bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract SY01-03: The obesity-inflammation connection: Implications for breast carcinogenesis.
Authors: Dannenberg Andrew J.
Published: August 2014

Obesity is a risk factor for the development of several malignancies including hormone receptor-positive breast cancer in postmenopausal women and has been associated with an increased risk of recurrence and reduced survival. Chronic inflammation increases the risk of multiple malignancies. A link between obesity, breast inflammation and hormone receptor-positive breast cancer was previously unknown. Obesity causes subclinical inflammation in visceral and subcutaneous white adipose tissue, characterized by macrophages surrounding dead adipocytes forming crown-like structures (CLS). The synthesis of estrogen is catalyzed by aromatase, which is encoded by CYP19. Recently, we found increased numbers of CLS, activation of the NF-κB transcription factor, increased levels of pro-inflammatory mediators (TNF-α, IL-1β, PGE2) and elevated aromatase levels and activity in the mammary glands of obese mice. These preclinical findings raised the possibility that the obesity→inflammation →aromatase axis is important for breast carcinogenesis. Importantly, these findings have now been translated to women. Breast tissue was obtained from women who underwent mastectomy. CLS of the breast (CLS-B) were found in nearly 50% of patient samples. The severity of breast inflammation, defined as the CLS-B index, correlated with both body mass index and adipocyte size. Consistent with our preclinical findings, increased NF-κB binding activity, increased levels of pro-inflammatory mediators and elevated aromatase expression and activity were found in the inflamed breast tissue of overweight and obese women. Collectively, these results suggest that the obesity→inflammation →aromatase axis is present in the breast tissue of most overweight and obese women and is likely to contribute to the increased risk of hormone receptor-positive breast cancer. The presence of CLS-B may be a biomarker of increased breast cancer risk or poor prognosis. The discovery of the connection between obesity, breast inflammation and changes in the expression of genes linked to breast cancer provides a mechanistic rationale for the development of behavioral, dietary and pharmacological strategies to reduce the risk of breast cancer. Recently conducted preclinical experiments provide proof-of-principle evidence that obesity-related mammary gland inflammation can be rapidly reversed with caloric restriction.

Citation Format: Andrew J. Dannenberg. The obesity-inflammation connection: Implications for breast carcinogenesis. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr SY01-03. doi:10.1158/1538-7445.AM2013-SY01-03
Abstract SY02-01: Regulators of in situ to invasive breast carcinoma progression.
Authors: Polyak Kornelia
Published: August 2014

A major clinical diagnostic criterion that differentiates in situ from invasive breast carcinoma is the presence of a continuous myoepithelial cell layer and basement membrane. In pre-invasive lesions such as DCIS, a relatively intact myoepithelial cell layer and basement membrane are still observed, but we have found that the molecular profiles of DCIS-associated myoepithelial cells are distinct from those from normal breast. The mechanisms underlying the loss of myoepithelial cells during the in situ to invasive breast carcinoma transition are unknown.

We hypothesized that the differentiation of breast epithelial progenitors into myoepithelial cells is progressively inhibited by signals from tumor epithelial cells and cells composing the microenvironment such as fibroblasts and leukocytes. As a consequence, the myoepithelial cell layer is progressively lost and eventually disappears resulting in progression to invasion.

We have been testing this hypothesis by characterizing myoepithelial cells from normal human breast tissues from nulliparous and parous women, including BRCA1 and BRCA2 mutation carriers. To dissect the functional properties of different types of myoepithelial cells, we have been using the MCFDCIS xenograft model. Our results will not only improve the current understanding of the role of myoepithelial cells but also have the potential to provide new prognostic markers to predict risk of invasive progression in DCIS. Furthermore, our results may help identify new targets for chemoprevention aimed at decreasing the risk of invasive breast tumors.

Citation Format: Kornelia Polyak. Regulators of in situ to invasive breast carcinoma progression. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr SY02-01. doi:10.1158/1538-7445.AM2013-SY02-01
Abstract SY02-04: Inhibition of Hedgehog signaling for prevention and treatment of basal cell carcinomas.
Authors: Epstein Ervin H.
Published: August 2014

Basal cell carcinomas, the most common of human cancers, differ from many other cancers not only in their frequency but also in the great rarity with which they metastasize and their routinely high cure rate following surgery. Because all BCCs are driven by mutational activation of the hedgehog signaling pathway in the tumor cells, small molecule hedgehog inhibitors are a “natural” approach. Indeed, not only the rare metastatic and locally advanced BCCs but also the high number of smaller individually less aggressive BCCs in patients with the Gorlin syndrome respond extremely well to small molecule Hedgehog inhibitors. This illustrates that interfering with critical pathways not only can treat existing tumors but also can prevent even the development of new tumors.

