bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3035: Decomposing oncogenic transcriptional signatures to generate maps of divergent cellular states
Authors: Kim William J. , Hahn William C. , Mesirov Jill , Tamayo Pablo 
Published: July 2017

Abstract
The systematic sequencing of the cancer genome has provided a powerful framework for identifying genetic alterations in cancer. However, a deeper understanding of the functional consequences of these alterations is necessary to guide appropriate therapeutic strategies. Here, we describe Onco-GPS (OncoGenic Positioning System), a data-driven analysis framework, and associated experimental and computational methodology, to organize individual tumor samples with shared oncogenic alterations onto a reference map defined by their underlying cellular states. Using this approach, we generated series of RAS/MAPK sub-signatures that reflect known and novel downstream pathways. These sub-signatures were then used to classify KRAS and BRAF mutant cancers into sub groups or cell states, as represented in the novel visual paradigm “OncoGPS map”. OncoGPS approach was first applied to cancers with BRAF mutations. The approach not only accurately classified three groups of BRAF mutant cancers that aligned with sensitivity to BRAF inhibitors, but also identified resistance mechanisms associated with each state, validating the overall approach. OncoGPS also identified four major cell states associated with KRAS mutant cancers. Further characterization of the four cell states showed that multiple molecular features representing epithelial-EMT states and activation of NF-κB pathway delineated two major “axes” of KRAS mutant cancers. In addition to the pathways and cell states defined in each group, the OncoGPS approach is able to identify effective drug combinations which was experimentally tested and confirmed. These results show that the Onco-GPS is an effective analytic framework to explore the complex landscape of oncogenic cellular states across cancers, and a powerful framework to summarize knowledge, establish relationships, and generate more effective disease models for research or as part of individualized precision medicine paradigms.
Citation Format: William J. Kim, William C. Hahn, Jill Mesirov, Pablo Tamayo. Decomposing oncogenic transcriptional signatures to generate maps of divergent cellular states [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 3035. doi:10.1158/1538-7445.AM2017-3035
Abstract 306: Antitumor effect of Wee1 inhibitor in gastric cancer cells
Authors: Kim Seongyeong , Min Ahrum , Kim So Hyeon , Ha Dong Hyeon , Jang Hyemin , Kim Yu JIn , Kim Hee Jun , Lee Kyung-Hun , Kim Tae-Yong , Oh Do-Youn , Bang Yung-Jue , Im Seock-Ah 
Published: July 2017

Abstract
Background: A cell cycle checkpoint is a key step to watch any damages and, it is needed to maintain genomic stability. Thus, to jeopardize cell cycle checkpoint is an attractive strategy for cancer treatment. Wee1 is a G2 cell cycle regulator that phosphorylate cdc2 on tyrosine 15 for inhibiting its activity. The activation of Wee1 can delay G2 phase progression and cells can have a chance to repair DNA damages. Therefore, to inhibit wee1 can accelerate DNA damage accumulation in the cell. AZD1775 is a first-in-class wee1 inhibitor. So far, previous studies showed the antitumor effect of AZD1775 as a mono-therapeutic agent or combination treatment with other chemo-agents. However, the activity of wee1 in gastric cancer (GC) cells is not yet fully understood. Thus, we would like to study whether AZD1775 has an antitumor effect against GC or not.
Materials and methods: We determined the antitumor effects of AZD1775 on GC cells using a cytotoxicity assay, cell cycle analysis, immunofluorescence assay and western blotting by AZD1775 treatment.
Results: AZD1775 effectively inhibit GC cell proliferation. The TP53 gene status or p-Wee1 expression levels were not associated with AZD1775 sensitivity. AZD1775 effectively down-regulated p-Wee1 and p-cdc2 expressions in SNU-601, a sensitive cell line. However, these effects were not significant in KATO-III cells, which is less sensitive to AZD1775. Cell cycle analysis revealed that the cells had different responses by AZD1775 treatment. SNU-601 cells were enriched in S phase when we decide cell cycle only by its DNA contents. However, KATO-III cells were arrested in G2/M phase. The sub-G1 population was dramatically increased only in SNU-601 cells. A population of BrdU-positive and p-HH3 positive cells was significantly increased in the SNU-601 cells which indicate that premature mitosis was increased. However, no differences were observed in KATO-III cells. Moreover, due to premature mitotic entry, multi-nucleated cells were observed only in SNU-601 cells.
Conclusion: AZD1775 effectively inhibited the growth of GC cell lines. The inhibition of cdc2 by AZD1775 was observed only in a sensitive cell line. Moreover, early mitotic entry was induced by AZD1775, and it led the induction of mitotic catastrophe. This result indicates that AZD1775 have an antitumor effect on GC and the possibility of adoption to the clinical trial design.
Citation Format: Seongyeong Kim, Ahrum Min, So Hyeon Kim, Dong Hyeon Ha, Hyemin Jang, Yu JIn Kim, Hee Jun Kim, Kyung-Hun Lee, Tae-Yong Kim, Do-Youn Oh, Yung-Jue Bang, Seock-Ah Im. Antitumor effect of Wee1 inhibitor in gastric 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 306. doi:10.1158/1538-7445.AM2017-306
Abstract 3064: Retinoic acid: An effective therapy for basal-like breast cancer
Authors: Coyle Krysta Mila , Dean Cheryl A. , Vidovic Dejan , Weaver Ian C. , Giacomantonio Carman A. , Marcato Paola 
Published: July 2017

