bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3068: MicroRNA 4723-5p is novel tumor suppressor microRNA in prostate cancer that directly regulates Abelson family of nonreceptor protein tyrosine kinases.
Authors: Arora Sumit , Saini Sharanjot , Majid Shahana , Shahryari Varahram , Yamamura Soichiro , Chiyomaru Takeshi , Fukuhara Shinichiro , Chang Inik , Deng Guoren , Tanaka Yuichiro , Dahiya Rajvir
Published: August 2014

The Abelson (c-Abl) proto-oncogene encodes a highly conserved nonreceptor protein tyrosine kinase that has been implicated in many cellular processes including regulation of cell growth and survival, oxidative stress and DNA-damage responses, actin dynamics and cell migration. Aberrant activity of this tyrosine kinase has been implicated in the stimulation of cancer growth and progression. Abl tyrosine kinase represents a target for specific anti-cancer therapy in prostate cancer and Abl inhibitors are being tested clinically for the treatment of prostate cancer bone metastasis. Here we report that Abl kinases are regulated by a novel microRNA- miR-4723-5p in prostate cancer. Expression profiling of miR-4723-5p expression in a cohort of prostate cancer clinical specimens showed that miR-4723-5p expression is widely attenuated in prostate cancer. Low miR-4723-5p expression was significantly correlated with poor survival outcome and tumor progression and recurrence in prostate cancer. Further, our analyses suggest that miR-4723-5p has significant potential as a disease biomarker for diagnosis and prognosis in prostate cancer. To evaluate the functional significance of decreased miR-4723-5p expression in prostate cancer, miR-4723-5p was reintroduced in prostate cancer cell lines followed by functional assays. The over expression of miR-4723-5p led to significant decreases in cell growth, clonability, invasion and migration. Importantly, miR-4723-5p reexpression led to dramatic induction of apoptosis in prostate cancer cell lines suggesting that miR-4723-5p is a pro-apoptotic microRNA that regulates prostate carcinogenesis. Analysis of putative miR-4723-5p targets showed that miR-4723-5p targets Integrin alpha 3 (ITGA3) and Methyl CpG binding protein (MeCP2) in addition to Abl1 and Abl2 kinases. In conclusion, we have identified a novel microRNA mediated regulation of Abl tyrosine kinases in prostate cancer. This study suggests that miR-4723-5p may be an attractive target for therapeutic intervention in prostate cancer.

Citation Format: Sumit Arora, Sharanjot Saini, Shahana Majid, Varahram Shahryari, Soichiro Yamamura, Takeshi Chiyomaru, Shinichiro Fukuhara, Inik Chang, Guoren Deng, Yuichiro Tanaka, Rajvir Dahiya. MicroRNA 4723-5p is novel tumor suppressor microRNA in prostate cancer that directly regulates Abelson family of nonreceptor protein tyrosine kinases. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3068. doi:10.1158/1538-7445.AM2013-3068
Abstract 3069: Pleiotropic tumor suppressor role of microRNA-34b in prostate cancer.
Authors: Majid Shahana , Dar Altaf A. , Saini Sharanjot , Shahryari Varahram , Arora Sumit , Chang Inik , Yamamura Soichiro , Tanaka Yuichiro , Chiyomaru Takeshi , Fukuhara Shinichiro , Deng Guoren , Carroll Peter R. , Dahiya Rajvir
Published: August 2014

CpG island hypermethylation is one of the most common causes of the loss of tumor-suppressor microRNAs (miRNA) in cancers. Here we show that miR-34b is silenced in human prostate cancer (PCa) and the mechanism is through CpG hypermethylation. We provide evidence that miR-34b directly targets methyltransferases (DNMT) and deacetylases (HDACs). We show that miR-34b expression could predict overall survival and recurrence free survival such that patients with high miR-34b levels had longer survival. Further we elucidate the tumor suppressor role of miR-34b using both in vitro and in vivo models. Functionally miR-34b inhibits cell proliferation, colony formation, migration/invasion and triggers G0/G1 cell cycle arrest and apoptosis in cancer cells. The mechanism is partly through the down regulation of AKT pathway as miR-34b directly targets AKT and causes depletion of its downstream genes. Our results show that over-expression of miR-34b caused a decline in the mesenchymal markers Vimentin, ZO1, N-cadherin and Snail whereas there was an increase in E-cadherin expression. Finally we demonstrated the antitumor effect of miR-34b in vivo. MiR-34b caused a dramatic decrease in tumor growth in nude mice compared to cont-miR. These findings offer new insight into the role of miR-34b in the inhibition of prostate cancer through demethylation, active chromatin modification and AKT pathways and may provide a rationale for the development of new strategies targeting epigenetic regulation of miRNAs for the treatment of prostate cancer.