Citation Format: Ervin H. Epstein. Inhibition of Hedgehog signaling for prevention and treatment of basal cell carcinomas. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr SY02-04. doi:10.1158/1538-7445.AM2013-SY02-04
Abstract SY10-02: Breast cancer subtypes have selective kinome reprogramming in response to kinase inhibitors.
Authors: Johnson Gary
Published: August 2014

Multiplexed Inhibitor Beads coupled with quantitative Mass Spectrometry (MIB/MS) allows study of over 60-70% of the expressed kinome simultaneously using lysates from cell lines, mouse tumors and human specimens. Cells or tumors are assessed before and after addition of agonists or inhibitors. Results show a systems kinome reprogramming in response to highly selective inhibitors that creates inhibitor resistance. The activation signatures and changes in the kinome activation profile (kinome reprogramming) are unique for each breast cancer subtype (Luminal, HER2+, Basal-like, Claudin-low) in response to highly selective, clinically relevant kinase inhibitors (MEKinh, mTOR/PI3Kinh). Window trials in patients with TNBC have shown kinome reprogramming in response to MEKinh, suggesting understanding kinome resiliency is necessary for rational design of effective combination therapies to treat cancer in individual patients.

Citation Format: Gary Johnson. Breast cancer subtypes have selective kinome reprogramming in response to kinase inhibitors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr SY10-02. doi:10.1158/1538-7445.AM2013-SY10-02
Abstract SY11-01: Plasma tumor DNA: Changing the paradigm for administering systemic therapies.
Authors: Beaver Julia A. , Valda Patricia , Jelovac Danijela , Higgins Michaela J. , Park Ben H.
Published: August 2014

The ability to accurately detect somatic cancer DNA alterations from cell free circulating plasma tumor DNA (ptDNA) using next generation genomic technologies has many potential applications for clinical oncology. The initial use of this technology has been to detect point mutations in peripheral blood that could serve as predictors of response to various targeted therapies. Thus the development of a “liquid biopsy” that could easily match the mutational status of a given cancer with a specific therapy had great therapeutic implications. For example, the ability to assess certain epidermal growth factor receptor (EGFR) mutations via blood versus an invasive lung biopsy would allow for the rapid determination of whether a patient would be a candidate for small molecule EGFR inhibitors such as gefitinib or erlotinib. We initially sought to evaluate the feasibility of detecting PIK3CA mutations in circulating ptDNA from patients with metastatic breast cancer using a novel technique of digital polymerase chain reaction (PCR) called BEAMing (for Beads, Emulsions, Amplification, Magnetics). We demonstrated that BEAMing is both sensitive and specific for identifying PIK3CA mutations in metastatic breast cancer patients, though we also confirmed the work of other groups that PIK3CA mutation status can change with progression to metastatic disease. An overview of these data will be presented. While these studies demonstrated the feasibility of using ptDNA in metastatic patients as a liquid biopsy for detecting specific cancer mutations, we are now focusing efforts to exploit the quantitative nature of digital PCR technology. Specifically, by analyzing the amount of ptDNA before and after primary breast surgery in early stage breast cancer patients, we will identify which patients truly have residual microscopic disease post surgery and therefore would be the most appropriate candidates for additional systemic therapies. Thus, in contrast to the current paradigm of “over” treating breast cancer patients in the adjuvant setting, detection of ptDNA using next generation digital PCR technologies will enable us to make rational decisions regarding which patients truly have need for adjuvant systemic therapies. Preliminary data and ongoing studies will be discussed as well as the implementation of these technologies in future clinical trials.

Citation Format: Julia A. Beaver, Patricia Valda, Danijela Jelovac, Michaela J. Higgins, Ben H. Park. Plasma tumor DNA: Changing the paradigm for administering systemic therapies. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr SY11-01. doi:10.1158/1538-7445.AM2013-SY11-01
Abstract SY24-03: Targeting IAP proteins in cancer: From molecular mechanism to therapeutic application.
Authors: Fulda Simone
Published: August 2014

Evasion of apoptosis is a hallmark of human cancers and contributes to tumor formation and progression as well as resistance to current cancer therapies, which largely rely on intact cell death pathways in cancer cells. Apoptosis resistance can be caused by aberrant expression of antiapoptotic proteins, for example, Inhibitor of Apoptosis“ (IAP) proteins, which are expressed at high levels in many human cancers. Since IAP proteins block apoptosis at the core of the apoptotic machinery by inhibiting effector caspases, they present promising therapeutic targets.

Among the therapeutic approaches that have been developed to target IAP proteins, the most widely used strategy is based on mimicking the IAP-binding motif of second mitochondria- derived activator of caspase (SMAC), which functions as an endogenous IAP antagonist. Alternative strategies include transcriptional repression and the use of antisense oligonucleotides. Current and future perspectives on neutralizing IAP proteins for therapeutic intervention in human cancers will be discussed.

Citation Format: Simone Fulda. Targeting IAP proteins in cancer: From molecular mechanism to therapeutic application. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr SY24-03. doi:10.1158/1538-7445.AM2013-SY24-03
Abstract SY28-01: Is mitosis the target of “anti-mitotic” cancer drugs.
Authors: Mitchison Timothy J.
Published: August 2014

Cytotoxic drugs, which mostly target DNA or microtubules, can be curative in some cancers, but how they kill tumor cells selectively compared to normal cells has long been mysterious. The textbook view holds that cytotoxic drugs gain efficacy and selectivity by targeting different phases of the cell cycle, mitosis in the case of anti-microtubule drugs such as paclitaxel. However, the proliferation rate in tumors is slow compared to bone marrow and gut, and drugs that target cells only during cell division have shown little tumor efficacy. It is thus unclear whether mitosis is really a druggable process for cancer treatment. We have investigated the cytotoxic actions of anti-mitotic drugs in cell culture and using intravital imaging in a xenograft tumor model. Comparing the same cell line growing in culture and xenografts, we find that paclitaxel kills via mitotic arrest in culture, but by a non-mitotic mechanism in tumors. Candidate cell-killing mechanisms and their implications for improving chemotherapy will be discussed.

