bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract B28: BET bromodomain inhibitors antagonize Brd4-Mediator complexes to undermine the acute myeloid leukemia cell state
Authors: Bhagwat Anand S. , Roe Jae-Seok , Mok Beverly A. , Vakoc Christopher R.
Published: May 2016

Acute myeloid leukemia (AML) is a hematologic malignancy with a 5-year survival rate of under 30%. We recently identified the bromodomain and extraterminal (BET) protein Brd4 as a therapeutic target in AML, and several trials are currently evaluating the clinical utility of BET inhibitors for this disease. BET inhibitors displace Brd4 from chromatin and subsequently reduce the expression of key oncogenes, such as Myc, leading to AML blast differentiation and cell death. However, the mechanism by which Brd4 maintains oncogene expression in AML is still unclear. We hypothesized that Brd4 functions by working with other coactivators in AML to promote expression of oncogenes. One such coactivator is the Mediator complex, which is comprised of ~30 subunits and directly contacts RNA Polymerase II to regulate its function. Initial purifications of Mediator from mammalian cells identified Brd4 as an associated factor. Using ChIP-seq analysis in AML cells, we show that Brd4 and Mediator closely co-localize across the genome. Moreover, chemical inhibition of Brd4 results in the displacement of Mediator from enhancer and promoter regions across the genome, an effect that occurrs within 30 minutes of treatment. While the genome-wide loss of Mediator occupancy is approximately 2-fold, a subset of promoters and enhancers exhibit dramatic loss of Mediator occupancy. Importantly, these regions are disproportionately associated with genes related to leukemia biology but only modestly overlap with super-enhancers. In addition, we show that shRNA-based knockdown of several Mediator subunits phenocopies the transcriptional and cellular effects of Brd4 inhibition without affecting levels of Brd4 in the cell. These effects include downregulation of Myc expression, induction of myeloid differentiation, and reduction of P-TEFb recruitment to chromatin. These findings support a model in which Brd4 functions in concert with the Mediator complex to maintain oncogenic gene expression programs in leukemia and shed light on the mechanisms of action underlying a promising new class of therapeutics for AML.

Citation Format: Anand S. Bhagwat, Jae-Seok Roe, Beverly A. Mok, Christopher R. Vakoc. BET bromodomain inhibitors antagonize Brd4-Mediator complexes to undermine the acute myeloid leukemia cell state. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr B28.
Abstract B31: EZH2 suppresses the interferon-stimulated gene response in non-Hodgkin lymphoma
Authors: Bradley William D. , Yuan Chih-Chi , Zhao Feng , Lee Christina , Williamson Kaylyn E. , Arora Shilpi , Hatton Charlie , Bryant Barbara M. , Trojer Patrick
Published: May 2016

Pharmacological inhibition of the histone lysine methyltransferase EZH2 has emerged as a therapeutic strategy for the treatment of non-Hodgkin Lymphoma (NHL), in particular for cases with mono-allelic mutations in the EZH2 catalytic domain. Potent, selective EZH2 small molecule inhibitors have achieved tumor regression in mutant EZH2-containing preclinical lymphoma models and several of these inhibitors are currently engaged in cancer-focused clinical trials. Here, we show that the presence of EZH2 mutations do not always confer EZH2 inhibitor sensitivity. We discovered that EZH2 is usurped by lymphoma cells to attenuate JAK/STAT signaling and to repress pro-apoptotic interferon response genes. EZH2 inhibition results in the broad induction of interferon-stimulated genes (ISGs) in several phenotypically sensitive NHL cell models. In mutant EZH2-containing insensitive models, EZH2 inhibitors synergize specifically with type I interferons (IFNs) in vitro and in vivo to induce ISGs and apoptosis. The profound combinatorial activity of EZH2 inhibitors and type I IFNs is not restricted to NHL models with mutant EZH2 and, is preferentially observed in models that are not affected by either single agent. Molecular consequences of EZH2 inhibitor and type I IFN combinatorial treatment include STAT1 activation, binding of STAT transcription factor complexes to ISGs, reduction of H3K27me3 levels and increase of H3K4me3 levels at ISG transcriptional start sites, and ISG transcriptional activation. The molecular and anti-proliferative effects of the combination can be suppressed by inactivation of the JAK/STAT signaling pathway, by using the JAK inhibitor ruxolitinib. We suggest that EZH2 inhibitors can be therapeutically combined with type I IFNs for the treatment of NHL.

