bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract A35: Innovative technologies for cancer research – NCI Strategy for supporting next generation of tools needed against cancer
Authors: Dickherber Tony
Published: May 2016

The development of highly innovative technologies continues to be a high priority for accelerating or challenging existing basic and clinical cancer research paradigms. Epigenetic regulation and chromatin structural biology have offered compelling new opportunities for cancer researchers, but existing tools for investigating this biology are insufficient and new technology development research is needed. The National Institutes of Health (NIH) is the principle biomedical research funding agency of the US federal government, and recognizes that it is often difficult to achieve support for such research through existing program structures. The National Cancer Institute (NCI) is the largest institute of the NIH, and has established the Center for Strategic Scientific Initiatives (CSSI) to pioneer unique scientific and technology initiatives that help keep the NCI ahead of the scientific curve with respect to new and exciting cancer research areas and discoveries. This has involved the development and application of advanced technologies (e.g., Clinical Proteomic Technologies Against Cancer initiative), synergy of large-scale and investigator-initiated research (e.g., NCI Physical Sciences Oncology Network and Alliance for Cancer Nanotechnology), and/or forging novel partnerships that emphasize innovation, trans-disciplinary teams and convergence of scientific disciplines (e.g., The Cancer Genome Atlas) to enable the translation of discoveries into new interventions, both domestically and internationally, to detect, prevent and treat cancer more effectively.

The longest standing program from CSSI is specifically tailored to address the need for highly innovative technology development necessary for advancing cancer research, and it is called the Innovative Molecular Analysis Technologies (IMAT) program. This program employs unique solicitation and review mechanisms better suited to appreciating the longer term potential of transformative technologies and designed to be more tolerant of the substantial risks often associated with such research. Research funding opportunities through this program were recently reissued, with a larger set-aside budget to grant up to 120 new awards through 2017. The unique aspects of both the solicitation and review of applications to this program will be presented, and several recently-supported research projects relevant to chromatin and epigenetics research will be highlighted to demonstrate the variety and high level of innovation evident in the IMAT portfolio of supported research. Potential projects of interest and identified technology gaps will also be discussed.

Citation Format: Tony Dickherber. Innovative technologies for cancer research – NCI Strategy for supporting next generation of tools needed against cancer. [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 A35.
Abstract A46: Effects of genistein supplementation on genome-wide DNA methylation and gene expression in patients with localized prostate cancer
Authors: Bilir Birdal , Lee Jeongseok Edward , Sharma Nitya V. , Lazarevic Bato , Svindland Aud , Kucuk Omer , Moreno Carlos S.
Published: May 2016

Prostate cancer is the most commonly diagnosed malignancy and the second leading cause of cancer death among men in the United States, with an estimated 220,800 new cases and 27,540 deaths in 2015. Epidemiological studies have shown that dietary compounds have significant effects on prostate carcinogenesis. Among dietary agents, genistein, the major isoflavone in soybean, is of particular interest because high consumption of soy products has been associated with a low incidence of prostate cancer, suggesting a preventive role of genistein in prostate cancer. In spite of numerous studies to understand the effects of genistein on prostate cancer, the mechanisms of action have not been fully elucidated. Here, we investigated the differences in methylation and gene expression levels of prostate specimens from a clinical trial of genistein supplementation prior to prostatectomy (Lazarevic B, et al. Nutr Cancer 2011). This study was a randomized, placebo-controlled, double-blind clinical trial on forty-seven Norwegian patients who received 30 mg genistein or placebo capsules daily for 3-6 weeks before prostatectomy. Whole genome methylation and expression profiling identified significantly differentially methylated sites and expressed sites between placebo and genistein groups. Differentially regulated genes were involved in developmental processes, stem cell markers, proliferation, and transcriptional regulation. These findings highlight the effects of genistein on global changes in DNA methylation and gene expression in prostate cancer, and provide additional insight into the multiple molecular pathways involved in prostate tumorigenesis.

Citation Format: Birdal Bilir, Jeongseok Edward Lee, Nitya V. Sharma, Bato Lazarevic, Aud Svindland, Omer Kucuk, Carlos S. Moreno. Effects of genistein supplementation on genome-wide DNA methylation and gene expression in patients with localized prostate cancer. [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 A46.
Abstract A51: DNA methylation in tumor, adjacent non-tumorous and normal breast tissues
Authors: Wagner Erin , Wu Wenting , Liu Yunlong , Nephew Kenneth , Han Jiali , He Chunyan
Published: May 2016

