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van Doormaal PTC, Thomas S, Ajroud-Driss S, Cole RN, DeVine LR, Dimachkie MM, Geisler S, Freeman R, Simpson DM, Singleton JR, Smith AG, Stino A, Höke A. Plasma proteomic analysis on neuropathic pain in idiopathic peripheral neuropathy patients. J Peripher Nerv Syst 2024; 29:88-96. [PMID: 37989721 DOI: 10.1111/jns.12606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/07/2023] [Accepted: 11/20/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND AND AIMS Why only half of the idiopathic peripheral neuropathy (IPN) patients develop neuropathic pain remains unknown. By conducting a proteomics analysis on IPN patients, we aimed to discover proteins and new pathways that are associated with neuropathic pain. METHODS We conducted unbiased mass-spectrometry proteomics analysis on blood plasma from 31 IPN patients with severe neuropathic pain and 29 IPN patients with no pain, to investigate protein biomarkers and protein-protein interactions associated with neuropathic pain. Univariate modeling was done with linear mixed modeling (LMM) and corrected for multiple testing. Multivariate modeling was performed using elastic net analysis and validated with internal cross-validation and bootstrapping. RESULTS In the univariate analysis, 73 proteins showed a p-value <.05 and 12 proteins showed a p-value <.01. None were significant after Benjamini-Hochberg adjustment for multiple testing. Elastic net analysis created a model containing 12 proteins with reasonable discriminatory power to differentiate between painful and painless IPN (false-negative rate 0.10, false-positive rate 0.18, and an area under the curve 0.75). Eight of these 12 proteins were clustered into one interaction network, significantly enriched for the complement and coagulation pathway (Benjamini-Hochberg adjusted p-value = .0057), with complement component 3 (C3) as the central node. Bootstrap validation identified insulin-like growth factor-binding protein 2 (IGFBP2), complement factor H-related protein 4 (CFHR4), and ferritin light chain (FTL), as the most discriminatory proteins of the original 12 identified. INTERPRETATION This proteomics analysis suggests a role for the complement system in neuropathic pain in IPN.
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Affiliation(s)
- Perry T C van Doormaal
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Neurology, Brain Center Rudolph Magnus, Utrecht Medical Center, Utrecht, The Netherlands
- Department of Neurology, Tergooi Medical Center, Hilversum, The Netherlands
| | - Simone Thomas
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Senda Ajroud-Driss
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Robert N Cole
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lauren R DeVine
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mazen M Dimachkie
- Department of Neurology, Kansas University Medical Center, Kansas City, Missouri, USA
| | - Stefanie Geisler
- Department of Neurology, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Roy Freeman
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - David M Simpson
- Department of Neurology, Icahn School of Medicine at Mount Sinai Medical Center, New York City, New York, USA
| | - J Robinson Singleton
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - A Gordon Smith
- Department of Neurology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Amro Stino
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Ahmet Höke
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Aisenberg WH, McCray BA, Sullivan JM, Diehl E, DeVine LR, Alevy J, Bagnell AM, Carr P, Donohue JK, Goretzki B, Cole RN, Hellmich UA, Sumner CJ. Multiubiquitination of TRPV4 reduces channel activity independent of surface localization. J Biol Chem 2022; 298:101826. [PMID: 35300980 PMCID: PMC9010760 DOI: 10.1016/j.jbc.2022.101826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Ubiquitin (Ub)-mediated regulation of plasmalemmal ion channel activity canonically occurs via stimulation of endocytosis. Whether ubiquitination can modulate channel activity by alternative mechanisms remains unknown. Here, we show that the transient receptor potential vanilloid 4 (TRPV4) cation channel is multiubiquitinated within its cytosolic N-terminal and C-terminal intrinsically disordered regions (IDRs). Mutagenizing select lysine residues to block ubiquitination of the N-terminal but not C-terminal IDR resulted in a marked elevation of TRPV4-mediated intracellular calcium influx, without increasing cell surface expression levels. Conversely, enhancing TRPV4 ubiquitination via expression of an E3 Ub ligase reduced TRPV4 channel activity but did not decrease plasma membrane abundance. These results demonstrate Ub-dependent regulation of TRPV4 channel function independent of effects on plasma membrane localization. Consistent with ubiquitination playing a key negative modulatory role of the channel, gain-of-function neuropathy-causing mutations in the TRPV4 gene led to reduced channel ubiquitination in both cellular and Drosophila models of TRPV4 neuropathy, whereas increasing mutant TRPV4 ubiquitination partially suppressed channel overactivity. Together, these data reveal a novel mechanism via which ubiquitination of an intracellular flexible IDR domain modulates ion channel function independently of endocytic trafficking and identify a contributory role for this pathway in the dysregulation of TRPV4 channel activity by neuropathy-causing mutations.
