bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2014: Alternative splicing is a frequent event in mouse PTEN-deficient prostate cancer
Authors: De Velasco Marco A. , Kura Yurie , Sakai Kazuko , Fujita Yoshihiko , Togashi Yosuke , Terashima Masato , Yoshikawa Kazuhiro , Nishio Kazuto , Uemura Hirotsugu 
Published: July 2016

Abstract
Castration-resistant prostate cancer (CRPC) remains an incurable disease and presents a major challenge for the development of novel treatment strategies. Alternative splicing occurs as a common natural phenomenon and promotes diversity, however, cancer-related alternative splicing events have been shown to contribute to disease progression and promote therapeutic escape. In prostate cancer, key genes required for normal biological function are frequently alternatively spliced resulting in altered phenotypes. Novel therapeutic strategies targeting the alternative splicing machinery are being developed and tested. Here, characterized the conditional PTEN-deficient mouse model of prostate cancer to determine its relevancy as preclinical tool for the development and efficacy determination of novel therapeutic strategies targeting aberrant alternative splicing. For this, we used the Affymetrix GeneChip mouse transcriptome assay to perform comparative analysis of the transcriptomes of normal prostate tissue and PTEN-deficient castration-naïve, castration-sensitive (4 weeks post-castration), and castration-resistant (10 weeks post-castration) prostate cancers. Clustering analysis revealed genes enriched with the functions involved in mRNA splicing and processing in mice with prostate tumors. Moreover, alternative splicing events were more prevalent in castration-sensitive tumors (&gt;2.5-fold) compared to castration-naïve and castration resistant tumors. Exon skipping (cassette exon), was the most common splicing event observed in all conditions. Additionally, alternative splicing was observed in several genes frequently associated with human prostate cancer including CD44, AR, p53, Bcl2l1 and Klf6 among others. Collectively, our data shows that alternative mRNA splicing is a frequent event in mouse PTEN-deficient prostate cancer and supports a role for alternative splicing dysregulation and the pathogenesis of the disease. Furthermore, this mouse model may also provide a suitable platform to study current therapeutic approaches targeting alternative splicing.
Citation Format: Marco A. De Velasco, Yurie Kura, Kazuko Sakai, Yoshihiko Fujita, Yosuke Togashi, Masato Terashima, Kazuhiro Yoshikawa, Kazuto Nishio, Hirotsugu Uemura. Alternative splicing is a frequent event in mouse PTEN-deficient 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 2014.
Abstract 203: Single cell imaging of kinase inhibitor-induced effects in breast cancer cell lines
Authors: Mills Caitlin , Andrews David , Sorger Peter 
Published: July 2016

Abstract
There is need for improved targeted therapies for the treatment of breast cancer. Kinase inhibitors are candidates to be used in this context. With the goal of uncovering specific vulnerabilities in differing cell lines, we treated five breast cancer cell lines representing triple negative (BT20, MDAMB231, and Hs578T), hormone receptor positive (MCF7), and Her2 amplified (SKBR3) disease and the non-malignant MCF10A line with a panel of 105 kinase inhibitors covering a broad range of targets. Cells were treated with doses between 0.1 and 10 μM for 24 hours, at which time they were stained with DRAQ5 (DNA) and TMRE (mitochondrial membrane potential). Live-cell images were acquired using a high throughput, confocal Opera microscope. Cell segmentation, based on the DRAQ5 staining, and feature extraction (intensity, morphology, and texture) were performed with Acapella software. Over 300 features were extracted for ∼1.5 million cells. Analytical methods have been applied to identify those treatments that induced significant changes to the cells. Over half of the kinase inhibitors queried had a significant effect within 24 hours in all cell lines at 10 μM. Cell cycle inhibitors had the most common effects across cell lines. Cell line specific effects were also uncovered, for example, MDAMB231 cells were the most sensitive to MAPK inhibitors. These, early time point, results have been compared with the effects of the same inhibitors on cell growth to better understand the mechanisms leading to cell line and pathway specific effects.
Citation Format: Caitlin Mills, David Andrews, Peter Sorger. Single cell imaging of kinase inhibitor-induced effects in breast cancer cell lines. [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 203.
Abstract 2034: Personalized chemotherapy regimen selection for breast cancer
Authors: Zhang Jinfeng , Yu Kaixian , Sang Qingxiang Amy , Tan Winston , Dargham Mayassa B. , Liu Jun S. , Lively Ty , Sheffield Cedric 
Published: July 2016