DNA methylation is an essential epigenetic mechanism involved in gene regulation. Aberrant DNA methylation plays an important role in breast cancer initiation and progression via inactivation of tumor suppressor genes and activation of oncogenes. Conventional approaches comparing DNA methylation profiles in tumor and adjacent non-tumorous tissue have shown that changes in DNA methylation contribute to deregulation of gene expression in breast cancer. However, adjacent non-tumorous tissue represents a suboptimal baseline control because its molecular profile may have been altered, and to some extent, similar to that of tumor. Consequently, important breast cancer-associated DNA methylation may not be identifiable in such comparisons. Using RNA-sequencing data generated from freshly-frozen breast tissue samples, we examined expression of methylation-related genes in 119 breast tumor, 47 adjacent normal-appearing breast tissue samples, and 23 normal breast tissue samples from healthy donors. Bowtie and RESM algorithms were used to align raw reads and quantify transcript abundance. Differential expression analyses were performed using edgeR software and normalized transcript counts. Normal breast tissue from healthy women compared to tumor from cancer patients identified differentially expressed cancer genes that are methylated in tumor, such as BRCA1, ESR1, ESR2, CDKN2A, HIC1, CDCP1, and SFRP1. A subset of these genes were found to be deregulated in adjacent non-tumorous tissue in a similar way as in tumor tissue, including PTGS2, SFN, SYK, FHIT , CST6, GADD45A, and THBS1, and are thus undetectable in the comparison between tumor and adjacent non-tumor tissue. In addition, a set of methylation-related genes were identified only in the comparison between tumor and normal tissue, including genes directly involved in the methylation/epigenetic process (HIST1H4A, KDM1B, MAT2B and SAP18) as well as novel target genes that may be methylated and play an important role in carcinogenesis (NFIA, ARHGAP18, and GRHL2). These findings suggest that normal breast tissue from healthy women is the most desirable control in comparison with tumor tissue to identify novel, tissue-specific methylation changes that may be important for carcinogenesis.

Citation Format: Erin Wagner, Wenting Wu, Yunlong Liu, Kenneth Nephew, Jiali Han, Chunyan He. DNA methylation in tumor, adjacent non-tumorous and normal breast tissues. [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 A51.
Abstract B20: Malignant transformation initiates a stochastic DNA methylation alteration pattern distinct from that in senescence
Authors: Xie Wenbing , Zhang Yang W. , Pan Li-Xia , Carvlho Fillipe , Kang Byung-Hak , Xia Limin , Murphy Lauren , Zahnow Cynthia A. , Baylin Stephen B. , Easwaran Hari
Published: May 2016

DNA methylation changes are a hallmark of cancers and occur during early tumorigenesis stages. Also, distinct DNA methylation patterns are reported to be characteristic of the anti-tumorigenic process of cell senescence. It is hypothesized that some cells escape senescence and retain the DNA methylation abnormalities manifest in cancers. We now re-visit, in a classic model of tumor progression in human fibroblasts, the relationships between genome-wide DNA methylation patterns associated with senescence, immortalization and transformation. We find that although DNA methylation alterations are a key feature during senescence, these changes are distinct from those we now find associated with malignant transformation in our model and which are classically seen in cancer. Both DNA methylation gains, predominantly at promoter CpG islands, and more balanced losses and gains at other loci, are seen by the time of pre-senescence and remain relatively stable until full senescence is reached. These DNA methylation alterations follow a reproducible pattern amongst independent senescent replicates involving genes in biological processes which positively regulate biosynthesis, gene transcription and macromolecule metabolism. In contrast, during immortalization and malignant transformation, the DNA methylation alterations appear to arise in a stochastic process resulting in heterogeneous methylation patterns amongst independently immortalized and transformed replicates. Gene ontology analysis shows that genes which gain DNA methylation in normally unmethylated promoter CpG island regions in independent transformation replicates enrich for functions involved in developmental regulation. Over the course of progression from immortalization to the transformed state in our model, gene promoter CpG island hypermethylation frequency increases, as does the numbers of associated genes that have decreased gene expression. Thus, a hallmark of the early transformation process is a stochastic accumulation of DNA methylation changes, distinct from those occurring during senescence, that converges to increasingly affect developmental biological processes and diminished transcription of many of the involved genes, which may help drive the process of tumor progression.

Citation Format: Wenbing Xie, Yang W. Zhang, Li-Xia Pan, Fillipe Carvlho, Byung-Hak Kang, Limin Xia, Lauren Murphy, Cynthia A. Zahnow, Stephen B. Baylin, Hari Easwaran. Malignant transformation initiates a stochastic DNA methylation alteration pattern distinct from that in senescence. [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 B20.
Abstract B24: High-dimensional genomic data integration and bias correction using MANCIE
Authors: Zang Chongzhi , Wang Tao , Deng Ke , Li Bo , Hu Sheng'en , Qin Qian , Xiao Tengfei , Zhang Shihua , Meyer Clifford A. , He Housheng Hansen , Brown Myles , Liu Jun S. , Xie Yang , Liu Xiaole Shirley
Published: May 2016

Most genomic and epigenomic experimental data are presented as high-dimensional matrices. Integrative analysis of such high-dimensional genomic data is challenging due to noises and biases in the high-throughput experiments from different platforms. We present MANCIE (Matrix Analysis and Normalization by Concordant Information Enhancement), a computational method for integrating two genomic datasets based on a Bayesian supported principal component analysis (PCA) approach. We demonstrate that data integration using MANCIE can reduce biases and improve the identification of tissue specificity from the Encyclopedia of DNA Elements (ENCODE) data, improve prognostic prediction from The Cancer Genome Atlas (TCGA) data, and improve the identification of genetic correlation in the Cancer Cell Line Encyclopedia (CCLE) data. MANCIE has broad applications in genomic and epigenomic data analysis in cancer research.