Citation Format: Shahana Majid, Altaf A. Dar, Sharanjot Saini, Varahram Shahryari, Sumit Arora, Inik Chang, Soichiro Yamamura, Yuichiro Tanaka, Takeshi Chiyomaru, Shinichiro Fukuhara, Guoren Deng, Peter R. Carroll, Rajvir Dahiya. Pleiotropic tumor suppressor role of microRNA-34b in prostate cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3069. doi:10.1158/1538-7445.AM2013-3069
Abstract 3085: Expression profiling of exosomal miRNAs derived from human esophageal cancer cells by Solexa high-through sequencing.
Authors: Liao Juan , Liu Ran , Yin Lihong
Published: August 2014

Background: Exosomes are small membrane vesicles of endocytic origin that are released into the extracellular environment on fusion of multivesicular bodies (MVB) with the plasma membrane. Studies showed that inside exosomes, cellular gene products including proteins, mRNAs, and microRNAs (miRNAs) are packaged and these molecules can be transferred to recipient cells to deliver their molecular signaling.

Objective: To explore the miRNA expression profile and distribution characteristics of exosomes derived from human esophageal cancer cells by Solexa high-throughput sequencing.

Methods: Exosomes were extracted from cell culture supernatants by ultracentrifugation. Exosomes were identified by transmission electronic microscopy and western blot assay with anti-CD63 antibody. The types and abundance of known and novel miRNAs in cells and exosomes were identified by Solexa high-throughput sequencing.

Results:There were 56421(2.94%) unique sequences in cells and 7727(0.63%) in exosomes matched the known miRNAs(Table 1). 64 in cells and 32 in exosomes novel miRNAs were predicted. Further analysis revealed extensive sequence variations (isomiRs) of cell and exosome miRNAs. The known miRNAs showed an increased expression in cells compared with exosomes. The expression level of hsa-miR-chr15_4885 and hsa-miR-chr18_7463 in exosomes were significantly higher than cells, with an average fold-change of 10 while hsa-miR-chr7_20613 and hsa-miR-chr19_8205 in cells were significantly higher than exosomes, with an average fold-change of thousands.

Conclusion: The miRNA expression profile in exosomes is different from that in cells. It suggested that the significantly enriched miRNAs in exosomes may be the result of an active uptaken by exosomes. These specific miRNAs expressed in exosomes may play an important role in intercellular communication.

Table 1. Distribution of sequence counts for the different classes of small RNAs in cells and exosomes Classification Unique RNA in cells Percentage (%) in cells Unique RNA in exosomes Percentage (%) in exosomes miRNA 56,421 2.94 7,727 0.63 mRNA 59,655 3.11 5,988 0.49 Repbase 31,421 1.64 5,066 0.41 rRNA 260,307 13.56 85,303 6.95 tRNA 80,635 4.20 119,500 9.74 snRNA 27,935 1.45 1,823 0.15 Unknown RNA 1,403,576 73.10 1,001,499 81.63 Total 1,919,950 100.00 1,226,905 100.00

Citation Format: Juan Liao, Ran Liu, Lihong Yin. Expression profiling of exosomal miRNAs derived from human esophageal cancer cells by Solexa high-through sequencing. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3085. doi:10.1158/1538-7445.AM2013-3085

Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.
Abstract 3086: Modulation of microRNA profile in lung adenocarcinoma cell line following TIMP-1 downregulation.
Authors: Ghoshal-Gupta Sampa , Kutiyanawalla Ammar , Jiwani Shahanawaz , Ojha Juhi , Kolhe Ravindra , Rojiani Amyn M. , Rojiani Mumtaz V.
Published: August 2014

Non-small cell carcinoma accounts for 85% of lung cancer cases and has a 5 year survival rate of only 17%. In recent years, tissue inhibitor of metalloproteinase-1 (TIMP-1) has emerged as an important prognostic marker. In several cancers including non-small cell lung cancer, high serum levels of TIMP-1 have been associated with poor prognosis. Previously, we have shown that overexpressing TIMP-1 in H2009, a lung adenocarcinoma cell line resulted in aggressive tumors when implanted in the mouse brain. In the present study, we have knocked down TIMP-1 expression in the non-small cell lung cancer cell line A549 using shRNA. In vitro assays using the TIMP-1 knockdown clones defined decreased migration in wound assays (p<0.01), as well as reduced invasion (p<0.05) using Boyden chamber assays. We investigated these functional alterations by examining microRNAs in these cell lines. MicroRNAs represent a class of small non-coding RNAs that regulate gene expression at the post-transcriptional level and control crucial signaling and physiological processes functioning either as oncogenes or tumor-suppressors. The miRNA expression profile of A549 cell line and its TIMP1 knockdown clone were evaluated using the Affymetrix miRNA microarray platform on Gene-Chip miRNA 3.0 array in A549 cell line. Following hybridization and data acquisition, we used Partek Genomics Suite ® software for RNA normalization and to determine statistically significant differences in miRNA expression between experimental groups by ANOVA and pairwise comparisons (two-sidedα=0.05). Using the Affymetrix miRNA array we have identified altered miRNAs expression in the clones, with 72 differentially regulated miRNAs following TIMP-1 knockdown. Using quantitative real time PCR we have selectively validated several of the miRNAs that showed the maximal difference. We have confirmed a 2 to 4-fold down regulation of MiR-10b, miR-29a and miR-30 and a 3-fold upregulation of miR-125a-5p. Based on KEGG pathway analysis, this group of validated miRNAs are involved in the MAPK signaling pathway. Western blot analysis showed activation of the apoptosis inducing p38 MAPK pathway in the knockdown clones. Additional mechanistic dissection of these changes and involved pathways will contribute further to our understanding of the role of TIMP-1 in lung cancer. (This research was supported by a Georgia Distinguished Cancer Scholar award to AMR).

