bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3525: The effects of Berberis vulgaris on bacterial inhibition and the p53 gene in cancerous Caenorhabditis elegans
Authors: Bhatt Jesal P. 
Published: July 2016

Abstract
Recently, there has been an interest in the use of natural products to inhibit bacterial growth rather than manufactured antibiotics due to the problem of bacterial resistance. This study aims at finding the most effective natural antibacterial remedy. The disk diffusion method was used to compare the antibacterial properties of manuka honey, barberry, aloe vera, and colloidal silver. After a 48-hour incubation period, the zone of inhibition was measured for the following bacteria: Bacillus megaterium, Serratia marcescens, Pseudomonas fluorescens, Rhodospirillum rubrum, and Escherichia coli. Barberry was the most efficient natural product (p = 0.02). Further tests were performed to determine whether barberry contained strong anticancer properties. Barberry was tested on Caenorhabditis elegans (C.elegans), strain JR1279, exposed to ultraviolet-C radiation and the population was counted daily. Prior to this experiment, barberry had never before been tested on a model organism. The purpose of this experiment would determine if barberry could increase the lifespan of the C.elegans by the addition of this reagent. It was shown that the C.elegans exposed to barberry had a longer lifespan than those that were not exposed to barberry (p = 0.01), indicating that barberry could be a potential anticancer supplement.
Citation Format: Jesal P. Bhatt. The effects of Berberis vulgaris on bacterial inhibition and the p53 gene in cancerous Caenorhabditis elegans. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3525.
Abstract 3527: Inhibition of autophagosome closure promotes iDISC-mediated apoptosis in AML cells
Authors: Tang Zhenyuan , Takahashi Yoshinori , Wang Hong-Gang 
Published: July 2016

Abstract
Macroautophagy (hereafter referred to as autophagy) is a lysosomal degradation process whereby cellular components, such as damaged organelles, are enclosed in double-membrane structures called autophagosomes and delivered to lysosomes for degradation and recycling. Autophagy is known to be essential for cancer pathogenesis and progression through its intimate crosstalk with programed cell death machinery, apoptosis. However, the role of autophagy in apoptosis pathway remains highly controversial and context-dependent, which makes developing autophagy-targeted anti-cancer treatments hard to achieve. We have previously reported that autophagosomal membranes can serve as a platform for caspase-8 activation through the assembly of an intracellular Death-Inducing Signaling Complex (iDISC). In the present study, we demonstrate that inhibition of phagophore closure by depleting Atg2A/B stabilizes iDISCs and induces caspase-8-initiated apoptosis in acute myeloid leukemia (AML) cells. We found that knockout of Atg2A/B, but not Atg7, promotes the oligomerization of caspase-8 on Atg16L- and LC3-positive phagophore membranes upon nutrient starvation. Starvation-induced capase-8 activation and apoptosis induction in Atg2A/B-deficient cells were strongly suppressed by the inhibition of caspase-8. These results suggest that autophagy inhibition at the phagophore closure step can shift cytoprotective autophagy to a pro-death mechanism and thus may be a promising strategy to enhance the efficacy of anticancer therapy.
Citation Format: Zhenyuan Tang, Yoshinori Takahashi, Hong-Gang Wang. Inhibition of autophagosome closure promotes iDISC-mediated apoptosis in AML cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3527.
Abstract 3544: Determining autophagic activity following cannabidiol treatment of melanoma: a potential new and novel treatment
Authors: Simmerman Erika L. , Qin Xu , Motamed Kouros , Yu Jack C. , Baban Babak 
Published: July 2016

Abstract
Introduction:
Autophagy is a catabolic pathway utilized for energy metabolism in nutrient-depleted tumors. Recent studies have reported autophagy to be a survival mechanism found in cancer during stress secondary to cancer progression or treatment. In this study we tested for autophagic activity in malignant melanoma tumors via detection of LC3 antibody following treatment with Cannabidiol (CBD) and cisplatin. The objective of this study was to investigate the effect of treatment with a cannabinoid derivative on autophagic activity in malignant melanoma.
Materials and Methods:
Murine B16F10 melanoma tumors were established subcutaneously in C57BL/6 mice. These mice were then subjected to treatment with local vehicle (PBS) injection (control - group 1, n = 5), systemic Cisplatin injection (group 2; n = 5), and local cannabidiol injection (group 3; n = 5). Tumor cells were subsequently submitted to immunohistochemistry, Brightfield microscopy, and quantitative analysis (Bioquant) for LC3 expression.
Results:
The expression level of LC3 was significantly reduced in groups 2 and 3 when compared to the control group 1. Quantitative measurement of the slides using Bioquant software confirmed our immunohistochemistry and microscopic results.
Conclusions:
If CBD does indeed decrease autophagic activity, it may represent a new and novel therapeutic target in the treatment of malignant melanoma. Additional studies to clarify the specific relationship between CBD and autophagy are in progress and will be reported upon completion.
Citation Format: Erika L. Simmerman, Xu Qin, Kouros Motamed, Jack C. Yu, Babak Baban. Determining autophagic activity following cannabidiol treatment of melanoma: a potential new and novel treatment. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3544.
Abstract 3553: A novel allosteric mechanism for molecular inhibition of anti-apoptotic MCL-1
Authors: Lee Susan , Wales Thomas E. , Gallagher Catherine , Cohen Daniel T. , Escudero Silvia , Luccarelli James , Huhn Annissa J. , Cohen Nicole A. , Bird Gregory H. , Engen John R. , Walensky Loren D. 
Published: July 2016

