bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 637: Antisense transcripts and R-loops caused by DNA topoisomerase I inhibition by camptothecin at human active CpG island promoters.
Authors: Marinello Jessica , Chillemi Giovanni , Bueno Susana , Manzo Stefano G. , Capranico Giovanni 
Published: August 2014

Abstract
DNA Topoisomerase I (Top1) is specifically inhibited by camptothecin (CPT), a natural product with effective anticancer activity. CPT can stabilize a DNA-Top1 DNA cleavage complex that can lead to irreversible DNA breakage at replication forks, and transcription-dependent genome instability. The bulk of cellular Top1 activity is required at transcribing regions to modulate DNA supercoils generated by elongating RNA polymerases. However, the molecular effects of CPT inhibition of Top1 at transcriptional levels are not fully established. By next generation sequencing analyses of bisulfite-treated RNAs extracted from human HCT116 cancer cells, we here show that CPT promoted high levels of antisense tags specifically at active promoters containing CpG islands (CGI). We found several not annotated transcripts close to Refseq genes, the majority of which were promoter-associated antisense transcripts increased by CPT. We identified 256 and 84 of such transcripts in HCT116 cells and Top1-silenced HCT116-siRNATop1 cells, respectively. We validated CPT-stimulated antisense transcripts by PCR in both cell lines, and found that several of them could form R-loops at corresponding genomic regions by affinity purification with a recombinant inactive mutant RNaseH1. Drug effects were independent from replication, and required both Top1 and ongoing transcription. In addition, CPT induced an immediate burst and a subsequent rapid reduction of Top1-DNA cleavage complexes at active, but not inactive, promoters indicating a partial, time-dependent removal of Top1 from chromatin. Our findings demonstrate that Top1 activity prevents accumulation of antisense R-loops and RNAs at human active CGI promoters by relaxing negative DNA supercoils. The transcriptional CPT effects can contribute to drug therapeutic activity in cancer and other diseases. We will discuss our findings in relation to transcription regulation and genome instability caused by interference with Top1 activity.
Citation Format: Jessica Marinello, Giovanni Chillemi, Susana Bueno, Stefano G. Manzo, Giovanni Capranico. Antisense transcripts and R-loops caused by DNA topoisomerase I inhibition by camptothecin at human active CpG island promoters. [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 637. doi:10.1158/1538-7445.AM2013-637
Abstract 638: PBF overexpression causes increased p53 ubiquitination and degradation via MDM2.
Authors: Ryan Gavin , Seed Robert , Read Martin , Fong Jim , Turnell Andrew , Smith Vicki , Franklyn Jayne , McCabe Christopher , Boelaert Kristien 
Published: August 2014

Abstract
The pituitary tumor-transforming gene-binding factor (PBF) is a relatively uncharacterised proto-oncogene, which is overexpressed in thyroid tumours. PBF elicits tumor growth in nude mice, whilst thyroid targeted transgenic overexpression in the PBF-Tg mouse induces hyperplasia and macrofollicular lesions, accompanied by induction of the E2 ubiquitin ligase Rad6. Our previous unpublished data showed that PBF binds to p53, and reduces stimulation of downstream target genes by competitive binding. Further, half-life studies of p53 showed reduced p53 stability when PBF was overexpressed in K1 and TPC-1 thyroid papillary cancer cell lines, and ubiquitination assays confirmed this was due to increased ubiquitination and subsequent degradation by the proteasome. Now, GST pull-down assays demonstrate direct binding between PBF and MDM2, the principal negative regulator of p53. The competitive inhibitor of p53-MDM2 binding, Nutlin-3, revealed that the increased degradation of p53 observed when PBF was overexpressed was mediated by MDM2. No change in p53-MDM2 binding stringency was detected when PBF expression was ameliorated by siRNA treatment, and MDM2 subcellular localisation was unchanged by PBF overexpression. However, co-immunoprecipitation assays revealed that PBF specifically interacts with Rad6, which has previously been shown to regulate p53 ubiquitination. Further, PBF-Tg mice demonstrated significantly induced genetic instability at 6 weeks of age, as determined by FISSR-PCR. Thus we propose that aberrantly expressed PBF functionally inactivates p53 via a complex interplay between Rad6 and MDM2, thus promoting genetic instability and tumorigenesis. Our studies, carried out in a panel of thyroid and colorectal cells lines, suggest this may be pertinent not only to thyroid cancer, but to colorectal and other tumour types.