Citation Format: Chongzhi Zang, Tao Wang, Ke Deng, Bo Li, Sheng'en Hu, Qian Qin, Tengfei Xiao, Shihua Zhang, Clifford A. Meyer, Housheng Hansen He, Myles Brown, Jun S. Liu, Yang Xie, Xiaole Shirley Liu. High-dimensional genomic data integration and bias correction using MANCIE. [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 B24.
Abstract B29: Inhibition of histone deacetylases 1 and 2 (HDAC1,2) perturbs DNA replication and DNA repair in cancer cells: Implications in mechanism-based therapeutic strategies
Authors: Johnson Danielle , Jones Simon , Quayle Steven , Shearstone Jeff , Bhaskara Srividya
Published: May 2016

Class I family enzymes, histone deacetylases 1 and 2 (HDAC1,2), are targets of FDA-approved small molecule inhibitors currently used in cancer therapy. HDAC inhibitors impair DNA repair and replication in cancer cells to trigger genotoxic stress and cause cell death. How HDAC1,2 function in genome maintenance processes, DNA replication and repair, in mammalian cells is far from fully understood. Using small molecules to selectively inhibit HDAC1,2 activities, we have systematically defined their direct functions in DNA replication and repair. Our studies show that HDAC1,2 inhibition reduces replication fork velocity and activates the replication stress associated DNA damage independent of its effect on transcription. HDAC1,2 inhibition increases histone H4K16 acetylation (H4K16ac) and nuclease sensitivity of nucleosomes associated with newly replicated DNA, suggesting that HDAC1,2 are required for chromatin compaction during DNA replication. Thus, mechanistically, HDAC1,2 activities are required for maintaining nascent chromatin structure and dynamics required for efficient progression of the replication fork. In addition to H4K16ac, we have found that HDAC1,2 inhibition activities increases H3K27ac and H4K91ac present on the histone tail and core regions, respectively. Increase in these histone acetyl marks perturbs the acetyl-methyl or the acetyl-ubiquityl switch during DNA repair leading to impaired EZH2-mediated H3K27me3-dependent DNA repair signaling and the H4K91ubiquityl-dependent 53BP1-mediated DNA repair signaling in chemoresistant EZH2 gain-of-function diffuse large B-cell lymphoma cells. We are currently investigating the therapeutic benefits of HDAC1,2 inhibition in mouse models of aggressive chemoresistant diffuse large B-cell lymphoma and in primary patient samples. Overall, our studies have uncovered novel functions for HDAC1,2 in genome maintenance processes and provide insight into the mode-of-action of HDAC1,2 inhibitors in overcoming chemoresistance in cancer cells (via targeting the DNA repair process) and in inducing DNA damage and death in the rapidly cycling cancer cells (via targeting DNA replication).

Note: This abstract was not presented at the conference.

Citation Format: Danielle Johnson, Simon Jones, Steven Quayle, Jeff Shearstone, Srividya Bhaskara. Inhibition of histone deacetylases 1 and 2 (HDAC1,2) perturbs DNA replication and DNA repair in cancer cells: Implications in mechanism-based therapeutic strategies. [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 B29.
Abstract B43: Dose and context-dependent roles for Arid1a in liver tumorigenesis
Authors: Sun Xuxu , Wang Sam , Nguyen Liem , Zhu Hao
Published: May 2016

Frequent Arid1a loss-of-function mutations suggest tumor suppressive roles, but the functional impact of Arid1a and SWI/SNF chromatin-remodeling aberrations in human cancer are not clear. Liver-specific Arid1a knockout mice do not develop cancer after 15 months and surprisingly, homozygous mice are potently protected from diethylnitrosamine (DEN) + carbon tetrachloride induced hepatocellular carcinoma (HCC). This is likely due to the fact that Arid1a deficient livers are resistant to chemical damage in a Cytochrome P450 dependent fashion. To determine if genetic drivers of cancer might reveal additional roles for Arid1a, we showed that Arid1a loss results in increased survival in a MYC driven liver cancer model. Given the physical interactions between MYC and Arid1a and a global reduction in mRNA levels, we hypothesize that MYC's transcriptional activities are constrained by the lack of normal SWI/SNF chromatin remodeling. Interestingly, in vivo anti-Arid1a siRNA delivery to mice overexpressing MYC also prolonged survival, demonstrating that mutation timing does not explain the lack of tumor suppressor activity. Our models build the case that Arid1a is not a bona fide tumor suppressor gene in many important contexts.

