bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1594: Transcriptome-wide association study analysis of nasopharyngeal carcinoma
Authors: Su Wen-Hui , Chan Fu-Chun 
Published: August 2019

Abstract
Arising from the epithelial cells in nasopharynx, nasopharyngeal carcinoma (NPC) is highly prevalent in Southeastern China, including Hong Kong and Taiwan. Genetic and environmental factors play important role in NPC susceptibility. Genome-wide association studies (GWASs) have identified single-nucleotide polymorphisms (SNPs) located in major histocompatibility complex (MHC) region with strong evidence for association with NPC. Recently, combination of GWAS and expression quantitative trait loci (eQTL) datasets, transcriptome-wide association study (TWAS) was used to identify novel associations in transcriptome level. In this study, we conducted TWAS in NPC using two in house GWAS datasets and GTEx eQTL datasets from public domain. Most of the significant results were located in chromosome six MHC region. Our analysis identified significant TWAS genes that explain the most of the GWAS signals : HLA-A, GABBR1 and HLA-F genes with P values of 5.08E-13, 5.78E-09 and 2.30E-08, respectively. One of the novel genes, ZNRD1 (P = 8.22 E-08), was known to be involved in the tumorigenesis of esophageal cancer and liver cancer. Further analysis should be needed to understand the mechanisms between ZNRD1 association in NPC.
Citation Format: Wen-Hui Su, Fu-Chun Chan. Transcriptome-wide association study analysis of nasopharyngeal carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1594.
Abstract 16: 3,3'-diindolylmethane induces cytoglobin expression and synergizes with poly ADP ribose polymerase inhibitor PJ34 to inhibit triple negative breast cancer cell growth
Authors: Wooten Jonathan V. , Mavingire Nicole , Rowland Leah , Matthews Jason , Brantley Eileen 
Published: August 2019

Abstract
Triple negative breast cancer (TNBC), characterized by tumors that lack expression of the estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2), carries a poor prognosis. While recently approved poly ADP ribose polymerase (PARP) inhibitor olaparib shows favorable activity in patients with TNBC harboring tumors deficient in DNA repair enzyme BRCA1, patients with TNBC possessing BRCA1-proficient tumors are largely unresponsive to olaparib. Emerging evidence suggests that small molecules that activate aryl hydrocarbon receptor (AhR) signaling have the capacity to confer anticancer actions. 3,3′-diindolylmethane (DIM), an AhR ligand, is the major metabolite of indole-3-carbinol (I3C) found in cruciferous vegetables such as broccoli. Patients often consume natural product-derived AhR ligands while undergoing chemotherapy. It is therefore crucial to enhance our understanding of nutraceutical-pharmaceutical interactions. We previously demonstrated the ability of synthetic AhR ligands to induce the expression of putative tumor suppressor cytoglobin (CYGB) and inhibit Akt signaling in breast cancer cells. Since PARP inhibitor PJ34 has been shown to synergize with Akt inhibitors we hypothesize that DIM induces CYGB expression and synergizes with PJ34 to inhibit TNBC cell growth. Using the Alamar Blue assay, we found that DIM substantially enhanced the sensitivity of TNBC BRCA1 proficient cells to PJ34, though knockdown of CYGB did not significantly influence the responsiveness of cells to DIM. Chromatin immunoprecipitation followed by next-generation sequencing data revealed that DIM promoted the binding of AhR to the CYGB promoter in breast cancer cells. Finally, DIM induced CYGB gene expression in TNBC cells as determined by quantitative PCR. Taken together, our data suggest that DIM upregulates CYGB in TNBC cells and synergizes with PJ34 to confer anticancer actions in TNBC. Our data provide a rationale for incorporating the use of natural product-derived AhR ligands as a strategy to enhance PARP inhibitor efficacy in patients with TNBC that have BRCA1-proficient tumors.
Citation Format: Jonathan V. Wooten, Nicole Mavingire, Leah Rowland, Jason Matthews, Eileen Brantley. 3,3'-diindolylmethane induces cytoglobin expression and synergizes with poly ADP ribose polymerase inhibitor PJ34 to inhibit triple negative breast cancer cell growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 16.
Abstract 1601: Genetic and epigenetic intratumor heterogeneity of lung adenocarcinoma
Authors: Zhao Wei , Hua Xing , Zhang Tongwu , Consonni Dario , Pesatori Angela Cecilia , Shi Jianxin , Landi Maria Teresa 
Published: August 2019