Citation Format: William D. Bradley, Chih-Chi Yuan, Feng Zhao, Christina Lee, Kaylyn E. Williamson, Shilpi Arora, Charlie Hatton, Barbara M. Bryant, Patrick Trojer. EZH2 suppresses the interferon-stimulated gene response in non-Hodgkin lymphoma. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr B31.
Abstract B32: Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses
Authors: Chiappinelli Katherine B. , Strissel Pamela L. , Desrichard Alexis , Li Huili , Henke Christine , Akman Benjamin , Hein Alexander , Rote Neal S. , Cope Leslie M. , Snyder Alexandra , Makarov Vladimir , Budhu Sadna , Wolchok Jedd , Zahnow Cynthia A. , Mergoub Taha , Chan Timothy A. , Strick Reiner , Baylin Stephen B.
Published: May 2016

DNA methyltransferase inhibitors (DNMTis) upregulate immune attraction, including the interferon response, in solid tumors. We now define viral defense signaling as one mechanism for this. In epithelial ovarian cancer cells DNMTis upregulate viral defense by cytosolic sensing of double-stranded RNA (dsRNA), triggering a Type I Interferon response, upregulation of downstream interferon response genes, and increased apoptosis. Knockdown of the dsRNA sensors TLR3 and MAVS and inhibition of the interferon alpha/beta receptor blunt the DNMTi induced dsRNA response. DNMTis cause apoptosis of cancer cells, which is partially rescued by inhibiting the interferon alpha/beta receptor. We observe upregulation and demethylation of hypermethylated endogenous retroviruses (ERVs) and overexpression of individual ERVs whose sense and anti-sense transcripts may be key candidates for triggering the above signaling. Overexpression of ERVs alone is sufficient to trigger an interferon response in the absence of DNMTis. Basal levels of ERV and viral defense gene expression significantly correlate in primary OC and basal expression of the viral defense signature separates primary TCGA samples for multiple tumor types into low versus high expression groups. In melanoma patients treated with an immune checkpoint therapy, high viral defense signature expression in tumors significantly associates with durable clinical response and DNMTi treatment sensitizes to anti-CTLA4 therapy in a pre-clinical melanoma model. We thus define a major mechanism for how DNMTis may induce cancer cells to increase immune attraction and possibly sensitize patients to immunotherapy. Experiments determining which Aza-upregulated molecules on tumor cells are necessary for attraction and activation of host immune cells are ongoing.

Citation Format: Katherine B. Chiappinelli, Pamela L. Strissel, Alexis Desrichard, Huili Li, Christine Henke, Benjamin Akman, Alexander Hein, Neal S. Rote, Leslie M. Cope, Alexandra Snyder, Vladimir Makarov, Sadna Budhu, Jedd Wolchok, Cynthia A. Zahnow, Taha Mergoub, Timothy A. Chan, Reiner Strick, Stephen B. Baylin. Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr B32.
Abstract IA09: Nucleosome barriers to transcription
Authors: Henikoff Steven , Weber Christopher M. , Teves Sheila S. , Ramachandran Srinivas
Published: May 2016

Nucleosomes are barriers to transcription in vitro, but is this the case in vivo? To address this question, we have introduced a simple and general method to comprehensively map the positions of elongating and arrested RNA polymerase II (RNAPII) at nucleotide resolution. We find that the nucleosomes are barriers to RNAPII elongation at essentially all genes, with the +1 nucleosome downstream of the transcriptional start site the strongest barrier. Depletion of the histone variant H2A.Z from a nucleosome strengthens the barrier to RNAPII, which suggests that H2A.Z has evolved to reduce nucleosome barrier strength. One potential mechanism for overcoming the nucleosome barrier to transcription is the DNA torsional stress created by RNA polymerase transit, which can unwrap and destabilize nucleosomes. We find that inhibiting topoisomerases results in both increased torsion measured at high resolution and increased turnover of nucleosomes, confirming this mechanism in vivo. We have also applied H4S47C-anchored cleavage mapping to identify non-canonical nucleosomes, leading to the characterization of chromatin remodeling intermediates at a subset of +1 nucleosome positions.

Citation Format: Steven Henikoff, Christopher M. Weber, Sheila S. Teves, Srinivas Ramachandran. Nucleosome barriers to transcription. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr IA09.
Abstract IA18: Functional characterization of the tumor suppressor lysine-specific methyltransferase KMT2D in lymphoma
Authors: Ortega-Molina Ana , Boss Isaac W. , Canela Andres , Pan Heng , Jiang Yanwen , Zhao Chunying , Jiang Man , Hu Deqing , Lee Ji-Eun , Chen Hua-Tang , Ennishi Daisuke , Scott David W. , Hother Christoffer , Liu Shichong , Cao Xing-Jun , Tam Wayne , Shaknovich Rita , Garcia Benjamin A. , Gascoyne Randy D. , Ge Kai , Shilatifard Ali , Elemento Olivier , Nussenzweig Andre , Melnick Ari M. , Wendel Hans-Guido
Published: May 2016

Genomic studies have revealed surprising new insights into the genetics of human B-cell lymphomas. Of particular note the lysine-specific methyl transferase KMT2D has emerged as one of the most frequently mutated genes in follicular lymphoma (FL) and in diffuse large B-cell lymphoma (DLBCL). However, the biological consequences of KMT2D mutations in lymphoma are not known. Here we show that KMT2D functions as a bona fide tumor suppressor and promotes lymphoma development in vivo. Integrative analyses of KMT2D function indicate specific and focal effects on H3K4 methylation and gene expression. These include B-cell growth and differentiation signals such as the CD40, JAK/STAT, and B-cell receptor pathways. Moreover, KMT2D targets include frequently mutated tumor suppressor genes such as TNFAIP3/A20, SOCS3, and TNFRSF14/HVEM. In this manner, KMT2D deficiency disrupts the physiological process of B-cell differentiation, facilitates malignant outgrowth, and can impede therapies acting on the CD40 and B-cell receptor pathways.

