tbuckley/cabot-search huggingface dataset:
Abstract 1081: APC regulation of breast cancer therapeutic resistance
Authors: Anne Arnason, Monica VanKlompenberg, Jenifer R. Prosperi
Journal: Cancer Research (2017)

Abstract Resistance to chemotherapy is one of the leading causes of death from breast cancer. Our lab discovered that Adenomatous Polyposis Coli (APC) loss in breast cancer cells results in an elevation of tumor-initiating cells (TICs) and resistance to chemotherapy-induced apoptosis. Given that TICs are often most resistant to standard chemotherapeutic compounds, we sought to understand the mechanism responsible for APC-mediated TIC enhancement. Our hypothesis is that the molecular mechanism involved in chemotherapeutic resistance parallels that promoting the TICs. APC-mutant cells have amplified activation of signal transducer and activator of transcription 3 (STAT3). Interestingly, inhibition of STAT3 with a small molecule inhibitor A69 decreases the TIC population and restores drug sensitivity. Studies are ongoing in the laboratory to investigate other molecular signaling pathways involved in APC-mediated enhanced TIC population and therapy resistance. These data have begun to reveal the molecular mechanisms of APC loss in breast cancer that can guide future treatment plans to counteract chemotherapeutic resistance. Note: This abstract was not presented at the meeting. Citation Format: Anne Arnason, Monica VanKlompenberg, Jenifer R. Prosperi. APC regulation of breast cancer therapeutic 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 1081. doi:10.1158/1538-7445.AM2017-1081
Abstract 5369: Epigenetic, transciptomic and ubiquitomic changes associated with BAP1 loss in uveal melanoma
Authors: Stefan Kurtenbach, Jeffim N. Kuznetsov, Matthew G. Field, Rohit Reddy, Margaret I. Sanchez, Christina L. Decatur, J William Harbour
Journal: Cancer Research (2017)

Abstract Uveal melanoma (UM) is the most common primary and aggressive ocular cancer. Up to 50% of the patients develop metastasis, which are notoriously resistant to all forms of therapy and despite medical treatment leads to death within a mean time of 5-7 months, with a mortality rate of over 90%. We previously described that gene expression profiling can be used to classy UM tumors into two basic categories, class 1 (low metastatic risk) and class 2 (high metastatic risk). We further described that inactivating mutations in the ubiquitin hydrolase BAP1 are found in over 85% of class 2 tumors. BAP1 is involved in removing ubiquitin from specific proteins to regulate their function, like histone H2A, thereby regulating gene expression. Building on these findings, we have generated uveal melanoma and melanocyte cell lines that allow for the inducible knockdown of BAP1. First, we performed RNAseq on multiple cell lines before and after BAP1 knockdown and compare the results to gene expression of class 1 and class 2 tumors. We identified significant overlap in key genes linked to metastasis between the primary tumors, uveal melanoma and melanocyte cell lines. Using ChIP-seq to interrogate uveal melanoma cells depleted of BAP1, we identified changes in genome wide histone marks and RNA polymerase localization associated with BAP1. To gain further insight into non-histone deubiquitination targets of BAP1, we performed ubiquitination proteomic profiling using the UbiScan® technology and identified a list of high probability BAP1 substrates. Taken together, these complementary genome-wide investigations provide a global picture of the cellular functions of BAP1 and they provide novel insights into the metastasis-promoting effect of BAP1 loss in UM. Citation Format: Stefan Kurtenbach, Jeffim N. Kuznetsov, Matthew G. Field, Rohit Reddy, Margaret I. Sanchez, Christina L. Decatur, J William Harbour. Epigenetic, transciptomic and ubiquitomic changes associated with BAP1 loss in uveal 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 5369. doi:10.1158/1538-7445.AM2017-5369
Abstract 147: Metformin suppresses triple-negative breast cancer stem cells by targeting KLF5 for degradation
Authors: Peiguo Shi, Zhongmei Zhou, Rong Liu, Ceshi Chen
Journal: Cancer Research (2017)

