tbuckley/cabot-search huggingface dataset:
Abstract 4136: Effect of prorenin receptor PRR knock down and telmisartan on endometrial cancer growth
Authors: Riazuddin Mohammed, Sarah J. Delforce, Yu Wang, Nicole M. Verrills, Eugenie R. Lumbers, Kirsty G. Pringle
Journal: Cancer Research (2017)

Abstract Endometrial cancer is the most common gynaecological malignancy and its incidence is increasing. Tissue renin angiotensin systems (RAS) are known to stimulate angiogenesis, cell proliferation and migration. All of these actions potentiate cancer growth and spread. We have previously demonstrated that endometrioid endometrial cancers express both prorenin and prorenin receptor ((P)RR) mRNA and have significantly greater levels of these proteins than normal adjacent endometrial tissue. Prorenin acting via the (P)RR can activate both RAS dependent and independent signalling pathways. Therefore we hypothesized that endometrial cancer growth can be inhibited by drugs that block Ang II/AT1R interactions and prorenin/(P)RR mediated signaling pathways. To determine the functional role of (P)RR in endometrial cancer growth, we used siRNA transfection to knock down (P)RR expression in three endometrial cancer cell lines (Ishikawa, HEC-1A and AN3CA) at 24h, 48h, 72h &amp; 96h. The effect of RAS blockers on cell viability was also assessed by Resazurin assay at 48h in the three endometrial cancer cell lines. All three of the endometrial cancer cell lines examined (Ishikawa, HEC-1A and AN3CA) expressed (P)RR and prorenin mRNA, however levels of (P)RR were much higher in Ishikawa cells. Transfection of the three cell lines with a (P)RR siRNA resulted in 90% knockdown of (P)RR mRNA expression and reduced the cell viability of both Ishikawa and AN3CA but not HEC-1A cells, as measured by a resazurin assay after 48h incubation. Aliskiren (a renin inhibitor) inhibited Ishikawa cell growth by 20%. There was no effect of Aliskiren on cell viability in HEC-1A and AN3CA cell lines. Perindoprilat (an ACE inhibitor) and Losartan (an angiotensin II type 1 receptor (AT1R) inhibitor) had no effect on cell viability in any cell line. Another AT1R antagonist, telmisartan, which also acts as a selective agonist of peroxisome proliferator-activated receptor gamma (PPAR-γ), did however significantly reduce cell viability in all cell lines (Ishikawa 75%, HEC-1A 50% and AN3CA 60%). Removal of the prorenin receptor inhibits the growth and development of some endometrial cancer cell lines. Only telmisartan, which has properties additional to Ang II antagonism, was effective in inhibiting endometrial cancer cell growth. (P)RR knockdown and telmisartan are therefore potential therapeutic drugs for the treatment of endometrial cancer. Citation Format: Riazuddin Mohammed, Sarah J. Delforce, Yu Wang, Nicole M. Verrills, Eugenie R. Lumbers, Kirsty G. Pringle. Effect of prorenin receptor PRR knock down and telmisartan on endometrial cancer growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4136. doi:10.1158/1538-7445.AM2017-4136
Abstract 4552: ssCOPA: a novel method with improved sensitivity to assess statistical significance for cancer outlier profile analysis of gene expression
Authors: Hong Gao, Sam Ng, Hinco J. Gierman
Journal: Cancer Research (2017)

Abstract To understand the genetic mechanism of disease, finding biomarkers and drug targets are a major focus of academic and pharmaceutical research. However, it has become clear that many important genes driving diseases like cancer, are deregulated in a relatively small group of outliers, e.g. amplified and fusion genes. Cancer outlier profile analysis (COPA), introduced by Tomlins et al, has raised interest in detecting genes with outlier expression within a group, particularly in cancer patients. However, the magnitudes of the COPA scores are not directly comparable across different studies or with different input parameters. Also, integrating COPA scores across multiple studies in a meta-analysis is problematic. Current solutions to performing meta-analyses, including rank-based methods and binomial test, require large study numbers without adjustment for the differences in study size. Also, within a single study