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The Application of a Characterized Pre-Clinical
THE APPLICATION OF A CHARACTERIZED PRE-CLINICAL GLIOBLASTOMA ONCOSPHERE MODEL TO IN VITRO AND IN VIVO THERAPEUTIC TESTING by Kelli M. Wilson A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland March, 2014 ABSTRACT Glioblastoma multiforme (GBM) is a lethal brain cancer with a median survival time (MST) of approximately 15 months following treatment. A serious challenge facing the development of new drugs for the treatment of GBM is that preclinical models fail to replicate the human GBM phenotype. Here we report the Johns Hopkins Oncosphere Panel (JHOP), a panel of GBM oncosphere cell lines. These cell lines were validated by their ability to form tumors intracranially with histological features of human GBM and GBM variant tumors. We then completed whole exome sequencing on JHOP and found that they contain genetic alterations in GBM driver genes such as PTEN, TP53 and CDKN2A. Two JHOP cell lines were utilized in a high throughput drug screen of 466 compounds that were selected to represent late stage clinical development and a wide range of mechanisms. Drugs that were inhibitory in both cell lines were EGFR inhibitors, NF-kB inhibitors and apoptosis activators. We also examined drugs that were inhibitory in a single cell line. Effective drugs in the PTEN null and NF1 wild type cell line showed a limited number of drug targets with EGFR inhibitors being the largest group of cytotoxic compounds. However, in the PTEN mutant, NF1 null cell line, VEGFR/PDGFR inhibitors and dual PIK3/mTOR inhibitors were the most common effective compounds. -
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. -
Options for the Treatment of Gemcitabine-Resistant Advanced Pancreatic Cancer
JOP. J Pancreas (Online) 2010 Mar 5; 11(2):113-123. REVIEW Options for the Treatment of Gemcitabine-Resistant Advanced Pancreatic Cancer Ioannis Gounaris, Kamarul Zaki, Pippa Corrie Oncology Centre, Cambridge University Hospitals NHS Trust. Cambridge, United Kingdom Summary Context Pancreatic cancer is noteworthy in that the number of patients dying from the disease is roughly equal to the number diagnosed. For more than a decade, gemcitabine has constituted the standard of care for the palliative treatment of the majority of patients who present with metastatic or relapsed disease, although the survival gains are limited. Despite a median survival of less than 6 months, there is a significant proportion of advanced pancreatic cancer patients who progress on gemcitabine that remains fit and these patients are candidates for second-line treatment. Methods The OVID MEDLINE database was searched from 1950 to present using the MeSH terms “pancreatic neoplasms”, “drug treatment” and “gemcitabine”. After excluding non-relevant results, 31 published studies were identified. These results were supplemented by searching the last three (2007-2009) American Society of Clinical Oncology (ASCO) Proceedings of Annual Meetings for studies published only in abstract form and reviewing reference lists of published articles. Results and discussion The evidence for second line treatments of metastatic pancreatic cancer consists mostly of single arm, small phase II studies. Oxaliplatin-fluoropyrimidine combinations appear promising and have shown increased survival compared to best supportive care. As the molecular pathways governing pancreatic cancer are unravelled, novel targeted therapies may offer the greatest promise for this disease either given alone, combined with one another, or with cytotoxic agents. -
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. -
LEUKEMIA CHEMOTHERAPY REGIMENS (Part 1 of 2) the Selection, Dosing, and Administration of Anti-Cancer Agents and the Management of Associated Toxicities Are Complex
