bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2079: FGFR1/MAPK pathway regulates transcription factor brachyury-driven epithelial-mesenchymal transition in lung cancer
Authors: Hu Yunping , Hsu Wesley 
Published: August 2015

Abstract
Lung cancer is the leading cause of cancer-related death worldwide. Failure of treatment is attributed to recurrence, metastasis, and chemotherapeutic resistance. Previous studies have demonstrated that the transcription factor brachyury is a potential regulator of epithelial-mesenchymal transition (EMT) and plays a role in tumor resistance to conventional antitumor therapies. However, the mechanisms underlining brachyury-induced EMT are unknown. Recent studies have revealed that fibroblast growth factor (FGF)/ fibroblast growth factor receptor (FGFR) signaling is activated in lung cancer, and suppression of FGFR results in cell growth inhibition and apoptosis. Here we investigated the role of FGFR signaling, a critical component of mesoderm induction during normal embryogenesis and a regulator of normal brachyury expression, in brachyury-driven lung cancer. Quantitative RT-PCR and Western Blot analysis showed that the chemotherapy-insensitive/metastatic lung cancer cell line H460 and adenocarcinoma tissues in patients had significantly high expressions of brachyury and FGFR1, 3 and 4 compared to the chemotherapy-sensitive/non-metastatic lung cancer cell line H440 and normal tissues adjacent to tumor. To further explore the association between FGFR and brachyury expression and its function, we specifically silenced FGFR using siRNAs for FGFR1, 2, 3 and 4 in H460 cells or overexpressed FGFR1, 3 and 4 in H441 cells. We found that only FGFR1 inhibition led to suppression of brachyury, whereas overexpression of FGFR1 induced brachyury expression, suggesting that brachyury is a potential target of FGFR1. Immunofluorescence staining and RT-PCR showed that silencing of FGFR1 led to inhibitions of brachyury and EMT (an increased epithelial marker E-cadherin expression and decreased mesenchymal biomarker Snail expression) in H460 cells. Overexpression of FGFR1 promoted EMT in H441 cells, but this effect was suppressed by concomitant knockdown of brachyury. In addition, the mitogen-activated protein kinases (MAPK)/extracellular signal-related kinase (ERK) inhibitor, PD184352, suppressed FGF1-upregulated brachyury and Snail expressions and invasion in H460 cells. PD184352 also inhibited FGFR1 overexpression-induced brachyury expression, EMT and invasion in H440 cells, indicating an important regulatory role of FGFR1 in brachyury-driven EMT through MAPK/ERK. These findings provide novel insights into the molecular mechanism of brachyury-driven EMT and highlight the FGFR1/MAPK/ERK pathway as a new therapeutic target for brachyury-driven lung cancer.
Citation Format: Yunping Hu, Wesley Hsu. FGFR1/MAPK pathway regulates transcription factor brachyury-driven epithelial-mesenchymal transition in lung cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2079. doi:10.1158/1538-7445.AM2015-2079
Abstract 2083: TFAP4 inhibits differentiation of MYCN-amplified neuroblastoma
Authors: Zhang Shuobo , Lopez Gonzalo , Yu Jiyang , Silva Jose , Kadenhe-Chiweshe Angela , Califano Andrea , Yamashiro Darrell 
Published: August 2015

