bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5256: A prospective study of inflammatory diet potential and risk of hepatocellular carcinoma (HCC)
Authors: Ma Yanan , Simon Tracey G. , Tabung Fred K , King Lindsay Y. , Chong Dawn Q. , Nguyen Long , VoPham Trang , Fuchs Charles S. , Meyerhardt Jeffrey A. , Corey Kathleen E. , Khalili Hamed , Smith-Warner Stephanie , Chung Raymond T. , Giovannucci Edward L. , Chan Andrew T. , Zhang Xuehong 
Published: August 2018

Abstract
Worldwide, hepatocellular carcinoma (HCC) is the fifth most common cancer and the second-leading cause of cancer-related death worldwide. In the U.S., the incidence rate of HCC has tripled since 1975. Although preliminary evidence suggesting a biological impact of diet on multiple inflammatory pathways implicated in hepatocarcinogenesis, the most comprehensive review by the WCRF/AICR concluded that the relationship between diet and HCC remains largely unknown. HCC is an inflammation-related cancer but few studies have investigated diet quality based on its inflammatory potential in relation to HCC risk. The empirical dietary inflammatory pattern scores (EDIP) score were calculated from validated food frequency questionnaires. It characterized dietary inflammatory potential based on circulating levels of inflammatory bio-markers. We prospectively followed 49,674 men in the Health Professionals Follow-up Study (1986-2012), and 74,139 women in the Nurses' Health Study (1984-2012). Cox regression analyses were used to calculate hazards ratios (HR) for HCC risk adjusting for body mass index, smoking, history of diabetes, race, physical activity, and regular aspirin use. We documented a total of 89 incident HCC cases (44 in women and 45 in men) over 28 years, encompassing 1,522,972 person-years of follow-up. Compared to the lowest tertile, the highest tertile of the EDIP score was associated with a multivariable HR for HCC of 2.86 (95%CI, 1.20-6.81) among women (P-trend=0.01) and of 0.68 (95%CI, 0.31-1.50) among men (P-trend=0.35). Future study is warranted to confirm this finding and elucidate the potential biological basis.
Key words: inflammation, dietary patterns, HCC
A. T. C. and X. Z contributed equally to this work.
Citation Format: Yanan Ma, Tracey G. Simon, Fred K Tabung, Lindsay Y. King, Dawn Q. Chong, Long Nguyen, Trang VoPham, Charles S. Fuchs, Jeffrey A. Meyerhardt, Kathleen E. Corey, Hamed Khalili, Stephanie Smith-Warner, Raymond T. Chung, Edward L. Giovannucci, Andrew T. Chan, Xuehong Zhang. A prospective study of inflammatory diet potential and risk of hepatocellular carcinoma (HCC) [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 5256.
Abstract 5266: Current smoking habit is a risk factor for poor surgical outcome of non-B, non-C hepatocellular carcinoma
Authors: Kai Keita , Koga Hiroki , Aishima Shinichi , Kawaguchi Atsushi , Yamaji Koutaro , Ide Takao , Ueda Junji , Noshiro Hirokazu 
Published: August 2018

Abstract
Background: Many factors are recognized as risks for the development of hepatocellular carcinoma (HCC) in non-B non-C (NBNC) patients. Although cigarette smoking has been recognized as one of the risk factors for HCC, the surgical outcomes and clinicopathological characteristics according to smoking habits of NBNC-HCC patients are unclear.
Methods: Consecutive cases of 83 NBNC-HCC patients who underwent curative surgical treatment for the primary lesion at Saga University Hospital were enrolled the study. The information about possibly carcinogenic factors such as alcohol abuse, diabetes mellitus, obesity and smoking habit were collected from medical records. Smoking habits were subcategorized as never, ex- and current smoker at the time of surgery. The diagnosis of non-alcoholic steatohepatitis (NASH) was based on both clinical information and pathological confirmation.
