bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1612: The effect of docosahexaenoic acid on androgen-dependent and androgen-independent prostate tumors in combination with abiraterone and enzalutamide
Authors: Cooper Andrew R. , Ma Irvin V. , Shao Andy , Kumar Prem , Pardini Ronald S. 
Published: August 2019

Abstract
Standard treatments for prostate cancer typically involve androgen deprivation therapy (ADT). In later stages of prostate cancer, the tumor typically evolves to become insensitive to ADT, otherwise known as castration-resistant prostate cancer (CRPC). Despite being hormone-insensitive, CRPC has been shown to respond to both abiraterone and enzalutamide. Although both treatments deprive the tumor of androgens, they both display different mechanisms of action. Abiraterone inhibits androgen production, and enzalutamide acts by interrupting the binding of androgens to the androgen receptor. Studies in our laboratory have shown that docosahexaenoic acid (DHA; C22:6, n-3), a long chain omega-3 polyunsaturated fatty acid (PUFA), inhibits tumorigenesis in both androgen-dependent (LNCaP) and androgen-independent (PC-3, DU145) prostate cancer cell lines in culture. Moreover, in vivo studies with n-3 supplementation have been shown to significantly reduce PC-3 and DU145 tumor growth compared to corn oil diets rich in linoleic acid (C18:2, n-6). With evidence suggesting that n-3 PUFA dietary supplementation can inhibit tumorigenesis in CRPC, this study investigated the efficacy of DHA in combination with both abiraterone and enzalutamide in a subset of prostate tumor phenotypes in vitro. PC-3 and LNCaP cell viability were reduced with DHA in combination with either enzalutamide or abiraterone compared to primary treatments of each. These results suggest that DHA enrichment can augment abiraterone and/or enzalutamide therapy with androgen-dependent and androgen-independent prostate tumors in vitro. The results of this study provide preliminary evidence of the effectiveness of nutritional supplementation in conjunction with cancer therapeutics, and it will serve as a prelude to a pilot clinical trial evaluating the effects of nutritional supplementation with high levels of omega-3 fatty acids on enzalutamide inhibition of CRPC.
Citation Format: Andrew R. Cooper, Irvin V. Ma, Andy Shao, Prem Kumar, Ronald S. Pardini. The effect of docosahexaenoic acid on androgen-dependent and androgen-independent prostate tumors in combination with abiraterone and enzalutamide [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 1612.
Abstract 1619: Cervical cancer screening knowledge and behavior among female undergraduates
Authors: Agboeze Joseph , Nwali Matthew Igwe , Ezeani Nkiru 
Published: August 2019

Abstract
Background; Cervical cancer is a highly preventable disease that disproportionally affects women in developing countries with an estimated incidence rate of 33 cases per 100,000 women in Nigeria.. Over the year’s awareness and uptake of cervical cancer screening services have remained poor in developing countries. Lack of knowledge and poor attitude towards the disease and risk factors can affect screening practice and development of preventive behavior for cervical cancer
Objective; This study assessed the level of knowledge and barriers towards cervical cancer screening among female university students.
Method; We conducted a cross-sectional study of 234 female students at Ebonyi State University Abakaliki Nigeria from March to July 2017 using multistage sampling technique. Apretested questionnaire was used to collect data on socio-demographic characteristics, knowledge, and screening history. Data were analysed with Epi info version 7.1.4.
Results; Participants’ mean age was 22 years (sd=3).Of the respondents 79.5% were not aware of cervical cancer screening while 58.9% and 78.5% had poor knowledge on cervical cancer and Human papilomavirus vaccination respectively. Major sources of information were health workers 70% and 35% Radio while only 4.0% have had Pap smear test. Common barriers include lack of centres where such services are obtainable 88% and fear of cancer being discovered 9%. Reported risk factors were multiple sexual partners 24.2% and early onset of sexual intercourse 19.8%. A significant association was found between institutional and personal barriers and having a Pap smear test.
Conclusion Comprehensive education on cervical cancer screening in universities is critical in reducing the morbidity and mortality associated with cervical cancer. Few screening centres contributed to poor cervical screening uptake.
Note: This abstract was not presented at the meeting.
Citation Format: Joseph Agboeze, Matthew Igwe Nwali, Nkiru Ezeani. Cervical cancer screening knowledge and behavior among female undergraduates [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 1619.
Abstract 1634: A topology based data analysis method to predict survival time
Authors: Huang Cheng , Sun Hui-Chuan , Chen Junda , Shi Lin , Li Fengqing , Lin Yihui , Yang Hanyan 
Published: August 2019

