bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5240: Epigenetic dysregulation of miR-196b in breast cancer
Authors: Marquez Rebecca T. , Smith Amber R. , Tsao Bryan , Xu Liang 
Published: May 2015

Abstract
Dysregulation of microRNA (miRNA) expression levels is a major cause of cancer development. miRNA expression profiles can determine tumor type, patient prognosis, reoccurrence and treatment outcome, with greater accuracy as compared to mRNA expression profiles. The expression of miRNAs can be epigenetically dysregulated by aberrant DNA methylation and histone deacetylation in breast cancer cells. Furthermore, one third of miRNA promoters are targets for aberrant methylation in breast cancer. Identifying miRNAs that are epigenetically silenced in breast cancer will provide new insight into breast cancer development as well as define novel signatures for predicting therapeutic response to epigenetic modifying agents. New studies have shown that using transient low doses of demethylating agents, such as decitabine (DAC), result in sustained changes in major cancer cell signaling pathways, therefore reducing tumorigenicity and cancer stem cell self-renewal. The goal of this project is to identify epigenetically-silenced miRNAs that can be reactivated upon low dose treatment of DAC. miR-196b has been shown to inhibit metastasis by targeting HOXC8. Using online datasets, we determined miR-196b is hypermethylated in breast cancer patient samples compared to normal breast samples. We used Taqman miRNA assays to measure the expression of miR-196b in breast cancer patient samples and found it was down-regulated in tumor samples compared to paired normal breast tissue. miR-196b is also down-regulated in MDA-MB-231 cells. We treated MDA-MB-231 cells with low dose (100 nM) DAC for 3 days and found miR-196b was upregulated 5-fold compared to DMSO control. The methylated CpG content of miR-196b-associated CpG island was measured using bisulfite sequencing DNA purified from DMSO and DAC treated cells. The miR-196b CpG loci in the DAC treatment was demethylated by 33% compared to DMSO control. Therefore, reactivation of miR-196b is associated with demethylation of miR-196b CpG loci. Interestingly, fourteen days after ending DAC treatment, miR-196b re-expression continued to increase up to 13-fold above DMSO control. In addition, we found that exogenously re-introduced mature miR-196b into MDA-MB-231 breast cancer cells resulted in upregulation of endogenous primary miR-196b. This suggests a novel positive feedback loop that allows miR-196b to regulate its own expression, possibly through epigenetic mechanisms. Future studies will involve identifying the mechanism associated with this re-expression, determining whether miR-196b regulates additional gene promoters, and the affect this has on breast cancer metastatic phenotype.
Citation Format: Rebecca T. Marquez, Amber R. Smith, Bryan Tsao, Liang Xu. Epigenetic dysregulation of miR-196b in breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5240. doi:10.1158/1538-7445.AM2014-5240
Abstract 5241: Accurate quantitation of micro RNA by chip-based digital PCR
Authors: Wu Yalei , Dahlhoff Victoria , He Lin , Chen Caifu 
Published: May 2015

Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that function to regulate gene expression at transcriptional and post-transcriptional level. Mature miRNAs are short, usually 18-23 nucleotides (nt) in length, with high homology in the seed region (position 2-8 from the 5′ end of a mature miRNA) within each family. This presents a great challenge when designing assays for quantitation by real-time polymerase chain reaction (PCR). Existing miRNA assays often trade in sensitivity and/or assay performance for specificity. Comparison between two different mature miRNAs with quantitative real-time PCR (qPCR) requires generating standard curves and characterizing PCR efficiency and sensitivity. Here we report a chip-based digital PCR technology. With this technology, we are able to accurately quantitate mature miRNAs without characterizing and optimizing the assay.
Briefly, we input the same amount (ratio=1:1) of synthetic hsa-miR-19b and hsa-miR-92a. We then quantitated the miRNAs using reverse transcription followed by quantitative RT-PCR or chip-based QuantStudio™ 3D digital PCR (dPCR). Data from qPCR showed a delta Ct=2.58 between the cDNAs. This converted to a 3.84 fold difference between the two mature miRNAs, which deviated 284% from the input ratio, which equals 1. However, the data from dPCR indicated that the ratio between the amounts of the two mature miRNAs was 0.94 ± 0.02 (SD). Although statistically different, the results from dPCR deviated only 5% from the input ratio. Compared to qPCR, dPCR significantly enhanced the precision in sample quantitation.
In summary, our study demonstrated that the chip-based dPCR technology has greatly increased precision in quantitating miRNA samples. The simplified workflow and improved output of dPCR are very useful features in broad applications such as revealing small changes in the miRNA expression levels.
Citation Format: Yalei Wu, Victoria Dahlhoff, Lin He, Caifu Chen. Accurate quantitation of micro RNA by chip-based digital PCR. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5241. doi:10.1158/1538-7445.AM2014-5241
Abstract 525: Automated microRNA detection in formalin-fixed, paraffin-embedded tissue samples
Authors: Jiang Zeyu (David) , Pedata Anne , Shingler Taylor , Behman Lauren , Chafin David , Day William 
Published: May 2015

