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A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Distinct Transcriptional Programming Drive Response to MAPK Inhibition in BRAF -Mutant Melanoma Patient-Derived Xenografts
Published OnlineFirst September 16, 2019; DOI: 10.1158/1535-7163.MCT-19-0028 Cancer Biology and Translational Studies Molecular Cancer Therapeutics Distinct Transcriptional Programming Drive Response to MAPK Inhibition in BRAFV600-Mutant Melanoma Patient-Derived Xenografts Tianshu Feng, Javad Golji, Ailing Li, Xiamei Zhang, David A. Ruddy, Daniel P. Rakiec, Felipe C. Geyer, Jane Gu, Hui Gao, Juliet A.Williams, Darrin D. Stuart, and Matthew J. Meyer Abstract Inhibitors targeting BRAF and its downstream kinase MEK are preferentially sensitive to MAPK inhibition. These gene- produce robust response in patients with advanced BRAFV600- expression programs are somewhat similar to the MITF-high mutant melanoma. However, the duration and depth of and -low phenotypes described in cancer cell lines, but response vary significantly between patients; therefore, pre- demonstrate an inverse relationship with drug response. dicting response a priori remains a significant challenge. Here, This suggests a discrepancy between in vitro and in vivo we utilized the Novartis collection of patient-derived xeno- experimental systems that warrants future investigations. grafts to characterize transcriptional alterations elicited by Finally, BRAFV600-mutant melanoma relies on either MAPK BRAF and MEK inhibitors in vivo, in an effort to identify or alternative pathways for survival under BRAF and MEK mechanisms governing differential response to MAPK inhibi- inhibition in vivo, which in turn predicts their response to tion. We show that the expression of an MITF-high, "epithelial- further pathway suppression using a combination of BRAF, like" transcriptional program is associated with reduced MEK, and ERK inhibitors. Our findings highlight the inter- sensitivity and adaptive response to BRAF and MEK inhibitor tumor heterogeneity in BRAFV600-mutant melanoma, and treatment. -
Exosome-Mediated MIR211 Modulates Tumor Microenvironment Via the DUSP6-ERK5 Axis and Contributes to BRAFV600E Inhibitor Resistan
bioRxiv preprint doi: https://doi.org/10.1101/548818; this version posted February 13, 2019. 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. Exosome-mediated MIR211 modulates tumor microenvironment via the DUSP6-ERK5 axis and contributes to BRAFV600E inhibitor resistance in melanoma. Bongyong Lee1,3, Anupama Sahoo3, Junko Sawada1,3, John Marchica1,3, Sanjay Sahoo3, Fabiana I. A. L. Layng4, Darren Finlay4, Joseph Mazar5, Piyush Joshi1, Masanobu Komatsu1,3, Kristiina Vuori4, Garth Powis4, Petrus R. de Jong4, Animesh Ray6,7, and Ranjan J. Perera 1,2,3* 1 Department of Cancer and Blood Disorders Institute, Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701 USA 2 Department of Oncology, Sydney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA 3 Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827 USA 4 Sanford Burnham Prebys Medical Discovery Institute, NCI-Designated Cancer Center, La Jolla, CA 92037, USA 5 Nemours Children Hospital, Orlando, FL 32827 USA 6 Keck Graduate Institute, Claremont CA 91711 USA, 7 Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA. *Correspondence: Ranjan Perera Tel: 1-727-767-3491 Email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/548818; this version posted February 13, 2019. 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. ABSTRACT The microRNA MIR211 is an important regulator of melanoma tumor cell behavior. -
CDH12 Cadherin 12, Type 2 N-Cadherin 2 RPL5 Ribosomal
