flow
Authors: Wang Jonathan T. , Lee Michael K. , Janaway Gordon A. , Koch Nathalie , Geuns Elke , Stevens Junko F. 
Published: February 2011

Abstract
BRCA1 and BRCA2 are the two primary breast cancer susceptibility genes in which identifying mutations is important to access cancer risk and decision for treatment. Prescreening of exons by High Resolution Melt (HRM) prior to sequencing can reduce effort in mutation screening in large transcripts such as the BRCA genes. Published methods for BRCA1 and 2 HRM screening have relied on complicated touchdown cycling protocols and custom reagent mixes that can lead to variable result. We have validated a streamlined workflow for adaptability in a clinical diagnostic environment. First, genomic DNA template was extracted on an automated sample processor using magnetic bead technology to purify genomic DNA directly from blood sample. Then, the PCR was performed using a PCR master mix optimized for HRM coupled with universal cycling conditions. We have successfully amplified all 120 amplicons covering exons of both BRCA genes using universal PCR condition. Potential variations identified by HRM screening were confirmed by direct sequencing of HRM PCR amplicons with M13 universal tags. By using unified protocol for PCR and universal sequencing for all amplicons the risk of incorrect procedure is greatly reduced. This simplified workflow for oncogene mutation screening using automated sample extraction and universal protocol for PCR and sequencing provides significant advantages for application in diagnostic settings.
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 2187.
Abstract 22: Cyclin E amplification, a novel mechanism of resistance to trastuzumab in HER2 amplified breast cancer
Authors: Scaltriti Maurizio , Eichhorn Pieter , Gili Magui , Guzman Marta , Aura Claudia , Jimenez José , Prudkin Ludmila , Green Simon R. , Cortés Javier , Chandarlapaty Sarat , Mai Sabine , Hudis Clifford A. , Rosen Neal , Baselga José 
Published: February 2011

Abstract
HER2 amplification/overexpression occurs in 20% of breast cancers and is associated with poor prognosis. Therapeutic agents against HER2, including monoclonal antibodies and tyrosine kinase inhibitors, have shown to improve the survival of these patients. However, primary and acquired resistance to these agents is a major barrier to the effective treatment of this disease.
Aiming to identify the molecular pathways responsible for resistance to anti-HER2 therapy we have established HER2 positive breast cancer cell lines refractory to the anti-proliferative effects of the therapeutic antibody trastuzumab. We have studied their acquired genetic aberrations by performing gene expression microarray and genome single nucleotide polymorphisms analyses. In trastuzumab resistant cells we identified an increase in copy number variation in locus 19q12. This chromosome region comprises seven genes, among them cyclin E1 (CCNE1). We further confirmed Cyclin E over-expression in trastuzumab resistant cells by western blot.
To test the hypothesis that increased cyclin E expression could play a role in the acquisition of trastuzumab resistance we have demonstrated that ablation of cyclin E expression by siRNA restores trastuzumab sensitivity in HER2 positive resistant cells. Furthermore, we have determined that trastuzumab resistant cells are highly sensitive to the specific CDK inhibitor seliciclib and its more potent derivative Cmpd. 5 (Cyclacel) both in vitro and in vivo. In addition, we have analyzed a cohort of HER2 positive breast cancer patients treated with trastuzumab-based therapy and identified a proportion of patients refractory to trastuzumab that harbor amplification of the cyclin E gene. Our results suggest that cyclin E amplification decreases trastuzumab sensitivity and may provide the rationale to test the efficacy of CDK2 inhibitors in breast cancer patients with cyclin E amplification that escaped trastuzumab therapy.
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 22.
Abstract 220: 14-3-3 zeta downregulation sensitizes head and neck cancer cells to chemotherapeutic agents
Authors: Ajay Matta , Desouza Leroi V. , Ralhan Ranju , Siu KW Michael 
Published: February 2011

