bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1829: The validation of a pyrosequencing KRAS mutation detection assay
Authors: Poulin Matthew L. , Meyer Ann , Mead E. Andrew , Xu Jessica , Drennan Ryan , Yan Liyin 
Published: July 2016

Abstract
Mutations in the KRAS gene, especially affecting the codon 12 and 13 region of the Kras protein, have implications in the treatment of certain cancer types. Because of the current potential for the FDA to oversee laboratory developed procedures (LPDs), it is imminently important that the validation of such tests be published to ensure that it is shown that these LPDs are properly reviewed and properly tested within the CLIA guidelines, thus keeping LPDs within the CLIA regulatory domain. We have developed a pyrosequencing assay that can detect eleven mutations in the codon 12 and 13 position of the KRAS gene. Our validation consisted of a sensitivity study in which a purified mutant PCR product was introduced into a wildtype DNA background and diluted down to undetectable levels. This sensitivity test was done on six different KRAS codon 12/13 mutants to determine the detection limit of the assay. Intra- and inter-assay precision and assay accuracy was determined by comparing assay results of over 40 total samples, both mutant and wild type, over five days carried out by two technicians. The results will show that this KRAS pyrosequencing assay falls within the acceptance criteria for sensitivity, accuracy and precision.
Citation Format: Matthew L. Poulin, Ann Meyer, E. Andrew Mead, Jessica Xu, Ryan Drennan, Liyin Yan. The validation of a pyrosequencing KRAS mutation detection assay. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1829.
Abstract 1841: Dissecting gene expression programs that define tumor aggression and patient outcome in pancreatic cancer
Authors: Fassler Danielle J. , Escobar-Hoyos Luisa F. , Shroyer Kenneth R. 
Published: July 2016

Abstract
By the year 2020, pancreatic cancer (PDAC) is projected to be the second leading cause of cancer deaths in the United States. Current systemic therapies offer limited survival advantages in subgroups of patients, suggesting underlying biological differences in this deadly cancer. Our lab has recently identified keratin-17 (K17) gene expression as a prognostic and predictive biomarker in PDAC. Furthermore, we found that K17 acts as an oncoprotein by promoting degradation of tumor suppressor p27KIP1, while knockdown of K17 limits tumor size and sensitizes cancer cells to chemotherapy agents. Together, these findings suggest that targeting K17 expression in PDACs may increase patient survival and response to treatment. The factors that lead to increased K17 gene expression in only a subset of PDAC cases, however, are unknown. K17 is expressed in embryonic ectoderm and aberrantly induced in keratinocytes from psoriasis patients through paracrine signaling from the microenvironment. To determine how K17 gene expression is upregulated in PDAC, we tested the effects of two major contributing factors in PDAC pathogenesis: driver mutations and inflammatory mediators present in tumor microenvironment. Using in vitro and in vivo loss- and gain-of function approaches, we modulated oncogene expression in and performed acute cytokine treatments on cells to test for changes in K17 gene expression. K17 expression was evaluated by qRT-PCR and western blot. We found that forced expression of oncogenes like KRASG12D, Q61K or TP53R248W significantly increase K17 expression, yet these cell-autonomous factors are not sufficient to explain K17 gene expression in PDACs. In addition, we found that pro-inflammatory cytokines, typically released by helper T cells, induce a strong increase in K17 gene expression. Together these findings suggest that K17 gene expression across otherwise clinically identical PDAC cases may be explained by early transformation events and maintained by positive feedback loops associated with patient specific adaptive immune response. Ongoing studies are seeking to test the combined effects of genetic and paracrine events in K17 expression, and understand the signaling pathways and transcription factors downstream of these inducing factors. Ultimately, insight into the mechanisms that mediate K17 overexpression in PDACs could help guide future research to develop K17 as a potential therapeutic target.
Citation Format: Danielle J. Fassler, Luisa F. Escobar-Hoyos, Kenneth R. Shroyer. Dissecting gene expression programs that define tumor aggression and patient outcome in pancreatic cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1841.
Abstract 1842: Overexpressing human endogenous retroviral elements (HERVs) in chemorefractory colorectal adenocarcinoma cells are repressed by antiviral drugs
Authors: Diaz-Carballo David 
Published: July 2016

