bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4033: A20 gene promoter methylation confers resistance to colorectal carcinoma cell lines
Authors: Siraj Abdul K. , Al-Rasheed Maha , Bavi Prashant , Hussain Azhar , Al-Sanea Nasser , Al-Dayel Fouad , Uddin Shahab , Al-Kuraya Khawla S. 
Published: August 2012

Abstract
Gene silencing associated with aberrant methylation of promoter region CpG islands is an acquired epigenetic alteration. It serves as an alternative to genetic defects in the inactivation of tumor suppressor and other genes in human cancers. Several genes have been shown to be epigenetically inactivated in a wide range of tumors and most neoplasms show hypermethylation of one or more genes. A20, also known as TNF alpha induced protein3 (TNFAIP3), is a tumor suppressor gene and a well-known negative regulator of the NF-kB pathway. In colorectal carcinoma (CRC), aberrant NF-kB regulation has been associated with poor prognosis and resistance to therapy. Previously, we elucidated the biological role of A20, mechanism of its inactivation and its prognostic role in colorectal carcinoma. Loss of A20 protein expression by immunohistochemistry and A20 deletions by FISH were studied in a microarray cohort of CRC cases and cell lines for mutations in A20 gene and A20 promoter methylation were also screened. We further elucidated the mechanism of A20 inactivation in colorectal carcinoma cell lines in this extended study. Methylation status of A20 promoter in CRC cell lines correlated with the degree of A20 protein expression: unmethylated cell line SW948 showed the highest expression of A20 protein whereas LOVO, which was methylated, showed almost complete loss of A20 expression. CRC cell lines with high levels of A20 expression (SW948 and COLO320), intermediate levels (HCT-15 and DLD-1) and very low levels (LOVO-1) were immunoblotted for detection of A20 protein expression. Treatment of methylated colorectal cell lines with the methyltransferase inhibitor, 5-aza-2′deoxy-cytidine resulted in partial demethylation and re-expression of A20 gene, suggesting the role of methylation in silencing the gene. In addition, demethylation of A20 gene by 5-aza-2′deoxy-cytidine also decreased cell viability by 15-20X in CRC cell lines, suggesting that A20 expression may play an important role in CRC tumorigenesis. In conclusion, A20 methylation may be a promising molecular marker to predict patient outcome in colorectal cancer, and may be used as therapeutic demethylating target.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4033. doi:1538-7445.AM2012-4033
Abstract 404: Regulation of NKG2D expression and NKG2D-positive T cell tumor-specific trafficking by doxorubicin and IL-12 in vivo
Authors: Hu Jiemiao , Zhu Shiguo , Xia Xueqing , Yokoyama Wayne M. , Li Shulin 
Published: August 2012

Abstract
IL-12 and doxorubicin treatment are known to polarize anti-tumor immune response and induce tumor cell death, respectively, when each is administered alone. IL-12 treatment can boost NKG2D receptor expression on immune cells, enhancing NK cell cytotoxicity against different tumor cell lines. However, IL-12 treatment alone can only modestly increase expression of NKG2D receptor. In tumor immuno-surveillance, it is important to create an environment in which spleen cells constitutively express the NKG2D receptor thereby triggering NKG2D-dependent tumor cell death. In an earlier study, we found that coadministration of the anti-neoplastic drug doxorubicin and IL-12 greatly boosted anti-tumor efficacy. This increased anti-tumor efficacy was associated with a substantial increase in immune cell infiltration at tumor sites, but the underlying mechanism by which the increased number of immune cells was trafficked into the tumors remains largely unknown. This report demonstrates that doxorubicin plus IL-12 treatment induces the higher expression of NKG2D receptor in CD8 T cells than IL-12 treatment alone, resulting in an increased infiltration of NKG2D-positive CD8 T cells, and leading to an NKG2D-dependent tumor growth inhibition in vivo. These in vivo observations are in agreement with our in vitro result, in which the encounter between NKG2D receptor-positive effector cells and NKG2D ligand-positive tumor cells yields an NKG2D-dependent tumor cell death as determined by cytolytic activity assay. Blocking the NKG2D receptor by using neutralization antibody impaired doxorubicin plus IL-12 treatment-mediated tumor eradication in vivo and effector cell-mediated tumor cell death in vitro. Together, the evidence links the higher IL-12 plus doxorubicin treatment-induced NKG2D expression to greater CD8 T cell infiltration into tumors, tumor cell death, and anti-tumor efficacy.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 404. doi:1538-7445.AM2012-404
Abstract 4044: Epigenetic repression of RARRES1 is mediated by methylation of a critical proximal promoter and a loss of CTCF binding
Authors: Lin Huey-Jen L. , Peng Zhengang , Shen Rulong , Li Yingwei , Teng Kun-Yu , Shapiro Charles 
Published: August 2012