Citation Format: Ana Ortega-Molina, Isaac W. Boss, Andres Canela, Heng Pan, Yanwen Jiang, Chunying Zhao, Man Jiang, Deqing Hu, Ji-Eun Lee, Hua-Tang Chen, Daisuke Ennishi, David W. Scott, Christoffer Hother, Shichong Liu, Xing-Jun Cao, Wayne Tam, Rita Shaknovich, Benjamin A. Garcia, Randy D. Gascoyne, Kai Ge, Ali Shilatifard, Olivier Elemento, Andre Nussenzweig, Ari M. Melnick, Hans-Guido Wendel. Functional characterization of the tumor suppressor lysine-specific methyltransferase KMT2D in lymphoma. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr IA18.
Abstract B1-06: Tumor genotyping using full cloud based pipeline
Authors: Ueda Hiroki , Yamamoto Shogo , Aburatani Hiroyuki
Published: May 2016

With emergence of Next Generation Sequencer (NGS), data processing using cloud computing and parallel computation becomes necessary. To process huge NGS data, especially yielded from illumina Hiseq2000 sequencer, we have developed a Hadoop/Spark based mapping soft “Volt” which used spaced hash index and Smith-Waterman algorithm with comparable speed and accuracy to existing NGS mapping software. This software can run both on standalone environment and Hadoop/Spark environment, and in later case, the software is directory integrated using Hadoop API and can read and write data to Hadoop Distributed File System (HDFS), and mapping process is distributed using MapReduce framework. To speedup mapping speed, the software uses two seeds match for near perfect hit, and uses full length seed hit for mismatched hit. Also, we have developed tumor genotyper “karkinos” which detects single nucleotide variation (SNV), copy number variation (CNV), calculate tumor cellularity simultaneously. In this genotyper, we proposed “Open genotyper format”, by using that, each heuristic filtering algorithm can be implemented by add on style development. We integrated software into one analysis pipeline and tested on large cohort of liver cancer data. Detailed algorithm and performance data will be shown at the meeting.

Citation Format: Hiroki Ueda, Shogo Yamamoto, Hiroyuki Aburatani. Tumor genotyping using full cloud based pipeline. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-06.
Abstract B1-08: Deep learning for the large-scale cancer data analysis
Authors: Tsuji Shingo , Aburatani Hiroyuki
Published: May 2016

The advanced cancer research fields have been producing vast amount of multi-omics data in various cancer types, and the most of the data are publicly available. It is unquestionably important to analyze these data with unbiased and generalized methodology for obtaining the deeper insights into cancer biology.

Machine learning algorithms, such as k-means clustering, Support Vector Machines (SVM), and Random Forests (RF), have been applied to biological data analysis including cancer research. In this area, deep learning is gaining attention due to its high performance and generalized characteristics for analyzing complex data.

To explore the possibilities for applying deep learning algorithms to the cancer multi-omics data analysis, we compared the performance among SVM, RF, and deep learning. We build the models for predicting cancer types of TCGA pan-cancer data set, and confirmed the advantages for deep learning.

When we applied the algorithm to multi-omics data such as gene expression, DNA methylation, and somatic mutations, the input nodes of the neural network represented each data type. Autoencoders, components of the deep learning models, involve the weighted relationships among the input nodes, therefore we can find the unknown dependencies of some nodes by analyzing the networks of the model.

The results suggested that the deep learning architecture would be promising methodology to progress the cancer research in the data explosion era.

Citation Format: Shingo Tsuji, Hiroyuki Aburatani. Deep learning for the large-scale cancer data analysis. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-08.
Abstract B1-11: Application of the CN-AVG method to reconstruct the evolutionary history of glioblastoma multiforme
Authors: Ballinger Tracy J. , Zerbino Daniel , Paten Benedict , Haussler David
Published: May 2016

We have constructed evolutionary histories of cancer genomes using a new method, the Copy Number Ancestral Variation Graph (CN-AVG). Unlike previous cancer evolutionary studies which infer the clonal structure and evolutionary history of a tumor using single nucleotide variant frequencies, the CN-AVG method predicts the ordering of structural rearrangements, such as inversions, duplications, and deletions, using copy number changes and breakpoints derived from whole genome sequencing data. Because finding the most parsimonious ordering of genomic rearrangements is an NP hard problem, we build a consensus history by merging a large number of possible evolutionary histories generated from MCMC sampling. We tested the CN-AVG method on simulated rearranged genomes and achieved an average accuracy of 62%. We also found that accuracy decreased with increasing complexity of the simulated rearrangements, as expected. We then applied the method to TCGA Glioblastoma Multiforme genomes to search for evolutionary patterns in this disease. The CN-AVG method may distinguish driver mutations as the early rearrangement events and passenger or secondary mutations as the later events in the reconstructed evolutionary history of the tumor, and will be powerful for both the clinic and for research.

