bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5261: Tocopherols inhibit the estrogen-stimulated expansion of cancer stem cells via down-regulation of OCT4 and NFκB
Authors: Bak Min Ji 
Published: July 2017

Abstract
Cancer stem cells have been suggested to play a role in tumor initiation, maintenance, resistance, and metastasis. Breast cancer stem cells are defined as CD44+/CD24- cell populations that have the properties of tumor-initiating ability, self-renewal and differentiation. Although the importance of estrogen in breast cancer is well established, the effects of estrogen on breast cancer stem cells are not fully understood. Vitamin E, which is consisted of different forms of tocopherols and tocotrienols, has anti-tumor effects in various cancers, including breast cancer. In the present study, we examined the effects of α-, γ-, and δ-tocopherol against estrogen-stimulated expansion of cancer stem cells. To determine the effects of tocopherols on breast cancer stem cells, the MCF-7 tumorsphere cell culture system, which enriches for mammary progenitor cells and putative breast cancer stem cells, was utilized. Treatment of MCF-7 tumorsphere with estrogen for four days resulted in an increase in CD44+/CD24- stem cell populations in tumorspheres as well as the number and size of tumorspheres. Tocopherols at 1 and 10 μM inhibited formation of estrogen-induced stem cell enriched tumorspheres, indicating that tocopherols reversed estrogen-induced expansion of breast cancer stem cells. Tocopherols decreased the expression of estrogen-related genes such as TFF/pS2, cathepsin D, progesterone receptor and SerpinA1 in estrogen-stimulated tumorspheres. In addition, the mRNA levels of stem cell markers, including OCT4, NFκB, SOX-2 and CD44, were upregulated by estrogen, which were downregulated by the treatment with tocopherols. Our results suggest that tocopherols repress the expansion of breast cancer stem cell population by regulating OCT4 and NFκB signaling. Tocopherols could be effective natural agents for the prevention and treatment of estrogen-induced breast cancer. (This work was supported in part by the National Institutes of Health grant R01 AT007036.)
Citation Format: Min Ji Bak. Tocopherols inhibit the estrogen-stimulated expansion of cancer stem cells via down-regulation of OCT4 and NFκB [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5261. doi:10.1158/1538-7445.AM2017-5261
Abstract 5270: Disease subtype independent biomarkers of breast cancer prevention by withaferin a
Authors: Hahm Eun-Ryeong , Samanta Suman K. , Sehrawat Anuradha , Kim Su-Hyeong , Pore Subrata K. , Singh Krishna B. , Christner Susan M. , Shuai Yongli , Beumer Jan H. , Roy Ruchi , Davidson Nancy E. , Singh Shivendra V. 
Published: July 2017