Citation Format: Sampa Ghoshal-Gupta, Ammar Kutiyanawalla, Shahanawaz Jiwani, Juhi Ojha, Ravindra Kolhe, Amyn M. Rojiani, Mumtaz V. Rojiani. Modulation of microRNA profile in lung adenocarcinoma cell line following TIMP-1 downregulation. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3086. doi:10.1158/1538-7445.AM2013-3086
Abstract 3101: The Role of MYC and the miR-17∼92 cluster in histone deacetylase inhibitor-induced apoptosis.
Authors: Talbert Dominique R. , Wappel Robert L. , Moran Diarmuid M. , Shell Scott A. , Bacus Sarah S.
Published: August 2014

In recent years histone deacetylase inhibitors (HDACi's) have emerged as promising therapeutics for cancer. While favorable responses to HDACi's as single agents have been shown in several hematological malignancies, very little efficacy has been demonstrated in solid tumors. c-Myc (Myc), an oncoprotein commonly over-expressed in cancer, has been shown by several studies to play a critical role in HDACi-mediated cellular death. To expand upon these findings and determine the role that Myc plays in this process in solid tumors, we compared the effect of two HDAC inhibitors, SAHA and LAQ824, on the proliferation of solid tumor cell lines expressing high versus low levels of Myc. We found that cells expressing high levels of Myc were more sensitive to HDACi. In addition, there were significant differences in the type of response to HDACi treatment between the two cell types with prominent apoptosis in cells expressing higher levels of Myc while cell cycle arrest was more commonly observed in cells expressing lower levels of Myc. Interestingly, HDACi reduced the expression of Myc and one of its well-known oncogenic miRNA targets, miR-17∼92 cluster, resulting in an increase in the expression of the master pro-apoptotic protein Bim. We propose that this novel mechanism may play a role in the potent anti-proliferative effects mediated by HDACi. Furthermore, these studies suggest that Myc expression could be used as a predictive biomarker to select patients with solid tumors who may be more responsive to HDACi treatment.

Citation Format: Dominique R. Talbert, Robert L. Wappel, Diarmuid M. Moran, Scott A. Shell, Sarah S. Bacus. The Role of MYC and the miR-17∼92 cluster in histone deacetylase inhibitor-induced apoptosis. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3101. doi:10.1158/1538-7445.AM2013-3101

Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.
Abstract 3115: Sumoylation enhances the stability of the proto-oncogene EVI1 however negatively regulates its DNA binding and transcriptional activity.
Authors: Singh Sneha , Chakraborty Soumen
Published: August 2014

Aberrant expression of the proto-oncogene EVI1 (Ecotropic virus integration site1) has been implicated not only in lymphoid or myeloid malignancies but also in several other solid tumors like colon, ovarian and breast cancer. Despite its crucial role in oncogenesis, the regulatory factors and mechanisms that control the function of EVI1 are partially known. Post translational modifications play a crucial role in regulating various cellular processes by controlling the function of several proteins. Here we show that EVI1, a transcription factor is post-translationally modified by SUMO1. Indirect immunofluorescence studies revealed that EVI1 and SUMO1 colocalized in the nuclear speckles in the cells transiently transfected with EVI1 and SUMO1 as well as cells that constitutively expresses EVI1. Sumoylation is known to stabilize their target protein which was also observed in case of EVI1 through pulse chase assay with cycloheximide. Reporter gene assay revealed that sumoylation impaired EVI1 mediated transactivation of Bcl-xL and SIRT1 promoters and also reduced the DNA binding efficiency of EVI1 which was confirmed through ChIP assay. PIAS proteins are known as SUMO E3 ligase which enhances the sumoylation of the proteins. PIAS proteins are also known to regulate the function of several proteins independent of its ligase activity. Co-immunoprecipiation assay revealed that EVI1 directly interacts with SUMO E3 ligase PIASy, which was also found to enhance EVI1 sumoylation. Our study also demonstrates that PIASy negatively regulated EVI1 transcription activity which is independent of its ligase activity. Thus PIASy was found to be an interacting partner that regulates the function of EVI1 in sumoylation dependent as well as independent manner. In summary, we present a new modifier of EVI1 which controls its stability and deregulates its transcriptional activity. Further study in context with EVI1-SUMO1-PIASy may give a better idea in understanding the functions and the regulation of EVI1 in normal and diseased cells.

Citation Format: Sneha Singh, Soumen Chakraborty. Sumoylation enhances the stability of the proto-oncogene EVI1 however negatively regulates its DNA binding and transcriptional activity. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3115. doi:10.1158/1538-7445.AM2013-3115
Abstract 312: A mouse model of chronic prostatic inflammation using a human prostate cancer-derived isolate of Propionibacterium acnes.
Authors: Biswal Shinohara Debika , Vaghasia Ajay , Yu Shu-Han , Nelson William G. , De Marzo Angelo M. , Yegnasubramanian Srinivasan , Sfanos Karen S.
Published: August 2014

Background: A causative role for infectious agents and chronic inflammation in prostate cancer etiology has been difficult to establish in humans. To study this potential link in an in vivo system, we have developed a mouse model of long-term bacteria-induced chronic inflammation of the prostate using a prostatectomy-derived strain of Propionibacterium acnes that may be of particular relevance to prostate cancer.

