bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2160: PTEN deletion is associated with metastatic disease and worse prognosis in pancreatic cancer
Authors: Wartenberg Martin , Centeno Irene , Zlobec Inti , Lugli Alessandro , Perren Aurel , Karamitopoulou Eva
Published: August 2015

Background: PTEN is a tumor suppressor gene encoding a phosphatase. PTEN inactivation is a frequent event in cancer, occurring through various genetic and epigenetic alterations. Here we investigate the role of PTEN alterations in the microenvironment of ductal pancreatic adenocarcinoma (PDAC).

Methods: Presence of PTEN was investigated by immunohistochemistry and mRNA-in-situ-hybridization (mRNA-ISH) by using multi-punch tissue microarrays (TMAs)containing at least 4 punches per tumor, in a set of 120 well characterized PDACs with full clinicopathological information. Expression was assessed separately in tumor and stromal cells. Multiplex ligation-dependent probe amplification (MLPA) of DNA probes to identify loss of heterozygosity (LOH) of the PTEN gene was additionally performed in 61 cases. Results were correlated with clinicopathological features including survival of the patients.

Results: Loss of PTEN protein (i.e. average immunohistochemical expression in <10% of the neoplastic cells across all tumor punches) was found in 62% of PDAC cases, mostly paralleled by the results of mRNA-ISH. In 22.2% of the cases PTEN protein and/or mRNA loss was additionally observed in the tumor stroma. Interestingly, protein loss in the stromal cells was associated with distant metastasis (p = 0.0045). MLPA identified PTEN LOH (all exons or only exon 1) in 51% of all examined cases and in 73.5% of the cases with PTEN protein/mRNA loss. The occurrence of PTEN LOH was slightly more frequent among cases with concomitant PTEN protein loss in tumor and stromal cells (80%). PTEN LOH as identified by MLPA was associated with higher tumor grade (p = 0.0412), vascular invasion (p = 0.0176), presence of distant metastases (p = 0.0082) and decreased overall survival (p = 0.0127). In 26.5% of the cases with PTEN protein/mRNA loss, no PTEN deletion could be found suggesting occurrence of other genetic changes or epigenetic mechanisms.

Conclusion: PTEN LOH is a major cause of PTEN loss in PDAC and is associated with aggressive tumor characteristics and worse patient prognosis. This is intensified by concomitant PTEN loss in tumor and stromal cells.

Citation Format: Martin Wartenberg, Irene Centeno, Inti Zlobec, Alessandro Lugli, Aurel Perren, Eva Karamitopoulou. PTEN deletion is associated with metastatic disease and worse prognosis in pancreatic cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2160. doi:10.1158/1538-7445.AM2015-2160
Abstract 2166: Analyses of protein expression of PI 3-kinase/AKT signaling in response to altered expression of motor protein MYO1C
Authors: Visuttijai Kittichate , Ejeskär Katarina , Behboudi Afrouz
Published: August 2015

In the previous work, a minimal region of recurrent deletion distal to the Tp53 gene was identified in BDII rat model for endometrial adenocarcinoma and the MYO1C gene was singled out as the tumor suppressor candidate in this region. Myo1c can bind to PIP2, the substrate of PI3-kinase, as well as to the mTOR complex, indicating a role for MYO1C in the PI3-kinase pathway. In this study, we assessed protein levels of 12 members of PI3-kinase/AKT signaling pathways in transient transfected HeLa cells expressing increasing amounts of MYO1C using Western blotting and densitometry analyses. Results revealed decreased protein levels of PTEN, AKT, and phosphorylated AKT, at both residues T308 and S473, and an increased expression of p110α protein in the cells transfected with the MYO1C gene expression constructs compared to the control cells transfected with empty plasmid. We next investigated potential effect of MYO1C protein depletion on serum-induced activation (phosphorylation) of AKT in the MCF10A cells that has de novo expression of MYO1C protein. Following serum stimulation, AKT was rapidly phosphorylated in its residue S473 (pAKTS473) in the cells transfected with MYO1C-siRNA, but with significantly lesser extent in the control cells. Overall, a negative correlation between the protein expression of MYO1C and AKT expression/activation was suggested, signifying a role for MYO1C as a negative regulator of PI3-kinsase/AKT signaling pathway. This is in agreement with the initial hypothesis of involvement of MYO1C in tumorigenesis pathways through its potential tumor suppressor activity. Further studies are required to fully understand the functional contribution of MYO1C to tumor development.

Citation Format: Kittichate Visuttijai, Katarina Ejeskär, Afrouz Behboudi. Analyses of protein expression of PI 3-kinase/AKT signaling in response to altered expression of motor protein MYO1C. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2166. doi:10.1158/1538-7445.AM2015-2166
Abstract 2168: BC-BET: an online bladder cancer biomarker evaluation tool
Authors: Dancik Garrett
Published: August 2015

Cancer is a genetic disease whose biology is driven by mutated and abnormally expressed genes. In the past ∼15 years, the identification of diagnostic and prognostic biomarkers from genomic data has increased our understanding of cancer biology and has led to advances in the personalized treatment of many cancers. Despite these advances, however, there are no clinically approved biomarkers for the treatment of bladder cancer, which is the fourth most common cancer in males in the United States and one of the most expensive cancers to treat.