Abstract
Background. Despite the identification of MYCN-amplification as an adverse prognostic marker in neuroblastoma, no drugs that target MYCN have yet been developed. An alternative approach is to identify genes synthetically lethal to MYCN-amplified neuroblastoma. Through a whole genome shRNA screen, we have previously identified transcription factor AP4 (TFAP4) as a synthetic lethal gene of MYCN-amplified neuroblastoma. Silencing of TFAP4, both in vitro and in vivo inhibited the growth of MYCN-amplified neuroblastoma. TFAP4 has previously reported to repress neuronal specific genes in non-neuronal cells (Kim et al, 2006). Here, we investigate the function of TFAP4 in inhibiting differentiation of MYCN-amplified neuroblastoma.
Methods: Master regulators specifically associated to MYCN amplified patients were identified by MARINA (Master Regulator Inference algorithm). TFAP4 expression was measured by real-time PCR, Western blot and immunohistochemistry. GAP43 expression was detected by Western blot. Gene expression changes after silencing of TFAP4 or retinoic acid treatment was determined by RNAseq.
Results: TFAP4 was identified as a master regulator specifically in MYCN amplified neuroblastoma patients in both NCI-TARGET dataset and a published GEO dataset (Kocak et al, 2013). We determined that TFAP4 is a direct target of MYCN and TFAP4 expression was highly correlated with Stage 4, MYCN-amplified neuroblastoma in both patient datasets. Neuronal markers TUBB3 and GAP43 expression were inversely correlated with TFAP4 expression in TARGET (P = 9.77e-03 and P = 7.78e-08). Silencing TFAP4 in MYCN amplified cells induced a differentiated phenotype, as shown by markedly increased the number of neurites, and an increase in the neuronal differentiation marker GAP43. Forty hours after silencing TFAP4, we observed 415 genes that were significantly up-regulated and 457 genes down-regulated (P&lt;0.01). Genes with increased expression were enriched for gene ontology terms associated with neuronal activity. Gene signature of TFAP4 also showed a strong correlation with the treatment signature of the differentiation agent retinoic acid in SKNDZ.
Conclusions. We demonstrated that TFAP4 is an important downstream effector of MYCN, that inhibits the neuronal differentiatin of MYCN-amplified neuroblastoma. This may provide novel targets for the treatment of neuroblastoma.
Citation Format: Shuobo Zhang, Gonzalo Lopez, Jiyang Yu, Jose Silva, Angela Kadenhe-Chiweshe, Andrea Califano, Darrell Yamashiro. TFAP4 inhibits differentiation of MYCN-amplified neuroblastoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2083. doi:10.1158/1538-7445.AM2015-2083
Abstract 2087: Regulation of p53 function by KLF5
Authors: Yang Yizeng , Zhou Taicheng , Zong Zhen , Lomberk Gwen , Urrutia Raul , Katz Jonathan 
Published: August 2015

Abstract
Background: The transcription factor Krüppel-like factor 5 (KLF5) is essential for normal homeostasis, stemness, and tumorigenesis. Typically, KLF5 functions as a transcriptional activator, including in esophageal epithelia where KLF5 promotes keratinocyte proliferation and migration by activating EGFR and ILK, respectively, and prevents transformation by activating Notch1. Yet, the function of KLF5 is context dependent, and mutation of the tumor suppressor p53 switches KLF5 from a transcriptional activator to a repressor of p21Waf1/Cip1 and from pro-proliferative to anti-proliferative. Interestingly, KLF5 also inhibits p53 itself, though the mechanism of this inhibition is unknown. We hypothesized that the functional switch of KLF5 from transcriptional activator to repressor involves the recruitment of a co-repressor.
Methods: Primary human esophageal keratinocytes immortalized with hTERT were stably infected with inducible lentivirus containing shRNA against KLF5 or Sin3A. p53 mRNA and protein levels were assessed by real-time quantitative PCR and Western blotting, respectively, and p53 protein stability was evaluated by pulse-chase experiments. We employed ChIP across a 4 kb region on the p53 gene, from 2 kb upstream to 2 kb downstream of the transcription start site, to identify the region of KLF5 binding on p53. Promoter activity was assessed with a series of luciferase reporters containing varying lengths of p53 and its upstream regulatory region. Protein-protein interaction was examined by co-IP.
Results: KLF5 knockdown significantly increased p53 both at the mRNA and protein levels. In unstressed cells p53 protein undergoes rapid degradation such that p53 levels are typically low. Yet, with KLF5 knockdown, despite increased p53 protein levels, we saw no changes in p53 protein stability. By ChIP, we identified a region of KLF5 binding to p53 between -600 to -356 bp upstream of the transcription start site. Several other KLF family members can interact with the co-repressor Sin3A, and we found that Sin3A also complexed with KLF5 in human primary esophageal keratinocytes. Knockdown of Sin3A abolished the inhibitory effect of KLF5 on p53, resulting in elevated p53 expression, growth inhibition, and increased apoptosis.
Conclusion: KLF5 transcriptionally represses p53 via the co-repressor Sin3A. Thus, KLF5 promotes cell proliferation in normal keratinocytes by both activating pro-growth signals and inhibiting the brake machinery of the cell cycle.
Citation Format: Yizeng Yang, Taicheng Zhou, Zhen Zong, Gwen Lomberk, Raul Urrutia, Jonathan Katz. Regulation of p53 function by KLF5. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2087. doi:10.1158/1538-7445.AM2015-2087
Abstract 2089: Role of Cdx2 in maintainining differentiated chromatin structure during tumor progression
Authors: Perekatt Ansu O. , Rana Ritu , Kumar Namit , Valdez Michael , Verzi Michael 
Published: August 2015

