tbuckley/cabot-search huggingface dataset:
Abstract 1097: Knockdown of splicing factor ESRP1 affects multiple splicing factors
Authors: Yesim Gökmen-Polar, Yaseswini Neelamraju, Xiaoping Gu, Gouthami Nallamothu, Sarath C. Janga, Sunil Badve
Journal: Cancer Research (2015)

Abstract Introduction: Tissue-specific alternative splicing (AS) is an important mechanism for regulating gene expression. Epithelial Splicing Regulatory Proteins 1 and 2 (ESRP1 and ESRP2), two RNA-binding proteins (RBPs) that promote splicing, are potential candidates that contribute to breast cancer recurrence and resistance to therapies. In our prior studies, we have shown that ESRPs are associated with endocrine resistance. In this study, we seek to investigate the impact of the ESRP1 knockdown in endocrine resistant breast cancer cells. Methods: Expression of ESRP1 was analyzed in endocrine resistant-LCC2 and LCC9 cells. Knockdown of ESRP1 expression in LCC2 and LCC9 cells was achieved using lenti-viral based shRNA approach (Mission TRC human shRNA constructs, Sigma). We next performed paired-end RNA-sequencing of LCC2 and LCC9 cells transfected with control and two clones representative of shRNA knockdown (Illumina HiSeq platform, SeqWright Genomic Services) according to the manufacturer's instructions. After processing and quality check of raw FASTQ data (Illumina CASAVA, FASTQ and FASTX toolkits), reads were aligned, and quantified using bioinformatics software tools (Tophat/Cufflinks and Sailfish). Results: Expression of ESRP1 is significantly elevated in ERα-positive endocrine -resistant cells (LCC2 and LCC9 cells). ESRP1 knockdown was confirmed using qRT-PCR analysis in LCC2 cell lines (clone1 - 80% reduction and clone 3- 95% reduction) and in LCC9 cells (clone 2- 90% reduction and clone 3- 50% reduction). RNA-seq analysis identified 5153 differentially regulated genes between ESRP1 knockdown and control LCC2 cell lines. Of the 5153 genes, 1117 and 2109 genes were unique to clone 1 and clone 3, respectively, while 1927 genes were common in both clones. Targeted RNA-seq analysis also revealed that ESRP1 regulates the expression of several genes including other splicing factors. Furthermore, a functional enrichment analysis of these genes revealed a possible role of altering important pathways such as cell-cell adhesion and cell signaling. Additionally, it was observed that neither ESR1 nor any of its downstream genes were affected by the knockdown of ESRP1. This data was similar to that obtained in knockdown of LCC9 cells. Conclusions: ESRP1 regulates splicing of multiple genes in ER+ breast cancer. The process is independent of ER pathway. Targeting splicing could be a novel modality for treating endocrine therapy resistant breast cancer. Citation Format: Yesim Gökmen-Polar, Yaseswini Neelamraju, Xiaoping Gu, Gouthami Nallamothu, Sarath C. Janga, Sunil Badve. Knockdown of splicing factor ESRP1 affects multiple splicing factors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1097. doi:10.1158/1538-7445.AM2015-1097
439. Oncolytic Newcastle Disease Virus Iraqi Virulent Strain Induce Apoptosis In Vitro through intrinsic Pathway and Association of Both Intrinsic and Extrinsic Pathways In Vivo
Authors: Ahmed M. Al-Shammari, Tagreed J. Humadi, Eman H. Al-Taee, Shalal M. Al-Atabi, Nahi Y. Yaseen
Journal: Molecular Therapy (2015)

Newcastle disease virus is very promising antitumor agent. Iraqi virulent strain showed pronounced oncolytic activity. This study aimed to investigate the specific pathway of apoptosis induced by Iraqi strain of Newcastle disease virus (NDV) on tumor cells In vitro and In vivo. Several cell lines were tested (Human Rhabdomyosarcoma cell line (RD), Human Glioblastoma multiforme culture (AMGM) and Murine mammary adenocarcinoma cell line (AMN3) for ability of Iraqi NDV strain to induce apoptosis and to give deep look about the main pathway that induce apoptosis in tumor cell lines by the virus. The cell lines were infected with Newcastle disease virus and investigated for apoptotic pathway by using immunocytochemistry for caspase 3, 8, and 9. The result of this in vitro experiment revealed that NDV induce apoptosis in tumor cell lines when compared to control group with marked increase in the percentage of cells expressing caspase 9 