Abstract
MCL-1 is an anti-apoptotic BCL-2 family protein that has emerged as a major pathogenic factor across a broad range of human cancers. Thus, pharmacologic inhibition of MCL-1 has been the focus of intensive drug development efforts. Like BCL-2, MCL-1 bears a C-terminal surface groove whose function is to bind and sequester the essential BH3 killer domains of pro-apoptotic BCL-2 family proteins, a mechanism harnessed by cancer cells to create formidable apoptotic blockades. Whereas drugging the BH3-binding groove has been successfully achieved for BCL-2, translating this approach to MCL-1 has been challenging. Here, we report an alternative mechanism for MCL-1 inhibition by small molecule covalent modification of an interaction site that is distant from the BH3-binding groove. Biochemical and hydrogen-deuterium exchange mass spectrometry analyses revealed that both the BH3-binding capacity of MCL-1 and its functional suppression of BAX-mediated membrane poration is impaired by molecular engagement, a phenomenon recapitulated by mutagenic mimicry at the novel regulatory region. This allosteric mechanism for disrupting the anti-apoptotic, BH3-binding activity of MCL-1 could inform a new therapeutic strategy for disarming MCL-1 in cancer.
Citation Format: Susan Lee, Thomas E. Wales, Catherine Gallagher, Daniel T. Cohen, Silvia Escudero, James Luccarelli, Annissa J. Huhn, Nicole A. Cohen, Gregory H. Bird, John R. Engen, Loren D. Walensky. A novel allosteric mechanism for molecular inhibition of anti-apoptotic MCL-1. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3553.
Abstract 3559: The rare BCL-2 isoform BCL-2β is associated with melanoma survival and the apoptotic response to UV and cisplatin
Authors: Warren Chloe , Vilain Ricardo E. , Ashton Katie A. , Almazi Juhura G. , Braye Stephen , Moscato Pablo , Bowden Nikola A. 
Published: July 2016

Abstract
There are two isoforms of the anti-apoptotic protein BCL-2. BCL-2α (wild-type) is well characterised and is known predominantly for its role in apoptosis, BCL-2β lacks the C-terminal transmembrane (TM) domain and its function has not yet been characterised. The aim of this study was to quantify and determine the biological role of the BCL-2β isoform in melanoma.
BCL-2α and BCL-2β isoforms were quantified at the mRNA and protein level in a cohort of 141 FFPE melanoma tumours using qPCR and multiple reaction monitoring (MRM) tandem mass spectrometry and compared to clinical parameters including age at diagnosis, gender, solar elastosis, BRAF/NRAS mutation, Breslow thickness, disease free survival and overall survival. The role of the BCL-2α and BCL-2β isoforms in apoptosis were investigated by quantifying transcript expression and apoptosis before and up to 72 hours after UVB irradiation (650J/m2) and cisplatin treatment (10ug/mL). siRNA knockdown targeted to each individual isoform transcript was used to verify the apoptotic response.
Expression of the BCL-2β isoform in tumours was significantly associated with increased overall survival (686.4 weeks, 95% CI 462.5-910.3). BCL-2α response to UVB and cisplatin (i.e. downregulation prior to apoptosis) was the same in melanocyte and melanoma cell lines. However, BCL-2β response was varied across the melanoma cell lines, but was similar to that of BCL-2α in melanocytes. siRNA knock-down of BCL-2α resulted in increased apoptosis and cell death in melanoma cell lines, but knock-down of BCL-2β delayed onset of apoptosis, suggesting the BCL-2β is pro-apoptotic.
Our current understanding of the role of BCL-2β is based on the concept that it lack the C-terminal transmembrane domain, and is incapable of localising to target organelles. It is currently thought that the isoform is of null function. However, these observations are based on studies of non-representative synthetic versions of BCL-2β. This is the first time the naturally transcribed version of the rare isoform has been studied. We have demonstrated herein that BCL-2β performs an apoptotic role, and that its regulation in melanoma may be a biomarker of better overall survival.
Citation Format: Chloe Warren, Ricardo E. Vilain, Katie A. Ashton, Juhura G. Almazi, Stephen Braye, Pablo Moscato, Nikola A. Bowden. The rare BCL-2 isoform BCL-2β is associated with melanoma survival and the apoptotic response to UV and cisplatin. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3559.
Abstract 3563: Ras-mediated regulation of cytochrome c-induced caspase activation is dependent on the status of extracellular matrix attachment
Authors: McCallister Chelsea M. , Rayavarapu Raju , Pagani Nicholas , Heiden Brendan , Shaw Melissa , Shuff Sydeny , Schafer Zachary T. 
Published: July 2016

