bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4021: Breaking the dogma: AWT1 hypermethylation in myeloid leukemia despite high expression
Authors: Guillaumet Amy , Sandoval Juan , Esteller Manel , Issa Jean-Pierre , Sibert Reiner , Monk David 
Published: August 2012

Abstract
Hematological malignancies are the sixth leading cause of cancer related death worldwide. The Wilms tumor 1 (WT1) gene is over-expressed in numerous cancers with respect to normal cells, and has either a tumor suppressor or oncogenic role depending on cellular context. WT1 has been shown to be detectable at low levels only in CD34+/CD38- hematological stem cells but is undetectable after differentiation. WT1 is reported to be an excellent marker for diagnosis and minimal residual disease in acute myeloid leukemia, but the underlying epigenetic alterations are unknown. Using 23 hematological cancer cell lines we confirm the high expression of WT1 and the transcripts derived the from alternative promoter regions (AWT1) in myeloid associated cancer cell lines. To determine if this expression profile is associated with lineage specific DNA methylation changes we performed bisulphite analysis across the loci. Surprisingly we observe hypermethylation of the AWT1 promoter region in despitehigh levels of expression. This hypermethylation is associated with the expected canonical histone modification signature, with high levels of H3K9me3 and low H3K4me3 or H3K9ac. Subsequent bisulphite pyrosequencing of the WT1 and AWT1 promoters in a 356 cytogenetically characterized hematological malignancies revealed that AWT1 was hypermethylated in 63% and WT1 in 8% of primary myeloid cancers at diagnosis, whereas only 26% and 27% where hypermethylated in primary lymphoid cancers. A subset of these patients were treated with decitabine (5-aza-2′-deoxycytidine), a DNA demethylation agent commonly used to treat myeloid leukemia and myeloproliferative disease. The AWT1 methylation state did not change during treatment suggesting that AWT1 methylation state does not correlate with drug response. Our data suggests that combining (A)WT1 expression and AWT1 methylation analyses will be a useful tool for diagnose and confirmation of myeloid-lineage malignancies.
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 4021. doi:1538-7445.AM2012-4021
Abstract 4024: Aberrant DNA methylation of Shisa3 is a novel prognostic biomarker for colorectal cancer
Authors: Jao Tzu-Ming , Tsai Ming-Hong , Chen Wen-Chi , Chen Chun-Chieh , Yu Sung-Liang , Yang Ya-Chien 
Published: August 2012

Abstract
Shisa3, a newly identified tumor suppressor, inhibits invasion and metastasis via regulation of epithelial-mesenchymal transition in non-small cell lung cancer. We first screened 11 colorectal cancer (CRC) cell lines as well as 10 pairs of primary tumors and matched normal mucosas for Shisa3 expression by semi-quantitative RT-PCR. Shisa3 gene was silenced or down-regulated in 8 (72.7%) cell lines and 8 (80%) CRC tumors, suggesting that Shisa3 might be also involved in colorectal tumorigenesis. Accordingly, we further confirmed Shisa3 expression was significantly decreased in 59.6% (31/52) of colorectal carcinomas compared with corresponding normal mucosas by real-time RT-PCR (P &lt; 0.001). Using gene copy number assay, we ruled out chromosomal instability pathway as the major mechanism resulting in Shisa3 silencing in CRC. While Shisa3 mRNA expression was restored in 66.7% (4/6) of CRC cell lines as exposure to DNA methylation inhibitor 5-Aza-2′-deoxycytidine. CpG islands spanning around Shisa3 gene were predicted via MethPrimer program. Aberrant methylation of 5 CpG loci in Shisa3 intron 1 was identified in CRC cell lines and primary tumors by bisulfite sequencing, and their methylation levels determined by pyrosequencing were inverse correlation with Shisa3 mRNA expression. In addition, among 127 pairs of CRC tissues, Shisa3 methylation levels in tumors were much higher than that in corresponding normal mucosas (P &lt; 0.001), and Shisa3 hypermethylation was significantly associated with disease recurrence in stages B and C patients (P = 0.008). Kaplan-Meier survival analysis showed that patients with Shisa3 hypermethylation revealed significantly shortened overall survival (P &lt; 0.001) and disease-free survival (P = 0.006). In conclusion, Shisa3 gene hypermethylation could serve as a molecular predictor of disease recurrence and poor prognosis in CRC.
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 4024. doi:1538-7445.AM2012-4024
Abstract 4032: Consequences of NEIL1 promoter hypermethylation in head and neck squamous cell carcinoma
Authors: Schmezer Peter , Chaisaingmongkol Jittiporn , Warta Rolf , Dyckhoff Gerhard , Oakes Christopher C. , Kuhmann Christine , Geiselhart Lea , Waas Peter , Herold-Mende Christel , Plass Christoph , Popanda Odilia 
Published: August 2012