5 6 6 5 . 4 2 1 1 1 2 4 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 A A A A A A A A A A A A A A A A A A A A C C C C C C C C C C C C C C C C C C C C R R R R R R R R R R R R R R R R R R R R B , B B B B B B B B B B B B B B B B B B B , 9 , , , , 4 , , 3 0 , , , , , , , , 6 2 , , 5 , 0 8 6 4 , 7 5 7 0 2 8 9 1 3 3 3 1 1 7 5 0 4 1 4 0 7 1 0 2 0 6 7 8 0 2 5 7 8 0 3 8 5 4 9 0 1 0 8 8 3 5 6 7 4 7 9 5 2 1 1 8 2 2 1 7 9 6 2 1 7 1 1 0 4 5 3 5 8 9 1 0 0 4 2 5 0 8 1 4 1 6 9 0 0 6 3 6 9 1 0 9 0 3 8 1 3 5 6 3 6 0 4 2 6 1 0 1 2 1 9 9 7 9 5 7 1 5 8 9 8 8 2 1 9 9 1 1 1 9 6 9 8 9 7 8 4 5 8 8 6 4 8 1 1 2 8 6 2 7 9 8 3 5 4 3 2 1 7 9 5 3 1 3 2 1 2 9 5 1 1 1 1 1 1 5 9 5 3 2 6 3 4 1 3 1 1 4 1 4 1 7 1 3 4 3 2 7 6 4 2 7 2 1 2 1 5 1 6 3 5 6 1 3 6 4 7 1 6 5 1 1 4 1 6 1 7 6 4 7 e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m -
The Regulatory Roles of Phosphatases in Cancer
Oncogene (2014) 33, 939–953 & 2014 Macmillan Publishers Limited All rights reserved 0950-9232/14 www.nature.com/onc REVIEW The regulatory roles of phosphatases in cancer J Stebbing1, LC Lit1, H Zhang, RS Darrington, O Melaiu, B Rudraraju and G Giamas The relevance of potentially reversible post-translational modifications required for controlling cellular processes in cancer is one of the most thriving arenas of cellular and molecular biology. Any alteration in the balanced equilibrium between kinases and phosphatases may result in development and progression of various diseases, including different types of cancer, though phosphatases are relatively under-studied. Loss of phosphatases such as PTEN (phosphatase and tensin homologue deleted on chromosome 10), a known tumour suppressor, across tumour types lends credence to the development of phosphatidylinositol 3--kinase inhibitors alongside the use of phosphatase expression as a biomarker, though phase 3 trial data are lacking. In this review, we give an updated report on phosphatase dysregulation linked to organ-specific malignancies. Oncogene (2014) 33, 939–953; doi:10.1038/onc.2013.80; published online 18 March 2013 Keywords: cancer; phosphatases; solid tumours GASTROINTESTINAL MALIGNANCIES abs in sera were significantly associated with poor survival in Oesophageal cancer advanced ESCC, suggesting that they may have a clinical utility in Loss of PTEN (phosphatase and tensin homologue deleted on ESCC screening and diagnosis.5 chromosome 10) expression in oesophageal cancer is frequent, Cao et al.6 investigated the role of protein tyrosine phosphatase, among other gene alterations characterizing this disease. Zhou non-receptor type 12 (PTPN12) in ESCC and showed that PTPN12 et al.1 found that overexpression of PTEN suppresses growth and protein expression is higher in normal para-cancerous tissues than induces apoptosis in oesophageal cancer cell lines, through in 20 ESCC tissues. -
Curcumin Alters Gene Expression-Associated DNA Damage, Cell Cycle, Cell Survival and Cell Migration and Invasion in NCI-H460 Human Lung Cancer Cells in Vitro
ONCOLOGY REPORTS 34: 1853-1874, 2015 Curcumin alters gene expression-associated DNA damage, cell cycle, cell survival and cell migration and invasion in NCI-H460 human lung cancer cells in vitro I-TSANG CHIANG1,2, WEI-SHU WANG3, HSIN-CHUNG LIU4, SU-TSO YANG5, NOU-YING TANG6 and JING-GUNG CHUNG4,7 1Department of Radiation Oncology, National Yang‑Ming University Hospital, Yilan 260; 2Department of Radiological Technology, Central Taiwan University of Science and Technology, Taichung 40601; 3Department of Internal Medicine, National Yang‑Ming University Hospital, Yilan 260; 4Department of Biological Science and Technology, China Medical University, Taichung 404; 5Department of Radiology, China Medical University Hospital, Taichung 404; 6Graduate Institute of Chinese Medicine, China