Results: Alcohol abuse, diabetes mellitus, obesity and NASH had no significant effect on the surgical outcomes. Current smoking status was strongly correlated with both overall survival (p=0.0058) and disease-specific survival (p=0.0105) by multivariate analyses. Subset analyses revealed that current smokers were significantly younger at the time of surgery (p=0.0002) and more likely to abuse alcohol (p=0.0188) and to have multiple tumors (p=0.023).
Conclusion: Current smoking habit at the time of surgery is a risk factor for poor long-term survival in NBNC-HCC patients. Current smokers tend to have multiple HCCs at a younger age than other patients.
Citation Format: Keita Kai, Hiroki Koga, Shinichi Aishima, Atsushi Kawaguchi, Koutaro Yamaji, Takao Ide, Junji Ueda, Hirokazu Noshiro. Current smoking habit is a risk factor for poor surgical outcome of non-B, non-C hepatocellular carcinoma [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 5266.
Abstract 5274: Role of obesity and dietary chemopreventive nutrients on risk for breast cancer among ethnically diverse women
Authors: Uppala Padma P. Tadi , Katuli Sozina , Mejia Alfredo , Brown-Fraser Sherine , Wong Brian Yuen Yau , Hayes Ryan , Senthil Maheswari , Garberoglio Carlos 
Published: August 2018

Abstract
Dietary factors have been inconsistently associated with breast cancer risk among various ethnicities. Diet however, may influence breast cancer through mechanisms of obesity. The purpose of this study was to compare intake of dietary chemopreventive nutrients and obesity across three racial/ethnic groups: Latina, African American and Asian women. Methods: Eighty subjects from Inland Empire, California were enrolled into the study from five different sites. Dietary intake was assessed using a validated food frequency questionnaire. The questionnaire includes 19 adjustment questions used to modify food-item responses in regard to fat, fiber, and sodium intake followed by 122 specific food item-lines that capture frequency and serving sizes for select foods. Women also completed a demographic and breast cancer survey. Chi-square tests were used for categorical variables, ANOVA, and Kruskal-Wallis one-way analysis of variance was used for nutrient variables. Results: The age of the study population ranged from 24 to 79. Subjects included 30 Latina, 35 African American and 15 Asian women. The mean body mass index for Latina, African American and Asian women was 26.8±4.2, 30.8±7.24, 24.41±3.85 respectively. Mean fat percent for the three races was 34.21±5.80 for Latina, 41.57±6.33 for African American and 35.5±8.74 for Asian. African American women were significantly (p=0.001) more obese compared to Latina and Asian women. Total breast cancer cases for Latina is 3, African American 6 and Asian 2. Family history of reported breast cancer among Latina, African American and Asian was 0, 11, 0 respectively. There was a significant difference among racially ethic groups in alcohol consumption (p=0.001), alpha carotene (p=0.005), beta-carotene (p=0.031), beta-Cryptoxanthin (p=0.022), Lycopene (p=0.000) MUFA (p=0.017), PUFA (p=0.000) animal protein (0.49) and total Vitamin A (0.044). Conclusion: Significant differences were found in obesity and dietary intake of chemopreventive nutrients among the three racial groups. African Americans had higher rates of obesity and lower consumption of total vegetable intake. This data is consistent with the general US population data in terms of obesity and risk for breast cancer. Further studies will include larger sample size to identify specific nutrients that may protect against breast cancer risk among diverse populations.
Citation Format: Padma P. Tadi Uppala, Sozina Katuli, Alfredo Mejia, Sherine Brown-Fraser, Brian Yuen Yau Wong, Ryan Hayes, Maheswari Senthil, Carlos Garberoglio. Role of obesity and dietary chemopreventive nutrients on risk for breast cancer among ethnically diverse women [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 5274.
Abstract 5291: Professional nurses' awareness and practice with sexual concerns of the oncology patient
Authors: Emeagi Maurel C. , Swardt Hester Rina De , Villiers Martjie De 
Published: August 2018

Abstract
Sexuality is an important aspect of quality of life (QOL). QOL after cancer therapy is an important aspect of patient care of which sexual wellbeing forms part of the holistic nursing care although sexuality assessment is recognized as an important part of nursing care, in practice it has been observed that professional nurses may experience some difficulties to this aspect.