Although gene expression profiles of bladder cancer patients are publicly available, their analysis is time-consuming and requires computational resources and bioinformatics expertise often not available to biologists or clinician-researchers. Here we describe BC-BET, an online Bladder Cancer Biomarker Evaluation Tool for evaluating candidate diagnostic and prognostic biomarkers in bladder cancer.

The BC-BET database contains gene expression data collected from 11 publicly available patient cohorts (N = 1041). For a chosen gene, BC-BET evaluates whether the gene is differentially expressed (P < 0.05) between normal cells and tumors, between low-grade (LG) and high-grade (HG) tumors, and between non-muscle invasive (NMI) and muscle invasive (MI) tumors. Survival analysis is carried out to evaluate whether gene expression is significantly associated with survival in all patients, or in clinically important subsets of patients with NMI, LG tumors, or in patients with MI, HG tumors. Results are summarized graphically and can be downloaded in an Excel spreadsheet. A user can also look at the relative expression of a gene or the correlation between the expression of two genes across 40 bladder cancer cell lines.

This tool is freely available to the cancer research community and will be updated as additional bladder cancer biomarker data becomes available. BC-BET is available from http://bioinformatics.easternct.edu.

Citation Format: Garrett Dancik. BC-BET: an online bladder cancer biomarker evaluation tool. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2168. doi:10.1158/1538-7445.AM2015-2168
Abstract 2178: Comparison and interpretation of variants in RNA and DNA from sarcoma cancer sample
Authors: Øster Bodil , Joecker Anika , Yip Rupert , Schacherer Frank , Basset Douglas , Salter Donald , Hayward Richard L. , Hupp Ted R.
Published: August 2015

Identification and interpretation of somatic variants using DNA from matched tumor/normal pairs is crucial for understanding the mechanisms behind cancer.

Studies have shown that a large proportion of variants present in the DNA are not present in the RNA and vice versa due to RNA-editing and other unknown molecular processes. In addition, recent publications show that RNA-editing plays an important role in cancer. These findings can have strong implications for clinical diagnostics where correct identification and interpretation of somatic variants from matched tumor/normal samples is essential.

In this study we will investigate somatic variants that are only present in the DNA or the RNA of pleomorphic undifferentiated sarcoma. For this approach we will first identify somatic variants in the DNA using Exome Sequencing data and in the RNA using RNA-Seq data from a matched tumor/normal pair. Somatic variants in DNA as well as RNA are then again filtered for germline variants using the DNA of the normal sample and the RNA of the normal sample. Somatic variants found in only DNA or only RNA are further investigated using Ingenuity's large Knowledge Base as well as HGMD and PGMD. We will show which class of proteins is mainly affected by the RNA editing events and which pathways are mainly affected. We will also highlight implications for clinical diagnostics using DNA only.

The complete analysis will be done using the new integrated QIAGEN tool suite of CLC Cancer Research Workbench, Ingenuity Variant Analysis and Biobase Genome Trax.

Citation Format: Bodil Øster, Anika Joecker, Rupert Yip, Frank Schacherer, Douglas Basset, Donald Salter, Richard L. Hayward, Ted R. Hupp. Comparison and interpretation of variants in RNA and DNA from sarcoma cancer sample. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2178. doi:10.1158/1538-7445.AM2015-2178
Abstract 2185: Informatics framework for clustering and deriving gene signatures for prognostic stratification of cancer patients
Authors: Jung Segun , Bi Yingtao , Davuluri Ramana V.
Published: August 2015

Stratification of cancer patients into different molecular groups is essential for developing targeted therapies. High-throughput technologies, such as microarrays and next-generation sequencing, have been extensively used for generating multi-omics data. Indeed, The Cancer Genome Atlas (TCGA) consortium, one of the most comprehensive and popular databases of cancer, has been accumulating large volumes of invaluable data for more than 30 cancer types, offering unprecedented opportunity to attain new insights in cancer biology. Despite the technological advances, analyzing, integrating and translating the gene signatures across different platforms remains a computationally challenging task.

Here, we developed a novel computational framework that integrates genomic and clinical data to stratify cancer patients into different molecular subgroups and predict clinically applicable phenotypes, such as survival. Application of this user-friendly framework derives platform-independent isoform-level gene signatures that can be translated from high-dimensional platforms (e.g., RNA-Seq) to clinically adaptable low-dimensional molecular assays (e.g., RT-PCR) for prognostic stratification. We applied the pipeline on two TCGA lung cancer datasets_Lung Adenocarcinoma (LUAD) and Lung Squamous Cell Carcinoma (LUSC). Using independent test data, we achieved about 93% (LUAD) and 98% (LUSC) classification accuracy using less than 70 isoform-level gene signature. The proposed informatics platform is applicable to other cancer types in TCGA data portal.

Note: This abstract was not presented at the meeting.

