tbuckley/cabot-search huggingface dataset:
Abstract 3499: Differentially expressed small noncoding RNAs in triple-negative breast cancer
Authors: Srinivas V. Koduru, Amit K. Tiwari, Ashley Leberfinger, Sprague W. Hazard, Yuka Imamura Kawasawa, Milind Mahajan, Dino J. Ravnic
Journal: Cancer Research (2017)

Abstract Cancer is the second leading cause of death in the United States and is a major public health concern worldwide. Basic, clinical and epidemiological research is leading to improved cancer detection, prevention, and outcomes. Recent technological advances have allowed unbiased and comprehensive screening of genome-wide gene expression. Small non-coding RNAs (sncRNAs) have been shown to play an important role in biological processes and could serve as a diagnostic, prognostic and therapeutic biomarker for specific diseases. Recent findings have begun to reveal and enhance our understanding of the complex architecture of sncRNA expression including miRNAs, piRNAs, sn/snoRNAs and their relationships with biological systems. We used publicly available small RNA sequencing data that was derived from 24 triple negative breast cancers (TNBC) and 14 adjacent normal tissue samples to remap various types of sncRNAs. We found a total of 55 miRNAs were aberrantly expressed (p&amp;lt;0.005) in TNBC samples (8 miRNAs upregulated; 47 downregulated) compared to adjacent normal tissues whereas the original study reported only 25 novel miRs. In this study, we used pathway analysis of differentially expressed miRNAs which revealed TGF-beta signaling pathways to be profoundly affected in the TNBC samples. Furthermore, our comprehensive re-mapping strategy allowed us to discover a number of other differentially expressed sncRNAs including piRNAs, sn/snoRNAs, rRNAs, miscRNAs and nonsense-mediated decay RNAs. We believe that our sncRNA analysis workflow is extremely comprehensive and suitable for discovery of novel sncRNAs changes, which may lead to the development of innovative diagnostic and therapeutic tools for TNBC. Citation Format: Srinivas V. Koduru, Amit K. Tiwari, Ashley Leberfinger, Sprague W. Hazard, Yuka Imamura Kawasawa, Milind Mahajan, Dino J. Ravnic. Differentially expressed small noncoding RNAs in triple-negative 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 3499. doi:10.1158/1538-7445.AM2017-3499
Abstract 1483: Alteration of miR-186 expression modifies inflammatory markers in normal epithelial and prostate cancer cell models
Authors: Suman Suman, Dominique Z. Jones-Reed, M. L. Schmidt, Geoffrey J. Clark, Carolyn Klinge, Shirish Barve, Kevin S. Kimbro, La Creis R. Kidd
Journal: Cancer Research (2017)

Abstract Dysregulation of miRNAs and chronic inflammation are strongly implicated in the development of various malignancies, including prostate cancer (PCa). Previously, our lab identified several inflammatory and immune response sequence variants in CCL5 and CCR5 significantly modified PCa risk. Recently, we propose an oncogenic role for miR-186-5p based on its up-regulation in serum from PCa patients and metastatic PCa cell lines. Moreover, miR-186-5p inhibition reduced proliferation, anchorage independent growth and invasion in metastatic PC cells (PC3, MDA-PCA-2b). We hypothesize dysregulation of inflammatory and immune response markers may enhance immune surveillance leading to a reduced aggressive tumor phenotype. Following modulations in miRNA-186 levels in normal prostate epithelial (RWPE1) and metastatic PCa (PC3) cell lines, we evaluated alterations in mRNA expression using micro-array analysis. Ectopic expression of miRNA-186 in the RWPE1 resulted in a 1.3-2.6-fold down-regulation in TLR2, IRAK2, CCL20, IL1RAP, IL1RAP, IL15, and IL17RD (FDR p-value ≥7.8x10-06). Whereas, inhibition of miR-186 in PC3 cells corresponded with a 1.4-fold up-regulation of IL18R1 (p=0.0095). Notably, these inflammatory markers are involved in cell invasion (TLR2), apoptosis (IL17RD), tumorigenesis (TLR2, IRAK2) and autoimmune diseases (CCL20). Validation of these targets is underway using qRT-PCR, western blots and luciferase reporter assays. We will assess the mechanism by which these miR-186 targets suppress aggressive cancer behavior using knock-out and knock-in cell and ultimately animal models. Future studies may identify inflammatory targets that may guide immune therapies for the effective treatment of aggressive prostate cancer. Citation Format: Suman Suman, Dominique Z. Jones-Reed, M. L. Schmidt, Geoffrey J. Clark, Carolyn Klinge, Shirish Barve, Kevin S. Kimbro, La Creis R. Kidd. Alteration of miR-186 expression modifies inflammatory markers in normal epithelial and prostate cancer cell models [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 1483. doi:10.1158/1538-7445.AM2017-1483
Abstract 5373: 3D genome architecture changes during cancer cell migration and metastasis
Authors: Rachel Patton McCord, Rosela Golloshi
Journal: Cancer Research (2017)

