bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5178: Genomic and transcriptomic alterations of chromatin factors in head and neck cancer
Authors: Cheng Hui , Bao Riyue , Waes Carter Van , Saloura Vassiliki 
Published: August 2019

Abstract
Chromatin factors play central roles in the transcriptional regulation and maintenance of genomic stability and have been implicated in cancer initiation and progression in multiple cancer types. No study has systematically investigated the genomic and expression alterations of chromatin factors in head and neck squamous cell carcinoma (HNSCC). To this purpose, we utilized the molecular profiles from over 510 HNSCCs in the Cancer Genome Atlas (TCGA), and thoroughly characterized the mutational, copy number and transcriptional alterations of 457 chromatin factors and histones. Over 75% of all HNSCC samples have genomic alterations in protein methyltransferases and protein demethylases. Protein lysine methyltransferases MLL2 and NSD1 are the most frequently mutated chromatin factors in this disease. Actin Like 6A (ACTL6A), a component of the SWI/SNF chromatin remodeling complex, SUMO specific peptidase 5 (SENP5) and Nuclear receptor binding SET domain protein 3 (NSD3) are the most frequently copy-number amplified and overexpressed chromatin factors. Interestingly, hierarchical clustering of gene expression of a set of chromatin factors identified a molecular subtype with significantly better overall survival (OS), regardless of HPV-status, stage and NSD1 mutation status, a factor recently reported to render better OS in HNSCC. Systematic characterization of the deregulation of chromatin factors may elucidate novel epigenetic mechanisms and provide novel targets for cancer therapy in HNSCC. Supported by NIDCD intramural projects ZIA-DC-000016, 73 and 74.
Note: This abstract was not presented at the meeting.
Citation Format: Hui Cheng, Riyue Bao, Carter Van Waes, Vassiliki Saloura. Genomic and transcriptomic alterations of chromatin factors in head and neck cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5178.
Abstract 518: Hypoxia and high interstitial pressure present within the tumor microenvironment can promote T cell suppression and exhaustion
Authors: Rancan Chiara , Marusinec Rachel , Lim James , Fong Lawrence 
Published: August 2019

Abstract
Introduction: The tumor microenvironment is thought to be hostile to the optimal functionality of immune cells. In addition to hypoxia, tumors have a higher interstitial pressure than normal tissue. We examined the impact of hypoxia and increased pressure on human T cell function in vitro. We hypothesize that hypoxia and high pressure induced a more profound and durable exhaustion of activated T cells.
Methods: We cultivated human healthy PBMCs stimulated with phytohemagglutinin (PHA) or CD3/CD28 beads under tumor hypoxic conditions (1%O2, 2PSI) and compared it to normoxic in vitro culture conditions (20% O2, 0 PSI). We utilized the AVATAR system (Xcellbio), a novel bioreactor with highly customable cultivation conditions that allows for the modulation of oxygen and pressure. Functionality and phenotypic changes induced by different cultivation conditions were assessed by flow cytometry and cytokine release assays.
Results: Upon stimulation of PBMCs for 3 days, we observed that hypoxia markedly reduced IFNγ and TNFα cytokine release. Additionally, hypoxia induced an overall decrease in surface expression of the activation and metabolic markers CD71 (transferrin) and CD98 (neutral amino acids transporter), while promoting an increased expression of the inhibitory receptor PD1. This was true for both CD4+ and CD8+ T cells. Following this initial 3-day “priming” stimulation, cells spent 2-days in a “resting period” and underwent a second stimulation under a different condition (cells under normoxia were cultured under hypoxia and vice versa). We found that cells initially primed under hypoxic conditions maintained higher levels of PD1 expression after the second stimulation, regardless of whether the latter condition was normoxic or hypoxic.
Conclusions: Taken together these observations suggest that T cell priming in hypoxic and high pressure conditions present in tumors induce an irreversible state of T cell exhaustion and point out a dominant effect of hypoxia over normoxia. Our data suggest that environmental culture conditions greatly affect T cell responses and should be taken into account when studying T cell functionality, especially in the investigation of novel therapeutic agents targeting the immune system.
Citation Format: Chiara Rancan, Rachel Marusinec, James Lim, Lawrence Fong. Hypoxia and high interstitial pressure present within the tumor microenvironment can promote T cell suppression and exhaustion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 518.
Abstract 5180: Enhanced and controlled chromatin extraction for chromatin-based epigenetic assays in FFPE tissues
Authors: Zhong Jian , Ye Zhenqing , Clark Chad , Lenz Samuel , Nguyen Justin , Yan Huihuang , Robertson Keith , Farrugia Gianrico , Zhang Zhiguo , Ordog Tamas , Lee Jeong-Heon 
Published: August 2019