Abstract
Background: The critical promoter element responsible for epigenetic silencing of retinoic acid receptor responder 1 (RARRES1) by methylation is unclear. Likewise, how aberrant methylation interplays effectors and thus affects breast neoplastic features remains largely unknown. Methodology/Principal Findings: We first compared methylation occurring at the sequences flanking the RARRES1 promoter in primary breast carcinomas to that in adjacent benign tissues. Surprisingly, tumor cores displayed significantly elevated methylation occurring solely at the upstream region, while the downstream element proximal to the transcription start site (+1) remained largely unchanged. Yet, hypermethylation at the former did not result in appreciable silencing effect. In contrast, the proximal sequence displayed full promoter activity and methylation of which remarkably silenced RARRES1 transcription. This phenomenon was recapitulated in breast cancer cell lines, in which methylation at the proximal region strikingly coincided with downregulation. We also discovered that CTCF occupancy was enriched at the unmethylayed promoter enriched with transcription-active histone markings. Furthermore, knocking-down CTCF expression hampered RARRES1 expression, suggesting CTCF positively regulated RARRES1 transcription presumably by binding to unmethylated promoter poised at transcription-ready state. Moreover, RARRES1 restoration not only impeded cell invasion but also promoted death induced by chemotherapeutic agents, denoting its tumor suppressive effects. Its role of attenuating invasion agreed with data generated from clinical specimens revealing that RARRES1 was generally downregulated in metastatic lymph nodes compared to the tumor cores. Conclusion/Significance: For the first time, this report delineated that silencing of RARRES1 by hypermethylation is occurring at a crucial proximal promoter element and is associated with a loss of binding to CTCF, an activator for RARRES1 expression. We also revealed the tumor suppressive roles exerted by RARRES1 in part by promoting breast epithelial cell death and by impeding cell invasion that is an important property for metastatic spread.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4044. doi:1538-7445.AM2012-4044
Abstract 4045: Intragenic ATM methylation in peripheral blood DNA as a biomarker of breast cancer risk
Authors: Brennan Kevin , Garcias-Closas Montserrat , Orr Nicholas , Fletcher Olivia , Jones Michael , Ashworth Alan , Swerdlow Anthony ,   KConFab Investigators, Riboli Elio , Vineis Paolo , Dorronsosro Mirren , Clavel Francoise , Panico Salvatore , Onland-Moret N. Charlotte , Trichopoulos Dimitrios , Kaaks Rudolf , Khaw Kay-Tee , Brown Robert , Flanagan James M. 
Published: August 2012

