bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract LB-245: Preclinical study of epigenetic drug-based differentiation therapy for neuroblastoma
Authors: Hattori Naoko , Mori Akiko , Kimura Kana , Kubo Emi , Asada Kiyoshi , Kawamoto Hiroshi , Ushijima Toshikazu 
Published: July 2016

Abstract
Neuroblastoma (NBL) is the most common extracranial solid tumor in children. We previously reported that the CpG island methylator phenotype (CIMP) of NBL was strongly associated with poor prognosis, and also suggested that CIMP may be a possible target for DNA demethylation therapy. Differentiation therapy with 13-cis-retinoic acid has already been established as the standard for high-risk NBLs in the USA.
In this study, we aimed to establish an “epigenetic drug-based differentiation therapy” using a combination of a DNA demethylating agent (5-aza-2’-deoxycytidine: 5-Aza-CdR) and a differentiation agent (tamibarotene: TBT), a new synthetic retinoid. Treatment with 5-Aza-CdR suppressed the growth of 12 NBL cell lines by increasing the number of cells in the S-phase. Genome-wide DNA methylation analysis revealed that 5-Aza-CdR treatment induced global DNA hypomethylation, and that genes related to cell death and neurological processes were enriched as hypomethylated genes, suggesting that DNA demethylation therapy might assist the differentiation agent in inducing neuron differentiation. TBT induced differentiation of five NBL cell lines along with induction of neural extension and upregulation of differentiation markers, such as HOXD4, NGFR, and NTRK1. Pretreatment with 5-Aza-CdR increased the expression levels of differentiation markers, indicating that 5-Aza-CdR enhanced TBT-induced differentiation in vitro. Finally, the tumor suppression effect of 5-Aza-CdR and TBT in vivo was investigated using a mouse xenograft model of KELLY and NB-1 cell lines. Although a synergistic effect of 5-Aza-CdR and TBT was not apparent, they could induce significant tumor regression without severe side-effects.
From these data, we concluded that 5-Aza-CdR and TBT had antitumor activity in vitro and in vivo, and that epigenetic drug-based differentiation therapy is a promising therapeutic strategy for NBL.
Citation Format: Naoko Hattori, Akiko Mori, Kana Kimura, Emi Kubo, Kiyoshi Asada, Hiroshi Kawamoto, Toshikazu Ushijima. Preclinical study of epigenetic drug-based differentiation therapy for neuroblastoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-245.
Abstract LB-251: Radiotherapy sensitizes pancreatic cancer to immunotherapy by promoting T cell infiltration
Authors: Zheng Wenxin , Skowron Kinga B. , Namm Jukes P. , Burnette Byron , Fernandez Christian , Arina Ainhoa , Liang Hua , Spiotto Michael T. , Posner Mitchell C. , Fu Yang-Xin , Weichselbaum Ralph R. 
Published: July 2016

Abstract
Pancreatic cancer patients often fail to respond to immunotherapy, such as vaccines or checkpoint inhibitors. It is unknown if an immune phenotype predicts the efficacy of immunotherapy for pancreatic cancer and what standard modalities are required to facilitate the response of pancreatic cancer to immunotherapy. We examined prognostic markers of immune cell infiltration in pancreatic cancer. Pancreatic cancer patients with low CD8+ T cell infiltration and high PD-L1 expression (CD8+ TloPD-L1hi) experienced worse outcomes compared to patients whose tumors demonstrate CD8+ TloPD-L1lo, CD8+ ThiPD-L1hi or CD8+ ThiPD-L1lo profiles. To understand how to improve tumor control in CD8+ TloPD-L1hi pancreatic cancers, we developed a mouse tumor fragment model with a trackable model antigen (SIYRYYGL or SIY) to mimic CD8+ TloPD-L1hi pancreatic cancers. Similar to pancreatic cancers, tumors arising from fragments contained few T cells, even after vaccination. Fragment tumors responded poorly to PD-L1 blockade, SIY vaccination or radiation as individual treatments. By contrast, local ionizing radiation coupled with vaccination increased CD8+ T cell infiltration that was associated with upregulation of CXCL10 and CCL5 chemokines in the tumor, but demonstrated modest inhibition of tumor growth. The addition of an anti-PD-L1 antibody enhanced the effector function of tumor-infiltrating T cells, leading to significantly improved tumor regression and increased survival compared to vaccination and radiation. These results indicate that combination of radiation, vaccination and checkpoint blockade could convert non-T cell-inflamed cancers to T cell-inflamed cancers, and thus effectively treat established pancreatic tumors with an initial CD8+ TloPD-L1hi phenotype. This suggests a novel immunostimulatory role for radiotherapy in the treatment of pancreatic cancer.