Abstract
Background: HERVs account for ca. 8% of all transposable elements found in the genome of humans and other animals. They represent a genetic footprint of ancestral germ-cell infections of exoviruses that is transmittable to the progeny by Mendelian segregation. Traces of human endogenous retroviruses are physiologically expressed in ovarial, testicular and placental tissues as well as in stem cells. In addition, a number of these fossil viral elements have also been related to carcinogenesis. However, a relation between endoretroviruses expression and chemoresistance has not been reported yet. Methods: Twenty colorectal carcinoma patient samples were analyzed for HERV-WE1 and HERV-FRD1 endoretroviruses using immunohistochemical approaches. In addition, to examine for differential expression of HERVs in chemotherapy refractory cells, a resistant HCT8 colon carcinoma subline was developed by serial etoposide exposure. Endoretroviral elements were detected by immunocytochemical staining, qPCR and ELISA. IC50-values of antiviral and cytostatic drugs in HCT8 cells were determined by MTT proliferation assay. The antivirals-cytostatics interaction was evaluated by the isobologram method. Results: In this work, we show for the first time that HERV-WE1, HERV-FRD1, HERV-31, and HERV-V1 are a) simultaneously expressed in treatment-naïve colon carcinoma cells from patients and b) upregulated after cytostatic exposure in colon-cancer cell lines, suggesting that these retroviral elements are intimately related to chemotherapy resistance. A number of antiviral drugs showed not only cytotoxic activity but also downregulation of HERV proteins in vitro. We also demonstrate that the use of different antiviral compounds alone or in combination with anticancer agents present synergistic antiproliferative activity and downregulation of different endoretroviral elements in highly chemotherapy-resistant colorectal tumor cells. Conclusions: Enhanced HERV-expression is associated with chemo-resistance in colon carcinoma cells which can be repressed by antiviral drugs alone or in combination with anticancer drugs. Therefore, the introduction of antiviral compounds to antiproliferative chemotherapy regimens potentially improves patient outcomes.
Citation Format: David Diaz-Carballo. Overexpressing human endogenous retroviral elements (HERVs) in chemorefractory colorectal adenocarcinoma cells are repressed by antiviral drugs. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1842.
Abstract 1859: Bioinformatic and experimental evaluation of regulatory variants in breast cancer susceptibility genes
Authors: Sevcik Jan , Burke Leslie , Gambino Gaetana , Brewster Brooke L. , Tudini Emma , Whiley Philip J. , Manoukian Siranoush ,   ENIGMA Consortium, van Overeem Hansen Thomas , Santamariña Pena Marta , Vega Ana , Caligo Maria A. , Radice Paolo , Peterlongo Paolo , Rouleau Etienne , Spurdle Amanda B. , Brown Melissa A. 
Published: July 2016

Abstract
Many germline DNA sequence variants in gene regulatory elements are associated with an increased risk of cancer. These include large genomic deletions of the promoter of the BRCA1 gene, through to single nucleotide variants in the promoter, UTRs and long-range enhancers of multiple other cancer related genes. Next generation sequence analysis of early onset and familial breast cancer cases is currently identifying an escalating number of variants in non-coding regions of the genome, however for most of these the significance in unknown. This project aims to determine the functional and clinical significance of breast cancer associated variants in regulatory regions of BRCA1 and BRCA2, as part of an international collaborative project arising from the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium. To date over two hundred variants mapping to promoter, UTR and deep intronic regions have been identified in early onset or familial breast cancer patients that have no identifiable coding or splicing changes in BRCA1 or BRCA2. Through a pipeline of bioinformatics analyses using ENCODE datasets, these variants have been prioritized for experimental evaluation. This has lead to the identification of several variants that significantly alter the regulation of BRCA1 or BRCA2 expression, through mechanisms including altered binding of transcription factors and microRNAs. These studies will lay the groundwork for comprehensive statistical analyses, in which bioinformatics and experimental data is combined with clinical and genetic data to establish multifactorial risk prediction models that can ultimately be used in a clinical setting.
Citation Format: Jan Sevcik, Leslie Burke, Gaetana Gambino, Brooke L. Brewster, Emma Tudini, Philip J. Whiley, Siranoush Manoukian, ENIGMA Consortium, Thomas van Overeem Hansen, Marta Santamariña Pena, Ana Vega, Maria A. Caligo, Paolo Radice, Paolo Peterlongo, Etienne Rouleau, Amanda B. Spurdle, Melissa A. Brown. Bioinformatic and experimental evaluation of regulatory variants in breast cancer susceptibility genes. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1859.
Abstract 1861: The role and regulation of MTA1-ETS2 axis in prostate cancer
Authors: Kumar Avinash , Dhar Swati , Butt Nasir , Rimando Agnes , Martinez Luis , Levenson Anait 
Published: July 2016

