bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract LB-225: Combination immunotherapy targeting HSP90 DNA-repair client proteins overexpressed in chemotherapy-resistant melanoma
Authors: Raveendran Subhara , Fecek Ronald , Carey Cara Donahue , Storkus Walter J.
Published: July 2016

DNA repair protein (DNA-RP) overexpression has been reported to involve post-translational protein stabilization mediated by the molecular chaperone heat shock protein 90(HSP90), thereby preventing proteasome-dependent degradation of these HSP90 “client” proteins. Overexpression of DNA-RP in a disease-stage associated manner has also been correlated to chemo resistance and poor overall prognosis. Hence, HSP90 inhibitors (HSP90i) have been heralded as co-therapy agents for cancer patients that have developed resistance to first-line treatments such as temozolomide (TMZ). In the presence of HSP90i, HSP90 client proteins rapidly become (poly)ubiquinated and undergo degradation resulting in the improved sensitization of cancer cells to chemo therapy. We observed that HSP90i promote the proteasome-dependent degradation of a broad range of DNA-repair client proteins. We have also identified 9 H-2Kb/Db-presented peptide epitopes derived from DNA-RPs that may be recognized by Type-1 CD8+ T cells after specific vaccination. When combined with adoptive cell therapy using DNA-RP-specific CD8+ T cells, HSP90i cotreatment yielded superior anti-tumor efficacy against established TMZ-resistant B16 tumors in C57BL/6 mice.

Citation Format: Subhara Raveendran, Ronald Fecek, Cara Donahue Carey, Walter J. Storkus. Combination immunotherapy targeting HSP90 DNA-repair client proteins overexpressed in chemotherapy-resistant melanoma. [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-225.
Abstract LB-228: Polo-like kinase 4: A potential new target for the management of prostate cancer
Authors: Singh Chandra K. , Shabbir Maria , Nihal Minakshi , Iczkowski Kenneth A. , Ahmad Nihal
Published: July 2016

Prostate cancer (PCa) is the most prevalent non-cutaneous cancer of males. According to an estimate from the American Cancer Society, it is expected that approximately 180,890 new cases of PCa will be diagnosed and 26,120 PCa-related deaths will occur in the United States in 2016. Therefore, identification of additional molecular target(s) could be useful in designing novel mechanism-based approaches for the prevention and/or therapy of PCa. PLK4 belongs to the polo-like kinase family of serine/threonine protein kinases that localizes to centrioles and regulates centriole duplication during the cell cycle. Essentially, PLK4 is a low abundance suicidal kinase that is known to auto-phosphorylate itself to promote its own destruction to limit centriole duplication once per cell cycle phase. Since centrosome aberrations are frequently seen in cancer, the central role of PLK4 in centriole duplication suggests its significance as a potential target for cancer management. However, the role and functional relevance of PLK4 in PCa development and progression has not been investigated. In this study, we determined the expression profile of PLK4 in PCa using immunohistochemical analysis of multiple tissue microarrays (TMAs) containing a variety of cancerous and benign human prostate tissues. The TMAs were immunostained for PLK4 and the images were scanned and analyzed for protein levels using Aperio ScanScope at 40x magnification. We found a significant upregulation of PLK4 in PCa, compared to benign prostatic tissues. Further, we found a significant upregulation of PLK4 protein and mRNA in human PCa cells, as assessed by western blot and qRT-PCR analyses, respectively. To further assess the relevance of PLK4 overexpression in PCa, we determined the effect of a small molecule inhibitor of PLK4, centrinone-B, on androgen-responsive 22Rν1 and androgen-independent DU145 human PCa cells. Centrinone-B treatment (0, 50, 100 and 200 nM; for 24 and 48 h) resulted in a marked decrease in growth and viability of PCa cells, as assessed i) by CytoTox-Glo™ cytotoxicity assay, and ii) microscopic evaluation of cells following staining with Nuclear Fast Red and Crystal Violet dyes. Further, centrinone-B treatment resulted in a G1 phase cell cycle arrest of human PCa cells. Taken together, our study provides first direct evidence of a pro-proliferative function of PLK4 in PCa. However, additional studies are required to ascertain the relevance of our in vitro findings to in vivo situations in relevant animal models.