Citation Format: Timothy J. Mitchison. Is mitosis the target of “anti-mitotic” cancer drugs. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr SY28-01. doi:10.1158/1538-7445.AM2013-SY28-01
Abstract SY30-01: Molecular characterization of single circulating tumor cells.
Authors: Haber Daniel A. , Yu Min , Ozkumar Emre , Ting David , Miyamoto David , Lee Richard , Shah Ajay , Bardia Aditya , Stott Shannon , Toner Mehmet , Maheswaran Shyamala
Published: August 2014

Circulating Tumor Cells (CTCs) are present at extraordinarily low levels in the blood of patients with advanced epithelial cancers. Our group has developed and tested three generations of microfluidic devices for the isolation of CTCs, each with further improvements in automation, processing throughput and downstream analytical capabilities. Isolation and molecular analyses of these cells has a number of significant potential clinical applications: rising or declining numbers of CTCs are well correlated with tumor progression or therapeutic response. Furthermore, CTCs bear genetic hallmarks of the primary cancer, offering a noninvasive “liquid biopsy” to enable initial and serial monitoring of tumor genotypes during cancer therapy. Most significantly, CTCs hold the key to understanding the process of blood-borne metastasis. Using next generation RNA sequencing strategies, we have initiated studies of expression profiles within CTCs. These have identified cellular pathways implicated in resistance of epithelial cells to anoikis in the circulation and in epithelial-mesenchymal transition - a phenomenon implicated in cancer invasion. The heterogeneity of CTC populations is evident in single cell imaging analyses and sequencing studies, with implications for understanding the complexity of therapeutic responses. Taken together, the application of novel bioengineering technologies to the isolation and analysis of CTCs across multiple different cancer types offers a unique window into the properties of cancer cells that invade into the bloodstream and give rise to metastases.

Citation Format: Daniel A. Haber, Min Yu, Emre Ozkumar, David Ting, David Miyamoto, Richard Lee, Ajay Shah, Aditya Bardia, Shannon Stott, Mehmet Toner, Shyamala Maheswaran. Molecular characterization of single circulating tumor cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr SY30-01. doi:10.1158/1538-7445.AM2013-SY30-01
Abstract A18: The role of histone demethylase JARID1C in tumorigenesis of clear cell renal cell carcinoma
Authors: Ler Lian Dee , Allen George Edward , Myint Swe Swe , Teh Bin Tean
Published: August 2014

Clear cell renal cell carcinoma (ccRCC) constitutes 75% of all RCC. It is characterized by inactivation of the tumor suppressor Von Hippel Lindau gene (VHL) in ~70% of sporadic ccRCC cases. Recent large scale screen of ~3,500 genes by PCR-based exon re-sequencing identified several new cancer genes in ccRCC including UTX, JARID1C and SETD2. These genes encode enzymes that demethylate and methylate key lysine residue of histone H3. In particular, JARID1C is a histone 3 lysine 4 (H3K4) demethylase involved in the demethylation of gene activating trimethyl H3K4 (H3K4me3) mark and was found to be mutated in 3-9% of ccRCC, independent of the mutation status of VHL. Using gene expression profiling, we revealed that major down-regulated pathways in primary RCCs harboring JARID1C inactivating mutation are pointing towards changes involving metastatic properties. The highlighted pathways include ECM-receptor interaction, focal adhesion, regulation of actin cytoskeleton, cell junction organization and cell junction assembly. Therefore, we focused on elucidating the role of JARID1C in ccRCC invasive properties. From in vitro assay, depletion of JARID1C by introducing JARID1C shRNA in ccRCC cells did not result in significant changes in cell migration. By contrast, in consistent with the findings from gene expression profiling, we showed that such depletion of JARID1C significantly enhances the invasiveness of ccRCC cells regardless of their VHL gene status. In summary, our findings establish the role of JARID1C in potentiating the invasive capabilities of ccRCC.

Citation Format: Lian Dee Ler, George Edward Allen, Swe Swe Myint, Bin Tean Teh. The role of histone demethylase JARID1C in tumorigenesis of clear cell renal cell carcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr A18.
Abstract A28: Targeting PCL3/PHF19 as an alternative therapeutic strategy to EZH2 inhibition in PRC2-deregulated cancers
Authors: Brien Gerard L. , Jerman Emilia , Campbell Matthew , Adrian Bracken P.
Published: August 2014