Abstract
We have identified a novel strategy to identify breast cancer patients who will benefit from an existing anti-cancer agent, retinoic acid (RA). While RA has not yet achieved success in the treatment of breast cancers, we hypothesized that it can be an effective therapy for a subset of triple-negative breast cancer (TNBC) patients. TNBC is among the most aggressive breast cancers, and lacks targeted therapies. TNBCs can be further subtyped into basal-like and claudin-low, which differ in gene expression and drug sensitivities. Understanding the molecular basis of these subtypes will lead to the development of more effective treatment options for TNBC. To test this hypothesis, we performed tumor growth assays on TNBC cell lines and patient-derived xenografts (PDXs). We found that RA treatment decreased the tumor growth of four basal-like TNBC cell lines (MDA-MB-468, HCC70, SUM149, HCC1937). In contrast, RA increased the tumor growth of two claudin-low TNBC cell lines (MDA-MB-231, MDA-MB-436). Gene expression and methylation analysis of these affected cell lines revealed subtype-specific expression of RA-inducible genes due to silencing by DNA methylation, e.g. of the RA-inducible tumor-suppressor gene RARRES1. RARRES1 is silenced by methylation in claudin-low cell lines, but is hypomethylated and expressed in basal-like cells. Use of the subtype-specific expression and methylation profiles allowed us to accurately predict the response of 4 PDXs to RA treatment. Continued classification of TNBCs into these two subtypes will enable clinical use of RA, in part due to the subtype-specific hypomethylation of RA-inducible tumor suppressor genes including RARRES1. We have identified additional subtype-specific biomarkers which can predict the response of patient tumors to RA treatment, thus identifying a novel targeted therapy strategy for TNBCs.
Citation Format: Krysta Mila Coyle, Cheryl A. Dean, Dejan Vidovic, Ian C. Weaver, Carman A. Giacomantonio, Paola Marcato. Retinoic acid: An effective therapy for basal-like breast cancer [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 3064. doi:10.1158/1538-7445.AM2017-3064
Abstract 3067: Galectin-3, a target for KRAS-addicted lung cancer
Authors: Seguin Laetitia , Camargo Maria F. , Wettersten Hiromi I. , Kato Shumei , Schalscha Tami von , Elliott Kathryn C. , Weis Sara M. , Cheresh David A. 
Published: July 2017