Citation Format: Wenxin Zheng, Kinga B. Skowron, Jukes P. Namm, Byron Burnette, Christian Fernandez, Ainhoa Arina, Hua Liang, Michael T. Spiotto, Mitchell C. Posner, Yang-Xin Fu, Ralph R. Weichselbaum. Radiotherapy sensitizes pancreatic cancer to immunotherapy by promoting T cell infiltration. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-251.
Abstract LB-266: Large oncosomes reprogram prostate fibroblasts toward a pro-angiogenic phenotype
Authors: Minciacchi Valentina , Spinelli Cristiana , Reis-Sobreiro Mariana , Zandian Mandana , Adam Rosalyn M. , Posadas Edwin M. , Michael Freeman R. , Cocucci Emanuele , Bhowmick Neil , Di Vizio Dolores 
Published: July 2016

Abstract
Introduction: Cancer cells communicate with different cells in the tumor microenvironment, establishing a supportive stroma that sustains tumor development and facilitates the first steps of metastasis. Extracellular vesicles (EVs) have emerged as key functional mediators of this process. Aim of this study was to determine the mechanism of intercellular communication mediated by the atypically large EVs produced by highly migratory and metastatic tumor cells, referred to as large oncosomes (LO), and prostate fibroblasts (NAF). Methods: Filtration, differential centrifugation followed by iodixanol gradient; flow cytometry and confocal imaging; RNA-seq; kinase assay; TF array; luciferase assay; tube formation; siRNA; RT-qPCR. Results: Active AKT1 is significantly more expressed and functional in LO than in exosomes (Exo). Patients with metastatic disease express abundant active AKT1 in plasma LO. Uptake of LO harboring active AKT1 by NAF results in AKT1 and c-MYC activation. Conditioned media from LO-treated NAF, but not from Exo-treated NAF, promoted endothelial morphogenesis. The Dynamin (DNM) inhibitor Dynasore (Dyn) inhibited LO-uptake, as well as MYC activation and tube formation. Transient silencing of DNM2 significantly reduced LO uptake, suggesting that uptake occurs by phagocytosis. LO treatment increased levels of MYC targets in NAF, suggesting that MYC is involved in LO-induced reprogramming of NAF. Accordingly, MYC expression was higher in activated fibroblasts than NAF, and MYC overexpression in NAF induced hyperplasia in normal prostate epithelium in mice, suggesting MYC activation is an early event in cancer development. Summary/Conclusion: Our results indicate that tumor-derived LO induce a novel, c-MYC mediated, pro-tumorigenic reprogramming of fibroblasts that can be reverted by selectively inhibiting LO uptake.
Support: National Institutes of Health NCI NIH R00 CA131472; NIH UCLA SPORE in Prostate Cancer award P50 CA092131; Avon Foundation Fund 02-2013-043 (to DDV).
Citation Format: Valentina Minciacchi, Cristiana Spinelli, Mariana Reis-Sobreiro, Mandana Zandian, Rosalyn M. Adam, Edwin M. Posadas, Freeman R. Michael, Emanuele Cocucci, Neil Bhowmick, Dolores Di Vizio. Large oncosomes reprogram prostate fibroblasts toward a pro-angiogenic phenotype. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-266.