Abstract Metastasis, the most deadly part of cancer, results from cancer cell migration and invasion from a tumor into surrounding tissues. During this migration, the cell often has to squeeze and deform its nucleus through tight spaces. This nuclear squeezing is a rate-limiting step in migration, and the deformations can even rupture the nucleus. The organization of the genome inside the nucleus into loops, domains, and territories is important for proper gene regulation, DNA replication, and genome repair. However, little is known about the characteristics of nuclear organization that might allow for the nuclear deformation of metastatic cancer cells. We are using Chromatin Conformation Capture (Hi-C) and microscopy techniques to study genome organization during cancer cell migration. Using photoconvertible fluorophore Dendra2-H4 we draw and monitor patterns on nuclei of cells migrating through dense collagen matrices, Transwell filters, or microfluidic channels. Our data show changes in these patterns, indicating spatial reorganization of the genome during migration. Previous work has suggested that cancer cell migration requires global condensation of the genome. Some cancer chemotherapeutics act on epigenetic marks to decondense chromatin. We are testing whether such chromatin decondensation affects the physical deformability of the nucleus and thus effective migration. We have used Transwell and wound healing migration assays to monitor migration of cells treated with histone deacetylase inhibitors and histone methyltransferase inhibitors. Our results show that the drugs inhibit migration in a Transwell assay but not in the wound healing assay. This suggests that genome decondensation prevents the passage of the nucleus through narrow 3D spaces. But, a condensed genome organization is not necessary for 2D cell motility, where nuclei are unconfined. Hi-C experiments on migrating cells with deformed nuclei and drug-treated cells will characterize the specific rearrangements in genome structure that occur during cancer cell migration and whether these specific changes are counteracted by epigenetically active drugs. Citation Format: Rachel Patton McCord, Rosela Golloshi. 3D genome architecture changes during cancer cell migration and metastasis [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 5373. doi:10.1158/1538-7445.AM2017-5373
Abstract 2371: Oncogenic transformation of FLT3-ITD is partially dependent on tyrosine 842 in the activation loop
Authors: Julhash U. Kazi, Lars Rönnstrand
Journal: Cancer Research (2017)

Abstract Acute myeloid leukemia (AML) is a heterogeneous disease of the blood. About 30 % of AML patients carry an oncogenic mutant of the type III receptor tyrosine kinase FLT3. Among the various mutations in FLT3, the internal tandem duplication (ITD) mutations in the juxtamembrane domain are the most common type of mutation, while point mutations in the kinase domain also occur. Although oncogenic FLT3 mutants are constitutively active, the wild-type receptor needs its ligand (FLT3 ligand, FL) for activation. Ligand binding to the receptor induces dimerization, auto-phosphorylation, and activation of the receptor. Tyrosine phosphorylation sites on FLT3 constitute docking sites for interacting proteins that transduce pro-survival and proliferative signals. The so-called activation loop tyrosine residue (in FLT3, Y842) is well conserved in all receptor tyrosine kinases and long been known essential for the activity of some but not all receptor tyrosine kinases. Recently we have shown that activation loop tyrosine residue in KIT is not essential for its activation but plays an important role in receptor stabilization and downstream signaling. However, so far the role of FLT3 activation loop tyrosine residue remains unknown. We generated 32D cell lines carrying a Y-to-F mutant (Y842F) of FLT3 in either the wild-type or ITD background to study the role of this tyrosine residue. We show that the Y842 residue is not necessary for FLT3 activation or stability but is required for oncogenic transformation. We observed that Y842F mutation results in reduced cell viability, proliferation and in vitro colony formation in semi-solid medium. In addition, cells expressing the Y842F mutant in FLT3-ITD background display a significant reduction in tumor volume and weight in a xenograft model in nude mice. Gene set enrichment analysis (GESA) shows that mutation of Y842 causes suppression of anti-apoptotic genes. Furthermore, we demonstrated that phosphorylated Y842 is one of the binding sites of the protein tyrosine phosphataseSHP2, which is required for activation of signaling through the RAS/ERK pathway. Taken together, our data suggest that activation loop tyrosine residue in FLT3 plays an important role in the cellular transformation which is regulated by RAS/ERK signaling. Citation Format: Julhash U. Kazi, Lars Rönnstrand. Oncogenic transformation of FLT3-ITD is partially dependent on tyrosine 842 in the activation loop [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 2371. doi:10.1158/1538-7445.AM2017-2371
Abstract 3052: Defining the role of EMT in breast cancer dormancy and metastasisin vivo
Authors: Hae-Yun Jung, Kay T. Yeung, Tiffany Lee, Jeff H. Tsai, Jing Yang
Journal: Cancer Research (2017)