Abstract
Background: Epigenetic dysregulation is involved in the etiology and progression of various human diseases. Formalin-fixed paraffin-embedded (FFPE) samples represent the gold standard for archiving pathology samples, and thus FFPE samples are a major resource of samples in clinical research. However, chromatin-based epigenetic assays in the clinical settings are limited to fresh or frozen samples and are hampered by low chromatin yield in FFPE samples due to the lack of reliable and efficient chromatin preparation methods. Here, we introduce a new chromatin extraction method from FFPE tissues (Chrom-EX PE) for chromatin-based epigenetic assays.
Results: During rehydration of FFPE tissues, applying tissue-level cross-link reversal to the deparaffinized tissue at 65°C dramatically increased chromatin yield in the soluble fraction. We found the resulting chromatin to be compatible with ChIP-qPCR and ChIP-seq analysis of histone marks (H3K4me3, H3K27me3, and H3K27Ac) and RNA polymerase II. The chromatin prepared by Chrom-EX PE showed a gradual fragmentation pattern with varying incubation temperature. At temperatures below 37°C, the majority of soluble chromatin was over 1 kb in size. The soluble chromatin prepared at 45-60°C showed a typical nucleosomal pattern shown in cell lines and frozen tissues. The majority of the chromatin prepared at 65°C is close to mononucleosomal size. These observations indicate that chromatin preparation from FFPE samples can be controlled for downstream chromatin-based epigenetic assays.
Conclusions: Our method achieves efficient extraction of high-quality chromatin from FFPE samples suitable for targeted and genome-wide epigenetic assays while minimizing degradation and damages. This approach provides a new platform for developing chromatin-based assays applicable to archived FFPE samples to circumvent the over-fixed nature of FFPE tissues.
This work was supported, in part, by National Institutes of Health grant P01DK068055 and the Mayo Clinic Center for Individualized Medicine Epigenomics Program.
Citation Format: Jian Zhong, Zhenqing Ye, Chad Clark, Samuel Lenz, Justin Nguyen, Huihuang Yan, Keith Robertson, Gianrico Farrugia, Zhiguo Zhang, Tamas Ordog, Jeong-Heon Lee. Enhanced and controlled chromatin extraction for chromatin-based epigenetic assays in FFPE tissues [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5180.
Abstract 5183: ONC201 induces acetylation of histone binding within the p21 (CDKN1A) gene promoter
Authors: Zhang Yiqun , Zhou Lanlan , Zhang Shengliang , Ralff Marie D. , Zhao Shuai , Abbosh Philip H. , Sidker Rahmat , El-Deiry Wafik S. 
Published: August 2019

Abstract
ONC201/TIC10 is a promising anticancer agent that upregulates cytotoxic TRAIL pathway signaling in cancer cells. Preliminary clinical data indicates ONC201 induces clinical benefit in a subset of patients with histone H3 K27M glioma, among other tumors. Since H3 K27M mutation reduces levels of H3K27 di- and tri-methylation and in turn alters the expression of genes by epigenetic modulation, we investigated ONC201 effects on epigenetic regulation in cancer. We treated the colorectal cancer cell line HCT116 with the histone deacetylase inhibitor entinostat or ONC201. Chromatin immunoprecipitation (ChIP) was performed with anti-histone H3 (acetyl K9) antibody using lysates from drug-treated tumor cells. Immunoprecipitated DNA was probed by PCR using primers across the promoter of p21 (WAF1; CDKN1A). The results indicate that both ONC201 and entinostat induce the acetylation of histone H3 binding within the p21 promoter. We further observed that ONC201 plus entinostat have synergistic effects in this p21 promoter acetylation activity. Activation of p21 gene expression by enhancing histone acetylation may be relevant in cancer suppression by ONC201.
Citation Format: Yiqun Zhang, Lanlan Zhou, Shengliang Zhang, Marie D. Ralff, Shuai Zhao, Philip H. Abbosh, Rahmat Sidker, Wafik S. El-Deiry. ONC201 induces acetylation of histone binding within the p21 (CDKN1A) gene promoter [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5183.
Abstract 5189: Activity of polycomb repressive complex 2 determines sensitivity to epigenetic therapy
Authors: Chen Fan , Brainson Christine F. 
Published: August 2019