Citation Format: Tracy J. Ballinger, Daniel Zerbino, Benedict Paten, David Haussler. Application of the CN-AVG method to reconstruct the evolutionary history of glioblastoma multiforme. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-11.
Abstract B1-18: Integrative analysis of gene expression and metabolism in isocitrate dehydrogenase 1 mutant acute myeloid leukemia and myeloid knock in mouse model
Authors: Tseng Alan , Li Wanda , Lee Kim-Chung , Yung Karrie , Lam Ching-Wan , Mak Tak
Published: May 2016

Isocitrate dehydrogenase 1 (IDH1) mutations are common drivers of acute myeloid leukemia (AML). While mutant IDH1 is known to disrupt DNA methylation, gene expression, and metabolism in cell lines, it is not known how mutant IDH1 alters global metabolism in vivo. The purpose of this study is to find differential enzymes and metabolites in IDH1 wild type versus mutant AML and knock in mice by integrating differential genes and metabolites in a metabolic network.

Differential genes were found by comparing gene expression and DNA methylation in IDH1 mutant (n = 12) and wild type (n = 89) cytogenetically normal AML patients from The Cancer Genome Atlas. Differential metabolites were found by untargeted liquid chromatography-mass spectrometry of urine, plasma, and bone marrow hematopoietic stem and progenitor cells from unpaired 1-2 year old mixed-sex IDH1 myeloid knock in (n = 13) and control mice (n = 14). Integrative analysis was performed using the MetScape 2 Cytoscape plugin.

71 differential genes and 52 differential metabolites were mapped to the global metabolic network. The set of differential genes and metabolites formed 10 connected subnetworks containing reactions in sphingolipid, phospholipid, and bile acid metabolism. Two enzymes in the subnetworks were differentially expressed in an independent IDH1 mutant versus wild type AML dataset: acyl-CoA thioesterase 4 (ACOT4) and galactosylceramidase (GALC) (P < 0.05, false discovery rate ≤ 0.3). ACOT4 and GALC were significantly upregulated (P < 0.02) in acute promyelocytic leukemia cells treated with all-trans retinoic acid.

In conclusion, we have found novel differential genes and metabolites in IDH1 mutant systems which may be relevant to leukemia differentiation treatment. Integrative analysis of gene expression and metabolite levels could be useful for finding dysregulated metabolic subnetworks in cancer.

Citation Format: Alan Tseng, Wanda Li, Kim-Chung Lee, Karrie Yung, Ching-Wan Lam, Tak Mak. Integrative analysis of gene expression and metabolism in isocitrate dehydrogenase 1 mutant acute myeloid leukemia and myeloid knock in mouse model. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-18.
Abstract B1-29: The effect of higher-order receptor clusters on TRAIL induced apoptotic signaling
Authors: Raue Andreas , Chai Diana , Hudson Hannah , Tam Eric , Schoeberl Birgit
Published: May 2016

The trimeric TNF-related apoptosis-inducing ligand (TRAIL) is an endogenous ligand that binds to trimeric death receptors (DR4/5). TRAIL is known to induce apoptosis mainly in malignant cells while normal cells remain unaffected. This makes TRAIL a most interesting target for cancer therapy.

We investigate the effects of ligand valency on the degree of Caspase-8 activation and apoptosis induction. As a model system we use the semi-sensitive cell line DU145 and multivalent anti-DR5 fibronectin domains that can potentially form higher-order receptor clusters. In order to disentangle the effects of receptor clusters of different size, a dynamic model of ligand-receptor binding and Caspase-8 activation is coupled to a model of cell growth and cell death. The dynamic model is calibrated using quantitative experimental data of ligand on cell binding, Caspase-8 activity and cell viability.

Our results show that higher-order receptor clusters do amplify apoptotic signaling. The model predicts that receptor clusters of size three and six are more abundant than others, indicating the special role of preformed receptor trimers. However, Caspase-8 activation only increases after receptor clusters of size larger than three. On the cell population level, the model can quantitatively predict the induction of apoptosis in this cell line. This work is an important step towards an integrative model of TRAIL induced apoptosis that finally aims at the understanding of heterogeneity both on a single cell level across cell lines.

Citation Format: Andreas Raue, Diana Chai, Hannah Hudson, Eric Tam, Birgit Schoeberl. The effect of higher-order receptor clusters on TRAIL induced apoptotic signaling. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-29.
Abstract B1-46: How collection, processing and storage of PBL samples impact the measurement of telomerase activity
Authors: Johnson Ruth A. , Druliner Brooke R. , Alleto Jill Washechek , Devine Donna Felmlee , Ruan Xiaoyang , Vanderboom Russell , Boardman Lisa A.
Published: May 2016

Introduction: Activation of telomerase and telomere lengthening in patient peripheral blood leukocytes (PBL) is associated with longer survival in cancer patients. There are few studies to date that have measured telomerase activity in clinical PBL samples, and it is unclear how initial collection and processing of PBL samples impact the measurement of telomerase activity. In this study, we assessed if telomerase activity measurement varies based on the method of blood collection, processing and storage.