Abstract
There are different methods to predict survival time, including traditional statistical regression, and modern neural network. Still, precise prediction of survival time remains as a challenge. In recent years algebraic topology was introduced as a novel method to infer information from high dimensional data set, where a mapper uses an algorithm to obtain geometric or topological features of the data set, and associate the features with the predicted variables. In this study, the data set includes gender, age, AFP, GGT, PPT, TB, ALT, tumor size, tumor number, BCLC stage, number of liver nodules, type of surgical approach etc., total 21 diagnostic variables. We use these variables to predicted OS and DFS, and the data set contains 329 records. In this study, the topology mapper is executed to acquire the topological features of all the data (including training and test sets), since this task is unsupervised, so the target values are not considered. Our method is to infer three new features of each data record, including the location of the record on the main branch of the topology, whether it is a branch node (i.e. has more than 2 branches), and whether it is an endpoint. A simple neural network with one hidden layer is designed and implemented with Tensorflow, and the three features will be added to the data set and provide valuable information for prediction of the target values. Without adding the new features from topology mapper, we have 72% accuracy (in predicting the survival time is greater or less than the mean value) on test set data when predicting OS, and we have 75% accuracy on test set data when predicting the DFS. With the new features from topology mapper, we have 83% accuracy on test set data when predicting OS, and 84% accuracy on test set data when predicting the DFS. The three new features inferred from the topology mapper have a significant effect on the accuracy of prediction and provide better accuracy. The topology based data analysis method in this study could be applied to other classification problems related to clinical trial data, and will need further verification.
Citation Format: Cheng Huang, Hui-Chuan Sun, Junda Chen, Lin Shi, Fengqing Li, Yihui Lin, Hanyan Yang. A topology based data analysis method to predict survival time [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 1634.
Abstract 165: CUCDC2 regulates malignant phenotype of triple-negative breast cancer through interacting with â-catenin
Authors: Han Shuyan , Han Hai-Bo , Jiao Yan-Na , Lo Pang-Kuo , Yao Yuan , Zhou Qun , Li Ping-Ping 
Published: August 2019

Abstract
Triple-negative breast cancer (TNBC) has the worst prognosis among all subtypes of breast cancer. CUE domain-containing protein-2 (CUEDC2) protein has reported to confer endocrine resistance in breast cancer by down-regulation of estrogen receptor α (ERα) expression. However, the function of CUEDC2 in TNBC subtype is unclear. Here, we showed CUEDC2 is expressed in triple-negative breast cancer and associated with its malignant phenotype. Knockdown of CUEDC2 not only inhibits TNBC cell proliferation, clone formation, migration, and invasion, but also suppresses TNBC stem cell mammosphere formation ability and cancer stem cell markers expression. While over-expression of CUEDC2 enhances its cell malignant phenotype. Furthermore, we determined that the ARM domain of β-catenin interacts with CUE domain of CUEDC2 through immunoprecipitation and pull-down assay. In the 34 TNBC samples, the expression levels of CUEDC2 and β-catenin also showed a positive correlation. Taken together, our study revealed CUEDC2 is associated with malignant phenotype and breast cancer stem cell properties of TNBC by interacting with β-catenin, and suggested that CUEDC2 may be a potential promising prognosis and therapy target for TNBC.
Citation Format: Shuyan Han, Hai-Bo Han, Yan-Na Jiao, Pang-Kuo Lo, Yuan Yao, Qun Zhou, Ping-Ping Li. CUCDC2 regulates malignant phenotype of triple-negative breast cancer through interacting with â-catenin [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 165.
Abstract 1660: Identification of allelic imbalance utilizing heterozygous genotype allele frequencies and intensities
Authors: Chang Kyle , Lucas Francis A. San , Ozcan Zuhal , Sivakumar Smruthy , Jakubek Yasminka A. , Fowler Richard G. , Scheet Paul 
Published: August 2019

