bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2078: A multiscale map of DNA damage response in human cells
Authors: Kratz Anton , Kim Minkyu , Zheng Fan , Koczor Christopher A. , Fong Samson , Li Jianfeng , Sobol Robert W. , Krogan Nevan , Ideker Trey 
Published: July 2021

Abstract
The DNA damage response (DDR) ensures error-free genome replication and transcription, but is often disrupted in cancer. We developed DDRAM, a multilayered map of DDR derived from our own high-throughput physical interaction screen as well as genome, transcriptome, and proteome datasets from published sources. DDRAM organizes 328 genes into 41 hierarchical pathways. We identify 55 (17%) novel DDR genes with functions distributed across various pathways, and novel and more specific roles for 153 (47%) of established DDR genes. We perform epistasis mapping to support novel pathway assignments of FOXK1 in nucleotide metabolism and XRCC3 in the Fanconi anemia pathway. Using quantitative imaging of a fluorescent probe, in some cases confirmed by epistasis mapping, we experimentally validate members of the Short Patch Base Excision Repair pathway over a time course, revealing a more complete model of poly(ADP-ribose)-dependent recruitment to sites of DNA damage.
Citation Format: Anton Kratz, Minkyu Kim, Fan Zheng, Christopher A. Koczor, Samson Fong, Jianfeng Li, Robert W. Sobol, Nevan Krogan, Trey Ideker. A multiscale map of DNA damage response in human cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2078.
Abstract 2081: Transcriptional silencing of CDK18 in BRG1 mutant lung cancer
Authors: Phillips Loryn Michelle , Johnston Christopher A. , Belinsky Steven A. , Tessema Mathewos 
Published: July 2021

Abstract
In ~10% of lung cancers, the BRG1 gene is mutated often causing a loss of function (LOF). BRG1 is a tumor suppressor that encodes a protein (SMARCA4), which is one of the mutually exclusive ATPase subunits of the Switch/Sucrose Non-fermentable (SWI/SNF) complex. The SWI/SNF complex functions to regulate transcription of many genes including tumor suppressor genes, through mediating chromatin remodeling and nucleosome repositioning by maintaining open chromatin and actively evicting polycomb repressive complexes (PRCs) from target genes and regions. Our previous research showed that BRG1 mutation occurs in approximately 9% of lung adenocarcinomas in smokers and 11% in smokers delineating BRG1 as a clinically relevant mutation. The goal of these studies is to elucidate the downstream effects of BRG1 LOF on gene expression. RNA sequencing of isogenic BRG1 wild type (WT) and knock out (KO) clones from malignant and transformed cell lines identified cell cycle control and chromosomal replication as the most significantly affected pathway. qRT-PCR was used to validate expression changes in 17 genes from this pathway in the WT and KO clones as well as wild type and mutant tumors lines. CDK18 was the most significantly affected target exhibiting a 78% reduction in expression (p&lt;0.001) comparing wild type to mutant cell lines. Ongoing studies are investigating the epigenetic mechanisms leading to transcriptional repression of CDK18 that include cytosine DNA methylation and histone methylation of H3K27. In addition, functional assays (e.g., soft agar, cell migration) are evaluating the role of epigenetically repressed CDK18 in lung carcinogenesis and cell cycle control through siRNA knock down of CDK18 in wild type BRG1 cell lines and carcinogen transformed human bronchial epithelial cells. Together, these studies will provide new insight into the role of LOF of CDK18 in BRG1 mutant cancer. (Supported by P30 CA11800).
Citation Format: Loryn Michelle Phillips, Christopher A. Johnston, Steven A. Belinsky, Mathewos Tessema. Transcriptional silencing of CDK18 in BRG1 mutant lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2081.
Abstract 2084: Single-cell multimodal glioma analyses reveal epigenetic regulators of cellular plasticity and environmental stress response
Authors: Johnson Kevin C. , Anderson Kevin J. , Courtois Elise T. , Gujar Amit D. , Barthel Floris P. , Varn Frederick S. , Luo Diane , Seignon Martine , Yi Eunhee , Kim Hoon , Estecio Marcos R. , Tang Ming , Navin Nicholas E. , Maurya Rahul , Ngan Chew Yee , Verburg Niels , Hamer Philip C. De Witt , Bulsara Ketan , Samuels Michael L. , Das Sunit , Robson Paul , Verhaak Roel G. 
Published: July 2021

