tbuckley/cabot-search huggingface dataset:
Abstract 4895: A one-tube assay for simultaneous detection of gene mutation, fusion, copy number alteration and expression
Authors: Zongli Zheng, Ranjit Shetty, Matthew Liebers, Jessica L. Cambry, Lindsay A. Bernardo, Darrell Borger, Long P. Le, John A. Iafrate
Journal: Cancer Research (2015)

Abstract There are growing demands for tumor genotyping in the clinic, with an ever-growing number of mutation/fusion targets and expression profiles needed for tumor diagnostics. We sought to develop a comprehensive yet efficient tumor genetic approach using next-generation sequencing (NGS) that would target the genomic DNA and mRNA components of a sample simultaneously, to decrease costs and labor in the lab, and take advantage of small/limited quantity tumor specimens. We describe here a novel method termed one-tube anchored multiplex PCR (OneAMP) for combined DNA-and-RNA targeted sequencing, allowing simultaneous detection of gene expression, rearrangements, single nucleotide variations (SNVs), insertion and deletions (Indels) and copy number variation (CNV). In this approach, total nucleic acid is used as input for the assay, starting with cDNA synthesis, shearing, adenylation, and ligation with a half-functional molecule-indexed Y adaptor. The molecular index is a random oligomer and serves as a tag for tracing and counting sample templates from ligation through sequencing. Target enrichment is then achieved by two rounds of hemi-nested PCR using gene specific primers and adaptor primers. Gene specific primers for priming genomic DNA (intronic primer extension to exons for SNVs, Indels and CNV) and for priming cDNA (exonic primer extension for gene fusion and expression) have been optimized so they can be combined in one tube for PCR. A distinctive feature of OneAMP is that mRNA expression is normalized to genomic DNA copy number for the same gene, eliminating the need for normalization to housekeeping genes, which can eliminate significant bias across tissue types and individuals. We developed a 210 gene OneAMP cancer panel that consists of important cancer genes that are mutated, fused, or with altered expression or copy number. We validated CNV calls with aCGH/FISH of the same samples and validated mRNA expression by comparing to array and qPCR. Finally SNVs, Indels, and fusions were validated with a large panel of samples with known mutation status. We demonstrate the potential of OneAMP for the comprehensive detection of genetic abnormalities, preserving precious tumor samples, and reducing reagent usage and time. Citation Format: Zongli Zheng, Ranjit Shetty, Matthew Liebers, Jessica L. Cambry, Lindsay A. Bernardo, Darrell Borger, Long P. Le, John A. Iafrate. A one-tube assay for simultaneous detection of gene mutation, fusion, copy number alteration and expression. [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 4895. doi:10.1158/1538-7445.AM2015-4895
S27 The effect of P2X3 antagonism (AF–219) on experimentally evoked cough in healthy volunteers and chronic cough patients
Authors: JA Smith, M Kitt, P Butera, A Ford
Journal: Thorax (2016)

<h3>Introduction and objectives</h3> Effective therapies for chronic cough are a significant unmet need. Recently a P2X3 antagonist (AF-219), markedly reduced cough frequency in two phase 2 trials, but the role of P2X3 receptors and their ligand (adenosine triphosphate, ATP) in chronic cough is not well-understood. This study assessed the effect of P2X3 antagonism on cough evoked by capsaicin and ATP in healthy volunteers and chronic cough patients. <h3>Method</h3> We performed a double-blind, placebo-controlled, randomised, 4-period crossover study. During each period (≥48 h apart), cough challenges were performed 2h after single doses of study medication [capsaicin (0.48–1000 μM) periods 1/2 and ATP (0.227–929 μmol/mL) periods 3/4]. Two cohorts were enrolled; cohort (1) 14 healthy volunteers (HV, mean age 37.5 yrs, 100% male) and 12 chronic cough (CC, mean age 60.3 yrs, 17% male) received AF-219 300mg/placebo and cohort (2) 12 HV (mean age 34.8 yrs, 100% male) and 12 CC (mean age 57.8 yrs, 25% male) received AF-219 50 mg/placebo. Cough challenges consisted of four