bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1787: Identification of factors governing sensitivity of NSCLC cell lines to inhibition of Poly (ADP-Ribose) Polymerase (PARP).
Authors: Kommajosyula Naveen , Cao Ye , Moreau Lisa , D'Andrea Alan , Shapiro Geoffrey I. 
Published: August 2014

Abstract
PARP inhibitors are emerging as important new anticancer agents, especially in cancers defective in homologous recombination (HR) repair, such as those lacking BRCA1 or BRCA2. To date, the potential role of PARP inhibition in NSCLC has not been extensively studied. As previously reported, we examined a panel of 26 genotypically-defined NSCLC cell lines for sensitivity to the PARP-1 inhibitor AG014699 (rucaparib) using colony formation assays. We identified 5 cell lines that are exquisitely sensitive (IC50 ≈ 50nM), 9 cell lines that are moderately sensitive (IC50 ≈ 60-500nM) and 12 cell lines that are resistant (IC50 &gt; 5 μM). These data were confirmed with a second PARP inhibitor, AZD2281 (Olaparib). To determine whether sensitive cell lines have defective HR compared to resistant cell lines, we examined the formation of RAD51 foci. Both sensitive and resistant cell lines demonstrated efficient formation of RAD51 foci as well as gamma-H2AX foci in response to DNA damaging treatments, indicating correct initiation of HR. In resistant cell lines, the repair process following PARP inhibition is completed within 24 hours, with resolution of RAD51 and gamma-H2AX foci. However, in sensitive cell lines, these foci persist greater than 30 hours following DNA damaging treatments. These results suggest that although sensitive lines are able to initiate HR repair, they are unable to complete the process, so that RAD51 foci are not resolved. The persistence of DNA damage in these cell lines is confirmed by persistent gamma-H2AX focus formation as well as S/G2 arrest, the latter representing intact checkpoint control. Our results suggest that proteins required downstream of RAD51, including helicases and Holliday junction resolvases, are lacking in the sensitive lines. Consistent with this hypothesis, NCI-H520 cells, a highly PARP inhibitor-sensitive cell line, lacks expression of WRN, RECQL4 and RECQL5. siRNA-mediated depletion of these proteins individually sensitizes the resistant A549 cell line to PARP inhibition, with reduction in rucaparib IC50 by 100 fold. Our results may define a novel subset of NSCLCs with a late-step defect in HR that can be approached with PARP inhibition as a novel treatment strategy.
Citation Format: Naveen Kommajosyula, Ye Cao, Lisa Moreau, Alan D'Andrea, Geoffrey I. Shapiro. Identification of factors governing sensitivity of NSCLC cell lines to inhibition of Poly (ADP-Ribose) Polymerase (PARP). [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1787. doi:10.1158/1538-7445.AM2013-1787
Abstract 1792: MDM2 promoter variants and mRNA expression in irradiated lymphocytes.
Authors: Gansmo Liv B. , Knappskog Stian , Lonning Per E. 
Published: August 2014

Abstract
Background. The ubiquitin ligase protein MDM2 plays an important role in cellular processes like growth arrest, senescence and apoptosis, and one of its main targets is the key cell cycle regulator p53. MDM2 is found overexpressed in several solid tumors, and its dysregulation is caused by gene amplification or by enhanced transcription or translation. The MDM2 gene has two main promoters; promoter P1 is constitutive while P2 is considered to be inducible in response to cellular stress. One polymorphism located in the MDM2 promoter P2 region, SNP309T&gt;G (rs2279744), has been shown to enhance Sp1 transcription factor binding and is associated with increased cancer risk. Recently we reported a second polymorphism SNP285G&gt;C (rs117039649) located 24 bp upstream of rs2279744. SNP285C resides on the SNP309G allele and was found to reduce Sp1 binding and lower the risk of ovarian, endometrial and breast cancer. A third SNP located in the same region, SNP344T&gt;A (rs1196333) has been found not to be associated with cancer risk. In this study we examined the expression levels from the two MDM2 promoters among individuals harboring the different SNP variants (SNP309T/G, SNP285G/C and SNP344T/A) before and after irradiation.