Citation Format: Segun Jung, Yingtao Bi, Ramana V. Davuluri. Informatics framework for clustering and deriving gene signatures for prognostic stratification of cancer patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2185. doi:10.1158/1538-7445.AM2015-2185
Abstract 2195: A high-throughput chemical screen identifies synergistic activity between crizotinib and transcriptional CDK inhibitors in ALK-mutated neuroblastoma
Authors: Moore Nathan F. , Chipumuro Edmond , Hatheway Clark M. , Zhang Tinghu , Gray Nathanael S. , George Rani E.
Published: August 2015

Activating mutations in the anaplastic lymphoma receptor tyrosine kinase (ALK) represent important therapeutic targets in neuroblastoma (NB). One of the more common mutations, ALKF1174L, is sensitive to the FDA-approved ALK inhibitor, crizotinib, only at high doses and mediates acquired resistance to crizotinib in ALK-rearranged cancers. To identify compounds that would potentiate the effect of crizotinib, we performed a high-throughput compound screen using ALKF1174L-dependent human NB SH-SY5Y cells and compared viability between cells treated with the screen compound alone and in combination with crizotinib. The strongest “hits” among the ∼8,000 compounds screened were inhibitors of cyclin dependent kinases (CDKs). The combination of crizotinib and two candidate pan-selective CDK inhibitors, AT7519 and SNS-032 resulted in synergistic activity with significantly increased apoptosis over that of either single agent alone. This effect was observed in NB cells expressing not only ALKF1174L, but also in those expressing ALKR1275Q, the most common NB-associated ALK mutation. Synergy was also seen with ceritinib (LDK378), a structurally unrelated ALK inhibitor, in combination with both AT7519 and SNS-032. We determined that the synergistic effect was mediated preferentially through the transcriptional, rather than the cell cycle activity of these CDK inhibitors, denoted by absence of cell cycle arrest, stalling of RNA polymerase II at representative gene promoters, and loss of Pol II phosphorylation at the transcription elongation marker serine 2 in treated cells. These findings were comparable with results obtained using agents that were highly selective for CDK9 or CDK7, CDKs with roles in transcription regulation. Finally, in murine xenogaft models of ALK-mutated NB, the combination resulted in inhibition of tumor growth and prolongation of survival compared to single agents alone. Together, these data support further pre-clinical and clinical efforts to explore the therapeutic potential of combining ALK inhibitors with transcriptional CDK inhibitors in ALK-mutated NB.

Citation Format: Nathan F. Moore, Edmond Chipumuro, Clark M. Hatheway, Tinghu Zhang, Nathanael S. Gray, Rani E. George. A high-throughput chemical screen identifies synergistic activity between crizotinib and transcriptional CDK inhibitors in ALK-mutated neuroblastoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2195. doi:10.1158/1538-7445.AM2015-2195
Abstract 2213: Evaluation of bias associated with high-multiplex, target-specific pre-amplification
Authors: Okino Steven T. , Kong Michelle , Wang Yan T.
Published: August 2015

We developed a novel PCR-based pre-amplification (PreAmp) technology that can increase the abundance of over 350 target genes one million-fold. To assess potential bias introduced by PreAmp we utilized ERCC RNA reference standards, a model system that quantifies measurement error in RNA analysis. We assessed three types of bias: amplification bias, dynamic range bias and fold-change bias. We show that our PreAmp workflow does not introduce significant amplification and fold-change bias under stringent conditions. We do detect dynamic range bias if a target gene is highly abundant and PreAmp occurred for 16 or more PCR cycles; however, this type of bias is correctable. To validate PreAmp performance in an actual gene expression profiling experiment, we analyzed a panel of genes that are regulated during differentiation using the NTera2 stem cell model system. We find that results generated using PreAmp are statistically equivalent to results obtained using standard qPCR without the pre-amplification step. Importantly, PreAmp maintains patterns of gene expression changes across samples; the same biological insights would be derived from a PreAmp experiment as with a standard gene expression profiling experiment. Our PreAmp technology can facilitate accurate analysis of extremely limited samples in gene expression profiling experiments.

Citation Format: Steven T. Okino, Michelle Kong, Yan T. Wang. Evaluation of bias associated with high-multiplex, target-specific pre-amplification. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2213. doi:10.1158/1538-7445.AM2015-2213
Abstract 2214: Dynamic transcriptome analysis of DNA damage pathways under hypoxia
Authors: Lo Winnie W. , Zafarana Gaetano , Bristow Robert G.
Published: August 2015

During the outgrowth of tumor, gradients of hypoxic regions develop due to reduced oxygen diffusion. Intratumoral hypoxia is a prognostic factor associated with decreased disease-free survival and increased resistance to radiotherapy and chemotherapy in different solid cancers. We have previously shown that chronic hypoxia suppresses DNA damage repair pathways partly through decreased protein translation efficiency. The RNA levels of repair pathway genes have also been shown to be downregulated in hypoxia; however, most of the RNA studies do not distinguish between RNA synthesis and degradation. Here, we use novel metabolic labeling of newly synthesized RNA to investigate the dynamic changes in transcription rates of DNA damage repair pathways under hypoxia.

4-thiouridine (4sU), a uridine analogue, was added to the media of DU145 cells (prostate cancer cell line) that have been cultured in 21% or 0.2% oxygen concentrations for 72 hours. Total RNA was extracted and 4sU-tagged RNA was biotinylated and separated from untagged pre-existing RNA using streptavidin coated magnetic beads. Real-time RT-PCR was used to quantify the expression of repair pathways in three RNA subsets (total, pre-existing, and newly synthesized). Parallel experiments were performed in RNA harvested from the cytoplasmic and nuclear factions of cells.