Methods: Prostates of C57BL/6J mice were inoculated, via urethral catheterization, with PBS (control) or a strain of P. acnes (PA2) isolated from human prostatectomy tissues. Animals were assessed at 2 days, 1 week, 2 weeks, or 8 weeks post-inoculation via histology and immunohistochemistry (IHC).

Results: PA2 inoculation resulted in severe acute and chronic inflammation confined to the dorsal lobe of the prostate. Chronic inflammatory infiltrates persisted for at least 8 weeks post-inoculation. Inflammatory lesions were associated with an increase in the Ki-67 proliferative index, and diminished Nkx3.1 and androgen receptor (AR) production. Interestingly, the observed response required live bacteria. Additionally, both IHC and in situ hybridization assays for P. acnes indicated a potential intracellular persistence of P. acnes in prostate epithelial cells.

Conclusions: To our knowledge, this is the first mouse model of long-term prostatic inflammation induced by P. acnes, and more generally, any prostatectomy tissue-derived bacterial isolate. This model may serve as a valuable preclinical model of chronic prostatic inflammation that can be used to mechanistically study the link between inflammation and prostate cancer and other prostate disease.

Citation Format: Debika Biswal Shinohara, Ajay Vaghasia, Shu-Han Yu, William G. Nelson, Angelo M. De Marzo, Srinivasan Yegnasubramanian, Karen S. Sfanos. A mouse model of chronic prostatic inflammation using a human prostate cancer-derived isolate of Propionibacterium acnes. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 312. doi:10.1158/1538-7445.AM2013-312
Abstract 314: Effect of dietary carbohydrates and exercise on prostate cancer progression in LNCaP xenograft model.
Authors: Ge Xiangfeng , Venier Natalie , Fleshner Neil , Klotz Laurence , Venkateswaran Vasundara
Published: August 2014

Introduction: Prostate cancer (PCa) is the second leading cause of death among North American men. There are many risk factors for PCa, dietary as well as physical activity play a role in the development and progression of the disease. Our lab has previously reported that increased intake of dietary carbohydrates was associated with increased tumor growth and activation of signaling pathways distal to the insulin receptor in a murine model of prostate cancer. In humans, one of the most potent stimulants for insulin production is glucose consumption and carbohydrate restriction reduces serum insulin and IGF-I levels to a greater extent than dietary fat restriction. Numerous studies have also found an inverse relationship between exercise and PCa progression. For example, a study by Barnard et al (2003) demonstrated that regular physical activity in PCa patients decreased serum insulin and IGF-I levels, and also elevated IGF binding protein I. However, the exact relationships between diet, exercise and PCa, as well as their underlying mechanisms, are unclear. Herein we aim to investigate the effect of sustained aerobic exercise on PCa tumour growth in animals placed on a high carbohydrate diet.

Methods: Athymic (6 -8 week old) nude mice (n=40) were inoculated subcutaneously with 1 million LNCaP cells. Mice were fed ad libitum with a high-carbohydrate (HC) diet or a low-carbohydrate (LC) diet. Animals were randomized into four groups: HC with and without exercise, LC with and without exercise. Exercise was implemented for 5 days/week (3 x 15 mins; 2-min breaks between cycles; 2.0-10.0 m/min) using a forced exercise wheel. Exercise was performed for a period of 10 weeks. Body weights, tumour volumes, and food consumption were recorded tri-weekly. Blood samples were obtained by sephenous vein bleeding at various times during the study period. Comparisons between groups over time were performed using RANOVA Type 3 Tests of Fixed Effects.

Results: There were no significant differences in animal weight and food consumption between groups. Tumour growth, wet tumour weights were not significantly different between groups. However it was very interesting to note that animals from the exercise group had a slower tumour growth rate compared to animals from the no exercise group.

Citation Format: Xiangfeng Ge, Natalie Venier, Neil Fleshner, Laurence Klotz, Vasundara Venkateswaran. Effect of dietary carbohydrates and exercise on prostate cancer progression in LNCaP xenograft model. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 314. doi:10.1158/1538-7445.AM2013-314
Abstract 3142: Whole genome sequencing of oligodendrogliomas identifies genes mutated at a low frequency that contribute to tumor formation.
Authors: Erdem-Eraslan Lale , de Wit Maurice , Heijsman Daphne , Kremer Andreas , van der Spek Peter J. , Sillevis Smitt Peter A.E. , French Pim J.
Published: August 2014

Background: Causal genetic changes in oligodendrogliomas (OD) with 1p/19q codeletion include mutations in IDH1, IDH2, CIC and FUBP1. Here, we have performed whole genome sequencing on three ODs to determine whether additional genetic changes contribute to tumor formation.