Abstract
Glioma intratumoral heterogeneity enables adaptation to challenging microenvironments and contributes to universal therapeutic resistance. Here, we integrated 914 single-cell DNA methylomes, 55,284 single-cell transcriptomes, and bulk multi-omic profiles across 11 adult IDH-mutant or IDH-wild-type gliomas to delineate sources of intratumoral heterogeneity. We found that local DNA methylation instability, or epimutation burden, was elevated in more aggressive tumors, reflected intratumoral variability, linked with transcriptional disruption, and associated with environmental stress response. We show that the activation of cell-state specific transcription factors is impacted by epimutations and that loosened epigenetic control may facilitate cellular plasticity. We validated the impact that the common environmental stressor hypoxia has on the epigenetic stability and shifts in cell states through perturbation-based in vitro experiments coupled with single-cell genomics. Our analyses support that glioma cells under stress hijack epigenetic mechanisms that regulate cell state transitions to overcome challenges posed by nutrient-poor microenvironments and therapeutic insults. We confirmed the link between cellular stress and epigenetic instability by analyzing larger cohorts of bulk longitudinally collected and spatially separated DNA methylation data. Increased DNA methylation instability was associated with accelerated disease progression, and recurrently selected DNA methylation changes were enriched for environmental stress response pathways. Our work provides an integrative framework to better understand glioma evolution and highlights the importance of epigenetic heterogeneity in shaping therapeutic response.
Citation Format: Kevin C. Johnson, Kevin J. Anderson, Elise T. Courtois, Amit D. Gujar, Floris P. Barthel, Frederick S. Varn, Diane Luo, Martine Seignon, Eunhee Yi, Hoon Kim, Marcos R. Estecio, Ming Tang, Nicholas E. Navin, Rahul Maurya, Chew Yee Ngan, Niels Verburg, Philip C. De Witt Hamer, Ketan Bulsara, Michael L. Samuels, Sunit Das, Paul Robson, Roel G. Verhaak. Single-cell multimodal glioma analyses reveal epigenetic regulators of cellular plasticity and environmental stress response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2084.
Abstract 2089: Epigenetic regulation of sprouty2 in colorectal cancer
Authors: Stuckel Alexei , Khare Sharad 
Published: July 2021

Abstract
Background: The specific role of Sprouty-2 in colorectal cancer (CRC) as either a tumor suppressor or an oncogene is unclear. This is further obscured by the fact that no known driver mutations of Sprouty-2 have been reported. Therefore, for the first time, alterations of DNA 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) were investigated to better understand the regulation of Sprouty-2 in CRC.
Methods: Sprouty-2 transcript expression was evaluated in CRC patient samples and Sprouty-2 protein expression was evaluated in CRC cells. The DNA methylation status spanning Sprouty-2 gene was evaluated using combined bisulfite restriction analysis (COBRA). The 5hmC status in the Sprouty-2 gene body and promoter was analyzed using previously performed nano-hmC-seal data from colon cancers and adjacent normal colonic mucosa. Publicly available RNA-seq and methylation data from The Cancer Genome Atlas (TCGA) were extracted from tumors from CRC patients.
Results: Variable Sprouty-2 mRNA expression was observed among CRC patient tumors compared to adjacent normal appearing colonocytes. For the first time, differential methylation between adjacent normal colon and CRC samples was identified in 2 CTCF binding sites and in the promoter near the Transcriptional Start Site (TSS) of Sprouty-2, where the 5mC status in 1 of the CTCF binding sites correlated with transcript abundance. In CRC, this is the first study to reveal increases of 5hmC deposition in the gene body and promoter region of Sprouty-2 compared to normal colon. In metastatic CRC, an inverse correlation of increased Sprouty-2 promoter 5mC and decreased mRNA expression was found in patients registered in TCGA.
Conclusions: In terms of tumor growth, epigenetic aberrations including Sprouty-2 promoter hypomethylation and increased 5hmC may play a prominent role in positive regulation of Sprouty-2 in CRC. In metastatic stages of CRC, increases in Sprouty-2 promoter 5mC may downregulate Sprouty-2 expression, which may ultimately label Sprouty-2 as a tumor suppressor in CRC.
Citation Format: Alexei Stuckel, Sharad Khare. Epigenetic regulation of sprouty2 in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2089.
Abstract 2090: TP73 expression may be influenced by DNA methylation in human tumorigenesis
Authors: Yao Zhixing , Yao David R. , Yu William , Malki Ahmed , Sherif Zaki A. 
Published: July 2021

