Trends and Developments in the Pharmacological Treatment of Psoriasis
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Cancer Subtype Identification Using Somatic Mutation Data
www.nature.com/bjc ARTICLE Genetics and Genomics Cancer subtype identification using somatic mutation data Marieke Lydia Kuijjer 1,2, Joseph Nathaniel Paulson1,2,3, Peter Salzman4, Wei Ding5 and John Quackenbush1,2,6 BACKGROUND: With the onset of next-generation sequencing technologies, we have made great progress in identifying recurrent mutational drivers of cancer. As cancer tissues are now frequently screened for specific sets of mutations, a large amount of samples has become available for analysis. Classification of patients with similar mutation profiles may help identifying subgroups of patients who might benefit from specific types of treatment. However, classification based on somatic mutations is challenging due to the sparseness and heterogeneity of the data. METHODS: Here we describe a new method to de-sparsify somatic mutation data using biological pathways. We applied this method to 23 cancer types from The Cancer Genome Atlas, including samples from 5805 primary tumours. RESULTS: We show that, for most cancer types, de-sparsified mutation data associate with phenotypic data. We identify poor prognostic subtypes in three cancer types, which are associated with mutations in signal transduction pathways for which targeted treatment options are available. We identify subtype–drug associations for 14 additional subtypes. Finally, we perform a pan-cancer subtyping analysis and identify nine pan-cancer subtypes, which associate with mutations in four overarching sets of biological pathways. CONCLUSIONS: This study is an important step toward understanding mutational patterns in cancer. British Journal of Cancer (2018) 118:1492–1501; https://doi.org/10.1038/s41416-018-0109-7 INTRODUCTION However, subtype classification using somatic mutations in Cancer is a heterogeneous disease that can develop in different cancer is challenging, mainly because the data are very sparse: tissues and cell types. -
Psoriasis and the New Biologic Agents: Interrupting a T-AP Dance
Review Synthèse Psoriasis and the new biologic agents: interrupting a T-AP dance Scott R.A. Walsh, Neil H. Shear Abstract corticosteroids, tar, anthralin, calcipotriol or tazarotene be- come cumbersome to apply as lesional surface area increases. PSORIASIS IS AN IMMUNE-MEDIATED SKIN DISEASE in which chronic T- Furthermore, potential side effects of these therapies increase cell stimulation by antigen-presenting cells (APC) occurs in the with the level of application. Nevertheless, topical treatment skin. This interplay between the T-cell and APC has been likened remains an adjunct in more severe disease to limit the re- to a “T-AP dance” where specific steps must occur in sequence to quirement for more aggressive therapies. Phototherapy is a result in T-cell activation and the disease phenotype; otherwise T- popular option in the treatment of more widespread disease. cell anergy would occur. Several novel engineered proteins de- However, ultraviolet light is generally only available in larger signed to block specific steps in immune activation (biologic treatment centres, requires a major time commitment (2–3 agents) have demonstrated efficacy in the treatment of psoriasis. times per week for many months) and can be associated with These agents include fusion proteins, monoclonal antibodies and an increased risk of cutaneous neoplasms.6 For moderate to recombinant cytokines. These medications act at specific steps during the T-AP dance either to inhibit T-cell activation, costimu- severe disease, oral systemic immunosuppressives such as lation and subsequent proliferation of T-cells, lead to immune de- methotrexate and cyclosporine or oral retinoids are generally viation or induce specific cytokine blockades. -
Infliximab, Adalimumab and Golimumab for Treating Moderately