Abstract
The human genome encodes more than one thousand short (17-24 base) non-coding microRNA molecules which regulate diverse cellular functions. Several of these functions are also involved in tumorigenesis including cell growth, motility, and immune surveillance. Not surprisingly, numerous clinical studies suggest that microRNAs could serve as potent prognostic and/or predictive biomarkers for a variety of diseases including breast, colorectal, lung, and prostate cancers. However, due to their short sequence length, technical obstacles exist for detection of these potential biomarker targets particularly in FFPE tissue samples: (i) limited target sequence limits probe length and subsequent target specificity as well as (ii) detection sensitivity since short probes require significant amplification technologies to generate a visible signal; lastly, (iii) short microRNA targets may be less stable in tissue (increased ribonuclease sensitivity and/or limited crosslinking to cellular components). In the current study, new RNA detection technologies, which include hapten-labeled oligonucleotide probes and sensitive tyramide-hapten/Silver detection designed for detection of longer RNA targets, were adopted for automated detection of microRNA targets in formalin-fixed, paraffin-embedded (FFPE) tissue.
DNP-labeled oligonucleotide probes, directed against four microRNA targets (miR-21, miR-200c, miR-25, and miR-200b) plus sequence-scrambled negative control were synthesized and combined with a modified VENTANA OptiView amplification kit and silver detection. The probes and new detection system catalyzed sensitive and specific detection of each microRNA target in MCF-7 xenograft FFPE tissues, which correlates well with microarray profiling data from MCF-7 cells by Fix et. al. (2010)*.
In summary, this study demonstrates a robust and fully automated ISH assay for microRNA targets in FFPE tissue and enables potential microRNA biomarkers being analyzed within tissue context.
* Fix et. al. Cancer Genomics & Proteomics (2010) 7:261-278.
Citation Format: Zeyu (David) Jiang, Anne Pedata, Taylor Shingler, Lauren Behman, David Chafin, William Day. Automated microRNA detection in formalin-fixed, paraffin-embedded tissue samples. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 525. doi:10.1158/1538-7445.AM2014-525
Abstract 5250: The effect of introducing a C118S mutation into the endogenous Kras gene on early tumorigenesis
Authors: Huang Lu , Counter Christopher M. 
Published: May 2015