Purpose: The purpose of this study was to gain a deeper understanding of the awareness, practice and possible barriers of professional nurses when engaging in conversation about sexuality with patients receiving cancer treatment in a private oncology care setting in Pretoria, South Africa.
Objectives: The research objectives were: Ø To explore and describe the awareness and practice of professional nurses to engage in conversation about sexuality with the patient receiving cancer treatment in a private oncology setting in Pretoria. Ø To describe possible barriers that prohibit professional nurses to engage in conversation with patients receiving cancer treatment in a private oncology setting regarding sexuality Ø To make recommendations to improve nursing practice with regard to nursing care related to sexuality in the private oncology care setting.
Method: An exploratory, descriptive and qualitative design was followed. A convenient purposive sample consisting of nine participants who met the inclusion criteria participated. Data were gathered through semi-structured interviews, while Creswell's method of data analysis was applied. Trustworthy measures included credibility, transferability, dependability and confirmability. This study obtained ethical clearance from all stakeholders.
Results: The themes embarrassment, cultural beliefs and values emerged as barriers to engage in conversation about sexuality while, referring to a specialist in the field as suggested support to cancer treated patients arose. Limited knowledge about intensive therapy featured as the last theme. The data revealed that professional nurses themselves had restricted views on sexuality and very often would see the patient's body image and associated sexuality as not their responsibility. The concept intensive therapy was not fully understood which led to limited referral to various specialist.
Conclusions: Professional nurses should be sensitized and empowered with the skills and knowledge on how patients' perception of their body image changed when been treated with cancer and the effect thereof. Reflective conversations about this sensitive topic could assist in this regard.
Citation Format: Maurel C. Emeagi, Hester Rina De Swardt, Martjie De Villiers. Professional nurses' awareness and practice with sexual concerns of the oncology patient [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 5291.
Abstract 5305: DNA methylation and gene expression in melanoma: A large-scale integrated analysis
Authors: Candido Saverio , Palumbo Giuseppe A. Parasiliti , Russo Giulia , Falzone Luca , Leonardi Giulia C. , Pappalardo Francesco , Libra Massimo 
Published: August 2018

Abstract
Dysregulation of DNA methyltransferase activity, through global hypomethylation and localized hypermethylation phenomena, has been associated with cancer development. Even though the role of promoter methylation in gene regulation has been widely described, the regulatory function of methylation status of intergenic and intragenic regions has been not yet clarified. High-throughput technology and bioinformatics analysis represent useful tools to investigate the functional role of global methylation patterns in gene regulation. Therefore, a specific bionformatic tool was generated to identify methylation hotspots as well as extended genomic methylation regions in order to analyze specific genetic methylation patterns associated with cancer gene deregulation. In the present study, melanoma was selected as tumor model for its aggressive phenotype. Melanoma samples were obtained from the Cancer Genome Atlas (TCGA) to analyze DNA methylation and gene expression profiling data. We developed an algorithm, using R language, that performs cyclic correlation analysis between gene expression and methylation levels of all genes.
Our results show that in melanoma there are different methylation patterns that positively and negatively correlate with gene expression. In particular, the hypomethylation of the promoter (TSS1500, TSS200, 5'UTR) leads to the over-expression of selected gene (p&lt;0.01) while the hypermethylation of gene body and 3'UTR regions were associated with gene over-expression. Furthermore, the frequency of genes showing a global hypomethylation status was higher compared to those that were hypermethylated (70% vs 30%). We have also identified the main individual CG probesets and methylated regions that are differentially correlated with gene expression. A further pathway analysis shows that the identified genes are implicated in central cellular processes associated with melanoma. Our algorithm allows the identification of methylation hotspots involved in the regulation of key genes for melanoma development. This may contribute to the development of new therapeutic strategies targeting methylome alterations in melanoma cells. Moreover, the identification of methylation hotspots associated to cancer initiation and progression can represent useful biomarkers for patients' risk stratification.