Materials and methods. Blood samples were collected from 219 healthy individuals. From this blood the buffy coat fraction was separated, divided into two and cultured. Prior to RNA extraction and subsequent cDNA synthesis, one half of the cells were irradiated with a dose equivalent to 3 Grey.
Each sample was investigated for SNP285, SNP309 and SNP44 status by sequencing, and MDM2 expression was determined by qPCR using hydrolysis probes. All statistical analyses were calculated using SPSS and GraphPad Prism 5.
Results. After stress (ionizing radiation) we observed, on average, a 8 and 60 fold increase in mRNA levels from promoter P1 and P2, respectively (p&lt;0,0001). Statistical analysis of MDM2 mRNA expression from promoter P1 and P2, showed no significant difference between individuals harboring the different genotypes of SNP309 (TT/TG/GG), SNP285 (GG/GC/CC) or SNP344 (TT/TA/AA) before or after stress. Since the SNP285C allele counteracts the effect of SNP309G (reduces Sp1 binding), we analyzed the impact of SNP309G in the subgroup of individuals harboring SNP285 GG, but found no correlation to higher expression levels in this subgroup either.
Conclusions. Despite their association with risk of several major solid tumor forms, we found no correlation between MDM2 promoter SNP285 or SNP309 with mRNA expression levels in WBC.
Citation Format: Liv B. Gansmo, Stian Knappskog, Per E. Lonning. MDM2 promoter variants and mRNA expression in irradiated lymphocytes. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1792. doi:10.1158/1538-7445.AM2013-1792
Abstract 1794: Cross-regulation of polycomb group protein BMI1 and WNT inhibitors.
Authors: Cho Joon-Ho , Dimri Manjari , Dimri Goberdhan P. 
Published: August 2014

Abstract
Polycomb group (PcG) proteins are evolutionarily conserved gene silencers, which determine cell fate decisions during development. These proteins are often aberrantly expressed in cancer cells. In particular, BMI1 and EZH2 are known to be overexpressed in a number of human malignancies including breast and prostate cancers. In vitro models of cancer development strongly support oncogenic role of overexpressed BMI1 in cancer and metastasis. BMI1 is known to be required for self-renewal of neural, hematopoietic, intestinal and mammary stem cells. In addition, BMI1 is downregulated in senescent cells, and this downregulation may contribute to age-related pathologies. BMI1 is also suspected to play a role in cancer stem cell development and increase stem cell-ness of tumors to promote drug resistance. Despite its role in cancer, stem cell phenotype, development and aging, very little is known about the signaling pathways that regulate the expression of BMI1. Here we report that BMI1 activates WNT pathway and upregulates its target genes such as Cyclin D1 and c-Myc. Using promoter-reporter assays, quantitative RT-PCR and Western blot analyses, we show that BMI1 auto-activates its expression via an E-box present in its promoter. Because auto-activation of BMI1 depends on E-box sequences present in its promoter, we hypothesized that BMI1 may regulate expression of c-Myc directly or indirectly via activation of WNT pathway. Indeed, our data suggest that BMI1 upregulated expression of c-Myc via activation of WNT pathway. Further dissection of this regulation revealed that BMI1 represses expression of WNT inhibitors, in particular DKK family of proteins such as DKK1, DKK2 and DKK3. Interestingly, we also found that DKK1 inhibits expression of BMI1, which also depends on E-box present in BMI1 promoter. Thus BMI1 and WNT inhibitors such as DKK1 cross-regulate each other's expression. We speculate that such regulation might favor BMI1 overexpression in cancer cells via increased WNT activity and c-Myc expression. On the other hand, increased expression of WNT inhibitors such as DKK1 might favor BMI1 downregulation in senescent and aged tissues. Thus, a fine tuned positive feedback loop controls BMI1 expression via WNT signaling pathway, and this feedback loop may be relevant to the role of BMI1 in cancer, stem cells and senescence.