Abstract
Despite the rapid progress in personalized cancer therapy (PCT) for breast cancer, no previous studies have used genomic predictors to choose among multiple chemotherapy regimens. It is unclear that given the current regimens how much PCT can improve the response rate for patients who will receive chemotherapy. In this study, we reanalyzed data from published studies of 1111 breast cancer patients who were treated with neoadjuvant chemotherapies. Those patients were divided into three regimen groups: an anthracycline alone, anthracycline plus paclitaxel, and anthracycline plus docetaxel. We developed a new strategy called PRES (Personalized REgimen Selection) to reassign the optimal regimen to each of the patients. First, a variable selection scheme was developed to identify significant genetic predictors for chemotherapy response. The selected genetic variables were then combined with clinical variables to build random forest models to predict the response of a patient to each regimen using pCR (pathological complete response) as the measure of response. The models were used to assign an optimal regimen to each patient to maximize the chance of pCR. We found that the expected rate of pCR was improved from 21.2% to 39.6% (95% CI: 34.6% - 43.0%). We also found that 31.1% of the patients may have been overtreated and 8.2% patients undertreated. A validation study on 21 cell lines showed that our prediction agrees with their paclitaxel-sensitivity profiles. We performed additional analysis on the Cancer Genome Atlas (TCGA) data and found that 18 of the 19 genes identified are significantly differentially expressed between normal and tumor tissues, and 2 of them, TAF6L and METRN (meteorin), are associated with overall survival. In conclusion, PRES could substantially increase response rates for breast cancer patients who will receive one of the widely-accepted chemotherapy regimens at present.
Citation Format: Jinfeng Zhang, Kaixian Yu, Qingxiang Amy Sang, Winston Tan, Mayassa B. Dargham, Jun S. Liu, Ty Lively, Cedric Sheffield. Personalized chemotherapy regimen selection for breast 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 2034.
Abstract 204: Disruption of the RACK1/PP2A complex results in a decrease in the adhesion, proliferation, migration and invasion capabilities of breast cancer cells
Authors: Kiely Maeve , O’Connor Rosemary , Adams David , Baillie George S. , Kiely Patrick A. 
Published: July 2016

Abstract
Conflicting reports implicate the scaffolding protein RACK1 in the progression of breast cancer. PP2A has a well-established role as a tumour suppressor within signalling pathways but is also known to play a pro-carcinogenic role in certain circumstances [1]. RACK1 has been identified as a direct binding partner of PP2A to regulate cell migration and stabilize PP2A activity [2]. Our objective was to further characterise the interaction between PP2A and RACK1 in breast cancer cells. The PP2A holoenzyme is assembled in MCF-7 cells and we found that both the C subunit and A subunit of PP2A are assembled on the RACK1 scaffold. We used immobilized peptide arrays representing the entire PP2A-Catalytic protein to identify amino acids on the C subunit of PP2A that are required for the binding of RACK1. Once identified, these sites were mutated and expressed in the context of the full length PP2A C subunit protein and stable cell lines were generated. When the RACK1/PP2A interaction was disrupted, cells exhibited reduced PP2A phosphatase activity, confirming the role for RACK1 in stabilizing PP2A activity. We used the stable cell lines to determine that disruption of the RACK1/PP2A complex also reduces the adhesion, proliferation, migration and invasion of this breast cancer cell model. The work has significantly advanced our understanding of the RACK1/PP2A complex and indicates a pro-carcinogenic role for the RACK1/PP2A complex. This work has highlighted a novel mechanism to target PP2A activity and may provide a potential therapeutic target in the treatment of breast cancer.
1. Kiely, M. and P.A. Kiely, PP2A: The Wolf in Sheep's Clothing? Cancers, 2015. 7(2): p. 648-669.
2. Kiely, P.A., et al., Tyrosine 302 in RACK1 is essential for insulin-like growth factor-I-mediated competitive binding of PP2A and β1 integrin and for tumor cell proliferation and migration. Journal of Biological Chemistry, 2008. 283(34): p. 22952-22961.
Citation Format: Maeve Kiely, Rosemary O’Connor, David Adams, George S. Baillie, Patrick A. Kiely. Disruption of the RACK1/PP2A complex results in a decrease in the adhesion, proliferation, migration and invasion capabilities of breast cancer cells. [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 204.
Abstract 2057: Dual peptide-mediated targeted delivery of siRNAs for the treatment of oral cancer
Authors: Alexander-Bryant Angela A. , Zhang Haiwen , Pugh William , Dinh Lu , Attaway Christopher , Eggart Laurence , Sansevere Robert , Cantini Liliana , Jakymiw Andrew 
Published: July 2016