COPA scores alone do not provide a P-value, and it is impossible to know which outlier genes are statistically significant. Here we developed three novel methods to address these problems by computing a significance for COPA scores, including Bootstrap resampling, Bootstrap + generalized Pareto distribution (GPD) and Binomial method for statistical significance of COPA (ssCOPA), to enable the comparison of COPA score across studies or parameters. We first evaluated our methods using two breast cancer studies. The P-values generated by Binomial method match closely to Bootstrap resampling using 10,000 randomizations, better than Bootstrap + GPD. In addition, the Binomial method requires significantly less computing time than the other methods. We further validated our methods with a meta-analysis of five breast cancer studies and compared the results with the top-ranking genes of a large-scale meta-analysis of 31 breast cancer studies by ONCOMINE. We show that our P-value-based approaches (P = 10-17~10-24) achieves significantly better concordance than the Binomial test (P = 10-14). Data and methods are available for use on the Illumina BaseSpace® CohortAnalyzer platform (formerly known as NextBio Clinical). Citation Format: Hong Gao, Sam Ng, Hinco J. Gierman. ssCOPA: a novel method with improved sensitivity to assess statistical significance for cancer outlier profile analysis of gene expression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4552. doi:10.1158/1538-7445.AM2017-4552
Abstract 4808: Effect of Merkel cell polyomavirus large and small T-antigen on the thrombospondin and the periostin promoter
Authors: Aelita Konstantinell, Ida Sofie Furuholmen, Baldur Sveinbjørnsson, Ugo Moens
Journal: Cancer Research (2017)

Abstract Merkel cell carcinoma (MCC) is a rare, but aggressive form of skin cancer with rising incidence and high mortality rate. Approximately 80% of MCC tumors are positive for Merkel cell polyomavirus (MCPyV), suggesting a causative relationship between MCPyV and MCC. Exosomes are 30-150 nm vesicles that contain proteins, lipids, mRNAs, lncRNAs, and miRNAs. Exosomes from virus-infected cells comprise also viral nucleic sequences and proteins. Because tumor cell-derived exosomes may contribute to cancer, we hypothesized that MCPyV may affect the composition of exosomes and play a role in tumorigenesis. Therefore, we compared the proteins in exosomes produced by MCPyV-positive MKL1 and MKL2 and MCPyV-negative MCC13 and MCC26 MCC cell lines. Our proteomic analysis of exosomes originating from polyomavirus-negative and polyomavirus-positive MCC cell lines revealed the presence of the oncogenic proteins periostin and thrombospondin. Western blot analysis of exosomes and lysates of these MCC cells confirmed the presence of these proteins in exosomes from all cell lines. Thrombospondin, but not periostin was detectable in cell lysates, and an enrichment of both proteins was detected in exosomes of all cell lines. The effect of MCPyV large T-antigen (LT-ag) and small t-antigen (st-ag) on the periostin and thrombospondin promoters was examined by transient transfection studies with luciferase reporter plasmids. Transfection experiments in MCC13 revealed that LT-ag, but not st-ag significantly increased the activity of the thrombospondin and periostin promoters. In MCC26 cells, neither LT-ag nor st-ag had a significant effect on the thrombospondin promoter activity, while both proteins alone or in combination significantly stimulated the periostin promoter strength. Our results suggest that MCPyV proteins may contribute to tumorigenesis by enhancing the expression of the oncoproteins thrombospondin and periostin and promote their secretion via exosomes. Citation Format: Aelita Konstantinell, Ida Sofie Furuholmen, Baldur Sveinbjørnsson, Ugo Moens. Effect of Merkel cell polyomavirus large and small T-antigen on the thrombospondin and the periostin promoter [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4808. doi:10.1158/1538-7445.AM2017-4808
Abstract 3735: Detection of microsatellite instable colorectal cancers from routine NGS panel sequencing data