Abstract LB-268: Androgen signaling in cancer-associated fibroblasts contributes to progression of prostate cancer
Authors: Liao Chun-Peng , Chen Leng-Ying , Luethy Andrea , Kim Youngsoo , MacLeod Robert , Gross Mitchell 
Published: July 2016

Abstract
Interactions between epithelial and stromal cells are important in the development of prostate cancer (PCa). Cancer-associated fibroblasts (CAFs) have been to support tumor progression, metastasis, and differentiation. Androgen receptor (AR) and related pathways are known to support the growth and survival of prostate epithelial cancer cells, the roles of AR-dependent processes in cancerous stroma are less clear. We sought to investigate if AR-dependent pathways present in CAF cells influence the growth and tumorogencity of epithelial cancer cells in relation to androgen-deprivation therapy in prostate cancer. Murine CAFs were isolated from a well-described PTEN-dependent cancer mouse model. A co-culture system was developed based on multiple lines of murine CAFs grown along with human prostate cancer epithelial cells, and a murine-specific anti-sense oligonucleotide (ASO) against murine AR was used to specifically suppress AR expression in murine CAFs in this system. Using this co-culture system, we found that murine CAFs promoted cell proliferation and colony formation in several human prostate cancer cell lines. Further, these processes were decreased by suppression of AR-expression in CAFs. Expression of genes related to tumorogenicity in epithelial cells were investigated by real-time quantitative PCR. Markers associated with epithelial-mesenchymal transition (EMT) and stemness were increased in human prostate cancer cells grown with low-AR CAFs. Our data indicates that suppression of AR in CAFs results in down-regulation in the growth and tumorogenecity of prostate cancer cells through pathways related to EMT and “cell reprograming”. As such, development of therapies which inhibit the tumor-promoting pathways present in stromal cells may be one approach to improve the treatment of prostate cancer.
Citation Format: Chun-Peng Liao, Leng-Ying Chen, Andrea Luethy, Youngsoo Kim, Robert MacLeod, Mitchell Gross. Androgen signaling in cancer-associated fibroblasts contributes to progression of prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-268.
Abstract LB-274: Microenvironment mediates the efficacy of Cabozantinib in prostate cancer
Authors: Tripathi Manisha , Nandana Srinivas , Billet Sandrine , Posadas Edwin M. , Chung Leland W.K. , Bhowmick Neil A. 
Published: July 2016

Abstract
Therapeutic targeting of the epithelial compartment alone in prostate cancer has resulted in unfavorable outcomes, including the development of resistance. Cabozantinib (XL184), a small molecule inhibitor of tyrosine kinases including c-MET and VEGFR2 has been shown to decrease tumor growth and metastasis. Our working rationale is that therapeutic strategies that target the prostate tumor microenvironment would have improved outcomes compared with those that solely target the cancer epithelia. Cabozantinib is demonstrated to have a role in inhibiting osteoclast and osteoblast differentiation and thereby limit prostate cancer (PCa) bone lesions, as determined by technetium-99 bone scan. However, the ultimate survival benefit of castrate resistant prostate cancer patients treated with cabozantinib has not born out in recent clinical trials for PCa patients with bone metastasis. In this study, utilizing various pre-clinical xenograft mouse models, prostate epithelial cell lines and human and mouse prostate fibroblasts, we investigated the effect of cabozantinib on prostate tumor microenvironment and delineated the cellular targets of cabozantnib. We found that cabozantinib affects prostate stromal cells at a significantly lower concentration compared with epithelial cells in vitro. We found that human cancer associated fibroblasts pre-treated with cabozantinib induced a significantly increased tumor growth in the intra-tibial mouse model of growth in the bone microenvironment. Further, in a novel and surprising discovery, we found that cabozantinib alters the immune microenvironment by reducing the M1 macrophages. However, cabozantinib depleted both basal and luminal epithelial progenitor cells in vivo. Taken together, we found that cabozantnib can have a tumor potentiating role by limiting M1 macrophages, yet the down regulation of carcinoma associated fibroblasts and associated epithelial progenitors could suggest interesting combination therapies. A lower dose of cabozantnib with traditional anti-proliferative therapies, like taxanes or radiation is supported by the pre-clinical experiments.