Citation Format: Chandra K. Singh, Maria Shabbir, Minakshi Nihal, Kenneth A. Iczkowski, Nihal Ahmad. Polo-like kinase 4: A potential new target for the management 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-228.
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

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

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

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

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

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

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

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

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.
Abstract LB-350: In vivo kinome screen reveals potential drivers of brain metastasis
Authors: Lowery Frank J. , Acharya Sunil , Xia Yong , Zhang Chenyu , Saunus Jodi M. , Yu Dihua
Published: July 2016

Brain metastasis remains an unmet medical need, as its incidence continues to rise while treatment options remain palliative. Advances in targeted therapy for breast cancer have prolonged patient survival through better control of the systemic disease, but an ever-increasing number of patients later recur with brain metastasis. As no effective therapies exist for brain metastasis, the median survival of patients is less than one year. To tackle this growing clinical challenge, we sought to better understand the biological mechanism of brain metastasis and to identify novel targets for intervention. We chose to focus on kinases, as they both occupy the central nodes of cancer cell signaling pathways and structurally lend themselves to targeting by small molecules. To identify novel therapeutic targets, we performed an unbiased kinome screen in vivo for determination of brain metastasis driver kinases. We injected MDA-MB-231 human breast cancer cells overexpressing pools of 16-20 kinase ORFs into the carotid artery of nude mice to form experimental brain metastasis. Several of the kinase pools led to decreased brain metastasis-specific survival, decreasing survival time by as much as 50% relative to controls. We then performed targeted next-generation sequencing (NGS) of the pre-and post-injection tumor cells to determine those kinases most enriched in vivo, revealing 31 ORFs that were significantly increased in vivo in multiple animals. To validate the clinical relevance of these potential targets, we examined their expression in a collection of 32 human brain metastases by RNA-seq, and observed that the majority of the ORFs (29/31) were indeed expressed. One of the kinases with the highest in vivo enrichment and expression in human brain metastases was hexokinase 2 (HK2), an important glycolysis regulator that has been previously implicated in brain metastasis and served to validate our findings. Several other candidate kinases were also related to glycolysis and other metabolic pathways, suggesting that these kinases enable metastatic cancer cells to survive in the nutrient-restricted brain environment. Functional validation of these newly identified kinases as true drivers of brain metastasis will reveal whether they have potential to serve as the first targets of brain metastasis-targeted therapy.

Citation Format: Frank J. Lowery, Sunil Acharya, Yong Xia, Chenyu Zhang, Jodi M. Saunus, Dihua Yu. In vivo kinome screen reveals potential drivers of brain metastasis. [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-350.
Abstract LB-359: Knowledge of prostate cancer and screening attitude of residents of a Nigerian community
Authors: Iweala Emeka E.J , Omonhinmin Conrad A. , Azuh Dominic E. , Okwudi Isioma J.
Published: July 2016

This study assessed the level of awareness and knowledge of prostate cancer amongst the residents of a Nigerian University and its environs. A cross-sectional descriptive study using self-administered questionnaires was carried out among 443 people, aged 20 to 80 residing in Covenant University, Nigeria and its environs. Data analysis was done with SPSS version 15.0. The level of significance was set at p <0.05. The majority (45.1%) of respondents was aged between 31 - 40 years and only 41.3% were aware of the existence of Prostate cancer. Educational background, occupation and religion were observed to significantly increase (p <0.05) awareness of prostate cancer while gender and age did not. The awareness and previous participation in prostate cancer screening negatively (p <0.05) influenced respondents’ decision to participate in future screening. Electronic media via radio and television was the commonest source of awareness for prostate cancer. Only 13.4% became aware through health facility or personnel. Only 30.5% correctly identified the location of the prostate. Most of the respondents identified poor diet and environmental conditions as risk factors while 13.7%, 2.0% and 5.9% identified aging, race and genetics respectively as the causes of prostate cancer. Most of the respondents (31.2%) correctly identified difficult urination as a symptom of prostate cancer. About 30.8% have a relative, family or friend that had prostate cancer out of which 18.5% resulted in deaths. Only one respondent had been previously diagnosed with an enlarged prostate. Majority of the respondents were unaware of a possible cure or therapy. Only 9.9%, of the respondents strongly agreed that prostate cancer was peculiar to all men while a low percentage (4.1%) of respondents strongly agreed that it is a health disparity issue among black men. Over all a very low percentage of 37.9% of the respondents considered prostate cancer to be a serious ailment. The study showed a generally poor knowledge and wrong conceptions about prostate cancer, screening and treatment. This suggests the need for public health education and screening programs on prostate cancer for this population and others.