Authors: Volker Endris, Martina Kirchner, Matthias Kloor, Anna-Lena Volckmar, Magnus von Knebel Doeberitz, Roland Penzel, Peter Schirmacher, Albrecht Stenzinger
Journal: Cancer Research (2017)

Abstract Introduction In about 15% of all colorectal cancers, microsatellite instability (MSI) caused by defects in the DNA mismatch repair machinery can be detected. MSI driven tumors have a better prognosis compared to microsatellite stable (MSS) tumors and show good response to drugs targeting the PD-1-PD-L1 axis. Current molecular diagnostic procedures for colorectal cancer are primarily focused on the detection of oncogenic mutations in RAS family genes by either classical Sanger sequencing or next-generation sequencing. Routine testingof MSI status for therapeutic purposes is still rare and usually carried out by a different array of methods including PCR and immunohistochemistry. Experimental procedures In our routine diagnostic CRC screening, we sequenced more than 600 colorectal tumors with an entity specific customized 180 amplicon NGS panel encompassing HotSpot regions of 31 genes. This panel includes several homopolymeric regions of genes that are known to be affected by MSI. We retrospectively analysed this data set for MSI signatures, including deletion/insertion mutations in 20 different homopolymeric regions (&amp;gt;7) and mutations/deletions of MLH1, MSH3, MSH6 and TGFBR2. Cases with an MSI signature detected by panel sequencing were reevaluated by PCR-based screening (Bethesda panel). Results From the 20 homopolymeric regions analyzed, several loci showed deletion/insertion mutations in MSI-positive patients. The highest discriminatory power presented a homopolymeric region within the ACVR2A gene showing a high analytical sensitivity and specificity towards MSI prediction. In combination with the readout of additional homopolymeric regions and the mutation status of MLH1, MSH3, MSH6 and TGFBR2, a sensitive and specific detection algorithm for MSI can be obtained from routine panel sequencing data. In conclusion, using only one assay, this approach facilitates simultaneous detection of mutations in RAS genes (and other druggable targets) and the MSI status in CRC As the assay is tissue sparing and time saving it may be advantageous over classic test approaches that are currently being employed in routine diagnostics. Note: This abstract was not presented at the meeting. Citation Format: Volker Endris, Martina Kirchner, Matthias Kloor, Anna-Lena Volckmar, Magnus von Knebel Doeberitz, Roland Penzel, Peter Schirmacher, Albrecht Stenzinger. Detection of microsatellite instable colorectal cancers from routine NGS panel sequencing data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3735. doi:10.1158/1538-7445.AM2017-3735
Abstract 740: Rapid detection of IDH1/2 mutations using RNaseH2 dependent, multiplex quantitative PCR Assays
Authors: Yun Bao, Aymen Baig, Yu Wang, A. John Iafrate, Caifu Chen, Darrell R. Borger
Journal: Cancer Research (2017)

Abstract Isocitrate dehydrogenase 1 (IDH1) and 2 (IDH2) are enzymes that normally catalyze the oxidative decarboxylation of isocitrate to α-ketoglutarate during glucose metabolism. Heterozygous mutations in the IDH1 and IDH2 genes have been identified in a specific subset of cancers. Mutations typically affect the enzyme active sites at codon R132 in the IDH1 gene, and R140 or R172 in the IDH2 gene. This confers neomorphic enzyme activity that produces the oncometabolite 2-hydroxyglutarate that is involved in cancer initiation and progression. The detection of IDH1/IDH2 mutations has important diagnostic, prognostic, and therapeutic implications and testing for these variants is being incorporated in clinical settings. In fact, the identification of IDH1 or IDH2 gene mutations is now required for the classification of tumors of the central nervous system under the 2016 WHO guidelines. Therefore, there is a significant need for an IDH1 + IDH2 test that can be performed in a rapid manner to support clinical diagnosis and treatment decisions. A strategy utilizing allele-specific quantitative PCR (qPCR) is well suited for evaluating a small number of hotspot variants in IDH1 and IDH2 from clinical tissue samples in a matter of few hours. Using RNase