Citation Format: Xuxu Sun, Sam Wang, Liem Nguyen, Hao Zhu. Dose and context-dependent roles for Arid1a in liver tumorigenesis. [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 B43.
Abstract B44: Accelerated mouse colorectal cancer progression in the presence of EHMT2 overexpression
Authors: Tai Kang-Yu , Yu I-Shing , Cha Shih-Ting , Lin Shu-Wha , Kuo Min-Liang , Chen You-Tzung
Published: May 2016

In the last 5 years, the prevalence of colorectal cancer (CRC) has increased worldwide and has surpassed that of liver cancer. Even after treatment for primary CRC, patients still have a high risk (30%–50%) of cancer recurrence, generally from metastasis. Thus, if we can uncover the progressive mechanisms of CRC and identify a novel drug target, current treatment regimens and the survival of patients with advanced stage CRC can be improved. Euchromatin histone lysine N-methyl transferase 2 (EHMT2) inhibition is considered an effective therapeutic strategy for cancer treatment because its inhibitors, BIX-01294 and UNC0639, can induce autophagy-dependent cell death. However, the function of EHMT2 in CRC progression remains largely unclear. In this study, we established a colonic stem-cell-specific EHMT2 activation combined with sporadic (AOM/DSS-induced) or hereditary (Apc mutant) CRC mouse models. In the EHMT2-overexpressed group, many colonic tumors larger than 3 mm in size were found in the 24 weeks after tumor induction. Histological analysis of these tumors showed that the adenocarcinomatous glands became highly irregular, and these glands were difficult to discern, one of the characteristic of malignant CRC. In the 52 weeks after tumor induction, we reproducibly observed CRC liver metastases. Further analysis by RNA sequencing combined with gene set enrichment analysis determined that the anti-apoptosis-related and Wnt-signaling gene sets can be enriched in the EHMT2-overexpressed group. Using the chromatin immunoprecipitation assay, we demonstrated that EHMT2 directly targeted the caspase8 proximal promoter region and increased the level of H3 lysine9 di-methylation in this region. Several functional assays supported that this gene regulation may have conferred opportunities for CRC cells to avoid the cytotoxicity of anticancer drugs. Overall, aberrant EHMT2 expression is conducive to CRC progression.

Citation Format: Kang-Yu Tai, I-Shing Yu, Shih-Ting Cha, Shu-Wha Lin, Min-Liang Kuo, You-Tzung Chen. Accelerated mouse colorectal cancer progression in the presence of EHMT2 overexpression. [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 B44.
Abstract B48: Epigenetic reprogramming of mitochondrial and metabolic functions plays a key role in arginine-deprivation based cancer therapy
Authors: Wang Hung-Jung , Yu Yen-Ling , Hsu Sheng-Chieh , Kuo Cheng-Chin , Wang Wen-Ching , Shuu Chin-Pin , Kung Hsing-Jien
Published: May 2016

Arginine deprivation has recently emerged as a promising cancer therapy, targeting tumor metabolism. This is due to the selective silencing of argininosuccinate synthetase 1 (ASS1) gene in many cancer types, rendering them “addicted” to external arginine. PEGylated arginine deiminase (ADI-PEG20), which effectively metabolizes arginine into citrulline and ammonia, has shown promising results in clinical trials for treating a variety of cancers. We have previously shown that ADI-PEG20 induces a novel type of tumor cell killing involving mitochondria dysfunction and chromatin autophagy, and that lysine demethylase KDM8 which regulates PKM2 plays an important role in tumor metabolism. We also observed in ADI-treated cells, the severe depletion of metabolites involved in glycolysis and glutaminolysis including alpha-ketoglutarate, a key cofactor for many of the KDMs. In parallel, many of the metabolic genes and nuclear genes involved in TCA cycles are coordinately down-modulated, which can be rescued by the addition of arginine. To study whether the coordinated gene repression is via epigenetic mechanism or due to the inhibition of KDMs, we analyzed the methylation status of histones at the promoter sites of metabolic genes, and found consistent accumulation of histone marks associated with transcriptional repression in ADI-PEG20-treated cells. Our results thus suggest that epigenetic reprogramming plays an important a role in the coordinated repression of metabolic gene expression in arginine-deprived cells.