The Polycomb Repressive Complex 2 (PRC2) is emerging as an attractive therapeutic target for the treatment of cancer. Several functional protein domains that are amenable to small-molecule inhibition exist within the complex and the recent development of chemical inhibitors of the EZH1/2 SET domain now offers a means to therapeutically target the complex. Here we explore the potential of targeting the sub-stoichiometric PRC2 component, PCL3/PHF19, as an alternative to EZH1/2 inhibition. We show, both in normal fibroblasts and in SNF5 deficient malignant rhabdoid sarcoma cells, that targeted depletion of PCL3/PHF19 leads to proliferative defects, owing, at least in part, to a loss of Polycomb binding at and de-repression of the tumour suppressor p16INK4A. Significantly, we show that ectopic expression of PCL3/PHF19 leads to p16INK4A repression and a bypass of cellular senescence. This correlates with increased recruitment of EZH2, accumulation of H3K27me3 and PRC1 components on the INK4A promoter, suggesting a potential oncogenic role for PCL3/PHF19. Consistent with this, PCL3/PHF19 is over-expressed in many cancers. Previously we demonstrated that the TUDOR domain of PCL3/PHF19 is required for the ability of the protein to read epigenetic modifications and facilitate the recruitment of EZH2 to chromatin. Taken together with the data presented here, we propose that the TUDOR domain of PCL3/PHF19 represents a viable alternative functional domain within the PRC2 complex for small-molecule inhibition.

Citation Format: Gerard L. Brien, Emilia Jerman, Matthew Campbell, Bracken P. Adrian. Targeting PCL3/PHF19 as an alternative therapeutic strategy to EZH2 inhibition in PRC2-deregulated cancers. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr A28.
Abstract A35: SMARCE1 mutations cause inherited multiple spinal meningiomas
Authors: Smith Miriam J. , O'Sullivan James , Bhaskar Sanjeev S. , Hadfield Kristen D. , Poke Gemma , Caird John , Sharif Saba , Eccles Diana , FitzPatrick David , Rawluk Daniel , Plessis Daniel du , Newman William G. , Evans D. Gareth
Published: August 2014

Meningiomas represent approximately one third of all primary central nervous system tumors in adults. Multiple meningiomas are usually associated with neurofibromatosis type 2 (NF2) disease, which is caused by mutations in the NF2 gene. Recent reports have also shown multiple meningiomas to be associated with schwannomatosis disease, which is caused by mutations in the SWI/SNF chromatin remodeling complex subunit, SMARCB1. In a subset of individuals, multiple meningioma disease is a discrete entity, inherited in an autosomal dominant manner unrelated to NF2 or SMARCB1 mutations.

We sought to discover novel genes associated with a predisposition to meningioma development by exome sequencing of germline DNA three unrelated individuals with familial multiple spinal meningiomas, who did not have germline NF2 or SMARCB1 mutations.

Two of these three individuals harbored heterozygous novel loss-of-function mutations in the SWI/SNF complex subunit, SMARCE1. Sanger sequencing of SMARCE1 in lymphocyte DNA from six additional individuals with spinal meningiomas identified another two novel heterozygous loss-of-function mutations. Tumors from individuals with germline SMARCE1 mutations were demonstrated a clear cell histological subtype and all demonstrated loss of SMARCE1 protein consistent with a tumor suppressor mechanism.

Our findings define multiple spinal meningioma disease as a novel discrete entity and implicate the SWI/SNF chromatin remodeling complex in the pathogenesis of meningiomas and tumors with clear cell histology.

Citation Format: Miriam J. Smith, James O'Sullivan, Sanjeev S. Bhaskar, Kristen D. Hadfield, Gemma Poke, John Caird, Saba Sharif, Diana Eccles, David FitzPatrick, Daniel Rawluk, Daniel du Plessis, William G. Newman, D. Gareth Evans. SMARCE1 mutations cause inherited multiple spinal meningiomas. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr A35.
Abstract A58: Systematic optimization of key parameters involved in the preparation of chromatin and the chromatin immunoprecipitation (ChIP) workflow
Authors: Cooke Tracy , Li Zirong , Saito Kan , Sturges Michael R. , Taganov Konstantin , Thyagarajan Bhaskar , Rosenfeld John M. , Solache Alejandra
Published: August 2014

The ChIP protocol is a fundamental tool that has been used to gain insight into the impact of epigenetic phenomenon and their effect on cancer development and progression. Despite the abundance of research tools that support ChIP, very little innovation has occurred around the ChIP method itself to make the process more reproducible and reliable. Issues surrounding antibody specificity and performance, lack of reliable high-throughput options for limited amounts of chromatin, and accepted criteria to make determinations on the quality of chromatin suitable for ChIP are just some of the challenges faced when performing this method. Improvements in the ChIP process would enable more reliable high resolution genomic mapping of chromatin events that are critical to unambiguously dissect epigenetic regulatory mechanisms and their influence on gene expression.

To address these issues, we have engaged in an iterative process of examining multiple parameters that influence ChIP data. For chromatin fragmentation, we prepared chromatin on a variety of devices and utilized various buffer systems to develop an approach to optimize this process. To allow rapid and evaluation of histone antibody specificity, we have produced tools that allow researchers to evaluate specificity utilizing a simple dot blot western blotting approach. In addition, we have developed low-cell protocol that simplifies the ChIP process, reduces variability and significantly improve signal-to-noise ratios. This protocol has been demonstrated to work in both a low throughput version as well as a high-throughput version that is amenable to automation. Our approach is well suited to those with limited experience in ChIP, but is also sufficiently robust and flexible to enable ChIP from either abundant or limited amounts of chromatin derived from cells or tissues. Using this systematic approach, we present data comparing the impact of different sonication protocols on ChIP, analysis of user-to-user variation, as well as approaches to optimize and control for factors that introduce variability in ChIP.

