bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 522: Histone deacetylase 6-let-7i-5p-thrombospondin-1 signaling axis suppresses CD47-dependent tumorigenic behavior of liver cancer
Authors: Yang Hee Doo , Eun Jung Woo , Shen Qingyu , Kim Hyung Seok , Kim Sang Yean , Nam Suk Woo
Published: August 2018

Histone deacetylase 6 (HDAC6) uniquely endows as tumor suppressor in liver tumorigenesis, but the underlying mechanisms leading to liver cancer are not fully understood. To identify the large-scale microRNA (miRNA) expression changes by HDAC6, we performed miRNA expression analysis in HDAC6-overexpressing Hep3B cells. From this, let-7i-5p was suggested as most highly associated miRNA with HDAC6 in liver cancer cells. We also found that let-7i-5p expression was up-regulated in a large cohort of HCC patients, and high expression of let-7i-5p was significantly associated with poor prognosis of HCC patients. Ectopic expression of antisense let-7i-5p (AS-let-7i-5p) caused cancer cell growth inhibition mediated by caspase-dependent cell death processing, and inhibited epithelial-mesenchymal transition (EMT) of liver cancer cells. Computational analysis suggested that thrombospondin-1 (TSP-1) is a specific target for let-7i-5p in liver cancer cells. Increased secretion of TSP1 was detected in AS-let-7i-5p transfected HCC cells. We found that partially purified TSP-1 from culture media (ppTSP-1) induced cellular death processing and simultaneously inhibited tumor angiogenesis and metastatic behavior of liver cancer cells. In addition, we observed that anti-TSP-1 antibody containing CD47 receptor binding motif (3F352) attenuated HDAC6, AS-let-7i-5p and TSP-1 effects on liver cancer cells. Furthermore, TSP-1 and ppTSP-1 treatments significantly enhanced macrophage phagocytosis through blocking CD47-dependent “Don't eat me” signal in liver cancer cells. Our findings suggest that HDAC6-let-7i-5p-TSP-1 signaling axis regulates CD47-dependent neoplastic and phagocytic behaviors of hepatocytes providing a novel target for the molecular treatment of liver malignancies.

Citation Format: Hee Doo Yang, Jung Woo Eun, Qingyu Shen, Hyung Seok Kim, Sang Yean Kim, Suk Woo Nam. Histone deacetylase 6-let-7i-5p-thrombospondin-1 signaling axis suppresses CD47-dependent tumorigenic behavior of liver cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 522.
Abstract 5244: Neratinib induced HER2 dependent and independent intracellular signaling events in human breast cancer cells and the clinical implications
Authors: Jiang W. G. , Martin Tracey A. , Owen Sioned , Xin Ling , Liu Yinhua , Ruge Fiona , Avogadri-Connors Francesca , Lalani Alshad S. , Bryce Richard P. , Davies Eleri
Published: August 2018

Background. Neratinib is an orally available irreversible pan-HER receptor tyrosine kinase inhibitor that has clinical benefit in patients with HER2-positive and HER2-mutated breast cancer. Neratinib also targets the other two members of the HER family, namely EGFR and HER4. However, tentative evidence suggests that neratinib may affect kinases of non-HER family. In the present study, we aimed to explore the pattern of kinases targeted by neratinib, in the context of HER2 non-amplified cancer cells and explored the potential clinical implications. Method. A panel of HER2-low/medium-expressing (MCF-7 and ZR-75-1) and HER2- negative (MDA-MB-231 and BT549) human breast cancer cells were used. The response of a panel of 304 kinases to neratinib was screened using the kinase antibody array. Cellular toxicity was quantified using a colorimetric method. Candidate neratinib-responsive kinases were subject to analyses against the survival of a breast cancer cohort as well as a public database for additional validation. The protein expression level of the kinase targets identified was also validated on tissue arrays from breast cancer by immunohistochemistry. Result. Of all the kinases tested, thirty-six were found to be influenced by neratinib, either via activation or suppression of their phosphorylation. Based on the differential responses to neratinib in HER2 negative and positive breast cancer cells, a small panel of the kinases were classified as HER2 independent. Using clinical cohorts, these kinases collectively had predictive value for the overall survival of the patients (p<0.0001). We further analysed one of the candidate kinases, namely salt inducible kinase-1 (SIK1) and the SIK family in relation with HER2. HER2 expression was found significantly correlated with both SIK1 (r=0.46, p<0.001) and also other two SIK family members. SIK1 protein staining in the tissue array was found to be aberrant in breast tumours. Conclusion. Neratinib has an effect on a subset of HER2 independent kinases in breast cancer cells. These kinases had a prognostic value on patient's survival and correlated with HER2 expression, as in the case of the SIK family.This finding may have important implication in understanding the biology of HER2 inhibitors such as neratinib.