Citation Format: Gavin Ryan, Robert Seed, Martin Read, Jim Fong, Andrew Turnell, Vicki Smith, Jayne Franklyn, Christopher McCabe, Kristien Boelaert. PBF overexpression causes increased p53 ubiquitination and degradation via MDM2. [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 638. doi:10.1158/1538-7445.AM2013-638
Abstract 646: Identification of novel epigenetic biomarkers for platinum-based chemotherapy resistance in high grade serous ovarian cancer.
Authors: Tomar Tushar , Alkema Nicolette G. , De Meyer Tim , van Criekinge Wim , Klip Harry G. , Meersma Gert Jan , van der Zee Ate GJ , de Jong Steven , Wisman G. Bea A. 
Published: August 2014

Abstract
Platinum-based chemotherapy has been standard of care for advanced stage ovarian cancer (OC) patients since the last 3 decades. However, majority of patients relapse within 6 months with drug-resistant disease, which entitle OC among the most lethal gynecological malignancy. Besides ‘’classic’’ clinicopathological features of the primary tumor, no biological parameters have shown clinically predictive and prognostic value for chemoresponse in OC. In the present study, we are focusing on the identification of novel DNA methylation markers in response to platinum-based chemotherapy in high grade serous OC. To accomplish this aim, we performed next generation sequencing on methylation-enriched genomic DNA, isolated from frozen OC patient material from responders (more than 18 months progression free survival) and non-responders (less than 6 months progression free survival) to platinum chemoresponse (n=10 in each group).
Subsequent robust biostatistics and comparative expression data analysis revealed a list of significantly differentially methylated genes of which a number were checked by methylation specific PCR (MSP) on a large platinum sensitive and resistance OC cell line panel. Gene ontology analysis showed that these genes are frequently associated with cell-fate determination, lineage commitment, transcriptional factor binding and ions-transporter system.
Selected candidate methylation markers are currently being validated by pyrosequencing. Moreover, these selected markers are in-silico validated with publically available methylation and expression databases. Next, selected candidate methylation markers will be validated by quantitative-MSP on an independent OC patient cohort. Ultimately, this study will provide a DNA methylation profile for identifying those patients that may benefit from platinum-based chemotherapy in combination with epigenetic treatment modalities.
Citation Format: Tushar Tomar, Nicolette G. Alkema, Tim De Meyer, Wim van Criekinge, Harry G. Klip, Gert Jan Meersma, Ate GJ van der Zee, Steven de Jong, G. Bea A. Wisman. Identification of novel epigenetic biomarkers for platinum-based chemotherapy resistance in high grade serous ovarian 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 646. doi:10.1158/1538-7445.AM2013-646
Abstract 675: Jarid2 is a novel target for lung cancer therapy.
Authors: Hong Young K. , Zhang Mary , Atay Scott , Raiji Manish , Upham Trevor , Hong Julie A. , Rao Mahadev , Schrump David S. 