Abstract
Allelic imbalance (AI) events, such as amplification, deletion or copy-neutral loss-of-heterozygosity (cn-LOH) can result in the activations of oncogenes or inactivations of tumor suppressor genes that are critical to the process of carcinogenesis and metastasis. However, tumor samples often have low tumor-cellularity and small subclones that require sensitive and robust algorithm for AI detections. To overcome this challenge, our lab has developed an original software application hapLOH (Vattathil and Scheet, 2013) that identifies AI with high sensitivity in SNP array data by utilizing heterozygous genotype allele frequencies in SNP array data using a Hidden Markov Model. Motivated by the plethora of next-generation sequencing (NGS) data, we carried this logic and functionality and developed hapLOHseq (San Lucas et al, 2016) for detection of subtle AI in NGS data using reference and alternate allele read depths and a set of haplotype estimates based on 1000 genome data. Recently, we sought to improve AI detection and provide support for different data types by developing haploh-cn. Haploh-cn extends our previous tools by supporting both SNP array and NGS data, and by incorporating intensity data and Log R ratios (LRR) into the underlying Hidden Markov Model for SNP array data, and incorporating sequencing depth for NGS data. In order to evaluate haploh-cn’s performances, we have downloaded The Cancer Genome Atlas Lung Adenocarcinoma whole exome sequencing data and corresponding Affymetrix SNP6 array data. Then, we simulated tumor cellularity by performing in-silico dilution of NGS and SNP array data. For NGS data, we down sampled tumor sequencing BAM files and mixed in matched-normal sequencing reads. For SNP6 array data, we combined the adjusted B allele frequencies of heterozygous sites in the tumor sample and matched-normal sample. Using the AI events detected in the undiluted tumor samples as the gold standard, we assessed the performance of haploh-cn in the computational diluted samples. Our results showed that haploh-cn had high sensitivity without sacrificing specificity in diluted tumor samples. In summary, haploh-cn is a robust and powerful method for profiling subtle AI in NGS and SNP array data.
Citation Format: Kyle Chang, Francis A. San Lucas, Zuhal Ozcan, Smruthy Sivakumar, Yasminka A. Jakubek, Richard G. Fowler, Paul Scheet. Identification of allelic imbalance utilizing heterozygous genotype allele frequencies and intensities [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 1660.
Abstract 1680: RhoGAP and PAP2 domain-containing fusions are recurrent and prognostic in gastric cancer
Authors: Kim Hark K. 
Published: August 2019

Abstract
We conducted an RNA sequencing study to identify novel in-frame gene fusions in 80 discovery dataset tumors collected from young Korean patients with diffuse gastric cancer. Twenty-five in-frame fusions were associated with diffuse gastric cancer, three of which (CLDN18-ARHGAP26, CTNND1-ARHGAP26, and ANXA2-MYO9A) were recurrent in 384 diffuse gastric cancers based on RT-PCR. All three fusions contained a RhoGAP domain in their 3’ partner genes. Patients with one of these three RhoGAP domain fusions had a significantly worse prognosis than those without such fusions. The median survival was 29.1 [95% CI, 5.7–not reached] and 94.6 [95% CI, 62.0–not reached] months, respectively (P=0.011, log-rank; HR, 2.8 [95% CI, 1.5–5.3]). Ectopic expression of CLDN18-ARHGAP26 promoted the migration and invasion capacities of diffuse gastric cancer cells. Parallel targeted RNA sequencing analysis additionally identified PAP2 domain-containing fusions as recurrent and poor prognostic in-frame fusions. Overall, in-frame gene fusions containing either RhoGAP or PAP2 domain clearly defined the aggressive subset (7.5%) of diffuse gastric cancer, and their prognostic impact (HR, 3.4 [95% CI, 2.0–5.7]) was greater than, and independent of, chromosomal instability and CDH1mutations. Our study may provide novel genomic insights guiding future strategies for managing diffuse gastric cancer.
Citation Format: Hark K. Kim. RhoGAP and PAP2 domain-containing fusions are recurrent and prognostic in gastric cancer [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 1680.
Abstract 1717: Variants of uncertain significance of the cancer predisposing genes in 3.5 thousand Japanese whole genome sequencing data
Authors: Yasuda Jun 
Published: August 2019