Citation Format: W. G. Jiang, Tracey A. Martin, Sioned Owen, Ling Xin, Yinhua Liu, Fiona Ruge, Francesca Avogadri-Connors, Alshad S. Lalani, Richard P. Bryce, Eleri Davies. Neratinib induced HER2 dependent and independent intracellular signaling events in human breast cancer cells and the clinical implications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5244.
Abstract 5259: Cancer incidence in relation to body fatness in China: Evidence from a large population-based cohort study
Authors: Wang Lu , Jin Guangfu , Yu Canqing , Lv Jun , Guo Yu , Bian Zheng , Yang Ling , Chen Yiping , Hu Zhibin , Chen Feng , Chen Zhengming , Li Liming , Shen Hongbing
Published: August 2018

Body fatness has been associated with several cancers in developed countries, but little is known in China. The purpose of this study was to examine the association between body fatness and cancer incidence, with different anthropometric measures, and compare their predicting values. Between June 2004 and July 2008, the China Kadoorie Biobank (CKB) study recruited 0.5 million adults aged 30-79 years from 10 geographically diverse areas across China, and followed up until December, 2015. Body-mass index (BMI), body fat percentage (BFP), waist circumference (WC), and waist-to-hip ratio (WHR) were measured at baseline. Cox regression yielded adjusted hazard ratios (HRs) associating incidence of all cancers and 15 site-specific cancers with different anthropometric measures, adjusting for education level, marital status, annual household income, alcohol consumption, smoking status and physical activity, and stratifying by age at risk, sex, and region. We compared the ability of cancer risk prediction between different anthropometric measures through a receiver operating characteristic (ROC) analysis. Among 508,362 participants, the overall mean (SD) BMI was 23.66 (3.38) kg/m2, 31.11% of men and 34.24% of women were overweight or obesity (BMI≥25.0kg/m2), and 4.41% of men and 4.26% of women were underweight (BMI<18.5kg/m2). 21,474 incident cancers were identified over an average of 8.94 years of follow-up. Each 5 kg/m2 increase in BMI was associated with an increased risk of endometrial (HR, 2.01; 95% CI, 1.72 to 2.35), postmenopausal breast (HR, 1.29; 95% CI, 1.18 to 1.40), colorectal (HR, 1.17; 95% CI, 1.10 to 1.25) and cervical (HR, 1.15; 95% CI, 1.03 to1.29) cancer, whereas it was associated with a reduced risk of oesophageal (HR, 0.73; 95% CI, 0.67 to 0.79), lung (HR, 0.78; 95% CI, 0.74 to 0.82), liver (HR, 0.85; 95% CI, 0.79 to 0.92), and stomach (HR, 0.88; 95% CI, 0.82 to 0.94) cancer. BMI was the best risk prediction measure for postmenopausal breast and endometrial cancer, whereas BFP were the best for oesophageal, lung, liver and stomach cancer, and WC and WHR did for colorectal cancer. BMI is related to the incidence of several cancers in China. Obesity and overweight, as well as underweight, contribute to the cancer incidence in China. Other anthropometric measures may add information for cancer-specific risk prediction.

Citation Format: Lu Wang, Guangfu Jin, Canqing Yu, Jun Lv, Yu Guo, Zheng Bian, Ling Yang, Yiping Chen, Zhibin Hu, Feng Chen, Zhengming Chen, Liming Li, Hongbing Shen. Cancer incidence in relation to body fatness in China: Evidence from a large population-based cohort study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5259.
Abstract 5269: Body mass index may not have causal association with thyroid cancer risk: A Mendelian randomization study
Authors: Kim Jeongseon , Lee Soo Ji , Nguyen Quy N. , Lee Jeonghee , Lee Eun Kyung , Hwangbo Yul , Sung Joohon
Published: August 2018

Background: Thyroid cancer (TC) is one of the endocrine tumors of which incidence rates have shown an upward trend worldwide. Obesity, another endemic health issue, has been recently reported in the association with increased TC risk. We attempted to examine if there is a causal association between body mass index (BMI) and TC using a Mendelian randomization approach.

Methods: Total 17,935 healthy individuals from the Korean Genome Epidemiology Study and 1,214 TC cases from National Cancer Center, Korea, and Seoul National University Hospital were selected with age, sex, BMI, and genetic information. Based on the thirteen previously reported single nucleotide polymorphisms associated with BMI, we constructed a genetic risk score (GRS) as a genetic instrumental variable (IV) representing BMI independent of possible confounding. IV analysis was performed using the ratio (or, Wald) method to test causal association.

Results: The odds of TC were 2.6 times higher in females than males. The cases were younger than the controls. The F-statistic from the regression of BMI on BMI GRS (IV) was 157.2 (usually, F larger than 10 indicates a strong and valid IV), and the IV explained 1.10% of the phenotypic variance for BMI. From IV analysis, genetically instrumented BMI was not associated with TC risk (causal odds ratio per 1kg/m2 increase in BMI 0.98 [0.79 - 1.20 95% confidence interval]).

Conclusion: Our analysis suggests that positive association between obesity and TC risk repeatedly reported from several meta-analyses may be null. Further investigation is needed as the incidence rates differ in different ethnicity.