Citation Format: Saverio Candido, Giuseppe A. Parasiliti Palumbo, Giulia Russo, Luca Falzone, Giulia C. Leonardi, Francesco Pappalardo, Massimo Libra. DNA methylation and gene expression in melanoma: A large-scale integrated analysis [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 5305.
Abstract 5311: Integrated approaches for design of precision cancer immunotherapies: Selection of Class I and Class II T cell neo-epitopes and removal of Treg epitopes
Authors: Richard Guilhem , Moise Lenny , Ardito Matthew , Terry Frances , Berdugo Gad , Martin William , Groot Anne De 
Published: August 2018

Abstract
Next-generation sequencing has opened the door to precision cancer therapies targeting mutations expressed by tumor cells. However, most neo-epitopes selected by traditional T cell epitope prediction algorithms prove to be non-immunogenic. Poor predictive performance may partially be due to inclusion of mutated epitopes cross-conserved with self-epitopes recognized by the T cell receptor of regulatory (Treg), anergic or deleted T cells. Vaccination with self-epitopes can lead to weak effector responses, active immune suppression, and toxicity due to immune-mediated adverse effects. We have developed Ancer, an advanced cancer T cell epitope identification and characterization tool, that streamlines the selection of Class I and Class II T cell neo-epitopes. Ancer leverages EpiMatrix and JanusMatrix, state-of-the-art predictive algorithms that have been extensively validated in prospective vaccine studies for infectious diseases [Moise et al., Hum. Vaccines Immunother 2015; Wada et al., Sci. Rep. 2017]. Distinctive features of Ancer are its ability to accurately predict Class II HLA ligands with EpiMatrix and its 82% positive predictive value, as estimated in previous prospective studies. Additionally, the application of JanusMatrix allows for the prioritization of neo-epitopes with reduced potential for Treg induction, that is responsible for diminished efficacy of current cancer therapies. We validated Ancer's predictive accuracy using datasets of HLA-bound peptides detected by mass spectrometry, which are independent of training sequence data used in model development. Analysis of sequences from Abelin et al., Immunity 2017 shows a 96% agreement between Ancer predictions and peptides eluted from common Class I HLAs, while only 86% of these sequences are accurately predicted by NetMHC or NetMHCpan. An additional retrospective analysis of a cancer immunogenicity study [Strønen et al., Science 2016] demonstrates that Ancer selects immunogenic neo-epitopes with 72% accuracy, as compared to 21% accuracy when using public prediction tools. These results demonstrate that Ancer may focus epitope candidate selection on higher value sequences than conventional algorithms. Class I and Class II neo-epitopes with low Treg activation potential may then be used to support the development of safer and more effective vaccines.
Citation Format: Guilhem Richard, Lenny Moise, Matthew Ardito, Frances Terry, Gad Berdugo, William Martin, Anne De Groot. Integrated approaches for design of precision cancer immunotherapies: Selection of Class I and Class II T cell neo-epitopes and removal of Treg epitopes [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 5311.