Abstract Breast cancer patients can develop metastases from dormant tumor cells years after primary tumor resection and treatment. Despite the clinical significance of metastatic latency, the exact cellular and molecular events regulating tumor dormancy remains largely unknown due to challenges in detecting single dormant tumor cells in vivo and characterizing the dormant tumor microenvironment. A developmental program termed Epithelial Mesenchymal Transition (EMT) has been shown to play an important role in tumor cell dissemination, tumor dormancy, and chemoresistance. During EMT, stationary epithelial cells lose their epithelial characteristics, including adherent junctions and apical-basal polarity, and acquire mesenchymal shape and properties. These cells gain the ability to migrate into the circulation, lodge into a distant organ, and form dormant tumor niches. We have previously shown that reversal of EMT is a key driving force in dormant tumor cell proliferation and macrometastasis formation in a skin carcinoma mouse model. Here, we present a novel metastatic breast cancer mouse model in which HER2-driven primary breast tumor cells are labelled with red fluorescent protein with inducible EMT transcription factor TWIST1. We established this mouse model by crossing the TetON-TWIST1 mice with the MMTV-rtTA mice to generate the MMTV-rtTA/TetON-TWIST1 double transgenic mice. To generate HER2-driven breast tumors in these mice, we administered concentrated lentivirus that expresses both the HER2 gene and the tdTomato fluorescent marker under one promoter via intraductal injection. This allows for rapid and synchronized development of primary tumors which recapitulate the formation of sporadic human breast cancer which arises in single cells in otherwise normally developed breast tissue. TWIST1 expression in the luminal layer of the mammary gland was then induced via oral doxycycline. Upon expression of TWIST1, Her2-driven breast tumor cells were found in circulation and in the lungs as micrometastases. We determined that disseminated breast tumor cells mostly remained in dormancy until TWIST expression was switched off by doxycycline withdrawal. We showed that tumor dormancy is partly due to the inability to reverse EMT and regain proliferative capacity. Lastly, using our mouse model to track disseminated breast cancer cells, we will characterize the associated dormant residing niche to further our understanding of tumor dormancy in connection with EMT and immune escape. Citation Format: Hae-Yun Jung, Kay T. Yeung, Tiffany Lee, Jeff H. Tsai, Jing Yang. Defining the role of EMT in breast cancer dormancy and metastasis in vivo [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 3052. doi:10.1158/1538-7445.AM2017-3052
Abstract 5530: Evidence linking aquaporin-3 loss to increased invasiveness in bladder cancer
Authors: Arpita Roy, Dinuka M. DeSilva, Donald P. Bottaro
Journal: Cancer Research (2017)