Abstract Out of the breast cancer subtypes, triple-negative breast cancer (TNBC) has the poorest prognosis without effective targeted therapies. A stem cell transcription factor KLF5 is over-expressed in basal type TNBC and promoting cell proliferation, survival and stemness. Previously, we demonstrated that Mifepristone suppresses basal TNBC stem cells by down-regulating KLF5 expression through inducing the expression of miR-153. In this study, Metformin, a first-line drug for type 2 diabetes mellitus, was demonstrated to target breast cancer stem cells selectively. However, the efficiency and the mechanism of action of metformin in TNBC are unclear. We demonstrated that metformin decreased the percentage of TNBC stem cells partially through the downregulation of the expression of KLF5 and its downstream target genes, such as Nanog and FGF-BP1, in TNBC cell lines. Metformin induced GSK3β-mediated KLF5 protein phosphorylation and degradation through the inhibition of PKA activity in TNBC cells. Consistently, PKA activators increased the expression levels of KLF5. We observed a positive correlation between p-CREB and KLF5 protein levels in human TNBC samples. These findings suggest that metformin suppresses TNBC stem cells partially through the PKA-GSK3β-KLF5 signaling pathway. Citation Format: Peiguo Shi, Zhongmei Zhou, Rong Liu, Ceshi Chen. Metformin suppresses triple-negative breast cancer stem cells by targeting KLF5 for degradation [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 147. doi:10.1158/1538-7445.AM2017-147
Abstract 530: The role of EGFR in c-fos-dependent osteosarcoma formation
Authors: Markus Linder, Elisabeth Glitzner, Sriram Srivatsa, Parastoo Shahrouzi, Latifa Bakiri, Monika Dumanic, Markus Mitterhauser, Erwin F. Wagner, Maria Sibilia
Journal: Cancer Research (2017)

Abstract The Epidermal Growth Factor Receptor (EGFR) is overexpressed or mutated in human carcinomas and glioblastomas, which are tumors of epithelial and glial origin, respectively. Some publications indicated that EGFR overexpression could occur in human osteosarcomas (OS). Using EGFR knockout mice (Egfr-/-), we have recently shown that EGFR plays a role in bone development and osteoblast function, raising the possibility that EGFR is also involved in OS formation. Here we show that Egfrf/f Runx2-Cre mice (EgfrΔOb), lacking the EGFR in osteo-chondroprogenitor cells, develop an increased zone of hypertrophic chondrocytes in long bones and decreased bone formation. When bred to c-fos transgenic mice (H2-c-fosLTR) that develop osteosarcomas with 100% penetrance, EgfrΔOb mice show reduced tumor incidence and burden. At the molecular level, tumors from EgfrΔOb mice exhibit decreased expression levels of c-Fos and Cyclin D1. In vitro experiments in primary bone tumor cells further show that EGFR inhibition leads to reduced proliferation and increased apoptosis. Importantly, Egfr and c-Fos also play an important role in human OS, as co-expression of both proteins in tumor sections correlated with significantly reduced survival in patients suffering from primary OS. Taken together our data suggest an essential role of EGFR signaling during both development and progression of c-Fos-dependent OS and newly identified molecular targets currently under investigation will be presented. Citation Format: Markus Linder, Elisabeth Glitzner, Sriram Srivatsa, Parastoo Shahrouzi, Latifa Bakiri, Monika Dumanic, Markus Mitterhauser, Erwin F. Wagner, Maria Sibilia. The role of EGFR in c-fos-dependent osteosarcoma formation [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 530. doi:10.1158/1538-7445.AM2017-530
Abstract 3782: Genetic analysis using a novel high-purity enrichment system for circulating tumor cells independent of epithelial cell antigen
Authors: Hidenori Takagi, Masahiro Kozuka, Hiroshi Ito, Soo Hyeon Kim, Mitsuharu Hirai, Teruo Fujii
Journal: Cancer Research (2017)