Medical University, Taichung 404; 7Department of Biotechnology, Asia University, Taichung 404, Taiwan, R.O.C. Received March 31, 2015; Accepted June 26, 2015 DOI: 10.3892/or.2015.4159 Abstract. Lung cancer is the most common cause of cancer CARD6, ID1 and ID2 genes, associated with cell survival and mortality and new cases are on the increase worldwide. the BRMS1L, associated with cell migration and invasion. However, the treatment of lung cancer remains unsatisfactory. Additionally, 59 downregulated genes exhibited a >4-fold Curcumin has been shown to induce cell death in many human change, including the DDIT3 gene, associated with DNA cancer cells, including human lung cancer cells. However, the damage; while 97 genes had a >3- to 4-fold change including the effects of curcumin on genetic mechanisms associated with DDIT4 gene, associated with DNA damage; the CCPG1 gene, these actions remain unclear. Curcumin (2 µM) was added associated with cell cycle and 321 genes with a >2- to 3-fold to NCI-H460 human lung cancer cells and the cells were including the GADD45A and CGREF1 genes, associated with incubated for 24 h. -
Targeting Protein Tyrosine Phosphatases in Cancer Lakshmi Reddy Bollu, Abhijit Mazumdar, Michelle I
Published OnlineFirst January 13, 2017; DOI: 10.1158/1078-0432.CCR-16-0934 Molecular Pathways Clinical Cancer Research Molecular Pathways: Targeting Protein Tyrosine Phosphatases in Cancer Lakshmi Reddy Bollu, Abhijit Mazumdar, Michelle I. Savage, and Powel H. Brown Abstract The aberrant activation of oncogenic signaling pathways is a act as tumor suppressor genes by terminating signal responses universal phenomenon in cancer and drives tumorigenesis and through the dephosphorylation of oncogenic kinases. More malignant transformation. This abnormal activation of signal- recently, it has become clear that several PTPs overexpressed ing pathways in cancer is due to the altered expression of in human cancers do not suppress tumor growth; instead, they protein kinases and phosphatases. In response to extracellular positively regulate signaling pathways and promote tumor signals, protein kinases activate downstream signaling path- development and progression. In this review, we discuss both ways through a series of protein phosphorylation events, ulti- types of PTPs: those that have tumor suppressor activities as mately producing a signal response. Protein tyrosine phospha- well as those that act as oncogenes. We also discuss the tases (PTP) are a family of enzymes that hydrolytically remove potential of PTP inhibitors for cancer therapy. Clin Cancer Res; phosphate groups from proteins. Initially, PTPs were shown to 23(9); 1–7. Ó2017 AACR. Background in cancer and discuss the current status of PTP inhibitors for cancer therapy. Signal transduction is a complex process that transmits extra- PTPs belong to a superfamily of enzymes that hydrolytically cellular signals effectively through a cascade of events involving remove phosphate groups from proteins (2). -
Bortezomib Inhibits Lung Fibrosis and Fibroblast Activation Without Proteasome
bioRxiv preprint doi: https://doi.org/10.1101/2021.02.26.433086; this version posted February 26, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Bortezomib inhibits lung fibrosis and fibroblast activation without proteasome 2 inhibition 3 4 Loka Raghu Kumar Penke, Jennifer Speth, Scott Wettlaufer, Christina Draijer and Marc 5 Peters-Golden1* 6 7 Affiliations 8 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, 9 University of Michigan, Ann Arbor, Michigan, USA. 10 1 Graduate Program in Immunology, University of Michigan, Ann Arbor, Michigan, USA. 11 12 Correspondence: 13 Marc Peters-Golden, M.D. 14 6301 MSRBIII, 1150 W. Medical Center Drive, Ann Arbor, MI 48109-5642 15 Tel: 734-936-5047 16 Fax: 734-764-4556 17 Email: [email protected] 18 Author Contributions: L.R.K.P. planned and performed experiments, analyzed the 19 data, organized data for presentation, and wrote the manuscript. J.M.S, S.H.W and C.D 20 performed experiments. M.P.-G. planned experiments, analyzed data, and wrote the 21 manuscript. 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.02.26.433086; this version posted February 26, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. -