Abstract Bladder cancer (BCa) is the most common type of urothelial cancer (UC). According to American Cancer Society, in 2016, diagnoses of 76,960 new cases of bladder cancer (BCa) and 16,390 BCa associated deaths have been estimated. More than 90% of bladder cancer starts in the innermost transitional epithelium (urothelium) of the bladder. Aquaporin 3 (AQP3), one of 13 members of a transmembrane channel forming protein family (AQP0-12), has an N-terminal basolateral sorting signal and localizes to the basolateral membrane in epithelial tissues. Recent studies have shown that AQP3 expression is decreased in UC thus supporting a new hypothesis that alteration of the expression of AQP3 plays a role in the pathogenesis of UC. However, it remains to be determined whether AQP3 is involved in the invasion and metastasis of UC cells. In the present study, human bladder cancer cell lines of different grades, SW780 (G1) and TCCSUP (G4) were studied. Transcript and protein levels of AQP3 expression were significantly higher in low grade, SW780 cells when compared to the higher-grade TCCSUP cells. Inhibition of AQP3 by CuSO4 or siRNA specific knockdown of AQP3 resulted in increased migration in the wound-healing scratch assay. Over-expression of AQP3 plasmid resulted in reduced migration. It is known that epithelial cell polarity contributes to tumor suppression and that loss of E-cadherin is a crucial step in epithelial-to-mesenchymal transition (EMT). Our results indicate that AQP3 overexpression induced expression of E-cadherin, consistent with a role for AQP3 as a tumor suppressor by maintaining epithelial cell polarity and inhibiting EMT in BCa. Conversely, reduced AQP3 levels leading to reduced E-cadherin levels in high-grade BCa cells may result in loss of cell polarity, increased invasiveness and increased EMT. Citation Format: Arpita Roy, Dinuka M. DeSilva, Donald P. Bottaro. Evidence linking aquaporin-3 loss to increased invasiveness in bladder 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 5530. doi:10.1158/1538-7445.AM2017-5530
Abstract 1413: Replication obstacles formed within common fragile sites under replication stress are targeted by the global genomic nucleotide excision repair pathway
Authors: Martin Mistrik, Lucie Beresova, Eva Vesela, Ivo Chamrad, Jiri Voller, Masayuki Yamada, Tomas Furst, Rene Lenobel, Katarina Chroma, Jan Gursky, Jiri Bartek
Journal: Cancer Research (2017)

Abstract CFS’s are genomic loci present in higher vertebrates that are particularly sensitive to various forms of replication stress and suffer from increased breakage and rearrangements in tumors. They have rather enigmatic evolutionary role and employ various DNA repair and checkpoint mechanisms promoting their stability. We used an original approach for identification of CFS’s associated factors based on DNA probe designed to match the high flexibility island sequences typically present in some of the highly expressed CFS’s. This probe was used as affinity bait for fishing specifically enriched proteins which were further identified using SILAC and quantitative mass spectrometry. Among already known CFS’s stabilizers we identified also hits so far not implicated in CFS’s maintenance. Interestingly, most of these novel hits are components of the global genomic nucleotide excision repair pathway (GG-NER). Knock down-based functional experiments revealed that GG-NER works most likely as an important trigger turning the CFS’s-associated replication obstacles into DNA lesion further recognized by the ATR-promoted cellular checkpoint which function is to block an escape of DNA replication intermediates into mitosis and the next cell generation. Work was supported by the Grant Agency of the Czech Republic 13-17555S, Czech-BioImaging project (LM2015062 funded by MEYS, CR) and Ministry of Education of the Czech Republic (LO1304). Citation Format: Martin Mistrik, Lucie Beresova, Eva Vesela, Ivo Chamrad, Jiri Voller, Masayuki Yamada, Tomas Furst, Rene Lenobel, Katarina Chroma, Jan Gursky, Jiri Bartek. Replication obstacles formed within common fragile sites under replication stress are targeted by the global genomic nucleotide excision repair pathway [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 1413. doi:10.1158/1538-7445.AM2017-1413
Abstract 2940: TH17: mediators of metastatic growth acceleration after surgery
Authors: Vikas Sud, Samer Tohme, Dirk J. van der Windt, Hai Huang, Allan Tsung
Journal: Cancer Research (2017)