Citation Format: Tracy Cooke, Zirong Li, Kan Saito, Michael R. Sturges, Konstantin Taganov, Bhaskar Thyagarajan, John M. Rosenfeld, Alejandra Solache. Systematic optimization of key parameters involved in the preparation of chromatin and the chromatin immunoprecipitation (ChIP) workflow. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr A58.
Abstract A63: Rsf-1, a chromatin remodeling protein, interacts with shelterin protein hRap1 and induces telomere shortening
Authors: Wu Ren-Chin , Guan Bin , Kobayashi Yusuke , Wang Tian-Li , Shih Ie-Ming
Published: August 2014

Background: Rsf-1, a chromatin remodeling factor that forms an ISWI chromatin-remodeling complex with SNF2H, has been implicated in the oncogenesis of a variety of human cancers, yet its functions in promoting tumor development remains unclear. In this study, we found Rsf-1 interacted with hRap1, a telomere binding protein involved in telomere length regulation. We aimed at characterizing the interaction between Rsf-1 and hRap1 and exploring the effect of Rsf-1 overexpression on telomere length in ovarian cancer cells.

Methods: Protein microarray and co-immunoprecipitation were employed to screen and validate Rsf-1 interaction proteins. Deletion mutants of both Rsf-1 and hRap1 were constructed to map the binding domains responsible for their interaction. To determine whether RSF complex was enriched in the telomeric regions, we performed chromatin immunoprecipitation (ChIP) -qPCR in two ovarian cancer cell lines (OVCAR3 with high RSF-1 gene amplification and Rsf-1 inducible SKOV3) with antibodies against Rsf-1 and SNF2H. A ChIP-sequencing dataset performed with Rsf-1 and SNF2H antibodies using OVCAR3 cells was also examined for enrichment of telomeric sequences. To investigate the effect of Rsf-1 overexpression on telomere length, we evaluated by qPCR the telomere length in two Rsf-1 inducible cell lines (SKOV3 and BRK).

Results: We identified hRap1, a telomere binding protein, as an interaction partner of Rsf-1 by protein microarray and co-immunoprecipitation. Protein interaction domain mapping revealed that C-terminal domain of hRAP1 and PHD domains and arginine-rich region of RSF1 were critical for this interaction. Both ChIP-qPCR and ChIP-sequencing demonstrated that Rsf-1 and SNF2H were enriched in the telomeres, suggesting that RSF complex was recruited by hRAP1 to the telomeres. Induction of RSF1 expression resulted in shortened telomere length in two different cell lines. The results suggest that RSF complex may be involved in the telomere length regulation mediated by hRAP1.

Conclusions: Rsf-1 interacted with hRap1 through the PHD domain and the arginine-rich region. RSF complex bound telomeres, probably through the interaction with hRap1. Rsf-1 overexpression led to telomere length shortening, which may contribute to genomic instability in cancer cells.

Citation Format: Ren-Chin Wu, Bin Guan, Yusuke Kobayashi, Tian-Li Wang, Ie-Ming Shih. Rsf-1, a chromatin remodeling protein, interacts with shelterin protein hRap1 and induces telomere shortening. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr A63.
Abstract B24: Ras-mediated epigenetic reprogramming: NF-κB-dependent and independent effects
Authors: Durand Joel , Baldwin Albert
Published: August 2014

In addition to many genetic alterations, cancer cells also harbor global epigenetic abnormalities, a fundamental hallmark of cancer. K-Ras, the most commonly mutated oncogene, has been shown to induce aberrant epigenetic changes, including the methylation and subsequent silencing of key tumor suppressors. Furthermore, in the majority of K-Ras-driven tumors, the NF-κB pathway is constitutively active and contributes to cellular transformation. Specifically, our lab has shown that knocking out the p65 subunit of NF-κB significantly reduces tumor development in a mouse model of K-Ras-induced lung cancer. NF-κB subunits have been shown to associate with HDAC1 and to promote DNMT1 recruitment to chromatin, suggesting the involvement of NF-κB in epigenetic regulation. However, the role of the NF-κB pathway in Ras-mediated epigenetic changes remains unclear. Based on the above, I hypothesize that oncogenic K-Ras cooperates with the NF-κB pathway to alter the epigenetic landscape and promote transformation. Using the Infinium Methylation Assay, we have uncovered genome-wide differences in DNA methylation in lung epithelial cells expressing K-RasG12V (SAKRAS) compared to wild-type (SALEB) cells. Expression of oncogenic K-RasG12V was accompanied by hypermethylation of many tumor suppressors and demethylation of established oncogenes. Notably, many of these changes in methylation correlated with changes in gene expression. Inhibition of the NF-κB pathway in SAKRAS cells also led to significant changes in the methylation profile of a subset of genes. Together, these preliminary results support a role for the K-Ras and NF-κB pathways in the epigenetic reprogramming observed in K-Ras-driven cancers.