Citation Format: Joon-Ho Cho, Manjari Dimri, Goberdhan P. Dimri. Cross-regulation of polycomb group protein BMI1 and WNT inhibitors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1794. doi:10.1158/1538-7445.AM2013-1794
Abstract 1795: Impact of ischemia time on mRNA and microRNA expression in surgical liver tissue.
Authors: Schuster Claudia , Thasler Wolfgang E. , Kirchner Thomas , Hlubek Falk 
Published: August 2014

Abstract
Human frozen tissues are one of the best sources for molecular analyses such as microarrays, qPCR or Next-Generation-Sequencing. In addition, frozen tissues are particularly valuable for biomarker identification. Several biobanks comprising non-fixed frozen tissues have been established alongside with corresponding clinical data repositories to facilitate biomarker studies relevant for clinical diagnostics. Apart from proteomic approaches, mRNA- and microRNA-expression profiles have shown to be highly valuable for biomarker studies. Since RNA is generally a fragile molecule, RNA integrity in tissue specimens has tremendous impact on gene expression analyses, requiring a rigorous quality assessment of biobank tissue samples. To address this issue, we established a tissue quality test system based on RNA integrity and differential gene expression. We used normal liver tissue, that was snap frozen after various periods of ischemia time. The RNA was isolated and the quality was assessed in four steps: First, the RNA was quantitated by spectrophotometry (NanoDrop) and total RNA quality was determined by on-chip electrophoresis (Experion). Second, the degree of RNA degradation and the maximum length of RNA molecules available for downstream applications was determined by amplicon length analysis using PCR amplification. Third, the RNA expression levels of selected genes were determined and correlated to the time and condition of ischemia. The genes analysed comprised highly regulated genes, signaling pathway genes and genes induced by hypoxia or apoptosis. Fourth, the expression of selected miRNAs involved in signaling pathway regulation was determined by quantitative PCR.
Taken together we analysed mRNA and miRNA stability in correlation to the time of warm and cold ischemia and its impact on signaling pathway regulation in liver tissue samples. The results enabled us to establish a RNA-based quality assessment procedure of tissue specimen for frozen tissue biobanks. This study may facilitate and optimise the logistics of biobanking processes.
Citation Format: Claudia Schuster, Wolfgang E. Thasler, Thomas Kirchner, Falk Hlubek. Impact of ischemia time on mRNA and microRNA expression in surgical liver tissue. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1795. doi:10.1158/1538-7445.AM2013-1795
Abstract 1808: Gene expression signature of malignant astrocytomas and its association with MGMT promoter methylation status.
Authors: Iuchi Toshihiko , Ohira Miki , Yokoi Sana , Kageyama Hajime , Hasegawa Yuzo , Kawasaki Koichiro , Sakaida Tsukasa , Nakagawara Akira 
Published: August 2014

Abstract
Background: MGMT promoter methylation has been reported as a predictive marker, not only for response to temozolomide (TMZ), but also for the longer survival of the patients with malignant astrocytomas (MAs) regardless of treatment with TMZ. This led us to hypothesize that methylation status of MGMT in MAs could somehow associate with epigenetic modification of other cancer-related gene promoters resulting in alterations of gene expression profiles and acquisition of therapy- sensitive characters. In this study, to elucidate the molecular characteristics that contribute to chemosensitivity and prognosis in MAs, we conducted gene expression profiling of the tumors with or without MGMT promoter methylation.
Materials and Methods: Forty-seven MAs including 5 anaplastic astrocytomas and 42 glioblastomas were enrolled in this study. Methylation status of MGMT gene promoter was evaluated by methylation-specific PCR and subsequent pyrosequencing. Gene expression profile was analyzed using 13,000 genes-cDNA microarray which was developed in our institute. Differentially expressed genes between MGMT-methylated and -unmethylated cases were picked up by statistical analysis (Wilcoxon test).