Methods: We performed whole genome sequencing of DNA from 3 ODs grade III with 1p/19q codeletion and matched germline DNA. Targeted resequencing of identified genes was performed in an additional 32 ODs with 1p19q LOH (28/32) or partial loss of 1p (2/32), 19q (2/32). All mutations were validated by Sanger sequencing. Constructs of wildtype and mutated genes were subsequently generated (n=13), fused to GFP for visualization. Established cell lines were created to perform functional analysis.

Results: Whole genome sequencing identified a total of 55 mutations in coding exons (range 8-32 mutations per tumor), including the known molecular abnormalities in IDH1 (2/3), IDH2 (1/3), CIC (2/3) and FUBP1 (1/3). Mutations in the ATRX gene were not identified. In addition to these known genes, we identified mutations in additional genes, most of which were previously not implicated in ODs. We first examined the mutation frequency of these genes in an additional 32 tumors. No additional mutations were identified. We then performed functional analysis on a subset of these mutations. For ZNF238, we observed a difference in the sub cellular localization between wildtype and mutant contructs; the wildtype protein localized to the nucleus while the mutant protein is present in the cytoplasm. In addition, stably transfected ZNF238 mutant cell line shows increased proliferation compared to wildtype.

Conclusion: Our results confirm that mutations in IDH, CIC and FUBP1 are present at high frequency in oligodendrogliomas with 1p/19q loss. Functional analysis of infrequently mutated genes provide evidence that they contribute to oncogenesis.

Citation Format: Lale Erdem-Eraslan, Maurice de Wit, Daphne Heijsman, Andreas Kremer, Peter J. van der Spek, Peter A.E. Sillevis Smitt, Pim J. French. Whole genome sequencing of oligodendrogliomas identifies genes mutated at a low frequency that contribute to tumor formation. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3142. doi:10.1158/1538-7445.AM2013-3142
Abstract 3154: Genomic landscape of metastatic colorectal cancer.
Authors: Krijgsman Oscar , Haan Josien , Carvalho Beatriz , Meijer Gerrit A. , Ylstra Bauke
Published: August 2014

Background: Colorectal cancer (CRC) results from the accumulation of multiple genetic and epigenetic alterations in the genome of colorectal epithelial cells. Next to large genomic DNA copy number changes, small focal alterations can be identified, often enriched for known cancer genes. However, not all tumors present the same pattern of alterations, as CRC is a heterogeneous disease. The varying underlying biology results in different clinical outcomes, such as response to treatment. The present study aimed to document the landscape of DNA copy number changes, with special focus on focal alterations, in primary tumors of a defined subset of colorectal cancer patients who develop metastatic disease and are eligible for systemic treatment. Material and methods: Tumors were selected from mCRC patients, who participated in two Dutch multicenter phase III clinical trials, i.e. CAIRO and CAIRO2 and were treated according to three different regimens . For all patients well-defined clinical data is available. Alterations were analyzed by high-resolution array comparative genomic hybridization (aCGH), with DNA isolated from formalin-fixed paraffin-embedded (FFPE) archival blocks of 349 patients. As a reference matched normal germ-line material was used. In this way only tumor specific alterations were identified. Also, frequent copy number variations present in the general population can be distinguished from actual somatic alterations. Results: Most frequently observed large chromosomal alterations were losses of chromosomes 8p and 18 and gains of chromosomes 7, 8q 13, and 20. Seven genomic regions were significantly associated with progression free survival (PFS). The focal alterations detected are significantly enriched for cancer genes and genes frequently mutated in colorectal cancer. The gene list includes PTEN, TP53, PARK2, A2BP2 and ATBP2 located in focal losses. On focal amplifications known drugtargets such as ERBB2, EGFR and VEGF were found. Conclusion: Based on initial results we hypothesize that DNA copy number profiling may be used for therapy selection and to guide individualized anticancer therapy. Chromosomal copy number alterations in CRC have been related to response to treatment. Moreover focal alterations were enriched for cancer genes. This study was performed within the framework of CTMM, the Center for Translational Molecular Medicine

Citation Format: Oscar Krijgsman, Josien Haan, Beatriz Carvalho, Gerrit A. Meijer, Bauke Ylstra. Genomic landscape of metastatic colorectal cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3154. doi:10.1158/1538-7445.AM2013-3154
Abstract 3163: ZMAT3, a signature gene for sporadic osteosarcoma.
Authors: Baciu Cristina , Porat Rinnat , Pienkowska Margaret , Alon Noa , Wasserman Jonathan , Malkin David
Published: August 2014

Osteosarcoma (OS) is a primary bone malignancy with high incidence in children and young adults. It frequently occurs in patients with strong cancer history (Li-Fraumeni syndrome, retinoblastoma), but the etiology of sporadic OS is still uncertain. The present study is an intensive investigation on susceptibility to sporadic osteosarcoma by genome wide copy number analysis. We evaluated the hypothesis that germline copy number variants (CNVs) could act as a source of genetic susceptibility that may contribute to the development of sporadic osteosarcoma. We analyzed 78 sporadic pediatric OS cases and 2375 controls using Affymetrix SNP 6.0 Array.