We found that with 30-minute 4sU incubation, most 4sU-tagged RNA is still in the nucleus, and is subjected to little degradation, thus reflecting the average transcription rate. The percentage of newly synthesized RNA is lower in hypoxic than in normoxic cells. Importantly, the transcript levels of homologous recombination (HR) repair pathway regulators, RAD51, BRCA1 and BRCA2, are decreased in both total and newly-synthesized RNA of hypoxic cells. Our results demonstrate that in addition to translational regulation, hypoxia may also downregulate repair pathways through suppression of transcription. This 4sU assay provides opportunities for further analysis of differential RNA synthesis and decay of DNA damage repair pathways between hypoxia and normoxia.

Citation Format: Winnie W. Lo, Gaetano Zafarana, Robert G. Bristow. Dynamic transcriptome analysis of DNA damage pathways under hypoxia. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2214. doi:10.1158/1538-7445.AM2015-2214
Abstract 228: A novel device to perform rapid high-throughput in vivo drug sensitivity testing and identify optimal drug therapy for personalized cancer treatment
Authors: Jonas Oliver
Published: August 2015

We have developed an implantable device that can perform drug sensitivity testing of a large number of anti-cancer agents inside the living tumor. This device contains reservoirs that release microdoses of single agents or drug combinations into distinct spatial regions of the tumor in local concentrations that are representative of concentrations achieved during systemic drug treatment. Local efficacy and drug concentration profile are evaluated for each drug or combination on the device, and the local efficacy was confirmed to be an excellent predictor of systemic efficacy across multiple drugs and tumor models.

Currently up to 16 individual drugs or combinations can be assessed independently, without systemic drug exposure, through minimally invasive biopsy of a small region of a single tumor. Moreover, this assay takes into consideration physiologic effects that contribute to drug response by allowing drugs to interact with the living tumor in its native microenvironment. Because these effects are crucial to predicting drug response we envision that these devices will help identify optimal drug therapy before systemic treatment is initiated and could significantly extend drug response prediction beyond the predictive biomarkers used today. These devices may also potentially be used in clinical drug development to safely gather efficacy data on new compounds before pharmacological optimization.

Note: This abstract was not presented at the meeting.

Citation Format: Oliver Jonas. A novel device to perform rapid high-throughput in vivo drug sensitivity testing and identify optimal drug therapy for personalized cancer treatment. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 228. doi:10.1158/1538-7445.AM2015-228
Abstract 2287: A model system to treat T-cell acute lymphoblastic leukemia with JAK inhibitors
Authors: Senkevitch Emilee , Hixon Julie , Li Wenqing , Durum Scott
Published: August 2015

The IL-7 Receptor signaling pathway is necessary for the proliferation and survival of T cells. Together with collaborators, we have shown that 9% of patients with T cell acute lymphoblastic leukemia (T-ALL) have gain of function mutations in IL-7R exon 6. These mutations promote homodimerization of IL-7Rα subunits, resulting in constitutive activation of this pathway via JAK1. Approximately 20% of T-ALL patients fail to respond to conventional chemotherapy, so there is a need for additional options for these patients. We hypothesized that JAK inhibitors could be used to treat T-ALL patients, particularly those with IL-7R mutations. We established a cell line model of T-ALL driven by constitutive IL-7R signaling which grew as a leukemia in RAG1-/- mice. The model cells were established by transforming the D1 thymocyte cell line with a mutated IL-7Rα derived from a patient sequence. These cells termed D1_hIL7R_P1 are also GFP+ which allows us to monitor the proliferation of the cells in vivo. D1_hIL7R_P1 cells delivered intravenously result in an aggressive leukemia with morbidity within 18-21 days. Currently we are studying the chemotherapeutic effects of two JAK inhibitors, Ruxolitinib and Tofacitinib on T-ALL. The maximum tolerated doses for Tofacitinib and Ruxolitinib are 50 mg/kg and 150 mg/kg, respectively. Ruxolitinib appears to be the most effective, showing a reduction of leukemogenesis detected in blood and tissues after just three days of oral treatment. Additionally, we have obtained samples derived from pediatric T-ALL patients. Once growth kinetics in NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mice is established, we will proceed to study the efficacy of the JAK inhibitors with human leukemia cells.

Citation Format: Emilee Senkevitch, Julie Hixon, Wenqing Li, Scott Durum. A model system to treat T-cell acute lymphoblastic leukemia with JAK inhibitors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2287. doi:10.1158/1538-7445.AM2015-2287
Abstract 2290: More than a biomarker: Studying the role of vimentin in lung cancer metastasis
Authors: Salgueiro Alessandra M. , Gilbert-Ross Melissa , Havel Lauren S. , Shupe John , Marcus Adam I.
Published: August 2015