Abstract Surgery is known to accelerate the growth and progression of metastases in patients undergoing oncological resections with 50-60% patients having recurrent metastasis after resection making it a major reason for treatment failure. This impedes the efficacy of adjuvant chemotherapy and overall prognosis of the patient. Studies have proved that inflammatory cascade initiated by surgery that increases metastatic growth and progression is mediated through a specific mechanism of neutrophil cell death called Neutrophil Extracellular Traps (NETs). We investigated the mechanism of how NET formation after surgical stress increases metastatic growth by influencing a pro-tumor microenvironment in order to specifically identify targets for perioperative therapy to keep metastases dormant and improve the effect of chemotherapy and overall prognosis. 12 week old male C57BL/6J mice (WT) and mice in which NET formation was inhibited, ie, WT mice injected with DNAse and global homozygous knockout of peptidyl arginine deaminase 4 (PAD4), an essential nuclear protein for NET formation, underwent splenic injection of 100,000 cells of the murine colorectal cancer cell line, MC-38, followed with either 70% hepatic ischemia-reperfusion (IR) for 60 minutes after 7 days or no IR. Livers were harvested at multiple time points and assessed for changes in both innate and adaptive immune cell populations by flow cytometry. On gross examination, the livers of the NET deficient mice had fewer tumors as compared to the WT mice. Mice, which underwent IR after tumor cell injection in both groups showed an increase in nodules formation versus those with just tumor cell injection, however were still more in WT than NET deficient mice. Flow cytometry revealed a decrease in both TH17 (0.36% of T cells in no IR mice vs 0.0036% in IR mice) and CD8 cells (71% of T cells in no IR mice vs 34.8% in IR mice) in mice subjected to IR versus those with only tumor injection. We found that increased tumors after surgical stress, which were mediated by NET formation, were caused due to a decrease in anti-tumor activity of CD8 cells regulated via TH17 cells. If controlled in the perioperative period, it may reduce acceleration in metastatic foci and improve the overall prognosis. We are further investigating the mechanism of NETs influencing the tumor immune environment. Citation Format: Vikas Sud, Samer Tohme, Dirk J. van der Windt, Hai Huang, Allan Tsung. TH17: mediators of metastatic growth acceleration after surgery [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 2940. doi:10.1158/1538-7445.AM2017-2940
Abstract 3887: GNA13 is a theranostic target that drives drug resistance and cancer stem-like phenotypes in solid tumors
Authors: Suhail Ahmed Kabeer Rasheed, Hui Sun Leong, Manikandan Lakshmanan, Anandhkumar Raju, Dhivya Dadlani, Fui-Teen Chong, Ravisankar Rajarethinam, Thakshayeni Skanthakumar, Ern Yu Tan, Jacqueline Siok Gek Hwang, Kok Hing Lim, Daniel Shao-Weng Tan, Paolo Ceppi, Mei Wang, Vinay Tergaonkar, Patrick J. Casey, N. Gopalakrishna Iyer
Journal: Cancer Research (2017)

Abstract Treatment failure in solid tumors occurs due to the survival of specific subpopulations of cells that possess stem cell-like (CSC) phenotypes. Studies have implicated G protein-coupled-receptors (GPCRs) in cancer progression and the acquisition of aggressive phenotypes. Many of the implicated GPCRs signal through the G12 subfamily, comprised of GNA12 and GNA13. In this study, we demonstrate that GNA13 is upregulated in many solid tumors and impacts survival and metastases in these patients. Consistent with this, we show that GNA13 expression modulates drug resistance through its effect on the CSC sub-population in a panel of patient-derived head and neck (HNSCC) and breast cancer cells. These data were validated in vivo, where GNA13 over-expression in patient-derived xenografts increased tumor initiating capacity, tumorigenicity and drug resistance, with no effect on growth or proliferation. Signaling through NFKB and MAPK pathways appear to be critical to the observed phenotype. Importantly, blockade of GNA13 expression, or select downstream pathways using small-molecule inhibitors, abrogates GNA13-induced CSCs, rendering cells vulnerable to standard-of-care cytotoxic therapy for these cancers. Taken together, these data indicate that GNA13 expression is a potential prognostic biomarker, and interfering with GNA13-induced signaling provides a novel strategy to block CSCs and drug resistance in solid tumors. Citation Format: Suhail Ahmed Kabeer Rasheed, Hui Sun Leong, Manikandan Lakshmanan, Anandhkumar Raju, Dhivya Dadlani, Fui-Teen Chong, Ravisankar Rajarethinam, Thakshayeni Skanthakumar, Ern Yu Tan, Jacqueline Siok Gek Hwang, Kok Hing Lim, Daniel Shao-Weng Tan, Paolo Ceppi, Mei Wang, Vinay Tergaonkar, Patrick J. Casey, N. Gopalakrishna Iyer. GNA13 is a theranostic target that drives drug resistance and cancer stem-like phenotypes in solid tumors [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 3887. doi:10.1158/1538-7445.AM2017-3887