Two independent methods, Genotyping Console™ (Affymetrix) and Birdsuite (Broad Institute) were employed to call for CNVs. Outliers with large genomic alterations and TP53 mutations were flagged and filtered out. Both bioinformatics methods show similar distribution of CNVs per chromosome, with slightly higher range depicted by Genotyping Console™, with an enriched set of CNVs in the diseased data. Bioinformatics analysis predicts overlap of copy number variable regions with several candidate genes (PIK3CA, STK11, AKT3, ZMAT3, BAI1), for selected samples. We validated these findings by performing real time quantitative PCR experiments that not only verified most of the computational results, but also identified more amplifications, in an extended selection of samples and regions. The most affected candidate gene, showing gain in 66% of osteosarcoma samples tested, is ZMAT3 (Chr. 3q26.32). A very recent method, digital droplet PCR (BioRAD), with very high sensitivity, also confirms qPCR results, although for a smaller number of samples.

In addition to calling for CNVs, pathways analyses have been also pursued, to address the hypothesis that disruption of multiple genes from the same pathway in the germline of a particular individual may cause susceptibility for developing osteosarcoma. DAVID software predicted several pathways that are enriched, p53 being one of them. Further investigations by KEGG suggest that several genes, including ZMAT3, are disrupted in the p53 signaling pathway. In order to validate these findings, functional assays on osteosarcoma derived lymphoblastoid cell lines are designed and currently in progress. In all, the current study suggests that ZMAT3 could represent a good candidate signature gene for susceptibility to sporadic osteosarcoma.

Citation Format: Cristina Baciu, Rinnat Porat, Margaret Pienkowska, Noa Alon, Jonathan Wasserman, David Malkin. ZMAT3, a signature gene for sporadic osteosarcoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3163. doi:10.1158/1538-7445.AM2013-3163
Abstract 3181: The genomic evolution of prostate cancer under the selective pressure of anti-androgen therapy.
Authors: Gsponer Joël R. , Dietsche Tanja , Rufle Alexander , Lenkiewicz Elisabeth , Zellweger Tobias , Bachmann Alexander , Von Hoff Daniel D. , Barrett M T. , Rentsch Cyrill , Ruiz Christian , Bubendorf Lukas
Published: August 2014

Background: The implementation of novel technologies such as array comparative genomic hybridization (aCGH) and next-generation sequencing has led to a deeper understanding of the genomic nature of cancer. However, these analyses have classically been done without respecting intra-tumor heterogeneity. Here, we applied a methodology that allows us analyzing the genomic profile of distinct tumor populations from individual tumors and their clonal evolution during the progression to castration-resistant disease. Methods: Matched pre- and post- hormone treated fresh frozen and/or formalin fixed prostate cancer samples were selected from our biobank. Clonal tumor populations were flow-sorted according to their nuclear DNA content. Sorted tumor populations were subjected to whole genome CGH and to full exome sequencing analyses by the use of Agilent SurePrint 2x400k microarrays and the SureSelect All Exon Kit, respectively. Results: The genomic analyses of the tumor samples underscore the presence of significant intra-tumoral heterogeneity. The analysis of matched tumor specimens allowed us to identify two particular patterns of tumor evolution during the progression after treatment: First, a more parallel pattern of tumor evolution, in which the ancestor population is breeding multiple aneuploid tumor clones. In this case, only the 2N ancestor population is able to withstand therapy by the acquisition of few specific genomic aberrations whereas the aneuploid populations are eradicated. Second, a more sequential pattern of tumor evolution with a tumor population that evolves out of a continuous line of clones. This population shows increasing signs of genomic instability over time, with a punctual event of chromothripsis (a massive destruction and rearrangement of chromosomal structures) resulting in castration-resistant clonal tumor populations. Conclusions: Genomic profiling of distinct clonal tumor populations during prostate cancer progression allows for analysis of intra-tumoral heterogeneity and the underlying clonal evolution. Importantly, this approach identifies genomic aberrations that were selected for under the pressure of hormone ablation therapy.

Citation Format: Joël R. Gsponer, Tanja Dietsche, Alexander Rufle, Elisabeth Lenkiewicz, Tobias Zellweger, Alexander Bachmann, Daniel D. Von Hoff, M T. Barrett, Cyrill Rentsch, Christian Ruiz, Lukas Bubendorf. The genomic evolution of prostate cancer under the selective pressure of anti-androgen therapy. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3181. doi:10.1158/1538-7445.AM2013-3181
Abstract 3186: Characterizing the antitumor effects of inhibiting translation initiation in glioblastoma multiforme.
Authors: Rajakumar Arjuna K. , Nalbantoglu Josephine
Published: August 2014