Abstract
Human endonuclease VIII-like1 (NEIL1) encodes a DNA glycosylase which is suggested to be involved in the repair of oxidative damage in association with DNA replication and transcription. We have recently demonstrated that hypermethylation of the NEIL1 gene promoter occurs in more than two third of head and neck squamous cell carcinoma (HNSCC) patients, and that this promoter hypermethylation correlated with a decreased expression both on the mRNA and protein levels. Further experiments were performed to investigate the relevance and functional consequence of these observations. Demethylation experiments using 5-aza-2′-deoxycytidine and DNMT1 knockdown demonstrated an up to 15-fold re-expression of NEIL1 mRNA in cultured HNSCC cells which initially carried hypermethylated promoter regions. The relevance of promoter methylation for NEIL1 expression was further studied by a luciferase promoter assay using CpG-free pCpGL vector constructs in 293T cells. A promoter construct covering the 5′ region of NEIL1 was treated with CpG methyltransferase (M.SssI) or remained untreated. Luciferase expression of the methylated NEIL1 promoter construct was significantly reduced compared to the unmethylated construct (p&lt;0.01, T-Test). Furthermore, NEIL1/2 glycosylase activity was measured in vitro using a bubble structure substrate containing 5-OHU and by quantifying the cleavage products. Nuclear extracts of HNSCC tissue samples which carried NEIL1 promoter hypermethylation showed a more than 2-fold decrease in NEIL1/2 activity when compared to extracts prepared from normal tissue samples without promoter hypermethylation. Taken together, the presented results strengthen the hypothesis that promoter hypermethylation can reduce NEIL1 gene expression and can lead to a significant loss of NEIL1/2 glycosylase activity in HNSCC tissue. NEIL1 hypermethylation may alter the cellular DNA repair capacity and thus play a role in modulating the response to DNA damaging therapies of HNSCC.
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 4032. doi:1538-7445.AM2012-4032
Abstract 4039: Loss of imprinting in PEG3, MEST and ARHI/DIRAS3 in invasive breast cancer
Authors: Barrow Timothy M. , Ellsworth Rachel E. , Harris Holly R. , Barault Ludovic , Valente Allyson , Shriver Craig D. , Michels Karin B. 
Published: August 2012

Abstract
Genomic imprinting is the epigenetic regulation of genes to enable monoallelic expression according to parental origin. Imprinting is established in the germline and is particularly important in the regulation of fetal development; loss of imprinting (LOI) has been implicated in the development of a variety of childhood disorders and several cancer types. We investigated loss of imprinting in PEG3, MEST and ARHI/DIRAS3 in breast cancer. Blood and tissue samples from women with benign breast disease or no abnormalities (n = 52) and patients with invasive breast cancer (n = 37) were provided by the Clinical Breast Care Project at the Walter Reed Army Medical Center (Washington, USA). DNA extracted from the samples was bisulfite converted and the methylation status of the three genes determined by pyrosequencing. Loss of PEG3 imprinting was observed in 2% of benign tissues and 34% of invasive cancers. LOI in MEST was similarly observed in 4% of benign tissues and 39% of invasive cancers, while in ARHI/DIRAS3 it was observed in 11% of benign samples and 54% of invasive ones. LOI was not observed in blood samples for any of the three genes, suggesting that these epigenetic alterations are highly tissue-specific. There was no correlation between the methylation profiles of the three genes (Spearman's rank correlation coefficient; p = &gt;0.25). Loss of imprinting in PEG3, MEST and ARHI/DIRAS3 appears to be a frequent event in breast cancer, and it is more common in invasive forms than benign proliferative breast disease. The impact of the observed methylation changes upon allele-specific expression is currently investigated.
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 4039. doi:1538-7445.AM2012-4039
Abstract 405: Innate immunity in taxol-mediated tumor regression
Authors: Kuhn Hallie E. , Orth James , Weissleder Ralph , Mitchison Timothy 
Published: August 2012