Citation Format: Emeka E.J Iweala, Conrad A. Omonhinmin, Dominic E. Azuh, Isioma J. Okwudi. Knowledge of prostate cancer and screening attitude of residents of a Nigerian community. [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-359.
Abstract NG01: Accumulation of somatic mutations in normal and cancerous tissues with age
Authors: Hoang Margaret L. , Kinde Isaac , Tomasetti Cristian , Rosenquist Thomas , Grollman Arthur P. , Kinzler Kenneth W. , Vogelstein Bert , Papadopoulos Nickolas
Published: July 2016

Fundamental theories in carcinogenesis and aging evoke the accumulation of rare somatic mutations in normal tissues over time. However, absence of a simple and systematic method to characterize somatic mutations in normal tissues precludes the understanding of their functional consequences. We present Bottleneck Sequencing System (BotSeqS), a next-generation sequencing method that quantitates rare somatic point mutations simultaneously across the mitochondrial and nuclear genomes. BotSeqS combines molecular barcoding with a simple dilution step immediately before library amplification. Using BotSeqS, we determine the mutation frequencies and spectra in normal brain, kidney, and colon from a total of 34 individuals ranging from < 1 to 98 years old. We show an age and tissue-dependent accumulation of rare point mutations and demonstrate that the somatic mutational burden in normal tissues can vary by several orders of magnitude depending on biological and environmental factors. For example, individuals with defects in the mismatch repair machinery or exposure to environmental carcinogens (smoking, aristolochic acid) show significant increases in mutational frequencies and altered mutational spectra compared to controls. We further show major differences between the mutational patterns of the mitochondrial and nuclear genomes in normal tissues. Lastly, we find that the mutational spectra of normal tissues were different from each other but similar to cancers from the same tissue type, suggesting that the differential mutational spectra observed in cancers are tissue-specific rather than cancer-specific. This technology can provide insights into the number and nature of genetic alterations in normal tissues and can be used to address a variety of fundamental questions about the genomes of diseased tissues.

Citation Format: Margaret L. Hoang, Isaac Kinde, Cristian Tomasetti, Thomas Rosenquist, Arthur P. Grollman, Kenneth W. Kinzler, Bert Vogelstein, Nickolas Papadopoulos. Accumulation of somatic mutations in normal and cancerous tissues with age. [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 NG01.
Abstract SY15-03: Drugging “undruggable” transcription factor drivers in cancer
Authors: Bushweller John
Published: July 2016

Dysregulation of gene expression is a hallmark of all cancers. It is critical for conferring stem cell like properties, such as self-renewal and chemo-resistance, on these cancer cells. Such properties contribute to the inability to completely eradicate cancer cells, thereby leading to relapse. The specific gene expression program that confers these properties derives from aberrant activity of specific transcription factors which are drivers of disease. There are numerous examples of such transcription factor drivers in cancer (ERG in prostate cancer, ETV1 in prostate cancer and GIST, RUNX1-ETO and CBFβ-SMMHC in acute myeloid leukemia, etc.). Clearly, the most direct and effective approach to alter this gene expression program is to target the activity of these transcription factors which are drivers of disease. While the paradigm is shifting significantly, transcription factors have traditionally been viewed as “undruggable”. This results from the challenges associated with targeting either the protein-DNA or protein-protein interactions that typically mediate their function. Recent successes in this area are clearly breaking down this paradigm.

Targeting of transcription factors is a very different approach to current approaches to targeted therapy which have heavily focused on kinase inhibitors. Targeting transcription factor drivers will likely alter the stem cell like properties of the cancer cell such as self-renewal, the DNA repair alterations which lead to enhanced rates of mutagenesis, and the chemo-resistance which limits effectiveness of chemotherapy drugs. It is also likely that agents targeting transcription factors will show synergy with appropriately targeted kinase inhibitors.