H2-dependent PCR (rhPCR) and a universal reporter system, we have developed new multiplex qPCR assays that effectively discriminate between closely related sequences that differ by only a single nucleotide base at the same position or adjacent position in a single tube reaction. In addition, the rhPCR mechanism of the assays also greatly reduces the impact of primer-primer interactions, further improving the multiplex capability of the assays. During initial testing, specificity, accuracy, and sensitivity were evaluated. Mutations present in patient samples at frequencies as low as 2% were identified with high reproducibility. The assays have been tested across 49 patient samples that included FFPE tissue, blood, and bone marrow aspirate with results that are concordant to those found using an orthogonal method of next generation sequencing. Our study showed that this assay provides a rapid method for detection of multiple IDH1 or IDH2 mutations in single rhPCR reactions with high accuracy, specificity, and sensitivity. Citation Format: Yun Bao, Aymen Baig, Yu Wang, A. John Iafrate, Caifu Chen, Darrell R. Borger. Rapid detection of IDH1/2 mutations using RNaseH2 dependent, multiplex quantitative PCR Assays [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 740. doi:10.1158/1538-7445.AM2017-740
Abstract 4846: The metastasis suppressor NME1 is recruited to DNA double strand breaks
Authors: Gemma S. Puts, Stuart G. Jarrett, Devin Snyder, Richard Vincent, Ying Wang, Katie Leonard, Ben Portney, Feyruz Rassool, Michal Zalzman, David M. Kaetzel
Journal: Cancer Research (2017)

Abstract NME1 is a potent suppressor of metastasis, and reduced expression has been associated with aggressive melanoma. The nucleoside diphosphate kinase and 3’-5’ exonuclease (3’-5’ EXO) activities of NME1 protein both contribute to its metastasis suppressor activity. 3’-5’ exonucleases are important for proofreading during DNA repair and synthesis, suggesting a potential role for NME1 in maintenance of genomic stability in melanoma. Although impairment of DNA repair activity has been implicated in melanoma risk, its contribution to melanoma initiation and progression is not well understood. We have shown previously that both enzymatic activities of NME1 are critical for repair of UV-induced DNA damage via nucleotide excision repair. In the current study, chromatin immunoprecipitation was used to demonstrate recruitment of NME1 to DNA double-strand breaks (DSBs), representing the first evidence of direct recruitment of NME1 to sites of DNA damage. Induction of DSBs with gamma irradiation (γ-IR) or bleomycin promoted rapid physical association of NME1 with γH2AX, ATM, NBS1 and RAD50. In addition, treatment of melanoma cells with γ-IR triggered a physical association of NME1 with XRCC4, an effector of the non-homologous end-joining (NHEJ) pathway. We are currently investigating whether knockout of NME1 induces a switch from NHEJ to the homologous recombination (HR) pathway, a slower but higher fidelity form of DSB repair, using plasmid repair assays. We are also using plasmid rescue to study the role of NME1 on the fidelity of NHEJ repair. Overall, our study indicates for the first time direct participation of NME1 in a molecular mechanism of DSB repair in both normal and transformed cells. In addition, these data suggest a novel mechanism of metastasis suppressor function for NME1, with loss of NME expression in tumor cells conferring genetic instability and enhanced metastatic potential. Citation Format: Gemma S. Puts, Stuart G. Jarrett, Devin Snyder, Richard Vincent, Ying Wang, Katie Leonard, Ben Portney, Feyruz Rassool, Michal Zalzman, David M. Kaetzel. The metastasis suppressor NME1 is recruited to DNA double strand breaks [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4846. doi:10.1158/1538-7445.AM2017-4846
Abstract 5907: Radiotherapy-induced damage to cancer-associated fibroblasts and its reciprocal influence on cancer progression: Impact of soluble factors
Authors: Olivier De Wever, Joke Tommelein, Marc Bracke, Tom Boterberg, Pieter Demetter, Laurin Verset
Journal: Cancer Research (2017)