Abstract
Taxol is a common chemotherapeutic used against many tumor types, including breast, ovarian and lung tumors. However, the mechanism by which it promotes tumor regression is unclear. While in cell culture taxol kills dividing cells, its ability to promote regression of slow growing tumors in some patients suggests it may have additional actions in vivo. To better understand taxol drug response in vivo we profiled xenograft tumors 1, 4, and 7 days post-drug treatment for changes gene expression and cytokine levels. Enrichment of genes associated with immune response pathways, and an increase in chemotactic cytokines Rantes and Mip-1α, suggest a pro-inflammatory immune response. In accordance, immunohistochemistry confirms that tumor associated macrophages (TAMs) are recruited following treatment. While TAMs are generally considered pro-tumorigenic, our system suggests that macrophages may play a cytotoxic role under certain conditions. Understanding the mechanisms by which macrophages can be pro or anti-tumor growth following drug treatment will shed light on the heterogeneity in patient response and may suggest more efficacious, targeted treatment strategies.
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 405. doi:1538-7445.AM2012-405
Abstract 4064: 3-D imaging of human colorectal cancer tissues with optical clearing: Spatial analysis of the tumor vasculature through transparent specimens
Authors: Liu Yuan-An , Pan Shien-Tung , Hou Yung-Chi , Tang Shiue-Cheng , Chung Yuan-Chiang 
Published: August 2012

Abstract
Introduction: Microscopic analysis of tumor vasculature in the endoscopic and surgical biopsies is a valuable diagnostic tool to evaluate cancer treatment at different stages. However, the standard microtome-based 2-dimensional (2-D) histology provides only limited perspective of the dispersed vasculature. To provide a global view of the vascular network, in this research we employed optical clearing to generate transparent specimens for penetrative, 3-dimensional (3-D) visualization of the tumor vasculature in the human colorectal cancer tissues. Methods: Colorectal cancer tissues were obtained from colectomies and endoscopic procedures. Samples of normal mucosa were obtained at least 5 cm apart from the carcinoma. Nuclear and CD34 immuno-staining were used to reveal the mucosal microstructure and vasculature. Optical clearing – use of immersion solution to reduce random scattering as light travels across media (Liu et al., Neurogastroenterol Motil 23:e446, 2011; Fu & Tang, Gastroenterology, 139:p1100, 2010) – was applied to prepare transparent specimens for 3-D imaging via confocal microscopy. Afterward, the specimens were extensively washed with saline to reverse the clearing step and then underwent the standard microtome-based 2-D histology. Avizo projection algorithms were used for image rendering and analysis. Results: The improved photon transmission resulting from optical clearing led to penetrative imaging (up to 300 µm) of the mucosal microstructure and vasculature with high definition. In the normal mucosa, we observed the peri-cryptic capillaries being orderly arranged as a network embedded in the hexagonal honeycomb structure of stroma. In comparison, the vessels in the colorectal carcinoma became dilated and distorted with irregular and disoriented architecture embedded in the deformed mucosa. Significantly, our 3-D image data provided a continuous flow of the anatomic information for panoramic projection and spatial analysis of the vessel density to compare and distinguish the normal and the tumor vasculature. In addition, matched tissue information was observed between the 3-D confocal and the standard H&E and IHC images, indicating our optical method is reversible and can serves as an add-on to the current 2-D histological evaluation of the colorectal cancer. Conclusion: Our optical method connects 3-D microscopy of the human colorectal cancer tissues to the standard microtome-based 2-D histology. This approach is particularly useful in 3-D projection and spatial analysis of the vasculature for future clinical evaluation of the colorectal carcinoma.
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 4064. doi:1538-7445.AM2012-4064
Abstract 4080: 5-Azacitydine augments the anti-glioma efficacy of Herpes-based oncolytic virotherapy
Authors: Okemoto Kazuo , Wagner Benjamin P. , Haseley Amy M. , Price Richard L. , Kaur Balveen , Chiocca Antonio E. 
Published: August 2012

Abstract
Oncolytic virotherapy (OV) using modified Herpes simplex virus (HSV) type 1, is currently being evaluated for safety and efficacy in numerous phase I-III clinical trials. However, the host innate immune response and a compromised ability to counter cellular defense responses in order to sustain efficient viral replication in tumor cells is still a major obstacle to efficacious virotherapy. Sodium valporate (VPA) is a simple branched-chain fatty acid FDA-approved medication used in treating epilepsy. We previously demonstrated that pretreatment of cultured glioma cells with VPA significantly increases OV replication. However, the mechanism underlying VPA mediated increased virus replication has not been fully elucidated. Understanding the mechanism of this effect can lead to the development of better pharmacologic sensitizers for OV therapy. We found that activation of STAT3 and inhibition of DNA methylation are involved in VPA's ability to enhance virus replication. Furthermore, we demonstrated that the combination of a DNA methylation inhibitor, 5-Azacitydine (5-Aza), at a 1-2 uM concentration coupled with IL-6-mediated (10ng/mL) STAT3 activation effectively enhanced OV replication 125 fold when compared with OV alone. This combination was comparable to what was previously observed when VPA alone was utilized to increase OV replication. The combination also showed increased anti-glioma activity (ED50 of 5-Aza: 2 uM; with IL-6, 0.3 uM) when compared to only VPA treatment. Given these in vitro results, we are currently performing experiments in mice assessing the effect of 5-Aza pretreatment on enhancing OV therapy of gliomas. Oncolytic HSV in combination with the DNA methylation inhibitor, 5-Aza, and activation of STAT3 represents a promising strategy for treating human gliomas.
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 4080. doi:1538-7445.AM2012-4080
Abstract 4083: Increased DNA methyltransferase activity and DNA methylation following epidermal growth factor stimulation in ovarian cancer cells
Authors: Samudio-Ruiz Sabrina L. , Hudson Laurie G. 
Published: August 2012