Methods: We first collected whole blood drawn in EDTA tubes from two healthy patients that were then processed three different ways. The first whole blood sample was spun down and the buffy coat was pipetted from the top of the red blood cells, and then placed directly into the -80°C freezer. The next two whole blood samples were isolated using an ACCUSPIN™ tube, which utilizes density gradient separation to recover the PBL without contamination of red blood cells. The resulting PBL from these two samples were suspended in freezing media containing RPMI and DMSO, with one sample also containing penicillin streptomycin glutamine, and then both samples were stored in liquid nitrogen following a slow freeze. We then measured enzymatic telomerase activity in each of the three PBL samples from the two different patients.

Results: We detected a comparable level of telomerase activity in all three PBL samples. These findings indicate that telomerase activity can be measured in buffy coat samples from patients independent of how the samples were processed and stored.

Conclusions: These findings are important because many biorepositories may not have collected or processed PBL samples by identical processes, therefore not allowing direct comparison across samples. Additionally, our finding that telomerase activity levels are comparable between PBL samples containing red blood cells and those processed using an ACCUSPIN™ tube is valuable because it eliminates the necessity for the extra cost of the ACCUSPIN™ tube, freezing media, antibiotics and use of liquid nitrogen storage tanks. Future studies will focus on the determining the relationship of telomerase activity between the PBL, normal colon and cancer tissue in colorectal cancer patients.

Citation Format: Ruth A. Johnson, Brooke R. Druliner, Jill Washechek Alleto, Donna Felmlee Devine, Xiaoyang Ruan, Russell Vanderboom, Lisa A. Boardman. How collection, processing and storage of PBL samples impact the measurement of telomerase activity. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-46.
Abstract B1-52: Analysis of the iCOGS breast cancer GWAS reveals 4 unique signals in the PTHLH region in patients of European origin
Authors: Freeman Adam N. , Martin T John , Henderson Michael A. , Makalic Enes , Kapuscinski Miroslaw K. , Schmidt Daniel F. , Hopper John
Published: May 2016

Parathyroid hormone-related protein (PTHrP), the product of the PTHLH gene, has long been implicated in breast cancer. Its expression is thought to favour and, potentially, facilitate metastasis to bone. Paradoxically, a prospective clinical study clinical suggests that its production in primary breast cancers is actually protective, affording a better prognosis than its absence. Multiple recent Genome-Wide Association Studies (GWAS) have confirmed a single susceptibility locus immediately upstream of the PTHLH gene to be associated with breast cancer. This was again reproduced in the recent iCOGS GWAS, which involved over 90,000 European subjects. In spite of a single SNP, rs10771399, being uniquely reported and reproduced by prior studies, we demonstrate 4 discrete overlapping signals by utilising forward selection logistic regression and LASSO techniques. Two of these signals are centred and superimposed around rs10771399, ~40kbp upstream of PTHLH, a third lies a further 100kbp upstream, and the fourth lies a further 250kbp upstream over the next gene, CCDC91. While the causation of this signal remains elusive, multiple putatively contributory variations are captured by these signals.

Citation Format: Adam N. Freeman, T John Martin, Michael A. Henderson, Enes Makalic, Miroslaw K. Kapuscinski, Daniel F. Schmidt, John Hopper. Analysis of the iCOGS breast cancer GWAS reveals 4 unique signals in the PTHLH region in patients of European origin. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-52.
Abstract B2-03: Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers
Authors: Lee Eunjee , Ito Koichi , Schadt Eric E. , Irie Hanna Y. , Zhu Jun
Published: May 2016

MicroRNAs (miRNAs) play a key role in regulating tumor progression and metastasis. However, miRNA's activity can't be measured by its expression level. We developed a computational approach, ActMiR, for identifying active miRNAs and miRNA-mediated regulatory mechanisms. Applying ActMiR to four cancer datasets in The Cancer Genome Atlas (TCGA), we showed that (1) miRNA activity was tumor subtype specific; (2) genes correlated with inferred miRNA activities were more likely to enrich for miRNA binding motifs; (3) expression levels of these genes and inferred miRNA activities were more likely to be negatively correlated. For the four cancer types in TCGA we identified 64~203 key miRNAs for each cancer subtype and annotated their biological functions. For ER-/HER2- breast cancers we identified activities of key miRNAs let-7d and miR-18a as potential prognostic markers and validated them in two independent ER-/HER2- breast cancer data sets. We experimentally validated their causal relationships with their target genes. Similarly, we showed that key miRNA activities but no miRNA expression level were consistently associated with clinical outcomes for other cancer types. Taken together, the inferred activity of key miRNA provided a functional link to its mediated regulatory network, and can be used to robustly predict patient's survival.