Abstract
Genomic studies have revealed remarkable intratumoral heterogeneity (ITH) in lung adenocarcinoma (LUAD) and increasing evidence suggests its impact in cancer treatment. However, to what extent epigenomic abnormalities and somatic copy number alterations (SCNAs) are involved in shaping genetic clones in lung tumors and are associated with clinical outcome is under-appreciated. Here we applied Infinium HumanMethylation450K BeadChips, Infinium Global Screening Arrays and ultra-deep (&gt;500X) targeted sequencing of 35 LUAD driver genes to 369 samples (including 77 normal tissues) from 84 LUAD patients to investigate the genetic and epigenetic architecture of subclonal diversification. SCNAs were mostly clonal events. For patients with more than three tumor regions assayed, 66% SCNAs were located on the trunk of the evolutionary trees. Similar evolutionary trajectories were inferred from SCNAs and DNA methylation. The driver genes’ sequencing depth allowed to identify subclonality even in TP53, EGFR, and BRAF mutations, which were largely reported as clonal events in previous studies. Elevated copy number ITH was associated with higher risk of death, while no significant association was found between clinical outcome and DNA methylation ITH or heterogeneous CpG island methylator phenotype (CIMP), in contrast with the observed prognostic capability of DNA methylation ITH in hematological malignancies. These findings expand our understanding of the coevolution of genetic and epigenetic aberrations in tumorigenesis, the subclonal complexity for therapeutic targets and the implication of ITH in cancer prognosis.
Citation Format: Wei Zhao, Xing Hua, Tongwu Zhang, Dario Consonni, Angela Cecilia Pesatori, Jianxin Shi, Maria Teresa Landi. Genetic and epigenetic intratumor heterogeneity of lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1601.
Abstract 1602: Genomic profiling of lung cancer associated with idiopathic pulmonary fibrosis
Authors: Noro Rintaro , Miyanaga Akihiko , Fukuizumi Aya , Kunugi Shinobu , Sugano Teppei , Omori Miwako , Minegish Yuji , Usuda Jitsuo , Seike Masahiro , Kubota Kaoru , Hirao Mamiko , Matsuda Kuniko , Gemma Akihiko 
Published: August 2019

Abstract
Idiopathic pulmonary fibrosis (IPF) is reportedly associated with an increased risk of lung cancer. However, optimal diagnosis and treatment for lung cancer associated with IPF remains unclear. In this study, we aimed to clarify the mechanism of carcinogenesis and progression in lung cancer with IPF. We used tumor tissues and adjacent non-tumor lung tissues from 29 lung cancer patients who had undergone complete surgical resection at Nippon Medical School Hospital between 2013 and 2017. Whole-Exon Sequencing was performed on 29 paired samples, consisted of 19 lung cancers with IPF (IPF group) and 10 lung cancers with normal lung (non-IPF group). The candidate gene alterations discriminating between the IPF and non-IPF group, were identified using the random-forest method, RelifF method along with the data from Catalogue Of Somatic Mutations In Cancer (COSMIC). Twenty-five gene alterations were specifically found in IPF tissues and/or tumor tissues with IPF. Whenever 5 of 25 genes including MUC2 and TTF1, were altered in both IPF tissues and tumor tissues, 20 of 25 genes including CADM1, were altered in only tumor tissues. We are undergoing the validation study using other tissues in independent cohorts. Among the candidate genes, Cell adhesion molecule genes (CADM1) gene alterations were frequently found in 15 out of 19 in only tumor tissues with IPF. The CADM1 protein expression was decreased in tumors than in non-tumor fibrotic tissues by western blotting. The CADM1 induced the epithelial-mesenchymal transition (EMT) on the multifunctional cell process involved in the pathogenesis of fibrosis in vitro study. Whenever the down-regulation of CADM1 was frequently detected in various human cancers through its allelic loss as well as hypermethylation within promoter region in addition to inactivate gene mutation, the up-regulation of CADM1 was frequently detected in paired IPF tissues. The CADM1 may be a target candidate in lung cancer associated with IPF.
Citation Format: Rintaro Noro, Akihiko Miyanaga, Aya Fukuizumi, Shinobu Kunugi, Teppei Sugano, Miwako Omori, Yuji Minegish, Jitsuo Usuda, Masahiro Seike, Kaoru Kubota, Mamiko Hirao, Kuniko Matsuda, Akihiko Gemma. Genomic profiling of lung cancer associated with idiopathic pulmonary fibrosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1602.
Abstract 1603: Valproic acid and hydralazine reverse increased mammary cancer risk and upregulate Cdkn2a/p16 in mice exposed to a high fat diet in utero
Authors: Hilakivi-Clarke Leena A. , Andrade Fabia de Oliveira , Nguyen Nguyen , Bouker Kerrie 
Published: August 2019