Abstract
Epigenetic events that cause alterations in gene expression are common in human cancers. The connection between TP73 expression and its epigenetic functionality in tumorigenesis has scarcely been explored. As a transcription factor, TP73 (aka, p73) like its cousin, p53, is activated in response to DNA damage and regulates the expression of downstream genes involved in cell cycle arrest and apoptosis. However, there are other compounding functions of this gene that reflect its non-tumor-related characteristics, thus making it very difficult to assess its specific role in tumorigenesis. Our previous work showed that DNA methylation activates TP73 expression in hepatocellular carcinoma (HCC) and gastrointestinal cancer. In this study, we determined TP73 expression in normal human mammary epithelial cells (HMECs), human non-cancerous Li-Fraumeni Syndrome (LFS) skin fibroblast cells, human breast cancer cell lines (MCF7, MDA-MB-231 & MDA-MB-468), prostate cancer cell lines (LNCaP & MDA-PCa2b), lung cancer cell lines (A549 & NCI-H596), neuroblastoma cell lines (IMR32 & SK-N-SH) and normal human skin fibroblast cell line (HS27). The results show that TP73 was expressed solely in cancer cells. Subsequent immunohistochemical analyses of TP73 expression in cancerous and adjacent non-cancerous liver tissues of HCC patients clearly showed that TP73 expression was exclusively evident in cancerous tissues but not in the adjacent normal liver tissues. Mechanistically, methylation-specific PCR and bisulfite sequencing studies revealed that TP73 promoter is activated only in cancer cells and this activation occurs via DNA methylation. Moreover, ChIP assays demonstrated that a CTCF (a chromosomal networking protein CCCTC binding factor) and tumor protein p53 (TP53) bind to TP73 promoter and regulate TP73 expression. Our observations demonstrate that a positive correlation in tumorigenesis exists between TP73 expression and DNA methylation in promoter regions of TP73. These findings suggest that TP73's role in carcinogenesis may prove to be pivotal for the development of future diagnostic and therapeutic applications.
Citation Format: Zhixing Yao, David R. Yao, William Yu, Ahmed Malki, Zaki A. Sherif. TP73 expression may be influenced by DNA methylation in human tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2090.
Abstract 2091: DNA methylation enhances apoptosis resistance of renal cancer cells
Authors: Miyakuni Kosuke , Nishida Jun , Ehata Shogo , Miyazono Kohei 
Published: July 2021

Abstract
Epigenetic modifications are important not only for carcinogenesis but also for metastasis of clear cell renal cell carcinoma (ccRCC). We previously reported that inflammation-related signaling is constitutively activated in advanced ccRCC through the formation of super enhancer. In addition to histone modification, methylation of the primary structure of DNA is implicated in the progression of ccRCC. Recent studies revealed that DNA hypermethylation was frequently observed in ccRCC and correlated with poor prognosis. However, unlike in other cancers, methylated genes responsible for cancer progression is still unclear in ccRCC. In this study, we tried to identify a target(s) for DNA methyltransferases (DNMTs) in ccRCC cells based on the genome-wide analysis. Its function for the regulation of cellular survival was examined. Our preclinical model of ccRCC using the serial orthotopic inoculation model exhibited the up-regulation of DNMT3B in advanced ccRCC. Pre-treatment of advanced ccRCC with 5-aza-dC attenuated a formation of a primary tumor through the induction apoptosis. DNA methylated sites were analyzed using methylation array in reference to RNA-sequencing data. As a result, ubiquinol cytochrome c reductase hinge protein (UQCRH), one of the components of mitochondrial complex III, was extracted as a methylation target in advanced ccRCC. Immunohistochemical analysis revealed that the expression of UQCRH in human ccRCC tissue was lower than normal adjacent tissue. Silencing of UQCRH attenuated the cytochrome c release in response to apoptotic stimuli and resulted in enhancement of primary tumor formation in vivo. Our results imply that DNA methylation induces the decreased expression of potential tumor suppressor gene UQCRH, which is essential for the completion of apoptotic process of ccRCC cells. These findings may contribute to the understanding of molecular mechanisms involved in the drug resistance of ccRCC cells and provide an important insight for the improvement of the efficacy of existing medicines.
Citation Format: Kosuke Miyakuni, Jun Nishida, Shogo Ehata, Kohei Miyazono. DNA methylation enhances apoptosis resistance of renal cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2091.
Abstract 2102: Development and validation of Predicine methylation assay towards early cancer detection
Authors: Xiang Binggang , Dai Chao , Wang Ming , Zhao Zhixin , Wang Amy Xiaohong , Zhou Kemin , Jia Shidong , Luo Shujun , Du Pan 
Published: July 2021