Citation Format: Eunjee Lee, Koichi Ito, Eric E. Schadt, Hanna Y. Irie, Jun Zhu. Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-03.
Abstract B2-10: Systems biology reveals role of cholesterol homeostasis in breast cancer metastasis
Authors: Zhao Weina , Sara Prijic , Urban Bettina , Tisza Michael , Mani Sendurai A. , Chang Jeffrey T.
Published: May 2016

New therapeutic targets that can inhibit cancer metastasis are desperately needed. To address this issue, we have leveraged a computational approach and performed an unbiased screen for therapies that can inhibit an epithelial-to-mesenchymal transition (EMT) gene expression profile, a phenotype that is believed to promote metastases. This yielded predictions of drugs that can both promote and inhibit an EMT transcriptional profile. Following up on these predictions, we confirmed experimentally that these drugs can induce or repress an EMT in a range of breast cancer cell lines. Furthermore, we discovered that they do so by altering the fluidity of the plasma membrane. An increase in plasma membrane fluidity is necessary and sufficient to induce and maintain an EMT state, increased motility, and increased mammosphere forming ability. Finally, we found that human cancers can regulate their membrane fluidity through cholesterol homeostasis pathways. Human breast tumors with altered cholesterol profiles have a significantly shorter time to metastasis. These data demonstrate that an unbiased systems approach can be used to discover novel pathways that underlie metastasis. Our multidisciplinary approach combining computational, cell biology, and mouse models reveal that plasma membrane fluidity is a cellular attribute that is leveraged by human tumors to increase metastatic capacity, and that it can, in principle, be targeted by therapeutics to prevent metastasis.

Citation Format: Weina Zhao, Prijic Sara, Bettina Urban, Michael Tisza, Sendurai A. Mani, Jeffrey T. Chang. Systems biology reveals role of cholesterol homeostasis in breast cancer metastasis. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-10.
Abstract B2-29: The reverse control of colorectal tumorigenesis based on Boolean network modeling of human signaling network
Authors: Sung-Hwan Cho , Sang-Min Park , Ho-Sung Lee , Hwang-Yeol Lee , Kwang-Hyun Cho
Published: May 2016

The intracellular processes are governed by a signal transduction network composed of complex interactions of a number of signaling proteins and various human diseases including cancer are known to be caused by the rewiring of the complex signaling network owing to the individual genetic mutations. There have been many studies on the dynamical analysis of the human signaling network to investigate the progression mechanism of human diseases, but most of the results were limited to small-scale signaling pathways. In this study, we have reconstructed a large-scale signaling network model composed of 197 nodes and 745 relations based on Boolean modeling and performed attractor landscape analysis to uncover the mechanism of colorectal tumorigenesis caused by driver mutations. In addition, we have investigated the reverse control of tumorigenesis by changing the attractor landscape of colorectal cancer state that has been deformed by the driver mutations. Our results show that colorectal tumorigenesis can occur by the expansion of the cancer attractor basin due to the accumulation of driver mutations. We found a minimal control set of network components that can reverse the cancerous state into a normal state. Together, these results suggest a new therapeutic strategy for the treatment of colorectal cancer and provide a new insight into the drug target excavation.

Acknowledgement: This work was supported by the National Research Foundation of Korea (NRF) grants funded by the Korea Government, the Ministry of Science, ICT & Future Planning (2014R1A2A1A10052404, 2013M3A9A7046303, and 2010-0017662).

Citation Format: Cho Sung-Hwan, Park Sang-Min, Lee Ho-Sung, Lee Hwang-Yeol, Cho Kwang-Hyun. The reverse control of colorectal tumorigenesis based on Boolean network modeling of human signaling network. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-29.
Abstract IA24: Computational dissection of phenotypic and functional heterogeneity in cancer
Authors: Pe'er Dana
Published: May 2016

Cells within a single tumor are known to display extensive phenotypic and functional heterogeneity. Many life-threatening features of cancer, including drug resistance, metastasis and relapse, are facets of intratumor heterogeneity. With emerging single-cell measurement technologies, the field is poised to make important strides in understanding and controlling this heterogeneity. However, these technologies require advances in analytical methods to interpret the complex data they produce. Using mass cytometry, which measures single cells in ~31 simultaneous proteomic features, we developed novel methods for analyzing phenotypic heterogeneity in cancer. We use AML as an example to demonstrate the power of our approach. The heart of our approach is Phenograph, a graph-based representation of single-cells which represents the phenotypic structure of the sample and can be partitioned into subsets of densely interconnected nodes, called communities. Using Phenograph, we deconstructed several AML samples into discrete phenotypes. Analyzing the resulting subpopulations provided insights into functional heterogeneity of AML. Phenograph can be applied to characterize heterogeneity and primitive subpopulations in additional cancers.