HEALTH TECHNOLOGY ASSESSMENT VOLUME 20 ISSUE 39 MAY 2016 ISSN 1366-5278 Infliximab, adalimumab and golimumab for treating moderately to severely active ulcerative colitis after the failure of conventional therapy (including a review of TA140 and TA262): clinical effectiveness systematic review and economic model Rachel Archer, Paul Tappenden, Shijie Ren, Marrissa Martyn-St James, Rebecca Harvey, Hasan Basarir, John Stevens, Christopher Carroll, Anna Cantrell, Alan Lobo and Sami Hoque DOI 10.3310/hta20390 Infliximab, adalimumab and golimumab for treating moderately to severely active ulcerative colitis after the failure of conventional therapy (including a review of TA140 and TA262): clinical effectiveness systematic review and economic model Rachel Archer,1* Paul Tappenden,1 Shijie Ren,1 Marrissa Martyn-St James,1 Rebecca Harvey,1 Hasan Basarir,1 John Stevens,1 Christopher Carroll,1 Anna Cantrell,1 Alan Lobo2 and Sami Hoque3 1Health Economics and Decision Science, School of Health and Related Research (ScHARR), University of Sheffield, Sheffield, UK 2Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK 3Barts Health NHS Trust, London, UK *Corresponding author Declared competing interests of authors: none Published May 2016 DOI: 10.3310/hta20390 This report should be referenced as follows: Archer R, Tappenden P, Ren S, Martyn-St James M, Harvey R, Basarir H, et al. Infliximab, adalimumab and golimumab for treating moderately to severely active ulcerative colitis after the failure of conventional therapy (including a review of TA140 and TA262): clinical effectiveness systematic review and economic model. Health Technol Assess 2016;20(39). Health Technology Assessment is indexed and abstracted in Index Medicus/MEDLINE, Excerpta Medica/EMBASE, Science Citation Index Expanded (SciSearch®) and Current Contents®/ Clinical Medicine. -
Suppression of Signal Transducer and Activator of Transcription 3 Activation by Butein Inhibits Growth of Human Hepatocellular Carcinoma in Vivo
Author Manuscript Published OnlineFirst on December 3, 2010; DOI: 10.1158/1078-0432.CCR-10-1123 AuthorPublished manuscripts OnlineFirst have been on peer December reviewed and 3, accepted 2010 as for 10.1158/1078-0432.CCR-10-1123 publication but have not yet been edited. Suppression of Signal Transducer and Activator of Transcription 3 Activation by Butein Inhibits Growth of Human Hepatocellular Carcinoma in vivo Peramaiyan Rajendran1, Tina H. Ong2, Luxi Chen1,3, Feng Li1, Muthu K Shanmugam1, Shireen Vali4, Taher Abbasi4, Shweta Kapoor4, Ashish Sharma4, Alan Prem Kumar1,3, Kam M. Hui2,5 Gautam Sethi1,5 1Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, 2Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research National Cancer Centre, Singapore 169610, 3Cancer Science Institute of Singapore, National University of Singapore, and 4Cellworks Group Inc., California 95070; 4Cellworks Research India Pvt. Ltd, Bangalore 560066, India. Running title: Butein inhibits STAT3 signaling in vitro and in vivo in HCC. 5To whom correspondence should be addressed: 1. Dr. Gautam Sethi, Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Phone: +65-65163267; Fax: +65- 68737690; Email: [email protected] Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Copyright © 2010 American Association for Cancer Research Downloaded from clincancerres.aacrjournals.org on September 27, 2021. © 2010 American Association for Cancer Research. Author Manuscript Published OnlineFirst on December 3, 2010; DOI: 10.1158/1078-0432.CCR-10-1123 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. -
Biological Pathways and in Vivo Antitumor Activity Induced by Atiprimod in Myeloma
Leukemia (2007) 21, 2519–2526 & 2007 Nature Publishing Group All rights reserved 0887-6924/07 $30.00 www.nature.com/leu ORIGINAL ARTICLE Biological pathways and in vivo antitumor activity induced by Atiprimod in myeloma P Neri1,2,3, P Tassone1,2,3, M Shammas1, H Yasui2, E Schipani4, RB Batchu1, S Blotta1,2,3, R Prabhala1, L Catley2, M Hamasaki2, T Hideshima2, D Chauhan2, GS Jacob5, D Picker5, S Venuta3, KC Anderson2 and NC Munshi1,2 1Jerome Lipper Multiple Myeloma Center, Department of Adult Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; 2Boston VA Healthcare System, Department of Medicine, Harvard Medical School, MA, USA; 3Department of Experimental and Clinical Medicine, University of ‘Magna Græcia’ and Cancer Center, Catanzaro, Italy; 4Endocrine Unit, Massachusetts General Hospital, Boston, MA, USA and 5Callisto Pharmaceuticals Inc., New York, NY, USA Atiprimod (Atip) is a novel oral agent with anti-inflammatory tion.7,8 Atip inhibits the inflammatory response and preserves properties. Although its in vitro activity and effects on signaling bone integrity in murine models of rheumatoid arthritis (RA),9–12 in multiple