Abstract
EZH2 is a histone methyltransferase that tri-methylates histone H3 at lysine 27 (H3K27me) in the context of the Polycomb Repressive Complex 2, and is highly correlated with poor prognosis of many cancers. However, recent data suggest a de-coupling of EZH2 expression from its enzymatic activity, and many poor prognosis tumors also have low H3K27me3. Therefore, we hypothesize that deletion of Ezh2 would drive more aggressive tumors which may have distinct epigenetic vulnerabilities. To test this hypothesis, we generated the LSL:KrasG12D/+; p53 flox/flox (LSL: lox-stop-lox) mice (Kras/p53 mice) with either zero, one or two floxed alleles of Ezh2 and induced lung tumors with intranasal adeno-Cre virus administration. Supporting our hypothesis, we observed mice with two floxed alleles of Ezh2 (Ezh2 null) had higher tumor burden, higher tumor grade and lower survival than Ezh2 wild-type or heterozygous Kras/p53 mice. Ezh2 null tumors also had a higher propensity to metastasize than Ezh2 wild-type tumors. Consistent with these results, Ezh2 null Kras/p53 tumors and cell lines had increased expression of genes involved in epithelial-mesenchymal transition (EMT), KRAS-driven tumorigenesis, metastasis, and cell cycle regulation. In order to examine the therapeutic vulnerabilities of Ezh2 depleted lung cancers, we built a panel of 2-dimensional cell lines and 3-dimensional organoid cultures of the Kras/p53 tumors that were Ezh2 null, heterozygous and wild-type. We reasoned that using the H3K27me3 demethylase inhibitor might be able to stabilize the residual H3K27me3 in Ezh2 null cells and decrease their aggressive properties. Intriguingly, while we observed no difference in sensitivity to H3K27me3 demethylase inhibitor in the various Ezh2 genotypes of 2-dimensional cultures, both 3-dimensional cultures and in vivo allografts demonstrated Ezh2 null tumors but not Ezh2 WT or heterozygous are sensitive to the H3K27me3 demethylase inhibitor. These data are interesting because they suggest that assays of 3-dimensional organoids may more faithfully recapitulate responses to epigenetic drugs than standard cell lines, and that aggressive tumors with low H3K27me3 might be selectively killed by demethylase inhibitor. We are now expanding our studies to include other targeting agents, including inhibitors of the kinase WEE1 and inhibitor of the chromatin reader BRD4.
Citation Format: Fan Chen, Christine F. Brainson. Activity of polycomb repressive complex 2 determines sensitivity to epigenetic therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5189.
Abstract 519: EVOEXS21546 is a novel non-brain penetrant A2AR inhibitor for cancer immunotherapy with accelerated drug development
Authors: Fons Pierre , Bell Andy , Esquerre Michael , Versluys Stephanie , Bertrand Florie , Hopkins-Navratilova Iva , Robinson Sean , Visentin Virgile , Schreyer Adrian , Cox Richard , Mirey Emilie , Pelissier Emilie , bergeaud Celia , Culurgioni Simone , Besnard Jeremy , Payne Andrew , Menegotto Jerome , Machet Frederic , Poussereau-Pomie Celine , Cogo Eric , Paillasse Michael , Ferigo Federica , Pagliarusco Sabrina , Lisztwan Joanna , Whittaker Mark , Johnstone Craig , Hopkins Andrew 
Published: August 2019