A major mechanism of metastasis is the epithelial to mesenchymal transition (EMT) where epithelial cells from the primary site undergo genetic and epigenetic alterations to become motile and mesenchymal. A canonical marker of EMT and a clinical marker of metastasis is the intermediate filament protein, vimentin. Vimentin expression correlates with increased metastatic potential and poor patient prognosis across most solid tumor types including lung, prostate, and breast cancers; however little is known about how vimentin functions to promote the metastatic cascade. Here we use a lung cancer mouse model to study the role of vimentin in lung cancer metastasis in vivo. We have re-developed an LSL-KrasG12D,LKB1fl/fl mouse model whereby intranasal administration of lentiviral Cre recombinase causes a KrasG12D mutation and LKB1 knockout in the lungs. Consequently, about half of the mice that develop primary lung tumors after 10 weeks also develop metastasis to the mediastinal lymph nodes by week 16. We crossed this mouse with a Vim-/- mouse to create a LSL-KrasG12D,LKB1fl/fl, Vim-/- (termed here KLV) mouse to determine if loss of vimentin prevents lung cancer metastasis in this model. Our findings show that the KLV mouse exhibits significantly less metastasis to the mediastinal lymph nodes (12%) as compared with its vimentin wild type counterpart but does not show a decrease in primary tumor formation. These knockout mice also exhibit less focal invasion at the primary tumor site while maintaining a well-differentiated adenocarcinoma histology independent of vimentin genotype. Taken together, our work indicates that vimentin is critical for lung cancer metastasis but not primary tumor formation.

Citation Format: Alessandra M. Salgueiro, Melissa Gilbert-Ross, Lauren S. Havel, John Shupe, Adam I. Marcus. More than a biomarker: Studying the role of vimentin in lung cancer metastasis. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2290. doi:10.1158/1538-7445.AM2015-2290
Abstract 2303: Impact of synbiotics administration on tumorigenesis of colon cancer mouse model
Authors: Saito Yasufumi , Hinoi Takao , Adachi Tomohiro , Shimomura Manabu , Miguchi Masashi , Niitsu Hiroaki , Kochi Masatoshi , Ohdan Hideki , Sentani Kazuhiro , Oue Naohide , Yasui Wataru
Published: August 2015

Introduction:

Previous study showed that Synbiotics might have beneficial effect in human and animal colitis like ulcerative colitis. However, it is not well known that the influence of Synbiotics for tumorigenesis in colon cancer. The aim of present study was to investigate the influence of Synbiotics in colon cancer mouse model and colitis associated cancer mouse model.

Methods:

Mouse stains carrying colon epithelium-preferential Apc mutation (CPC;Apc mice), that show sporadic colorectal adenomas and carcinomas are used in this study. We also used CPC;Apc mice consumed 1%Dextran Sulfate Sodium (DSS) as colitis associated colon cancer model, developing apploximately fourfold more adenomas and adenocarcinomas than CPC;Apc not consumed. At first, 9 of CPC;Apc mice were administerated symbiotics (Probiotics (Lactobacillus) 0.1g + Prebiotics (Oligosaccharide) 10mg/0.3ml/body) between 7 and 20 age in weeks and 10 was not administerated. Secondaly, using 9 of CPC;Apc consumed 1%DSS was administrated Symbiotics, 8 of not administrated, 7 of only Probiotics, and 7 of only Prebiotics. Body weight was measured weekly. Fecal microbial analysis was performed. At sacrifice in 21 age in weeks, the small and large bowel were histologically assessed.

Results:

Synbiotics administration group has no differences of tumorigenesis comparing to control group (tumor incidence rate(88.9%(8/9) vs. 62.5% (5 / 8); control vs. Synbiotics; p = 0.21)average tumor number(3.2 vs. 2.1; p = 0.38), average tumor greatest diameter 5.8 vs. 5.1 mm; p = 0.51). Using CPC;Apc consumed 1%DSS, Symbiotics administration group showed inhibiting morbidity (50% (8 / 16) vs. 80% (8 / 10); control vs. Synbiotics; p = 0.04) and weight loss, and less tumor incidence than control (18.8 vs. 9.6; control vs. Synbiotics; p = 0.01). On the other hands, administration of probiotics or prebiotics alone had no significant differences of tumorigeneis.

Conclusion:

This data suggest that Synbiotics administration may have influence of inhibiting tumorigenesis in the colitis associated colon cancer.

Citation Format: Yasufumi Saito, Takao Hinoi, Tomohiro Adachi, Manabu Shimomura, Masashi Miguchi, Hiroaki Niitsu, Masatoshi Kochi, Hideki Ohdan, Kazuhiro Sentani, Naohide Oue, Wataru Yasui. Impact of synbiotics administration on tumorigenesis of colon cancer mouse model. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2303. doi:10.1158/1538-7445.AM2015-2303
Abstract 2307: Targeted agents and chemotherapeutic treatments of genetically engineered Basal-like breast cancer mouse model
Authors: Contreras Cristina M. , Silva Grace O. , Pfefferle Adam D. , Perou Charles M.
Published: August 2015

Background: Genomic characterization of human breast tumors has resulted in the identification of at least five distinct tumor subtypes (Luminal A and B, HER2-enriched, Claudin-low, and Basal-like). These subtypes each show their own unique biology, which correlates with distinct patient outcomes. Basal-like Breast Cancer (BLBC) is associated with high grade, BRCA1 mutation status, younger patient age, and increased frequency in African Americans. In order to identify novel therapeutic strategies for BLBC, we developed a genetically engineered mouse model based upon two common human BLBC genetic events, namely BRCA1 and TP53 loss.