Abstract
DNA methylation is one of the earliest signatures during cancer development. DNA methylation patterns from different cancer types can provide distinct epigenetic signatures. Several methods are available for sequencing DNA methylation throughout the genome, including whole genome bisulfite sequencing (WGBS) and antibody-dependent DNA immunoprecipitation (MeDIP). As a non-invasive approach, plasma cfDNA and urinary cfDNA (ucfDNA) have been widely explored for clinical applications. More recently, in virtue of its cancer-specific methylation signatures, cfDNA has been adopted for early cancer detection and further identification of cancer tissue of origin. Predicine has developed a liquid biopsy methylation assay that can robustly detect methylation using genomic and circulating cell-free DNA in body fluids. Predicine's methylation assay has great improvement over WGBS in reducing DNA damage, GC bias and increasing NGS reads mapping rate, and mapping quality score. In this study, we report the clinical utility of Predicine's methylation assay, which efficiently distinguishing healthy donors from patients of various types of cancer. Combined with its genomics NGS counterpart, Predicine's methylation platform is a powerful tool for early cancer detection and real-time monitoring of cancer progression.
Citation Format: Binggang Xiang, Chao Dai, Ming Wang, Zhixin Zhao, Amy Xiaohong Wang, Kemin Zhou, Shidong Jia, Shujun Luo, Pan Du. Development and validation of Predicine methylation assay towards early cancer detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2102.
Abstract 2110: Platinum-inducedBRCA1 promoter DNA hypermethylation and altered metabolic profile promotes chemoresistance in ovarian cancer
Authors: Sood Riddhi , Xiao Sikai , Sriramkumar Shruthi , Hassel Christiane , Nephew Kenneth , O'Hagan Heather 
Published: July 2021

Abstract
High grade serous ovarian cancer (HGSOC) is the most common and aggressive type of ovarian cancer (OC). Platinum resistance is a common occurrence in HGSOC leading to tumor relapse and patient mortality. Multiple mechanisms contribute to platinum resistance in OC, including enrichment of ovarian cancer stem cells (OCSCs), which is observed in relapsed tumors. Platinum treatment activates the DNA damage response (DDR) and the DNA repair protein BRCA1 is an OC susceptibility factor. In our study, we demonstrate that platinum treatment induces a decrease in BRCA1 levels that leads to an increase in activity of ALDH, an OCSC marker. In a parallel pathway that is associated with G2/M arrest, platinum treatment also induces an increase in NAMPT expression and NAD+ levels, the cofactor required for ALDH activity. BRCA1 is repressed through platinum-induced promoter DNA hypermethylation. Importantly, combination of platinum with decitabine, a DNA methyltransferase (DNMT) inhibitor, prevents the platinum-induced increase in OCSCs. This study uniquely provides preclinical support for the use of DNMT inhibitors in the neoadjuvant setting in combination with platinum treatment for OC patients.
Citation Format: Riddhi Sood, Sikai Xiao, Shruthi Sriramkumar, Christiane Hassel, Kenneth Nephew, Heather O'Hagan. Platinum-inducedBRCA1 promoter DNA hypermethylation and altered metabolic profile promotes chemoresistance in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2110.
Abstract 2132: Ezh2-Y641F mutation interacts with Stat3 to regulate the melanoma tumor immune response via disruption of IFN signaling
Authors: Zimmerman Sarah M. , Nixon Samantha , Souroullas George P. 
Published: July 2021