Citation Format: Jeongseon Kim, Soo Ji Lee, Quy N. Nguyen, Jeonghee Lee, Eun Kyung Lee, Yul Hwangbo, Joohon Sung. Body mass index may not have causal association with thyroid cancer risk: A Mendelian randomization study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5269.
Abstract 527: Identification of novel target mRNAs of microRNA-143 in glioblastoma cells
Authors: Lozada-Delgado Eunice , Valiyeva Fatma , Marcos Maria , Vivas Pablo
Published: August 2018

The purpose of this study is to assess the biological role of microRNA-143 (miR-143) in Glioblastoma multiforme (GBM). In the United States, the incidence of GBM is about 17% of all primary brain tumors and about 60-75% of all Astrocytomas. Many patients recur even after therapy with a median survival rate of 15 months. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression post-transcriptionally. Deregulated miRNAs have been identified in cancer including GBM. In this study, we aim to thoroughly uncover the role of miR-143 by using GBM cell lines, mouse models, and patient samples. Previous qPCR data from FFPE samples of Puerto Rican GBM patients showed a higher relative expression of miR-143 in GBM patients compared to control individuals and paired surrounding non-cancerous tissue suggesting an oncogenic role. Moreover, in vitro data of transient transfections of a miR-143 oligonucleotide inhibitor in GBM cells showed reduced cell proliferation (clonogenic assay), increased apoptosis and cell cycle arrest in the G0/G1-S phase (flow cytometry and western blot analysis). Furthermore, we want to identify novel target mRNAs of miR-143 in GBM cells that may explain these results. Using in silico analysis tools and a qPCR analysis we identified 5 candidate genes as potential miR-143 targets. Western blot analysis of the proteins encoded by these genes using miR-143 overexpressing cells showed that the Integral membrane protein 2B (ITM2B) and Zinc transporter 8 (SLC30A8) protein levels were reduced and when miR-143 was transiently inhibited their protein levels where increased. These results suggest that miR-143 targets these mRNAs. Ongoing luciferase reporter assays will determine direct binding of miR-143 to the 3'UTR of these mRNAs in GBM cells.

Citation Format: Eunice Lozada-Delgado, Fatma Valiyeva, Maria Marcos, Pablo Vivas. Identification of novel target mRNAs of microRNA-143 in glioblastoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 527.
Abstract 5278: Tobacco and areca nut use among Chuukese youth in Guam
Authors: Somera Lilnabeth P. , Simsiman Brayan , Badowski Grazyna , Lee Hye-ryeon , Cassel Kevin
Published: August 2018

Background: Little is known regarding the tobacco use of Micronesian population in Guam. According to the Youth Risk Behavior Survey (YRBS) 2013, Micronesian youth have a higher prevalence rate of current smokers (27.2% vs. 15.7% for U.S.) and current smokeless tobacco users (39.7% vs. 8.8% for US) compared to the U.S. They also have the highest rate among all ethnic groups in Guam. This study aims to investigate tobacco use and areca nut use, which may explain high lung and bronchus cancer incidence and mortality rates among Micronesians. The survey in this study focuses on Chuukese youth, the largest group among Micronesians in Guam.

Methods: Respondent-driven sampling method (RDS) was used to recruit 364 Chuukese youth (ages 13-19) to complete the survey. YRBS question items that measured cigarette, cigar, and smokeless tobacco use were included in the survey. Measures for areca nut use were also included. Chi-square tests were performed by bivariate analysis. Only high school-level youth are included in the analysis.

Results: A total of 237 Chuukese high school students completed the survey. Fourteen percent of the participants currently smoke cigarettes, 6.4% currently smoke cigars, and 23.7% currently use smokeless tobacco. In addition, smokeless tobacco remains highest regarding daily use (11%) within the past 30 days prior the survey. Although there is high use of smokeless tobacco among participants, there are significant associations between gender and cigarette and gender and cigar use only. Boys smoke cigarettes and cigar at higher rates than girls. Among the recruited participants, 32% are areca nut users with tobacco product as an ingredient. There is significantly high association between smokeless tobacco users and areca nut with tobacco users. The majority of cigarette smokers (82.4%) have tried to quit smoking. Fifty-six percent of the smokeless tobacco users have tried to quit as well. However, only 17% of the participants are aware of the Guam Youth Quitline.

Conclusion: Results suggest the need to raise awareness among Chuukese youth on tobacco cessation programs on Guam, particularly the smoking cessation quitline. Tobacco cessation efforts should not focus on cigarette use only, but must also be expanded to include the use of smokeless tobacco products and chewing areca nut. Future studies should investigate the roles and implications of tobacco as an ingredient of areca nut chewing among Micronesian youth.

Citation Format: Lilnabeth P. Somera, Brayan Simsiman, Grazyna Badowski, Hye-ryeon Lee, Kevin Cassel. Tobacco and areca nut use among Chuukese youth in Guam [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5278.
Abstract 5294: CIMerge: A machine learning approach for merging and genotyping complex indel calls from NGS data
Authors: Zheng Tian , Li Yang , Geng Yu , Zhao Zhongmeng , Zhang Xuanping , Wang Jiayin
Published: August 2018