inhalations of each doubling concentration of tussive agent, from a dosimeter 30s apart. Coughs in the first 15s were counted and challenges continued to the maximum tolerated dose. The concentrations evoking at least 2 and 5 coughs, C2 and C5 (from inhalation 1) were analysed using mixed effect models; pharmacodynamic modelling was used to estimate Emax/ED50. <h3>Results</h3> AF-219 had no effect on capsaicin C2 or C5 at 300 mg or 50 mg in HV or CC (all p &gt; 0.05). For ATP challenges, AF-219 300 mg significantly increased C2 in CC (AF-219 10.8 μmol/mL vs. placebo 2.3 μmol/mL, p = 0.005) but not HV (p = 0.135), whereas AF-219 50mg significantly increased C2 in both groups (CC 40.4 μmol/mL vs. 2.8 μmol/mL, p = 0.002 and HV 114.4 μmol/mL vs. 20.7 μmol/mL, p = 0.046). AF-219 had no significant effect on ATP C5 at either dose in HV (all p &gt; 0.05), but in CC patients 50mg AF-219 (but not 300mg) increased C5 (70.1 μmol/mL vs. 17.1 μmol/mL, p = 0.027). Of note, ATP inhalation evoked less coughing than capsaicin, limiting the utility of the C5 endpoint. <h3>Conclusions</h3> P2X3 antagonism reduced cough responses to ATP, particularly in patients with CC, but did not alter cough responses to an off-target tussive agent.
Abstract 2524: Combination with vorinostat overcomes ABT-263 resistance of small cell lung cancer
Authors: Wataru Nakajima, Mark A. Hicks, Kanika Sharma, Ngoc Le, Geoffrey W. Krystal, Hisashi Harada
Journal: Cancer Research (2015)

Abstract Lung cancer is the most common cause of cancer related mortality worldwide, with small cell lung cancer (SCLC) representing 15% of cases, accounting for 30,000 new cases in the US each year. While SCLC is initially a highly chemotherapy-responsive disease, relapse and progressive development of chemotherapy resistance is the rule. One promising approach to overcome the therapeutic resistance would be to utilize agents targeting molecular abnormalities regulating resistance to apoptosis. Tumor cell death induced by chemotherapy or lack of appropriate cellular survival signals is mediated by the BCL-2 family-dependent mitochondrial apoptotic pathway. We and others have shown that the pro-survival member BCL-2, as well as BCL-XL and MCL-1, is overexpressed in SCLC. BH3 mimetic antagonists have been developed to block the function of pro-survival BCL-2 family members. ABT-737 and its orally available derivative ABT-263 bind to and block BCL-2 and BCL-XL, but not MCL-1 function. Although SCLC is the only non-hematologic malignancy against which ABT-737/ABT-263 are effective as single agents, the sensitivity of SCLC to these drugs varies over a broad range in vitro and in clinical trials. We have shown in a model SCLC system that expression of Noxa, a BH3-only pro-apoptotic BCL-2 family protein, is a critical determinant of ABT-737 sensitivity, demonstrating that Noxa specifically binds to and recruits MCL-1 from the cytosol to the mitochondria. Recent integrative genome analysis in SCLC implicates histone modification as a major feature of SCLC. It has also been demonstrated that Noxa is transcriptionally activated by HDAC inhibitors. Thus, we hypothesized that alteration of histone modification by a HDAC inhibitor, vorinostat could induce Noxa to enhance cell death by ABT-737/263 treatment. We have found that combination of ABT-263 and vorinostat efficiently induces apoptosis in a variety of SCLC cell lines, even in the ABT-263 resistant cells. Cell death induced by combined treatment is Noxa- and/or BIM-dependent in some cell lines but in others appears to be mediated by an alternative mechanism. These results suggest that combination of HDAC inhibitors and BCL-2 inhibitors could be an alternative effective regimen for SCLC treatment. Citation Format: Wataru Nakajima, Mark A. Hicks, Kanika Sharma, Ngoc Le, Geoffrey W. Krystal, Hisashi Harada. Combination with vorinostat overcomes ABT-263 resistance of small cell lung cancer. [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 2524. doi:10.1158/1538-7445.AM2015-2524
Tolerability of PTK787/ZK 222584 in a Phase II Study of Post-Transplant Maintenance Therapy in Patients with Multiple Myeloma Following High-Dose Chemotherapy and Autologous Stem Cell Transplant.
