bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 437: Leveraging new methods in single-cell copy number analysis and clonotype detection to uncover and characterize hidden subclones within standard cell lines
Authors: Villarreal Enrique I. Velazquez , Kumar Vijay , Yin Yifeng , Carpten John D. , Craig David W. 
Published: August 2018

Abstract
Single-cell sequencing is an important and powerful tool for improving our understanding of cancer heterogeneity. While previous reports have largely focused on single-cell RNA-seq, we examined the utility of novel approaches for single-cell copy-number analysis and clonotype detection using 10x Chromium™ Technology capable of processing thousands of single cells. In contrast to bulk sequencing, this technology is able to call cell clonotypes down to 1% of 1,000 cell inputs, while providing detection of CNVs down to 100 Kb events on clones consisting of 10 or more cells. As a pilot study, we processed 300 single cells from COLO829 through the system, generating a barcoded short-read library, which was sequenced to a raw depth of approximately 600 million reads. Previous efforts had characterized COLO829 by bulk whole-genome sequencing of tumor/normal cell-line lineages grown and sequenced across four laboratories to help establish tumor/normal reference standards. We used barcode-aware bioinformatic analysis to recover reads derived from single cells, analyzing them in 20 Kb cassettes of reads providing both regional copy number and genome-wide ploidy estimates. This high resolution of CNV detection is enabled by aggregation of reads across cells within the same clone. Somewhat surprisingly, we find the presence of multiple clones within a single cell line growth evident by large-scale copy number changes, in some cases spanning entire chromosome arms. We show an ability to better resolve absolute copy number, whereas previous analysis approaches on bulk sequencing have lagged due to a reliance on indirect inferences. Consideration of prior publications on this cell line are consistent with the undescribed existence of clonal heterogeneity in these, and when considered with these data provide greater insight into copy number-driven events. Overall, our results suggest that single-cell copy number provides unique and important insight into larger-scale events, providing unique and distinct insight into cancer heterogeneity.
Citation Format: Enrique I. Velazquez Villarreal, Vijay Kumar, Yifeng Yin, John D. Carpten, David W. Craig. Leveraging new methods in single-cell copy number analysis and clonotype detection to uncover and characterize hidden subclones within standard cell lines [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 437.
Abstract 4370: Regulation of AGO2-KRAS interaction through epidermal growth factor receptor
Authors: Siebenaler Ronald F. , Shankar Sunita , Tien Jean C. , Dommeti Vijaya L. , Mody Malay , Kumar-Sinha Chandan , Chinnaiyan Arul M. 
Published: August 2018

Abstract
The RAS gene family is among the most commonly mutated genes within cancer. While much research has elucidated its major functions and downstream pathways, little progress has been made in successfully targeting RAS mutations. We recently identified Argonaute 2 (AGO2) of the RNA-induced silencing complex (RISC) as a novel partner of the Switch II domain of KRAS. We have found that stable knockdown of AGO2 in KRAS-dependent cell lines lead to a decrease in KRAS protein expression with a subsequent decrease in cellular proliferation. In addition, we observed a decrease in microRNA unwinding in the presence of mutant KRAS, suggesting this interaction inhibits the endogenous RNAi function of AGO2. Despite this clear connection between KRAS and AGO2 in KRAS mediated oncogenesis, the precise function of this interaction remains unclear in both normal and cancer biology.
In order to identify endogenous regulators of AGO2-RAS, we investigated the ability of EGFR signaling to modulate the AGO2-RAS interaction. We established two mouse embryonic fibroblast cell lines (NIH-3T3 and MEF) with complete knockout of AGO2. When compared to normal control cells, we found that knockout of AGO2 resulted in an increase in WT RAS-GTP activation levels, phosphorylation of Y1068-EGFR, and MAPK/ERK and PI3K/AKT signaling. Rescue of AGO2 knockout resulted in a return to normal levels of active RAS-GTP, pEGFR, and downstream signaling.
Recent studies have described EGFR phosphorylation of AGO2 under hypoxic cell conditions, resulting in the inhibition of AGO2 association with RISC members. In order to better characterize the relationship between EGFR-AGO2-RAS, we found that overnight serum starvation followed by stimulation with EGF led to a decrease in AGO2-RAS co-IP in WT KRAS cells. Blocking AGO2 phosphorylation with a Y393F mutant of AGO2 prevented AGO2-RAS dissociation following EGFR stimulation. While WT KRAS cell lines displayed regulation of AGO2-RAS via EGFR, the phosphorylation of AGO2Y393 was unable to disrupt the interaction of AGO2 with mutant KRAS following stimulation with EGF. Together these results suggest a unique EGFR-AGO2-RAS signaling axis, and its dysregulation by mutant KRAS could increase oncogenic growth through promotion of AGO2-RAS interaction in cancer.
Citation Format: Ronald F. Siebenaler, Sunita Shankar, Jean C. Tien, Vijaya L. Dommeti, Malay Mody, Chandan Kumar-Sinha, Arul M. Chinnaiyan. Regulation of AGO2-KRAS interaction through epidermal growth factor receptor [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 4370.
Abstract 4372: SET/PP2A/SHP-1/Lyn oncogenic signaling contributes to tumor aggressiveness in diffuse large B cell lymphoma
Authors: Chen Ji-Lin , Tsai Wen-Chun , Lan Tien-Yun , Huang Chun-Teng , Chu Pei-Yi , Lee Chia-Han , Lau Ka-Yi , Wang Wan-Lun , Chen Kuen-Feng , Shiau Chung-Wai , Liu Chun-Yu 
Published: August 2018