Abstract
Many of the cancer predisposing genes are known to be associated with juvenile cancer syndromes such as Li Fraumeni syndrome. The responsible variants of the juvenile cancer syndromes are usually very deleterious and show strong biological effects on the gene functions. It is not so easy to estimate the clinical significance of the moderately deleterious variants in those genes that may have clinically significant effects on the hosts’ cancer predisposition and these moderately deleterious (or hypomorphic) variants are now classified as variants of uncertain significance (VUSs). The insight that VUSs may have moderate but clinically significant effects on cancer susceptibility now attracts cancer geneticists. To elucidate the state of VUSs of more than 150 cancer predisposing genes in general population, we functionally annotate the single nucleotide variants (SNVs) in the genes from a 3,552 whole genome sequence dataset (3.5KJPN) obtained from participants in a genome cohort by Tohoku Medical Megabank Organization. Frequency spectrum of the Combined Annotation-Dependent Depletion (CADD) and deleterious annotation of genetic variants using neural networks (DANN) scores of the more than 150 cancer predisposing genes will be discussed. Finally, the association of the CADD and DANN scores with the past and family histories will be analyzed.
Citation Format: Jun Yasuda. Variants of uncertain significance of the cancer predisposing genes in 3.5 thousand Japanese whole genome sequencing data [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 1717.
Abstract 1719: Copper levels and the p53 protein: A delicate balance
Authors: Muller Patricia , Grabowiecki Yannick von , Hall Callum 
Published: August 2019

Abstract
The tumor suppressor p53 is mutated in 50% of all cancers and in about 90% of small lung cancers. Mutations lead to loss of p53 expression or the expression of mutant p53 proteins. These mutants often lose WT function, but they have also been shown to acquire invasive and metastatic functions. p53 requires a zinc molecule in its core domain to fold properly and to function as a transcription factor and tumor suppressor. Loss of this zinc through competition with copper causes p53 to unfold and to lose its transcription function. Copper is an essential heavy metal required for a large variety of biological processes as it is required for the function of many enzymes. In cancer patients, increased serum levels of copper have been found and people with a predisposition for copper accumulation in the liver (Wilson’s disease, mutations in ATP7B) are prone to develop liver cancers. Our preliminary results have indicated that an unfolded WT p53 molecule does not only lose its transcription function, but also gains mutant p53-like functions in promoting invasion. Copper-induced unfolded p53 interacted with the mutant p53 specific interacting proteins Dicer, Ago, p63 and p73 and impaired p63 function. These results raise the question as to why a WT molecule would lose its function and whether it perhaps could act as a redox sensor. Experiments are ongoing to explore p53 mediated transcription in response to copper exposure. In addition, we are setting up mouse models to investigate p53 folding in vivo in response to mild increases in copper serum levels and we are developing methods to better determine p53 folding in patients and in mice. These results will help us assess p53 status in relation to serum metal levels in vivo and determine whether p53 is important in the development of cancers and metastasis.
Citation Format: Patricia Muller, Yannick von Grabowiecki, Callum Hall. Copper levels and the p53 protein: A delicate balance [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 1719.
Abstract 1722: Spectrum of solid malignancies associated with mutations in CYLD gene
Authors: Ellis Michelle , Swensen Jeff , Gatalica Zoran 
Published: August 2019