Abstract
Cancer genetic sequencing studies have identified systematic alterations of epigenetic and chromatin modifiers in most cancers, consistent with the fact that chromatin modifiers, such as the Polycomb Repressive Complex 2 (PRC2), regulate the expression of tumor suppressors. In melanoma, 10% of patients exhibit amplifications or point mutations in EZH2, the enzymatic subunit of PRC2; however, the oncogenic mechanisms of EZH2 mutations in melanoma remain elusive. Previously, we observed that expression of Ezh2-Y641F in melanoma cells resulted in upregulation of IFN-related genes. We thus sought to better understand this mutation and the consequences of IFN signaling changes on tumor growth and the tumor immune response. We discovered that Ezh2-Y641F directly interacts with and methylates Stat3, a known regulator of interferon signaling. To understand the effects of this interaction, we performed ChIP-seq for Ezh2 and Stat3 in melanoma cells and found that the binding profiles of Stat3 and Ezh2 are greatly changed in Ezh2-Y641F cells. Furthermore, Ezh2 and Stat3 binding sites co-localized at several genomic loci in Ezh2-Y641F cells, including a region that regulates Ezh2. Knockdown of Stat3 in melanoma cells decreased Ezh2 expression and partially reduced expression of the IFN-related genes that were initially upregulated by Ezh2-Y641F. Analysis of the tumor-infiltrating immune cells by flow cytometry revealed increased CD8+ T cells and decreased myeloid cells in Ezh2-Y641F melanomas, consistent with a more favorable immune response, although tumor growth was unchanged. Genetic inhibition of Stat3 expression via shRNA rescued this phenotype. Our data suggest a novel interaction between the PRC2 complex and Stat3 in melanoma, which has significant physiological consequences on the tumor immune response. Molecular and genomic analysis suggest that Ezh2 and Stat3 together regulate gene expression, including Ezh2 itself. Overall, these data highlight the significant role of chromatin regulators on the tumor immune response.
Citation Format: Sarah M. Zimmerman, Samantha Nixon, George P. Souroullas. Ezh2-Y641F mutation interacts with Stat3 to regulate the melanoma tumor immune response via disruption of IFN signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2132.
Abstract 2135: Functional models of chromosome arm aneuploidies in lung squamous cell carcinoma
Authors: Taylor Alison Marie , Jain Sejal , Shih Juliann , Cherniack Andrew D. , Beroukhim Rameen , Meyerson Matthew 
Published: July 2021

Abstract
Aneuploidy, which we define as whole chromosome or chromosome arm copy number imbalance, is a near-universal characteristic of human cancers. Cancer subtypes are often characterized by tumor specific patterns of chromosome arm copy number alterations; for example, squamous cell carcinomas (SCCs) from different tissues of origin (including lung, head and neck, esophagus, and bladder) have a pattern of chromosome 3p loss and chromosome 3q gain. Although these alterations are frequent, they are not well understood due to difficulty in modeling specific aneuploidy alterations in the matching cell type. However, recent advances in genome engineering allow generation of large chromosomal alterations. We used the CRISPR-Cas9 system to delete one copy of chromosome 3p in human immortalized lung epithelial cells most similar to upper airway basal cells. Deletion of chromosome 3p was validated by whole genome sequencing and karyotyping. Consistent with patient data, expression of 3p genes was decreased upon deletion, as well as increased expression of interferon response genes. Phenotypic characterization revealed that cells with chromosome 3p deletion initially proliferated more slowly than their siblings. These chromosome 3p deleted cells had increased G1 arrest but did not undergo increased apoptosis or cell death. Interestingly, after several passages in culture, the proliferation defect was rescued in chromosome 3p deleted cells. Genome sequencing and karyotype analyses found that evidence of chromosome 3 duplication, transitioning the cell to a state of chromosome 3q gain. We isolated sibling cells with chromosome 3p deletion or chromosome 3q gain and demonstrated that duplication of chromosome 3 could indeed rescue proliferation rates. With our cellular model of chromosome arm-level aneuploidy, we uncovered a selection mechanism that allowed aneuploidy tolerance in vitro, and a possible explanation for joint alteration of both arms of chromosome 3. In conclusion, our genome engineering approach to model chromosome arm-level deletions provides a robust model that will address a gap in our understanding of aneuploidy in cancer.
Citation Format: Alison Marie Taylor, Sejal Jain, Juliann Shih, Andrew D. Cherniack, Rameen Beroukhim, Matthew Meyerson. Functional models of chromosome arm aneuploidies in lung squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2135.