Abstract
Purpose:
Diffuse large B-cell lymphoma (DLBCL) is aggressive non-Hodgkin lymphoma. It is a heterogeneous disease and is classified as germinal center B-cell like (GCB) and activated B-cell like (ABC) subtypes according to gene-expression profiling. The oncogenic pathways in DLBCL are potential targets for new therapies. In present study, the role and regulation of SET/PP2A/SHP-1/Lyn axis in DLBCL were investigated.
Experimental design: U2932, OCL-Ly3, OCI-Ly7, SU-DHL-6 and DB DLBCL cell lines were used for this study. TD-19, a novel SET/PP2A protein-protein interaction inhibitor, was used to address the molecular events of SET signaling. Cell viability was measured by MTT assay. The apoptotic cells were examined by PI/Annexin V staining and Western blotting. SHP-1, Lyn and pLyn were analyzed by immunohistochemistry on lymphoma tissue microarrays from DLBCL patients.
Results:
We first examined the effects of two different SET inhibitors, TD-19 that is a SET/PP2A protein protein interaction inhibitor, and FTY720 which is a sphingosine analogue that targets SET, on DLBCL cells. TD-19 and FTY720 significantly decreased cell viability and induced apoptosis. SET inhibition activated PP2A and SHP-1 by reducing pPP2AY307 and pSHP-1S591 and inactivated Lyn by decreasing pLynY396. Overexpression of SET rescued these molecular events, and promoted cell growth and migration. Interestingly, we observed the level of SET was declined by TD-19 and TFY720 treatment. We hypothesized Lyn might up-regulate SET expression. Overexpression of Lyn increased SET level, and was accompanied with phosphorylation of PP2A (pPP2AY307) and SHP-1 (pSHP-1S591). Lyn elevated cell growth and migration and suppressed PP2A and SHP-1 activities. Moreover, exogenous SET restored the FTY720- and TD-19-suppressed pSHP-1 and pLyn. Immunohistochemically, high SHP-1 level was linked to low pLyn level of patient with DLBCL and vice versa.
Conclusion: This study established the existence of positive feedback of SET/PP2A/SHP-1/Lyn axis in DLBCL cells, and targeting SET could disrupt this regulation.
Citation Format: Ji-Lin Chen, Wen-Chun Tsai, Tien-Yun Lan, Chun-Teng Huang, Pei-Yi Chu, Chia-Han Lee, Ka-Yi Lau, Wan-Lun Wang, Kuen-Feng Chen, Chung-Wai Shiau, Chun-Yu Liu. SET/PP2A/SHP-1/Lyn oncogenic signaling contributes to tumor aggressiveness in diffuse large B cell lymphoma [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 4372.
Abstract 4378: Novel CARP-1- H2AX interaction regulates apoptosis in breast cancer cells
Authors: Sekhar Sreeja C. , Cheriyan Vino T. , Rishi Arun K. 
Published: August 2018