Published: August 2014

Abstract
Increasing evidence indicates that aberrant expression/activity of polycomb repressive-complex-2 (PRC-2) contributes to the pathogenesis of a variety of human malignancies including lung cancers. In recent studies we have demonstrated that depletion of EZH2- a core component of PRC-2, either by biochemical or pharmacologic techniques inhibits the malignant phenotype of lung cancer cells, indicating that PRC-2 is a target for epigenetic therapy of lung cancer. In the present study, we sought to further examine the potential efficacy of targeting PRC-2 in lung cancers via depletion of Jarid2, which modulates gene expression in stem cells in part via targeting PRC-2 to DNA. Quantitative RT-PCR and immunoblot experiments demonstrated over-expression of Jarid2 in cultured lung cancer cells and primary lung cancers relative to normal respiratory epithelia or histologically normal lung tissues. In subsequent experiments, shRNA techniques were used to inhibit Jarid2 expression in lung cancer cells. Quantitative RT-PCR and immunoblot experiments demonstrated that knock-down of Jarid2 had relatively modest effects on global H3K27Me3 levels in lung cancer cells. These finding were in contrast to knock-down of EZH2, which markedly inhibited H3K27 trimethylation in these cancer cells. Interestingly, knock-down of Jarid2 inhibited in vitro proliferation of lung cancer cells by approximately 70% relative to respective controls, and significantly diminished growth of subcutaneous lung cancer xenografts in athymic nude mice. The anti-proliferative effects of Jarid2 knock-down were relatively comparable to those observed following depletion of EZH2 in lung cancer cells. Jarid2 knock- down only modestly enhanced cytotoxicity mediated by DZNep in lung cancer cells. Microarray experiments are currently in progress to compare gene expression profiles in lung cancer cells mediated by Jarid2 knock-down relative to EZH2 depletion or DZNep treatment, and to delineate the mechanisms by which Jarid2 enhances the malignant phenotype of lung cancer cells. Collectively, these preliminary findings warrant further analysis of Jarid2 expression during pulmonary carcinogenesis, and suggest that Jarid2 may be a novel target for lung cancer therapy.
Citation Format: Young K. Hong, Mary Zhang, Scott Atay, Manish Raiji, Trevor Upham, Julie A. Hong, Mahadev Rao, David S. Schrump. Jarid2 is a novel target for lung cancer therapy. [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 675. doi:10.1158/1538-7445.AM2013-675
Abstract 684: Novel potent curcumin analogues EF-31 and UBS109 inhibit DNA methylation and induce SPARC expression in pancreatic cancer.
Authors: Ganji Purnachandra Nagaraju , Zhu Shijun , Mamoru Shoji , El-Rayes Bassel 
Published: August 2014

Abstract
Purpose/Objectives: DNA methylation is an essential step in epigenetic modification and carcinogenesis. HSP90 and NF-κB have a central role in DNA methylation. Curcumin down regulates HSP90 and NF-kB. UBS109 and EF-31 are potent synthetic analogues of curcumin. We tested the hypothesis that EF-31 and UBS-109 can inhibit DNA methylation and induce SPARC through inhibition of NF-kB and HSP90 in pancreatic cancer cell lines.
Methods: Two pancreatic cancer cell lines were used, PANC-1 and Mia-PaCa2. Cells were either untreated (control) or treated with curcumin (20μM), EF-31 (750nM) and UBS-109 (250nM) for 24 hours. Western blot and RT-PCR analyses were carried out to determine the effect of curcumin and its analogues EF-31 and UBS-109 on different signal molecules involved in carcinogenesis. Electromobility shift assay (EMSA) was performed in pancreatic cells to evaluate the effects of ganetespib on NF-kB activity. Immunocyto and histo chemistry assays were also performed.
Results: The treatment of pancreatic cancer cell lines with curcumin and its analog EF-31 and UBS-109 inhibited NF-κB and HSP90 at transcriptional and translational level resulting in inhibition of DNMT1, decrease in CpG island methylation and up-regulation of SPARC. EF-31 and UBS109 were more potent at inhibition of DNMT1 than curcumin. To confirm that the observed effects were mediated by NF-kB, a stable transfection with p65 (NF-kB) was performed. Cells with overexpression of NF-κB resulted in increased DNMT-1, HSP90 protein and decreased SPARC. Inhibition of NF-kB using EF31 or UBS109 resulted in up-regulation of SPARC and inhibition of the DNMT due to NF-κB down-regulation. Similar effects were observed in tumors from animals treated with EF-31 and UBS-109.
Conclusion: UBS109, EF31 and curcumin can inhibit DNA methylation through down-regulation of DNMT-1 expression by NF-kB. Inhibition of methylation was associated with expression of silenced genes such as SPARC. UBS109 and EF31 are significantly more potent than curcumin. UBS109 and EF31 are promising agents for therapy in pancreatic cancer.