Citation Format: Joel Durand, Albert Baldwin. Ras-mediated epigenetic reprogramming: NF-κB-dependent and independent effects. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr B24.
Abstract B42: An integrated view on genetic and epigenetic mechanisms revealed aberrant DNA methylation as an important source for miRNA deregulation in prostate cancer
Authors: Bogatyrova Olga , Wuttig Daniela , Gu Lei , Assenov Yassen , Kuner Ruprecht , Baer Constance , Feuerbach Lars , Gerhäuser Clarissa , Weichenhan Dieter , Schlomm Thorsten , Simon Ronald , Sauter Guido , Sültmann Holger
Published: August 2014

Prostate cancer (PCa) the most common malignant tumor in males and the third leading cause of cancer-related deaths in Western developed countries. The clinical spectrum of PCa ranges from indolent tumors requiring no therapy to highly aggressive and often metastatic diseases. MicroRNAs (miRNAs) have emerged as important regulators in human tumorigenesis and tumor progression during the last decade. miRNA expression is strongly deregulated in many human cancers including PCa. We investigated the contribution of genetic and epigenetic events to the deregulation of miRNAs in PCa by utilizing the profiling data of 19 Early-Onset Pca (EOPC) from International Cancer Genome Consortium (ICGC) (http://www.icgc.org). For 31% (154/491) of the downregulated miRNAs and for 23% (133/578) of the upregulated miRNAs, DNA hyper- and hypomethylation respectively of a promoter region was observed in at least one of the 13 PCa. Deletions were detected for 26% (126/491) of the downregulated miRNAs in at least one sample. We observed a single translocation event leading to disruption of miR-1244-2 from its putative regulatory region that might contribute to expression decrease. We did not detect any SNV within miRNA precursors. Only one miRNA precursor (miR-4307) was amplified in one patient, but the corresponding mature miRNA was not expressed at all. We demonstrated that, among deletions, methylation of miRNA promoters is one of the major mechanisms leading to miRNA silencing or activation, respectively in PCa. 37 miRNA were downregulated by hypermethylation of regulatory regions and 10 miRNAs were upregulated by hypomethylation in both the ICGC EOPC cohort and the validation dataset on 50 prostate cancer and 48 normal prostate tissues. 82% (9/11) of the miRNAs/miRNA clusters analyzed regulate genes that are involved in PI3K/AKT/PTEN signaling, which represents one of the PCa key pathways being deregulated in more than one third of primary PCa.

Note: This abstract was not presented at the conference.

Citation Format: Olga Bogatyrova, Daniela Wuttig, Lei Gu, Yassen Assenov, Ruprecht Kuner, Constance Baer, Lars Feuerbach, Clarissa Gerhäuser, Dieter Weichenhan, Thorsten Schlomm, Ronald Simon, Guido Sauter, Holger Sültmann. An integrated view on genetic and epigenetic mechanisms revealed aberrant DNA methylation as an important source for miRNA deregulation in prostate cancer. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr B42.
Abstract IA11: The epigenetic stability of pluripotent and somatic cell states
Authors: Hanna Jacob H.
Published: August 2014

The identity of somatic and pluripotent cells can be epigenetically reprogrammed and forced to adapt a new functional cell state by different methods and distinct combinations of exogenous factors. The aspiration to utilize such ex vivo reprogrammed pluripotent and somatic cells for therapeutic purposes necessitates understanding of the mechanisms of reprogramming and elucidating the extent of equivalence of the in vitro derived cells to their in vivo counterparts. I will present and analyze our recent advances toward understanding these fundamental questions, and discuss the role of chromatin remodeling complexes in influencing the characteristics of pluripotency and reprogramming. I will further highlight future possibilities for utilizing epigenetic reprogramming for experimental and theoretical modeling of gene expression regulation, cell fate decisions and early mammalian development.

Citation Format: Jacob H. Hanna. The epigenetic stability of pluripotent and somatic cell states. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr IA11.
Abstract IA16: Reactivating epigenetically silenced genes
Authors: Jones Peter A.
Published: August 2014

Chromatin is inherently refractory to the initiation of transcription and to the binding of regulatory factors. Nucleosomes need to be moved or destabilized from DNA sequences by processes involving remodelers. We have designed a new approach called NOME-Seq which allows us to examine DNA methylation patterns and nucleosomal positioning on individual DNA molecules thus digitizing the analysis of accessible chromatin areas. We have used this approach genome wide to analyze the precise nature and physical sizes of nucleosome depleted regions (NDRs) and examined the effects of mutations in chromatin remodelers on these accessible areas. We have also followed the alterations in chromatin accessibility immediately following drug treatment with DNA demethylation agents. Results from these studies give insights as to the mechanisms of action of the drugs and provide opportunities for future drug development.