Authors: James C. Mosley, Shachar Peles, Alisa Ruddell, Feng Gao, Camille Abboud, Amanda Cashen, Geoffrey Uy, Peter Westervelt, John F. DiPersio, Ravi Vij
Journal: Blood (2007)
Deletion of OLFM4 Rescues Defective Host Defense Against Staphylococcus Aureus, but Not Aspergillus Fumigatus in Murine X-Linked Chronic Granulomatous Disease
Authors: Wenli Liu, Janyce A Sugui, Hongzhen Li, Kyung J Kwon-Chung, Griffin P. Rodgers
Journal: Blood (2012)
632. Alpha-1 Antitrypsin Gene Therapy Prevented Bone Loss in an Ovariectomy Induced Osteoporosis Mouse Model
Authors: Mohammad A. Akbar, Jay J. Cao, Yuanqing Lu, David Nardo, Mong-Jen Chen, Ahmed S. Elshikha, Rubina Ahamed, Mark Brantly, Lung-ji Chang, Lexie Shannon Holliday, Sihong Song
Journal: Molecular Therapy (2016)

Osteoporosis is a major healthcare burden affecting mostly postmenopausal women characterized by compromised bone strength and increased risk of fragility fracture. Although pathogenesis of this disease is complex, inflammation is clearly involved in bone loss at menopause. Therefore, anti-inflammatory strategies hold great potential for the prevention of postmenopausal osteoporosis. Human alpha-1 antitrypsin (hAAT) is a multifunctional protein that has anti-inflammatory and cytoprotective properties. In this study, we investigated the protective effect of hAAT against bone loss. In vitro studies showed that hAAT significantly inhibited osteoclast formation and function in a dose-dependent manner. Treatment of hAAT inhibited M-CSF (macrophage colony-stimulating factor) induced cell surface RANK receptor expression by downregulating cFos mRNA expression. To test the protective effect of hAAT in an osteoporosis mouse model, we treated ovariectomized (OVX) mice with rAAV8-CB-hAAT, or mesenchymal stem cells (MSCs) infected with a lentiviral vector expressing hAAT (MSC-Lenti-hAAT) or phosphate buffer saline (PBS). Sham operated age-matched animals were used as controls. Eight weeks after the treatment, animals were sacrificed and subjected to µCT scanning for the evaluation of vertebral bone microarchitecture. Gene and stem cell-based hAAT therapies significantly increased bone volume density, trabecular number and decreased structure model index compared to PBS injection in OVX mice. Gene therapy also increased connectivity, density and trabecular thickness compared to PBS injection in OVX mice. We also observed that both therapies inhibited RANK gene expression in bone, which is consistent with the results of our in vitro study. These results demonstrate that hAAT gene and MSCs based therapies mitigate ovariectomy-induced bone loss in a mouse model, possibly through inhibition of osteoclast formation by reducing RANK gene expression. Considering the safety profile of the hAAT and rAAV vector in human, our results provide a new insight for the treatment of osteoporosis.
Safety and Efficacy in Patients Receiving Maintenance Rituximab for Follicular Lymphoma: Early Results From Phase IIIb MAXIMA Trial.
Authors: Mathias Witzens-Harig, Guy van Hazel, Dalton FA Chamone, Klaus Ruffert, Jacob M. Rowe, Mario Lazzarino, Robin Foà, Irina Poddubnaya, Anthony D. Ho, Valentina Ivanova, Andrej Vranowsky, Joachim Hipp, Stefan Oertel
Journal: Blood (2009)
Phase IA/II Study of Oral Panobinostat (LBH589), a Novel Pan- Deacetylase Inhibitor (DACi) Demonstrating Efficacy in Patients with Advanced Hematologic Malignancies.