Citation Format: Hung-Jung Wang, Yen-Ling Yu, Sheng-Chieh Hsu, Cheng-Chin Kuo, Wen-Ching Wang, Chin-Pin Shuu, Hsing-Jien Kung. Epigenetic reprogramming of mitochondrial and metabolic functions plays a key role in arginine-deprivation based cancer therapy. [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 B48.
Abstract IA02: Genomic organization of yeast chromatin and gene regulatory complexes
Authors: Pugh B. Franklin
Published: May 2016

The large number of genes across eukaryotic genomes begs the question as to whether they are all fundamentally regulated in the same manner. Clearly, sequence-specific factors direct gene-specific regulation, but then do all downstream events proceed along a common path? To begin to address this question, we use ChIP-exo to map the precise contact points of proteins along genomic DNA. The near single-bp readout provides structural insights into how proteins are organized into complexes across genomes, and how they might position nucleosomes to regulate gene expression. Multiple classes of complexes occupy nucleosome-free promoter regions: an ensemble of sequence-specific factors and their coactivators, the core transcription machinery, chromatin remodelers and nucleosomes. This talk will focus on identifying common principles that determined how factors and chromatin organize themselves at promoters across co-regulated genes, and in genes in general.

Citation Format: B. Franklin Pugh. Genomic organization of yeast chromatin and gene regulatory complexes. [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 IA02.
Abstract IA04: How DNA methylation organizes the cancer epigenome
Authors: Jones Peter A.
Published: May 2016

The holistic role of DNA methylation in the organization of the cancer epigenome is not well understood. We performed a comprehensive, high-resolution analysis of chromatin structure to compare the landscapes of HCT116 colon cancer cells and a DNA methylation deficient derivative. The NOMe-seq accessibility assay unexpectedly revealed symmetrical and transcription-independent nucleosomal phasing across active, poised and inactive genomic elements. DNA methylation abolished this phasing primarily at enhancers and CpG Island (CGI) promoters, with little effect on insulators and non-CGI promoters. Abolishment of DNA methylation led to the context-specific reestablishment of the poised and active states of normal colon cells, which were marked in methylation-deficient cells by distinct H3K27 modifications and the presence of either well-phased nucleosomes or nucleosome depleted regions, respectively. Taken together, our results demonstrate the nuanced and context-dependent role of DNA methylation in the functional, multi-scale organization of cancer epigenomes.

Citation Format: Peter A. Jones. How DNA methylation organizes the cancer epigenome. [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 IA04.
Abstract IA10: Regulating transcription elongation at stimulus responsive genes
Authors: Adelman Karen , Scruggs Benjamin S. , Henriques Telmo , Burkholder Adam , Fargo David C.
Published: May 2016

The majority of mammalian protein-coding genes display transcription in both sense and anti-sense directions. At such bidirectional promoters, Pol II has been shown to initiate transcription and undergo promoter-proximal pausing near both the sense-strand mRNA transcription start site (TSS) and from within the upstream region in the anti-sense direction. This enigmatic, dual promoter structure raises fundamental questions about the specificity, purpose and regulation of upstream anti-sense transcription. Interestingly, transcription in the anti-sense direction is generally non-processive and creates short, unstable non-coding RNAs (ncRNAs). Intriguingly, many distal enhancer regions display bidirectional transcription and generate short unstable ncRNAs, raising parallels between enhancers and anti-sense promoters near protein-coding genes.

Importantly, enhancers and upstream anti-sense promoters show exquisite cell type specificity in their location and activity, suggesting key roles in establishing cell state and behavior. Further, perturbation of either transcription or chromatin structure at such non-coding loci has been implicated in the development of cancer and disease, with a profound impact on maintenance of cell state and responsiveness to stimuli. These recent findings raise a number of intriguing questions about the communication between promoters and non-coding loci.

Our work has recently defined a mechanism through which upstream anti-sense transcription impacts stimulus-responsive gene expression. Specifically, we found that the distance between sense and anti-sense TSSs at bidirectional promoters strongly influences activation of pro-inflammatory genes in macrophages. We discovered that anti-sense TSSs organize chromatin structure, creating a region of open chromatin between bidirectional TSSs that is optimal for recruitment of the transcription machinery and signal-dependent transcription factors like NF-kB. Further, we discovered that key inflammatory genes possess enhancer-like histone modifications around the anti-sense TSS, and that this characteristic selectively marks genes that are highly activated upon immune stimulation.

Citation Format: Karen Adelman, Benjamin S. Scruggs, Telmo Henriques, Adam Burkholder, David C. Fargo. Regulating transcription elongation at stimulus responsive genes. [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 IA10.
Abstract PR04: Targeting super-enhancer driven oncogene transcription through cyclin-dependent kinase inhibitors
Authors: Krajewska Malgorzata , Moore Nathan F. , Chipumuro Edmond , Zhang Tinghu , Marco Eugenio , Hatheway Clark , Sharma Bandana , Kwiatkowski Nicholas , Yuan Guo-Cheng , Young Richard A. , Gray Nathanael S. , George Rani E.
Published: May 2016