Abstract
DNA methylation is an important epigenetic modification that could affect cancer risk through direct effects on disease, and/or mediating effects of genetic and environmental factors. Global and gene-specific DNA methylation levels in white blood cells (WBC) have been related to risk of breast and other cancers, however, evidence is generally weak. We analysed WBC DNA methylation of two ATM intragenic loci (ATMmvp2a and ATMmvp2b) and genome-wide DNA methylation in LINE1 repetitive elements in three breast cancer studies with pre-diagnostic blood samples. Studies included a case-control study with cases derived from a prospective cohort of high-risk breast cancer families (KConFab), and nested case-control studies in two prospective cohorts: the Breakthrough Generations Study (BGS) and the European Prospective Investigation into Cancer and Nutrition (EPIC). Total sample size was 640 incident cases of invasive breast cancer and 741 controls. Bisulphite pyrosequencing was used to quantify methylation in WBC DNA. Quintile analyses of the combined data for ATMmvp2a showed an increased risk of breast cancer limited to women in the highest quintile of methylation (OR =1.89 (1.36-2.64), p= 1.64x10-4). We found no significant differences in estimates across studies, however, the largest differences in ATMmvp2a methylation levels were observed for familial cases in KConFab compared to controls. We observed no significant differences in LINE1 or ATMmvp2b methylation levels between cases and controls. These results indicate that WBC DNA methylation levels at ATM could be a marker of breast cancer risk and further support the pursuit of epigenome-wide association studies in peripheral blood DNA methylation. Funding: Breast Cancer Campaign Fellowship and Cancer Research UK Program C536/A6689.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4045. doi:1538-7445.AM2012-4045
Abstract 4047: Introducing a novel acoustic imaging tool for breast cancer detection
Authors: Alizad Azra , Whaley Dana H. , Urban Matthew M. , Greenleaf James F. , Fatemi Mostafa 
Published: August 2012

Abstract
Objective: This paper introduces an alternative non-invasive and non-ionizing breast imaging tool called vibro-acoustography (VA). This method is based on low-frequency harmonic vibrations induced in the object by the radiation force of ultrasound. Contrast in Vibro-acoustography images represent several properties of the object, including the dynamic characteristics at the audio frequency and scattering and absorption properties at the ultrasound frequency. X-ray mammography and ultrasound are the main imaging modality used today for detection of breast lesions. X-ray mammography, however, is ionizing and its sensitivity is greatly reduced in dense breasts. Ultrasound images suffer from speckles or other or artifact that prevents the physician from delineating the mass lesion from the background tissue. Hence, VA may be used as a stand-alone imaging device or as a tool to provide supplementary information to other existing imaging modalities. Materials & Methods: Matching vibro-acoustography and mammography images of human breast are acquired using a combined mammography/vibro-acoustography machine. Images of various types of breast masses are investigated and their characteristics features are compared. Image features, such as lesion borders, interior texture, and speculation pattern, are studied. Results: Resulting images show soft tissue structures, breast lesions and microcalcifications within breast with high contrast, high resolution, and no speckles. The results have been verified using x-ray mammograms of the breast. Vibro-acoustography images demonstrate that calcified masses normally show sharp borders, benign non-calcified masses have smooth texture, and, in some cases, malignant masses are characterized with spiculation. Conclusion: The encouraging results which are based on the data collected from an ongoing study indicate that the above mentioned image features may be used for differentiation of breast masses and suggest that further development of vibro-acoustography technology may lead to a new clinical tool for various imaging applications. Work supported in part by Grant CA121579-01A1from NIH and Grant BCTR#0504550 from Susan G. Komen Breast Cancer Foundation.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4047. doi:1538-7445.AM2012-4047
Abstract 4057: Quantitative assessment of 3D nuclear architecture in colon epithelial cells by micro-optical computed tomography
Authors: Nandakumar Vivek , Hernandez Kathryn F. , Rodolpho Beatriz L. , Senechal Patti , Bussey Kimberly J. , Johnson Roger H. , Meldrum Deirdre R. 
Published: August 2012