Abstract
Tumor progression often coincides with the appearance of tumor cells with dedifferentiated or stem-like properties; the ontogeny of these cells is unclear, but they are thought to carry a more malignant capacity than their differentiated counterparts. Cdx2 is a transcriptional factor that specifies cell fate of the intestinal epithelium. Epigenetic studies have demonstrated that Cdx2 loss alters chromatin structure in the intestinal epithelium. Cdx2 loss is often observed during colon tumor progression and is correlated with de-differentiation. Our current study is aimed to test the hypothesis that the Cdx2 prevents tumor progression by maintaining the tumor epigenome. To this end, we have generated two mouse models to determine the effect of Cdx2 loss on chromatin structure in a tumorigenic environment and in primary tumors. Our current studies are aimed at comparing Cdx2 binding sites on the genome in a normal and tumorigenic environment, and in defining how Cdx2 loss affects chromatin structure in primary tumors. These studies will shed light on how alterations in chromatin structure can contribute to the epigenomic mechanisms of colon tumor progression.
Note: This abstract was not presented at the meeting.
Citation Format: Ansu O. Perekatt, Ritu Rana, Namit Kumar, Michael Valdez, Michael Verzi. Role of Cdx2 in maintainining differentiated chromatin structure during tumor progression. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2089. doi:10.1158/1538-7445.AM2015-2089
Abstract 2105: An EWS-FLI1/MRTF gene regulatory network in Ewing sarcoma
Authors: Katschnig Anna M. , Kauer Maximilian , Schwentner Raphaela , Aryee Dave N.T , Lawlor Elizabeth , Kovar Heinrich 
Published: August 2015

Abstract
The pediatric bone cancer Ewing sarcoma (ES) is characterized by the expression of the chimeric transcription factor EWS-FLI1, derived from a chromosomal translocation t(11;22)(q24;q12). The early onset of metastasis in ES leads to poor overall survival and limited treatment options. Remodeling of the actin cytoskeleton is a prerequisite of a tumor cell in order to become metastatic. Previous studies suggest that EWS-FLI1 alters cell morphology and deregulates various cytoskeletal genes. The major point of convergence of extracellular signals influencing cytoskeletal regulation is the Rho pathway. Activation of Rho GTPases promotes polymerization of monomeric G-actin into stress fibers (F-actin) thereby releasing the myocardin-related transcription factor family (MRTF-A, MRTF-B) of transcriptional coactivators. MRTFs translocate to the nucleus and interact with the transcription factor serum response factor (SRF) bound on CArG promoter elements of genes. However, the ternary complex factor (TCF) family, a class of transcriptional coactivators activated downstream of Ras signaling, competes with MRTFs for SRF binding in presence of ets binding sites adjacent to the CArG consensus sequence. The ets-transcription factor EWS-FLI1 has been shown to substitute for TCFs and interact with SRF. We hypothesized that EWS-FLI1 competes with MRTFs for SRF binding and uncouples target gene expression from Rho signaling. In combinatorial knockdown experiments of MRTFA/B and EWS-FLI1 we demonstrate that global changes in gene expression elicited by EWS-FLI1 silencing largely depend on the presence of MRTFs, suggesting that the fusion oncogene prohibits MRTF activity. Using gene expression analysis we identified six different patterns of MRTF/EWS-FLI1 interaction, with predominance of EWS-FLI1 inversely regulating MRTF target genes. Furthermore, we found MRTF transcriptional effects are already present in the absence of serum in A673 ES cells. MRTFB, however, is cytoplasmic under serum starved conditions and translocates to the nucleus only upon serum stimulation unless latrunculin B (LatB), an actin polymerization inhibitor, is added. In contrast, MRTFA is constitutively nuclear even under serum starved conditions or upon LatB treatment indicating that MRTFA might be uncoupled from actin regulation. These findings reveal a previously unknown role of MRTFs and the “CArGome” in EWS-FLI1 driven transcriptional dysregulation. Supported by the Liddy Shriver Sarcoma Initiative.
Citation Format: Anna M. Katschnig, Maximilian Kauer, Raphaela Schwentner, Dave N.T Aryee, Elizabeth Lawlor, Heinrich Kovar. An EWS-FLI1/MRTF gene regulatory network in Ewing sarcoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2105. doi:10.1158/1538-7445.AM2015-2105
Abstract 2108: Regulation of nucleotide metabolism by mutant p53 contributes to its gain-of-function activities
Authors: Martinez Luis A. , Kollareddy Madhusudhan 
Published: August 2015