Results: We developed a genetically engineered mouse (GEM) model of breast cancer by inactivating TP53 and BRCA1 genes using Cre-LOX technology in the mammary gland (K14-cre / TP53 L/L / BRCA1 L/L). As part of the characterization of this GEM model, we performed gene expression profiling and DNA copy number analysis using aCGH arrays on the Basal-like tumors from this model (25/27 total tumors were Basal-like). We found a number of chromosomal regions that were similarly altered and found to be specific to mouse and human BLBC including gains of mouse chromosome 1q and 12q and losses in chromosomes 3F1 and 15q. Subsequently two tumors from the murine Basal-like group were taken and expanded into an orthotopic syngeneic model where they passaged in wild type FVB mice. These two tumors lines were then tested extensively with chemotherapeutics (Doxorubicin, Carboplatin, Cytoxan, Paclitaxel) and biologically targeted agents (MEK inhibitor/AZD6244, PI3K Inhibitor/BEZ235, PARP Inhibitor/ABT888 and mTOR Inhibitor/Everolimus). The DNA damaging agents exhibited exceptional efficacy (i.e. ABT888, Cytoxan, and Carboplatin), whereas the biologically targeted agents tended to at best, only slow tumor growth, even in combination.

Conclusions: Genetic engineering of mice using TP53 and BRCA1 loss results in tumors of predominantly the Basal-like subtype phenotype. As expected, these tumors were exquisitely sensitive to DNA damaging chemotherapeutics including cytoxan and carboplatin, yet generally insensitive to the 3 tested kinase inhibitors. Novel combinations of targeted agents and chemotherapeutics are now being tested.

Citation Format: Cristina M. Contreras, Grace O. Silva, Adam D. Pfefferle, Charles M. Perou. Targeted agents and chemotherapeutic treatments of genetically engineered Basal-like breast cancer mouse model. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2307. doi:10.1158/1538-7445.AM2015-2307
Abstract 2308: The role of LKB1 in development of lung squamous cell carcinoma in mice
Authors: Liu Jian , Cho Sung-Nam , Zhang Yiqun , Creighton Chad J. , DeMayo Francesco J.
Published: August 2015

LKB1 is frequently dysregulated in human lung cancer and has been shown to be one of the critical genes controlling the development of lung squamous cell carcinoma (SCC) in mice1,2. However, it's unclear that the contribution of LKB1 in the development of lung SCC in mice. Here we took advantage of our new enhanced Cre (CCSPiCre) to efficiently deplete Lkb1 in the mouse airway epithelial cells. Although ablation of Lkb1 failed to show any discernable morphological changes, microarray analysis revealed 503 genes and 202 LincRNAs were significantly altered after single ablation of Lkb1. Ingenuity Pathway Analysis (IPA) showed that LXR/RXR activation and inflammatory pathways were significantly dysregulated by ablation of Lkb1. Using the CCSPiCre mouse, we ablated Pten in addition to Lkb1. As previously reported by Xu and coworkers who used Adenoviral delivery of Cre recombinase to achieve Lkb1 and Pten ablation2, the resulting phenotype was SCC while much rapider tumor initiation age, higher mouse metastasis ratio and a worse mortality were observed in this efficient mouse model. Analysis of the tumor development showed progression from mucous cell hyperplasia of the large airways to a papillary transition stage, then to the SCC phenotype. Mice with airway specific loss of Lkb1 and only one allele of Pten (CCSPiCrePtenf/+Lkb1f/f) showed slower tumor progression with the strong metastasis ability to multiple organs, such as liver, uterus, intestine and spleen. Comparison of the microarrays of CCSPiCrePtenf/f and CCSPiCrePtenf/fLkb1f/f in the pretumor stage showed 1463 genes and 339 LincRNAs were significantly altered. Again the major altered pathways were inflammatory and cholesterol biosynthesis. Using this model the developmental progression of lung SCC and the contribution of LKB1 to lung SCC progression were determined.

References

1.

Ji, H., et al. LKB1 modulates lung cancer differentiation and metastasis. Nature 448, 807-810 (2007).

2.

Xu, C., et al. Loss of Lkb1 and Pten leads to lung squamous cell carcinoma with elevated PD-L1 expression. Cancer cell 25, 590-604 (2014).

Citation Format: Jian Liu, Sung-Nam Cho, Yiqun Zhang, Chad J. Creighton, Francesco J. DeMayo. The role of LKB1 in development of lung squamous cell carcinoma in mice. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2308. doi:10.1158/1538-7445.AM2015-2308
Abstract 2320: Prox1 marks a stem cell population that promotes tumor progression in intestinal adenomas
Authors: Wiener Zoltan , Högström Jenny , Hyvönen Ville , Kallio Pauliina , Heino Sarika , Alitalo Kari
Published: August 2015