LEUKEMIA CHEMOTHERAPY REGIMENS (Part 1 of 2) The selection, dosing, and administration of anti-cancer agents and the management of associated toxicities are complex. Drug dose modifications and schedule and initiation of supportive care interventions are often necessary because of expected toxicities and because of individual patient variability, prior treatment, and comorbidities. Thus, the optimal delivery of anti-cancer agents requires a healthcare delivery team experienced in the use of such agents and the management of associated toxicities in patients with cancer. The chemotherapy regimens below may include both FDA-approved and unapproved uses/regimens and are provided as references only to the latest treatment strategies. Clinicians must choose and verify treatment options based on the individual patient. REGIMEN DOSING Acute Myeloid Leukemia (AML) Induction Therapy Cytarabine (Cytosar-U; ARA-C) + Days 1–3: An anthracycline (eg, daunorubicin at least 60mg/m2/day IV, an anthracycline idarubicin 10–12mg/m2/day IV, or mitoxantrone 10–12mg/m2/day IV), plus (daunorubicin [Cerubidine], Days 1–7: Cytarabine 100–200mg/m2/day continuous IV infusion. idarubicin [Idamycin], OR mitoxantrone [Novantrone])1, 2 Days 1–3: An anthracycline (eg, daunorubicin 45mg/m2/day IV, idarubicin 12mg/m2/day IV, or mitoxantrone 12mg/m2/day IV), plus Days 1–7: Cytarabine 100mg/m2/day continuous IV infusion. Intermediate-dose cytarabine3 Cycle 1 Days 1–7: Cytarabine 200mg/m2/day continuous IV infusion, plus Days 5–6: Idarubicin 12mg/m2/day IV. Cycle 2 Days 1–6: Cytarabine 1,000mg/m2 continuous IV infusion for 3 hrs twice daily, plus Days 3, 5 and 7: Amsacrine 120mg/m2/day. -
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. -
(DAC) Followed by Clofarabine, Idarubicin, and Cytarabine (CIA) in Acute Leukemia 2012-1064
2012-1064 September 02, 2014 Page 1 Protocol Page Phase I/II Study of Decitabine (DAC) followed by Clofarabine, Idarubicin, and Cytarabine (CIA) in Acute Leukemia 2012-1064 Core Protocol Information Short Title Decitabine followed by Clofarabine, Idarubicin, and Cytarabine in Acute Leukemia Study Chair: Nitin Jain Additional Contact: Allison Pike Jeannice Y. Theriot Leukemia Protocol Review Group Department: Leukemia Phone: 713-745-6080 Unit: 428 Full Title: Phase I/II Study of Decitabine (DAC) followed by Clofarabine, Idarubicin, and Cytarabine (CIA) in Acute Leukemia Protocol Type: Standard Protocol Protocol Phase: Phase I/Phase II Version Status: Terminated 01/12/2018 Version: 12 Submitted by: Jeannice Y. Theriot--4/26/2017 2:13:38 PM OPR Action: Accepted by: Melinda E. Gordon -- 5/1/2017 7:55:15 AM Which Committee will review this protocol? The Clinical Research Committee - (CRC) 2012-1064 September 02, 2014 Page 2 Protocol Body Phase I/II Study of Decitabine (DAC) followed by Clofarabine, Idarubicin, and Cytarabine (CIA) in Acute Leukemia 1. OBJECTIVES Phase I Primary: To determine the maximal tolerated dose (MTD) of clofarabine to be used in portion II of the study Phase II Primary: To determine the response rate of the DAC-CIA regimen Secondary: A) To determine the toxicity of the combination regimen B) To determine the disease-free survival (DFS) and overall survival (OS) rates 2. RATIONALE 2.1 Acute Myelogenous Leukemia Acute myelogenous leukemia (AML) is the most common acute leukemia in adults. It is estimated that 13,780 men and women will be diagnosed with and 10,200 men and women will die of acute myeloid leukemia in the year 2012.1 AML is a disease with a poor prognosis with a 5-year survival of only around 30%.2,3 Certain subgroups of AML have a particularly worse Page 1 of 34 outcome such as patients with relapsed and/or refractory AML and AML arising from antecedent myelodysplastic syndrome (MDS) or myeloproliferative neoplasms (MPNs). -
Drug Name Plate Number Well Location % Inhibition, Screen Axitinib 1 1 20 Gefitinib (ZD1839) 1 2 70 Sorafenib Tosylate 1 3 21 Cr
Drug Name Plate Number Well Location % Inhibition, Screen Axitinib 1 1 20 Gefitinib (ZD1839) 1 2 70 Sorafenib Tosylate 1 3 21 Crizotinib (PF-02341066) 1 4 55 Docetaxel 1 5 98 Anastrozole 1 6 25 Cladribine 1 7 23 Methotrexate 1 8 -187 Letrozole 1 9 65 Entecavir Hydrate 1 10 48 Roxadustat (FG-4592) 1 11 19 Imatinib Mesylate (STI571) 1 12 0 Sunitinib Malate 1 13 34 Vismodegib (GDC-0449) 1 14 64 Paclitaxel 1 15 89 Aprepitant 1 16 94 Decitabine 1 17 -79 Bendamustine HCl 1 18 19 Temozolomide 1 19 -111 Nepafenac 1 20 24 Nintedanib (BIBF 1120) 1 21 -43 Lapatinib (GW-572016) Ditosylate 1 22 88 Temsirolimus (CCI-779, NSC 683864) 1 23 96 Belinostat (PXD101) 1 24 46 Capecitabine 1 25 19 Bicalutamide 1 26 83 Dutasteride 1 27 68 Epirubicin HCl 1 28 -59 Tamoxifen 1 29 30 Rufinamide 1 30 96 Afatinib (BIBW2992) 1 31 -54 Lenalidomide (CC-5013) 1 32 19 