Results: MGMT promoter methylation was found in 26 out of 47 cases. Among the 13,000 genes examined, 163 genes demonstrated statistically significant difference in expression between MGMT-methylated and -unmethylated cases. 22 genes demonstrated lower expression in MGMT-methylated cases, while the remaining 141 genes showed higher expression in methylated cases. When we classify the cases into two groups according to the expression profiles of these 163 genes, survival of the patients were clearly divided (median survival: 18.9m vs. 9.7m, p=0.039). Annotation analysis indicated that the 22 genes with lower expression in MGMT-methylated tumors include those which actively participate in tumor progression, invasion and metastasis, and one of these showed a significant prognostic power in 47 MAs examined (p=0.049). Validation of methylation status of these gene promoters is underway.
Conclusion: We identified a gene expression signature strongly correlated with MGMT methylation in MAs, which might contribute to predict chemosensitivity of tumors as well as prognosis of the patients with MA in combination of MGMT methylation.
Citation Format: Toshihiko Iuchi, Miki Ohira, Sana Yokoi, Hajime Kageyama, Yuzo Hasegawa, Koichiro Kawasaki, Tsukasa Sakaida, Akira Nakagawara. Gene expression signature of malignant astrocytomas and its association with MGMT promoter methylation status. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1808. doi:10.1158/1538-7445.AM2013-1808
Abstract 1817: Expression of the Kaiso-binding partner Znf131 negatively correlates with cell proliferation in murine intestinal and human breast tumor tissues.
Authors: Longo Joseph , Robinson Shaiya , Chaudhary Roopali , Daniel Juliet M. 
Published: August 2014

Abstract
Znf131 is a relatively uncharacterized member of the POZ-ZF family of transcription factors with suspected roles in both vertebrate development and carcinogenesis. Previous studies from our lab identified Znf131 as a specific binding partner of another POZ-ZF protein, Kaiso, which has been implicated as a regulator of the canonical Wnt signaling pathway. Our lab successfully generated an intestinal-specific Kaiso overexpressing (KaisoTg/+) mouse model, which was found to exhibit enlarged crypts and mild hyperplasia in the small intestine. Several lines of evidence implicate Znf131 in cell proliferation, but whether Znf131 expression increases or decreases cell proliferation has yet to be elucidated. To determine whether Znf131 expression correlates with increased proliferation in hyperplastic KaisoTg/+ crypts, the expression and localization of Znf131 was correlated with the proliferation marker Ki-67 in KaisoTg/+ and wildtype (WT) mouse intestinal tissues. Znf131 nuclear expression was localized to the Paneth cell region of the crypts in both the KaisoTg/+ and WT small intestinal tissues, but decreased Znf131 expression was observed in the KaisoTg/+ model. Intriguingly, Ki-67 was localized to the progenitor cell region of the crypts and was excluded from Znf131-positive nuclei. In contrast to our hypothesis, these results suggest that Znf131 negatively correlates with cell proliferation. Since Znf131 has also been implicated as a regulator of ERα, we repeated these experiments using human breast tumor tissues to determine whether the observed results were tissue specific. We detected decreased nuclear expression of Znf131 in breast tumor tissues compared to matched normal tissues, and we observed a negative correlation between the nuclear expression of Znf131 and the histologic grade and stage of the tumor. Collectively, our results from both murine intestinal and human breast tumor tissues suggest a negative correlation between Znf131 nuclear expression and cell proliferation and raise the possibility that Znf131 may act as a tumor suppressor.
Citation Format: Joseph Longo, Shaiya Robinson, Roopali Chaudhary, Juliet M. Daniel. Expression of the Kaiso-binding partner Znf131 negatively correlates with cell proliferation in murine intestinal and human breast tumor tissues. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1817. doi:10.1158/1538-7445.AM2013-1817
Abstract 1836: Long noncoding RNA HOTAIR enhances aggressive biological behavior and is associated with short disease-free interval in human non-small cell lung cancer.
