HSP90 Is Necessary for the ACK1-Dependent Phosphorylation of STAT1 and MARK STAT3
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Mutation-Specific and Common Phosphotyrosine Signatures of KRAS G12D and G13D Alleles Anticipated Graduation August 1St, 2018
MUTATION-SPECIFIC AND COMMON PHOSPHOTYROSINE SIGNATURES OF KRAS G12D AND G13D ALLELES by Raiha Tahir A dissertation submitted to The Johns Hopkins University in conformity with the requirement of the degree of Doctor of Philosophy Baltimore, MD August 2018 © 2018 Raiha Tahir All Rights Reserved ABSTRACT KRAS is one of the most frequently mutated genes across all cancer subtypes. Two of the most frequent oncogenic KRAS mutations observed in patients result in glycine to aspartic acid substitution at either codon 12 (G12D) or 13 (G13D). Although the biochemical differences between these two predominant mutations are not fully understood, distinct clinical features of the resulting tumors suggest involvement of disparate signaling mechanisms. When we compared the global phosphotyrosine proteomic profiles of isogenic colorectal cancer cell lines bearing either G12D or G13D KRAS mutations, we observed both shared as well as unique signaling events induced by the two KRAS mutations. Remarkably, while the G12D mutation led to an increase in membrane proximal and adherens junction signaling, the G13D mutation led to activation of signaling molecules such as non-receptor tyrosine kinases, MAPK kinases and regulators of metabolic processes. The importance of one of the cell surface molecules, MPZL1, which found to be hyperphosphorylated in G12D cells, was confirmed by cellular assays as its knockdown led to a decrease in proliferation of G12D but not G13D expressing cells. Overall, our study reveals important signaling differences across two common KRAS mutations and highlights the utility of our approach to systematically dissect the subtle differences between related oncogenic mutants and potentially lead to individualized treatments. -
Src-Family Kinases Impact Prognosis and Targeted Therapy in Flt3-ITD+ Acute Myeloid Leukemia
Src-Family Kinases Impact Prognosis and Targeted Therapy in Flt3-ITD+ Acute Myeloid Leukemia Title Page by Ravi K. Patel Bachelor of Science, University of Minnesota, 2013 Submitted to the Graduate Faculty of School of Medicine in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Pittsburgh 2019 Commi ttee Membership Pa UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE Commi ttee Membership Page This dissertation was presented by Ravi K. Patel It was defended on May 31, 2019 and approved by Qiming (Jane) Wang, Associate Professor Pharmacology and Chemical Biology Vaughn S. Cooper, Professor of Microbiology and Molecular Genetics Adrian Lee, Professor of Pharmacology and Chemical Biology Laura Stabile, Research Associate Professor of Pharmacology and Chemical Biology Thomas E. Smithgall, Dissertation Director, Professor and Chair of Microbiology and Molecular Genetics ii Copyright © by Ravi K. Patel 2019 iii Abstract Src-Family Kinases Play an Important Role in Flt3-ITD Acute Myeloid Leukemia Prognosis and Drug Efficacy Ravi K. Patel, PhD University of Pittsburgh, 2019 Abstract Acute myelogenous leukemia (AML) is a disease characterized by undifferentiated bone-marrow progenitor cells dominating the bone marrow. Currently the five-year survival rate for AML patients is 27.4 percent. Meanwhile the standard of care for most AML patients has not changed for nearly 50 years. We now know that AML is a genetically heterogeneous disease and therefore it is unlikely that all AML patients will respond to therapy the same way. Upregulation of protein-tyrosine kinase signaling pathways is one common feature of some AML tumors, offering opportunities for targeted therapy. -
Supplementary Table 1. in Vitro Side Effect Profiling Study for LDN/OSU-0212320. Neurotransmitter Related Steroids