Citation Format: Dana Pe'er. Computational dissection of phenotypic and functional heterogeneity in cancer. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr IA24.
Abstract PR06: Nucleation of transcriptional super-enhancers at tumor oncogenes
Authors: Abraham Brian J. , Kwiatkowski Nicholas , Weintraub Abraham S. , Hnisz Denes , Hannett Nancy , Young Richard A.
Published: May 2016

Transcriptional super-enhancers drive expression of oncogenes in many cancers and are being targeted with novel transcriptional and epigenetic therapeutics (1,2,3,4). Super-enhancers are acquired in cancers through multiple mechanisms, including DNA translocation of an extant super-enhancer and focal amplification. We recently discovered a novel mechanism by which super-enhancers are nucleated in T cell acute lymphoblastic leukemias (T-ALLs) (5). In this case, a small, monoallelic insertion creates a DNA binding site for a master transcription factor protein, which binds and recruits additional factors to nucleate the super-enhancer, which in turn drives high levels of the TAL1 transcription factor. We describe here a method for unbiased identification of similar genomic insertions that nucleate potentially oncogenic regulatory elements in cancers. This approach uses data from genome-wide ChIP-Seq studies that map locations of enhancer-binding proteins to identify sequences missing from reference genomes. We have found many additional genomic insertions in many additional cancers. I will describe new insights into the regulation of cancer that occur due to nucleation of novel regulatory elements.

1 Hnisz, Abraham, Lee, et al., Cell 2013

2 Loven, Hoke, Lin, et al., Cell 2013

3 Kwiatkowski, et al., Nature, 2014

4 Chipumoro, et al., Cell, 2014

5 Mansour et al., Science 2014

Citation Format: Brian J. Abraham, Nicholas Kwiatkowski, Abraham S. Weintraub, Denes Hnisz, Nancy Hannett, Richard A. Young. Nucleation of transcriptional super-enhancers at tumor oncogenes. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr PR06.
Abstract IA02: Genome regulation by long noncoding RNAs
Authors: Chang Howard Y.
Published: May 2016

The discovery of extensive transcription of long noncoding RNAs (lncRNAs) provide an important new perspective on the centrality of RNA in gene regulation. I will discuss genome-scale strategies to discover and characterize lncRNAs. Genome-wide mapping of RNA secondary structures, termed the structurome, provides important clues to potential functions of regulatory RNAs. An emerging theme from multiple model systems is that lncRNAs form extensive networks of ribonucleoprotein (RNP) complexes with numerous chromatin regulators, and target these enzymatic activities to appropriate locations in the genome. Consistent with this notion, long noncoding RNAs can function as modular scaffolds to specify higher order organization in RNP complexes and in chromatin states. The importance of these modes of regulation is underscored by the newly recognized roles of long RNAs in developmental patterning and cancer.

Citation Format: Howard Y. Chang. Genome regulation by long noncoding RNAs. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr IA02.
Abstract P1-11-01: Depression and anxiety after adjuvant ovarian function suppression in premenopausal breast cancer patients
Authors: Yi HW , Nam SJ , Kim SW , Lee JE , Lee SK , Bae SY , Park S , Paik H-J , Ryu JM
Published: May 2016

Purpose

The results of the Suppression of Ovarian Function Trial (SOFT) and the Tamoxifen and Exemestane Trial (TEXT) showed that ovarian function suppression (OFS) in premenopausal early breast cancer patients improves disease control. However, mood swings after OFS is one of the chief complaints to make patients stop undergoing endocrine therapy. Studies about complications of OFS in breast cancer patients are not established well. We designed this randomized controlled trial to evaluate psychological functioning of patients after undergoing adjuvant OFS by goserelin.

Patients and Methods

We randomly assigned 64 premenopausal women with hormone receptor positive early breast cancer to the tamoxifen or tamoxifen plus goserelin group for a period of 1 year. Participants were screened for depression and generalized anxiety disorder using Hamilton Rating Scale for Depression (HAMD), Hamilton Rating Scale for Anxiety (HAM-A), Anxiety Sensitivity Index (ASI) and Albany panic and phobia questionnaire (APPQ) at baseline, 6 months and 12 months. Brain-derived Neurotrophic Factor (BDNF) levels were measured, as well. The results were analyzed by using a linear mixed model and a generalized linear mixed model.

Results

Thirty two patients were distributed in each group, equally. Linear mixed-mixed model analyses revealed that, compared with HAM-A scores of each group at baseline, HAM-A scores at 12 months showed increments (p=0.0078). Among HAM-A questions, Questions for intellectual, sensory and autonomic status were scored significantly high at 12 months (p=0.0018, p=0.0132, p=0.0006). Platelet BDNF levels reported a statistically significant rise at 12 months (p=0.0006). There was no significant time-by-study group effect in all scales.

Conclusion

Compared with the patients without OFS, patients with Goserelin showed no difference in anxiety or depression scales. Thought the levels of anxiety of each group at 12 months were increased, they do not indicate medical interventions. Patients with increased levels of BDNF at 12 months are expected to have good recovery from anxious and depressive symptoms.