Abstract
The Ras family of small GTPase, comprised of HRAS, NRAS, and KRAS, have been found mutated to remain in an active oncogenic state in many different human cancers, which is well established to promote tumorigenesis. All three RAS isoforms contain a conserved C118, of which the thiol group can be post-translationally modified by processes such as S-nitrosylation, which have been reported to promote RAS activation. To investigate the effect of blocking such modifications on RAS function in vivo, a C118S mutation, which lacks the reactive thiol group, was knocked into the endogenous Kras gene in mice. We now report that KrasC118S/C118S mice were born at the expected ratio with no overt phenotypes. To explore the effect of this mutation on early tumorigenesis, Kras+/+, KrasC118S/+, and KrasC118S/C118S mice were treated with the carcinogen urethane to induce oncogenic mutations in Kras and lung lesions. Interestingly, both KrasC118S/+ and KrasC118S/C118S mice developed fewer and smaller lung tumors than control Kras+/+ mice, suggesting that KrasC118S impairs lung tumorigenesis. Such a reduction in tumorigenesis could be the consequence of the C118S mutation on either the unaffected Kras allele or the Kras allele with the oncogenic mutation. To evaluate the first possibility, we tested and found that mice harboring a Cre-activated LSL-KrasG12D allele formed a similar number and size of lung tumors after activation of this allele when the remaining Kras allele was wild-type or C118S mutant. These data indicate that the reduction in tumor lesions observed in KrasC118S/+ and KrasC118S/C118S mice treated with urethane was unlikely to be the consequence of the C118S mutation on the non-oncogenic Kras allele. To evaluate the second possibility, we tested and found that oncogenic mutations occurred preferentially in the native compared to the C118S mutant Kras allele in KrasC118S/+ mice treated with urethane, suggesting a selection against oncogenic mutations on the KrasC118S allele. These results are consistent with the hypothesis that post-translational modifications such as S-nitrosylation on C118 enhance the oncogenic activity of Kras in vivo, and demonstrate for the first time that blocking the ability of a protein to be modified by processes like S-nitrosylation has a biological consequence in vivo.
Citation Format: Lu Huang, Christopher M. Counter. The effect of introducing a C118S mutation into the endogenous Kras gene on early tumorigenesis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5250. doi:10.1158/1538-7445.AM2014-5250
Abstract 5251: ASCL1 and RET expression define a clinically relevant subgroup of lung adenocarcinoma characterized by neuroendocrine differentiation
Authors: Kosari Farhad , Ida Cristiane M. , Aubry Marie Christine , Yang Lin , Kovtun Irina V. , Klein Janet L. Schaefer , Tomaszek Sandra C. , Murphy Stephen J. , Yang Ping , Wigle Dennis , Vasmatzis George 
Published: May 2015

Abstract
ASCL1 is an important regulatory transcription factor in pulmonary neuroendocrine cell development, but its value as a biomarker of neuroendocrine differentiation in lung adenocarcinoma (AD) and as a potential prognostic biomarker remains unclear. We examined ASCL1expression in lung cancer samples of varied histologic subtype, clinical outcome, and smoking status and compared to expression of traditional neuroendocrine markers. ASCL1 mRNA expression was found almost exclusively in smokers with AD, in contrast to non-smokers. ASCL1 protein expression by immunohistochemistry (IHC) correlated best with synaptophysin compared to chromogranin and CD56/NCAM. Analysis of a compendium of 367 microarray-based gene expression profiles in stage I lung adenocarcinomas identified significantly higher expression levels of the RET oncogene in ASCL1 positive tumors (ASCL1+) compared to ASCL1- tumors (q-value &lt; 10 - 9). High levels of RET expression in ASCL1+ but not in ASCL1- tumors was associated with significantly shorter overall survival in stage 1 (p = 0.007) and in all AD (p = 0.037). RET protein expression by IHC had an association with overall survival in the context of ASCL1 expression. In silico gene set analysis and in vitro experiments by ASCL1 shRNA in AD cells with high endogenous expression of ASCL1 and RET implicated ASCL1 as a potential upstream regulator of the RET oncogene. Also, silencing ASCL1 in AD cells markedly reduced cell growth and motility. These results suggest that ASCL1 and RET expression define a clinically relevant subgroup of approximately 10% of AD characterized by neuroendocrine differentiation.
Citation Format: Farhad Kosari, Cristiane M. Ida, Marie Christine Aubry, Lin Yang, Irina V. Kovtun, Janet L. Schaefer Klein, Sandra C. Tomaszek, Stephen J. Murphy, Ping Yang, Dennis Wigle, George Vasmatzis. ASCL1 and RET expression define a clinically relevant subgroup of lung adenocarcinoma characterized by neuroendocrine differentiation. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5251. doi:10.1158/1538-7445.AM2014-5251
Abstract 5253: PTEN represses oncogene expression by regulating Daxx-H3.3 deposition in the chromatin
Authors: Benitez Jorge A. , Cavenee Webster K. , Furnari Frank F. 
Published: May 2015