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Affiliation(s)
- William H Aisenberg
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brett A McCray
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jeremy M Sullivan
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Erika Diehl
- Department of Chemistry, Biochemistry Section, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Lauren R DeVine
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jonathan Alevy
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Anna M Bagnell
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Patrice Carr
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jack K Donohue
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Benedikt Goretzki
- Institute of Organic Chemistry and Macromolecular Chemistry, Cluster of Excellence 'Balance of the Microverse', Friedrich-Schiller-Universität, Jena, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, Frankfurt am Main, Germany
| | - Robert N Cole
- Institute of Organic Chemistry and Macromolecular Chemistry, Cluster of Excellence 'Balance of the Microverse', Friedrich-Schiller-Universität, Jena, Germany
| | - Ute A Hellmich
- Institute of Organic Chemistry and Macromolecular Chemistry, Cluster of Excellence 'Balance of the Microverse', Friedrich-Schiller-Universität, Jena, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, Frankfurt am Main, Germany
| | - Charlotte J Sumner
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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Akimov SS, Jiang M, Kedaigle AJ, Arbez N, Marque LO, Eddings CR, Ranum PT, Whelan E, Tang A, Wang R, DeVine LR, Talbot CC, Cole RN, Ratovitski T, Davidson BL, Fraenkel E, Ross CA. Immortalized striatal precursor neurons from Huntington's disease patient-derived iPS cells as a platform for target identification and screening for experimental therapeutics. Hum Mol Genet 2021; 30:2469-2487. [PMID: 34296279 PMCID: PMC8643509 DOI: 10.1093/hmg/ddab200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 11/12/2022] Open
Abstract
We have previously established induced pluripotent stem cell (iPSC) models of Huntington's disease (HD), demonstrating CAG-repeat-expansion-dependent cell biological changes and toxicity. However, the current differentiation protocols are cumbersome and time consuming, making preparation of large quantities of cells for biochemical or screening assays difficult. Here, we report the generation of immortalized striatal precursor neurons (ISPNs) with normal (33) and expanded (180) CAG repeats from HD iPSCs, differentiated to a phenotype resembling medium spiny neurons (MSN), as a proof of principle for a more tractable patient-derived cell model. For immortalization, we used co-expression of the enzymatic component of telomerase hTERT and conditional expression of c-Myc. ISPNs can be propagated as stable adherent cell lines, and rapidly differentiated into highly homogeneous MSN-like cultures within 2 weeks, as demonstrated by immunocytochemical criteria. Differentiated ISPNs recapitulate major HD-related phenotypes of the parental iPSC model, including brain-derived neurotrophic factor (BDNF)-withdrawal-induced cell death that can be rescued by small molecules previously validated in the parental iPSC model. Proteome and RNA-seq analyses demonstrate separation of HD versus control samples by principal component analysis. We identified several networks, pathways, and upstream regulators, also found altered in HD iPSCs, other HD models, and HD patient samples. HD ISPN lines may be useful for studying HD-related cellular pathogenesis, and for use as a platform for HD target identification and screening experimental therapeutics. The described approach for generation of ISPNs from differentiated patient-derived iPSCs could be applied to a larger allelic series of HD cell lines, and to comparable modeling of other genetic disorders.
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Affiliation(s)
- Sergey S Akimov
- Division of Neurobiology, Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Mali Jiang
- Division of Neurobiology, Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Amanda J Kedaigle
- Department of Biological Engineering, Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Nicolas Arbez
- Division of Neurobiology, Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Leonard O Marque
- Division of Neurobiology, Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Chelsy R Eddings
- Division of Neurobiology, Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Paul T Ranum
- The Department of Pathology and Laboratory Medicine, The University of Pennsylvania, The Raymond G Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Emma Whelan
- Division of Neurobiology, Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Anthony Tang
- Division of Neurobiology, Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ronald Wang
- Division of Neurobiology, Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Lauren R DeVine
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Conover C Talbot
- The Johns Hopkins School of Medicine, Institute for Basic Biomedical Sciences, Baltimore, MD 21205, USA
| | - Robert N Cole
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tamara Ratovitski
- Division of Neurobiology, Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Beverly L Davidson
- The Department of Pathology and Laboratory Medicine, The University of Pennsylvania, The Raymond G Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- The Department of Pathology and Laboratory Medicine, The University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Christopher A Ross
- Division of Neurobiology, Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Neurology, Neuroscience and Pharmacology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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Noel G, In JG, Lemme-Dumit JM, DeVine LR, Cole RN, Guerrerio AL, Campbell JD, Kovbasnjuk O, Pasetti MF. Human Breast Milk Enhances Intestinal Mucosal Barrier Function and Innate Immunity in a Healthy Pediatric Human Enteroid Model. Front Cell Dev Biol 2021; 9:685171. [PMID: 34327199 PMCID: PMC8313895 DOI: 10.3389/fcell.2021.685171] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/18/2021] [Indexed: 12/20/2022] Open
Abstract
Breastfeeding has been associated with long lasting health benefits. Nutrients and bioactive components of human breast milk promote cell growth, immune development, and shield the infant gut from insults and microbial threats. The molecular and cellular events involved in these processes are ill defined. We have established human pediatric enteroids and interrogated maternal milk's impact on epithelial cell maturation and function in comparison with commercial infant formula. Colostrum applied apically to pediatric enteroid monolayers reduced ion permeability, stimulated epithelial cell differentiation, and enhanced tight junction function by upregulating occludin. Breast milk heightened the production of antimicrobial peptide α-defensin 5 by goblet and Paneth cells, and modulated cytokine production, which abolished apical release of pro-inflammatory GM-CSF. These attributes were not found in commercial infant formula. Epithelial cells exposed to breast milk elevated apical and intracellular pIgR and enabled maternal IgA translocation. Proteomic data revealed a breast milk-induced molecular pattern associated with tissue remodeling and homeostasis. Using a novel ex vivo pediatric enteroid model, we have identified distinct cellular and molecular events involved in human milk-mediated improvement of human intestinal physiology and immunity.