We have developed a specific, potent, and effective protein-protein interaction inhibitor for the CBFβ-SMMHC fusion protein which is a driver in inv(16) acute myeloid leukemia (Illendula et al. Science 347: 779-784 (2015)). The efficacy of this inhibitor of a critical protein-protein interaction of the CBFβ-SMMHC transcription factor fusion protein clearly demonstrates the utility of directly targeting transcription factor drivers in cancer. Based on this success, we are targeting other transcription factor drivers in leukemia as well as in other cancers. Two examples of our efforts in this area will be presented.

Citation Format: John Bushweller. Drugging “undruggable” transcription factor drivers in 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 SY15-03.
Abstract SY16-02: The discovery of Mcl-1 inhibitors using fragment-based methods and structure-based design
Authors: Fesik Stephen W.
Published: July 2016

Myeloid cell leukemia 1 (Mcl-1) is a member of the Bcl-2 family of proteins that is overexpressed and amplified in a wide variety of cancers and causes resistance to many chemotherapies. Although a very promising cancer target, it exerts its activity through protein-protein interactions and is very challenging to drug with small molecules. Indeed, there are no Mcl-1 inhibitors that have entered clinical trials. In this presentation, I will describe the discovery of picomolar Mcl-1 inhibitors using fragment-based methods and structure-based design that show promise as therapeutic agents for the treatment of heme malignancies and solid tumors.

Citation Format: Stephen W. Fesik. The discovery of Mcl-1 inhibitors using fragment-based methods and structure-based design. [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 SY16-02.
Abstract SY27-02: Targeting leukemia stem cells with small molecule inhibitors of PRC1
Authors: Cierpicki Tomasz
Published: July 2016

Bmi1 is a stem cell gene, which determines the proliferative capacity and self-renewal potential of normal and leukemic stem cells. Multiple studies identified Bmi1 to be able to induce oncogenic transformation and promote tumor growth in a variety of in vitro and in vivo animal models. Bmi1 is a central component of the Polycomb Repressive Complex 1 (PRC1) and interacts with Ring1B protein to form an active E3 ligase, which ubiquitinates histone H2A on lysine K119. This epigenetic modification of H2A is required to maintain transcriptionally repressive state of many genes. Small molecule inhibitors of the Ring1B-Bmi1 E3 ligase activity have not been reported to date, but are highly desired as potential therapeutic agents targeting cancer stem cells. Employing fragment screening approach we identified small molecule inhibitors of Ring1B-Bmi1. Using medicinal chemistry, we developed potent compounds that bind to Ring1B-Bmi1 and inhibit its E3 ubiquitin ligase activity with low micromolar affinities. In cells, Ring1B-Bmi1 inhibitors revealed robust downregulation of H2A K119 ubiquitination. Treatment of model cell lines enriched in leukemia initiating cells show that the Ring1B-Bmi1 inhibitor blocks the self-renewal capacity and induces cellular differentiation. Our approach validates that RING ligases represent novel class of ‘druggable’ epigenetic targets.

Citation Format: Tomasz Cierpicki. Targeting leukemia stem cells with small molecule inhibitors of PRC1. [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 SY27-02.
Abstract SY29-01: Deciphering oncogenic translation programs
Authors: Wendel Hans-Guido
Published: July 2016

New technologies provide precise measures of translation across the transcriptome. In particular, transcriptome-scale ribosome foot printing in conjunction with deep RNA sequencing developed by N. Ignolia and colleagues has shifted the focus in the field towards the output of mRNA translation. We can now measure differential mRNA translation programs and determine RNA sequence and structural features that guide translational responses to cellular and environmental cues. This has direct implications to cancer and beyond. It also extends our understanding of gene expression from transcriptional control to the regulation of protein production. We will provide examples of how these new approaches to studying mRNA translation are leading to new insight into cancer biology and therapy.

Citation Format: Hans-Guido Wendel. Deciphering oncogenic translation programs. [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 SY29-01.
Abstract SY38-03: Quantifying tumor heterogeneity in the microenvironment
Authors: Markowetz Florian
Published: July 2016

Cancer has long been understood as a somatic evolutionary process, but many details of tumor progression remain elusive. Here, I will talk about computational methods to infer evolutionary pathways leading to tumour heterogeneity.