Abstract
Two major hurdles for small interfering RNA (siRNA)-mediated therapies are cell/tissue-type targeted delivery and endosomal entrapment of siRNAs, resulting in inefficient gene silencing. As a result, the objective of this study was to examine the feasibility of utilizing two peptides, one with cancer cell-targeting specificity and the second with endosome-disruptive properties, to co-deliver bioactive siRNAs into oral cancer cells overexpressing the epidermal growth factor receptor (EGFR) and induce silencing of the targeted oncoprotein, CIP2A. Previously, we designed a novel endosome-disruptive peptide, termed 599, that was demonstrated to mediate intracellular delivery of bioactive siRNAs targeting CIP2A (siCIP2A) in vitro. Furthermore, we recently demonstrated that 599 peptide-mediated delivery of siCIP2A into tumor tissues via intratumoral injections reduced the expression of CIP2A and significantly inhibited tumor growth. In order to induce targeted uptake via systemic administration, we designed the EGFR targeting peptide, GE11R9, which was found to deliver siRNAs specifically to EGFR-overexpressing oral cancer cells; however, it was incapable of mediating the delivery of bioactive siRNAs due to endosomal entrapment. Consequently, we developed a novel dual peptide delivery strategy, combining the 599 peptide, with the GE11R9 peptide and examined their ability to co-deliver siRNAs. Our results demonstrated that the dual peptide complex exhibited effective binding and specific uptake of siRNAs into EGFR-overexpressing cells compared to low-EGFR-expressing cells. The co-addition of the 599 peptide with the GE11R9 peptide also restored siRNA functionality. Furthermore, when administered systemically to mice bearing xenograft oral tumors, the dual peptide complex mediated increased targeted delivery of siRNAs into tumor tissues in comparison to the 599 peptide alone. Together, these data demonstrate the clinical potential of the dual peptide strategy for RNAi-based therapeutics by synergistically mediating the effective targeting and delivery of bioactive siRNAs into EGFR-overexpressing cancer cells.
Citation Format: Angela A. Alexander-Bryant, Haiwen Zhang, William Pugh, Lu Dinh, Christopher Attaway, Laurence Eggart, Robert Sansevere, Liliana Cantini, Andrew Jakymiw. Dual peptide-mediated targeted delivery of siRNAs for the treatment of oral 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 2057.
Abstract 206: Cytochrome c oxidase subunit 5a (COX5A) is identified as a potential therapeutic target for lung cancer with high therapeutic index through a pooled shRNA screen
Authors: Kato Toshio , Sato Mitsuo , Kondo Masashi , Kakumu Tomohiko , Yogo Naoyuki , Hase Tetsunari , Morise Masahiro , Hasegawa Yoshionori , Minnna John D. , Girard Luc 
Published: July 2016