Abstract Background Genetic analysis of circulating tumor cells (CTCs) is useful as a liquid biopsy. However, there are 3 challenging issues in processing of CTC samples for clinical use of the analysis: [1] numerous residual blood cells in processed samples, [2] loss of CTCs that do not express epithelial markers, and [3] very laborious process. Here, we developed a novel system capable of overcoming all of these problems. Methods Our CTC analysis system is composed of 3 steps: [1] filtering of whole blood followed by immunostaining and magnetic labeling of cells trapped on the filter, [2] depletion of white blood cells (WBCs) in the cells recovered from the filter by magnetic separation, and [3] trapping the resultant cells at an observation chamber in a microfluidic enrichment device using dielectrophoresis, followed by recovering them as a concentrated sample after fluorescence microscope observation. SNV and CNV analysis was conducted using the collected concentrated sample, and the system performance was substantiated. Genetic mutations of the cells in the collected sample were detected by the Quenching Probe method. On the other hand for CNV analysis, cells in the collected concentrated sample were immobilized on slide glass and analysis of gene amplification conducted by FISH. Results With SNV analysis, our system successfully detected EGFR, KRAS or PIK3CA mutations of cancer cell lines spiked in 8 mL of whole blood (Table). The detection sensitivity of our method was 1 cell/mL, and both the cancer cells and their genetic mutations were detected within 9 hours of starting the processing of whole blood. Additionally, with CNV analysis, HER2 gene amplification was confirmed with cell lines spiked in 8 mL of blood. This detection result was obtained within 48 hours. Conclusion Our system would be useful for the analysis of gene mutations in a wide range of CTC types independent of certain epithelial antigens, such as CK and EpCAM, and can be used for various genetic analyses. Table Results of spiking test for SNV analysisSpiked cell linesExpected count[cells/8ml]No. of detected spiked cells [cells]No. of detected remained WBCs [cells]Detected genotypesNCI-H197512979EGFR L858RNCI-H16508225EGFR exon19 deletionSW6208648KRAS codon12, 13SNU-1124154KRAS codon12, 13MCF-777341PIK3CA G1633A Citation Format: Hidenori Takagi, Masahiro Kozuka, Hiroshi Ito, Soo Hyeon Kim, Mitsuharu Hirai, Teruo Fujii. Genetic analysis using a novel high-purity enrichment system for circulating tumor cells independent of epithelial cell antigen [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 3782. doi:10.1158/1538-7445.AM2017-3782
Abstract 2428: The cytidine deaminase APOBEC3B is a regulator of gene expression in breast cancer
Authors: Manikandan Periyasamy
Journal: Cancer Research (2017)

Abstract The APOBEC3B (A3B) cytidine deaminase gene has been implicated driving the mutational landscape in breast and other cancer types. We have discovered that A3B is a co-activator of estrogen receptor (ER) mediated gene expression in breast cancer. Mechanistic studies established that A3B regulates gene expression by promoting C-to-U deamination at ER binding regions. We show that these C-to-U changes lead to the generation of DNA strand breaks through activation of base excision repair (BER) and to repair by non-homologous end-joining (NHEJ) pathways. We have performed RNA-seq and A3B ChIP-seq, in multiple ER+ and ER- breast cancer cell lines. Remarkably, these studies demonstrate that A3B regulates the expression of many genes in inflammatory and interferon signaling pathways, in addition to the regulation of ER target genes. These findings, together with other data to be presented, provide a clear role for A3B in transcription regulation. These findings also raise the possibility that transcription factor mediated recruitment of A3B to DNA may facilitate acquisition of A3B driven cancer mutations. Citation Format: Manikandan Periyasamy. The cytidine deaminase APOBEC3B is a regulator of gene expression in 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 2428. doi:10.1158/1538-7445.AM2017-2428
Abstract 1897: The role of nuclear deformation and rupture in breast cancer cell migration
Authors: Alexandra L. McGregor, Joshua J. Elacqua, Emily S. Bell, Jan Lammerding
Journal: Cancer Research (2017)