with low percentage of cells expressing caspase 8 in NDV treated group at 24,48hr. These results indicated the role of NDV Iraqi strain in inducing apoptosis through intrinsic mitochondrial pathway in vitro. The in vivo experiment included female mice transplanted with mammary adenocarcinoma transplantable tumor line (AM3), after tumor growth; tumor bearing mice randomly divided into groups, first group treated by NDV by intratumoral injection, second group treated by NDV intrapretonially. Caspase 3, caspase 8, and caspase 9 expression in tumor sections were checked after 24hrs, 48hrs, 72hrs, 7 and 14 days of treatment with NDV. The results revealed that NDV induce apoptosis significantly in treated tumors by both ways IT and IP when compared with control group. There is significant (p<0.05) marked increase in the mean percentage of cells expressing caspase 9 in NDV treated groups compared with mean percentage of cells expressing caspase 8 and untreated control group at 24,48,72, 1week, 2 weeks post single injection treatment. Moreover, Caspase-8 expression in IT and IP groups was significantly higher than control untreated group. These results revealed that NDV had a powerful effect on inducing mitochondrial (intrinsic) apoptotic pathway in vivo in association of extrinsic pathway. This association can explained by NDV induction for antitumor immune response and this immune response can trigger tumor killing by extrinsic pathway. The current work suggest that Iraqi oncolytic virulent strain of NDV induce apoptosis through intrinsic pathway directly as the results of in vitro study and induce extrinsic pathway indirectly through immune stimulation properties of NDV.
210. Complete Control of Tumor Growth In Vivo By a Synthetic Consensus Multi-Antigen DNA Immune Therapy for Prostate Cancer
Authors: Bernadette Ferraro, Jewell N. Walters, Emma L. Reuschel, Amrthia Balakrishnan, Matthew P. Morrow, Jian Yan, Amir S. Khan, Niranjan Y. Sardesai, Laurent M. Humeau, David B. Weiner
Journal: Molecular Therapy (2015)

Prostate cancer (PCa) is one of the leading causes of cancer deaths among men with limited treatment options. Accordingly, new approaches, such as immunotherapy, may represent important approaches for PCa treatment. Electroporation (EP) delivered DNA vaccines has recently shown promising results for therapeutic treatment of HPV early disease in humans. Application of this technology for PCa immunotherapy strategies has been limited to single antigen and epitope targets with limited success. We hypothesized that a broader collection of antigens adjuvanted by plasmid encoded IL-12 would bypass immune tolerance and improve the breadth and effectiveness of a PCa immunotherapy approach. We tested this hypothesis in NHP for immune tolerance effects as well as in the highly relevant TRAMP-C2 challenge model. We developed highly optimized DNA vectors encoding consensus antigens for important PCa targets prostate-specific antigen (SynCon PSA), prostate-specific membrane antigen (SynCon PSMA), and human six-transmembrane epithelial antigen of the prostate (STEAP). In mice the vaccines demonstrated potent IFNγ production by ELISpot (2740 SFU) and robust immune responses in the CD4+ (0.53%) and CD8+ (3.0%) T cell compartments. Further, sera from immunized mice reacted in ELISA with relevant targets and specifically stained LNCaP cells, a human PCa cell line, as well as human PCa tumor sections, supporting that the vaccine antigens induced relevant antibody responses. Vaccination of Rhesus Macaques, which share greater than 98% identity with humans, showed robust anti-PSA, PSMA and STEAP IFNγ production (612 SFU), potential for cytotoxic T cell function, and antigen specific seroconversion supporting the ability of these constructs to break tolerance. The therapeutic potential of PSMA, STEAP, and the combination of PSMA and STEAP, alone or with the molecular adjuvant IL-12, was evaluated in mice in the TRAMP-C2 tumor model. Alone, PSMA, STEAP or PSMA+STEAP demonstrated prolonged survival and a modest impact on tumor growth. However, the combination of synthetic vaccine antigens with IL-12 resulted in 100% efficacy in treatment and clearance of tumors resulting in 100% survival. These data support further study of this novel immune therapy of PCa.