Abstract
Colorectal cancer (CRC) is a commonly diagnosed cancer and the third leading cause of cancer-related deaths in the United States. About 50,000 people will die from this disease in 2011. CRCs develop through an accumulation of genetic and epigenetic aberrations and have been broadly classified into three molecular subtypes - chromosomal instability (CIN), microsatellite instability (MSI), and CpG Island Methylator Phenotype (CIMP). Research studies on CRC have predominantly focused on its molecular biological and genetic basis, but very little is known about the three-dimensional cell morphological variations between these subclasses. We investigated alterations in the three-dimensional (3D) nuclear architecture of the three molecular subtypes of CRC, comparing them to a benign adenoma, using representative epithelial cell line models: AAC1 (benign), AAC1-SB10 (CIN), HCT-116 (MSI) and RKO (CIMP). We applied micro-optical computed tomography (Cell-CT) to image one hundred individual hematoxylin-stained cells of each of the four types with submicron, isotropic spatial resolution. We performed automated 3D image analysis on the volumetric cell images, quantifying fifty descriptors (features) to characterize the nuclear morphology and coarse chromatin organization. We evaluated the statistical efficacy of our 3D features in distinguishing among the cell types. Our results demonstrated previously unreported morphological variations among the controls and three types of CRC. Relative to the benign adenoma cells, in contrast to CIN and MSI, the CIMP subtype exhibited markedly smaller cell and nuclear sizes, smaller nucleus-to-cytoplasm (NC) ratio and a predominantly smooth nuclear interior, lacking in clumpy chromatin. However, the CIMP cell nuclei exhibited the highest optical density among the four cell classes. MSI cells showed the clumpiest nuclear texture, followed by the benign adenoma cell nuclei. These results offer new perspectives on nuclear structure variations in benign colon adenoma and colorectal cancer cells, warranting further investigation. They suggest that the hypermethylation seen in the CIMP phenotype may result in demonstrable chromatin compaction with a concomitant reduction in nuclear size. The chromatin clumpiness observed in the MSI cells may reflect increased mutations at nuclear scaffold binding sites, which tend to be characterized by single and di-nucleotide repeats. We intend to pursue studies on human biopsy cells with ultimate goal of testing the efficacy of Cell-CT for CRC diagnosis, subtyping and staging.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4057. doi:1538-7445.AM2012-4057
Abstract 406: Monitoring inflammation and therapeutic response with clinically translational 19F MRI
Authors: Helfer Brooke M. , Balducci Anthony , Wesa Amy 
Published: August 2012

Abstract
Non- invasive monitoring of inflammation to both diagnose disease and evaluate treatment is critically needed. V-Sense, a perfluorocarbon tracer agent that labels circulating inflammatory cells, which are then recruited out of circulation to sites of inflammation, enables detection by 19F MRI. Due to negligible 19F background in the host, detection of 19F and thus inflammation is highly-specific. Inflammation is a noted predecessor to several types of cancer such as colon, ovarian, pancreatic and prostate cancer and also contributes to the progression of metastatic disease. Using a collagen-induced arthritis model, where the inflammatory process is well understood, we demonstrate the ability to monitor development, progression, and treatment of inflammation. Disease progression in the rat hind limbs was monitored by caliper measurements and 19F MRI on days 14, 21 and 28, including the height of clinically symptomatic disease. Naïve rats served as controls. The capacity of V-Sense to assess the effectiveness of therapy was studied in a cohort of rats administered oral prednisolone on days 14 to 28. Terminal histopathological analysis was also performed. Comparison of caliper measurements to the 19F accumulation, from 19F MRI, validated the quanitative nature of this approach. This study supports the use of V-Sense to monitor and quantify the inflammatory process in disease, including the development of and treatment cancer.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 406. doi:1538-7445.AM2012-406
Abstract 4062: A kinetic live-cell imaging approach to measuring cytotoxicity in vitro
Authors: OClair Belinda A. , Endsley Eric W. , Groppi Vince E. , Appledorn Daniel M. 
Published: August 2012