Citation Format: Peter A. Jones. Reactivating epigenetically silenced genes. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr IA16.
Abstract IA22: Cancer as a single process of a dysregulated epigenome
Authors: Feinberg Andrew P.
Published: August 2014

Since the discovery of altered DNA methylation in cancer in 1982, most studies of cancer epigenetics have focused on epimutations which could serve as surrogates of mutation. In the past decade, we and our collaborators have been leading efforts to develop whole genome approaches to epigenetic analysis of human disease, that include novel approaches to array-based analysis and whole genome bisulfite sequencing. This has led to the first whole genome bisulfite sequencing methylation map of the cancer genome. Surprising results have been the discovery of CpG island shores and large hypomethylated blocks corresponding to nuclear lamina / heterochromatin regions, and accounting for the vast majority of epigenetic changes in cancer. These results point to the possibility that at least solid tumors represent epigenetically a single process with common molecular characteristic, namely increased epigenetic plasticity that allows selection of the tumor cells at the expense of the host. This view can explain most of the hallmarks of cancer, as well as offering a strategy for powerful new approaches to risk detection and treatment.

Citation Format: Andrew P. Feinberg. Cancer as a single process of a dysregulated epigenome. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr IA22.
Abstract PR05: Reversing the oncogenic roles of misdirected chromatin remodeling: Disruption of mSWI/SNF (BAF) complexes by the SS18-SSX fusion in human synovial sarcoma
Authors: Kadoch Cigall , Crabtree Gerald R.
Published: August 2014

Recent exon- and genome-wide sequencing studies of human cancers have revealed frequent mutations in genes encoding subunits of mSWI/SNF or BAF complexes and implicated them as tumor suppressors. Indeed, we estimate that they are mutated in >20% of human cancers (Kadoch et al, Nature Genetics 2013). Interestingly, the subunits most commonly mutated are not required for chromatin remodeling in vitro and thus may contribute to chromatin regulation in a novel way. One difficultly in understanding the oncogenic role(s) of these complexes is distinguishing primary driving mutations from passenger mutations. To investigate the mechanism underlying oncogenesis, we studied human synovial sarcoma (SS), in which transformation results from a remarkably precise and uniform translocation of exactly 78 amino acids of SSX (SSX1, 2 or 4) to the SS18 protein. In a proteomic study we discovered that SS18 is a dedicated, non-exchangeable subunit of BAF complexes. We demonstrate that the hallmark SS18-SSX fusion incorporates into BAF complexes, evicting both the wild-type SS18 protein and the tumor suppressor, hSNF5 (BAF47), which is known to be biallelically inactivated in malignant rhabdoid tumors. The altered complex binds the Sox2 locus, reversing polycomb-mediated H3K27me3 repression and activating Sox2. Sox2 is uniformly expressed in SS tumors and is essential for proliferation. Remarkably, increasing the concentration of wild-type SS18 leads to reassembly of wild-type complexes, retargeting of BAF complexes, returned polycomb-mediated repression at the Sox2 locus and cessation of SS cell proliferation. This mechanism of transformation depends on a two amino acid hydrophilic region of SSX and hence provides a potential foundation for therapeutic intervention.

Citation Format: Cigall Kadoch, Gerald R. Crabtree. Reversing the oncogenic roles of misdirected chromatin remodeling: Disruption of mSWI/SNF (BAF) complexes by the SS18-SSX fusion in human synovial sarcoma. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr PR05.
Abstract PR07: SNF5 is an essential executor of epigenetic regulation during differentiation
Authors: You Jueng Soo , Carvalho Daniel D. De , Dai Chao , Liu Minmin , Pandiyan Kurinji , Zhou Xianghong , Liang Gangning , Jones Peter A.
Published: August 2014

Nucleosome occupancy controls the accessibility of the transcription machinery to DNA regulatory regions and serves an instructive role for gene expression. Chromatin remodelers, such as the BAF complexes, are responsible for establishing nucleosome occupancy patterns, which are key to epigenetic regulation along with DNA methylation and histone modifications. Some reports have assessed the roles of the BAF complex subunits and stemness in murine embryonic stem cells. However, the details of the relationships between remodelers and transcription factors in altering chromatin configuration, which ultimately affects gene expression during cell differentiation, remain unclear. Here for the first time we demonstrate that SNF5, a core subunit of the BAF complex, negatively regulates OCT4 levels in pluripotent cells and is essential for cell survival during differentiation. SNF5 is responsible for generating nucleosomedepleted regions (NDRs) at the regulatory sites of OCT4 repressed target genes such as PAX6 and NEUROG1, which are crucial for cell fate determination. Concurrently, SNF5 closes the NDRs at the regulatory regions of OCT4 activated target genes such as OCT4 itself and NANOG. Furthermore, using loss and gain of function experiments followed by extensive genome-wide analyses including gene expression microarrays and ChIP-sequencing, we highlight that SNF5 plays dual roles during differentiation by antagonizing the expression of genes that were either activated or repressed by OCT4, respectively. Together, we demonstrate that SNF5 executes the switch between pluripotency and differentiation.

This abstract is also presented as Poster A39.

Citation Format: Jueng Soo You, Daniel D. De Carvalho, Chao Dai, Minmin Liu, Kurinji Pandiyan, Xianghong Zhou, Gangning Liang, Peter A. Jones. SNF5 is an essential executor of epigenetic regulation during differentiation. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr PR07.
Abstract A15: High-Content screen for inhibitors of cell migration in cancer metastasis using adenoviral knock-down
Authors: de Pril Remko , Lekkerkerker Annemarie , van Steenhoven Desire , Maghrani Ilhem , Perera Tim , Arts Janine , Fischer David , Janssen Richard
Published: August 2014

Enhanced cell migration is a hallmark of metastatic cancer cells. The propensity of cancer cells to close an open wound in a cell monolayer is thought to predict this ability. Using our adenoviral shRNA knockdown library we have established a high-throughput wound healing assay to identify novel genes involved in cell migration. A 96-pin tool was designed to apply a constant mechanical scratch-wound in the cellular monolayer. We used transmitted light imaging for segmentation and quantification of the scratch wound that remained open.