<i>Notes from the Field:</i> New Delhi Metallo-β-Lactamase–Producing Carbapenem-Resistant Enterobacteriaceae Identified in Patients Without Known Health Care Risk Factors — Colorado, 2014–2016
Authors: Sarah J. Janelle, Alexander Kallen, Tom de Man, Brandi Limbago, Maroya Walters, Alison Halpin, Karen Xavier, Joyce Knutsen, Elizabeth Badolato, Wendy M. Bamberg
Journal: MMWR Morbidity and Mortality Weekly Report (2016)
Molecular markers of the EGFR pathway in erlotinib-treated patients with advanced pancreatic cancer (APC): Translational analyses of a randomized, cross-over AIO phase III trial.
Authors: S. H. Boeck, A. Jung, R. P. Laubender, J. Neumann, R. Egg, C. Goritschan, U. Vehling-Kaiser, C. Winkelmann, L. Fischer von Weikersthal, M. R. Clemens, T. C. Gauler, A. Marten, S. Klein, G. Kojouharoff, M. Barner, M. Geissler, T. F. Greten, U. Mansmann, T. Kirchner, V. Heinemann
Journal: Journal of Clinical Oncology (2011)

4047 Background: Within a cross-over phase III trial, we compared gemcitabine/erlotinib followed by capecitabine with capecitabine/erlotinib followed by gemcitabine in patients with treatment-naive APC (Boeck S et al, ASCO 2010, LBA4011). Valid translational data are still lacking from APC phase III trials. Methods: 281 patients (pts) were randomized; archival formalin fixed paraffin embedded (FFPE) tumor tissue was available from 208 pts. We centrally analysed KRAS exon 2 mutation status (PCR), EGFR expression (immunohistochemistry, IHC and fluorescence in-situ hybridization, FISH), PTEN expression (IHC), as well as the EGFR intron 1 polymorphism [PM] (PCR) and the EGFR exon 13 R497K PM (PCR). Translational biomarker data were correlated (either as dichotomous or continuous variables, respectively) with overall survival (OS) by using Kaplan-Meier estimates and the log rank test. Results: KRAS mutations (all in codon 12) were found in 121/173 pts (70%), EGFR expression was detected in 174/181 pts (96%) by IHC, and 77/166 pts (46%) had an EGFR gene amplification by FISH; 30/171 pts (18%) had a loss of PTEN expression. Median number of CAn repeats in the intron 1 PM (allele 1+2, n=186) was 34 (range 28-41) and 112/194 pts (58%) had the GG wildtype sequence for the exon 13 R497K PM of the EGFR gene. EGFR intron 1 PM showed no correlation with EGFR expression either by IHC (p=0.264) or FISH (p=0.311). Median OS for all 208 pts was estimated with 6.2 months. In univariate biomarker analyses KRAS mutation status was significantly associated with OS (HR 1.68, 95% CI 1.17-2.41, p=0.005); no significant correlation was found for EGFR-IHC (HR 1.01, p=0.985), EGFR-FISH (HR 1.22, p=0.252), PTEN-IHC (HR 0.77, p=0.216), EGFR intron 1 PM (HR 1.02, p=0.540) or EGFR exon 13 R497K PM (HR 0.83, p=0.231). None of the 6 molecular biomarkers analysed correlated with the occurrence of skin rash. Conclusions: Translational research with archival FFPE tissue is feasible in APC phase III trials. Molecular markers of the EGFR pathway may be associated with treatment outcome in erlotinib-treated pts with APC.