Abstract
Overexpression of the chromatin modifier protein, metastasis associated 1 (MTA1) in prostate cancer contributes to tumor aggressiveness, but the molecular mechanism involved has not been fully elucidated. MTA1 ChIP-Seq analysis in prostate tissues from the prostate-specific Pten heterozygous mice, which exhibit elevated levels of MTA1 revealed MTA1 recruitment onto the ETS2 promoter. Loss of function studies with MTA1 in various prostate cancer cell lines exhibited reduced expression for ETS2 at both mRNA and protein levels. We also observed increased expression of ETS2 at both mRNA and protein levels in prostate tissues from the prostate-specific MTA1 transgenic mice. Meta-analysis of prostate cancer samples in the GEO database exhibited a positive correlation between MTA1 and ETS2 levels. These results suggested that MTA1 functions as a coactivator for regulating ETS2 expression in prostate cancer. We found direct interaction between MTA1 and ETS2 in cells expressing ectopic MTA1 and ETS2. Interestingly, the prostate-specific Pten heterozygous mice, when fed with diet supplemented with pterostilbene, a natural pharmacological inhibitor of MTA1, showed a decrease in ETS2 mRNA and protein levels, perhaps due to decreased recruitment of MTA1 onto the ETS2 promoter. These results suggest that MTA1 functions as a coactivator for regulating ETS2 expression in prostate cancer at the transcriptional level and co-operates with ETS2 to promote prostate cancer progression. At the same time, pterostilbene may become a novel chemopreventive and therapeutic candidate for clinical development in prostate cancer due to its ability to target the MTA1-ETS2 axis.
Citation Format: Avinash Kumar, Swati Dhar, Nasir Butt, Agnes Rimando, Luis Martinez, Anait Levenson. The role and regulation of MTA1-ETS2 axis in prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1861.
Abstract 1865: Areca nut-induced JNK/ATF2/Jun axis regulates TGF-beta signaling contributing to pre-cancerous oral submucous fibrosis
Authors: Pant Ila , Kondaiah Paturu 
Published: July 2016