Abstract
KRAS-mutant cancers are notoriously therapy-resistant. While responsible for oncogenesis, mutant KRAS or the sustained activation of KRAS-driven effectors may or may not be required throughout the course of cancer progression. Thus, understanding which tumors remain dependent on oncogenic KRAS could lead to the identification of unique vulnerabilities and opportunities to treat them. We previously discovered that the carbohydrate-binding Galectin-3 (Gal-3) brings together KRAS with integrin αvβ3 at the cell membrane in epithelial cancer cells to promote tumor progression. Here, we show that by directly binding to the cell surface receptor integrin αvβ3, Gal-3 drives addiction to oncogenic KRAS by enhancing macropinocytosis and reducing mitochondrial reactive oxygen species (ROS). This pathway drives increased expression of SOD2, a superoxide dismutase that clears mitochondrial ROS to protect against cell death. Targeting Gal-3 with a clinically active drug decreases macropinocytosis and increases ROS to eradicate KRAS-addicted lung cancer in patient-derived xenografts and spontaneous KRAS-driven lung cancer in mice. Our work reveals Gal-3 as a druggable target for KRAS-addicted lung cancer, and indicates integrin αvβ3 as a biomarker to identify this dependence.
Citation Format: Laetitia Seguin, Maria F. Camargo, Hiromi I. Wettersten, Shumei Kato, Tami von Schalscha, Kathryn C. Elliott, Sara M. Weis, David A. Cheresh. Galectin-3, a target for KRAS-addicted lung cancer [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 3067. doi:10.1158/1538-7445.AM2017-3067
Abstract 307: TRIB3 regulates cell cycle progression and programmed cell death in non-small cell lung cancer
Authors: Almiman Abeer , Nie Daotai , Adom Jamila 
Published: July 2017

Abstract
Introduction: The pseudokinase Tribbles pseudokinase 3 (TRIB3) is known as a regulator in cellular responses to a variety of stresses such as glucose insufficiency and (ER) stress. TRIB3 has been described in some studies as a tumor suppressor due to its effect on inactivating PI3K/Akt pathway, but other studies suggest TRIB3 as a stimulator of tumor progression. In this study, we aimed to define the functions of TRIB3 in in non-small cell lung cancer.
Methods: TRIB3 expression was altered using a lentiviral vector to overexpress TRIB3 in non-small cell lung cancer. A CRISPR-CAS9 construct with guiding sequence matching to TRIB3 gene was used to knock out its expression. Cell proliferation was evaluated using MTS and trypan blue assays. Boyden chamber assay was used to assess the cell migration while cell cycle phases were determined using flow cytometry. Heatmap analysis was performed to assess the changes in the expressions of genes in cell cycle progression and apoptosis.
Results: TRIB3 overexpression led to reduced cell proliferation and migration. Moreover, it contributed to the increased of cell cycle arrest at G0/G1 phase. QPCR analyses of cell cycle related genes showed an upregulation of CDK inhibitors in (NCI-H358) TRIB3 overexpression cells, while depletion of TRIB3 led to the down-regulation of CDK inhibitors. TRIB3 overexpression led to downregulation of LC3B and other autophagy markers while increasing the expression of apoptotic genes.
Conclusion: Increased TRIB3 expression in non-small cell lung cancer cells inhibited proliferation by blocking cell cycle progression through the upregulation of CDK inhibitors, led to activation of cell death through apoptosis. Our study reveals a significant role of TRIB3 in regulating cell cycle progression, apoptosis and autophagy.
Citation Format: Abeer Almiman, Daotai Nie, Jamila Adom. TRIB3 regulates cell cycle progression and programmed cell death in non-small cell lung cancer [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 307. doi:10.1158/1538-7445.AM2017-307
Abstract 3074: Selective lethality of cisplatin in pancreatic cancer is dependent on mitotic functions of BRCA2
Authors: Orelli Barbara , Maurer Hans C. , Palermo Carmine , Sastra Steven A. , Olive Kenneth P. 
Published: July 2017