Supplementary Table 1. In vitro side effect profiling study for LDN/OSU-0212320. Percent Inhibition Receptor 10 µM Neurotransmitter Related Adenosine, Non-selective 7.29% Adrenergic, Alpha 1, Non-selective 24.98% Adrenergic, Alpha 2, Non-selective 27.18% Adrenergic, Beta, Non-selective -20.94% Dopamine Transporter 8.69% Dopamine, D1 (h) 8.48% Dopamine, D2s (h) 4.06% GABA A, Agonist Site -16.15% GABA A, BDZ, alpha 1 site 12.73% GABA-B 13.60% Glutamate, AMPA Site (Ionotropic) 12.06% Glutamate, Kainate Site (Ionotropic) -1.03% Glutamate, NMDA Agonist Site (Ionotropic) 0.12% Glutamate, NMDA, Glycine (Stry-insens Site) 9.84% (Ionotropic) Glycine, Strychnine-sensitive 0.99% Histamine, H1 -5.54% Histamine, H2 16.54% Histamine, H3 4.80% Melatonin, Non-selective -5.54% Muscarinic, M1 (hr) -1.88% Muscarinic, M2 (h) 0.82% Muscarinic, Non-selective, Central 29.04% Muscarinic, Non-selective, Peripheral 0.29% Nicotinic, Neuronal (-BnTx insensitive) 7.85% Norepinephrine Transporter 2.87% Opioid, Non-selective -0.09% Opioid, Orphanin, ORL1 (h) 11.55% Serotonin Transporter -3.02% Serotonin, Non-selective 26.33% Sigma, Non-Selective 10.19% Steroids Estrogen 11.16% 1 Percent Inhibition Receptor 10 µM Testosterone (cytosolic) (h) 12.50% Ion Channels Calcium Channel, Type L (Dihydropyridine Site) 43.18% Calcium Channel, Type N 4.15% Potassium Channel, ATP-Sensitive -4.05% Potassium Channel, Ca2+ Act., VI 17.80% Potassium Channel, I(Kr) (hERG) (h) -6.44% Sodium, Site 2 -0.39% Second Messengers Nitric Oxide, NOS (Neuronal-Binding) -17.09% Prostaglandins Leukotriene, -
TRK Inhibitors: Tissue-Agnostic Anti-Cancer Drugs
pharmaceuticals Review TRK Inhibitors: Tissue-Agnostic Anti-Cancer Drugs Sun-Young Han Research Institute of Pharmaceutical Sciences and College of Pharmacy, Gyeongsang National University, Jinju-si 52828, Korea; [email protected] Abstract: Recently, two tropomycin receptor kinase (Trk) inhibitors, larotrectinib and entrectinib, have been approved for Trk fusion-positive cancer patients. Clinical trials for larotrectinib and entrectinib were performed with patients selected based on the presence of Trk fusion, regardless of cancer type. This unique approach, called tissue-agnostic development, expedited the process of Trk inhibitor development. In the present review, the development processes of larotrectinib and entrectinib have been described, along with discussion on other Trk inhibitors currently in clinical trials. The on-target effects of Trk inhibitors in Trk signaling exhibit adverse effects on the central nervous system, such as withdrawal pain, weight gain, and dizziness. A next generation sequencing-based method has been approved for companion diagnostics of larotrectinib, which can detect various types of Trk fusions in tumor samples. With the adoption of the tissue-agnostic approach, the development of Trk inhibitors has been accelerated. Keywords: Trk; NTRK; tissue-agnostic; larotrectinib; entrectinib; Trk fusion 1. Introduction Citation: Han, S.-Y. TRK Inhibitors: Tropomyosin receptor kinases (Trk) are tyrosine kinases encoded by neurotrophic Tissue-Agnostic Anti-Cancer Drugs. tyrosine/tropomyosin receptor kinase (NTRK) genes [1]. Chromosomal rearrangement of Pharmaceuticals 2021, 14, 632. https:// NTRK genes is found in cancer tissues [2]. The resulting fusion proteins containing part of doi.org/10.3390/ph14070632 the Trk protein have a constitutively active form of kinase that transduces deregulating signals. -
The Non-Receptor Tyrosine Kinase TNK2/ACK1 Is a Novel Therapeutic Target in Triple Negative Breast Cancer
www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 2), pp: 2971-2983 Research Paper The non-receptor tyrosine kinase TNK2/ACK1 is a novel therapeutic target in triple negative breast cancer Xinyan Wu1,2,*, Muhammad Saddiq Zahari1,2,*, Santosh Renuse1,2,5, Dhanashree S. Kelkar1,2, Mustafa A. Barbhuiya2, Pamela L. Rojas1,2, Vered Stearns3, Edward Gabrielson3,4, Pavani Malla6, Saraswati Sukumar3, Nupam P. Mahajan6,7, Akhilesh Pandey1,2,3,4 1Department of Biological Chemistry, Johns Hopkins University School of Medicine Baltimore, MD 21205, U.S.A 2McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, U.S.A 3Department of Oncology, Johns Hopkins University School of Medicine Baltimore, MD 21205, U.S.A 4Department of Pathology, Johns Hopkins University School of Medicine Baltimore, MD 21205, U.S.A 5Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India 6Department of Drug Discovery, Moffitt Cancer Center, Tampa, FL 33612, U.S.A 7Department of Oncologic Sciences, University of South Florida, Tampa, FL 33612, U.S.A *These authors have contributed equally to this work Correspondence to: Xinyan Wu, email: [email protected] Nupam P. Mahajan, email: [email protected] Akhilesh Pandey, email: [email protected] Keywords: TNK2, triple negative breast cancer, tyrosine kinase, phosphorylation Received: March 11, 2016 Accepted: October 10, 2016 Published: November 25, 2016 ABSTRACT Breast cancer is the most prevalent cancer in women worldwide. About 15-20% of all breast cancers do not express estrogen receptor, progesterone receptor or HER2 receptor and hence are collectively classified as triple negative breast cancer (TNBC). -