Abstract
Breast cancer is a rather complex and heterogeneous disease broadly grouped into four major subtypes, including luminal-type, basal-like, HER2 amplified, and normal-like, and each with a distinct molecular signature. A non-toxic chemopreventive intervention efficacious against different subtypes of breast cancer is still a clinically unmet need. The present study not only demonstrates chemoprevention of breast cancer in rats by the Ayurvedic medicine phytochemical withaferin A (WA) but also identifies its mechanistic biomarkers common to different subtypes of this disease. Chemopreventive efficacy of WA (4 and 8 mg per kg body weight) was determined using a rat model of breast cancer induced by N-methyl-N-nitrosourea (MNU). The mechanisms underlying breast cancer chemoprevention by WA were elucidated by western blotting, biochemical assays, immunohistochemistry, and cytokine profiling using plasma and tumors from the MNU-rat and/or mouse mammary tumor virus-neu (MMTV-neu) models. Inhibitory effect of WA on exit from mitosis and leptin-induced oncogenic signaling was determined using MCF-7 and MDA-MB-231 cells. Incidence, multiplicity, and burden of MNU-induced breast cancer in rats were decreased by WA administration. For example, the tumor weight in the 8 mg per kg group was lower by 67% compared with controls (P = 0.004). Mitotic arrest and apoptosis induction were common determinants of breast cancer chemoprevention by WA in the MNU-rat and MMTV-neu models. Cytokine profiling showed suppression of plasma leptin levels by WA in rats. WA inhibited leptin-induced oncogenic signaling in cultured MCF-7 and MDA-MB-231 cell lines. WA is a promising phytochemical with the ability to inhibit at least two different subtypes of breast cancer, including neu-driven estrogen receptor negative (ER-) breast cancer in MMTV-neu model and MNU-induced ER+ breast cancer in rats. This study was supported by the grant RO1 CA142604-07 awarded by the National Cancer Institute.
Citation Format: Eun-Ryeong Hahm, Suman K. Samanta, Anuradha Sehrawat, Su-Hyeong Kim, Subrata K. Pore, Krishna B. Singh, Susan M. Christner, Yongli Shuai, Jan H. Beumer, Ruchi Roy, Nancy E. Davidson, Shivendra V. Singh. Disease subtype independent biomarkers of breast cancer prevention by withaferin a [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5270. doi:10.1158/1538-7445.AM2017-5270
Abstract 5323: Obesity and ovarian cancer survival revisited
Authors: Bandera Elisa V. , Lee Valerie , Qin Bo , Rodriguez Lorna , Powell Bethan , Kushi Lawrence H. 
Published: July 2017

Abstract
Research on the impact of obesity on ovarian cancer survival is inconsistent but previous studies did not consider the possible impact of ascites, bowel obstruction, or cachexia, which commonly occur in late-stage disease. We evaluated this association in a cohort study of primary invasive epithelial ovarian cancers diagnosed from 2000-2013 in Kaiser Permanente Northern California (KPNC) (n=1,157). Deaths were identified through December 2014, with median follow-up of 37 months. Proportional hazards regression was used to estimate overall and ovarian cancer-specific mortality, accounting for prognostic variables including age at diagnosis, race, stage, grade, histology, comorbidities, treatment, post-treatment CA125 levels, ascites, and bowel obstruction. There was no evidence of an association between BMI and overall or ovarian cancer-specific survival. However, we found strong effect modification by stage (Pinteraction&lt;.01). Compared to normal pre-diagnosis BMI (18.5-24.9 kg/m2), for women who were obese before diagnosis (BMI≥35 kg/m2) risk of ovarian cancer-specific mortality was increased among those diagnosed at stages I/II (Hazard ratio [HR]: 3.40; 95% confidence interval [CI]: 1.16-9.99), but reduced among those diagnosed with stage IV disease (HR: 0.58; 95%CI: 0.35-0.96). Associations persisted after excluding those diagnosed with cachexia (n=91) and further adjusting for ascites and bowel obstruction, with no evidence of effect modification by these factors. Associations of obesity with ovarian cancer survival differ by stage, with decreased survival among those with localized disease and increased survival among those with late-stage disease. Stage-specific effects of obesity on survival suggest a tailored approach to improve prognosis may be appropriate.
Citation Format: Elisa V. Bandera, Valerie Lee, Bo Qin, Lorna Rodriguez, Bethan Powell, Lawrence H. Kushi. Obesity and ovarian cancer survival revisited [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5323. doi:10.1158/1538-7445.AM2017-5323
Abstract 5340: Retrovirus insertion induces syncytin mediated exosomes delivery in prostate cancer cells
Authors: Uygur Berna , Chernomordik Leonid 
Published: July 2017

