bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 537: TRAF3 serves as a tumor suppressor in HPV-associated head and neck squamous cell carcinomas
Authors: Chen Tony W. , Zhang Jialing , Yang Xinping , Chen Zhong , Waes Carter Van 
Published: July 2017

Abstract
The molecular mechanisms that control transformation and tumorigenicity of human papillomavirus-associated (HPV+) head and neck squamous cell carcinomas (HNSCCs) are currently being investigated. The number of HPV+ HNSCC cases has increased sharply in recent years, especially in tonsil and oropharyngeal cancers. These HPV+ HNSCCs often respond differently to treatments. Recently, The Cancer Genome Atlas (TCGA, 2015) identified novel loss-of-function genomic alterations of TNF receptor-associated factor 3 (TRAF3) in HPV+ HNSCCs. TRAF3 is a ring-finger E3 Ubiquitin Ligase which inhibits downstream alternative NF-κB signaling and promotes anti-viral immunity by promoting degradation of ubiquitinated proteins. To assess TRAF3’s role in HPV+ HNSCCs, we identified cell lines with lower level of TRAF3 protein, consistent with deficient TRAF3 expression identified in TCGA data. Functional studies showed that TRAF3 expression led to decreased steady-state protein levels of the alternative NF-κB pathway components RELB and NF-κB2/p52, as assessed by Western blot, reporter assays and immunofluorescence. Additionally, TRAF3 expression led to decreased cell proliferation, tumorigenic activity and migration, and increased sensitivity to chemotherapy agent cisplatin. Interestingly, TRAF3 increases the steady state protein level of the classical tumor suppressors RB and p53 in HPV+ HNSCC cell lines as assessed by Western blot. Further in vitro characterization of TRAF3’s function in HPV+ HNSCCs was assessed using clinically identified TRAF3 loss-of-function mutagenic isoforms, mimicking both TCGA data and HNSCC cell line data for TRAF3 defects. In contrast to wtTRAF3, these mutant forms of TRAF3 do not as strongly restore p53 or inhibit RELB and NF-κB2/p52 protein levels. One specific mutation which causes a frameshift at residue 210 greatly inhibits TRAF3 function as assessed by Western blot. To further assess effects of wt or TRAF3 loss-of-function mutants in vitro and in vivo, an inducible HPV+ HNSCC line expressing TRAF3 using the TET-ON system, and TRAF3 knockout in HPV+ HNSCC line and Human Oral Keratinocyte (HOK) line using CRISPR-Cas9 genomic editing are generated. In conclusion, the ring-finger E3 ubiquitin ligase TRAF3 inhibits the pro-survival alternative NF-κB signaling pathway and restores TP53 and RB, thereby serving as a tumor suppressor in HPV+ HNSCCs.
(Supported by NIDCD intramural project ZIA-DC-000016, 73 and 74)
Citation Format: Tony W. Chen, Jialing Zhang, Xinping Yang, Zhong Chen, Carter Van Waes. TRAF3 serves as a tumor suppressor in HPV-associated head and neck squamous cell carcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 537. doi:10.1158/1538-7445.AM2017-537
Abstract 5370: Examination of DNA looping near oncogenes reveals variable patterns of epigenetic landscapes in cancer
Authors: Perez Monika , Johannes Ty 
Published: July 2017