Abl P210 and P190 Kinases in Leukemia Cells Defined By
OPEN Leukemia (2017) 31, 1502–1512 www.nature.com/leu ORIGINAL ARTICLE Differential signaling networks of Bcr–Abl p210 and p190 kinases in leukemia cells defined by functional proteomics S Reckel1, R Hamelin2, S Georgeon1, F Armand2, Q Jolliet2, D Chiappe2, M Moniatte2 and O Hantschel1 The two major isoforms of the oncogenic Bcr–Abl tyrosine kinase, p210 and p190, are expressed upon the Philadelphia chromosome translocation. p210 is the hallmark of chronic myelogenous leukemia, whereas p190 occurs in the majority of B-cell acute lymphoblastic leukemia. Differences in protein interactions and activated signaling pathways that may be associated with the different diseases driven by p210 and p190 are unknown. We have performed a quantitative comparative proteomics study of p210 and p190. Strong differences in the interactome and tyrosine phosphoproteome were found and validated. Whereas the AP2 adaptor complex that regulates clathrin-mediated endocytosis interacts preferentially with p190, the phosphatase Sts1 is enriched with p210. Stronger activation of the Stat5 transcription factor and the Erk1/2 kinases is observed with p210, whereas Lyn kinase is activated by p190. Our findings provide a more coherent understanding of Bcr–Abl signaling, mechanisms of leukemic transformation, resulting disease pathobiology and responses to kinase inhibitors. Leukemia (2017) 31, 1502–1512; doi:10.1038/leu.2017.36 INTRODUCTION experimental conditions, the expression of p190 lead to a disease The Bcr–Abl kinase and its inhibitors (imatinib and successors) are with a shorter latency and more B-ALL, whereas p210 mice 9,11–13 a paradigm for targeted cancer therapy.1 Bcr–Abl is a constitu- developed CML-like leukemias. -
Amplification of the Human Epidermal Growth Factor Receptor 2 (HER2) Gene Is Associated with a Microsatellite Stable Status in Chinese Gastric Cancer Patients
387 Original Article Amplification of the human epidermal growth factor receptor 2 (HER2) gene is associated with a microsatellite stable status in Chinese gastric cancer patients He Huang1#, Zhengkun Wang2#, Yi Li2, Qun Zhao3, Zhaojian Niu2 1Department of Gastrointestinal Surgery, The First Hospital of Shanxi Medical University, Shanxi, China; 2Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China; 3Department of Gastrosurgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China Contributions: I) Conception and design: Z Niu, Q Zhao, H Huang; (II) Administrative support: Z Niu, H Huang, Z Wang; (III) Provision of study materials or patients: All authors; (IV) Collection and assembly of data: Z Wang, Q Zhao; (V) Data analysis and interpretation: Z Niu, H Huang; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors. #These authors contributed equally to this work. Correspondence to: Zhaojian Niu. Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, No. 16, Jiangsu Road, Shinan District, Qingdao 260003, China. Email: [email protected]; Qun Zhao. Department of Gastrosurgery, The Fourth Hospital of Hebei Medical University, No. 12 Jiankang Road, Shijiazhuang 050011, China. Email: [email protected]. Background: Gastric cancer (GC) is one of the most common cancers worldwide. However, little is known about the combination of HER2 amplification and microsatellite instability (MSI) status in GC. This study aimed to analyze the correlation of HER2 amplification with microsatellite instability (MSI) status, clinical characteristics, and the tumor mutational burden (TMB) of patients. Methods: A total of 192 gastric cancer (GC) patients were enrolled in this cohort. To analyze genomic alterations (GAs), deep sequencing was performed on 450 target cancer genes. -