Cyclin-dependent kinases (CDKs) with primary roles in transcription regulation are emerging as tractable therapeutic targets in cancers driven by the aberrant expression of oncogenic transcription factors. Our goal is to disrupt the myriad and pleomorphic features of oncogenic MYC through inhibiting CDKs involved in its transcriptional amplifier role. CDK7 participates in transcription initiation by phosphorylating the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II and also functions as a CDK-activating kinase, while CDK12 functions in transcription elongation and RNA processing. Using a novel covalent CDK7 inhibitor, THZ1, we demonstrated striking activity and selectivity in neuroblastoma (NB) cells driven by high MYCN expression. This response translated to significant tumor regression in a mouse model of high-risk NB, without introducing discernible toxicity. We determined that this effect was associated with global inhibition of MYCN-dependent transcriptional amplification. THZ1 led to preferential downregulation of Pol II occupancy at super-enhancer-associated genes, including MYCN and other master transcription factors critical to neuronal development such as PHOX2B, GATA2, and DBH. Similarly, inhibition of CDK12 activity using a novel, first-in-class small molecule inhibitor, THZ-5-31-1, resulted in potent antitumor activity in MYCN-overexpressing NB cells. THZ-5-31-1 doses sufficient to induce PARP cleavage did not lead to significant inhibition of global transcription elongation. Rather, cytotoxicity was associated with preferential downregulation of RNA processing factors and a higher percentage of immature mRNA transcripts. Together, these results suggest that transcriptional CDK inhibitors, by affecting different aspects of the transcription machinery, may inhibit the growth of cancers driven by oncogenic transcription factors such as MYC.

Citation Format: Malgorzata Krajewska, Nathan F. Moore, Edmond Chipumuro, Tinghu Zhang, Eugenio Marco, Clark Hatheway, Bandana Sharma, Nicholas Kwiatkowski, Guo-Cheng Yuan, Richard A. Young, Nathanael S. Gray, Rani E. George. Targeting super-enhancer driven oncogene transcription through cyclin-dependent kinase inhibitors. [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 PR04.
Abstract PR08: GC skew defines distinct RNA polymerase pause sites in CpG island promoters
Authors: Bell Joshua SK , Kellner Wendy A. , Vertino Paula M.
Published: May 2016

Promoter-proximal pausing of RNA Pol II (Pol II) is a near universal feature of human genes and plays a central role in governing levels of transcription and modulating rapid response to stimuli. Here we show that at CpG island (CGI)- associated promoters, Pol II encounters an additional barrier to elongation distinct from the promoter-proximal pause that occurs at the downstream boundary of the CGI domain. For most CGI associated promoters, Pol II exhibits a dominant pause at either the promoter-proximal or this distal site that correlates, both in position and in intensity, with local regions of high GC skew, a sequence feature known to promote the formation of unique secondary structures. Indeed, we find that distally paused genes manifest longer or more stable R-loops, a structure suggested to protect CGI domains from DNA methylation. Interestingly, the link between GC-skew and Pol II pausing is conserved in Drosophila. Upon signal-induced gene activation, long-range enhancer contacts at the dominant pause site are selectively enhanced, suggesting a new role for enhancers at CGI boundaries. Consistent with this idea, we find a correlation between enrichment of the cohesin complex, important for DNA looping, and the position of the dominant pause site. These findings unearth a novel transcriptional regulatory step at CGI-associated genes that is dictated by the underlying DNA sequenceand linked to the integrity of the CGI domain.

Citation Format: Joshua SK Bell, Wendy A. Kellner, Paula M. Vertino. GC skew defines distinct RNA polymerase pause sites in CpG island promoters. [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 PR08.
Abstract PR12: MED12 methylation by CARM1 sensitizes human breast cancer cells to chemotherapy drugs
Authors: Lu Wang , Zeng Hao , Wang Qiang , Zhao Zibo , Boyer Thomas G. , Bian Xiuwu , Xu Wei
Published: May 2016

Chemotherapy continues to be an important treatment to reduce the risk of metastatic breast cancer recurrence. However, many tumors relapse due to the development of multidrug resistance, the mechanisms of which remain poorly understood. Therefore, there is a pressing need to elucidate mechanisms of resistance and discover a sensitive biomarker that could predict patient response to chemotherapeutic drugs. We discovered that chemosensitivity can be predicted by methylation of a mediator of RNA polymerase II transcription subunit 12 (MED12) by coactivator associated arginine methyltransferase 1 (CARM1). MED12 is frequently mutated in human cancers, and loss of MED12 has been shown to induce drug resistance through activation of TGF-βR signaling. We showed that MED12 is a novel substrate of CARM1. Not only are the expression levels of CARM1 and MED12 positively correlated but their high expression predicts better prognosis in human breast cancers after chemotherapy. MED12 was primarily methylated at R1862 by CARM1, and mutation of this site in cell lines resulted in resistance to chemotherapy drugs (e.g. 5-FU). A change in chemosensitivity by altering the methylation status of a single protein in breast cancer cells is unprecedented. Mechanistically, we showed that the methylation-dependent drug response mechanism is distinct from activation of TGF-βR signaling. Further, we found that methylated MED12 potently suppresses p21/WAF1 transcription. Cells defective in MED12 methylation have up-regulated p21 protein, which correlates with poor prognosis in breast cancer patients treated with chemotherapy. Collectively this study identifies MED12-methylation as a sensor for predicting response to commonly used chemo-drugs in human cancers.