Authors: Oliver G. Ottmann, Andrew Spencer, H. Miles Prince, Kapil N. Bhalla, Thomas Fischer, Angela Liu, Kathryn Parker, Muhammad Jalaluddin, Glen Laird, Margaret Woo, Jeffrey W. Scott, Daniel J. DeAngelo
Journal: Blood (2008)
238. BTK-Promoter LV Vectors Utilizing Conserved Intron Element Mediate Functional Rescue in Murine XLA
Authors: Swati Singh, Brenda Seymour, Karen Sommer, Iram Khan, Socheath Khim, Malika Hale, Courtnee Clough, David J. Rawlings
Journal: Molecular Therapy (2015)

X-linked agammaglobulinema (XLA) is a rare immunodeficiency disorder caused by a mutation in the gene coding Bruton's tryosine kinase (BTK). BTK is required for signal transduction downstream of the B cell antigen receptor (BCR) and is essential for normal B cell development, activation, and survival. Patients lacking BTK have very few mature B cells, markedly reduced antibody production, and suffer from recurrent and life-threatening infections. XLA is an ideal candidate for hematopoietic gene therapy, as B cells that express BTK are positively selected during development. We previously developed a SIN-lentiviral (LV) construct that used the human BTK promoter (BTKp) to drive BTK expression. We also incorporated a truncated, 0.7 kb, fragment derived from the HNRPA2B1/CBX3 ubiquitously acting chromatin opening element (UCOE) upstream of the BTKp to facilitate stable BTK expression over time. Bone marrow transplantation in a murine XLA model (BTK-/-Tec-/- mice) using LV transduced hematopoietic stem cells (HSCs) reconstituted myeloid and B cell numbers, BCR-dependent B cell proliferation and T-dependent antibody responses. The goal of the current study was to further optimize BTK expression in B and myeloid cells while reducing the viral copy number (VCN) required for efficient functional reconstitution. Using the ENCODE database, we identified several highly conserved upstream and intronic regions exhibiting histone modifications and transcription factor binding profiles in B cells consistent with enhancer regions. These conserved elements were introduced individually or in tandem into the LV construct between the UCOE and BTKp and tested for their ability to rescue BTK expression and B cell development in the murine XLA model. Addition of two key intronic regions led to consistent BTK expression and rescued the development and function of B cells, despite a >5-fold reduction in VCN per splenic B cell. Our findings illustrate the usefulness of this strategy for improving the efficacy of endogenous promoter-based genetic therapies. This new LV vector, UCOE. I4-5.BTKpro-hBTK, is currently being evaluated using mobilized CD34+ stem cells isolated from XLA patients and in additional pretoxicology studies designed to support its application in a future LV clinical trial for XLA.
114. Integrins Are Required for Adenovirus 5 Transduction in Cells of Lymphocyte Origin
Authors: Payal Agarwal, Elizabeth A. Yanchak, Abdul Mohin Sajib, Maninder Sandey, Bruce F. Smith
Journal: Molecular Therapy (2015)

Adenovirus serotype 5 (Ad5) is the most widely used vector in cancer gene therapies. The high efficiency and broad range of host transduction, easy genome manipulation, non-integration into the host genome, and the well-characterized molecular biology of adenovirus have made them an excellent choice for cancer therapeutics. Ad5 infects cells by binding to the coxsackie-adenovirus receptor (CAR) followed by internalization mediated by binding of viral penton RGD motifs to cell surface integrins (avb3, avβ5). Low levels of Ad5 infection of both human and murine lymphocytes have been linked to the absence of CAR on these cells. We have previously reported that low levels of integrins on canine lymphoma cells are a potential obstacle to Ad5 infection. In the current report we have evaluated CAR and integrins at the molecular level by using quantitative reverse transcriptase PCR (Q-RT-PCR) in a broad range of canine tumor cells including lymphomas (OSW, 17-71), mast cells (BR, MPT1), melanocytes (CML7, CML10), histiocytoma (DH82) and mammary adenocarcinomas (CMT28). Normal canine fibroblasts, peripheral blood mononuclear cells (PBMC) and HEK293 cells were used as controls. All of the cell lines were exposed to Ad5G/L virus at multiplicities of infection (MOI) of 10, 100, and 1000 viral particles per cell. Ad5G/L is a replication incompetent virus vector that infect cells utilizing the classical CAR and integrin infection mechanism. Ad5G/L expresses both GFP and luciferase after infecting cells. Fluorescence microscopy demonstrated that Ad5G/L successfully infected CMT28, DH82, HEK293, CML7, CML10, and NCF at 48 hrs. post infection at all 3 multiplicities of infection. There was limited or no Ad5G/L infection in the lymphoma cell lines, PBMCs, and MPT1 mast cells. The mast cell line BR was the exception, showing relatively high levels of infection. Q-RT-PCR results showed low level of integrins in MPT1, 17-71, OSW, and PBMC cells in comparison to CMT28, DH82, and BR cells. Interestingly, CAR mRNA levels were comparatively higher in MPT1, 17-71, OSW, and PBMC cells. These data indicate that lack of integrins and not CAR is the primary reason for the inability of Ad5G/L infection to infect cells of lymphocyte origin. The defect in cell surface integrins must be addressed if Adenoviral vectors are to be used to transfer genes to lymphocytes or tumors in cells of lymphocyte origin.