Abstract
Activation of retroviruses in normal cells can induce tumors and a wide array of cancers contains retrovirus-like particles. The potential role of these endogenous retroviruses in the development and progression of tumors has been discussed in many studies. However the effects of retrovirus insertion into cancer cells have not yet been fully examined. In this study, we explore genetic material transfer either between retrovirus-transduced prostate cancer PC3 cells or between PC3 cells and their host environment through extracellular vesicles (EV) and virus-like particles. For these purposes, we transduced PC3 cells with either GFP-encoding retrovirus or with m-cherry-encoding lentivirus. Co-incubation of GFP-expressing cells with m-cherry-expressing cells for 72h yielded yellow PC3 cells. Yellow cells were also observed in the experiments where lentiviral m-cherry expressing PC3 cells were cultured with tissue culture medium from retrovirus GFP expressing PC3 cells. These results indicated that horizontal genetic information transfer involves neither fusion nor contact between the cells. Since incubation of the retrovirus GFP-expressing PC3 cells with the medium from the lentivirus m-cherry expressing PC3 cells, did not yield yellow cells the genetic material transfer requires retrovirus insertion in PC3 cells. Using Western blot and Q-PCR, we found the exosomes from the medium generated by retrovirus GFP expressing PC3 cells to carry human endogenous retroviral proteins syncytin 1 and 2 and contain RNAs encoding these proteins. Exosomes from the lentivirus m-cherry expressing PC3 cells had lower protein expression of Syncytin 1&2 than exosomes from retrovirus GFP expressing PC3 cells. Application of Syncytin 1 or 2 antibodies to the medium generated by or co-cultured retrovirus GFP expressing PC3 and lentivirus m-cherry expressing PC3 cells suppressed horizontal transfer of the genetic information from retrovirus GFP expressing PC3 cells to other cells. The specific mechanisms by which retroviral transduction and syncytins control the generation of a GFP-encoding pseudotyped retrovirus or EV and the delivery of their content, as well as the role of the virus/EV-mediated horizontal genetic material transfer between prostate cancer cells and between prostate cancer and their microenvironment remain to be clarified.
Citation Format: Berna Uygur, Leonid Chernomordik. Retrovirus insertion induces syncytin mediated exosomes delivery in prostate cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5340. doi:10.1158/1538-7445.AM2017-5340
Abstract 5347: Molecular barcoding improves confidence in variant calling with low input FFPE tissue samples
Authors: Arezi Bahram , Hsue Bilan , Chen Keith , Rogers Brenda , Lecocq Christian , Ashutosh Ashutosh , Ghosh Jayati , Amparo Gilbert , Ramaiah Madhuvanthi , Pabon Carlos , Hogrefe Holly 
Published: July 2017

Abstract
FFPE tissue archiving is the most widely used method for clinical sample preservation, and provides a valuable source of diverse genetic information for cancer biomarker discovery. NGS library preparation is often challenging, however, as FFPE-derived DNAs exhibit varying degrees of fragmentation and chemical modification depending on how tissues were handled and processed. Moreover, the presence of low allele frequency variants because of tumor heterogeneity, sample degradation, and high rate of formalin-induced mutations make SNV calling a challenging task. To improve variant calling and consistency across FFPE samples of varying quality, we developed a complete workflow solution that features DNA pre-qualification, molecular barcodes for uniquely tagging each DNA fragment, pre-capture indexing for tracking up to 192 samples, accelerated hybrid capture, and one-tube library prep, to enable the preparation of complex enriched libraries in less than 8 hours from 10-200ng of FFPE-derived DNA. We incorporate molecular barcodes at the ligation step to enable de-duplication and generation of consensus reads using SureCall software, which significantly improves confidence of variant calling (99% of calls &gt;150 variant call quality threshold) at low allelic frequencies.
Using ClearSeq Comprehensive Cancer Panel which targets 151 genes frequently mutated in solid and hematological cancers, we routinely obtain high quality libraries (with 1000X sequencing depth and after deduplication) with &gt;99% of the targeted region covered at 20X for high quality gDNA (FF tissue), and greater than 95% and 90% covered at 20X for medium and low quality FFPE samples, respectively. Using multiplex reference samples, we demonstrate detection of low frequency variants (at 1-5%) including SNVs, small indels, and RET and ROS1 translocations. As we will further show, FFPE integrity scores determined by qPCR and TapeStation (ddCq and DIN) enable researchers to choose the appropriate quantification method, PCR cycling, and sequencing depth for optimal sequencing coverage.
Citation Format: Bahram Arezi, Bilan Hsue, Keith Chen, Brenda Rogers, Christian Lecocq, Ashutosh Ashutosh, Jayati Ghosh, Gilbert Amparo, Madhuvanthi Ramaiah, Carlos Pabon, Holly Hogrefe. Molecular barcoding improves confidence in variant calling with low input FFPE tissue samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5347. doi:10.1158/1538-7445.AM2017-5347
Abstract 5367: Ngago: no evidence of targeted endonuclease activity
Authors: Topka Sabine , Kazzaz Sara , Offit Kenneth , Joseph Vijai 
Published: July 2017