Citation Format: Wang Lu, Hao Zeng, Qiang Wang, Zibo Zhao, Thomas G. Boyer, Xiuwu Bian, Wei Xu. MED12 methylation by CARM1 sensitizes human breast cancer cells to chemotherapy drugs. [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 PR12.
Abstract B1-05: R2: Accessible web-based genomics analysis and visualization platform for biomedical researchers
Authors: Koster Jan , Molenaar Jan J. , Versteeg Rogier
Published: May 2016

In this era of explosive high throughput (HT) genomics data generation, there is a growing need for accessible software solutions that can help unlock biological/clinical characteristics from such data. With the biomedical researcher (with limited or no bioinformatics skills) in mind, we developed a comprehensive web-based system called R2 (http://r2.amc.nl). R2 aids in the analysis and visualization of private/shielded as well as public high throughput data and their associated annotated features.

The R2 platform consists of a database storing both publicly accessible as well as shielded datasets with unified gene annotation, supplemented with a large suite of tools that can be used on these data, and their associated annotation. As such the user experiences the same look & feel throughout the mining process.

In the public section, R2 hosts over 60,000 HT samples. Next to gene expression (microarray and RNA-seq), the platform is also being employed in the integration, analysis and visualization of other data types, such as aCGH, SNP, ChIP, methylation, miRNA, and NGS whole genome sequencing information.

R2 contains an expanding set of interactive analyses which are heavily inter-connected, allowing users to quickly hop from one view (representation of the data) to another. Analyses include, correlation, differential expression, gene sets, gene ontology, transcription factor binding sites, PCA, kmeans, Kaplan Meier scans, signature creation etc. Visualizations include, various gene oriented plots, heatmaps, circos, embedded genome browser, Venn, etc.

Many parts of the R2 platform are publicly accessible through the http://r2.amc.nl portal. The R2 gene expression analysis tools have thus far been used in more than 180 peer-reviewed scientific publications including journals as Nature, Nature Genetics and Cell. R2 also supports restricted / shielded use and is used in many (inter)national collaborative efforts involving unpublished datasets. The webservers have been serving over 900.000 pages over the past 12 months (Nov 2014).

Citation Format: Jan Koster, Jan J. Molenaar, Rogier Versteeg. R2: Accessible web-based genomics analysis and visualization platform for biomedical researchers. [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 B1-05.
Abstract B1-20: Gene regulation by transcription factors and microRNAs in ovarian cancer
Authors: Kuijjer Marieke Lydia , Glass Kimberly , Quackenbush John
Published: May 2016

Conventional methods to analyze genomic data do not make use of the connectivity between different data types, such as transcriptional regulation and gene expression, thereby often failing to identify the cellular processes that are unique to cancer and cancer subtypes. An example of this are the four recently characterized high-grade serous ovarian cancer transcriptomic subtypes – differentiated, immunoreactive, mesenchymal, and proliferative ovarian cancer. These subtypes have not been associated with significant differences in survival, and their discovery has not lead to the identification of subtype-specific therapies. Uncovering the regulatory mechanisms mediating differences in expression between these subtypes may identify new therapeutic interventions, and ultimately help cancer patients.

We modeled regulatory networks of the four ovarian cancer subtypes using PANDA, a network inference approach that uses genomic data to search for an optimal network by modeling information flow between regulators and target genes. Because not only transcription factors, but also microRNAs play an important role in gene regulation, we modified the PANDA algorithm to account for the regulatory effects of microRNAs in addition to transcription factors (miR-PANDA, in preparation). We compared the networks defining gene regulation in each subtype using different network comparison metrics. We observed a very striking pattern in out-degree differences that suggests transcription factors and microRNAs play a major role in driving the different subtypes. Using gene set enrichment analysis on in-degree differences of target genes, we identified several cancer-related pathways that are highly targeted in specific subtypes, such as regulation of Notch signaling by microRNAs in the immunoreactive subtype, and regulation of Wnt signaling by transcription factors in the proliferative subtype. These results may point to new therapeutic interventions and advance personalized treatments for ovarian cancer patients.