Abstract
Maternal or paternal high fat (HF) diet that modifies the epigenome in germ cells and fetal somatic cells can program increased susceptibility to breast cancer among offspring. Resulting epigenetic changes include transgenerational upregulation of DNA methyltransferases (DNMTs). We studied here if this increased breast cancer risk can be reversed by treating HF offspring with a well-tolerated drug that inhibits DNA methyl transferase (DNMT; hydralazine), combined with a histone deacetylase (HDAC) inhibitor valproic acid (VPA). Adult C57BL/6NTac mouse offspring of dams fed either corn oil -based HF or control diet during pregnancy were treated with 5 g/kg/day VPA and 5 mg/kg/day hydralazine in drinking water, starting after mice received 7,12-dimethylbenz[a]anthracene (DMBA) to initiate mammary cancer. Treatment with VPA/hydralazine prevented the increase in mammary cancer risk associated with in utero HF diet exposure: it reduced mammary tumor multiplicity and lengthened tumor latency, compared with non-treated HF offspring. These drugs downregulated DNMT3a protein levels, and reversed down-regulation of Cdkn2a/p16 mRNA in the mammary tumors of HF offspring. p16 is a tumor suppressor that is often epigenetically silenced in human breast cancers. However, in control offspring not exposed to HF diet in utero, VPA/hydralazine increased mammary tumor incidence and burden. Further, this treatment upregulated genes involved in the unfolded protein response pathway in in utero control diet exposed animals that were already upregulated in non-VPA/hydralazine treated mammary tumors from in utero HF diet exposed animals, including HIF-1α, NFkB, PERK and SQSTM1 p62. Thus, VPA and hydralazine had opposing effects on breast cancer risk in HF and control offspring, suggesting the importance of individually tailoring breast cancer prevention strategies.
Citation Format: Leena A. Hilakivi-Clarke, Fabia de Oliveira Andrade, Nguyen Nguyen, Kerrie Bouker. Valproic acid and hydralazine reverse increased mammary cancer risk and upregulate Cdkn2a/p16 in mice exposed to a high fat diet in utero [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1603.
Abstract 1604: Modulating effects of genistein in a mouse model of conditional BRCA1 deletion and triple negative breast cancer cells
Authors: Donovan Micah G. , Selmin Ornella I. , Doetschman Thomas C. , Romagnolo Donato F. 
Published: August 2019