Abstract
One of the most mutated and deleted gene in cancer is the tumor suppressor gene pten (phosphatase and tensin homology, deleted on chromosome ten). To further understand how PTEN inactivation contributes to cancer predisposition, we investigated how PTEN regulates gene expression. We found that the histone chaperon protein Daxx (death domain-associated protein) associates with PTEN, in vivo and in vitro, and regulates PTEN stability through acetylation and ubiquitination. We observed that PTEN regulates Histone 3.3 (H3.3 variant) loading in the chromatin by limiting Daxx interactions, and thereby controls expression of several tumor driver genes. Furthermore, when Daxx expression is disrupted in pten-deficient glioma stem cells, we observed a dramatic diminution of pluripotency transcription factors, a decrease in differentiation and sphere-forming capacity, and an increase in radiation sensitivity. In conclusion, this work supports a novel chromatin-associated function for PTEN that regulates H3.3 deposition, and gene expression, through Daxx interaction. This nominates Daxx as a therapeutic target to treat patients with gliomas and other types of cancers in which PTEN is mutated.
Citation Format: Jorge A. Benitez, Webster K. Cavenee, Frank F. Furnari. PTEN represses oncogene expression by regulating Daxx-H3.3 deposition in the chromatin. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5253. doi:10.1158/1538-7445.AM2014-5253
Abstract 5263: Identification of a lipid raft protein that is required for H-Ras activation and breast cancer aggressiveness
Authors: Yong Hae-Young , Kim Eun-Sook , Koh Minsoo , Son Hwajin , Jeon You Rim , Hwang Jin-Sun , Kim Myeong-Ok , Cha Yujin , Choi Wahn Soo , Noh Dong-Young , Lee Kyung-Min , Kim Ki-Bum , Lee Jae-Seon , Kim Hyung Joon , Kim Hong-Hee , Kim Eun Joo , Park So Yeon , Kim Hyeong-Reh Choi , Moon Aree 
Published: May 2015

Abstract
In an attempt to identify biomarkers and/or therapeutic targets for malignant breast cancer, the present study showed a comparative proteome profiling of invasive MCF10A human breast epithelial cells engineered to express active H-Ras and non-invasive cells expressing active N-Ras. Here, we identified a lipid raft protein DS-20, a crucial regulator of H-Ras activation, as a potential marker for invasive breast cancer. DS-20 (amino acid residues 1-38) interacted with H-Ras (residues 166-189) in lipid rafts and their interaction was important for H-Ras activation. DS-20 knockdown inhibited H-Ras activation and invasion in Hs578T triple-negative breast cancer cells (TNBC) and T24 bladder carcinoma cells in which H-Ras is endogenously activated, suggesting a crucial role of DS-20 in the invasive program which relies on the activation of H-Ras. We further showed that DS-20 was required for epidermal growth factor-induced H-Ras activation, but not that of N-Ras, in MDA-MB-231 TNBC cells. Intravasation of MDA-MB-231 cells treated with shRNA DS-20 in the chick chorioallantoic membrane model was markedly reduced, indicating that DS-20 is required for an invasive capacity in vivo. In a xenograft mice tumor model, DS-20 was essential for in vivo tumor aggressiveness of Hs578T cells, suggesting DS-20 as a potential target for the treatment of breast cancer. Using human breast cancer samples, we provide clinical evidence for the tumorigenic potential of DS-20 and its association with H-Ras. Taken together, our findings provide a new insight into the molecular basis of Ras isoform-specific interplay with plasma membrane leading to cell invasion.
Citation Format: Hae-Young Yong, Eun-Sook Kim, Minsoo Koh, Hwajin Son, You Rim Jeon, Jin-Sun Hwang, Myeong-Ok Kim, Yujin Cha, Wahn Soo Choi, Dong-Young Noh, Kyung-Min Lee, Ki-Bum Kim, Jae-Seon Lee, Hyung Joon Kim, Hong-Hee Kim, Eun Joo Kim, So Yeon Park, Hyeong-Reh Choi Kim, Aree Moon. Identification of a lipid raft protein that is required for H-Ras activation and breast cancer aggressiveness. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5263. doi:10.1158/1538-7445.AM2014-5263
Abstract 5265: S100P increases Twist expression and triggers FAK/AKT signaling in lung cancer
Authors: Liang Yung-Yu , Kuo Po-Lin , Hsu Ya-Ling 
Published: May 2015