Colorectal cancer (CRC) initiation and growth is often attributed to stem cells, yet little is known about the regulation of this cell population. We have shown that a subpopulation of cells expressing the Prox1 transcription factor have stem cell activity in intestinal adenomas, but not in the normal intestine. Using in vivo models and 3D ex vivo organoid cultures of mouse adenomas and human CRC, we found that Prox1 deletion reduced the number of stem cells and cell proliferation and decreased intestinal tumor growth in multiple CRC model systems. Loss of Prox1 also decreased autophagy and the survival of hypoxic tumor cells in tumor transplants. Thus, Prox1 is essential for the expansion of the stem cell pool in intestinal adenomas and CRC without being critical for the normal functions of the gut. To further study the adenoma stem cells in relation to the Prox1-positive cell population, we analyzed Apc-mutant intestinal organoids derived from Prox1-CreER; tdTomatoflox/Stop/flox; Apcmin/+ mice. In this lineage tracing model, the induction of Cre activity results in the expression of the red fluorescent protein tdTomato only in the Prox1-positive adenoma cells. FACS sorted tdTomato-positive cell population displayed a highly elevated capability to form new organoids compared to the tdTomato-negative cells, consistent with stem cells enrichment in the Prox1-positive cell population. Gene expression analysis provided new clues about the identity of the Prox1 positive cells.

Citation Format: Zoltan Wiener, Jenny Högström, Ville Hyvönen, Pauliina Kallio, Sarika Heino, Kari Alitalo. Prox1 marks a stem cell population that promotes tumor progression in intestinal adenomas. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2320. doi:10.1158/1538-7445.AM2015-2320
Abstract 2324: The histone acetyltransferase inhibitor CPTH6 selectively targets lung cancer stem-like cells
Authors: Di Martile Marta , Desideri Mariannna , De Luca Teresa , Gabellini Chiara , Eramo Adriana , Milella Michele , Secci Daniela , Carradori Simone , Buglioni Simona , Del Bufalo Donatella , Trisciuoglio Daniela
Published: August 2015

Targeting epigenetic regulators is emerging as a promising strategy for cancer therapy. In this context, we recently identified the thiazole derivative 3-methylcyclopentylidene-[4-(4′-chlorophenyl)thiazol-2-yl]hydrazone (CPTH6) as a novel pCAF and GCN5 histone acetyltransferase inhibitor. CPTH6 exerts in vitro anti-tumoral effect in a panel of human tumor cell lines derived from different histotypes. In this study, we evaluated the efficacy of CPTH6 as a novel drug that targets Lung Cancer Stem-like Cells (LCSC) derived from non-small cell lung cancer (NSCLC) patients. We found that CPTH6 has a stronger growth-inhibitory effect in patient-derived LCSC than in established NSCLC lines. Unlike LCSC models, in which CPTH6 treatment induces cell cycle perturbation and apoptosis even at low doses, in established NSCLC lines CPTH6 triggers a cell cycle perturbation associated to DNA damage only at higher concentrations. Of note, differentiated progeny of LCSC lines are more resistant to CPTH6 cytoxicity when compared to their undifferentiated counterparts. Interestingly, CPTH6 treatment is also associated with reduced expression of the CD133 stemness marker in LCSC lines. Analysis of the CD133+ subpopulation in LCSC lines indicates that CD133+ cells not only undergo apoptosis following CPTH6 treatment but also shift toward a more differentiated phenotype. Furthermore, the growth inhibitory effect seems to be tightly related to baseline expression of acetylated alpha-tubulin, which was particularly prominent in sensitive LCSC lines. In vivo experiments confirmes the antitumor efficacy of CPTH6, particularly in LCSC-derived models, where a pronounced apoptosis induction and growth inhibitory effect is observed after CPTH6 treatment. Overall, our studies propose histone acetyltransferase inhibition as an attractive target for cancer therapy of NSCLC.

Citation Format: Marta Di Martile, Mariannna Desideri, Teresa De Luca, Chiara Gabellini, Adriana Eramo, Michele Milella, Daniela Secci, Simone Carradori, Simona Buglioni, Donatella Del Bufalo, Daniela Trisciuoglio. The histone acetyltransferase inhibitor CPTH6 selectively targets lung cancer stem-like cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2324. doi:10.1158/1538-7445.AM2015-2324
Abstract 2342: Characterization of inflammatory markers and mast cells in association with prostate cancer
Authors: Hempel Heidi , Kulac Ibrahim , Cuka Nathan S. , Cornish Toby C. , Platz Elizabeth A. , DeMarzo Angelo M. , Sfanos Karen S.
Published: August 2015

Evidence suggests that there is a strong association between chronic inflammation and prostate cancer development and/or progression. While chronic inflammation is known to serve as an “enabling characteristic” in many cancers, the mechanism whereby it contributes to carcinogenesis and progression is still very controversial. This is particularly true for cells of the innate immune system, such as mast cells, that have been shown to possess both pro- and anti-tumor properties. The role of mast cells in prostate cancer is of particular interest, as evidence suggests that they influence cancer progression and immune modulation. The current study seeks to characterize mast cell density and mast cell-to-epithelial ratio in relation to prostate cancer recurrence using a unique set of tissue microarrays (TMAs) from a case-control study nested in a cohort of prostate cancer patients who underwent radical prostatectomy. These studies are aided by novel digital image analysis using a software framework integrating whole slide imaging, virtual microscopy, and ImageJ based analysis algorithms. Our preliminary results, obtained via analysis of a prostate cancer TMA containing matched cancer and benign tissues from 727 cases of radical prostatectomy patients, correlated with the literature in that the mast cell density (mast cell number/total tissue area) was significantly higher in cancer versus benign (p = 0.0016). We will expanded this study to determine if mast cell number correlates with epithelial area in the same cohort and to examine mast cell density in correlation to the presence, grade, or progression of prostate cancer. Furthermore, we will be examining this in a large full tissue slide cohort in relation to Gleason grade and stage. Finally, we are expanding this study to explore a possible role for mast cells in the racial disparity in prostate cancer incidence and prognosis.