Figure S1. HAEC ROS Production and ML090 NOX5-Inhibition
Figure S1. HAEC ROS production and ML090 NOX5-inhibition. (a) Extracellular H2O2 production in HAEC treated with ML090 at different concentrations and 24 h after being infected with GFP and NOX5-β adenoviruses (MOI 100). **p< 0.01, and ****p< 0.0001 vs control NOX5-β-infected cells (ML090, 0 nM). Results expressed as mean ± SEM. Fold increase vs GFP-infected cells with 0 nM of ML090. n= 6. (b) NOX5-β overexpression and DHE oxidation in HAEC. Representative images from three experiments are shown. Intracellular superoxide anion production of HAEC 24 h after infection with GFP and NOX5-β adenoviruses at different MOIs treated or not with ML090 (10 nM). MOI: Multiplicity of infection. Figure S2. Ontology analysis of HAEC infected with NOX5-β. Ontology analysis shows that the response to unfolded protein is the most relevant. Figure S3. UPR mRNA expression in heart of infarcted transgenic mice. n= 12-13. Results expressed as mean ± SEM. Table S1: Altered gene expression due to NOX5-β expression at 12 h (bold, highlighted in yellow). N12hvsG12h N18hvsG18h N24hvsG24h GeneName GeneDescription TranscriptID logFC p-value logFC p-value logFC p-value family with sequence similarity NM_052966 1.45 1.20E-17 2.44 3.27E-19 2.96 6.24E-21 FAM129A 129. member A DnaJ (Hsp40) homolog. NM_001130182 2.19 9.83E-20 2.94 2.90E-19 3.01 1.68E-19 DNAJA4 subfamily A. member 4 phorbol-12-myristate-13-acetate- NM_021127 0.93 1.84E-12 2.41 1.32E-17 2.69 1.43E-18 PMAIP1 induced protein 1 E2F7 E2F transcription factor 7 NM_203394 0.71 8.35E-11 2.20 2.21E-17 2.48 1.84E-18 DnaJ (Hsp40) homolog. -
Genetic Alterations of Protein Tyrosine Phosphatases in Human Cancers
Oncogene (2015) 34, 3885–3894 © 2015 Macmillan Publishers Limited All rights reserved 0950-9232/15 www.nature.com/onc REVIEW Genetic alterations of protein tyrosine phosphatases in human cancers S Zhao1,2,3, D Sedwick3,4 and Z Wang2,3 Protein tyrosine phosphatases (PTPs) are enzymes that remove phosphate from tyrosine residues in proteins. Recent whole-exome sequencing of human cancer genomes reveals that many PTPs are frequently mutated in a variety of cancers. Among these mutated PTPs, PTP receptor T (PTPRT) appears to be the most frequently mutated PTP in human cancers. Beside PTPN11, which functions as an oncogene in leukemia, genetic and functional studies indicate that most of mutant PTPs are tumor suppressor genes. Identification of the substrates and corresponding kinases of the mutant PTPs may provide novel therapeutic targets for cancers harboring these mutant PTPs. Oncogene (2015) 34, 3885–3894; doi:10.1038/onc.2014.326; published online 29 September 2014 INTRODUCTION tyrosine/threonine-specific phosphatases. (4) Class IV PTPs include Protein tyrosine phosphorylation has a critical role in virtually all four Drosophila Eya homologs (Eya1, Eya2, Eya3 and Eya4), which human cellular processes that are involved in oncogenesis.1 can dephosphorylate both tyrosine and serine residues. Protein tyrosine phosphorylation is coordinately regulated by protein tyrosine kinases (PTKs) and protein tyrosine phosphatases 1 THE THREE-DIMENSIONAL STRUCTURE AND CATALYTIC (PTPs). Although PTKs add phosphate to tyrosine residues in MECHANISM OF PTPS proteins, PTPs remove it. Many PTKs are well-documented oncogenes.1 Recent cancer genomic studies provided compelling The three-dimensional structures of the catalytic domains of evidence that many PTPs function as tumor suppressor genes, classical PTPs (RPTPs and non-RPTPs) are extremely well because a majority of PTP mutations that have been identified in conserved.5 Even the catalytic domain structures of the dual- human cancers are loss-of-function mutations. -