Abstract
CCAR1/CARP-1 is a peri-nuclear phosphoprotein that regulates apoptosis signaling by breast cancer therapeutic Doxorubicin and a novel class of CARP-1 Functional Mimetic (CFM) compounds. Prior reports have established that Doxorubicin exposure causes DNA damage in cells. Phosphorylation of histone 2AX (often referred as γH2AX) protein is involved in regulating DNA damage repair and apoptosis signaling. Although, currently it is unclear whether CFMs also induce DNA damage, we found that Doxorubicin or CFM-4.16 treatments caused elevated CARP-1 and γH2AX in HBC cells. In fact, a robust nuclear or peri-nuclear co-localization of CARP-1 and γH2AX occurred in HBC cells undergoing apoptosis. Knock-down of CARP-1 abolished increase of CARP-1 and γH2AX, their co-localization, and apoptosis in CFM-4.16 or Doxorubicin-treated HBC cells. We found that CARP-1 directly binds with H2AX, and the H2AX-interacting epitope is located within CARP-1 amino acids 600 to 652. We generated HBC cells that have stable expression of myc-tagged, wild-type CARP-1 (1-1150) or CARP-1 (1-1150; Δ600-652) mutant. Further analyses revealed that CARP-1 (1-1150), but not CARP-1 (1-1150; Δ600-652) mutant, interacted with H2AX. Moreover, HBC cells expressing CARP-1 (1-1150; Δ600-652) mutant were resistant to apoptosis by Doxorubicin or CFM-4.16, and had diminished levels of γH2AX, when compared with their counterparts expressing wild-type CARP-1. We have earlier reported involvement of the Stress-Activated Protein Kinases (SAPKs) such as p38 and JNKs in apoptosis by Doxorubicin or CFMs. Since the PI3K family of serine-threonine kinases ATM/ATR, as well as JNK SAPKs, phosphorylate serine-139 of H2AX following DNA damage, our current studies are investigating whether H2AX binding with CARP-1 serves to facilitate phosphorylation of CARP-1 and H2AX proteins for transduction of apoptosis signaling.
Citation Format: Sreeja C. Sekhar, Vino T. Cheriyan, Arun K. Rishi. Novel CARP-1- H2AX interaction regulates apoptosis in 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 4378.
Abstract 4381: Cordycepin promotes apoptosis in renal carcinoma cells by activating the MKK7-JNK signaling pathway through inhibition of cFLIPL expression
Authors: Jang Ik-Soon , Jang Hyun-Jin , Jo Eunbi 
Published: August 2018

Abstract
Cellular FLICE inhibitory protein (c-FLIP) is a key anti-apoptotic regulator that associates with the signaling complex downstream of NF-κB, negatively interfering with apoptotic signaling. The role of c-FLIP downregulation by negative regulation of NF-κB signaling during apoptosis is poorly understood. Here, we demonstrate that NF-κB-mediated c-FLIPL negatively regulates the JNK signaling pathway, and that cordycepin treatment of human renal cancer cells leads to apoptosis induction through c-FLIPL inhibition. TNF-α-induced inflammatory microenvironments stimulated NF-κB signaling and the c-FLIP long form (c-FLIPL) in TK-10 cells. Specifically, cordycepin inhibited TNF-α-mediated NF-κB activation, which induced renal cancer cell apoptosis. Cordycepin downregulated GADD45B and c-FLIPL, but upregulated MKK7 and phospho-JNK, by preventing nuclear mobilization of NF-κB. Furthermore, siRNA-mediated knockdown of GADD45B in cordycepin-treated TK-10 cells considerably increased MKK7 compared to cordycepin alone. siRNA-mediated knockdown of cFLIPL prevented TNF-α-induced JNK inactivation, whereas c-FLIPL overexpression inhibited cordycepin-mediated JNK activation. The JNK inhibitor SP600125 strongly inhibited Bax expression. In nude mice, cordycepin significantly decreased tumor volume. Taken together, the results indicate that cordycepin inhibits TNF-α-mediated NF-κB/GADD45B signaling, which activates the MKK7-JNK signaling pathway through inhibition of c-FLIPL expression, thus inducing TK-10 cell apoptosis.
Citation Format: Ik-Soon Jang, Hyun-Jin Jang, Eunbi Jo. Cordycepin promotes apoptosis in renal carcinoma cells by activating the MKK7-JNK signaling pathway through inhibition of cFLIPL expression [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 4381.
Abstract 4383: CD44s is a crucial ATG7 downstream regulator for formation of sphere, a key stem-like property, invasion and lung metastasis of human bladder cancer/BC cells
Authors: Hua Xiaohui , Che Xun , Xu Jiheng , Huang Chuanshu , Huang Grace , Dai Wei 
Published: August 2018