myeloma (MM) have been previously reported, here targets macrophages, inhibits phospholipase A and C in rat we investigated its molecular and in vivo effects in MM. Gene 13,14 expression analysis of MM cells identified downregulation of alveolar macrophages and exhibits antiproliferative and 15–17 genes involved in adhesion, cell-signaling, cell cycle and bone antiangiogenic activities in human cancer models. Impor- morphogenetic protein (BMP) pathways and upregulation of tantly, we have previously reported that Atip inhibits MM cell genes implicated in apoptosis and bone development, follow- growth, induces caspase-mediated apoptosis, blocks the phos- ing Atip treatment. -
Classification Decisions Taken by the Harmonized System Committee from the 47Th to 60Th Sessions (2011
CLASSIFICATION DECISIONS TAKEN BY THE HARMONIZED SYSTEM COMMITTEE FROM THE 47TH TO 60TH SESSIONS (2011 - 2018) WORLD CUSTOMS ORGANIZATION Rue du Marché 30 B-1210 Brussels Belgium November 2011 Copyright © 2011 World Customs Organization. All rights reserved. Requests and inquiries concerning translation, reproduction and adaptation rights should be addressed to [email protected]. D/2011/0448/25 The following list contains the classification decisions (other than those subject to a reservation) taken by the Harmonized System Committee ( 47th Session – March 2011) on specific products, together with their related Harmonized System code numbers and, in certain cases, the classification rationale. Advice Parties seeking to import or export merchandise covered by a decision are advised to verify the implementation of the decision by the importing or exporting country, as the case may be. HS codes Classification No Product description Classification considered rationale 1. Preparation, in the form of a powder, consisting of 92 % sugar, 6 % 2106.90 GRIs 1 and 6 black currant powder, anticaking agent, citric acid and black currant flavouring, put up for retail sale in 32-gram sachets, intended to be consumed as a beverage after mixing with hot water. 2. Vanutide cridificar (INN List 100). 3002.20 3. Certain INN products. Chapters 28, 29 (See “INN List 101” at the end of this publication.) and 30 4. Certain INN products. Chapters 13, 29 (See “INN List 102” at the end of this publication.) and 30 5. Certain INN products. Chapters 28, 29, (See “INN List 103” at the end of this publication.) 30, 35 and 39 6. Re-classification of INN products. -
Modifications to the Harmonized Tariff Schedule of the United States To
U.S. International Trade Commission COMMISSIONERS Shara L. Aranoff, Chairman Daniel R. Pearson, Vice Chairman Deanna Tanner Okun Charlotte R. Lane Irving A. Williamson Dean A. Pinkert Address all communications to Secretary to the Commission United States International Trade Commission Washington, DC 20436 U.S. International Trade Commission Washington, DC 20436 www.usitc.gov Modifications to the Harmonized Tariff Schedule of the United States to Implement the Dominican Republic- Central America-United States Free Trade Agreement With Respect to Costa Rica Publication 4038 December 2008 (This page is intentionally blank) Pursuant to the letter of request from the United States Trade Representative of December 18, 2008, set forth in the Appendix hereto, and pursuant to section 1207(a) of the Omnibus Trade and Competitiveness Act, the Commission is publishing the following modifications to the Harmonized Tariff Schedule of the United States (HTS) to implement the Dominican Republic- Central America-United States Free Trade Agreement, as approved in the Dominican Republic-Central America- United States Free Trade Agreement Implementation Act, with respect to Costa Rica. (This page is intentionally blank) Annex I Effective with respect to goods that are entered, or withdrawn from warehouse for consumption, on or after January 1, 2009, the Harmonized Tariff Schedule of the United States (HTS) is modified as provided herein, with bracketed matter included to assist in the understanding of proclaimed modifications. The following supersedes matter now in the HTS. (1). General note 4 is modified as follows: (a). by deleting from subdivision (a) the following country from the enumeration of independent beneficiary developing countries: Costa Rica (b). -
Investigating the Mechanism of Hepatocellular Carcinoma Progression by Constructing Genetic and Epigenetic Networks Using NGS Data Identification and Big Database Mining Method