Citation Format: Manisha Tripathi, Srinivas Nandana, Sandrine Billet, Edwin M. Posadas, Leland W.K. Chung, Neil A. Bhowmick. Microenvironment mediates the efficacy of Cabozantinib in prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-274.
Abstract LB-317: Energy distruptor 2-deoxyglucose mitigates bacterial infection responsive hyperplasia and/or colitis
Authors: Ahmed Ishfaq , Umar Shahid , Papineni Rao V. 
Published: July 2016

Abstract
Transmissible murine crypt hyperplasia (TMCH) is a pathological outcome of Citrobacter rodentium (CR) infection, accompanied by intestinal inflammation during colitis though excessive induction of epithelial regeneration and repair mechanisms. The TMCH model, provides an excellent template to determine how alterations in intestinal stem cells promote trans-differentiation, crypt regeneration or colon carcinogenesis following bacterial infection. CR is a valuable infection model for the study of pathogenesis of the clinically significant human pathogens, enteropathogenic Escherichia coli (EPEC) and enterohaemorrhagic E. coli (EHEC). During TMCH, there is a complex interplay between the Notch and Wnt/β-catenin pathways in colonic crypt hyperplasia. Blocking Notch signaling via chronic dibenzazepine (DBZ) administration inhibits both Notch and Wnt signaling, and disrupts the intestinal barrier during CR induced colitis. 2-deoxyglucose (2DG) is a glycolytic inhibitor has been used for cancer therapy exploiting the cancer cell's high metabolic state. Added, the similarity of 2DG to mannose produces improper N-linked glycosylation resulting in an unfolded protein response (UPR) slowing growth of tumors. Here, using CR infection model, we show that dietary treatment of 2DG (0.4%) mitigates C. rodentium- and Notch signaling blocker dibenzazepine (DBZ)-induced colitis in NIH:Swiss mice. The survival curve shows no loss in mice administered with 2DG, compared to 40% loss in mice with vehicle alone during CR infection together with DBZ treatment. At tissue level, 2DG dietary intervention resulted in restoration of Hes-1, and β-catenin protein levels as observed from the western analyses of the C. rodentium-infected and DBZ-treated mice crypts. Histological staining show reduced dysbiosis upon 2DG intervention, as seen from reduced infiltration of inflammatory response cells during CR infection and the therapeutic effects are further substantiated with the Ki-67 staining. Thus, the energy distruptor 2-deoxyglucose (2DG) is described for the first time here to mitigate bacterial infection and its responsive hyperplasia/colitis. The current model in this novel mechanism of action will be presented.
Citation Format: Ishfaq Ahmed, Shahid Umar, Rao V. Papineni. Energy distruptor 2-deoxyglucose mitigates bacterial infection responsive hyperplasia and/or colitis. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-317.
Abstract LB-331: Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations
Authors: Seshagiri Somasekar , Stawiski Eric , Goldstein Leonard , Durinck Steffen , Modrusan Zora , Gnad Florian , Nguyen Thong T. , Jaiswal Bijay , De Rienzo Assunta , Richards William , Bueno Raphael 
Published: July 2016

Abstract
Malignant pleural mesothelioma (MPM) is an aggressive cancer arising from the mesothelial cells of the pleura. About 80% of mesothelioma cases are linked to asbestos exposure, while the remainder may be related to prior chest radiation, genetic predisposition or spontaneous occurrence.