Citation Format: Purnachandra Nagaraju Ganji, Shijun Zhu, Shoji Mamoru, Bassel El-Rayes. Novel potent curcumin analogues EF-31 and UBS109 inhibit DNA methylation and induce SPARC expression in pancreatic 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 684. doi:10.1158/1538-7445.AM2013-684
Abstract 691: Methylation of APC and GSTP1 in non-neoplastic tissue adjacent to prostate tumour and mortality from prostate cancer.
Authors: Grasso Chiara Celestina , Richiardi Lorenzo , Fiano Valentina , Zugna Daniela , Gillio Tos Anna , Delsedime Luisa , Merletti Franco 
Published: August 2014

Abstract
Prostate cancer is the most common tumour in men in many populations, with a crude incidence of 120-130 per 105 in Europe and the United States. The incidence of prostate cancer has increased dramatically since the introduction of prostate-specific antigen (PSA) testing at the end of the 1980s; opportunistic PSA-based screening for prostate cancer is widespread, although its ability to decrease mortality is still being debated.
We studied gene methylation in non-neoplastic tissue adjacent to prostate tumours (NTAT) in association with prostate cancer mortality, as a marker to discriminate between indolent and aggressive prostate tumours.
From two cohorts of consecutive prostate cancer patients diagnosed at one pathology ward in Turin, Italy, we selected 157 patients with available NTAT and followed them up for more than 14 years. We obtained DNA from NTAT in paraffin-embedded prostatic tumour tissues and used probe real-time PCR to analyse methylation of the glutathione S-transferase (GSTP1) and adenomatous polyposis coli (APC) gene promoters. Prevalence of APC and GSTP1 methylation in the NTAT was between 40 and 45%. It was associated with methylation in prostatic tumour tissue for the same two genes as well as with high Gleason. The hazard ratio (HR) of prostate cancer mortality was 2.16 (1.13-4.13) for APC methylation, and 2.83 (1.42-5.65) for GSTP1 methylation in NTAT. It changed to 1.75 (0.95-3.22) and 1.61 (0.80-3.22) after adjusting for Gleason score and methylation in prostatic tumour tissue. Comparison of 2 vs. 0 methylated genes in NTAT revealed a HR of 3.84 (1.83-8.03), which decreased to 2.12 (1.03-4.37) after adjustment. Results were stronger in the first 5 years of follow-up (adjusted HR: 3.03, 95% CI: 1.20-7.67) and in the biopsy sub-cohort (HR: 5.91, 95% CI: 1.00-35.0).
This results show that changes in gene methylation are an early event in prostate carcinogenesis and may play a role in cancer progression. Gene methylation in NTAT is a possible prognostic marker.
Citation Format: Chiara Celestina Grasso, Lorenzo Richiardi, Valentina Fiano, Daniela Zugna, Anna Gillio Tos, Luisa Delsedime, Franco Merletti. Methylation of APC and GSTP1 in non-neoplastic tissue adjacent to prostate tumour and mortality from prostate 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 691. doi:10.1158/1538-7445.AM2013-691
Abstract 7: Berg Interrogative Biology™ platform unravels novel biomarkers FLNB and LY9 in combination with PSA enhances specificity in serum of patients with prostate cancer.
Authors: Sarangarajan Rangaprasad , Chan Joyce , Grund Eric , Vishnudas Vivek K. , Luan Shen , Akmaev Viatcheslav R. , Narain Niven R. 