Abstract
[Background]Recent advances in high throughput analysis of genetic and epigenetic alterations revealed numerous changes in lung cancer cells. It is vital to sort out genes that substantially contribute to oncogenic properties of cancer cells from these numerous altered genes by performing a functional screening because such genes could serve as valuable therapeutic targets. To this end, we performed a screening with a pooled shRNA library for genes critical for survival and/or proliferation in lung cancer cells. [Methods and Results]A pooled shRNA library comprising 5,000 genes, with 3 to 7 constructs per gene, were transduced in NCI-H460 lung cancer cell line. Subsequently, genomic DNA was extracted from the transduced cells and numbers of shRNA for each gene were quantified by next generation sequencing. Through a stringent filtering process we narrowed down genes to a list of 24 candidates as potentially target genes. Next, we integrated data of genome-wild gene expression and copy number analyses of a panel of lung cancer cell lines to narrow down to genes more relevant to lung cancer. Through these processes, we listed up several candidate genes. Among them, we focused on Cytochrome c oxidase subunit 5a (COX5A), one of the nuclear encoded subunits of cytochrome c oxidase, the terminal protein of the mitochondrial electron transport chain. Importantly, COX5A knockdown didn't suppress growth of HBEC3, a normal control cell line, suggesting that therapeutics of targeting COX5A may have high therapeutic index.
[Conclusions]Our results suggest that inhibiting COX5A may be an attractive strategy for the treatment of NSCLC with high therapeutic index.
Citation Format: Toshio Kato, Mitsuo Sato, Masashi Kondo, Tomohiko Kakumu, Naoyuki Yogo, Tetsunari Hase, Masahiro Morise, Yoshionori Hasegawa, John D. Minnna, Luc Girard. Cytochrome c oxidase subunit 5a (COX5A) is identified as a potential therapeutic target for lung cancer with high therapeutic index through a pooled shRNA screen. [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 206.
Abstract 2060: Polymer mediated RNAi-based combination therapy for treating prostate cancer
Authors: Danquah Michael 
Published: July 2016

Abstract
Purpose. To determine whether RNAi-based combination therapy targeting androgen receptor (AR) and XIAP signaling pathways using polymeric micelles can treat prostate cancer.
Methods. Potency of siRNAs targeting AR and XIAP genes was assessed using real time RT-PCR, Western Blot and ELISA. Cell viability was determined by MTT assay. A library of polymers designed to degrade via hydrolysis and enhance siRNA delivery was synthesized by conjugating hexylamine, pentaethylenehexamine and 3-morpholinopropylamine to poly(ethylene glycol)-block-poly(5-methyl-5-carboxyl-propylene carbonate) backbone using EDC/HOBT coupling chemistry. Polymer structure and molecular weight were verified with proton NMR and Gel Permeation Chromatography, respectively.
Results. Three siRNA sequences targeting different regions of the AR and XIAP genes were designed, blasted against the human genome database to eliminate cross-silencing of nontarget genes and their potency screened in LNCaP and C4-2 cells following transfection. All siRNAs targeting AR (start site: 1172, 1648 and 1768) used in this study silenced AR mRNA and protein expression in both cell lines. Furthermore, 1172 was identified as the most potent sequence resulting in approximately 75% knockdown regardless of cell type. Also, the three siRNAs targeting XIAP (start site: 264, 297 and 458) down-regulated XIAP mRNA and protein levels in both cells and were generally more potent in C4-2 cells compared to LNCaP cells. C4-2 cells transfected with siRNA targeting AR (start site: 1172) and XIAP (start site: 264) alone or in combination and assayed after 96 hours revealed XIAP and AR down-regulation resulted in approximately 20% and 50% growth inhibition in C4-2 cells, respectively, compared to control. However, combined silencing of XIAP and AR genes decreased cell growth by 62% and was more potent in inhibiting cell proliferation compared to monotherapy. Additionally, combination of siRNA targeting AR (start site: 1172) and XIAP (start site: 264) significantly increased percentage of cells undergoing apoptosis (85%) compared to control or monotherapy. Poly(ethylene glycol)-block-poly(5-methyl-5-carboxyl-propylene carbonate) copolymer was synthesized by ring opening polymerization and conjugated with various ratios of hexylamine, pentaethylenehexamine and 3-morpholinopropylamine moieties. The resulting copolymer (PEG-b-P(CC-g-PHEXYL-g-PMORPH-g-PPHEA) were non-toxic even at concentration of 1500 μg/mL and successfully condensed siRNA at N/P of 25 with average hydrodynamic diameter of approximately 175 nm.
Conclusions. Combination based therapy using siRNA targeting AR and XIAP can potentially treat prostate cancer.
Citation Format: Michael Danquah. Polymer mediated RNAi-based combination therapy for treating 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 2060.
Abstract 2072: Inhibition of breast cancer stem cells by Hedgehog-inhibitory peptide conjugated with Elastin-like biopolymers
Authors: Ryu Jung Su , Raucher Drazen 
Published: July 2016