We analyzed transcriptomes (n = 211), whole exomes (n = 99), and targeted exomes (n = 103) from 216 malignant pleural mesothelioma (MPM) tumors. Four distinct molecular subtypes, sarcomatoid (S), epithelioid (E), biphasic-E, and biphasic-S were identified using RNA-seq data. Using exome analysis we found BAP1, NF2, TP53, SETD2, DDX3X, ULK2, RYR2, CFAP45, SETDB1, and DDX51 to be significantly mutated MPM genes. We identified recurrent mutations in several genes including splice complex factor SF3B1 (∼2% [4/216]) and TRAF7 (∼2% [5/216]). SF3B1 mutant samples showed a distinct splicing profile compared to wild-type tumors. Mutations in TRAF7 occurred primarily in the WD40 domain and except in one case were mutually exclusive with NF2 mutations. We found recurrent gene fusions and splice alterations to be frequent mechanisms for inactivation of NF2, BAP1 and SETD2. We analyzed the tumors for infiltrating immune cells and found that M2 macrophage to T-cell ratio was predictive of reduced overall survival. Further we found sarcomatoid subtype had a significantly higher level of PD-L1 expression suggesting that this group might be prioritized for checkpoint inhibitor therapy. Integrated analysis of alterations identified changes in Hippo, mTOR, Histone methylation, RNA helicase and p53 signaling pathways in MPMs.
Overall our study significantly expands on the previous genomic studies and provides a comprehensive genomics profile of mesothelioma and identifies several previously unknown alterations and biological pathways that are potential targets for drug discovery and treatment. Incorporating genomic analysis for detection of actionable alterations as part of MPM patient care will help in developing rational individualized therapy.
Citation Format: Somasekar Seshagiri, Eric Stawiski, Leonard Goldstein, Steffen Durinck, Zora Modrusan, Florian Gnad, Thong T. Nguyen, Bijay Jaiswal, Assunta De Rienzo, William Richards, Raphael Bueno. Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-331.
Abstract LB-340: A novel method for estimating somatic mutations cellular prevalence in cancer using whole genome haplotype phasing
Authors: Chedom-Fotso Donatien , Ahmed Ahmed , Yau Christopher 
Published: July 2016

Abstract
The process of malignant transformation results in the acquisition of complex chromosomal copy number alterations and somatic mutations. Moreover, cancer exhibits extensive intra-tumor heterogeneity with multiple sub-populations of tumor cells containing both common and private genomic alterations. Within- and between-patient tumor heterogeneity is now seen as one of the major obstacles for precision medicine and the development of effective treatment strategies. Revealing the proportion of cells affected by particular somatic changes is emerging as a key factor for designing targeted therapies, characterizing tumor evolution and understanding chemotherapy-resistance mechanisms. Determining the proportion of cells harboring a particular mutation (the so called cellular prevalence) is a difficult task as it is confounded by several variables. Normal cell contamination, local copy number profile and the temporal relationship between the mutation and the copy number alteration represent some of the key variables. In order to more effectively quantify the cellular prevalence of somatic mutations we developed a novel method, which uses a combination of side, and haplotype phase information obtained from long fragment read sequencing to more accurately compute mutational prevalence. The method utilizes three sources of information: the phasing information, the copy number variation and the allele counts for prevalence estimation using a simple equation in both a linear and a non-linear form. We present theoretical examples of known genomics alterations and show using simulation that our method was able to accurately estimate the cellular prevalence compared to standard methods. We also apply our method to a real data set obtained from dense long fragment read sequencing of a single ovarian cancer and demonstrate the highly accurate estimation of cellular prevalence. Finally we provide an implementation of the method in the statistical software.
Citation Format: Donatien Chedom-Fotso, Ahmed Ahmed, Christopher Yau. A novel method for estimating somatic mutations cellular prevalence in cancer using whole genome haplotype phasing. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-340.