Abstract
Pancreatic ductal adenocarcinoma (PDA) is an aggressive malignancy with a 5-year survival rate of just 8%. Mutations in BRCA2 are among the most common known germline alterations that predispose to PDA. While the sensitivity of BRCA2-mutant breast and ovarian tumors to platinum compounds has long been recognized, the recent approval a PARP inhibitor in BRCA2-mutant ovarian cancer confers hope that such tumors might be targeted with greatly reduced toxicity. To test whether PDA exhibits a similar genetic susceptibility to these agents, we carried out preclinical intervention studies in Kras/p53-mutant genetically engineered mouse models (KPC mice) with or without the additional mutation of BRCA2 (KPCB2 mice). Mice were enrolled based on 3D ultrasound imaging criteria to assure similar initial tumor burden, and tumor growth was monitored longitudinally by ultrasound. To our surprise, loss of Brca2 failed to sensitize pancreatic tumors to Parp inhibition and did not provide additional benefit in combination with cisplatin treatment. By contrast, cisplatin induced substantial regressions in most KPCB2 tumors, leading to a &gt;3-fold increase in overall survival, while having no effect on the growth or survival of mice with wild-type BRCA2. More surprisingly, the efficacy of cisplatin was not shared with oxaliplatin, even at higher doses.
While BRCA2 is primarily known for its role in homology-directed repair, a network biology analysis of the function of BRCA2 in human pancreatic cancer led us to investigate the role of BRCA2 in mitosis. Wild type BRCA2 protein localizes to the midbody- a structure formed during the final stages of telophase- and plays and poorly understood role in the final abscission of cytoplasm between two dividing cells. Timelapse video microscopy of KPCB2 tumor cells treated once weekly for 2 hours with cisplatin revealed the frequent induction of endoreduplication and eventual formation of polyploid giant cells subsequent death. Similar cells were found throughout KPCB2 tumors during regression in response to cisplatin treatment, but were largely absent from tumors in other treatment arms. Mechanism studies found that BRCA2 deficient PDA cells are susceptible to replicative stress following cisplatin treatment that selectively leads to the formation of radial chromosomes that cannot be resolved during mitosis. These studies argue for the consideration of cisplatin-based (rather than oxaliplatin-based) regimens for the treatment of BRCA2-mutant pancreatic tumors.
Citation Format: Barbara Orelli, Hans C. Maurer, Carmine Palermo, Steven A. Sastra, Kenneth P. Olive. Selective lethality of cisplatin in pancreatic cancer is dependent on mitotic functions of BRCA2 [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 3074. doi:10.1158/1538-7445.AM2017-3074
Abstract 3078: The role of extracellular vesicles in chemotherapy resistance in gastric cancer
Authors: Cassinela Edson , Landemberger Michele C. , Oliveira Gabriela P. de , Martins Vilma Regina 
Published: July 2017

Abstract
Gastric adenocarcinoma (GAd) is the fourth most common cancer and the second cause of cancer death in the world. Chemotherapy has been largely used to treat this disease however acquired drug resistance is a common event and is associated to the development of new more aggressive clones of tumor cells. Herein, a gastric adenocarcinoma cell line (AGS) resistant to the 5-fluorouracil (rAGS-FU) was generated in order to establish mechanisms associated to acquire drug resistance. In the presence of 5-FU (10μM) resistant cells show a 2-3 times higher proliferation ratio than parental cells, a plating efficiency of 38% compared to 1% of parental cells and a higher invasive phenotype. Remarkable, when compared to parental cells, rAGS-FU resistant cells secreted 2-3 times more extracellular vesicles, EVs (85-175nm). When parental cells were treated with EVs from rAGS-5-FU resistant cells they acquired the same phenotype of the latter cells regarding higher proliferation, plating efficiency and invasion. The proteomic analysis of parental and rAGS-FU cells showed 306 differentially expressed proteins, while 66 differentially expressed proteins were found when EVs secreted from these cells were compared. Our data suggest that cells resistant to chemotherapy have a more aggressive phenotype and are able to transfer these characteristics to non-resistant cells. These findings point to mechanisms of chemoresistance mediated by components that are carried from cell to cell by EVs, what may indicate novel approaches that can be addressed to impair drug resistance and improve treatment response.
Supported by FAPESP
Citation Format: Edson Cassinela, Michele C. Landemberger, Gabriela P. de Oliveira, Vilma Regina Martins. The role of extracellular vesicles in chemotherapy resistance in gastric cancer [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 3078. doi:10.1158/1538-7445.AM2017-3078
Abstract 3082: Deficient NOXA in HER2-amplified breast cancer drives kinase inhibitor resistance
Authors: Floros Konstantinos V. , Song Kyung-A , Lochmann Timothy L. , Hughes Mark T. , Heisey Daniel A. , Harada Hisashi , Hu Bin , Koblinski Jennifer , Souers Andrew J. , Leverson Joel D. , Faber Anthony C. 
Published: July 2017