Clinical and Biological Characterization of Adult Patients with Acute Myeloid Leukemia Bearing T(7;11)(p15;p15)—Analysis of 536 Patients
Authors: Wen-Chien Chou, Chien-Yuan Chen, Hsin-An Hou, Liang-In Lin, Jih-Luh Tang, Ming Yao, Woei Tsay, Bor-Shen Ko, Shan-Yi Huang, Hwei-Fang Tien
Journal: Blood (2008)
No Benefit of Combining Additional Compounds with Standard High Dose Cytarabine Consolidation: Results of the Prospective Randomized AML2003 Study
Authors: Stefani Parmentier, Martin Bornhäuser, Christian Thiede, Christoph Röllig, Michael Kramer, Mathias Haenel, Regina Herbst, Norbert Schmitz, Reingard Stuhlmann, Hannes Wandt, Kerstin Schäfer-Eckart, Walter E. Aulitzky, Martin Kaufmann, Anthony D. Ho, Alwin Krämer, Wolfgang E. Berdel, Carsten Müller-Tidow, Hubert Serve, Gerhard Ehninger, Markus Schaich
Journal: Blood (2011)
Abstract 4898: Full-length isoform sequencing of the human MCF-7 cell line using PacBio long reads
Authors: Elizabeth Tseng, Tyson Clark, Meredith H. Ashby, Gloria Shenykman
Journal: Cancer Research (2015)

Abstract While advances in RNA sequencing methods have accelerated our understanding of the human transcriptome, isoform discovery remains a challenge because short read lengths require complicated assembly algorithms to infer the contiguity of full-length transcripts. This inability to resolve full-length isoforms hinders researchers’ ability to identify key isoform changes and fusion transcripts associated with human diseases. With the PacBio® long-read technology, one can now sequence full-length transcript isoforms up to 10 kb. The PacBio Iso-Seq™ protocol produces reads that originate from independent observations of single molecules, and no assembly is needed if a read spans the entire length of the transcript. In this study, we sequenced the human MCF7 cell-line using the Clontech SMARTer® cDNA preparation kit. Using the PacBio Iso-Seq bioinformatics software, we obtained 55,770 unique, full-length, high-quality transcript sequences that were subsequently mapped back to the human genome with ≥ 99% accuracy. The full-length transcripts ranged from 300 bp to 9.5 kb with a mean length of 2.1 kb. Out of 16,868 expressed loci, 149 had more than 20 isoforms, with a total average of 3 isoforms per loci. Additionally, we identified more than 100 candidate fusion transcripts, many of which were confirmed through previously published experimental validations or computation predictions. For the BCAS3-BRCA4 fusion, we detected 3 different fusion transcripts, two of which were entirely novel. To validate the full-length isoforms, we compared the predicted peptides from the MCF-7 data against a previously published mass spectrometry dataset from the same cell line. 41,699 peptides mapped to 23,729 PacBio-predicted open reading frames (i.e. protein sequences), confirming the translation of a majority of sequenced transcripts. Notably, 251 peptides were novel and not annotated in the UniProt protein database. These peptides confirm abundant cases of single amino acid polymorphisms, cassette exon splicing, and potential alternative protein coding frames encoded in the MCF-7 proteome. To conclude, the Iso-Seq protocol provides a new opportunity for researchers to study the complex splicing events that occur in cancer cells. Citation Format: Elizabeth Tseng, Tyson Clark, Meredith H. Ashby, Gloria Shenykman. Full-length isoform sequencing of the human MCF-7 cell line using PacBio long reads. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4898. doi:10.1158/1538-7445.AM2015-4898
425. Production of Gene Corrected T Cell Precursors for Therapy of SCID X1
Authors: Chantal Lagresle-Peyrou, Cécile Roudaut, Aurélie Gabrion, Laure Caccavelli, Hanem Sadek, Myriam Chouteau, Christian Reimann, Salima Hacein-Bey-Abina, Marina Cavazzana, Isabelle André-Schmutz
Journal: Molecular Therapy (2016)