Abstract
Hyperactivating mutations in Ras are found in a significant percentage of cancers, with a particularly high frequency in pancreatic and colon carcinomas. The hyperactivation of Ras drives a vast number of distinct downstream signaling pathways that play an important role in disease progression. One outcome of overactive oncogenic Ras signaling is the inhibition of anoikis, a form of apoptotic cell death caused by detachment from the extracellular matrix (ECM). It is well-established that one mechanism of anoikis inhibition by Ras involves impaired mitochondrial cytochrome c release. In addition, here, we have found that Ras-mediated anoikis inhibition can also occur downstream of mitochondrial cytochrome c release. Our data suggest that anoikis inhibition following cytochrome c release is not dependent on changes in the abundance of the Apaf-1, pro-caspase-9, or pro-caspase-3. Instead, our data suggest that Ras signaling leads to an inhibition in the ability of caspase-9 to bind Apaf-1 which thereby inhibits proper formation of the apoptosome and caspase activation. Interestingly, in stark contrast to the inhibition of cytochrome c-induced apoptosis in ECM-detached cells, the overexpression of oncogenic Ras in ECM-attached cells results in enhanced sensitivity to exogenous cytochrome c. This sensitization was found to be due to upregulation of apoptosomal proteins (e.g. Apaf-1, pro-caspase-9) in an ERK/MAPK dependent manner. In aggregate, our data suggest that in addition to inhibiting the release of cytochrome c in both attachment and detachment, oncogenic Ras drives additional mechanisms that prevent apoptosome formation and caspase activation in detachment. Furthermore, our data support a model whereby ECM-attached cells containing oncogenic Ras mutations could be selectively eliminated by cytochrome c or agents that mimic its action.
Citation Format: Chelsea M. McCallister, Raju Rayavarapu, Nicholas Pagani, Brendan Heiden, Melissa Shaw, Sydeny Shuff, Zachary T. Schafer. Ras-mediated regulation of cytochrome c-induced caspase activation is dependent on the status of extracellular matrix attachment. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3563.
Abstract 3601: Evaluation and quantification of biomarkers of DNA damage in human plucked hair
Authors: Bonavita Aude-Marine , Walker Liam , Boanas Adam , Tonge Nicola , Tudor Gregory , Booth Cath , Reed Ben 
Published: July 2016

Abstract
The hair follicle is a well vascularised structure that contains rapidly dividing epithelial cells. As a result it is a potentially useful surrogate biomarker for less accessible but highly similar tissues, such as rapidly proliferating tumours. We have developed an ex vivo culture method to validate target expression changes following exposure to DNA damage and/or potential therapeutics. Proof of concept studies performed ex vivo can then inform the design of clinical validation studies. Earlier work evaluated the response of targets such as pERK, pAKT and pSMAD2 to various kinase inhibitors, whilst recently we have used the model to measure the DNA damage response (DDR) following exposure to UV radiation (as a model damaging agent) and more clinically relevant chemotherapeutic agents.
Human plucked hair was placed in maintenance media in the presence of known chemotherapeutic agents (such as Gemcitabine, DNA topoisomerase inhibitor I, Irinotecan and Paclitaxel) or exposed to 0.2-0.5J/cm2 UVB radiation. Hairs were then fixed at a range of time points post-exposure and longitudinal sections labelled for various markers including pChk1, gamma-H2AX, p53, Ki67 and thymine dimers (TDM1). Quantitative image analysis to measure the level of labelling was performed using an Aperio® ScanScope®.
Following UVB exposure thymine dimer formation occurred immediately on the hair and was stronger on the side directly facing the source of radiation. It was followed rapidly by phosphorylation of Chk1 localised in the inner root sheath at first (10min to 1h after injury), then gamma-H2AX and p53 induction in the outer root sheath. Further studies are looking at DNA damage response in an UV dose dependent manner.
Chemotherapeutic agents known for their different mechanism of actions were tested at two concentrations with various responses depending on their mechanism of action. For example, Gemcitabine, which is linked to DNA polymerase inhibition, strongly induced p53 after 24h but no gamma-H2AX activity was seen above background level. We have profiled the large panel of responses for each chemotherapeutic agent, over an acute time course.
The ex vivo plucked hair follicle method is a rapid and convenient way of studying the DDR induced by exposure to various DNA damage agents. This model allows for screening of novel chemotherapeutic agents to test their efficacy in preventing or treating DNA damage.
Citation Format: Aude-Marine Bonavita, Liam Walker, Adam Boanas, Nicola Tonge, Gregory Tudor, Cath Booth, Ben Reed. Evaluation and quantification of biomarkers of DNA damage in human plucked hair. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3601.
Abstract 361: Single cell detection of protein and RNA: Development of a novel method combining immunocytochemistry and in situ hybridization in breast cancer cells
Authors: Ma Lisa J. , Frank Richard T. , Li Xiaoxiao , Lai Steve , Schmidt Jeanette , Just Peggy , Becker-Catania Sara 
Published: July 2016