Abstract Invasion of tumor cells into the surrounding tissue is a critical step in the metastatic cascade, which is responsible for the vast majority of cancer-related deaths. Recent findings have begun to demonstrate that the biophysical properties of the cell nucleus play a critical role in this process. During invasion, cancer cells must often pass through interstitial spaces much smaller than the cell nucleus. While the cell cytoplasm easily maneuvers through confined spaces, the deformability of the nucleus, which is the largest and stiffest organelle, ultimately determines how efficiently a cell can pass through a tight space. Furthermore, as the nucleus deforms to move through a confined space, it can exhibit transient loss of nuclear envelope (NE) integrity, where the nuclear membranes rupture and nuclear and cytoplasmic components interchange. We previously showed that chromatin is exposed to the cell cytoplasm during NE rupture, and cells can incur DNA damage. While this work revealed that cancer cell migration requires nuclear deformation and can involve NE rupture, it is currently unknown whether such events correlate with metastatic potential. We used a panel of human breast cancer cells lines, including claudin-low, basal-like, and lumen-like cells. Cells were stably labeled with a green fluorescent protein fused to a nuclear localization sequence (NLS-copGFP) to investigate whether some cell lines were particularly well suited to migrate through tight spaces, and if any were particularly prone to NE rupture. The cells were loaded into microfluidic devices that were designed to mimic interstitial in vivo spacing and monitored by time-lapse microscopy. Devices contained constrictions 5 µm tall and 1, 2, or 15 µm wide. We found that claudin-low cell lines such as BT-549 migrated through confined spaces (1+2 µm wide constrictions) significantly faster and more efficiently than basal-like HCC70 cancer cells. In contrast, the various cell lines displayed similar migration rates in the 15 µm wide constrictions, which do not require nuclear deformation. Thus, the differences observed between the cell lines reflect specific defects in migration through confined spaces, and not general migration defects. We are currently expanding our studies to a larger panel of cancer cell lines and to mouse breast cancer models. If confirmed, these results could indicate that highly invasive cancer cells may benefit from more deformable nuclei that facilitate movement through tight spaces encountered in the tissue microenvironment. Citation Format: Alexandra L. McGregor, Joshua J. Elacqua, Emily S. Bell, Jan Lammerding. The role of nuclear deformation and rupture in breast cancer cell migration [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 1897. doi:10.1158/1538-7445.AM2017-1897
Abstract 4985: Understanding the vulnerabilities in cancer cells upon inhibition of glutathione synthesis
Authors: Isaac S. Harris, Jennifer E. Endress, Joan S. Brugge
Journal: Cancer Research (2017)

Abstract A hallmark of cancer is the rewiring of cellular metabolic pathways, including those that mediate oxidative stress. Cancer initiation and progression, which demands increased production of ATP and synthesis of proteins, also results in elevated generation of toxic by-products such as reactive oxygen species (ROS). Cancer cells counteract ROS by increasing the production of antioxidants, which convert ROS into benign species. It has been shown that production of glutathione (GSH), the most abundant intracellular antioxidant, is necessary for many cancers to initiate malignant transformation. Whether inhibition of GSH synthesis can impact the survival of established malignant tumors remains poorly understood. In this study we investigated the extent to which GSH is required in cancer cells and across different subtypes of breast cancer. Profiling of an extensive panel of breast cancer cell lines demonstrated that the majority of cells are resistant to death after acute GSH depletion, while only luminal breast cancer cells are sensitive to chronic GSH depletion. To understand how most tumor cells are resistant to GSH depletion and oxidative stress, we conducted a small-molecule high-throughput screen interrogating more than 500 compounds in a 10-point dilution format. Importantly, screening plates were imaged and cell numbers quantified to avoid any false positives/negatives potentially associated with interrogating cellular metabolism using classical high throughput techniques, such as CellTiter-Glo. This screen revealed that depletion of glutathione sensitized breast cancer cells to inhibition of deubiquitinases, resulting in a drastic induction of a proteotoxic stress response. Furthermore, this sensitivity was found to be specific to malignant cells, as non-transformed cells were resistant to the combined treatments. It has been hypothesized that GSH, acting as an abundant thiol group, non-enzymatically reacts with ubiquitin and limits ubiquitination of proteins. Loss of glutathione, in combination with deubiquitinase inhibitors, leads to deregulation of ubiquitinated protein pools, and cancer cells undergo proteotoxic stress and cell death. These findings elucidate a novel vulnerability in cancers cells and shed light on an unexpected relationship between cancer metabolism and protein homeostasis. Citation Format: Isaac S. Harris, Jennifer E. Endress, Joan S. Brugge. Understanding the vulnerabilities in cancer cells upon inhibition of glutathione synthesis [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 4985. doi:10.1158/1538-7445.AM2017-4985
Abstract 3721: DLL3 analysis of circulating tumor cells predict treatment outcome in phase 1 rova-T study in small cell lung cancer
Authors: Somdutta Roy, Kevin Martinez, Archana Dilip, Holger Karsunky, Scott Dylla
Journal: Cancer Research (2017)