Abstract
INTRODUCTION:
The compaction of chromatin in the nucleus into hierarchical three-dimensional (3D) structures plays a key role in the regulation of gene expression. Advancements in high-throughput chromatin conformation capture assays have enabled the determination of this hierarchical structure in a variety of cell states, including cancer. Of note, recent studies have implicated pathogenic alterations in 3D topology of the genome with the activation of proto-oncogenes in a multitude of cancers.
METHODS:
To characterize the topological changes associated with different cancer phenotypes, we examine publically available epigenetic profiles from the ENCODE Project, including 3D data from Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) from breast cancer and leukemia cell lines. Integrating the chromatin topology data with transcription factor binding, DNase accessibility, and histone modification data, we uncover variable epigenetic landscapes associated with differentially active oncogenes in these cancer cell lines.
RESULTS:
We provide evidence of topological variability influencing differentially expressed oncogenes and tie these observations to other epigenetic changes. In particular, we show insulated-neighborhoods mediated by CTCF looping partition segments of the genome containing active oncogenes away from repressive markings like H3K4me3. Additionally, we show that variation in topology differentially localizes H3K27ac in distal regulatory regions to promoters of oncogenes, providing a means for gene activation in non-coding regions.
CONCLUSIONS:
Variable patterns of chromatin topology provide a unique signature and mechanism of oncogenes for cancerous phenotypes. We use publically available data to show mechanisms of activity associated with chromatin topology variation.
Citation Format: Monika Perez, Ty Johannes. Examination of DNA looping near oncogenes reveals variable patterns of epigenetic landscapes in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5370. doi:10.1158/1538-7445.AM2017-5370
Abstract 5372: Alterations in the chromatin accessibility in nonalcoholic steatohepatitis-associated hepatocellular carcinoma
Authors: Dechassa Mekonnen Lemma 
Published: July 2017

Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. Accumulated evidence in the past decade has stablished that NASH, in addition to other well-identified risk factors, is becoming a major cause of HCC in United States. In the present study, we investigated cancer-associated chromatin alterations in the Stelic Animal Model (STAM) of NASH-related HCC. Using Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq), we identified 1666 differentially opened chromatin regions in HCC tumor tissue as compared to normal livers. Annotation of these regions showed that they were associated with 1773 differentially expressed genes, which were enriched in lipid and steroid metabolism, obesity, and cancer. Among the differentially opened chromatin regions, 10% resided within 5 kb from the transcription start site (TSS), while the remaining 90% were located distal to the TSS (&gt; 5 kb). By combining ATAC-seq and transcriptomic profiles, we demonstrated that 182 of the up-regulated genes were associated with open chromatin regions in tumor tissue. Furthermore, 24 of these up-regulated genes, including Apoa4, Nupr1, Anxa2, and Igfbp1, had accessible chromatin regions located proximal to the TSS. Importantly, analysis of histone modifications at the open chromatin regions of the over-expressed cancer-related Apoa4 and Anxa2 genes demonstrated enrichment by H3K4 mono-methylation (H3H4me1) and H3K27 acetylation (H3K27ac), histone marks that associated with the active gene promoters (H3K27ac) and enhancers (H3Kme1 and H3K27ac). In conclusion, these data provide evidence for alterations in the chromatin accessibility in tumor tissue and potential role of open chromatin regions in the over-expression of critical cancer-related genes in HCC.
Citation Format: Mekonnen Lemma Dechassa. Alterations in the chromatin accessibility in nonalcoholic steatohepatitis-associated hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5372. doi:10.1158/1538-7445.AM2017-5372
Abstract 538: The cytosolic domain of a disintergrin and metalloprotease (ADAM) 15 promotes non-small cell lung cancer (NSCLC) anti-apoptosis ability
Authors: Hou Hsin-Han , Yu Chong-Jen 
Published: July 2017