Vorinostat (SAHA, MK0683) 1 33 38 Rucaparib (AG-014699,PF-01367338) phosphate1 34 14 Lenvatinib (E7080) 1 35 80 Fulvestrant 1 36 76 Melatonin 1 37 15 Etoposide 1 38 -69 Vincristine sulfate 1 39 61 Posaconazole 1 40 97 Bortezomib (PS-341) 1 41 71 Panobinostat (LBH589) 1 42 41 Entinostat (MS-275) 1 43 26 Cabozantinib (XL184, BMS-907351) 1 44 79 Valproic acid sodium salt (Sodium valproate) 1 45 7 Raltitrexed 1 46 39 Bisoprolol fumarate 1 47 -23 Raloxifene HCl 1 48 97 Agomelatine 1 49 35 Prasugrel 1 50 -24 Bosutinib (SKI-606) 1 51 85 Nilotinib (AMN-107) 1 52 99 Enzastaurin (LY317615) 1 53 -12 Everolimus (RAD001) 1 54 94 Regorafenib (BAY 73-4506) 1 55 24 Thalidomide 1 56 40 Tivozanib (AV-951) 1 57 86 Fludarabine -
Corporate Overview May 2017
Corporate Overview May 2017 DEVELOPING PRECISION MEDICINES TO TREAT CANCER Forward Looking Statements This presentation contains forward-looking statements. Such statements include, but are not limited to, statements regarding our research, pre-clinical and clinical development activities, plans and projected timelines for tipifarnib, KO- 947 and KO-539, plans regarding regulatory filings, our expectations regarding the relative benefits of our product candidates versus competitive therapies, and our expectations regarding the therapeutic and commercial potential of our product candidates. The words “believe,” “may,” “will,” “estimate,” “promise,” “plan”, “continue,” “anticipate,” “intend,” “expect,” “potential” and similar expressions (including the negative thereof), are intended to identify forward-looking statements. Because such statements are subject to risks and uncertainties, actual results may differ materially from those expressed or implied by such forward-looking statements. Risks that contribute to the uncertain nature of the forward-looking statements include: our future preclinical studies and clinical trials may not be successful; the U.S. Food and Drug Administration (FDA) may not agree with our interpretation of the data from clinical trials of our product candidates; we may decide, or the FDA may require us, to conduct additional clinical trials or to modify our ongoing clinical trials; we may experience delays in the commencement, enrollment, completion or analysis of clinical testing for our product candidates, or significant issues regarding the adequacy of our clinical trial designs or the execution of our clinical trials may arise, which could result in increased costs and delays, or limit our ability to obtain regulatory approval; our product candidates may not receive regulatory approval or be successfully commercialized; unexpected adverse side effects or inadequate therapeutic efficacy of our product candidates could delay or prevent regulatory approval or commercialization; we may not be able to obtain additional financing. -
(12) United States Patent (10) Patent No.: US 8,911,786 B2 Desai Et Al
US00891. 1786B2 (12) United States Patent (10) Patent No.: US 8,911,786 B2 Desai et al. (45) Date of Patent: Dec. 16, 2014 (54) NANOPARTICLE COMPRISING RAPAMYCIN A61K 45/06 (2013.01); A61K 47/42 (2013.01); AND ALBUMINAS ANTICANCERAGENT A61N 5/10 (2013.01); A61N 7700 (2013.01) (75) Inventors: Neil P. Desai, Los Angeles, CA (US); USPC ............ 424/491; 424/489: 424/490; 424/500 Patrick Soon-Shiong, Los Angeles, CA (58) Field of Classification Search (US); Vuong Trieu, Calabasas, CA (US) USPC .......... 424/465-489, 490, 491, 500: 514/19.3 See application file for complete search history. (73) Assignee: Abraxis Bioscience, LLC, Los Angeles, CA (US) (56) References Cited (*) Notice: Subject to any disclaimer, the term of this patent is extended or adjusted under 35 U.S. PATENT DOCUMENTS U.S.C. 154(b) by 344 days. 5,206,018 A * 4/1993 Sehgal et al. ................. 424,122 5,362.478 A 11/1994 Desai et al. (21) Appl. No.: 12/530,188 5.439,686 A 8, 1995 Desai et al. 5,498.421 A 3, 1996 Grinstaffet al. (22) PCT Filed: Mar. 7, 2008 5,505,932 A 4/1996 Grinstaffet al. 5,508,021 A 4/1996 Grinstaffet al. (86). PCT No.: PCT/US2O08/OO3O96 5,512,268 A 4/1996 Grinstaffet al. 5,540,931 A 7/1996 Hewitt et al. S371 (c)(1), 5,560,933 A 10/1996 Soon-Shiong et al. (2), (4) Date: Mar. 4, 2010 5,635,207 A 6/1997 Grinstaffet al. 5,639,473 A 6/1997 Grinstaffet al. -
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