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bioRxiv preprint doi: https://doi.org/10.1101/259192; this version posted February 2, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. INKA, an integrative data analysis pipeline for phosphoproteomic inference of active phosphokinases Thang V. Pham1,2, Robin Beekhof1,2, Carolien van Alphen1,2, Jaco C. Knol1, Alex A. Henneman1, Frank Rolfs1, Mariette Labots1, Evan Henneberry1, Tessa Y.S. Le Large1, Richard R. de Haas1, Sander R. Piersma1, Henk M.W. Verheul1, Connie R. Jimenez1 * 1 OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands 2 These authors contributed equally to this work * Correspondence should be addressed to C.R.J. ([email protected]) Running Title: Integrative tool ranks active kinases Character Count: 50,356 1 bioRxiv preprint doi: https://doi.org/10.1101/259192; this version posted February 2, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Abstract 2 3 Identifying (hyper)active kinases in cancer patient tumors is crucial to enable individualized 4 treatment with specific inhibitors. Conceptually, kinase activity can be gleaned from global 5 protein phosphorylation profiles obtained with mass spectrometry-based phosphoproteomics. A 6 major challenge is to relate such profiles to specific kinases to identify (hyper)active kinases that 7 may fuel growth/progression of individual tumors. Approaches have hitherto focused on 8 phosphorylation of either kinases or their substrates. -
Entry by Multiple Picornaviruses Is Dependent on a Pathway That Includes TNK2, WASL, and NCK1 Hongbing Jiang*, Christian Leung, Stephen Tahan, David Wang*
RESEARCH ARTICLE Entry by multiple picornaviruses is dependent on a pathway that includes TNK2, WASL, and NCK1 Hongbing Jiang*, Christian Leung, Stephen Tahan, David Wang* Department of Molecular Microbiology, Pathology and Immunology, School of Medicine, Washington University, St. Louis, United States Abstract Comprehensive knowledge of the host factors required for picornavirus infection would facilitate antiviral development. Here we demonstrate roles for three human genes, TNK2, WASL, and NCK1, in infection by multiple picornaviruses. CRISPR deletion of TNK2, WASL, or NCK1 reduced encephalomyocarditis virus (EMCV), coxsackievirus B3 (CVB3), poliovirus and enterovirus D68 infection, and chemical inhibitors of TNK2 and WASL decreased EMCV infection. Reduced EMCV lethality was observed in mice lacking TNK2. TNK2, WASL, and NCK1 were important in early stages of the viral lifecycle, and genetic epistasis analysis demonstrated that the three genes function in a common pathway. Mechanistically, reduced internalization of EMCV was observed in TNK2 deficient cells demonstrating that TNK2 functions in EMCV entry. Domain analysis of WASL demonstrated that its actin nucleation activity was necessary to facilitate viral infection. Together, these data support a model wherein TNK2, WASL, and NCK1 comprise a pathway important for multiple picornaviruses. Introduction Picornaviruses cause a wide range of diseases including the common cold, hepatitis, myocarditis, *For correspondence: [email protected] (HJ); poliomyelitis, meningitis, and encephalitis (Melnick, 1983). Although vaccines exist for poliovirus [email protected] (DW) and hepatitis A virus, there are currently no FDA approved antivirals against picornaviruses in the United States. As obligate intracellular pathogens, viruses are dependent on the host cellular Competing interests: The machinery to complete their lifecycle. -
Human Breast Cancer Associated Fibroblasts Exhibit Subtype Specific
Tchou et al. BMC Medical Genomics 2012, 5:39 http://www.biomedcentral.com/1755-8794/5/39 RESEARCH ARTICLE Open Access Human breast cancer associated fibroblasts exhibit subtype specific gene expression profiles Julia Tchou1*, Andrew V Kossenkov2, Lisa Chang2, Celine Satija1, Meenhard Herlyn2, Louise C Showe2† and Ellen Puré2† Abstract Background: Breast cancer is a heterogeneous disease for which prognosis and treatment strategies are largely governed by the receptor status (estrogen, progesterone and Her2) of the tumor cells. Gene expression profiling of whole breast tumors further stratifies breast cancer into several molecular subtypes which also co-segregate with the receptor status of the tumor cells. We postulated that cancer associated fibroblasts (CAFs) within the tumor stroma may exhibit subtype specific gene expression profiles and thus contribute to the biology of the disease in a subtype specific manner. Several studies have reported gene expression profile differences between CAFs and normal breast fibroblasts but in none of these studies were the results stratified based on tumor subtypes. Methods: To address whether gene expression in breast cancer associated fibroblasts varies between breast cancer subtypes, we compared the gene expression profiles of early passage primary CAFs isolated from twenty human breast cancer samples representing three main subtypes; seven ER+, seven triple negative (TNBC) and six Her2+. Results: We observed significant expression differences between CAFs derived from Her2+ breast cancer and CAFs from TNBC and ER + cancers, particularly in pathways associated with cytoskeleton and integrin signaling. In the case of Her2+ breast cancer, the signaling pathways found to be selectively up regulated in CAFs likely contribute to the enhanced migration of breast cancer cells in transwell assays and may contribute to the unfavorable prognosis of Her2+ breast cancer. -