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 7, No. 48 Research Paper Investigating the mechanism of hepatocellular carcinoma progression by constructing genetic and epigenetic networks using NGS data identification and big database mining method Cheng-Wei Li1, Ping-Yao Chang1, Bor-Sen Chen1 1Laboratory of Control and Systems Biology, National Tsing Hua University, Hsinchu, Taiwan Correspondence to: Bor-Sen Chen, email: [email protected] Keywords: DNA methylation, multiple potential drugs, hepatocarcinogenesis, miRNAs, principal network projection Received: February 19, 2016 Accepted: October 26, 2016 Published: November 04, 2016 ABSTRACT The mechanisms leading to the development and progression of hepatocellular carcinoma (HCC) are complicated and regulated genetically and epigenetically. The recent advancement in high-throughput sequencing has facilitated investigations into the role of genetic and epigenetic regulations in hepatocarcinogenesis. Therefore, we used systems biology and big database mining to construct genetic and epigenetic networks (GENs) using the information about mRNA, miRNA, and methylation profiles of HCC patients. Our approach involves analyzing gene regulatory networks (GRNs), protein-protein networks (PPINs), and epigenetic networks at different stages of hepatocarcinogenesis. The core GENs, influencing each stage of HCC, were extracted via principal network projection (PNP). The pathways during different stages of HCC were compared. We observed that extracellular signals were further transduced to -
Spotlight Review
Leukemia (2009) 23, 10–24 & 2009 Macmillan Publishers Limited All rights reserved 0887-6924/09 $32.00 www.nature.com/leu SPOTLIGHT REVIEW Bone marrow microenvironment and the identification of new targets for myeloma therapy K Podar, D Chauhan and KC Anderson Department of Medical Oncology, LeBow Institute for Myeloma Therapeutics, Dana Farber Cancer Institute, Jerome Lipper Multiple Myeloma Center, Harvard Medical School, Boston, MA, USA The development of multiple myeloma (MM) is a complex multi- Signaling cascades activated by cytokines, growth factors and/ step process involving both early and late genetic changes in or adhesion in MM cells include the Ras/Raf/MEK/MAPK- the tumor cell as well as selective supportive conditions by the k bone marrow (BM) microenvironment. Indeed, it is now well pathway, PI3K/Akt-pathway, the JAK/Stat3-pathway, the NF B- established that MM cell-induced disruption of the BM homeo- pathway and the Wnt-pathway. Promising intracellular targets stasis between the highly organized cellular and extracellular for novel therapies also include protein kinase C (PKC) and SPOTLIGHT compartments supports MM cell proliferation, survival, migra- heat-shock proteins (HSPs). Moreover, genomic profiling has tion and drug resistance through activation of various signaling now identified additional stage-specific intracellular targets, (for example, PI3K/Akt, JAK/Stat-, Raf/MEK/MAPK-, NFjB- and which are now under investigation as novel potential therapeutic Wnt-) pathways. Based on our enhanced understanding of the 2,4 functional importance of the MM BM microenvironment and its targets. inter-relation with the MM cell resulting in homing, seeding, Cell surface receptors include integrins, cadherins, selectins, proliferation and survival, new molecular targets have been syndecans, and the immunoglobulin superfamily of cell adhe- identified and derived treatment regimens in MM have already sion molecules including syndecan-1 (CD138), H-CAM (CD44), changed fundamentally during recent years. -
10. M. P. MARTINEZ MONTIEL 23/5/06 08:40 Página 265
10. M. P. MARTINEZ MONTIEL 23/5/06 08:40 Página 265 1130-0108/2006/98/4/265-291 REVISTA ESPAÑOLA DE ENFERMEDADES DIGESTIVAS REV ESP ENFERM DIG (Madrid) Copyright © 2006 ARÁN EDICIONES, S. L. Vol. 98. N.