Abstract
Mutant p53 (mtp53) is an oncogene that drives cancer cell proliferation. We found that mtp53 associates with the promoters of numerous nucleotide metabolism genes (NMG). Mtp53 knockdown reduced NMG expression and substantially depleted nucleotide pools. Decreased GTP levels correlated with reduced activation of GTP dependent proteins (GTPases) and reduced invasiveness. Addition of exogenous GTP restored the invasiveness of mtp53 knockdown cells, suggesting that mtp53 promotes invasion by increasing GTP. Additionally, mtp53 creates a dependency on the nucleotide salvage pathway enzyme deoxycytidine kinase (dCK) for the maintenance of a proper balance in dNTP pools required for proliferation. These data indicate that mtp53 harboring cells have acquired a synthetic sick or lethal phenotype relationship with the nucleotide salvage pathway. Finally, elevated expression of NMG correlates with mutant p53 status and poor prognosis in breast cancer patients. Thus, mtp53's control of nucleotide biosynthesis has both a driving and sustaining role in cancer development.
Citation Format: Luis A. Martinez, Madhusudhan Kollareddy. Regulation of nucleotide metabolism by mutant p53 contributes to its gain-of-function activities. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2108. doi:10.1158/1538-7445.AM2015-2108
Abstract 2109: Short isoform ARID5B protein is expressed in endometrial cancer cell lines by usage of the second translation initiation codon
Authors: Kawamata Norihiko , Itakuara Keiichi 
Published: August 2015

Abstract
ARID5B, also known as MRF2, is a transcription factor with the ARID-type DNA binding domain. The ARID5B gene generates two types of mRNA isoforms (short and long isoforms) using alternative first exons; the long and short mRNA isoforms encode 130kDa long and 100kDa short isoform ARID5B proteins, respectively. The ARID5B gene is highly mutated in endometrial cancer. Nonsense and frame-shift mutations, generating premature termination codons, are common. This transcription factor may play a role as a tumor suppressor in development of endometrial cancer and the inactivation of the gene by the mutations may contribute to carcinogenesis of this cancer.
To characterize functional significance of the gene products in this cancer, we analyzed the ARID5B gene in three endometrial cancer cell lines (Ishikawa, HEC59, and KLE).
Two cell lines, Ishikawa and HEC59, predominantly expressed the long isoform mRNA while KLE expressed both the long and short isoform mRNAs. However, surprisingly, all the cell lines predominantly expressed the 100 kDa protein, which was detected by an antibody recognizing the ARID-domain. To characterize the 100kDa protein, we generated rabbit anti-serum recognizing amino-terminus of the long isoform protein, which failed to detect the 100kDa protein. The data suggested that the 100kDa protein lacked the N-terminus of the long isoform ARID5B protein. Internal ribosome entry site (IRES) activity was found in the sequence between the first and second ATGs of the long isoform ARID5B mRNA by the bicistronic reporter gene assay. Our data suggested that the second translation initiation codon was used to generate the short isoform ARID5B protein in the cell lines.
To elucidate functional property of this short isoform ARID5B protein expressed in the cell lines, we suppressed the expression of the ARID5B protein by shRNA. The expression was decreased by 50% using the shRNA constructs. Colony formation assay of Ishikawa cells transfected with the shRNA constructs showed that repression of ARID5B short isoform protein decreased the number of the colonies. In summary, the short isoform ARID5B protein generated by usage of the second translation initiation site was indispensable in these endometrial cancer cells.
Citation Format: Norihiko Kawamata, Keiichi Itakuara. Short isoform ARID5B protein is expressed in endometrial cancer cell lines by usage of the second translation initiation codon. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2109. doi:10.1158/1538-7445.AM2015-2109
Abstract 211: A novel FRET assay for the intracellular activation of ADC linkers
Authors: Lee Byoung-Chul , Chalouni Cecile , Nalle Sam , Doll Sophia , Darwish Martine , Mellman Ira , Vandlen Richard 
Published: August 2015