Abstract 5315: Frequent downregulation of SALL3 by recurrent genetic and epigenetic alterations is involved in triple-negative breast cancers
Authors: Matsushita Yosuke , Komatsu Masato , Kiyotani Kazuma , Yoshimaru Tetsuro , Suzuki Hiromu , Miyoshi Yasuo , Sasa Mitsunori , Katagiri Toyomasa 
Published: August 2018

Abstract
Triple negative breast cancers (TNBC), defined by the lack of estrogen and progesterone receptors and HER2 gene amplification, is a heterogeneous and clinically aggressive disease due to the lack of beneficial therapeutic targets. Even though one of the most major risk for the development of TNBC is carrying a deleterious germline and somatic mutations of BRCA1 are not frequently found in sporadic cases of TNBC. Therefore, we aimed to search genomic alterations in TNBC cases by whole-exome sequencing analysis of genomic DNAs from 36 Japanese patients with TNBC compared with their corresponding normal. We identified 36 genes that were recurrently mutated (&gt;10% of cases) in TNBC cases, including TP53 and PIK3CA as described in the previous next generation sequencing analysis of TNBC cases. Remarkably, we identified a number of epigenetic-related genes involved in histone modification and DNA methylation, which were mutated in 20 out of 36 (55.6%) cases. Among them, we focused on spalt like transcription factor 3 (SALL3) gene which shows recurrent somatic mutations, and are most frequently downregulated in TNBC cases. Nonsense-mutation of SALL3 (E169X) completely abolish its binding to DNAMT3A. Ectopic overexpression of the wildtype SALL3, but not the somatically mutated SALL3 into BT549 breast cancer cells, which expresses low level of SALL3 gene, caused the significant suppression of cell growth. Importantly, SALL3 gene was frequently hypermethylated and transcriptionally silenced in only TNBC cases, but not in other types of breast cancer using TCGA data sets. Moreover, the expression of SALL3 was restored after treatments of 5-aza-2'-deoxycitidine (5-aza-dC) in TNBC cell line, HCC1937. Notably, siRNA-mediated knockdown of SALL3 expression in BT20 cells enhanced chemoresistance against paclitaxel and docetaxel, respectively. Moreover, low expression of SALL3 was associated with significantly shorter relapse free survival. Our findings provide the evidence of a pathophysiological role for SALL3 as a tumor suppressor which is possibly associated with carcinogenesis for TNBC.
Citation Format: Yosuke Matsushita, Masato Komatsu, Kazuma Kiyotani, Tetsuro Yoshimaru, Hiromu Suzuki, Yasuo Miyoshi, Mitsunori Sasa, Toyomasa Katagiri. Frequent downregulation of SALL3 by recurrent genetic and epigenetic alterations is involved in triple-negative breast 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 5315.
Abstract 5322: Normal breast tissue 5-hydroxymethylcytosine is enriched at DNA regulatory elements of breast cancer cells
Authors: Wilkins Owen Michael , Johnson Kevin C. , Houseman E. Andres , King Jessica E. , Marsit Carmen J. , Christensen Brock C. 
Published: August 2018

Abstract
DNA methylation is an established modulator of gene expression in normal mammalian cells. Emerging evidence suggests that the oxidized 5-methylcytosine (5mC) product, 5-hydroxymethylcytosine (5hmC), has distinct biological functions and its dysregulation may contribute to cancer pathogenesis. While 5hmC levels in normal breast tissue have been shown to be elevated relative to several other tissue types, we lack a complete knowledge of the genomic distribution of 5hmC in breast tissue, as well as its potential biological functions. Here, we determined the genome-wide distribution of 5hmC and 5mC using methylation array data from 18 normal breast tissue samples. To disambiguate 5hmC from 5mC, we performed parallel processing of bisulfite and oxidative-bisulfite treated DNA, followed by statistical estimation of the 5mC and 5hmC proportions. Based on the distribution of 5hmC, we identified genomic loci with consistently elevated levels of 5hmC across normal breast tissues. In addition, we showed 5hmC is enriched within transcriptionally active chromatin in breast myoepithelial cells, marked by H3K4 trimethylation. Conversely, 5hmC was depleted within active promoters (H3K9ac-marked DNA) and transcriptionally inactive chromatin (H3K9me3 and H3K27me3-marked DNA). Importantly, the loci with high 5hmC in normal breast tissue were enriched among regulatory elements, including transcription factor binding sites, in transformed normal-like breast MCF10A cells, as well as in multiple breast cancer cell lines. These findings provide a genome-wide distribution of 5hmC in normal breast tissue. Furthermore, these findings identify DNA-regulatory regions in breast cancer cell lines that show statistical enrichment for those sites with elevated 5hmC in normal breast tissue, suggesting deregulation of 5hmC within these elements may contribute to breast carcinogenesis.
Citation Format: Owen Michael Wilkins, Kevin C. Johnson, E. Andres Houseman, Jessica E. King, Carmen J. Marsit, Brock C. Christensen. Normal breast tissue 5-hydroxymethylcytosine is enriched at DNA regulatory elements of breast cancer 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 5322.