Citation Format: Yi HW, Nam SJ, Kim SW, Lee JE, Lee SK, Bae SY, Park S, Paik H-J, Ryu JM. Depression and anxiety after adjuvant ovarian function suppression in premenopausal breast cancer patients. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-11-01.
Abstract P2-03-08: miR-621 suppresses the metastatic cascade in breast cancer patients
Authors: Xue J , Chi Y , Chen J , Yang B , Wu J
Published: May 2016

Purpose: In previous study, we had shown that miR-621 could sensitize breast cancer to chemotherapy by suppressing FBXO11 and enhancing p53 activity. In this study, we aimed to define miR-621 prognosis value in breast cancer patients, and to explore the potential molecular mechanisms.

Experimental Design: 70 patients with stages II and III breast cancer were included as validation set. The correlation between miR-621 expression level and prognosis in breast cancer patients was confirmed. In parallel, in vitro and in vivo analyses were carried out to determine the potential mechanisms of miRNA-dependent prognosis.

Results: We validated that lower than higher miR-621 expression level was markedly associated with poor metastasis-free survival in breast cancer patients(P=0.03). In breast cancer cell lines, ectopic overexpression of miR-621 inhibited proliferation, migration, invasion, and metastasis both in vitro and in vivo. The potential miR-621-target genes were determined by TargetScan and miRNA CLIP-seq database. Among those, PAK7 was verified as one of the direct targets of miR-621 in breast cancer cells, whose expression level positively associated with recurrence and metastasis in breast cancer patients. The molecular mechanisms by which miR-621/PAK7 axis regulates recurrence and metastasis may involve regulation of epithelial-mesenchymal transition (EMT) in breast cancer cells.

Conclusions: Our study revealed a strong correlation between miR-621 expression and metastasis in breast cancers. High level of miR-621 was negatively associated with poor metastasis-free survival. The increased metastasis-free survival may be mediated by down-regulation of PAK7 gene, which leads to reduced EMT in breast cancer cells. Therefore, miR-621 may represent a therapeutic target for early metastasis breast cancer.

Citation Format: Xue J, Chi Y, Chen J, Yang B, Wu J. miR-621 suppresses the metastatic cascade in breast cancer patients. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-03-08.
Abstract P3-07-14: Prosigna® intrinsic subtyping predicts response to neoadjuvant combination therapy in study that includes herceptin within HER2+ (IHC) patients
Authors: Santonja Á , Ribelles N , Jiménez-Rodríguez B , Sánchez Rovira P , Álvarez M , Vicioso L , Isabel Fernandez A , de Luque V , Fernández de Sousa C , Villar E , Zarcos I , Ramírez C , González-Hermoso C , Jeiranian A , Dowidar N , Schaper C , Buckingham W , Ferree S , Jiménez A , Prat A , Alba E
Published: May 2016

Background: The role of the HER2-enriched (HER2E) subtype determined by the Prosigna Assay in the neoadjuvant setting has remained largely uncharacterized. In this study, we examine whether Prosigna can identify a subgroup of HER2+ patients for whom combination neoadjuvant therapy that includes trastuzumab (Herceptin) is associated with a greater likelihood of pathological complete response (pCR). Methods: In this single-arm retrospective analysis, 75 patients determined to be HER2+ by IHC were treated with a neoadjuvant regimen (NAC) consisting of 8-12 cycles of anthracyclines and taxanes as well as Herceptin. The Prosigna Assay was performed on the NanoString nCounter® Dx Analysis System at HU Virgende la Victoria de Málaga/CIMES-UMA. pCR was used as the endpoint for this study and was determined using the Miller & Payne scoring criteria. Results: Mean patient age for this study population was 49 (±11.1yr) and all patients were determined to be HER2+ by IHC. The overall pCR rate in this patient population was 46.2%. Of the 75 patient samples analyzed for this study, 59 (78.6%) were HER2E, 4 (5.3%) were Luminal A and 12 (16.1%) were Luminal B, as identified by the Prosigna Assay. Of the 16 tumors classified as Luminal (A or B) by Prosigna within this HER2+ population, only 2 (12.5%) responders were observed. Categorical analysis revealed that Prosigna subtype predicted response to a NAC regimen combined with Herceptin (Odds ratio [Her2E vs. non-Her2E]=6.4, p=0.023). Further analysis of the Her2E subtype revealed that tumors with profile expression that correlated well with the prototypical Her2E centroid were significantly more likely to respond to combination NAC and Herceptin (Odds ratio [Unit increase of 1 in Her2E correlation]=88.2, p=0.004). Conclusions: The results of this study indicate that HER2+ patients with greater correlations to the HER2E subtype have an increased likelihood of response to combination neoadjuvant regimens that included HER2-targeted therapy.

Citation Format: Santonja Á, Ribelles N, Jiménez-Rodríguez B, Sánchez Rovira P, Álvarez M, Vicioso L, Isabel Fernandez A, de Luque V, Fernández de Sousa C, Villar E, Zarcos I, Ramírez C, González-Hermoso C, Jeiranian A, Dowidar N, Schaper C, Buckingham W, Ferree S, Jiménez A, Prat A, Alba E. Prosigna® intrinsic subtyping predicts response to neoadjuvant combination therapy in study that includes herceptin within HER2+ (IHC) patients. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-14.