In Vivo Mobilization of Leukemic Human Precursor-B-ALL Cells by the CXCR4-Antagonist AMD3100 Is Via Secretion of SDF-1 and Synergistically by Catecholamine Action.
Authors: Eike C. Buss, Alexander Kalinkovich, Amir Schajnovitz, Orit Kollet, Ayelet Dar, Melania Tesio, Stefan Fruehauf, Marc Hotfilder, Anthony D. Ho, Leonard D. Shultz, Tsvee Lapidot
Journal: Blood (2008)
509. Regulated Expression of IL-12 as Gene Therapy Concomitant with Blockade of PD-1 for Treatment of Glioma
Authors: John A. Barrett, Hongliang Cai, John Miao, Margaret Murray, Paul Gonzales, Suma Krishnan, Francois Lebel, Laurence J.N. Cooper
Journal: Molecular Therapy (2016)

The utility of immunotherapy in the treatment of glioma may be improved through combination therapies that enhance cytotoxic immune-activation while concomitantly reducing immunosuppression. We provide data in mice to support evaluation of combining controlled local interleukin 12 (IL-12) administration and blockade of programmed cell death protein 1 (PD-1) in humans. To circumvent challenges surrounding the uncontrolled activation, we have implemented clinical trials using a replication-incompetent adenovirus engineered to conditionally express IL-12 (Ad-RTS-IL-12), via our RheoSwitch Therapeutic System® (RTS®) gene switch. When directly injected intra-tumorally in pre-clinical or clinical studies, IL-12 expression is "off" when devoid of the activator ligand (veledimex, V) and IL-12 production is turned "on" (in a dose-dependent manner) by oral administration of veledimex. PD-1 inhibitors using therapeutic monoclonal antibodies (mAbs) demonstrate an ability to reverse tumor immunosuppression and are effective in the treatment of some cancers. In the present pre-clinical study we assessed the effects of Ad-RTS-mIL-12+veledimex (Ad+V) alone, Ad 5×109 viral particles (vp) + V 10-30mg/m2/day for 14 days or in combination with the antiPD-1-specific mAb RMP1-14 (antiPD-1, 7.5 & 15.0 mg/m2 for 4/day for 5 days i.p.) in the orthotopic GL-261 mouse model. All mice without treatment succumb to disease progression by Day 35. Eighty days after immunotherapy, 70-80% receiving Ad +V monotherapy survived, 30-40% receiving antiPD-1 monotherapy survived and 100% receiving Ad +V 30 mg/m2 + antiPD-1 15.0 mg/m2 combination survived. There was an increase in tumor IL-12 (100 pg/mg) which was 15-times greater than that of plasma peak 5 days after Ad +V. Furthermore, the combination of Ad +V+antiPD-1 sustained peak IL-12 levels in tumor which was associated with a 100-150% increase of activated T cells in the spleen compared with the minimal changes observed with either immunotherapy alone. In addition, there was an additive reduction in regulatory T cells (FOXP3) compared with monotherapies. In summary we demonstrate that controlled local immunostimulation with IL-12 combined with inhibition of PD-1 is an attractive approach for the treatment of glioma. Since both Ad-RTS-IL-12 and mAb blocking PD-1 are clinically available, these data provide impetus for evaluating this combination immunotherapy in humans.