Abstract
Evaluating the intracellular activation of ADC by a novel FRET assay.
Despite the recent success of ADCs as cancer therapeutics, their mechanisms of action are not fully understood. In this study, we developed ADCs using a novel fluorescence resonance energy transfer (FRET) linker in order to facilitate monitoring the details of intracellular uptake, vesicular trafficking and payload release. In the FRET linker, the cathepsin-cleavable dipeptide of val-cit was inserted between a fluorescence donor Alexa Fluor 488 (or later, fluorescein) and an acceptor tetramethylrhodamine (TAMRA). Upon cleavage of the val-cit linker, a fluorescence signal from Alexa Fluor 488 or fluorescein is expected to appear as a probe for monitoring intracellular activation of ADC.
We used two in-vitro human cancer cell lines, SKBR3 and PC3. SKBR3 is a Her2-positive breast cancer cell line and PC3 is a prostate cancer cell line that has been engineered to express a prostate cancer-specific growth factor receptor, tomoregulin-2 (TenB2). We assessed the intracellular processing of the FRET conjugates using flow cytometry. We found that 74% and 41% of the linker was cleaved in PC3 and SKBR3 cells after 20 hours of treatment, respectively.
In the live-celling imaging of the FRET probe in SKBR3 and PC3 cells, Anti-Her2 and TenB2 FRET ADCs showed a remarkable difference of internalization pathways and cleavage following receptor-mediated endocytosis. In PC3 cells, FRET ADCs were internalized and congregated into a certain localized area during the early stage of uptake in 2 to 3 hours. The ADC-containing vesicles were spread over the cytosol and near the plasma membrane in a subset of cells. A similar directed localization at the early stage of uptake was not observed for the SKBR3 cells. The endosomal vesicles in SKBR3s were spread over the cytosol during the course of ADC internalization. The amount of the release payload in the cytosol of SKBR3s was 3-fold greater than that of PC3 cells, suggesting that the endosomal/lysosomal membrane of SKBR3 may be more permeable than that of PC3.
In summary, our ADC FRET probes allowed for the facile, robust and non-invasive evaluation of intracellular processing for ADC linkers. Quantitative measurements for the rate of antigen-mediated intracellular cleavage of the FRET linker as well as cytosolic release could be evaluated by our FRET probes.
Citation Format: Byoung-Chul Lee, Cecile Chalouni, Sam Nalle, Sophia Doll, Martine Darwish, Ira Mellman, Richard Vandlen. A novel FRET assay for the intracellular activation of ADC linkers. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 211. doi:10.1158/1538-7445.AM2015-211
Abstract 2122: RNA editing reveals new regulatory functions in tumorigenesis
Authors: Hu Landian 
Published: August 2015

Abstract
RNA Editing is a widespread post-transcriptional event that could increase the diversity of transcriptome. In humans, the most common type of RNA editing is adenosine-to-inosine (A-to-I) editing which is catalyzed by a family of enzymes called adenosine deaminase acting on RNA (ADARs). Over 90% A-to-I RNA editing sites locate in Alu elements, the most abundant transposable elements in human genome. We picked up 83 CEU individuals and 89 YRI individuals for RNA editing analysis. 94,315 credible sites are obtained after series of strict computational procedures. Those genes whose transcripts harbor numerous RNA sites are found to be enriched in several cancer-related pathways such as small cell lung cancer pathway, p53 signaling pathway and apoptosis pathway. Our work provides new insight into the regulation mechanism of RNA editing acting on tumorigenesis.
Citation Format: Landian Hu. RNA editing reveals new regulatory functions in tumorigenesis. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2122. doi:10.1158/1538-7445.AM2015-2122