Using a study in ovarian cancer I will describe how summary statistics of phylogenetic quantification of genetic heterogeneity can predict patient survival.

Then, I will present probabilistic frameworks to reconstruct intra-tumor evolution from data obtained by bulk bisulfite sequencing of mixed tumor samples or single cell genomes. Our approaches jointly estimates the number and composition of clones in the sample as well as the most likely tree connecting them.

I will finish with an outlook how to put cancer genomes in a tissue context by using image analysis and deconvolution of gene expression data.

Citation Format: Florian Markowetz. Quantifying tumor heterogeneity in the microenvironment. [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 SY38-03.
Endovascular Therapy for Large Vessel Stroke in the Elderly: Hope in the New Stroke Era
Authors: Lima Andrey , Haussen Diogo C. , Rebello Leticia C. , Dehkharghani Seena , Grossberg Jonathan , Grigoryan Mikayel , Frankel Michael , Nogueira Raul G.
Published: July 2016

Background and Purpose: Acute ischemic stroke (AIS) in the elderly encompasses approximately one-third of all AIS cases. Outcome data have been for the most part discouraging in this population. We aim to evaluate the outcomes in a large contemporary series of elderly patients treated with thrombectomy. Methods: Retrospective analysis of a single-center endovascular database for consecutive elderly (≥80 years) patients treated for anterior circulation large vessel occlusion AIS between September 2010 and April 2015. Univariate- and multivariate analyses were performed to identify the predictors of good clinical outcome (90-day modified Ranking Scale [mRS] ≤2). Receiver operating characteristic curves were used to calculate the optimal final infarct volume (FIV) threshold to predict good outcomes. Results: A total of 111 patients met our inclusion criteria (mean age 84.8 ± 4.2 years; National Institutes of Health Stroke Scale [NIHSS] score 19.1 ± 5.6; time from last-known normal to puncture, 349.6 ± 246.6 min; 33% male; 68% Alberta Stroke Program Early CT Score [ASPECTS] ≥8). The rates of successful reperfusion (modified treatment in cerebral ischemia ≥2b), symptomatic intracranial hemorrhage and 90-day mortality were 80%, 7% and 41%, respectively. The overall rate of good outcome was 29% (n = 32/111) but was 52% (n = 13/25) in patients with baseline mRS score of 0-2 who were selected based on CT perfusion and treated with stent retrievers. On multivariate analysis, only ASPECTS (OR 2.17; 95% CI 1.28-3.67.7; p = 0.004) and baseline NIHSS score (OR 0.87; 95% CI 0.77-0.97; p = 0.013) were independently associated with good outcome. A FIV ≤16 ml demonstrated the greatest accuracy for identifying good outcomes (sensitivity 75.0%, specificity 82.6%). Conclusions: Our results are encouraging demonstrating nearly one-third of elderly patients achieving full independence at 90 days. Contemporary treatment paradigms employing optimized patient selection and modern thrombectomy technology may result in even better outcomes.
The Default Computation of Negated Meanings
Authors: Papeo Liuba , Hochmann Jean-Rémy , Battelli Lorella
Published: July 2016

Negation is a fundamental component of human reasoning and language. Yet, current neurocognitive models, conceived to account for the cortical representation of meanings (e.g., writing), hardly accommodate the representation of negated meanings (not writing). One main hypothesis, known as the two-step model, proposes that, for negated meanings, the corresponding positive representation is first fully activated and then modified to reflect negation. Recast in neurobiological terms, this model predicts that, in the initial stage of semantic processing, the neural representation of a stimulus' meaning is indistinguishable from the neural representation of that meaning following negation. Although previous work has shown that pragmatic and task manipulations can favor or hinder a two-step processing, we just do not know how the brain processes an utterance as simple as “I am not writing.” We implemented two methodologies based on chronometric TMS to measure motor excitability (Experiment 1) and inhibition (Experiment 2) as physiological markers of semantic access to action-related meanings. We used elementary sentences (Adverb + Verb) and a passive reading task. For the first time, we defined action word-related motor activity in terms of increased excitability and concurrently reduced inhibition. Moreover, we showed that this pattern changes already in the earliest stage of semantic processing, when action meanings were negated. Negation modifies the neural representation of the argument in its scope, as soon as semantic effects are observed in the brain.