Complex insertion and deletion (complex indel) is a rare category of genomic structural variations, which is formed by inserting one or multiple DNA fragments into the genomic location where a deletion occurs. A recent study conducts a systematic analysis from over 8,000 pan-cancer cases, which reports hundreds of complex indels in cancer-associated genes, some of which are considered potentially druggable. Several approaches are proposed to detect complex indels from the new-generation sequencing data (both 2nd and 3rd generation). However, as different data-mining algorithms vary the preferences on capturing data patterns, different approaches may report the conflicted complex indel calls. Here, we propose a machine learning approach to correct the conflicted calls from different approaches and further estimate the genotype of each call. The proposed approach, implemented as CIMerge, adopts a relevance vector machine framework. For each candidate call, CIMerge first extracts a set of features on the candidate region, which includes the read depth, variant allelic frequency, number of the splitting/unmapped reads, number of the discordant paired-end reads, aligned contig, etc. CIMerge also considers another set of features on data-mining algorithm(s) that reported the candidate call, which includes the parameter settings, etc. Both sets of features are trained by the relevance vector machine framework, which outputs the probability of each candidate of the conflicted call. As a byproduct, it outputs the genotype of the candidate call with highest likelihood. We tested CIMerge on multiple datasets generated by different simulation configurations and compared it to several state-of-the-art approaches. The experiment results demonstrate that CIMerge outperforms the existing approaches. The average success rate of recognition is approaching 90%, while Pindel and Gindel are reported as 62.53% and 65.202%, respectively. The software package CIMerge is freely available for academic uses at https://github.com/xjtu712-lab/CIMerge.

Citation Format: Tian Zheng, Yang Li, Yu Geng, Zhongmeng Zhao, Xuanping Zhang, Jiayin Wang. CIMerge: A machine learning approach for merging and genotyping complex indel calls from NGS data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5294.
Abstract 5295: Toward high throughput immune infiltrate analysis from H&E stained images
Authors: Rawat Rishi R. , Ruderman Daniel , Agus David B.
Published: August 2018

Our appreciation of the immune system in breast cancer is rapidly evolving. New methods to quantify the composition and spatial distribution of the immune infiltrate from pathology images are urgently needed to develop better strategies to activate the anti-tumor immune response. Existing methods to quantify the immune infiltrate are tedious (manual counting) or rely on immunohistochemistry (IHC) staining to identify immune cells. While significant efforts are underway to develop machine learning tools to categorize cells based on morphologic features in hematoxylin and eosin (H&E) stained histopathology images, all approaches are limited by the scarcity of large, annotated ground truth training sets. In this work, we propose a new approach, leveraging “style-transfer” algorithms from the computer vision community to generate large quantities of training data from IHC stains. Using style transfer, we generate synthetic H&E images from IHC stains for immune markers, such as CD45, CD8 and CD4. The generated images have pixel-perfect ground truth provided by IHC, and do not need manual labeling. We investigate the impact of training on increasing numbers of synthesized images and validate our algorithms on an independent test set annotated by a pathologist (n=100 patients, 3064 identified lymphocytes). Our baseline classifier achieves a 83% accuracy, compared to the pathologist ground truth. This work provides a novel, tractable, and efficient way to train data-hungry algorithms to identify multiple cell types from H&E stained images. This work is supported by a grant from the Breast Cancer Research Foundation (BCRF-17-002)

Citation Format: Rishi R. Rawat, Daniel Ruderman, David B. Agus. Toward high throughput immune infiltrate analysis from H&E stained images [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5295.
Abstract 5298: The accurate noninvasive staging of liver fibrosis using deep learning radiomics: A prospective multicenter study
Authors: Zhou Hui , Wang Kun , Tian Jie
Published: August 2018

Purpose: We developed the deep learning Radiomics of elastography (DLRE) as a noninvasive method to assess liver fibrosis stages,which is essential for prognosis, surveillance of chronic hepatitis B (CHB) patients.

Methods and Materials: 402 patients were prospectively enrolled from 12 hospitals, and finally 2010 images were included into analysis randomly.DLRE adopted the CNN method, one of the deep learning radiomic techniques, for the automatic analysis of 2D-SWE images. This study was conducted to assess the accuracy of DLRE in comparison with 2D-SWE, transient elastography (TE), transaminase-to-platelet ratio index (APRI), and fibrosis index based on the four factors (FIB-4), by using liver biopsy as the gold standard. Analysis of receiver operating characteristic (ROC) curve were performed to calculate optimal area under it (AUC) for cirrhosis (F4), advanced fibrosis (≥F3), and significance fibrosis (≥F2) for all diagnostic approaches.

Results: AUCs of DLRE were both 0.98 for cirrhosis (95% confidence interval [CI]: 0.95-0.99) and advanced fibrosis (95% CI: 0.94-0.99), which were significantly better than other methods, as well as 0.76 (95% CI: 0.72-0.81) for significance fibrosis (significantly better than APRI and FIB-4).

Conclusion: DLRE shows the best overall performance in predicting liver fibrosis stages comparing with 2D-SWE, TE, and serological examinations. It is valuable and practical for popularized application of noninvasive diagnosis of liver fibrosis stages in HBV infected patients.