Abstract
Cytotoxicity assays play a critical role in the identification of potential anti-cancer chemotherapeutic agents. Commonly used in vitro cytotoxicity assays evaluate a range of end point parameters such as the release of lactate dehydrogenase (LDH) and glutathione (GSH) following membrane rupture, generation of reactive oxygen species (ROS), cell proliferation, and disruption of mitochondrial trans-membrane potential. Critical factors contributing to the predictive nature of these assays include compound concentration, and more importantly, the time allowed for the compound to elicit an effect. Although these multiplexed assays are able to simultaneously measure multiple indicators of in vitro cytotoxicity, they typically assess a single time point and are unable to assess the biological activity over time. We present data showing that we are able to kinetically measure cell wall integrity, while simultaneously monitoring cell death associated morphological changes using a commercially available cell impermeable DNA dye, YOYO-1, coupled with the IncuCyte™ FLR live-cell imaging system. This no-wash, mix-and-read assay provides a statistically robust method to study the kinetic induction of cytotoxicity in vitro. Specifically we use HT 1080 fibrosarcoma cells, MDA-MB-231 breast adenocarcinoma cells, and HeLa cervical adenocarcinoma cells in conjunction with the cytotoxic agents staurosporine and camptothecin, and the cytostatic agent, cycloheximide. These data illustrate the ability to kinetically detect, quantify, and analyze cytotoxicity data in a 96-well plate format using images collected in real time. We show that the quantitative data obtained in this study is amenable to moderate throughput screening protocols with Z’ values &gt;0.6 achieved in both intra- and inter-assay reproducibility studies. We also provide evidence that that the high definition phase contrast images provide qualitative verification of quantitative results allowing for the discrimination between cytotoxic and cytostatic compounds. This strategy combines automated data acquisition and analysis to provide an informative and efficient approach to detecting pharmacological or genetic manipulations that alter cell viability.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4062. doi:1538-7445.AM2012-4062
Abstract 4071: PAXgene Tissue: A new tissue fixation technology for simultaneous preservation of morphology and nucleic acids
Authors: Grölz Daniel , Dettmann Nadine , Blassnig Isabell , Wyrich Ralf , Rainen Lynne 
Published: August 2012

Abstract
Introduction: PAXgene Tissue (PAXgene) is a new, formalin-free fixation technology developed for simultaneous preservation of morphology and biomolecules in tissue samples. PAXgene fixed, paraffin embedded (PFPE) tissue is suitable for conventional histochemical and immunohistochemical staining as well as for extraction of high quality nucleic acids. Material and Methods: Cases of human lung, breast and colorectal cancer were divided and fixed in formalin, PAXgene, or snap frozen in liquid nitrogen (LN2). PAXgene fixed, stabilized specimens were stored for up to four days at room temperature prior to processing. Formalin fixed, paraffin embedded (FFPE) and PFPE tissue morphologies were compared using H&E stain. RNA, miRNA and DNA were isolated from FFPE, PFPE and LN2 tissue. RNA expression was analyzed in 96-well RT-qPCR arrays with pre-designed assays, and miRNA expression profiling was performed with single Sybr-green or primer/probe based assays. DNA was analyzed by agarose gel electrophoresis, long-range, and multiplex PCR. Results: Morphology of PFPE samples was similar to or indistinguishable from FFPE tissue. A high correlation of both RNA and miRNA gene expression results was observed between PFPE and LN2 samples. For all PCR assays, Ct values were within +/− 2 Ct. In contrast, poor correlation was observed between RNA from FFPE compared to RNA from LN2 with differences of up to 10 Cts. Correlation of FFPE to LN2 was higher in the case of miRNA but was still not as high as that of miRNA from PFPE. High molecular weight DNA which performed well in PCR could be isolated from LN2 and PFPE tissue, but DNA from FFPE failed in long-range PCR and showed biased or no amplification in multiplexed PCR. Conclusion: The PAXgene Tissue fixation technology preserves morphology and nucleic acids in tissue samples. It enables morphological and multimodal research biomarker testing with one sample. PAXgene Tissue is for research use only. It is not intended for diagnostic use.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4071. doi:1538-7445.AM2012-4071