Abstract 2543: Akt and Myc cooperate to promote cell proliferation in Lck-Dlx5 T-cell lymphomas
Authors: Yinfei Tan, Eleonora Sementino, Joseph Testa
Journal: Cancer Research (2015)

Abstract Constitutive activation of AKT is a frequent occurrence in the development of human T-cell acute lymphocytic leukemia/lymphoma (T-ALL), due largely to inactivation of PTEN. Up regulation of MYC is also commonly observed in T-ALL. We previously demonstrated that transgenic expression of a constitutively active form of Akt2 alone is sufficient to initiate T-cell lymphoma in mice, and that tumor formation typically requires up regulation of c-Myc or Dlx5 caused by specific chromosomal rearrangements. Here we report that transgenic overexpression of Dlx5 specifically in the mouse thymus can also drive T-cell lymphomagenesis. Tumors from these mice were characterized by loss of Pten expression and trisomy 15. Proliferation of these lymphoma cells was highly sensitive to the Akt pathway inhibitors BEZ235 and RAD001 as well as to the Myc inhibitor JQ1. Additionally, BEZ235 was found to cooperate with JQ1 to induce a more profound effect on cell cycle arrest and apoptosis. Moreover, BEZ235 potentiated vincristine-induced apoptosis when cells were treated with both drugs simultaneously, whereas pretreatment with BEZ235 antagonized the cell-killing effect of vincristine. These findings suggest that combination therapies with AKT and MYC inhibitors hold promise for the treatment of T-ALL in the clinic. Citation Format: Yinfei Tan, Eleonora Sementino, Joseph Testa. Akt and Myc cooperate to promote cell proliferation in Lck-Dlx5 T-cell lymphomas. [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 2543. doi:10.1158/1538-7445.AM2015-2543
Increased Incidence of Therapy Related Myeloid Neoplasia (t-MN) After Initial Therapy for CLL with Fludarabine-Cyclophosphamide (FC) Vs Fludarabine (F): Long-Term Follow-up of US Intergroup Study E2997
Authors: Mitchell R Smith, Donna Neuberg, Ian W. Flinn, Michael R. Grever, John M. Bennett, Gordon Dewald, Elisabeth M Paietta, Mark R. Litzow, Jacob M. Rowe, David Lucas, Shinichi Kitada, Diane F. Jelinek, John G. Gribben, John C. Byrd, John C. Reed, Mohamad A. Hussein, Frederick R. Appelbaum, Richard A. Larson, Dennis F Moore, Martin S. Tallman
Journal: Blood (2010)
Imatinib Mesylate and Nilotinib Affect the MHC-Class I Presentation by Modulating the Proteasomal Processing of Antigenic Peptides.
Authors: Stefanie Held, Stefan Tenzer, Thomas Rückrich, Karin von Schwarzenberg, Anita Bringmann, Annkristin Heine, Hansjörg Schild, Christoph Driessen, Peter Brossart
Journal: Blood (2009)
Feasibility Analysis of Nonmyeloabltive Allogeneic Stem Cell Transplantation (NST) in Patients with Chronic Lymphocytic Leukemia (CLL) and 17p- Deletion,
Authors: Yvonne Hsu, Rima M Saliba, Grace-Julia Okoroji, Susan o'Brien, Alessandra Ferrajoli, Lynne V. Abruzzo, Richard Champlin, Michael J Keating, Issa F. Khouri
Journal: Blood (2011)
Results of a Nonrandomized, Open-Label, Phase II Study of Combined Gemcitabine, Mitoxantrone, and Rituximab in Relapsed or Refractory Mantle Cell Lymphoma.
Authors: Lawrence E. Garbo, Patrick J. Flynn, Margaret A. MacRae, Mary A. Rauch, Yunfei Wang, Kathryn S. Kolibaba
Journal: Blood (2007)