Gene therapy for SCID and CID usually leads to a more efficient T-cell reconstitution as compared to HSCT from a mismatched related donor. However, as observed in ADA, SCID X1 and WAS gene therapy trials, T cell recovery is sometimes slow and associated with morbidity and mortality due to viral infections. In order to shorten post-transplant immunodeficiency and to reduce the frequency of these complications, one possible strategy is to transplant gene-corrected T-cell committed precursors. We have recently set up a protocol for transplanting in vitro-committed T-cell precursors able to seed the thymus and generate a wave of mature and polyclonal T-cells significantly faster than is usually observed. This protocol is based on a 3 to 7 day-culture of CD34+ cells in the presence of immobilized Notch ligand Delta-like-4 (DL-4), an adhesion molecule and a combination of cytokines; this culture system enables the in vitro generation of large amounts of T-cell precursor cells that (i) display the phenotypic and molecular signatures (i.e. gene expression pattern and TCR rearrangement pattern) of early thymic progenitor cells and (ii) have a high T-lymphopoietic potential in vitro and in vivo when transferred into NOD/SCPD/γc knock-out (NSG) mice (Reimann C, Stem Cells, 2012). The goal of the present project was to combine exposure to DL-4 and gene therapy approaches (DL-4/GT). For this purpose, gene correction of CD34+ cells from SCID-X1 patients was performed on DL-4 coated plates and the ex vivo transduced cells were either seeded on OP9/DL-1 culture or injected into NSG mice to determine their in vitro and in vivo capacity to generate mature and diverse T cells. In the DL-4/GT condition, the frequency and number of CD7+CD5+commited T-cell precursors was increased as compared to GT condition alone. Experiments to assess if the DL-4/GT condition accelerate T cell differentiation of gene corrected cells are currently ongoing. Altogether, our results suggest that a short exposure to the Notch ligand DL-4 might be an useful tool to generate large amounts of corrected T-cell precursors.
Abstract 4762: Cessation of Rivaroxaban in Post-ACS Patients is Not Associated With Clinical Evidence of Rebound Hypercoagulability: An ATLAS ACS-TIMI 46 Substudy
Authors: Jessica L Mega, Eugene Braunwald, Mary Lee, Frank Misselwitz, Satishkumar Mohanavelu, Ravi Notani, Gary Peters, C. Michael Gibson
Journal: Circulation (2009)

Introduction : In vitro and outcome studies suggest that rebound hypercoagulability is present after cessation of some anticoagulants. Rivaroxaban is an oral, direct factor Xa inhibitor that has been shown to reduce major atherothrombotic events in post-ACS patients. Whether rivaroxaban is associated with rebound hypercoagulability in this population remains undefined. Methods : ATLAS ACS-TIMI 46 randomized post-ACS patients to placebo or rivaroxaban (5–20 mg) for 6 mos, with a 30 day follow-up visit. This analysis included 3367 subjects with ≥1 day follow-up after last study drug administration. Cox regression was used to assess the risk of events (primary: death, MI, stroke, or severe recurrent ischemia requiring revascularization; secondary: death, MI, or stroke) within 10 days of cessation of study drug. Results : Among subjects who completed the treatment period (N=2808), cessation of rivaroxaban and placebo was associated with a similar rate of the primary (HR 1.03, 95% CI 0.19–5.64) and secondary (HR 0.77, 95% CI 0.13–4.64) endpoints. Moreover, among subjects who discontinued study drug early (N±559), there were no significant differences in the risk of events after cessation of rivaroxaban and placebo (Figure ). Overall (N=3367), the risk of death or cardiovascular events after discontinuation of study drug was similar with rivaroxaban and placebo (primary: HR 1.28, 95% CI 0.59–2.77; secondary: HR 1.11, 95% CI 0.51–2.44). Conclusion : In post-ACS patients, discontinuation of rivaroxaban as compared with placebo is not associated with an increase in death or cardiovascular events, and thus there does not appear to be clinical evidence of rebound hypercoagulability.