Citation Format: Hui Zhou, Kun Wang, Jie Tian. The accurate noninvasive staging of liver fibrosis using deep learning radiomics: A prospective multicenter study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5298.
Abstract 5306: SAUCIE: Sparse autoencoder for unsupervised clustering, imputation, and embedding
Authors: Amodio Matthew , Srinivasan Krishnan , Dijk David van , Mohsen Hussein , Yim Kristina , Muhle Rebecca , Moon Kevin , Montgomery Ruth , Noonan James , Wolf Guy , Krishnaswamy Smita
Published: August 2018

Handling the vast amounts of single-cell RNA-sequencing and CyTOF data, now being generated in patient cohorts, presents a computational challenge due to the noise, complexity, sparsity and batch effects present. Here, we propose a unified deep neural network approach to automatically process and extract structure from these massive datasets. Our unsupervised architecture, called SAUCIE (Sparse Autoencoder for Unsupervised Clustering, Imputation, and Embedding), simultaneously performs several key tasks for single-cell data analysis including 1) clustering, 2) batch correction, 3) visualization, and 4) denoising/imputation. SAUCIE is trained to recreate its own input after reducing its dimensionality in a 2-D embedding layer which can be used to visualize the data. Additionally, it uses two novel regularizations: (1) an information dimension regularization to penalize entropy as computed on normalized activation values of the layer, and thereby encourage binary-like encodings that are amenable to clustering and (2) a Maximal Mean Discrepancy penalty to correct batch effects. Thus SAUCIE has a single architecture that denoises, batch-corrects, visualizes and clusters data using a unified representation. We show results on artificial data where ground truth is known, as well as mass cytometry data from patients undergoing immunotherapy, dengue-infected patients, and single-cell RNA-sequencing data from embryonic mouse brain.

Citation Format: Matthew Amodio, Krishnan Srinivasan, David van Dijk, Hussein Mohsen, Kristina Yim, Rebecca Muhle, Kevin Moon, Ruth Montgomery, James Noonan, Guy Wolf, Smita Krishnaswamy. SAUCIE: Sparse autoencoder for unsupervised clustering, imputation, and embedding [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5306.
Abstract 5313: Occupational exposure to trichloroethylene and DNA methylation: a cross-sectional study
Authors: Zhang Jinming , Zhang Luoping , Vermeulen Roel , Hu Wei , Bassig Bryan A. , Wong Jason Y. , Shen Min , Ji Bu-Tian , Reiss Boris , Purdue Mark , Smith Martyn T. , Lan Qing , Rothman Nathaniel
Published: August 2018

Trichloroethylene (TCE) is a chlorinated solvent that is often used in occupational settings for vapor degreasing of metal parts. In 2012, TCE was classified as a known human carcinogen (Group 1) by the International Agency for Research on Cancer, largely based on evidence for kidney cancer. Animal studies have suggested that TCE may modulate DNA methylation. We performed a cross-sectional study to examine the associations of DNA methylation of individual CpG sites with TCE exposure. We enrolled 80 workers from factories where TCE was used, as well as 96 unexposed controls from food and clothes manufacturing factories in the same region, and 69 exposed workers and 77 controls were available for analyses in this study. Personal exposure measurements (2-3 per subject) were collected for a full work shift using a 3MTM badge in both exposed workers and a subgroup of the control workers. Blood samples were collected from each subject and CpG methylation was assayed on the Illumina Infinium HumanMethylation450 BeadChip. After quality controls procedures, 485,512 CpG probes were available for analyses. We used separate multivariable linear regression models to examine the associations of TCE exposure and the methylation level at each single CpG site. All models were adjusted for age, sex, current smoking status, current alcohol consumption, recent infection, and body mass index. The median TCE exposure level in exposed subjects was 12 ppm (10th percentile: 2 ppm; 90th percentile: 45 ppm). We found 29 CpG probes that achieved genome-wide significance (p < 1.04x10-7) when comparing TCE exposed workers with controls. TCE exposure was associated with hypomethylation at nearly all (28/29) of those CpG probes. Of these 29 CpG probes, 6 CpGs showed a significant (p < 1.04x10-7) exposure-response relationship across the categories of controls and lower- (<12ppm) and higher-exposed (≥12 ppm) workers, and were mapped to 6 different chromosomes. To our knowledge, this is the first report that TCE exposure is associated with alterations in DNA methylation in a molecular epidemiologic study. Our findings may provide insight into potential biological mechanisms linking exposure to TCE and adverse health outcomes.

Citation Format: Jinming Zhang, Luoping Zhang, Roel Vermeulen, Wei Hu, Bryan A. Bassig, Jason Y. Wong, Min Shen, Bu-Tian Ji, Boris Reiss, Mark Purdue, Martyn T. Smith, Qing Lan, Nathaniel Rothman. Occupational exposure to trichloroethylene and DNA methylation: a cross-sectional study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5313.
Abstract 5317: JAK2 regulates oxidative damage-induced epigenetic alterations
Authors: Ding Ning , Miller Sam , O'Hagan Heather
Published: August 2018