Abstract
Evotec and Exscientia are collaborating to develop an innovative drug discovery platform for accelerating small molecule development in Immuno-Oncology. The primary focus is to target the immunosuppressive adenosine pathway. We have firstly sought to generate a novel and selective, non-brain penetrant A2AR antagonist. EVOEX21546 has been selected as our lead candidate with in vitro potency on primary human CD3+ T-lymphocytes for inducing the recovery of IL-2 production after CADO-mediated inhibition of T-cell activation. In addition, we have demonstrated the compound’s effect on other key biological features of T-cell activation including IFN-gamma production and T-cell proliferation. ADME/DMPK data show that EVOEX21546 has a favourable pharmacological profile consistent with its evaluation in syngeneic tumour models. Furthermore, we are pursuing efforts to understand the Mechanism-of-Action of EVOEXS21546 in order to identify the most relevant biomarker of activity for clinical translation. Finally, from the perspective to accelerate the IND submission, EVOEXS21546 entered an INDiGO campaign, an integrated and rapid process to reach IND complemented by high-end integrated CMC. These results, generated in the frame of the A2AR inhibitor pathway, have paved the way to an optimized process for identifying, improving and accelerating the path from drug discovery to the entering into the clinic for Immuno-Oncology drugs.
Citation Format: Pierre Fons, Andy Bell, Michael Esquerre, Stephanie Versluys, Florie Bertrand, Iva Hopkins-Navratilova, Sean Robinson, Virgile Visentin, Adrian Schreyer, Richard Cox, Emilie Mirey, Emilie Pelissier, Celia bergeaud, Simone Culurgioni, Jeremy Besnard, Andrew Payne, Jerome Menegotto, Frederic Machet, Celine Poussereau-Pomie, Eric Cogo, Michael Paillasse, Federica Ferigo, Sabrina Pagliarusco, Joanna Lisztwan, Mark Whittaker, Craig Johnstone, Andrew Hopkins. EVOEXS21546 is a novel non-brain penetrant A2AR inhibitor for cancer immunotherapy with accelerated drug development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 519.
Abstract 5190: EZH2 epigenetically silences anti-tumor immunity in melanoma via dual histone and DNA methylation
Authors: Tiffen Jessamy , Gunatilake Dilini , Gallagher Stuart , Hersey Peter 
Published: August 2019

Abstract
Despite major advances in immuno- and targeted therapies for metastatic melanoma, not all patients respond to such treatments and the development of therapy resistance remain key obstacles. Novel targets are required and the epigenetic modifier EZH2 may represent such a solution.
EZH2 methylates histones causing chromatin compaction and silencing of gene expression. Additionally, EZH2 has been shown to interact with DNA methyltransferases (DNMTs). Aberrant EZH2 in cancer results in the silencing of hundreds of tumor suppressor genes that would normally constrain cancer growth, and 26% of patients in the Australian Melanoma Genome Project (AMGP) display such abnormal EZH2.
Using ChIP-seq, microarrays and DNA methylation sequencing, we identified a subset of EZH2 target genes that are silenced by both histone and DNA methylation in melanoma. Interestingly many of these genes play a role in the anti-tumor immune response, including RASSF5 and ITGB2 that facilitate lymphocyte infiltration into tumors and correlate with better survival outcomes in melanoma patients when their expression is high. We show that such genes can be significantly up-regulated by combined treatment with inhibitors of both EZH2 and DNMT in melanoma cells in vitro.
Our studies suggest that aberrant EZH2 in melanoma drives aggressive disease via suppression of genes that would normally trigger the anti-tumor immune response. The progression of several preclinical, small molecule inhibitors of EZH2 and DNMTs remains promising.
Citation Format: Jessamy Tiffen, Dilini Gunatilake, Stuart Gallagher, Peter Hersey. EZH2 epigenetically silences anti-tumor immunity in melanoma via dual histone and DNA methylation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5190.
Abstract 5195: Efficacy of histone deacetylase inhibitors in a 3D cell culture model
Authors: Irigoyen Macarena , Castillo Gonzalo 
Published: August 2019