Abstract
Emerging evidence has indicated that proteins of a disintergrin and metalloprotease (ADAM) family contribute to cancer progression and metastasis. One member of this family, ADAM15, has been shown to be upregulated in multiple cancers, including gastric, lung, breast, and prostate cancers, and the enzymatic activities of its extracellular metalloprotrease domain promote breast cancer proliferation and migration through mediating ErbB signaling pathway. The patients with ADAM15 high-expressing lung tumors have shorter survival time and ADAM15 has been proved to enhance synovial fibroblasts anti-apoptosis ability via focal adhesion kinase signaling pathway. We firstly demonstrated other than extracellular enzymetic activity, the longest isoform of ADAM15 (ADAM15 i6), which contains the most cytoplasmic Src homology 3 (SH3) binding motifs, significantly upregulated in primary lung cancer tissues and promoted NSCLC proliferation via growth factor receptor-bound protein 2 (Grb2) and Src homolog 2 domain containing (Shc) association. In this study, we further explore the roles of ADAM15 cytosolic domain in NSCLC apoptosis resistance. Overexpression of ADAM15 i6 promoted CL1-0 cell anti-apoptosis ability according to the trypan blue inclusion assay. Ablation of nephrocystin (NPHP1) attenuated the ADAM15 i6-promoted anti-apoptosis ability. Thus, we identified a novel mechanism of the ADAM15 cytoplasmic domain in NSCLC tumor progression, which will shed light on the molecular mechanisms of ADAM proteins, and facilitate development of novel therapy in NSCLC.
Note: This abstract was not presented at the meeting.
Citation Format: Hsin-Han Hou, Chong-Jen Yu. The cytosolic domain of a disintergrin and metalloprotease (ADAM) 15 promotes non-small cell lung cancer (NSCLC) anti-apoptosis ability [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 538. doi:10.1158/1538-7445.AM2017-538
Abstract 5386: Does chemotherapeutics contribute to DNMT1 expression level in colorectal cancer cells
Authors: VAROL NURAY , TERZİ SUNA ARIKAN , SOYLEMEZ ZAFER , YILDIZ HANDAN , OZDEMİR MUJGAN , SOLAK MUSTAFA 
Published: July 2017

Abstract
Epigenetic modifications, particularly DNA methylation in selected gene promoters is a pivotal role in the development of colorectal cancer. DNA methylation is considered as one of the most important epigenetic mechanisms and it is catalyzed by DNA methyltransferases (DNMTs). DNMT1 abundance has been frequently seen in colorectal cancers but the reasons are not well understood. We investigated to the effect of chemotherapeutics used in treatment of colorectal cancer on expression of DNMT1 and this effect is achieved over which signalling pathway. In this study, GSK3β; IWP2 for β-catenin) and chemotherapeutics (oxaliplatin, fluorouracil, irinotecan) were detected by WST1. DNMT1 expression level was determinated by real-time PCR; and protein levels of GSK3β, pGSK3β(Ser9), Akt1, pAkt1(Ser473), β-catenin, pβ-catenin(Ser675) and DNMT1 by western blot. Our results indicated taht Akt1 increased the protein level of DNMT1 expression with coordinate transcriptional change via β-catenin pathway. Fluorouracil and irinotecan decreased DNMT1 expression at both transcriptional and translational levels but not oxaliplatin. Oxaliplatin increased DNMT1 expression at mRNA and protein levels. This effect is achieved by specific phosphorylation of β-catenin protein. The results revealed that use of some chemotherapeutic, particularly oxaliplatin, with spesific inhibitors (such as β-catenin inhibitor) in combination led to a reduced DNMT1 expression. Our findings may offer a new approach for determining the molecular effects of β-catenin signal pathway on DNMT1. This may allow us to identify new molecular targets for the treatment of colorectal cancers. However, the results revealed that some chemotherapeutics may contribute the aberration of DNA methylation.
Citation Format: NURAY VAROL, SUNA ARIKAN TERZİ, ZAFER SOYLEMEZ, HANDAN YILDIZ, MUJGAN OZDEMİR, MUSTAFA SOLAK. Does chemotherapeutics contribute to DNMT1 expression level in colorectal cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5386. doi:10.1158/1538-7445.AM2017-5386
Abstract 5387: Droplet digital PCR for sensitive quantification of DNA methylation in non-invasive material: Development of a robust control
Authors: Pharo Heidi D. , Andresen Kim , Jeanmougin Marine , Lind Guro E. 
Published: July 2017