Elevated levels of reactive oxygen species at sites of chronic inflammation cause oxidative DNA damage in epithelial cells, contributing to carcinogenesis. Aberrant silencing of key genes by promoter CpG island DNA hypermethylation occurs in many cancers that form at sites of chronic inflammation. Yet, it is not completely understood how these aberrant DNA methylation alterations are initiated. We hypothesize that the recruitment of epigenetic silencing proteins to sites of oxidative DNA damage is important for initiating DNA methylation. Here we demonstrate that after hydrogen peroxide (H2O2) treatment, mismatch repair proteins MSH2 and MSH6 become localized to sites of oxidative DNA damage, resulting in the recruitment of DNA methyltransferase 1 (DNMT1) and Polycomb repressive complex 2 (PRC2) members to chromatin. This recruitment results in the formation of repressive chromatin in the promoters of tumor-suppressor genes and the concomitant transient reduction in their expression. We sought to further understand the mechanism that drives H2O2-induced MSH2 and MSH6 chromatin binding. Janus kinase 2 (JAK2) is a kinase that is canonically known to be activated by cytokines and growth hormones and phosphorylate the transcription factor signal transducer and activator of transcription (STATs). Here, we demonstrate that in response to treatment with H2O2, but not interleukin 6 (IL-6), JAK2 translocates to the nucleus and interacts with MSH2 and MSH6. Nuclear JAK2 is important for H2O2-induced chromatin interaction of MSH2, MSH6, DNMT1 and PRC2 members. Interestingly, H2O2-induces a global and site-specific increase in trimethylation of histone H3 at lysine 27 (H3K27me3) that is also dependent on JAK2. Furthermore, by analyzing TCGA datasets, we demonstrate high JAK2 mRNA expression correlates with CpG island methylator phenotype (CIMP) status in gastric and colorectal cancer. All together, these findings suggest JAK2 plays a key role in initiating oxidative damage-induced epigenetic alterations during inflammation-driven tumorigenesis. Ultimately, understanding the mechanism of initiation of cancer-specific promoter DNA hypermethylation may lead to treatment strategies to reduce aberrant epigenetic changes induced by chronic inflammation and therefore reduce tumorigenesis.

Citation Format: Ning Ding, Sam Miller, Heather O'Hagan. JAK2 regulates oxidative damage-induced epigenetic alterations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5317.
Abstract 5333: Methylation profiling identifies two subclasses of cutaneous squamous cell carcinoma related to distinct cell types of origin
Authors: Paredes Manuel Rodríguez , Bormann Felix , Raddatz Günter , Gutekunst Julian , Lucena-Porcel Carlota , Köhler Florian , Wurzer Elisabeth , Schmidt Katrin , Röwert-Huber Joachim , Denisova Evgeniya , Feuerbach Lars , Herpel Esther , Nindl Ingo , Hofmann Thomas G. , Winnefeld Marc , Lyko Frank
Published: August 2018

Cutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer type and arises from keratinocytes. Most cSCC progress from a UV-induced precancerous lesion termed actinic keratosis (AK). Despite various efforts to characterize these lesions molecularly, the etiology of AK and its progression to cSCC remain only partially understood. Here we have used Infinium MethylationEPIC BeadChips to interrogate the DNA methylation status of about 850.000 CpGs in epidermis samples from healthy skin, AK and cSCC. Importantly, we found that the premalignant AK samples displayed classical features of cancer methylomes and were highly similar to cSCC methylomes. Further analysis identified typical features of stem cell methylomes, such as a reduced DNA methylation age, non-CpG methylation and stem cell-related keratin and enhancer methylation patterns. Interestingly, this signature was detected only in one half of the AK and cSCC samples, while the other half showed keratin and enhancer methylation patterns that were more closely related to the control epidermis. These findings suggest the existence of two distinct subclasses of AK and cSCC that originate from distinct keratinocyte differentiation stages.

Citation Format: Manuel Rodríguez Paredes, Felix Bormann, Günter Raddatz, Julian Gutekunst, Carlota Lucena-Porcel, Florian Köhler, Elisabeth Wurzer, Katrin Schmidt, Joachim Röwert-Huber, Evgeniya Denisova, Lars Feuerbach, Esther Herpel, Ingo Nindl, Thomas G. Hofmann, Marc Winnefeld, Frank Lyko. Methylation profiling identifies two subclasses of cutaneous squamous cell carcinoma related to distinct cell types of origin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5333.
Abstract 5337: The epigenetic feedback loop of the CpG demethylase TET family genes in head and neck cancers
Authors: Misawa Kiyoshi , Imai Atsushi , Mochizuki Daiki , Kanazawa Takeharu
Published: August 2018

Purpose: The aim of this study is that clarifying the epigenetic regulation of TET family genes can provide insights into the mechanisms of tumorigenesis and the risk of disease recurrence in HNSCC.

Experimental Design: We generated methylation profiles of TET family genes in tumor samples obtained from 233 patients with head and neck squamous cell carcinoma (HNSCC); these included 57 hypopharynx, 44 larynx, 69 oral cavity, and 63 oropharynx tumor samples. TET family genes mRNA expression and promoter DNA methylation were examined via quantitative reverse transcription (Q-RT-PCR) and methylation-specific PCR (Q-MSP), respectively. Promoter methylation was compared with various clinical characteristics and methylation index.

Results: The TET methylation index (TE-MI) as the number of TET family genes methylation events was positively correlated with alcohol consumption (P = 0.004), HPV status (P = 0.004) and disease recurrence (P = 0.002). Simultaneous methylation analysis of TET family genes significantly correlated with reduced disease-free survival in unfavorable event groups (log-rank test, P = 0.026). In the multivariate Cox proportional hazards analysis, TET3 methylation of T1/2 patients, oropharyngeal cancer patients and oral cancer patients exhibited the high association with poor survival (hazard ratio: 2.64, P = 0.014; 3.55, P = 0.048; 2.63, P = 0.028, respectively). Joint analysis of tumor suppressor genes methylation index (TS-MI) showed a significant trend toward higher TE-MI increased.