Abstract
Oral Submucous Fibrosis (OSF) is an inflammatory, pre-cancerous condition of the oral submucosa. It affects individuals with prolonged areca nut chewing habit and therefore areca nut is regarded as the etiological agent for OSF manifestation. Transforming Growth Factor beta is an established promoter of cancer and fibrosis. Up-regulation of TGF-β and its target genes has also been reported in OSF. However, the underlying mechanism for the regulation of TGF-β by areca nut has not been elucidated.
The present study demonstrates that TGF-β pathway is activated in epithelial cells after two hour exposure to areca nut extract. Areca nut increases TGF-β transcript as well as protein and thereby the downstream canonical Smad2/3 signaling. Pre-treatment with various pathway inhibitors showed JNK pathway activation as a pre-requisite to TGF-β pathway activation by areca nut. Areca nut activated JNK pathway within half an hour of treatment and this was reversed by atropine treatment suggesting involvement of muscarinic acid receptor signaling. Second messengers upstream to JNK activation and regulated by areca nut were calcium/CAMKII and reactive oxygen species. Further, areca nut treatment resulted in JNK dependent phosphorylation of ATF2 and c-Jun transcription factors. These were found to bind TGF-β promoter, as revealed by chromatin immunoprecipitation experiments. Expectedly, knockdown of these transcription factors abrogated areca nut induced TGF-β pathway activation.
Based on the data obtained a model is proposed to elucidate activation of TGF-β pathway by areca nut extract involving activation of JNK and ATF2, c-Jun resulting in the over expression of TGF-β in epithelial cells which may contribute to the manifestation of OSF. Thus, this study highlights ATF2/c-Jun as the critical nodes for therapeutic intervention to prevent TGF-β over production in OSF.
Funding by DST and CSIR is acknowledged.
Citation Format: Ila Pant, Paturu Kondaiah. Areca nut-induced JNK/ATF2/Jun axis regulates TGF-beta signaling contributing to pre-cancerous oral submucous fibrosis. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1865.
Abstract 1872: Development of reference reagents to accelerate research on the RAS pathway
Authors: Esposito Dominic , Mehalko Jennifer , Wall Vanessa , Grose Carissa , Gillette William , Stephens Robert 
Published: July 2016

Abstract
The RAS Reference Reagents program within the NCI RAS Initiative is produces and distributes qualified DNA vectors, cell lines, and viruses to the external community to facilitate research into RAS biology and development of RAS cancer therapeutics. DNA vectors representing a variety of RAS mutations, as well as a complete collection of 180 genes in the RAS pathway are available as Gateway-compatible Entry clones. These clones represent the most commonly expressed transcript forms of the 180 genes, many of which were not previously available in full-length, wildtype forms. The vectors can be used with the FNLCR combinatorial cloning library to easily generate a large number of different types of expression clones with various promoters, fusion tags, and plasmid backbones. Additional reagents under construction include validated plasmid and lentiviral reagents for shRNA and CRISPR delivery, qualified cell lines for use in research into the RAS pathway, and systems for the generation of highly purified and characterized Ras and Ras-related proteins. A highlight of these reagents are materials for the high yield production of properly processed, prenylated KRAS protein using an engineered insect cell expression system. This system could be used to produce other prenylated small GTPases at levels not previously attainable. All of the resources of the RAS Reference Reagents program are readily available to the academic community through simple mechanisms, and can be licensed to industry scientists as well. The program is also interested in identifying the needs of the community for additional RAS-related resources, and is developing methods for vetting requests from the outside to provide additional reagents.
Citation Format: Dominic Esposito, Jennifer Mehalko, Vanessa Wall, Carissa Grose, William Gillette, Robert Stephens. Development of reference reagents to accelerate research on the RAS pathway. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1872.
Abstract 1873: The role of p21-activated kinase 4 (PAK4) in cancer stemness and epithelial-to-mesenchymal transition
Authors: Azmi Asfar S. , Muqbil Irfana , Aboukameel Amro , Senapedis William , Baloglu Erkan , Landesman Yosef , Shacham Sharon , Kauffman Michael , Philip Philip A. , Mohammad Ramzi M. 
Published: July 2016