Abstract
Over half a million US residents are suffering with bladder cancer (BC), which costs a total $4 billion in treatment annually. Although recent studies report that autophagy-related gene 7 (ATG7) is overexpressed in BCs, the regulatory effects of ATG7 on stem-like phenotypes and invasion have not been explored yet. Current studies demonstrated that the deficiency of ATG7 by its specific shRNA dramatically reduced Sphere formation and invasion in vitro, as well as lung metastasis in vivo in invasive BC cells. Further studies indicated that the knockdown of ATG7 attenuated the expression of CD44 and CD133, while ectopic introduction of CD44s, but not CD133, was capable of completely restoring sphere formation, invasion, and lung metastasis in T24T(shATG7) cells. Mechanistic studies revealed that ATG7 overexpression stabilized CD44s proteins accompanied with upregulating USP28 proteins. Upregulated USP28 was able to bind to CD44s and remove the ubiquitin group from CD44's protein, resulting in the stabilization of CD44s protein. Moreover, inhibition of ATG7 stabilized AUF1 protein and in turn reduced tet1 mRNA stability and expression, which was able to demethylate usp28 promoter, thereby reduced USP28 expression, finally promoting CD44s degradation. In addition, CD44s was defined to inhibit degradation of RhoGDIβ, which in turn promotes BC invasion. Our results demonstrate that CD44s is a key ATG7 downstream regulator of the sphere formation, invasion, and metastasis of BCs, providing significant insight into understanding the BC invasions, metastasis, and stem-like properties.
Citation Format: Xiaohui Hua, Xun Che, Jiheng Xu, Chuanshu Huang, Grace Huang, Wei Dai. CD44s is a crucial ATG7 downstream regulator for formation of sphere, a key stem-like property, invasion and lung metastasis of human bladder cancer/BC 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 4383.
Abstract 4384: The differential induction of apoptosis in MCF-7 and MDA-MB-231 breast cancer cells in response to RBBP6 silencing is associated with p53 expression
Authors: Moela Pontsho , Motadi Lesetja Raymond 
Published: August 2018

Abstract
Breast cancer remains a female-related health problem on a global scale, accounting for over a million newly estimated cases that are still on the rise. More than 50% cases of breast tumorigenesis are due to mutations or inactivation of p53, a tumor suppressor gene involved in the regulation of cell cycle and apoptosis. In breast cancer, the frequency of TP53 mutations varies greatly between the heterogeneous subtypes, with basal-like breast cancers having the highest frequency whereas the luminal subtypes have been shown to generally express wt. p53. Active p53 is responsible for sensing any cellular stress signal with a potential to damage DNA, thus deciding the cell's fate depending on whether the damage is reversible or not. Therefore cellular p53 levels remain in check by the MDM2 regulatory protein, which promotes the degradation of unwanted p53 via a negative feedback loop mechanism using its E3 ligase activity. However, this interaction between MDM2 and wild-type p53 is cancer promoting in the same way that E6 oncoprotein is capable of leading to the degradation of wild-type p53 in cervical cancer. Negative regulators of p53, therefore, threaten cancer repression and play a role in drug resistance among cancer patients. Of particular interest in this study is RBBP6, another negative regulator of p53 that uses the E3 ligase activity as well in order to promote p53 degradation. Previous studies have shown that silencing RBBP6 in breast cancer restores p53 followed by apoptosis induction. However, it is unclear whether the observed apoptosis is linked to the recovered p53. To test this hypothesis, we aim to analyze the differential susceptibilities of MCF-7 and MDA-MB-231 cells expressing wt. p53 and mt. p53, respectively, to RBBP6 silencing. Real-time cell analysis revealed a clear distinction between the growth of the two cell lines, with MCF-7 showing a significantly reduced proliferation in comparison to MDA-MB-231. Apoptosis induction was also high in MCF-7 AND lower is MDA-MB-231, as was further confirmed by the differential expression of pro-apoptotic genes between the two cell lines. These findings suggest that difference in p53 statuses of the two cell lines play a role in apoptosis induced by RBBP6 silencing. These findings are necessary for reaching a better understanding of molecular mechanisms that impact patient response and resistance to candidate therapeutics and may be helpful in developing more effective treatment strategies for different subtypes of breast cancer.
Citation Format: Pontsho Moela, Lesetja Raymond Motadi. The differential induction of apoptosis in MCF-7 and MDA-MB-231 breast cancer cells in response to RBBP6 silencing is associated with p53 expression [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 4384.
Abstract 4388: Anti-cancer effects of oleuropein olive leaf extract in K562 leukemia cells
Authors: Fagan Sophia , Fulco Natalie , Gilbertson Justin , Dyke Aaron R. Van , Phelan Shelley A. 
Published: August 2018