Authors: Nakagawa Takayuki 
Published: August 2014

Abstract
Lung cancer is the most common cause of cancer death worldwide. Non- small cell lung cancer (NSCLC) occupies more than 80% of all lung cancer. Overall, less than 10% of patients diagnosed with NSCLC survive five years after the diagnosis. Multidisciplinary management of NSCLC which contains surgery, chemotherapy and radiotherapy does not satisfactorily improve the patients’ prognosis. The pathogenic mechanisms contributing to the resistance to various therapeutic approaches in this cancer still remain to be clarified. HOTAIR is one of the large intervening noncoding RNA and interacts with the polycomb repressive complex 2 (PRC2) in the regulation of gene activities. Recently, the enhanced expression of this molecule has been shown to be associated with metastasis and/or poor prognosis of several human carcinomas such as breast, liver, colon and pancreas. However, little is known about the roles of this gene in lung cancer. Thus, we examined the involvement of HOTAIR in the development of NSCLCs. The expression of HOTAIR was examined in 77 NSCLCs and their corresponding normal lung tissues, and 6 metastatic lesions to brain by quantitative real-time RT-PCR. The high expression of HOTAIR (tumor/normal ratio &gt; 2) was detected in 17 patients (22.1%) and was frequently found in patients with advanced stage, lymph node metastasis or lymphovascular invasion. The NSCLC patients with high expression of HOTAIR also showed significantly short disease free interval compared with those with low expression. Furthermore the metastatic lesions to brain demonstrated significantly higher HOTAIR expression than primary tissues. Accordingly, HOTAIR transfected A549 cells showed induced migration in vitro, and injected HOTAIR expressing cells into the tail vein of immunodeficient mice formed more metastases to liver or bone compared to empty vector transfected cells. We also found that the enhanced HOTAIR expression in lung cancer cells demonstrated the reduced expression of LAMB2 and LAMC3 both of which are downstream targets of PRC2. Taken together, these results might indicate that the evaluation of HOTAIR expression predict the poor outcome of NSCLC patients and that the overexpression of HOTAIR enhanced the aggressive biological behavior of NSCLC cells, at least in part, through the regulation of PRC2.
Citation Format: Takayuki Nakagawa. Long noncoding RNA HOTAIR enhances aggressive biological behavior and is associated with short disease-free interval in human non-small cell lung cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1836. doi:10.1158/1538-7445.AM2013-1836
Abstract 1840: Clinical significance of lincRNA-p21 in colorectal cancer.
Authors: Zhai Haiyan , Fesler Andrew , Schee Kristina , Fodstad Øystein , Flatmark Kjersti , Ju Jingfang 
Published: August 2014

Abstract
Large Intergenic Noncoding RNAs (LincRNAs) have been recently shown to be novel regulators for both transcription and posttranscriptional/translation. One of them, lincRNA-p21, was regulated by p53 and contributed to apoptosis in mouse embryonic fibroblasts. However, the impact of such regulation on colorectal cancer (CRC) is remained to be determined. In this study, we discovered that the expression level of lincRNA-p21 was increased by elevated wild type p53 induced by Nutlin in HCT116 colon cancer cells. The clinical significance of lincRNA-p21 was further investigated in 2 CRC patient cohorts. The expression of lincRNA-p21 was quantified by the real time qRT-PCR analysis using total RNAs extracted from snap fresh frozen CRC samples. Our results reveal that the expression level of lincRNA-p21 is significantly (P = 0.0208) lower in CRC tumor tissue when compared to the paired normal tissue from the same patient. There is no significant correlation of lincRNA-p21 with p53 status (wild type vs. mutant). Tumors in rectum show higher level of lincRNA-p21 than the ones in colon (P = 0.00005). In addition, lincRNA-p21 in stage III patients was significantly higher than stage I patients (P = 0.007). Elevated level of lincRNA-p21 was significantly associated with higher pT (P = 0.037 between pT 2 and 3), and vascular invasion (P = 0.017). LincRNA-p21 was not significantly associated with patient's overall survival. These results indicate that lincRNA-p21 may contribute to CRC disease progression.
Citation Format: Haiyan Zhai, Andrew Fesler, Kristina Schee, Øystein Fodstad, Kjersti Flatmark, Jingfang Ju. Clinical significance of lincRNA-p21 in colorectal cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1840. doi:10.1158/1538-7445.AM2013-1840