Abstract
Background: Droplet digital PCR (ddPCR) is a highly sensitive method for quantification of nucleic acids, with great potential for detection of biomarkers present in low quantities. As for DNA methylation analyses using ddPCR, there is no consensus on whether or not a control should be included. The aim of the present study was to; 1) demonstrate that use of a control is essential in such analyses, and 2) develop a robust control with better performance than the existing alternatives.
Results and methods: A 4-gene control panel was developed in our lab, and its performance compared to the existing alternatives ACTB and C-LESS-C1. This was done through analyzing the methylation level of four target genes in DNA from 34 colon cancer cell lines. All ddPCRs were performed using the QX200™ PCR platform (BioRad). Details will be presented.
Conclusions: In summary, use of a control is essential for robust and consistent ddPCR based DNA methylation, and can prevent erroneous interpretation of technical artifacts.
Citation Format: Heidi D. Pharo, Kim Andresen, Marine Jeanmougin, Guro E. Lind. Droplet digital PCR for sensitive quantification of DNA methylation in non-invasive material: Development of a robust control [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5387. doi:10.1158/1538-7445.AM2017-5387
Abstract 5389: A personalized medicine approach to identifying dysregulated epigenetic enzyme activity in the development of castrate-resistant prostate cancer
Authors: Lee Jin-Hee , Boersma Melissa , Yang Bing , Damaschke Nathan , Corey Eva , Denu John , Jarrard David F. 
Published: July 2017

Abstract
Purpose: Recent advances in proteomic and chromatin immunoprecipitation tools have been vital in studying cancer epigenetics, but the ability to measure directly the enzyme activities of dysregulated histone-modifiers understudied. We utilize a novel approach to identify altered histone-modifying enzymes in the progression from hormone sensitive (HS) to castrate-resistant prostate cancer (CRPC) progression.
Methods: We developed, validated and utilized a high-throughput peptide microarray assay to identify altered histone lysine (de)acetylation activity in tumor lysates. Functional assays, novel HS and CRPC human tumor arrays and xenografts were utilized to confirm these findings.
Results: This microarray-based activity assay revealed up-regulated histone acetyltransferase (HAT) activity against specific histone H3 sites in a castrate-resistant (CR) PCa cell line compared to its hormone-sensitive (HS) isogenic counterpart. NAD+-dependent deacetylation assays revealed down-regulated Sirtuin activity in validated CR lines. Levels of acetyltransferases GCN5, PCAF, CBP and p300 were unchanged between matched HS and CR cell lines. However, auto-acetylation of p300 at K1499, a modification known to enhance HAT activity and a target of deacetylation by SIRT2, was highly elevated in CR cells, while SIRT2 protein level was reduced in CR cells. Interrogation of HS and matched CR xenograft lines reveals that H3K18 hyperacetylation, increased p300 activity, and decreased SIRT2 expression are associated with progression to CR in 8/12 (66%). Tissue microarray analysis revealed that hyperacetylation of H3K18 is a feature of CRPC. Inhibition of p300 results in lower H3K18ac levels and increased expression of androgen receptor.
Conclusions: This novel microarray approach provides a method to identify commonly dysregulated chromatin enzymes during progression providing a personalized therapeutic strategy to direct available drugs to target enzymes. Reduced SIRT2 expression and increased p300 activity lead to a concerted mechanism of hyperacetylation at specific histone lysine sites (H3K9, H3K14, and H3K18).Support: DOD PCRP (Jarrard)
Citation Format: Jin-Hee Lee, Melissa Boersma, Bing Yang, Nathan Damaschke, Eva Corey, John Denu, David F. Jarrard. A personalized medicine approach to identifying dysregulated epigenetic enzyme activity in the development of castrate-resistant prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5389. doi:10.1158/1538-7445.AM2017-5389
Abstract 5401: Assessment of whole genome amplification for whole exome sequencing in detecting genetic mutation
Authors: Xue Crystal , Gardner Laura , Jiang Guanglong , Shen Fei , Schneider Bryan 
Published: July 2017