Citation Format: Marieke Lydia Kuijjer, Kimberly Glass, John Quackenbush. Gene regulation by transcription factors and microRNAs in ovarian 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 B1-20.
Abstract B1-33: Network analyses identify hidden regulators of TGFa shedding
Authors: Wilson Jennifer L. , Fraenkel Ernest , Lauffenburger Douglas A. , Herrlich Andreas
Published: May 2016

It is well known that components of the ADAM17/EGFR ligand axis, ADAM17, TGFa, and AR, are upregulated in aggressive, metastatic forms of triple negative breast cancer (TNBC). Furthermore, we know that activation of alternate receptor-tyrosine kinase (RTK) ligands can decrease sensitivity to kinase inhibitor treatments (such as the EGFR-targeting erlotinib) and that locally-shed growth ligands are one source of RTK reactivation1. Unfortunately, directly targeting ADAM17 activity is a poor therapeutic option due to non-specific effects. It is currently unknown what regulators affect ligand shedding, the extent of specificity in this regulation and what connections, if any, exist between ligand shedding regulation and RTK re-activation, cell growth and metastasis in TNBC. We hypothesize that ligand shedding regulation is an important component of altered growth factor pathway signaling and that targets within these pathways contribute to the reactivation of growth factor pathways and chemotherapy resistance in TNBC. Here we use the Prize-Collecting Steiner Forest (PCSF), an interactome-based network construction tool, to identify candidate regulators of ectodomain shedding and leverage TNBC patient data to identify regulators with relevance to TNBC pathology.

Citation Format: Jennifer L. Wilson, Ernest Fraenkel, Douglas A. Lauffenburger, Andreas Herrlich. Network analyses identify hidden regulators of TGFa shedding. [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 B1-33.
Abstract B2-04: Time lapse to cancer: Defining the transition from polyp to colorectal cancer based on telomere metrics
Authors: Druliner Brooke R. , Johnson Ruth , Ruan Xiaoyang , Vanderboom Russell , Devine Donna Felmlee , Aletto Jill Washechek , Boardman Lisa A.
Published: May 2016

Despite advances in prevention and early detection strategies, colorectal cancer (CRC) remains the second leading cause of cancer death in the United States. The majority of CRC arises from adenomatous polyps. However, only 5% of all people who receive a colonoscopy will have a lesion determined to be at high risk for malignant transformation. Adenomas are primarily classified based on histology, size, degree of dysplasia and limited genetic mutation information. Further characterization of what contributes to or underlies the malignant transformation of polyps is currently lacking, but is essential to further understand the transition from polyp to cancer and factors that lead only a small portion of polyps to progress onto cancer.

Although telomere length is a recognized biomarker in multiple cancers, few studies have addressed the comprehensive role of telomeres in CRC progression. Telomere shortening is a fundamental feature of dividing cells related to the age of the cell and is implicated in carcinogenesis. Telomere length is not solely determined by attrition resulting from cell division, but also through telomere maintenance mechanisms (TMM), which are often exploited in malignant cells. In this study, we will measure the telomere profile (consisting of telomere length and TMM) in normal colon epithelium, polyps and the adjacent tumor trios and normal colon epithelium and cancer-free polyp pairs. Our aim is to determine which telomere features distinguish cancer adjacent polyps from cancer free polyps. This is an innovative approach for identifying the definable telomere-related properties that distinguish polyps with malignant potential that remain benign from those that transform to cancer and progress to invasive lesions. Further characterization of the molecular profile of polyps undergoing the transition to cancer that differentiate cancer free polyps has the potential to be utilized in designing optimal treatment options for patients with polyps that carry the risk of CRC.

Citation Format: Brooke R. Druliner, Ruth Johnson, Xiaoyang Ruan, Russell Vanderboom, Donna Felmlee Devine, Jill Washechek Aletto, Lisa A. Boardman. Time lapse to cancer: Defining the transition from polyp to colorectal cancer based on telomere metrics. [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 B2-04.
Abstract B2-34: Model guided understanding of synergistic combination therapies in the DNA damage response pathway
Authors: Raue Andreas , Alkan Ozan , Drummond Daryl , Schoeberl Birgit
Published: May 2016

Most commonly used anti-cancer therapies involve the systemic administration of anti-proliferative and DNA damaging agents. Deregulation of DNA damage response (DDR) pathways can cause resistance to DNA damaging therapies. Synergistic combination strategies of novel DDR pathway modulators promise to re-sensitize to and amplify currently used standard-of-care therapies.

Our goal is to gain mechanistic understanding of the DDR pathway by developing a predictive computational model using single cell microscopy phenotypic data and signaling data from a panel of cancer cell lines. We focus on synergistic and potentiating effects of drug combinations using standard-of-care drugs such as doxorubicin, gemcitabine and irinotecan, and DDR pathway modulators. Our computational model explains the mechanisms of synergistic or additive phenotype that are observed for various modulators and was validated using DDR signaling data.

The presented computational model rationalizes the design of novel combination therapies targeting the DDR pathway, includes heterogeneity of different cell lines and is an important step towards the design of a biomarker strategy.

Citation Format: Andreas Raue, Ozan Alkan, Daryl Drummond, Birgit Schoeberl. Model guided understanding of synergistic combination therapies in the DNA damage response pathway. [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 B2-34.