Abstract
Epigenetic dysregulation, changes in gene expression not due to changes in the DNA sequence, is the underlying cause of many diseases including cancer. Identification of enzymatic chromatin-complex modulators that can restore chromatin homeostasis is critical to developing better therapeutic agents for both, hematologic and solid tumors. 3D cell culture models have been developed to overcome the limitations of monolayer in vitro assays, to include the complexity of the tumor microenvironment known to modulate epigenetic factors, such as cell-cell interaction and allowing for formations of metabolic gradients, factors known to play a role in epigenetic drug efficacy and resistance. In this study, we evaluated the efficacy of class I and II Inhibitors of histone deacetylases, SAHA and Trichostatin A, in a 3D cell culture in vitro assay across several human tumor carcinoma cell lines. The cell lines were grown in 3D cell cultures, and efficacy of the drugs was evaluated at 72 hours and ten days. All the cell lines grown as spheroids proved to be highly sensitive to SAHA and Trichostation A. AGS, a stomach adenocarcinoma cell line, showed the highest sensitivity to SAHA with an IC50 of 270 nM. Trichostatin A, on the other hand, displayed higher sensitivity to the ovarian carcinoma cell line, SKOV3, with an IC50 of 190 nM. In all cases, maximum potency was seen at the 10-day incubations with IC50s below 1 µM for all the cell lines in the panel. Drug-drug combinations with the epigenetic drugs were also studied, the results are discussed.
Citation Format: Macarena Irigoyen, Gonzalo Castillo. Efficacy of histone deacetylase inhibitors in a 3D cell culture model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5195.
Abstract 5197: Histone deacetylase inhibitors promote breast cancer metastasis by elevating NEDD9 expression
Authors: Hu Zong-long , Wang Ya-fang , Su Yi , Shen Yan-yan , Fang Yan-fen , Ding Jian , Chen Yi 
Published: August 2019

Abstract
The approved pan-histone deacetylase (HDAC) inhibitors have brought impressive therapeutic benefits for patients with a few subtypes of hematologic malignancies. Favorable outcomes in breast cancer have not been observed, although multiple HDAC inhibitors have been therapeutically validated in preclinical breast cancer models. Here, we report that pan-HDAC inhibitors provoke breast cancer metastasis in vitro and in vivo, which will severely impede their clinical benefits. Given the role of HDAC inhibitors in the epigenetic control of transcription, we utilized RNA sequencing (RNA-seq) analysis to analyze global gene-expression changes following LBH589 treatment of MCF-7 cells. Pathway enrichment analysis of the 1591 identified genes based on GO analysis showed that 146 GO were significantly altered. Interestingly, most of the changes were related to cytoskeletal, cell junction, and biological adhesion pathways. Genes in the above mentioned GO were intersected to obtain seven genes by Venn analysis. NEDD9 was among the most significantly upregulated transcripts by LBH589, for which was suggested as a metastasis marker in the last decade. We substantiated this result by detecting the mRNA and protein levels of NEDD9 in HDAC inhibitors treated cells. As with the RNA-seq results, a notable upregulation of NEDD9 mRNA and protein were induced by HDAC inhibitors in breast cancer in vitro and in vivo. Mechanistically, pan-HDAC inhibitors enhance acetylation of H3K9 at the NEDD9 gene promoter to upregulate NEDD9 expression via inhibition of HDAC4, and activate FAK phosphorylation. Notably, we demonstrated that FAK inhibitor can reverse pan-HDAC inhibitor-induced breast cancer metastasis, which may improve HDAC inhibitors efficacy for breast cancer. In summary, we demonstrated an NEDD9-FAK signaling pathway, which was induced by pan-HDAC inhibitors, leading to breast cancer metastasis, and thereby caused limitation of the clinical benefits of HDAC inhibitors on breast cancer. We propose that HDAC4 has an upstream regulatory role in NEDD9 expression, leading to FAK phosphorylation and subsequent stimulation of breast cancer metastasis through epigenetic regulation. Our results suggest a need for increased isoform selective HDAC inhibitor research and development.
Citation Format: Zong-long Hu, Ya-fang Wang, Yi Su, Yan-yan Shen, Yan-fen Fang, Jian Ding, Yi Chen. Histone deacetylase inhibitors promote breast cancer metastasis by elevating NEDD9 expression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5197.