Abstract
Whole exome sequencing (WES) has been widely used for studying genetic mutations in DNA coding regions to elucidate cancer etiology and for identifying biomarkers to optimize chemotherapy. However, these studies can be limited when only small amount of DNA is available. Whole genome amplification (WGA) technology can be combined with WES to make these studies technically possible. Here, we evaluated WGA using a phi 29 polymerase prior to library preparation for WES in samples with various DNA concentrations. WES was performed by targeted exon amplification followed by massively parallel sequencing. We compared the base calls of single nucleotide variants for individual same samples with or without WGA prior to library construction to determine the concordance rate of variant calls. We also assessed genetic variant call rate in the same samples with or without WGA. The number of variants obtained ranged from 159,851,999 to 390,784 in the non-amplified samples and from 353,215 to 384,118 in the same amplified samples. The average concordance rate of identical variants in the samples with or without WGA was 96.5%. Our results indicate that WGA in prior to WES can increase detection efficiency of single nucleotide variants in samples with relatively small amount of DNA and/or low DNA concentration.
Citation Format: Crystal Xue, Laura Gardner, Guanglong Jiang, Fei Shen, Bryan Schneider. Assessment of whole genome amplification for whole exome sequencing in detecting genetic mutation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5401. doi:10.1158/1538-7445.AM2017-5401
Abstract 5402: Single cell sequencing of high grade serous ovarian cancer
Authors: Starr Timothy K. , Winterhoff Boris , Maile Makayla , Beckman Kenneth , Daniel Jerry , Geller Melissa , Bazzaro Martina , Klein Molly , Hellweg Raffaele , Abrahante Juan , Mitra Amit K. , Sebe Atilla , Mullany Sally A. 
Published: July 2017

Abstract
We performed RNA sequencing of single cells derived from a high grade serous ovarian cancer (HGSOC) specimen to determine the extent of heterogeneity and to determine if it was feasible to identify cancer stem cells or gene expression signatures of chemo resistance. To perform RNA sequencing we enzymatically digested a fresh specimen from an HGSOC derived from the ovary. Immune cells were depleted by flow cytometry and single cell sequencing was performed using the Fluidigm C1 chip in tandem with Illumina HiSeq 2500 sequencing. Multiple bioinformatics tools were used to identify subgroups and activated pathways. Immunohistochemistry was performed on an adjacent tumor section to analyze markers of epithelium, stroma and stem cells. We found that gene expression patterns in single cells could be used to separate cells into stroma-like and epithelial-like groups. Gene set enrichment analysis identified proliferative genesets (oxidative phosphorylation and MYC targets) associated with the epithelial-like cells while epithelial-to-mesenchymal-transition (EMT) genes associated with the stroma-like cells. Neither group was significantly associated with genesets derived from chemo-resistant cells. Using known marker analysis, we could identify a small percentage of cells that expressed ovarian cancer stem cell markers and we could group cells into functional categories. Using four molecular subtypes established from large-scale bulk sequencing studies we show that single cells from a single patient are heterogeneous and each molecular subtype is represented. In conclusion, we show the feasibility of performing single cell sequencing on an epithelial ovarian cancer and reveal a heterogeneous population of cells. Expanding these findings to a larger cohort of patients could allow for identification of targetable sub-populations of cells that were previously undetectable in studies that use bulk samples to interrogate the transcriptome and genome of ovarian cancer patients.
Citation Format: Timothy K. Starr, Boris Winterhoff, Makayla Maile, Kenneth Beckman, Jerry Daniel, Melissa Geller, Martina Bazzaro, Molly Klein, Raffaele Hellweg, Juan Abrahante, Amit K. Mitra, Atilla Sebe, Sally A. Mullany. Single cell sequencing of high grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5402. doi:10.1158/1538-7445.AM2017-5402