Abstract
The development of a versatile and easy to use genome editing tool based on the bacterial CRISPR/Cas9 system has led to a vast increase in applications of genome editing in laboratories around the world. As an extremely powerful and versatile tool it has facilitated important discoveries in both basic and translational research as well as in a potentially wide range of therapeutic applications. Natronobacterium gregoryi Argonaute (NgAgo) protein was described as a favorable alternative to Cas9 due to its simplicity and higher endonuclease specificity. Thus far, there are no formal reports documenting the success of NgAgo in other laboratory settings and cellular systems. Utilizing the identical cellular background and protocol that was made publicly available by the authors of the initial study, we were unable to reproduce the endonuclease function of NgAgo. These results do not support the role of NgAgo in gene editing experiments.
Note: This abstract was not presented at the meeting.
Citation Format: Sabine Topka, Sara Kazzaz, Kenneth Offit, Vijai Joseph. Ngago: no evidence of targeted endonuclease activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5367. doi:10.1158/1538-7445.AM2017-5367
Abstract 5399: Investigating phenotypic plasticity in breast cancer with high-throughput nanogrid single-nucleus RNA sequencing
Authors: Gao Ruli , Kim Charissa , Sei Emi , Yang Jie , Chan Leo , Srinivasan Maithreyan , Zhang Hong , Meric-Bernstam Funda , Navin Nicholas E. 
Published: July 2017

Abstract
Single-cell RNA sequencing (RNA-seq) is a powerful tool for investigating rare tumor subpopulations and resolving intra-tumor heterogeneity, but is low throughput, expensive, and requires fresh tissue samples. To address these limitations, we developed a 5’ high-throughput single-nucleus RNA sequencing (SNRS) approach that uses nanogrid technology to perform single-cell imaging and sequencing of 500-2500 nuclei in parallel. The automated image scanning procedure allowed us to exclude doublets and select live cells with DAPI/PI staining. This approach allows the transcriptomic profiling of frozen tissue samples, in which the cytoplasmic membrane is ruptured in cells, but leaves the nuclear membrane intact. We validated SNRS in a breast cancer cell line (SK-BR-3) and compared the transcriptomes of 500 nuclei to 500 whole cells, which revealed a high concordance in the number of genes expressed as well as their expression levels. We also performed bulk RNA-seq of isolated nuclear and cellular fractions from 5 breast cancer cell lines, which showed a high concordance in genes and expression levels. Differentially expressed genes in the nucleus mainly included lincRNAs, pseudogenes and mitochondria genes, but did not affect most cancer genes and pathway analysis. We further applied SNRS to sequence 500 nuclei from a triple-negative breast cancer patient and identified diverse phenotypes in tumor cells, including variation in cell proliferation, migration, invasion, and epithelial-to-mesenchymal transition. These studies demonstrated the technical feasibility of using a nanogrid platform to perform high-throughput single-cell RNA sequencing and showed that nuclei from cell lines and tumors can be used to study signaling pathways and gene networks that play an important role in tumor progression.
Citation Format: Ruli Gao, Charissa Kim, Emi Sei, Jie Yang, Leo Chan, Maithreyan Srinivasan, Hong Zhang, Funda Meric-Bernstam, Nicholas E. Navin. Investigating phenotypic plasticity in breast cancer with high-throughput nanogrid single-nucleus RNA sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5399. doi:10.1158/1538-7445.AM2017-5399
Abstract 540: Deep learning to determine breast cancer estrogen receptor status from nuclear morphometric features in H&E images
Authors: Rawat Rishi R. , Ruderman Daniel , Agus David B. , Macklin Paul 
Published: July 2017