Abstract
Introduction: The CYLD gene product is a de-ubiqutinating enzyme involved in regulation of NF-kappaB signaling. Inactivating germline mutations in CYLD are the cause of Brooke-Spiegler syndrome characterized by multiple cutaneous tumors (cylindromas, trichoepitheliomas and spiradenomas) and tumors of salivary glands. Little is known about the role of CYLD in the development of solid organ malignancies.
Methods: We retrospectively analyzed CYLD gene mutations detected in a large database of solid tumors genetically profiled (NGS of 592 genes) at a reference laboratory (Caris Life Science, Phoenix, AZ).
Results: CYLD pathogenic mutations were identified in 235 tumor samples (0.4% of the tumors analyzed). The most common primary sites included lung (60), endometrium (15) and anus (10). Histologically, the majority of the tumors were classified as squamous (71) and adenocarcinoma (59). A number of mutations were identified, most commonly affecting codons p.N722fs (27), p.S371* (16) and p.P771S/p.P771L (12). 38 cases had only CYLD mutations detected, while the majority of associated mutations occurred in TP53 (45%). Numerous co-occurring pathogenic mutations were present in oncogenes (e.g. PIK3CA in 41, KRAS in 33, BRAF 17) and/or tumor suppressor genes (e.g. APC in 40, PTEN in 36, BRCA2 in 25, RB1 in 23).
Conclusion: Our study provides the largest database analysis of CYLD gene mutations in solid tumors and shows the distribution in numerous primary tumor sites previously unrecognized in association with CYLD. Additional studies may reveal unexpected germ-line associations and will be pursued in the future.
Citation Format: Michelle Ellis, Jeff Swensen, Zoran Gatalica. Spectrum of solid malignancies associated with mutations in CYLD gene [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 1722.
Abstract 1757: The effect of Zc3h8 expression levels on sensitivity to DNA damage and repair in mouse mammary cells
Authors: Li Spencer , Schmidt John A. , Knepper Janice E. 
Published: August 2019

Abstract
Localized in PML nuclear bodies, the fetal liver zinc finger protein (Fliz), or ZC3H8, has been shown to increase cell proliferation, migration, and tumorigenesis in mouse mammary cell lines. While the exact function of ZC3H8 is unclear, PML nuclear bodies are critical centers for genome maintenance. Previous studies have suggested that these nuclear bodies act as deposits of sequestered DNA damage response proteins including SUMO-1, TP53, and BRCA-1. In addition to their localization to PML nuclear bodies, the phosphorylation of ZC3H8 by CK2 leads to dispersion of PML nuclear foci. For these reasons, we speculated that increased expression of Zc3h8, leading to greater protein availability, is involved in the suppression of DNA repair. This in return would increase genome instability and cancer cell aggression. This study uses the single cell comet assay to measure DNA damage repair following treatment with the topoisomerase inhibitor and chemotherapy drug etoposide. Two mouse mammary tumor cells lines, cV1A 01-51 and cV1A 03-31 were transfected to drive an shRNA targeting ZC3H8 (Flizout). In addition, the cV1A 03-31 Flizout line was rescued with a Zc3h8 construct with altered base coding to make transcribed products immune to shRNA targeting (SynFliz). We have also developed a constitutively charged cV1A 03-31 T32E mutant and a non-phosphorylatable T32A mutant. The nontumorigenic Comma1-D cell line was transfected with a vector to increase Zc3h8 expression. Ability to repair after etoposide treatment in these mutants was compared to controls carrying endogenous levels of Zc3h8. Etoposide leads to double strand breaks in the DNA during replication, and all cell lines were sensitive to etoposide and able to undergo repair. For the cV1A 01-51 lines, the control and Flizout mutants had a nonsignificant difference in post-repair comet length (p = 0.06) but a significant difference in tail moment (p = 0.003). Between the control and the mutants, the difference in overall comet length was 4.7%, and the difference in tail moment was 15.8%, with cells expressing higher levels of Zc3h8 being less adept in carrying out repair of double strand DNA breaks. This suggests an inverse relationship between Zc3h8 expression and DNA damage repair. This may indicate that evaluating Zc3h8 expression could be considered for determining the ability of tumor cells to respond to chemotherapy agents. Furthermore, altering its expression may be a novel approach for cancer treatment.
Citation Format: Spencer Li, John A. Schmidt, Janice E. Knepper. The effect of Zc3h8 expression levels on sensitivity to DNA damage and repair in mouse mammary 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 1757.