Abstract
Lung cancer accounts for 12% of all new cases of cancers worldwide and is the leading cause of cancer-related death. S100P, a calcium binding protein, has been reported to involve in cancer metastasis. However, the role of S100P is poorly known in lung cancer. This study first reports that S100P enhances the migration and invasion ability of lung cancer cells through the Twist1 upregulation and FAK (focal adhesion kinase)/Src/AKT signaling pathway. Compared to low invasive CL1-0, the expression of S100P is greater in that of high invasive CL1-5 cells. Overexpression of S100P increases the migration and invasion in CL1-0 cells, whereas knockdown of S100P expression decreases the migration and invasion of CL1-5 cells. Enhancement of S100P expression triggers FAK activation, which in turn increases the activation of Src and AKT signaling. Blockade of FAK by specific inhibitor prevents S100P-mediated cell migration and invasion. In the other hand, S100P also increases Twist1, which is responsible for epithelial-mesenchymal transition in lung cancer. More important, elevated expression of S100P protein was also found in human lung cancer specimen. This study demonstrates that S100P may be a novel anticancer target gene for the prevention of non-small cell lung cancer metastasis. In other way, it also can be a biomarker for prognosis of lung cancer metastasis.
Citation Format: Yung-Yu Liang, Po-Lin Kuo, Ya-Ling Hsu. S100P increases Twist expression and triggers FAK/AKT signaling in lung cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5265. doi:10.1158/1538-7445.AM2014-5265
Abstract 5266: Role of nuclear Met receptor in hepatocellular carcinoma
Authors: Yam Judy Wai Ping , Tey Sze Keong 
Published: May 2015

Abstract
Met is a receptor tyrosine kinase encoded by c-Met proto-oncogene which triggers a wide range of normal physiological signaling cascades upon activation by hepatocyte growth factor (HGF). However, aberrant Met expression and activity are commonly found in human cancers. Emerging evidence has shown the presence of nuclear Met (nMet) in some cancerous tissues and cell lines, suggesting that nMet could have unexplored functions in the nucleus. Met is an attractive therapeutic target for human cancers. Indeed, therapeutic antibodies and inhibitors that antagonize dysregulated Met are currently in clinical trials. However, the classic therapeutic strategies against the Met surface receptor will unequivocally exhibit limitations in acting against nMet. Despite the oncogenic role of Met in hepatocellular carcinoma (HCC), the existence and functions of nMet in HCC has never been reported. In this study, we aim to evaluate the clinical relevance and characterize the functions of nMet in HCC. We studied nMet expression in 103 human HCC paired samples by immunohistochemistry. Our data showed that nMet was overexpressed in 89.3% of HCC tissues and its expression was progressively increased along HCC development. Nonetheless, nMet overexpression was significantly associated with venous invasion and poorer overall survival. We found that nMet, which has a lower molecular weight than Met, could only be detected using an antibody against the carboxyl terminus of Met (C28) in tumorous tissues. This finding suggests that nMet only comprises the carboxyl cytoplasmic region of full length Met. Immunofluorescence microscopy showed that juxtamembrane deletion of Met accumulates in the nucleus whereas truncated tyrosine kinase domain accumulates in the cytoplasm, implying a region important for nuclear localization of the cytoplasmic fragment. Cellular fractionation also confirmed the existence of nMet in the nuclear fraction of HCC cells. To explore the functional role of nMet, expression vector was constructed to express the cytoplasmic protein of Met in cells. In vitro functional study showed that overexpression of nMet augments the invasiveness of HCC cells suggesting the unexplored functional effect of nMet exerted within nucleus in promoting HCC invasiveness. Furthermore, we showed that nMet activates NF-kappaB reporter activity which might enhance the pro-metastatic gene expression to promote tumor invasiveness and aggressiveness.
Citation Format: Judy Wai Ping Yam, Sze Keong Tey. Role of nuclear Met receptor in hepatocellular carcinoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5266. doi:10.1158/1538-7445.AM2014-5266