Oncogene addiction is the process by which a tumor cell becomes increasingly dependent on the expression of a particular gene for the maintenance of its tumorigenicity. Alleviating this dependence via genetic or pharmacological means may profoundly inhibit tumor growth. However many cancers are not dependent on a single gene for survival. Glioblastoma Multiforme (GBM) presents itself with many genetic aberrations contributing to its aggressive phenotype. These include loss of PTEN, amplification of CDK4 and EGFR among others, making targeting a single genetic node ineffective where other oncogenic networks may buffer any therapeutic benefit. Over the last 10 years it has been shown that targeting protein translation initiation results in the simultaneous targeting of many oncogenic pathways. Translation initiation is highly implicated in tumorigenesis with over 10 initiation factors acting as either proto-oncogenes or tumor suppressors, the most well described being the eIF4E. The overexpression of eIF4E in many cancers results in messenger RNA discrimination giving rise to an increased translation of a subset of oncogenic mRNAs with highly structured 5’UTRs. However the precise role translation initiation plays in maintaining tumorigenicity in GBM and the subsequent anti-neoplastic properties of its inhibition are not known. Here, we characterize the anti-tumor effects of targeting protein translation in three glioblastoma cell lines U87MG, U251N and the highly aggressive U87ΔEGFR, using a small molecule inhibitor of eIF4E, 4EGI-1. We show that 4EGI-1 severely impairs cell survival over a 72 hour time interval, in a dose-dependent manner. This is marked by an arrest of cell proliferation starting at 24 hours, induction of apoptosis at 48 hours with increased annexin V staining and a decrease in cell motility. We found these effects coincide with a decrease in protein expression of several oncogenes with highly structured 5’UTRs after treatment with 4EGI-1 including cell proliferation proteins c-Myc and Cyclin D1 which are completely lost by 48 hours and regulators of apoptosis such as Bcl-xL, Mcl-1 and Survivin which decrease and are lost by 72 hours, while not affecting overall transcription of these genes. Our results demonstrate the sensitivity of gliomas towards inhibition of translation initiation. This further highlights translation regulation control as a strong force in cancer therapy, particularly in glioblastoma where options are limiting.

Citation Format: Arjuna K. Rajakumar, Josephine Nalbantoglu. Characterizing the antitumor effects of inhibiting translation initiation in glioblastoma multiforme. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3186. doi:10.1158/1538-7445.AM2013-3186
Abstract 3187: Nucleolin-induced cap-independent translational pathway involved in Sp1 accumulation in tumorigenesis.
Authors: Hsu Tsung-I , Hung Jan-Jong , Chang Wen-Chang
Published: August 2014

Sp1 is a transcriptional factor to regulate numbers genes related to cell proliferation, apoptosis and tumor progression. Previous studies indicate that Sp1 is induced significantly through modulating its transcriptional activity and protein stability. To detail study the level of Sp1 protein and mRNA in tumorigenesis found that Sp1 mRNA was just increased a little, but Sp1 protein was increased dramatically, implying that enhancement of translational activity by nucleion might be important in the Sp1 accumulation in tumor progression. Here we found a Y-shift motif within the 5’-UTR of the Sp1 mRNA, and to study the contribution in Sp1 level found that the 5’-URT could enhance the translational efficiency of Sp1. Using this Y-shift motif as a probe fished the interacted proteins. Several RNA binding proteins were identified by LC/MS/MS, and nucleolin is one of them. To further address the effect of nucleolin in Sp1 induction found that nucleolin overexpression did not alter the level of Sp1 mRNA, but increased the translational activity obviously. In addition, the signal transduction pathway was also studied, and found that EGFR and Kras pathways might be involved in the induction in the cap-independent pathway in Sp1 induction in tumorigenesis. Taken the previous studies and this study together, during tumor formation, several strategies including increasing the transcriptional activity, protein stability and translational efficiency were used to induce the Sp1 level to regulate many oncogenes to enhance the cancer progression.

Keywords: Nucleolin, Sp1, Cap-independent pathway,

Citation Format: Tsung-I Hsu, Jan-Jong Hung, Wen-Chang Chang. Nucleolin-induced cap-independent translational pathway involved in Sp1 accumulation in tumorigenesis. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3187. doi:10.1158/1538-7445.AM2013-3187
Abstract 3190: Inhibition of the translation of A-myb mRNA by tumor suppressor protein Pdcd4.
Authors: Biyanee Abhiruchi , Klempnauer Karl-Heinz
Published: August 2014

Pdcd4 (Programmed cell death protein 4) was first identified as a protein to be expressed during apoptosis. Later it was shown that Pdcd4 acts as a tumor suppressor protein and regulates the cellular processes on various levels, encompassing transcription and translation. Pdcd4 interacts with the translation initiation factor eIF4A and inhibits its helicase activity which is required to unwind secondary structures in the 5’UTRs of mRNAs. Previous studies on artificial mRNAs have revealed that it inhibits the translation of mRNAs with secondary structures in their 5’ UTRs. Recently, c-myb mRNA was identified as a natural target RNA of Pdcd4. A-myb is a member of the myb family which is expressed in certain hematopoietic cells, such as B-cells, but also in certain non-hematopoietic cells. We have observed that Pdcd4 inhibits the translation of A-myb mRNA in co-transfection experiments using Pdcd4 expression vectors as well as on the endogenous level, as demonstrated by the analysis of a Pdcd4 knock-out model in the Chicken B-cell line DT40. We found that a mutant of Pdcd4 which no longer interacts with eIF4 is still able to inbihit the translation of A-myb RNA, suggesting that Pdcd4 acts in an eIF4A independent manner and contradicting the current view of how Pdcd4 suppresses translation. Similar to the situation in the case of c-myb RNA we have localized the Pdcd4 responsive region in the coding region of A-myb mRNA. We therefore conclude that Pdcd4 suppresses the translation of A-myb RNA by a novel mechanism. Ribosome density profiling technique is widely used nowadays to explore the topography of the various stages of translation. Currently we aim to exploit the technique of ribosome density profiling to further understand how Pdcd4 affects the translation of A-myb RNA.