Abstract 1541: Secreted serglycin in tumor microenvironment promotes tumor malignancies in a CD44-dependent manner
Authors: Jing-You Guo, Shiaw-Wei Tyan, Han-Shui Hsu, Fen-Yau Li, Jeou-Yuan Chen
Journal: Cancer Research (2015)

Abstract Tumor microenvironment (TME) plays an important role in cancer progression; however, the communication between TME and cancer cells remains largely unclear. CD44, a type I cell surface receptor functioning in cell-cell and cell-extracellular matrix interactions, has been implicated in tumor formation and progression. Using gain-of-function and loss-of-function approaches, we report in this study that serglycin (SRGN), a glycoprotein secreted from cancer-associated fibroblasts (CAFs) as well as aggressive cancer cells, works to promote the malignant behaviors of non-small cell lung cancer cells through its interaction with CD44. We showed that SRGN promotes cell transformation and tumor formation and metastasis using in vitro and in vivo tumorigenic assays. Furthermore, we showed that SRGN induced lung cancer cell stemness in a CD44-dependent manner. SRGN enhanced cancer cells sphere formation via Nanog induction, accompanied with increased drug resistance and resistance to anoikis. We also demonstrated that SRGN promotes cell migratory activity through promoting epithelial-mesenchymal transition (EMT) and enhancing adhesions turnover by upregulating vimentin expression and SRC activity via CD44/NF-KB/Claudin-1 axis. In support, Claudin-1 expression was tightly associated with SRGN expression in primary lung cancer tissues (p &amp;lt; 0.0001). In summary, we demonstrate that the crosstalk between tumor cells and TME promotes malignant phenotypes through the interaction of tumor-borne CD44 and CAF- or tumor-derived SRGN, suggesting that targeting CD44 or its ligands may represent an attractive strategy for development of cancer therapy. Citation Format: Jing-You Guo, Shiaw-Wei Tyan, Han-Shui Hsu, Fen-Yau Li, Jeou-Yuan Chen. Secreted serglycin in tumor microenvironment promotes tumor malignancies in a CD44-dependent manner. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1541. doi:10.1158/1538-7445.AM2015-1541
Analysis of Cooperating Genetic Events in MLLT3-MLL Rearranged Acute Myeloid Leukemia (AML) by Targeted Next-Generation Sequencing of 16 Leukemia-Related Genes Reveals Frequent Mutations Affecting Growth Factor Signalling Pathways and Provides Evidence for Clonal Heterogeneity
Authors: Klaus H. Metzeler, Nadine Sandhöfer, Tanja Hinrichsen, Evelyn Zellmeier, Bianka Ksienzyk, Annika Dufour, Stephanie Schneider, Purvi M. Kakadia, Philipp A Greif, Marion S. Subklewe, Stefan K Bohlander, Hanns-Georg Klein, Wolfgang Hiddemann, Karsten Spiekermann
Journal: Blood (2012)
Mutational Status of Splenic Marginal Zone Lymphoma Revealed by Whole Exome Sequencing.
Authors: Nerea Martinez, Ignacio Varela, Jose P. Vaque, Sophia Derdak, Sergi Beltran, Manuela Mollejo, Margarita Sanchez-Beato, Laura Cereceda, Monica Bayes, Marta Gut, David Oscier, Jose L. Rodriguez-Peralto, Francesc Sole, Maximo Fraga, Juan F. Garcia, Elena Sebastian, Ivo G. Gut, Miguel A. Piris
Journal: Blood (2012)