° 4, pp. 265-291, 2006 POINT OF VIEW Biologic therapies for chronic inflammatory bowel disease M. P. Martínez-Montiel and M. T. Muñoz-Yagüe Service of Digestive Diseases. Hospital Universitario 12 de Octubre. Madrid, Spain ABSTRACT Martínez-Montiel MP, Muñoz-Yagüe MT. Biologic therapies for chronic inflammatory bowel disease. Rev Esp Enferm Dig Crohn's disease (CD) and ulcerative colitis (UC) make up the 2006; 98: 265-291. so-called chronic inflammatory bowel disease (IBD). Advances in the understanding of IBD pathophysiologic mechanisms in the last few years have allowed the development of novel therapies such as biologic therapies, which at least theoretically represent a more INTRODUCTION specific management of this disease with fewer side effects. Cur- rently, the only effective and widely accepted biologic therapy for the treatment of intraluminal, fistulizing CD, both for remission in- Crohn’s disease (CD) and ulcerative colitis (UC) make duction and maintenance, is infliximab. The role of other mono- up the so-called inflammatory bowel disease (IBD). Ad- clonal antibodies such as adalimumab is not clearly established. It vances in the knowledge of this condition’s etiopathogene- could be deemed an alternative for patients with allergic reactions sis have been correlated to the development of novel thera- to infliximab, and for those with lost response because of anti-in- peutic agents. Medical treatment is currently the fliximab antibody development. -
Protein Design Labs, Inc. 2002 Annual Report Rti Einlb,Ic 2002Annual Report Protein Design Labs, Inc
PROTEIN DESIGN LABS, INC. 2002 ANNUAL REPORT PROTEIN DESIGN LABS, INC. 2002 ANNUAL REPORT WE HAVE THE RIGHT ASSETS, RIGHT HERE, RIGHT NOW. HERE’S WHAT WE’RE GOING Protein Design Labs, Inc. 34801 Campus Drive Fremont, CA 94555 TO DO WITH THEM. www.pdl.com Protein Design Labs, Inc. is a leader in the development of humanized monoclonal antibodies to treat various disease conditions. We currently have antibodies in clinical development for autoimmune and inflammatory conditions, asthma and cancer. We hold fundamental patents that cover our antibody humanization technology. This technology is also used by numerous other pharmaceutical and biotechnology companies, many of which have licensed our patents, and have agreed to pay royalties to us on any sales of licensed products. We receive royalties on sales of four currently marketed humanized antibodies. Client: Protein Design Labs Acct. Director: Bob Prow (x21) Creative Director: Bob Prow (x21) Client: Protein Design Labs Acct. Director: Bob Prow (x21) Creative Director: Bob Prow (x21) Job No: PDL02-199F Client Contact: Jim Goff Designer: Kristin Ritchie Job No: PDL02-199F Client Contact: Jim Goff Designer: Kristin Ritchie 1 Job Title: 2002 Annual Report Client Phone: Revised By: Kristin Ritchie (x22) 7 Job Title: 2002 Annual Report Client Phone: Revised By: Kristin Ritchie (x22) Refine and focus our research and development processes for humanized antibody products by 2003. Place an average of two proprietary product candidates into clinical trials each year after 2004. Initiate at least one pivotal clinical trial by 2005. Validate our own commercial manufacturing facility by 2006. OUR STRATEGY: MARKET OUR OWN MEDICINE TO BRING FULLER LIVES TO PATIENTS BY 2007. -
Alteration of Epileptogenesis Genes
Neurotherapeutics: The Journal of the American Society for Experimental NeuroTherapeutics Alteration of Epileptogenesis Genes Amy R. Brooks-Kayal,*† Yogendra H. Raol,* and Shelley J. Russek‡ *Division of Neurology, Department of Pediatrics, University of Colorado Denver School of Medicine, †The Children’s Hospital, Aurora, Colorado 80045, and ‡Laboratory of Translational Epilepsy, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, Massachusetts 02118 Summary: Retrospective studies suggest that precipitating expression and function have been reported in adult animals events such as prolonged seizures, stroke, or head trauma in- beginning immediately after prolonged seizures (status epilepticus crease the risk of developing epilepsy later in life. The process [SE]) and continue as animals become chronically epileptic. Pre- of epilepsy development, known as epileptogenesis, is associ- vention of GABAA receptor subunit changes after SE using viral ated with changes in the expression of a myriad of genes. One gene transfer inhibits development of epilepsy in an animal model, of the major challenges for the epilepsy research community suggesting that these changes directly contribute to epileptogen- has been to determine which of these changes contributes to esis. The mechanisms that regulate differential expression of epileptogenesis, which may be compensatory, and which may GABAA receptor subunits in hippocampus after SE have recently be noncontributory. Establishing this for any given gene