Abstract
The Hedgehog(Hh) signaling pathway has been reported to play a pivotal role in cancer. Studies have shown that suppression of this aberrantly activated Hh pathway may be effective in controlling the development and proliferation of many cancers. However, to date, there is no drug in clinical application that can be used to inhibit the Hh signaling pathway and suppress cancer growth.
In attempt to address this problem, we developed a thermally responsive polypeptide inhibitor of the Hh pathway. This polypeptide is derived from a mammalian tropo-elastin protein which will aggregate and accumulate at the tumor site where local hyperthermia is applied. For this study, ELP was fused to a peptide that inhibits Hh signaling by blocking interaction of Sonic Hh ligand (Shh) with the Patch-1 docking site. To improve bioavailability, ELP was further modified by adding the cell penetrating peptide, Tat.
The anti-proliferative activity of Tat-Hhi-ELP was examined in three breast cancer cell lines: MCF7, MDA-MB-231, and SKBR-3. Treatment of the cells with 20 uM of peptide for 2 days resulted in maximally 40% inhibition of cell proliferation. Observed cytotoxicity was further increased two fold by application of hyperthermia.
To validate that Tat-Hhi-ELP is targeting the Hh pathway, we determined the levels of GLI-1, which is a downstream target in the Hh pathway. Treatment of the breast cancer cells with Tat-Hhi-ELP resulted in reduction of GLI-1 levels, indicating that the cytotoxicity is based on hedgehog pathway inhibition. Furthermore, the formation of mammospheres was significantly reduced by treatment with Tat-Hhi-ELP in SKBR-3 cells. These results suggest that thermal targeting of ELP-based Hedgehog inhibitory peptides to breast cancer cells may be an effective and promising treatment strategy against breast cancer stem cells.
Citation Format: Jung Su Ryu, Drazen Raucher. Inhibition of breast cancer stem cells by Hedgehog-inhibitory peptide conjugated with Elastin-like biopolymers. [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 2072.
Abstract 2074: Mangostin-encapsulated PLGA nanoparticles inhibit pancreatic cancer stem cell characteristics by suppressing sonic hedgehog pathway
Authors: Yu Wei , Ma Yiming , Shankar Sharmila , Srivastava Rakesh K. 
Published: July 2016

Abstract
Pancreatic cancer is the fourth leading cause of cancer-related deaths in US, with a 5-year survival rate of approximately 6%. Patients develop resistance to currently used anticancer drugs which are mainly toxic and also demonstrate severe side effects. Cancer stem cells (CSCs) / tumor initiating cells (TICs) have been proposed for tumor initiation, promotion, metastasis, and chemotherapy failure. Thus, there is an urgent need to develop novel strategies for the management of pancreatic cancer. Sonic hedgehog (Shh) pathway has been implicated in pancreatic carcinogenesis and is constitutively active in CSCs. The α-Mangostin is derived from the plant mangosteen (Garcinia mangostana) which is a tropical evergreen tree. Mangosteen contains Mangnoids, such as α-Mangostin, and other phytochemicals. The main objective of the study was to demonstrate the biological activities of α-Mangostin-encapsulated PLGA nanoparticles (Mang-NPs) in human pancreatic CSCs and cells lines. We have also performed docking of α-Mangostin on to the DNA binding sites of Gli to assess whether α-Mangostin disrupts Gli-DNA binding and acts as a Gli inhibitor. Mang-NPs inhibited cell proliferation, colony formation, and induced apoptosis in pancreatic cancer AsPC-1, PANC-1 and Mia-Paca-2 cell lines, and CSCs. However, Mang-NPs had no effect on human pancreatic normal ductal epithelial cells. In addition, Mang-NPs inhibited epithelial to mesenchymal transition. α-Mangostin disrupted Gli-DNA binding activity. Western blot analysis has demonstrated that Mang-NPs inhibited pluripotency maintaining factors Nanog and c-Myc. Furthermore, Mang-NPs inhibited the expression of Gli1, Gli2, Patched1 and Patched2, and Gli transcriptional activity in pancreatic CSCs. Our data demonstrate that Mang-NPs can inhibit pancreatic CSC characteristics by disrupting Gli-DNA binding activity and may act as a Gli transcription inhibitor.
Citation Format: Wei Yu, Yiming Ma, Sharmila Shankar, Rakesh K. Srivastava. Mangostin-encapsulated PLGA nanoparticles inhibit pancreatic cancer stem cell characteristics by suppressing sonic hedgehog 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 2074.