Abstract
Germline mutations in BRCA1 (BRCA1+/-) confer ~72% risk of breast cancer, the majority of which are triple negative breast cancer (TNBC). Hypermethylation of BRCA1 is observed at high frequency in sporadic TNBC and may play a role in tumor development in BRCA1 mutation carriers. The aryl hydrocarbon receptor (AhR) coordinates epigenetic silencing of BRCA1 and is overexpressed in some TNBC. The purpose of our study is to investigate the effect of dietary genistein on BRCA1 epigenetic regulation, the AhR pathway and mammary tumorigenesis in BRCA1+/- and BRCA1+/+ mice. We used Cre-lox recombination to derive a mouse model of conditional BRCA1+/-. We used BRCA1F22/24 (The Jackson Laboratory, stock no. 017835) mice, which harbor loxP sites flanking exons 22-24 of the BRCA1 gene. We crossed dams that were heterozygous for BRCA1F22/24 (BRCA1+/FL) and transgenic for Cre recombinase (TG) under control of the mouse mammary tumor virus (MMTV) promoter with wildtype NJ males to derive our colony. Breeding pairs were administered either control or genistein-enriched (4 ppm) diets upon set up, which were continued throughout the life of the offspring. Changes in mRNA expression and protein levels were determined, respectively, by RT-PCR and Western blot. Crewas not expressed in mammary glands of non-TG offspring and Cre expression had no effect on BRCA1 mRNA levels in BRCA1+/+ mice, which do not harbor BRCA1 loxP sites. BRCA1 expression was ~40% decreased in mammary glands of TG, BRCA1+/FL mice compared with TG, BRCA1+/+ mice. Hepatic BRCA1 expression was not changed, confirming conditional BRCA1 knockdown. Preliminary data indicate BRCA1 expression in mammary glands of genistein-fed TG, BRCA1+/+ mice was elevated (~1.3 fold) compared with control-fed mice. Moreover, the genistein diet induced a compensatory increase in BRCA1 expression in mammary glands of TG, BRCA1+/FL mice. We found genistein rescued BRCA1 levels in TNBC HCC38 cells that have constitutively active AhR and hypermethylated BRCA1. These data suggest dietary genistein may have protective effects against tumorigenesis in these mice. To that end, we are currently monitoring tumor development, BRCA1 methylation, and changes in the AhR pathway in BRCA1+/+ and BRCA1+/FL mice fed either the genistein-enriched or control diet.
Citation Format: Micah G. Donovan, Ornella I. Selmin, Thomas C. Doetschman, Donato F. Romagnolo. Modulating effects of genistein in a mouse model of conditional BRCA1 deletion and triple negative breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1604.
Abstract 1605: Time-dependent maternal soybean genistein exposure leads to later-life breast cancer chemoprevention in mice
Authors: Li Yuanyuan , Chen Min , Li Shizhao , Tollefsbol Trygve 
Published: August 2019

Abstract
Breast cancer is the most common type of cancer and the second leading cause of death among women in the United States. Studies have shown that both environmental and genetic factors contribute to breast cancer risk over women's lifespans. Early-life nutritional status has a significant impact on the uterine environment and subsequent fetal development, predisposing the developing fetus to certain diseases such as breast cancer in adult life. During these windows of susceptibility including maternal pre-pregnancy, pregnancy and lactation periods, certain dietary exposure during these critical time periods may change breast cancer risk in an individual’s later life. Alterations of the maternal diet have been shown to induce modifications in the fetal epigenome. Nevertheless, the vulnerability to maternal nutrition status during the critical developmental stage provides an excellent opportunity to re-program epigenetic profiles that may lead to a beneficial outcome such as cancer prevention in the offspring. The bioactive dietary component, genistein (GE) enriched in soybean products, is an important epigenetic modulator that can prevent various cancers including breast cancer. Our study focuses on how maternal dietary soybean GE exposure during the specific time periods may prevent breast cancer in later-life and the potential mechanisms. In this study, we included multiple exposure time points of maternal GE diet (250 mg/kg) including prior-pregnancy (PP-GE), long-term (LT-GE) and short-term (ST-GE) exposures to further determine the efficacy of these strategies on transplacental chemoprevention of breast cancer in the progenies of two spontaneous breast cancer transgenic mouse models. Our pilot study indicates a time-dependent effect of maternal GE exposure on early-life breast cancer development in spontaneous breast cancer mouse models. We also integrated transcriptome and methylome data from mouse breast tumors and identified several candidate genes such as Trp63 and Tprg in response to maternal GE treatment, and considered to play important roles in regulation of development and tumorigenesis. These results suggest that an appropriate exposure window to soybean dietary GE could be a key factor for prevention of human breast cancer and comprehensive mechanisms may be involved in dietary GE-induced in utero breast cancer intervention.
Citation Format: Yuanyuan Li, Min Chen, Shizhao Li, Trygve Tollefsbol. Time-dependent maternal soybean genistein exposure leads to later-life breast cancer chemoprevention in mice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1605.
Abstract 1608: Time-restricted feeding attenuates pulmonary metastasis of Lewis lung carcinoma in mice fed a high-fat diet
Authors: Yan Lin , Sundaram Sneha 
Published: August 2019