Citation Format: Abhiruchi Biyanee, Karl-Heinz Klempnauer. Inhibition of the translation of A-myb mRNA by tumor suppressor protein Pdcd4. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3190. doi:10.1158/1538-7445.AM2013-3190
Abstract 320: New metastatic murine prostate cancer cell lines and preclinical model of human prostate cancer.
Authors: Ju Xiaoming , Pestell Richard G.
Published: August 2014

Defining oncogene-specific molecular pathways required for the induction and maintenance of prostate cancer is essential for the rational design of new therapies. Identifying molecular predictors of prostate cancer patient survival is important for patient therapeutic substratification.

We generated murine prostate cancer cell lines via selective transduction with a single oncogene (c-Myc, Ha-Ras, NeuT, and v-Src). These cell lines demonstrate contact-independent growth characteristics in soft agar, and have the substantial growth advantage over primary prostate epithelial cells. Each of the prostate lines grew tumor in immune competent mice after subcutaneous injection, and develop lung metastasis in c-Myc, Ha-Ras, and v-Src cell line groups. RNA samples were prepared from the these cell lines, Microarray analysis identified a total of 2635 out of 22115 genes that were significantly altered in expression (at least two-fold change) in oncogene over-expressing cell lines when compared with prostate epithelial cell control samples. The distinct oncogene expression signature was compared to gene signatures obtained from other published databases to identify similarities to human prostate cancer phenotypes. Comparisons were performed against gene signatures representative of differential expression in advanced state vs. early stage prostate cancer, high grade vs low grade prostate cancer, recurrent vs. nonrecurrent, the results indicate a significant degree of similarity between the prostate oncogene expression signature and high-grade disease; between the oncogene expression signature and the advanced stage disease phenotype. Interrogation of two distinct cohorts of Prostate cancer patient samples using the oncogene signature demonstrated an ability to distinguish tumor from normal prostate with a predictive value for prostate cancer of 98 - 99%. The signature provided in blinded study independent substratification of reduced recurrence free survival by Kaplan-Meier analysis.

The generation of new oncogene-specific prostate cancer cell lines that recapitulate human prostate cancer gene expression, that metastasize in immune-competent mice, are a valuable new resource for testing targeted therapy. The molecular signatures identified herein provide further value over current markers of prediction and outcome.

Citation Format: Xiaoming Ju, Richard G. Pestell. New metastatic murine prostate cancer cell lines and preclinical model of human prostate cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 320. doi:10.1158/1538-7445.AM2013-320
Abstract 322: Dual targeting of the PI3K/mTOR pathways by PF-04691502 or PF-05212384 exhibits therapeutic effects against the metastatic disease progression in the Ovcar 3 disseminated model.
Authors: Yan Zhengming , Fang Douglas , Simmons Brett , Yuan Jing , Kan Julie , Zhang Cathy C.
Published: August 2014

Ovarian cancer has the highest mortality rate of all gynecological cancers primarily due to the high incidence of metastatic spread prior to diagnosis. Understanding the biology of this malignancy and developing models that reflect the patient disease phenotype will create better pre-clinical opportunities for testing targeted therapy. We used the Ovcar 3 cell line to establish a metastasis model through serial in vivo passage. The dual PI3K/mTOR inhibitors PF-04691502 and PF-05212384 were then investigated in this model for their therapeutic effect against metastatic disease progression. Notably, the stromal environment and tumor initiating subpopulation play critical roles on the Ovcar 3MET disease invasiveness and progression. Based on the molecular profile, these invasive Ovcar 3MET cells exhibited a more EMT phenotype when compared to parental cells. Impairing PI3K/mTOR pathway with the dual PI3K/mTOR inhibitors resulted in significant anti-metastatic activity and increased survival in the Ovcar 3MET model. Serum CA125 level, which is a validated clinical marker, correlated with anatomic measurement of tumor burdens via BLI and mouse survival time in these studies, providing means for longitudinal monitoring of disease progression and response to therapy. In addition, using ex vivo tumorsphere analysis under serum-free condition, both PF-04691502 and PF-05212384 demonstrated robust activity against the self-renewal ability of Ovcar 3 tumor cells. In summary, this translational tumor model may serve as a valuable tool for testing targeted therapies such as PI3K/mTOR inhibitors for their ability to impact progression of metastatic ovarian disease.

Citation Format: Zhengming Yan, Douglas Fang, Brett Simmons, Jing Yuan, Julie Kan, Cathy C. Zhang. Dual targeting of the PI3K/mTOR pathways by PF-04691502 or PF-05212384 exhibits therapeutic effects against the metastatic disease progression in the Ovcar 3 disseminated model. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 322. doi:10.1158/1538-7445.AM2013-322