Potentiating Therapeutic Effects of Epidermal Growth Factor Receptor Inhibition in Triple-Negative Breast Cancer
pharmaceuticals Review Potentiating Therapeutic Effects of Epidermal Growth Factor Receptor Inhibition in Triple-Negative Breast Cancer Kyu Sic You 1,2,† , Yong Weon Yi 3,† , Jeonghee Cho 3 , Jeong-Soo Park 1,* and Yeon-Sun Seong 1,2,3,* 1 Department of Biochemistry, College of Medicine, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea; [email protected] 2 Graduate School of Convergence Medical Science, Dankook University, Cheonan 3116, Chungcheongnam-do, Korea 3 Department of Nanobiomedical Science, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea; [email protected] (Y.W.Y.); [email protected] (J.C.) * Correspondence: [email protected] (J.-S.P.); [email protected] (Y.-S.S.); Tel.: +82-41-550-3876 (J.-S.P.); +82-41-550-3875 (Y.-S.S.) † These authors contributed equally to this work. Abstract: Triple-negative breast cancer (TNBC) is a subset of breast cancer with aggressive charac- teristics and few therapeutic options. The lack of an appropriate therapeutic target is a challenging issue in treating TNBC. Although a high level expression of epidermal growth factor receptor (EGFR) has been associated with a poor prognosis among patients with TNBC, targeted anti-EGFR therapies have demonstrated limited efficacy for TNBC treatment in both clinical and preclinical settings. However, with the advantage of a number of clinically approved EGFR inhibitors (EGFRis), combi- nation strategies have been explored as a promising approach to overcome the intrinsic resistance of TNBC to EGFRis. In this review, we analyzed the literature on the combination of EGFRis with Citation: You, K.S.; Yi, Y.W.; Cho, J.; other molecularly targeted therapeutics or conventional chemotherapeutics to understand the current Park, J.-S.; Seong, Y.-S. -
Identification and Characterization of Tyrosine Kinase Nonreceptor 2 Mutations in Leukemia Through Integration of Kinase Inhibitor Screening and Genomic Analysis
Published OnlineFirst December 17, 2015; DOI: 10.1158/0008-5472.CAN-15-0817 Cancer Therapeutics, Targets, and Chemical Biology Research Identification and Characterization of Tyrosine Kinase Nonreceptor 2 Mutations in Leukemia through Integration of Kinase Inhibitor Screening and Genomic Analysis Julia E. Maxson1,2,3, Melissa L. Abel1,2, Jinhua Wang4, Xianming Deng4, Sina Reckel5, Samuel B. Luty1,2, Huahang Sun6, Julie Gorenstein6, Seamus B. Hughes3, Daniel Bottomly1,7, Beth Wilmot1,7,8, Shannon K. McWeeney1,7,8, Jerald Radich3, Oliver Hantschel5, Richard E. Middleton6, Nathanael S. Gray4, Brian J. Druker1,2,9, and Jeffrey W. Tyner2,10 Abstract The amount of genomic information about leukemia cells exhibited oncogenic capacity. Importantly, the integration of currently far exceeds our overall understanding of the precise functional and genomic data using HitWalker allowed for genetic events that ultimately drive disease development and prioritization of rare oncogenic mutations that may have been progression. Effective implementation of personalized medi- missed through genomic analysis alone. These mutations were cine will require tools to distinguish actionable genetic altera- sensitive to the multikinase inhibitor dasatinib, which antag- tions within the complex genetic landscape of leukemia. In this onizes TNK2 kinase activity, as well as novel TNK2 inhibitors, study, we performed kinase inhibitor screens to predict func- XMD8-87 and XMD16-5, with greater target specificity. We also tional gene targets in primary specimens from patients with identified activating truncation mutations in other tumor types acute myeloid leukemia and chronic myelomonocytic leuke- that were sensitive to XMD8-87 and XMD16-5, exemplifying mia. Deep sequencing of the same patient specimens identified the potential utility of these compounds across tumor types genetic alterations that were then integrated with the function- dependent on TNK2.