Abstract
Circadian rhythms, which cycle approximately every 24 hours, control patterns of daily functions, e.g. feeding and fasting, rest and activity, and sleeping and waking. Altering the finely tuned circadian rhythms by an erratic lifestyle (e.g. disruption of the daily feeding and fasting pattern) leads to metabolic disorders, including obesity. Obesity is a risk factor for cancer. Obese cancer patients are at a greater risk of recurrence and metastasis than patients with normal body weight. We hypothesized that time-restricted feeding (TRF) attenuates high-fat diet-enhanced metastasis. In a metastasis model of Lewis lung carcinoma (LLC), male C57BL/6 mice were fed the standard AIN93G diet (16% of energy from soybean oil) or a high-fat diet (HFD) containing 45% of energy from soybean oil with or without dark phase restricted feeding (12 hours per day) for 10 weeks. Pulmonary metastases from a primary tumor, established by subcutaneous injection of LLC cells, were quantified. The percent fat body mass of the TRF group was lower than that of the HFD group and remained similar to that of the AIN93G group. There was no difference in energy intake between the TRF and HFD groups. The number and size of lung metastases were significantly higher in the HFD group than in the AIN93G group; however, there were no differences in these measurements between the TRF and the AIN93G groups. Time-restricted feeding prevented HFD-induced increases in plasma concentrations of glucose, insulin, proinflammatory cytokines (leptin, monocyte chemotactic protein-1, and plasminogen activator inhibitor-1), and angiogenic factors (angiopoietin-2, hepatic growth factor, and vascular endothelial growth factor). We conclude that TRF attenuates the HFD-enhanced pulmonary metastasis of LLC. This protection may be through the entrainment of metabolic regulators to the fixed feeding time that results in reductions in body adiposity and associated cancer-promoting inflammatory and angiogenic factors.
Citation Format: Lin Yan, Sneha Sundaram. Time-restricted feeding attenuates pulmonary metastasis of Lewis lung carcinoma in mice fed a high-fat diet [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1608.
Abstract 1614: Coconut kernel extract as a novel chemopreventive agent that target cancer stemness
Authors: Sorra Sandhya , Talukdar Joyeeta , Gogoi Gayatri , Li Hong , Baishya Debabrat , Das Bikul 
Published: August 2019

Abstract
Cancer stemness can be defined as integrated molecular programs that confer stem cell phenotype to cancer cells. Cancer stemness is associated with drug resistance, immune evasion and metastasis. Our ongoing work indicates that oncogene MYC may enhance cancer stemness. We are interested to identify novel dietary agents that can target MYC mediated cancer stemness pathway. Coconut (Cocos nucifera L.) kernel extract (CKE) is traditionally used in tradition Indian medicine as anti-inflammatory diet. Here, we have investigated the potential CKE mediated targeting of MYC mediated skin carcinogenesis.
Methods: To determine tumor-suppressing activity of isolated CKE in vivo, we used a DMBA/TPA-mediated skin cancer in Balb/c mice. C-MYC expression in skin tumor was studied by immuno-histochemistry. The bioactive component of CKE was studied by performing histopathology and immunohistochemistry.
Results: CKE treatment decreased DMBA/TPA induced tumorigenicity by 200-fold (p&lt;0.001, n=10). Histological and Immuno histo-chemistry studies suggested that CKE treatment significantly inhibited over expression of c-Myc protein on skin tumorigenesis induced by DMBA/TPA. Additionally, CKE treatment also shows significant inhibitory effect on lipid peroxidase and stimulatory effect on glutathione, catalase and superoxide dismutase activities in tissues treated with DMBA/TPA. Additionally, in vitro study showed that CKE reduces DMBA/TPA induced stemness in skin keratinocytes. CKE contains lauric acid as per analysis performed by high performance liquid chromatography and Nuclear magnetic resonance. However, purified lauric acid alone did not exhibit potent anti-stemness activity in vitro as compared to CKE.
Conclusions: These findings demonstrate that CKE is a tumor suppressing agent for chemically induced skin cancer. CKE prevent DMBA/TPA induced oxidative stress and potentially act as an inhibitor of MYC-induced cancer stemness.
Citation Format: Sandhya Sorra, Joyeeta Talukdar, Gayatri Gogoi, Hong Li, Debabrat Baishya, Bikul Das. Coconut kernel extract as a novel chemopreventive agent that target cancer stemness [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1614.