Abstract
We hypothesized that the spatial arrangement of nuclei in a hematoxylin and eosin (H&E) stained image contains a vast quantity of latent information that is currently underutilized. We tested this hypothesis on the classification of breast cancer biopsies as estrogen receptor (ER) positive or negative. While determining ER status typically requires immunohistochemistry (IHC) staining, we aimed to recapitulate this step by predicting ER status directly from H&E stained slides. By training a deep neural network on nuclear-morphometric features, we demonstrate the power of machine learning to provide insights about cancer biology, and aim to scale precision oncology for the developing world.
We constructed a learning pipeline that segments nuclei from H&E stained slides scanned into digital images, extracts shape and orientation descriptors, and uses a deep neural network to learn spatial features to predict ER status. After training the pipeline on 57 tissue cores of invasive ductal carcinoma (IDC), we were able to predict ER status in patients with IDC in a statistically significant manner (AUC=0.72, 95%CI=0.55-0.88, n=56) and ductal carcinoma in situ (AUC=0.82, 95%CI=0.74-0.89, n=106).
To our knowledge, this is the first work to show that nuclear morphometric information can be used to predict the molecular status of a breast cancer tumor. An initial analysis of the features learned by the deep neural network provides a glimpse into the mechanistic differences between ER+ and ER- cancers: suggesting the importance of spatial heterogeneity in distinguishing between ER+ and ER-.
We anticipate that further analysis will provide deeper insights about the morphological differences between ER+ and ER- cancers, and that this type of analysis can be applied to other markers and cancers. Moreover, an optimized version of this pipeline may serve patients in the developing world by providing a means to predict marker status directly from H&E images.
Citation Format: Rishi R. Rawat, Daniel Ruderman, David B. Agus, Paul Macklin. Deep learning to determine breast cancer estrogen receptor status from nuclear morphometric features in H&E images [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 540. doi:10.1158/1538-7445.AM2017-540
Abstract 5400: Accurate identification of single nucleotide variants in whole genome amplified single cells
Authors: Dong Xiao , Zhang Lei , Milholland Brandon , Lee Moonsook , Maslov Alexander Y. , Wang Tao , Vijg Jan 
Published: July 2017

Abstract
Single cell sequencing for analyzing DNA mutations across the genome in somatic tissues is critically important for studying development, cancer and aging. However, current procedures are prone to artifacts and to date a reliable protocol for single-cell somatic mutation analysis remains to be developed. Here we address the two largest sources of artifacts, i.e., DNA denaturation-related cytosine deamination and allelic bias-driven whole genome amplification errors. We first reconfigured multiple displacement amplification (MDA) into an efficient protocol for whole genome amplification of single cells without cytosine deamination artifacts, i.e., Single Cell MDA (SCMDA). We then developed a new single-cell SNV caller (SCcaller) that distinguishes real somatic mutations and amplification errors by utilizing a SNP-based localized estimate of allelic amplification bias. The procedure was validated by comparing SCMDA-amplified single cells with unamplified clones derived from single cells from the same population. Together with SCcaller, SCMDA provides a firm foundation for analyzing cellular heterogeneity in somatic mutational landscapes in tumor and surrounding, normal tissues.
Citation Format: Xiao Dong, Lei Zhang, Brandon Milholland, Moonsook Lee, Alexander Y. Maslov, Tao Wang, Jan Vijg. Accurate identification of single nucleotide variants in whole genome amplified single cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5400. doi:10.1158/1538-7445.AM2017-5400