Abstract
Immunocytochemistry (ICC) utilizes antibodies to visualize the localization of specific proteins in cells while in situ hybridization (ISH) is a useful research tool for examining the presence and changes in levels of gene expression in cells. The ability to simultaneously visualize the co-localization of protein and RNA species in individual cells is necessary to address important biological questions. Additionally, studying both protein and RNA can be useful in cases where expression levels vary between mRNA and protein and to detect post-translational modifications. However, a combined technique has proved challenging due to the incompatibility of ICC and ISH protocols. Furthermore, traditional ISH methods have lacked sensitivity to detect low abundance RNA species and have limited multiplexing capability. Here, we describe a novel technique combining ICC staining with RNA ISH (based on the ViewRNA Assay), which utilizes branched DNA signal amplification technology allowing for single copy mRNA sensitivity. We demonstrate the utility and versatility of this technique using a variety of antibody and probe combinations relevant for cancer research. We compared expression of protein and mRNA of HER2, estrogen receptor alpha, and progesterone receptor in several breast cancer cell lines (MCF7, SKBR3, MDA-MB-175, MDA-MB-231, and BT474) known to express differential levels of these targets. We also compared expression of several microRNAs (let-7a, miR-17, miR-30d, miR-107, and miR-93) known to play a role in cancer development in combination with staining for proteins involved in proliferation (Ki-67), anti-apoptosis (survivin), and cell structure (tubulin). We show successful detection of low abundance RNA species together with various protein markers. This novel technique is a valuable tool not only for cancer researchers, but also for investigators across numerous fields in biological research.
Citation Format: Lisa J. Ma, Richard T. Frank, Xiaoxiao Li, Steve Lai, Jeanette Schmidt, Peggy Just, Sara Becker-Catania. Single cell detection of protein and RNA: Development of a novel method combining immunocytochemistry and in situ hybridization in breast cancer cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 361.
Abstract 3611: SMRT® sequencing of DNA samples extracted from formalin-fixed and paraffin embedded tissues
Authors: Baybayan Primo , Weiand Michael , Eng Kevin , Durin Guillaume , Kujawa Steve 
Published: July 2016

Abstract
Recent advances in next generation sequencing have led to the increased use of formalin-fixed and paraffin-embedded (FFPE) tissues for medical samples in disease and scientific research. Single Molecule Real-Time (SMRT®) sequencing offers a unique advantage in that it allows direct analysis of FFPE samples without amplification. However, obtaining ample long read information from FFPE samples has been a challenge due to the quality and quantity of the extracted DNA. DNA samples extracted from FFPE often contain damaged sites, including breaks in the backbone and missing or altered nucleotide bases, which directly impact sequencing and amplification. Additionally, the quality and quantity of the recovered DNA also vary depending on the extraction methods used.
We have evaluated the Adaptive Focused Acoustics (AFA™) system by Covaris® as a method for obtaining high molecular weight DNA suitable for SMRTbell template preparation and subsequent single molecule sequencing. Using this method, genomic DNA was extracted from normal kidney FFPE scrolls acquired from Cooperative Human Tissue Network (CHTN), University of Pennsylvania. Damaged sites present in the extracted DNA were repaired using a DNA Damage Repair step, and the treated DNA was constructed into SMRTbell libraries suitable for sequencing on the RSII System. Using the same repaired DNA, we also tested PCR efficiency of target gene regions of up to 5 kb. The resulting amplicons were constructed into SMRTbell templates for full-length sequencing on the RS II System.
We found the Adaptive Focused Acoustics (AFA™) system by Covaris® to be effective and efficient. This system is easy and simple to use, and the resulting DNA is compatible with SMRTbell™ library preparation for targeted and whole genome SMRT sequencing. The data presented here demonstrates single molecule sequencing of DNA samples extracted from tissues embedded in FFPE.
Citation Format: Primo Baybayan, Michael Weiand, Kevin Eng, Guillaume Durin, Steve Kujawa. SMRT® sequencing of DNA samples extracted from formalin-fixed and paraffin embedded tissues. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3611.