Abstract Preoperative radiotherapy is a mainstay in current management of colorectal cancer. Several tumor types, including colorectal cancer, show an abundant desmoplastic stroma, characterized by cancer-associated fibroblasts (CAFs). Nevertheless the effects of radiation to the CAFs in the stroma and its reciprocal impact on the response of CRC cells to irradiation have not been studied. We investigated the functional (cell number, morphotype) and biochemical (transcriptomics, metabolomics and kinomics) phenotype of CRC cells in response to paracrine signals from irradiated CAFs. Using neutralizing antibodies and small molecule inhibitors, we analysed the role of tyrosine-kinase receptor activation in CRC cells in response to supernatants from irradiated CAFs. Furthermore, the impact of tyrosine-kinase receptor neutralization in combination with RT was evaluated in an orthotopic CRC model. The level of mTOR activation, a downstream tyrosine-kinase receptor intermediate, was analysed in response to neoadjuvant treatment in human CRC specimens. Further work will reveal which soluble factor(s) are implicated in the communication between irradiated CAFs and colorectal cancer cells. Citation Format: Olivier De Wever, Joke Tommelein, Marc Bracke, Tom Boterberg, Pieter Demetter, Laurin Verset. Radiotherapy-induced damage to cancer-associated fibroblasts and its reciprocal influence on cancer progression: Impact of soluble factors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5907. doi:10.1158/1538-7445.AM2017-5907
Abstract LB-247: Early detection of gastric cancer using global and gene-specific promoter DNA methylation in endoscopic biopsies
Authors: Francesca Pirini, Sassan Noazin, Martha Jahuira Arias, Sebastian Rodriguez-Torres, Leah Friess, Christina Michailidi, Jaime Cok, Juan Combe, Goria Vargas, William Prado, Ethan Soudry, Jimena Perez, Tikki Yudin, Andrea Mancinelli, Helen Unger, Carmen Ili, Priscilla Brebi, Douglas Berg, Masamichi Hayashi, David Sidransky, Robert Gilman, Rafael E. Guerrero-Preston
Journal: Cancer Research (2017)

Abstract Clinically useful molecular tools to triage gastric cancer patients are not currently available. We aimed to develop a molecular tool to predict gastric cancer risk in endoscopy-driven biopsies obtained from high-risk gastric cancer clinics in low resource settings. We discovered and validated a DNA methylation biomarker panel in endoscopic samples obtained from 362 patients seen between 2004 and 2009 in three high-risk gastric cancer clinics in Lima, Perú, and validated it in 306 samples from the Cancer Genome Atlas project (“TCGA”). Global, genome wide and gene-specific DNA methylation analyses were used in a Phase I Biomarker Development Trial to identify a continuous biomarker panel that combines a Global DNA Methylation Index (GDMI) and promoter DNA methylation levels of IRF4, ELMO1, CLIP4 and MSC. We observed an inverse association between the GDMI and histological progression to gastric cancer, when comparing gastritis patients without metaplasia (mean= 5.74, 95% CI, 4.97-6.50), gastritis patients with metaplasia (mean= 4.81, 95% CI, 3.77-5.84), and gastric cancer cases (mean=3.38, 95% CI, 2.82-3.94), respectively (p&amp;lt;0.0001). Promoter methylation of IRF4 (p &amp;lt;0.0001), ELMO1 (p &amp;lt;0.0001), CLIP4 (p &amp;lt;0.0001), and MSC (p &amp;lt;0.0001), is also associated with increasing severity from gastritis with no metaplasia to gastritis with metaplasia and gastric cancer. Our findings suggest that promoter methylation of IRF4, ELMO1, CLIP4 and MSC and a GDMI &amp;gt; 4, is a useful molecular tool for gastric cancer risk stratification in endoscopic biopsies. Citation Format: Francesca Pirini, Sassan Noazin, Martha Jahuira Arias, Sebastian Rodriguez-Torres, Leah Friess, Christina Michailidi, Jaime Cok, Juan Combe, Goria Vargas, William Prado, Ethan Soudry, Jimena Perez, Tikki Yudin, Andrea Mancinelli, Helen Unger, Carmen Ili, Priscilla Brebi, Douglas Berg, Masamichi Hayashi, David Sidransky, Robert Gilman, Rafael E. Guerrero-Preston. Early detection of gastric cancer using global and gene-specific promoter DNA methylation in endoscopic biopsies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-247. doi:10.1158/1538-7445.AM2017-LB-247