Abstract
Ovarian cancer progression is correlated with accumulation of aberrant CpG island methylation. In patients with ovarian cancer, ascites fluid builds up and contains abundant levels of Epidermal-Growth-Factor-Receptor (EGFR) activators. This fosters a tumor microenvironment of constant EGFR activation. Signaling pathways downstream of EGFR, such as RAS, regulate DNA methylation and expression of DNA methyltransferases. We hypothesized that mimicking this microenvironment of chronic EGFR activation in culture could alter DNA methylation or expression of DNA methyltransferases in ovarian cancer cells. We found evidence that EGFR activation increased DNA methyltransferase activity by ∼3 fold acutely and by ∼7 fold following long term EGFR activation. Furthermore, this increase in activity was dependent on continued EGFR activity and resulted in a 50% increase in global DNA methylation. We also found that constitutive EGFR activation can decrease expression of DNMT3A. However, this decrease does not explain the observed increases in DNMT activity or methylation, thus future experiments will focus on a potential mechanism that mediates these EGF induced alterations to DNMT activity and DNA methylation. The data support a role for EGFR in the process of DNA methylation and accumulation during ovarian cancer progression; thus, suggesting that epigenetic therapy, used in combination with conventional chemotherapy, may be beneficial at preventing cancer progression.
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 4083. doi:1538-7445.AM2012-4083
Abstract 4086: Location matters: The impact of the location of CpG sites on the specificity of methylation biomarkers for HCC
Authors: Jain Surbhi , Chen Sitong , Lin Selena Y. , Boldbaatar Batbold , Xie Lijia , Chang Ting-Tsung , Hu Chi-Tan , Hamilton James P. , Evans Alison A. , Song Wei , Meltzer Stephen J. , Block Timothy M. , Su Ying-Hsiu 
Published: August 2012

Abstract
Hepatocellular carcinoma (HCC) is the second fastest growing cancer and one of the top 10 causes of cancer deaths in the United States. The 5-year survival rate is 14%, ranging from 26% among early stage tumors to only 2% in late stage HCC. The only available biomarker for screening, serum alpha-fetoprotein (AFP), has a low sensitivity of detection (40%-60%), so the need for a better detection method is urgent. Given the heterogeneous nature of HCC, a panel of genetic and epigenetic biomarkers would be needed to obtain high sensitivity for the early diagnosis of HCC. In the course of assembling a panel of epigenetic markers for HCC, we noticed variable HCC specificity of three extensively studied potential methylation biomarkers, APC, GSTP1, and RASSF1A. We hypothesized that the specificity of promoter methylation of the tumor suppressor genes APC, GSTP1, and RASSF1A as a biomarker for HCC could depend upon the location of the CpG sites analyzed. To test this hypothesis, we used bisulfite-PCR sequencing to compare the methylation status of the promoter region of these three genes in DNA isolated from HCC, matched adjacent non-HCC, cirrhosis, hepatitis, and normal liver. We identified HCC-specific CpG methylation sites and unique liver-specific methylation patterns in the promoter region of the APC (Jain et. al, PloSOne 2011) and GSTP1 genes and in a more HCC-specific promoter region (p &lt; 0.05 by Fisher's exact test) of the RASSF1A gene. Together, these results proved our hypothesis and provided an interpretation for the variability in the literature. Using PCR-based technology, we have developed assays for a panel of genetic and epigenetic markers for liver cancer screening. These assays were first tested in tissue to determine their ability to distinguish HCC (n=120) from cirrhosis (n=35) and hepatitis (n=35). The AUROC is 0.809 for mAPC, 0.756 for mGSTP1, 0.887 for mRASSF1, and 0.733 for TP53. When combined, this panel of DNA markers had an AUROC of 0.931 and identified 90% of AFP-negative tumors. This study clearly demonstrates (1) the importance of location of CpG site methylation for HCC specificity and the way in which liver-specific DNA methylation should be considered when an epigenetic DNA marker is studied for detection of HCC and (2) the potential of a sensitive DNA test for HCC screening. An analysis of the performance of this panel of markers in peripherals (blood and urine) for HCC screening is in progress.
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 4086. doi:1538-7445.AM2012-4086