Conclusions: TET family genes methylation status was independently associated with aggressive tumor behavior and forming a DNA methylation feedback loop in patients with HNSCC.

Citation Format: Kiyoshi Misawa, Atsushi Imai, Daiki Mochizuki, Takeharu Kanazawa. The epigenetic feedback loop of the CpG demethylase TET family genes in head and neck cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5337.
Abstract 5340: The methylation burden is determined by the duration of exposure to carcinogenic factors
Authors: Yamada Harumi , Takeshima Hideyuki , Niwa Tohru , Toyoda Takeshi , Yamashita Satoshi , Ushijima Toshikazu
Published: August 2018

Aberrant DNA methylation accumulated in normal tissues, namely methylation burden, is closely associated with risk of carcinogenesis, especially in cancers related to chronic inflammation. Methylation burden is known to be influenced by multiple factors, such as genetic factors and strengths of carcinogens. However, the impact of the duration of exposure to a carcinogen is still unclear. Here, using a Mongolian gerbil model of Helicobacter pylori (H. pylori)-induced chronic gastritis, we aimed to clarify the impact of the duration of exposure on the methylation burden in normal gastric tissues (gastric mucosae). Following infection with H. pylori, DNA methylation levels at four CpG islands, HE6, SA9, SB5, and SD2, increased, depending upon the exposure duration. After eradication of H. pylori, DNA methylation levels decreased, but tended to be higher in gastric mucosae with a longer infection period. DNA molecules with dense DNA methylation, but not those with sparse DNA methylation, increased depending upon the infection period. DNA methylation levels at one of the four CpG islands, SA9, tended to be higher in the gastric mucosae of gerbils infected with H. pylori than in those of non-infected gerbils, even 50 weeks after eradication. These results showed, for the first time, that the methylation burden in normal tissues is influenced by the duration of exposure to a carcinogenic factor.

Citation Format: Harumi Yamada, Hideyuki Takeshima, Tohru Niwa, Takeshi Toyoda, Satoshi Yamashita, Toshikazu Ushijima. The methylation burden is determined by the duration of exposure to carcinogenic factors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5340.
Abstract 5345: Somatic mutation status in cfDNA between therapy responders and non-responders of oropharyngeal squamous cell carcinoma patients
Authors: Khandelwal Alok R. , Greer Adam , Orgeron Rhett , Hamiter Mickie , Ma Xiaohui , Moore-Medlin Tara , Yin Hong , Mills Glenn , Nathan Cherie-Ann O.
Published: August 2018

Circulating tumor DNA (ctDNA) could potentially be utilized as a biomarker in Oropharyngeal Squamous Cell Carcinoma (SCC) patients. The objective of this study was to determine if somatic variants could be detected in circulating cell-free DNA (cfDNA) of Oropharyngeal SCC patients using Next Generation Sequencing (NGS). Somatic mutations have been reported in Orophayngeal SCC cases. The identification and detection of somatic variants in circulating cell-free DNA in patient's plasma may predict response to therapy, help monitor disease progression, guide therapy, and determine likelihood of recurrence. In this study, we compared the somatic mutation status between therapy responders and non-responders among Orophayngeal SCC patients. IRB approval was obtained and 23 Oropharyngeal SCC patients were identified in our patient database. Genomic DNA was isolated from frozen tumor tissue using NucleoSpin Tissue kit by Clontech. Cell-Free (cfDNA) was then extracted from patient's plasma samples using Zymo's Quick-cfDNATM serum and plasma kit. The quality and size of DNA was determined by Agilent 2200 TapeStation. If genomic DNA contamination was identified it was removed with Zymo Select-a-Size DNA kit. Libraries were prepared with 10 to 25 ηg of cfDNA using Accel-Amplicon 56G Oncology Panel of Swift Biosciences. DNA sequencing was then performed on MiSeq platform with Miseq Reagent Kit. Variants were identified using Biomedical Genomic Workbench and Genialis's online data analysis platform for Swift Biosciences's Accel-amplicon panels. From the 23 matched samples, 8 somatic non-synonymous variants were found in both tissue and plasma, 7 of which were present in non-responders. The variants and their allele frequencies in the non-responder group were as follows (tumor DNA /cfDNA in %) HRAS Gly12Cys (36.54/0.45), TP53 Glu298* (5.48/0.21), CDKN2A Pro114Arg (48.11/1.52), TP53 Arg282Trp (46.47/1.77), FBXW7 Arg505Gly (30.17/0.58), FBXW7 Arg505Leu (30.46/0.64), TP53 Arg273Cys (38.91/2.51), and one variant in the responder group PTEN (21.07/0.67) Arg130Gln. In conclusion, somatic non-synonymous variants can be identified in cfDNA from Oropharyngeal SCC patients using NGS. The number of detected variants is far greater in the non-responder group suggesting somatic variant detection could be a prognostic marker for Oropharyngeal SCC patients.