Abstract
Introduction. Advancements in treatment modalities have not translated into marked improvement in the prognosis of Head and Neck squamous cell carcinoma (HNSCC) patients. Major emphasis is being laid on designing new therapeutic strategies for more effective disease management. Recently, using iTRAQ-labeling and liquid chromatography-mass spectrometry (MS), we identified a panel of biomarkers, including 14-3-3 zeta and 14-3-3 sigma in HNSCC and oral pre-malignant lesions. Retrospective study of HNSCC revealed correlation of increased expression of both these biomarkers with poor disease prognosis. Herein, we report preliminary results on determining the potential of 14-3-3 zeta as a molecular target for HNSCC therapy.
Methods. Small interfering RNA (siRNA) targeting 14-3-3 zeta was used to down-regulate its expression in head and neck cancer cell lines (SCC4 / HSC2). Transient transfection of siRNAs targeting 14-3-3 zeta in these cultured cells was done using LipofectAMINE 2000. The chemosensitivity of transfected cells was determined by measuring the cell death using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, Flow cytometry-based cell cycle analysis, Annexin V dye binding assay and TUNEL assay.
Results: Knockdown of 14-3-3 zeta showed reduced cell viability and G2/M arrest in head and neck cancer cells transfected with 14-3-3 zeta siRNA (100 nM, 48 hours). Importantly, doxorubicin / cisplatin treatment of 14-3-3 zeta siRNA transfected head and neck cancer cells (SCC4 / HSC2), showed increased cell death at lower doses in comparison to cells treated with doxorubicin or cisplatin alone. Increased sub-G0 phase was observed in SCC4 cells (showing reduced 14-3-3 zeta expression) on treatment with any of these chemotherapeutic agents. Annexin V staining and TUNEL assay revealed increased apoptosis. Western blot analysis showed cleaved caspase 9 and caspase 3, confirming the induction of apoptosis.
Conclusions: Our results showed that 14-3-3 zeta downregulation sensitizes head and neck cancer cells to chemotherapeutic agents by induction of apoptosis. We propose that down-regulation of 14-3-3 zeta may serve as a novel strategy to improve the efficacy of chemotherapeutic agents in the management of head and neck 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 220.
Abstract 2201: Pathway analysis of breast cancer genome wide association study highlights three pathways and one canonical signaling cascade
Authors: Menashe Idan , Maeder Dennis , Garcia-Closas Montserrat , Figueroa Jonine D. , Bhattacharjee Samsiddhi , Rotunno Melissa , Kraft Peter , Hunter David J. , Chanock Stephen J. , Rosenberg Philip S. , Chatterjee Nilanjan 
Published: February 2011

Abstract
Genome-wide association studies (GWAS) focus on relatively few highly significant loci while less attention is given to other genotyped markers. Employing pathway analysis to existing GWAS data may shed light on relevant biological processes, and illuminate new candidate genes. We employed a pathway-based approach to the breast cancer GWAS data of the National Cancer Institute (NCI) Cancer Genetic Markers of Susceptibility (CGEMS) project that includes 1145 cases and 1142 controls. Pathways were retrieved from three databases: KEGG, BioCarta, and the NCI's Protein Interaction Database (PID). Genes were represented by their most strongly associated SNP, and an enrichment score (ES) reflecting the overrepresentation of gene-based association signals in each pathway was calculated using a weighted Kolmogorov-Smirnov procedure. Finally, hierarchical clustering was used to identify pathways with overlapping genes, and clusters with excess of association signals were determined by the adaptive rank-truncated product (ARTP) method. A total of 421 pathways containing 3962 genes were included in our study. Of these, three pathways (‘Syndecan-1-mediated signaling ‘, ‘Signaling of Hepatocyte Growth Factor Receptor’ and ‘Growth Hormone Signaling’) were highly enriched with association signals (PES &lt; 0.001, False Discovery Rate (FDR) = 0.118). Our clustering analysis revealed that pathways containing key components of the RAS/RAF/MAPK canonical signaling cascade, were significantly more likely to have excess of association signals than expected by chance (PARTP = 0.0051, FDR = 0.07). These results suggest that genetic alterations associated with these three pathways and one canonical signaling cascade may contribute to breast cancer susceptibility.
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 2201.