Abstract Small cell lung cancer (SCLC) is an aggressive neuroendocrine tumor with early dissemination and poor prognosis that accounts for 15-20% of all lung cancer cases worldwide. Most cases are inoperable and biopsies to investigate SCLC biology are rarely obtainable. Circulating tumor cells (CTCs), which are prevalent in SCLC, present a readily accessible liquid biopsy. Here we present CTC data from aggressive, late stage SCLC patients who were enrolled on a Phase 1 trial studying Rova-T (anti-DLL3 antibody drug conjugate). CTCs were captured using a microfluidic platform (IsoFlux) that uses flow control and immunomagnetic capturing of epithelial cell surface marker (EpCAM)-positive cells. CTCs were isolated before dosing (baseline) of Rova-T and at successive time points post treatment. CTCs from each time point were distinguished and enumerated using DAPI, EpCAM and the cytoplasmic marker (pan-CK), in addition to the absence of CD45. Enriched CTCs were also collected for RT-PCR for expression analysis of genes confirmed to be absent in blood cells. The number of CTCs varied among the 58 baseline samples collected, ranging from 5-1000 CTCs per 7.5ml of blood. When the CTCs were assessed for DLL3 target expression, 37/58 baseline samples expressed DLL3 by RT-PCR. Interestingly, the expression of DLL3 on the baseline CTCs correlated with treatment outcome. When additional time points after treatment were enumerated for CTCs, patients that presented with DLL3 expression on CTC at baseline showed a significant decrease in CTCs after treatment. This suggests that Rova-T might kill DLL3-expressing CTCs. These data support continued investigation of DLL3 expression on CTC in SCLC patients with the goal of facilitating a liquid biopsy able to assess DLL3 status as a prospective companion diagnostic for Rova-T. Citation Format: Somdutta Roy, Kevin Martinez, Archana Dilip, Holger Karsunky, Scott Dylla. DLL3 analysis of circulating tumor cells predict treatment outcome in phase 1 rova-T study in 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 3721. doi:10.1158/1538-7445.AM2017-3721
Abstract 196: Identification of small molecule inhibitors of the notch transcriptional activation complex
Authors: Luisana Astudillo, Anthony Capobianco
Journal: Cancer Research (2017)

Abstract Deregulation of the Notch pathway underlies many aspects of cancer physiology depending on cell type and context. In many human cancers, aberrant Notch activity has been demonstrated to play a role in the initiation and maintenance of the neoplastic phenotype. Notch also plays a central role in cancer stem cells, which may underlie a role in metastasis and resistance to therapy. The important and diverse role played by Notch in cancer makes it an exceedingly attractive target for anti-neoplastic therapeutics. However, the full range of potential targets in the pathway have been under-explored. Through computer-aided drug design we explored potential ligand binding sites and screened for compounds that could disrupt the assembly of the Notch transcriptional activation complex. An in vitro assay that quantitatively measures the assembly of the Notch transcriptional complex on DNA was used for screening. We have recently reported the identification and characterization of a small molecule inhibitor of the Notch transcriptional activation complex, termed Inhibitor of Mastermind Recruitment-1 (IMR-1). Herein we report the characterization of small molecule inhibitors of Notch derived from IMR-1 that were identified through a combination of structure-activity relationship studies and molecular docking simulations. We demonstrate that these compounds inhibit the growth of Notch dependent cell lines and decrease Notch target gene transcription. Citation Format: Luisana Astudillo, Anthony Capobianco. Identification of small molecule inhibitors of the notch transcriptional activation complex [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 196. doi:10.1158/1538-7445.AM2017-196