Citation Format: Heidi Hempel, Ibrahim Kulac, Nathan S. Cuka, Toby C. Cornish, Elizabeth A. Platz, Angelo M. DeMarzo, Karen S. Sfanos. Characterization of inflammatory markers and mast cells in association with prostate cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2342. doi:10.1158/1538-7445.AM2015-2342
Abstract 2361: TGFβ signaling deficiency enhances tumor associated inflammation in colon cancer
Authors: Principe Daniel R. , DeCant Brian , Mangan Riley J. , Wayne Elizabeth A. , Diaz Andrew M. , Vitello Dominic , Munshi Hidayatullah G. , Grippo Paul , Jung Barbara
Published: August 2015

In early colon cancer development, there is considerable evidence suggesting that transforming growth factor-β (TGFβ) serves as a tumor suppressor due to its growth-inhibitory effects in the epithelium. This is in contrast to observations suggesting that in advanced disease, TGFβ promotes tumor progression by contributing to metastasis. Therefore, to better understand the effects of TGFβ signaling on colon cancer, we examined the effect of global or epithelial reduction in TGFβ signaling on tumor progression in the APC murine model of colon cancer. Initially, we examined the relationship between TGFβ signaling and inflammation in human colon cancer specimens. We found that loss of SMAD4 in epithelial cells correlates with increased inflammation in tissue from colon cancer patients. Moreover, APC mice with global TGFBR deficiency (ATG mice) demonstrated increased inflammation that was also associated with loss of SMAD4 in epithelial cells. In contrast, APC mice with epithelial loss of TGFBR signaling (ATC mice) do not demonstrate loss of SMAD4, but have even more pronounced inflammation concomitant with rectal bleeding and prolapse, significant weight loss, the presence of crypt abscesses and lymphoid aggregates, and increased mortality. Similarly, ATC mice, in contrast to the ATG and the APC mice, show markedly increased tumor infiltrating macrophages, splenic macrophages, and serum levels of the cancer-associated cytokines IL8, TGFβ1, and TNFα. Overall, these findings demonstrate that loss of TGFβ signaling, particularly in epithelial cells, dramatically worsens tumor progression. Yet, the attempt to reduce metastasis by treating colon cancer patients with TGFβ inhibitors may result in worse outcome by invoking a robust inflammatory response.

Citation Format: Daniel R. Principe, Brian DeCant, Riley J. Mangan, Elizabeth A. Wayne, Andrew M. Diaz, Dominic Vitello, Hidayatullah G. Munshi, Paul Grippo, Barbara Jung. TGFβ signaling deficiency enhances tumor associated inflammation in colon cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2361. doi:10.1158/1538-7445.AM2015-2361
Abstract 2412: Assessment of clinical applications of circulating tumor DNA using an enhanced TAm-Seq platform
Authors: Lawson Andrew RJ , Plagnol Vincent , Fahem Abdelaziz , Forshew Tim , Brenton James D. , Gale Davina , Rosenfeld Nitzan
Published: August 2015

Novel biomarkers are required to assess tumor burden and response in cancer as conventional biopsies are invasive, costly and only provide a snapshot of the mutational profile at a given time and location. A promising biomarker is the detection of genomic material released from tumors into the blood plasma of patients, known as circulating tumor DNA (ctDNA). ctDNA has been detected in plasma for a wide range of solid tumors and can be distinguished from other (germline) cell-free DNA by the presence of tumor-specific DNA alterations or known hotspot mutations. However, the potential of ctDNA as a biomarker has not yet been fully realized due to technical challenges associated with its detection and analysis, including the short fragment sizes (140-170 bp), small number of amplifiable copies and low/variable allele fractions of ctDNA.

We have developed an enhanced platform for tagged-amplicon deep sequencing (TAm-Seq™). Using a combination of improved library preparation and bespoke data analysis methods, this platform can be used to sequence established cancer hotspots and the entire coding regions of selected genes, while preserving high levels of specificity and sensitivity. Using this approach, we have developed an assay that analyzes ∼20 kb of the genome (including regions of interest in more than 30 genes) with sensitivity down to a few mutant copies. Performance of this assay has been demonstrated using spike-in experiments, dilution series and clinical sample cohorts. Proof of concept studies have shown the potential of ctDNA to be used to assess tumor mutation status, monitor tumor dynamics, assess response to treatment and identify mutations associated with acquired drug resistance and disease progression. This non-invasive approach - a “liquid biopsy” - offers a revolution in how cancer can be detected, monitored and treated.

Citation Format: Andrew RJ Lawson, Vincent Plagnol, Abdelaziz Fahem, Tim Forshew, James D. Brenton, Davina Gale, Nitzan Rosenfeld. Assessment of clinical applications of circulating tumor DNA using an enhanced TAm-Seq platform. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2412. doi:10.1158/1538-7445.AM2015-2412