Genes whose knockdown inhibit cell migration can be identified by their effect on the open wound. We demonstrated that two knockdown constructs targeting a known player in motility, CXCR4, inhibit wound healing, thereby validating our approach. Using this wound healing assay we have identified a number of novel genes associated with cancer cell motility. These targets have consecutively been validated for their role in 3-D invasion using Boyden chambers. As our adenoviral knockdown libraries focus on druggable targets, these validated targets can quickly be employed to generate small-molecule compounds or antibody therapeutics targeting cancer metastasis.

Citation Format: Remko de Pril, Annemarie Lekkerkerker, Desire van Steenhoven, Ilhem Maghrani, Tim Perera, Janine Arts, David Fischer, Richard Janssen. High-Content screen for inhibitors of cell migration in cancer metastasis using adenoviral knock-down [abstract]. In: Proceedings of the AACR Special Conference on Chemical Systems Biology: Assembling and Interrogating Computational Models of the Cancer Cell by Chemical Perturbations; 2012 Jun 27-30; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2012;72(13 Suppl):Abstract nr A15.
Abstract A20: Molecular Detection of Prostate-Specific Membrane Antigen in Canine Prostate Carcinoma Cells
Authors: Wu Lisa Y. , Liu Tiancheng , Vanwie Bernard , Davis William C. , Berkman Clifford E.
Published: August 2014

Apart from the man, the dog develops prostate cancer spontaneously. Although the diseases in both species have several clinical aspects in common, not much is known about the expression of markers in the canine prostate cancer due to the lack of study in canine prostate cancer research. Therefore, the vast majority of canine prostate cancers at the time of diagnosis are end-staged. Numerous prostate cancer cell lines have been developed, but few cell lines develop bone metastases and no cell lines have been reported to cause brain metastases except the Ace-1 and the Leo canine prostate cancer cell lines. Prostate-specific membrane antigen (PSMA), which is known as a prostate cancer biomarker in humans, its usefulness in canine specimens has not been examined fully in these cell lines. Although there has been a considerable effort toward the development of PSMA-targeted diagnostic and therapeutic technologies for dogs, methods for detecting circulating and invasive prostate tumor cells currently remain limited. Previously, we developed a prostate circulating tumor cell (PCTC) detection method by a fluorescent PSMA inhibitor. The focus of the study is to evaluate PSMA expression on the Ace-1 and Leo cell lines by fluorescent conjugated PSMA inhibitor in flow cytometry. It is expected that the results will enable the development of detecting PSMA expressing canine cells in circulation for prognosis and diagnosis of canine prostate cancer.

Citation Format: Lisa Y. Wu, Tiancheng Liu, Bernard Vanwie, William C. Davis, Clifford E. Berkman. Molecular Detection of Prostate-Specific Membrane Antigen in Canine Prostate Carcinoma Cells [abstract]. In: Proceedings of the AACR Special Conference on Chemical Systems Biology: Assembling and Interrogating Computational Models of the Cancer Cell by Chemical Perturbations; 2012 Jun 27-30; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2012;72(13 Suppl):Abstract nr A20.
Abstract A21: High-throughput small molecule screening of genetically diverse glioblastoma stem cells
Authors: Strohbehn Garth W. , Zhou Jiangbing , Fu Michael , Patel Toral R. , Piepmeier Joseph M. , Saltzman W. Mark
Published: August 2014

Survival statistics for glioblastoma multiforme (GBM) have remained static despite years of research. Mounting evidence suggests that glioblastoma stem cells (GSCs) are a primary cause of GBM growth, spread, vascularity, and chemotherapeutic resistance. Increasing survival, therefore, demands a therapeutic strategy with efficacy against GSCs. To address this, we have conducted a high-throughput screen of over 3,000 small molecule compounds for activity against three independently derived GSC lines that vary in their expression of TCGA subtype-related genes. Our fluorescence-based assay is sensitive, reliable, and largely free of row- and column-based systematic errors. We identify novel compounds that impair the viability of all three of these genetically diverse GSC lines but have comparably limited toxicity against a normal human glial cell line. Many of these compounds are small and lipophilic, as well, making them ideal candidates for follow-up in vivo evaluation either through intravenous delivery or through encapsulation in polymeric nanoparticles.

Citation Format: Garth W. Strohbehn, Jiangbing Zhou, Michael Fu, Toral R. Patel, Joseph M. Piepmeier, W. Mark Saltzman. High-throughput small molecule screening of genetically diverse glioblastoma stem cells [abstract]. In: Proceedings of the AACR Special Conference on Chemical Systems Biology: Assembling and Interrogating Computational Models of the Cancer Cell by Chemical Perturbations; 2012 Jun 27-30; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2012;72(13 Suppl):Abstract nr A21.