Macrophage DUSP3 Genetic Deletion Confers M2-Like
DUSP3 Genetic Deletion Confers M2-like Macrophage−Dependent Tolerance to Septic Shock This information is current as Pratibha Singh, Lien Dejager, Mathieu Amand, Emilie of September 27, 2021. Theatre, Maud Vandereyken, Tinatin Zurashvili, Maneesh Singh, Matthias Mack, Steven Timmermans, Lucia Musumeci, Emmanuel Dejardin, Tomas Mustelin, Jo A. Van Ginderachter, Michel Moutschen, Cécile Oury, Claude Libert and Souad Rahmouni Downloaded from J Immunol 2015; 194:4951-4962; Prepublished online 15 April 2015; doi: 10.4049/jimmunol.1402431 http://www.jimmunol.org/content/194/10/4951 http://www.jimmunol.org/ References This article cites 35 articles, 9 of which you can access for free at: http://www.jimmunol.org/content/194/10/4951.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 27, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2015 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology DUSP3 Genetic Deletion Confers M2-like Macrophage–Dependent Tolerance to Septic Shock Pratibha Singh,*,1 Lien Dejager,†,‡,1 Mathieu Amand,*,1 Emilie Theatre,x Maud Vandereyken,* Tinatin Zurashvili,* Maneesh Singh,* Matthias Mack,{ Steven Timmermans,†,‡ Lucia Musumeci,* Emmanuel Dejardin,‖ Tomas Mustelin,#,** Jo A. -
GATA2 Regulates Mast Cell Identity and Responsiveness to Antigenic Stimulation by Promoting Chromatin Remodeling at Super- Enhancers
ARTICLE https://doi.org/10.1038/s41467-020-20766-0 OPEN GATA2 regulates mast cell identity and responsiveness to antigenic stimulation by promoting chromatin remodeling at super- enhancers Yapeng Li1, Junfeng Gao 1, Mohammad Kamran1, Laura Harmacek2, Thomas Danhorn 2, Sonia M. Leach1,2, ✉ Brian P. O’Connor2, James R. Hagman 1,3 & Hua Huang 1,3 1234567890():,; Mast cells are critical effectors of allergic inflammation and protection against parasitic infections. We previously demonstrated that transcription factors GATA2 and MITF are the mast cell lineage-determining factors. However, it is unclear whether these lineage- determining factors regulate chromatin accessibility at mast cell enhancer regions. In this study, we demonstrate that GATA2 promotes chromatin accessibility at the super-enhancers of mast cell identity genes and primes both typical and super-enhancers at genes that respond to antigenic stimulation. We find that the number and densities of GATA2- but not MITF-bound sites at the super-enhancers are several folds higher than that at the typical enhancers. Our studies reveal that GATA2 promotes robust gene transcription to maintain mast cell identity and respond to antigenic stimulation by binding to super-enhancer regions with dense GATA2 binding sites available at key mast cell genes. 1 Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA. 2 Center for Genes, Environment and Health, National Jewish Health, Denver, CO 80206, USA. 3 Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, ✉ CO 80045, USA. email: [email protected] NATURE COMMUNICATIONS | (2021) 12:494 | https://doi.org/10.1038/s41467-020-20766-0 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-020-20766-0 ast cells (MCs) are critical effectors in immunity that at key MC genes.