Abstract
The purpose of this study is the development of a novel combination therapy that targets HER2-amplified breast cancer. About one quarter of breast cancers harbor amplification of HER2. HER2 is a transmembrane receptor tyrosine kinase (RTK) belonging to the ERBB family of receptors (ERBB1-4). Upon hetero- and homo-dimerization, HER2 activates several key intracellular pathways, regulating many cellular functions including proliferation and survival. HER2 inhibitors (HER2i) (e.g. the receptor tyrosine kinase (RTK) inhibitor, lapatinib) are now part of standard care for treating HER2-amplified breast cancers. However, despite their anti-cancer benefit, these drugs have limited efficacy as monotherapies, which contrasts to other RTK inhibitors in other RTK-driven cancers. To better understand this apparent dichotomy, in the present study, we evaluated potential modifiers of HER2i therapy. Here, we found that the pro-apoptotic NOXA, a member of the B-cell CLL/lymphoma 2 (BCL2) family which acts mainly via inhibitory binding of the pro-survival MCL-1, was markedly down-regulated in breast cancers compared to other cancers, and this was largely attributed to the HER2-amplified subset. Experimentally, overexpressing NOXA or silencing MCL-1 dramatically sensitizes HER2 amplified breast cancer cell lines to lapatinib via apoptosis. Consistently, pharmaceutical inhibition of MCL-1 sensitizes HER2-amplified breast cancers to lapatinib in vitro and in vivo. Mechanistically, disruption of MCL-1:BIM complexes and MCL-1:BAK underlie dual HER2i/MCL-1i therapy. Therefore, deficient NOXA expression constitutes a bonafide apoptotic block in HER2 amplified breast cancers, contributes to mitigated HER2i responses, and presents a rational combination therapy that may improve HER2i responses.
Citation Format: Konstantinos V. Floros, Kyung-A Song, Timothy L. Lochmann, Mark T. Hughes, Daniel A. Heisey, Hisashi Harada, Bin Hu, Jennifer Koblinski, Andrew J. Souers, Joel D. Leverson, Anthony C. Faber. Deficient NOXA in HER2-amplified breast cancer drives kinase inhibitor resistance [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 3082. doi:10.1158/1538-7445.AM2017-3082
Abstract 3084: Therapeutic implications of sex hormone signaling in melanoma
Authors: Natale Christopher , Zhang Junqian , Dahal Ankit , Ridky Todd 
Published: July 2017

Abstract
Female gender, early age of first birth, and multiparity are associated with less aggressive melanoma; however, the mechanisms underlying the apparent clinical benefit are undefined. Previously we reported that 17β-estradiol drives melanocyte differentiation through G-protein coupled estrogen receptor (GPER), a nonclassical sex hormone receptor. Here, we use genetically-defined human skin xenograft melanoma to show that pregnancy antagonizes oncogenic BRAF and inhibits melanomagenesis. Transient GPER activation drives stable melanocyte differentiation that persists after removal of the activating ligand. Consistent with this, brief exposure of melanoma cells to GPER agonists prior to xenografting inhibited subsequent tumor growth. Systemic treatment with GPER agonists cooperated with PD-1 blockade in melanoma bearing mice to greatly prolong survival longer than that observed with either agent alone. The combination of differentiation-based therapies with immunotherapy may have significant therapeutic benefit for melanoma.
Citation Format: Christopher Natale, Junqian Zhang, Ankit Dahal, Todd Ridky. Therapeutic implications of sex hormone signaling in melanoma [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 3084. doi:10.1158/1538-7445.AM2017-3084