Published: August 2014

Abstract
Prostate Specific Antigen (PSA) test is the predominant screening test for prostate cancer. Utility is limited by the low predictive power to differentiate patients with indolent tumors from aggressive disease with potential for metastasis. Identification of potential biomarkers to increase prediction of patient population with propensity for progression to metastatic disease remains the overarching unmet need in prostate cancer screening. This study reports the identification of a panel of potential biomarkers using the Berg Interrogative Biology™ platform, a novel non-hypothesis driven approach to characterize disease specific molecular signatures for the identification of physiological drivers of disease etiology. Filamin B (FLNB) and lymphocyte antigen 9 (LY9) were two of several markers identified from a high confidence causal network of prostate cancer model using the Berg Interrogative Biology™ platform. Both FLNB and LY9 were validated in a small case-control retrospective study in human serum samples of patients with prostate cancer and age-matched normal controls. The utility of FLNB and LY9 as potential biomarkers in prostate cancer was determined by comparing the serum levels to that of PSA to establish benchmark comparison. Statistically significant elevation of the PSA, FLNB, and LY9 concentrations was detected in the prostate cancer group compared to the age-matched normal control group. Statistical analyses were performed to determine the sensitivity and specificity of the molecular markers by ROC curve analysis. The predictive power of FLNB or LY9 alone was comparable to that of the PSA test. The combination of FLNB and LY9 with PSA out-performed PSA alone with AUC=0.975 in the study. The study provides data in support of FLNB and LY9 as biomarkers with potential to improve screening outcomes when used in combination with PSA. Efforts are currently underway in large patient cohorts to validate the clinical utility of FLNB and LY9 as candidate biomarkers for use in the screening of prostate cancer with correlate to the Gleason score to enable more instructive data to the practitioner.
Citation Format: Rangaprasad Sarangarajan, Joyce Chan, Eric Grund, Vivek K. Vishnudas, Shen Luan, Viatcheslav R. Akmaev, Niven R. Narain. Berg Interrogative Biology™ platform unravels novel biomarkers FLNB and LY9 in combination with PSA enhances specificity in serum of patients with prostate 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 7. doi:10.1158/1538-7445.AM2013-7
Abstract 704: Inhibitors of telomerase and of poly(ADP-Ribose)polymerases synergize to limit the lifespan of pancreatic cancer cells.
Authors: Burchett Katrina M. , Ouellette Michel M. 
Published: August 2014

Abstract
Telomerase is required for the unlimited lifespan of cancer cells. Pancreatic cancers are almost always positive for telomerase activity and inhibiting telomerase in these cells could limit their lifespan. In this project, we have characterized the biology of telomeres in a panel of 11 pancreatic cancer cell lines and have examined the effects of GRN163L (Imetelstat), a potent telomerase inhibitor, on these cells. GRN163L inhibited telomerase in all 11 pancreatic cancer cell lines, with IC50 ranging from 50 nM to 200 nM. Continuous exposure of AsPC-1, CAPAN1 and CD18 cells to 1 μM GRN163L resulted in telomere shortening, induction of crisis, and loss of the cultures. Crisis In these cells was accompanied by activation of a DNA damage response (γ-H2AX) and evidence of both senescence (SA-β-galactosidase) and apoptosis (Floating cells, sub-G1 DNA content, PARP1 cleavage). In L3.6 cells, continuous GRN163L exposure led to the emergence of a GRN163L-resistant sub-population of cells. Over the last year, these cells have been expanded at successively higher concentrations of GRN163L and are still dividing in the presence of 10 μM GRN163L. To shorten telomeres and limit the lifespan of these cells, an alternate approach was to use inhibitors of poly(ADP-ribose)polymerases (PARP) to block the parsylation of TRF1 and TRF2, thereby enhancing the telomerase-inhibitory activity of the Shelterin complex. Our results show that combining GRN163L with the general PARP inhibitor 3-aminobenzamide (3AB) was sufficient to shorten telomeres and limit the lifespan of the GRN163L-L3.6 resistant cells. These experiments were then repeated in the parental L3.6 cells to determine if 3AB could be used to block the development of GRN163L-resistance. Whereas 3AB alone was not sufficient to induce crisis, 3AB did synergize with GRN163L to accelerate the timing of crisis and block the emergence of GRN163L resistant cells. These results raise the possibility that inhibitors of poly(ADP-ribose)polymerases could be exploited in the clinic to accelerate the effects of anti-telomerase therapies.
Citation Format: Katrina M. Burchett, Michel M. Ouellette. Inhibitors of telomerase and of poly(ADP-Ribose)polymerases synergize to limit the lifespan of pancreatic cancer cells. [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 704. doi:10.1158/1538-7445.AM2013-704