Citation Format: Alok R. Khandelwal, Adam Greer, Rhett Orgeron, Mickie Hamiter, Xiaohui Ma, Tara Moore-Medlin, Hong Yin, Glenn Mills, Cherie-Ann O. Nathan. Somatic mutation status in cfDNA between therapy responders and non-responders of oropharyngeal squamous cell carcinoma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5345.
Abstract 5396: Identification of meningioma patients in high risk of tumor recurrence using microRNA profiling
Authors: Srovnal Josef , Balik Vladimir , Slavik Hanus , Megova Magdalena Houdova , Vaverka Miroslav , Hrabalek Lumir , Ehrmann Jiri , Staffova Katerina , Hajduch Marian
Published: August 2018

Introduction: Meningioma represents one of the most common intracranial tumors. They are generally thought to progress from low to high-grade lesions and relapse. However, the molecular mechanisms underlying their pathogenesis remains to be ellucidated. Identification of meningioma patients with higher risk of recurrence may have significant impact for future clinical management. Methods and patients: Formalin-fixed paraffin embedded tumor samples were obtained from 45 meningioma patients (15 recurrent patients, 30 patients without recurrence) and 5 healthy controls (dura mater). Comprehensive clinical-pathological data were mined. There were 15 males and 30 females; median age was 54 years, range 28 - 99 years. Total RNA was purified from FFPE samples after pathological verification using miRNeasyMini kit (QIAGEN). Microarray analysis was performed using the MiRNA 4.0 Array and FlashTagTM Biotin HSR(Affymetrix). Affymetrix CEL files have been read with read.celfiles function from oligo package and preprocessed with rma function (Bioconductor). The expression dataset was analyzed with Wilcoxon exact two-sample test (exactRankTestsR package) in order to discover significantly altered miRNAs. Results: We revealed different miRNA profiles in primary meningioma tumors that will relapse in comparison with non-recurrent tumors. 54 differentially expressed miRNAs were identified in meningeoma patients at high risk of recurrence. High-risk patients had significantly higher expression of miR-572 and miR-320c, and lower expression of miR-140 and miR-16-5p. Sixteen candidate miRNAs (including miR-107, miR-16-5p, miR-320c, miR-371b-5p and miR-15a-5p) were chosen for further qPCR validation on independent dataset. Moreover, miRNA expression levels were also compared in paired samples (primary and recurrent tumors) of 15 meningioma patients. However, only small differences in miRNA expression were detected. Conclusion: We have found different miRNA profiles in meningioma patients identifying patients in high risk of recurrence. Sixteen candidate miRNAs (including miR-107, miR-16-5p, miR-320c, miR-371b-5p and miR-15a-5p) were further validated. Acknowledgment: This work was financially supported by Ministry of Health of the Czech Republic, grant nr. 15-29021A, IGA UP LF 2017_013, NPU LO1304 and NCMG LM2015091.

Citation Format: Josef Srovnal, Vladimir Balik, Hanus Slavik, Magdalena Houdova Megova, Miroslav Vaverka, Lumir Hrabalek, Jiri Ehrmann, Katerina Staffova, Marian Hajduch. Identification of meningioma patients in high risk of tumor recurrence using microRNA profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5396.
Abstract 5397: ExomiRs can distinguish tumor-associated from normal stroma: Potential biomarkers in colorectal cancer
Authors: Bhome Rahul , Goh Rebecca , Pillar Nir , Shomron Noam , Sayan Emre , Mirnezami Alex
Published: August 2018

There is urgent need for prognostic markers to stratify intermediate-stage colorectal cancer (CRC) patients for the benefit of adjuvant therapy. Tumor heterogeneity is a major obstacle in stratification attempts as rare cancer cell populations may display stem cell properties and allow generation of therapy resistance. Tumor stroma, on the other hand, is less susceptible to genetic alterations than cancer cells, providing signals that are more reproducible across patient samples. Exosome encapsulated microRNAs (exomiRs) are particularly amenable to biomarker development because they circulate, closely resemble the tissue of origin and are inherently stable. We sought to identify a stromal exomiR signature in colorectal cancer with biomarker potential. Paired primary tumor-associated and normal fibroblasts were extracted from human colonic tissue. Exosomes were isolated by differential ultracentrifugation, validated according to International Society for Extracellular Vesicles recommendations, and profiled for over 800 microRNAs (miRNAs) by NanoString. Data preprocessing and normalization was conducted prior to differential expression analysis. Candidate miRNAs were validated by qPCR. Pathway and network analyses were conducted using miRPath and Ingenuity Pathway Analysis. Forty one exomiRs were differentially present in tumor-associated and normal fibroblasts. Of these, 21 were more abundant in tumor-associated fibroblasts. Thirty-six KEGG pathways were found to be regulated by this exomiR signature, such as “PI3K-Akt” and “colorectal cancer.” A potential target of these exomiRs is PHLPP2, which encodes a phosphatase acting on AKT. In keeping with this, exposure to fibroblast exosomes increased AKT phosphorylation and that of its direct target Bad, in CRC cells, potentially due to a decrease in PHLPP2 protein abundance. Consequently, these cells were protected from drug-induced apoptosis. For the first time, stromal exomiRs have been profiled in colorectal cancer. Tumor-associated and normal stroma can be distinguished by a specific exomiR signature, which is potentially functionally important. Further mechanistic characterization is now required to identify the clinical significance of stromal exomiRs.

Citation Format: Rahul Bhome, Rebecca Goh, Nir Pillar, Noam Shomron, Emre Sayan, Alex Mirnezami. ExomiRs can distinguish tumor-associated from normal stroma: Potential biomarkers in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5397.