Abstract
Olive leaves come from a Mediterranean plant that many believe to have positive effects on human health, including anti-cancer properties. Oleuropein is one of the two main phenolic compounds derived from olive leaves, and it has been shown to increase apoptosis in many types of cancer cells. Numerous studies have found that the polyphenols contained in olive leaves possess strong antioxidant properties, suggesting that the compound could be effective in anti-cancer treatments. The purpose of this study was to examine the effects of oleuropein extract on cell growth and viability in K562 human leukemia cells, and begin to investigate possible molecular mechanisms of action. We purified our own extract from olive leaves for these studies. Oleuropein was microwave extracted from olive leaf powder using methanol and water as solvent. The oleuropein was successfully identified using HPLC to characterize elution time in comparison to an authentic standard. HPLC was then used in purification and fractions were lyophilized. Isolated oleuropein was greater than 94% in comparison to the authentic standard. We next demonstrated that K562 cells treated with 50-150 ug/ml of oleuropein exhibited significant reduction in cell growth and cell viability after four days when compared to 70% ethanol-treated controls. This effect was markedly greater after 6 days . Current studies are being conducted to determine the most effective concentration and duration of treatment for oleuropein-induced cell death. We are also examining cellular cyytotoxicity and cell cycle progression in these experiments using LDH assay and cell cycle staging, and further studies are being conducted to examine inflammatory and antioxidant pathways for their involvement in the anti-cancer effect of the compound in these cells. Given the observation that many of the cytotoxic effects of oleuropein are cancer-cell specific, this research provides a promising new avenue for the use of natural products as anti-cancer agents.
Citation Format: Sophia Fagan, Natalie Fulco, Justin Gilbertson, Aaron R. Van Dyke, Shelley A. Phelan. Anti-cancer effects of oleuropein olive leaf extract in K562 leukemia 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 4388.
Abstract 4397: Tak-1 inhibition re-sensitizes cancer cells to TNFα
Authors: Scarneo Scott , Sell Madeline , Totzke Juliane , Carlson David , Hughes Phillip , Haystead Tim 
Published: August 2018

Abstract
Identifying new pharmaceutical targets in cancer has been a long lasting goal of academia. Complex genomic changes coupled with a cancer cell's ability to adapt make tumors particularly difficult to target. To this end, we have identified the TAK1 kinase in the TNFα pathway as a potential mediator of cell survival or apoptosis. Here we evaluate the apoptotic effects of a novel TAK1 inhibitor, Takinib. The selectivity of Takinib was established with an IC50 of 9nm for TAK1, followed by an IC50 for IRAK4 and IRAK1 at 120nm and 390nm respectively. Treatment of MDA-MB-231 cells with Takinib on its own is not sufficient to induce consequential cell death. However, combination therapy with TNFα induces caspase 3/7 activity and subsequent cell death in a dose-dependent manner. Genetic knock out of TAK1 expression in MDA-MB-231 cells with the CRISPR/Cas9 system significantly sensitized previous resistant cells to TNFα. Furthermore, we have shown that activation of human THP-1 cells with LPS is sufficient to produce TNFα levels necessary to facilitate Takinib mediated cell death, indicating that potential immunotherapy applications may be possible. Together these findings support the idea that TAK1 may be an effective target in the TNFα pathway, shifting the cellular mechanisms from pro survival to pro apoptosis.
Citation Format: Scott Scarneo, Madeline Sell, Juliane Totzke, David Carlson, Phillip Hughes, Tim Haystead. Tak-1 inhibition re-sensitizes cancer cells to TNFα [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 4397.