Abstract
The p21-activated kinase 4 (PAK4) is a key downstream effector of the Rho family GTPases. PAK4 is found to be over-expressed in many oncogenic Ras-driven cancers and cell lines but not in their normal counterparts. Mesenchymal pancreatic ductal adenocarcinoma (PDAC) stem cells (CSCs) that are triple positive for stemness markers (CD133+, CD44+, and EpCam+) as well as Ras and snail transduced human mammary epithelial cells (HMLER-snail) showed enhanced expression of PAK4 along with activation of Rho, Rac1 and CDC42. PAK4 RNA interference resulted in disruption of PDAC CSC spheroids, reduction of mesenchymal markers (i.e. vimentin and snail) and suppression of CSCs potential to form subcutaneous tumors in mice. These findings point to a novel role of PAK4 in promoting oncogenic Ras-driven EMT and stemness. Using PDAC CSCs (MiaPaCa-2 and L3.6pl) and human mammary epithelial cells (HMECs) that are transduced with Ras and the EMT promoter snail (HMLE-Snail and HMLER-Snail), we investigated the impact of PAK4 allosteric modulators [PAMs (KPT-7189, KPT-7523, KPT-9274 and KPT-9307)] on the reversal of EMT and stemness. The toxicity and efficacy of PAMs were evaluated in vitro and in multiple sub-cutaneous xenograft models. PAMs show anti-proliferative activity in vitro against different PDAC CSCs and HMECs while sparing normal cells. Cell growth inhibition was concurrent with apoptosis induction, suppression of colony formation and reversal of mesenchymal morphology to epithelial (MET). PAMs not only reduced PAK4 RNA and protein steady state levels but also inhibited proliferative and anti-apoptotic signals downstream of PAK4. PAMs caused suppression of EMT markers (EpCAM, vimentin and snail) and re-expression of an epithelial promoter E-cadherin. PAM treatment inhibited RhoA, Rac1 and CDC42 activation in GLISA assays. KPT-9274 showed remarkable anti-tumor activity in sub-cutaneous xenograft models of CSCs and residual tumors showed suppression of EMT markers that was concurrent with inhibition of PAK4 signaling. These studies open a novel therapeutic opportunity against EMT and cancer stem cells through PAK4 inhibition.
Citation Format: Asfar S. Azmi, Irfana Muqbil, Amro Aboukameel, William Senapedis, Erkan Baloglu, Yosef Landesman, Sharon Shacham, Michael Kauffman, Philip A. Philip, Ramzi M. Mohammad. The role of p21-activated kinase 4 (PAK4) in cancer stemness and epithelial-to-mesenchymal transition. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1873.
Abstract 1876: Reduced Pak1 activity sensitizes FA/BRCA-proficient breast cancer cells to PARP inhibition
Authors: Villamar-Cruz Olga , Prudnikova Tatiana , Johnson Neil , Chernoff Jonathan , Arias Romero Luis E. 
Published: July 2016

Abstract
Cells that are deficient in homologous recombination, such as those that have mutations in any of the Fanconi Anemia (FA)/BRCA pathway genes, are hypersensitive to inhibition of poly(ADP-ribose) polymerase (PARP). However, FA/BRCA-deficient tumors represent only a small fraction of breast cancers, which might restrict the therapeutic utility of PARP inhibitor monotherapy. p21-activated kinase 1 (Pak1) is a serine/threonine protein kinase located in the chromosome 11q13 and is amplified and/or overexpressed in several human cancer types including 25-30% of breast tumors. This enzyme controls many cellular processes by phosphorylating its downstream substrates; in addition to its role in the cytoplasm, Pak1 also affects gene transcription due to its nuclear localization and association with chromatin. It is now recognized that Pak1 activation is a component of the DNA damage response. Here, we show that depletion or inhibition of Pak1 down-regulated the expression of several genes involved in the FA/BRCA pathway and compromised the ability of cells to repair DNA by homologous recombination, induced cell cycle arrest, promoted apoptosis and resulted in reduced colony formation. Combined inhibition of Pak1 and PARP in pak1 amplified breast cancer cells had a synergistic effect, enhanced apoptosis, resulted in reduced colony formation and delayed tumor growth in a xenograft setting. Inhibition of Pak1 did not sensitize non-transformed or Pak1 non-amplified cells to inhibition of PARP. Because reduced Pak1 activity impaired FA/BRCA function and consequently, repair by homologous recombination, inhibition of this kinase in pak1 amplified and/or overexpressing breast cancer cells represents a plausible strategy for expanding the utility of PARP inhibitors to FA/BRCA-proficient cancers.
Citation Format: Olga Villamar-Cruz, Tatiana Prudnikova, Neil Johnson, Jonathan Chernoff, Luis E. Arias Romero. Reduced Pak1 activity sensitizes FA/BRCA-proficient breast cancer cells to PARP inhibition. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1876.