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Affiliation(s)
- Gaelle Noel
- Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Julie G. In
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of New Mexico Health Science Center, Albuquerque, NM, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jose M. Lemme-Dumit
- Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Lauren R. DeVine
- Department of Biological Chemistry, Johns Hopkins Mass Spectrometry and Proteomics Facility, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Robert N. Cole
- Department of Biological Chemistry, Johns Hopkins Mass Spectrometry and Proteomics Facility, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Anthony L. Guerrerio
- Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology and Nutrition, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - James D. Campbell
- Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Olga Kovbasnjuk
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of New Mexico Health Science Center, Albuquerque, NM, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Marcela F. Pasetti
- Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
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Goodier JL, Soares AO, Pereira GC, DeVine LR, Sanchez L, Cole RN, García-Pérez JL. C9orf72-associated SMCR8 protein binds in the ubiquitin pathway and with proteins linked with neurological disease. Acta Neuropathol Commun 2020; 8:110. [PMID: 32678027 PMCID: PMC7364817 DOI: 10.1186/s40478-020-00982-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/26/2020] [Indexed: 02/08/2023] Open
Abstract
A pathogenic GGGCCC hexanucleotide expansion in the first intron/promoter region of the C9orf72 gene is the most common mutation associated with amyotrophic lateral sclerosis (ALS). The C9orf72 gene product forms a complex with SMCR8 (Smith-Magenis Syndrome Chromosome Region, Candidate 8) and WDR41 (WD Repeat domain 41) proteins. Recent studies have indicated roles for the complex in autophagy regulation, vesicle trafficking, and immune response in transgenic mice, however a direct connection with ALS etiology remains unclear. With the aim of increasing understanding of the multi-functional C9orf72-SMCR8-WDR41 complex, we determined by mass spectrometry analysis the proteins that directly associate with SMCR8. SMCR8 protein binds many components of the ubiquitin-proteasome system, and we demonstrate its poly-ubiquitination without obvious degradation. Evidence is also presented for localization of endogenous SMCR8 protein to cytoplasmic stress granules. However, in several cell lines we failed to reproduce previous observations that C9orf72 protein enters these granules. SMCR8 protein associates with many products of genes associated with various Mendelian neurological disorders in addition to ALS, implicating SMCR8-containing complexes in a range of neuropathologies. We reinforce previous observations that SMCR8 and C9orf72 protein levels are positively linked, and now show in vivo that SMCR8 protein levels are greatly reduced in brain tissues of C9orf72 gene expansion carrier individuals. While further study is required, these data suggest that SMCR8 protein level might prove a useful biomarker for the C9orf72 expansion in ALS.
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Affiliation(s)
- John L. Goodier
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Alisha O. Soares
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Gavin C. Pereira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Lauren R. DeVine
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Laura Sanchez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Robert N. Cole
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Jose Luis García-Pérez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
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Datta Chaudhuri A, Dasgheyb RM, DeVine LR, Bi H, Cole RN, Haughey NJ. Stimulus‐dependent modifications in astrocyte‐derived extracellular vesicle cargo regulate neuronal excitability. Glia 2019; 68:128-144. [DOI: 10.1002/glia.23708] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Amrita Datta Chaudhuri
- Department of Neurology, Richard T Johnson Division of Neuroimmunology and Neurological InfectionsJohns Hopkins University School of Medicine Baltimore Maryland
| | - Raha M. Dasgheyb
- Department of Neurology, Richard T Johnson Division of Neuroimmunology and Neurological InfectionsJohns Hopkins University School of Medicine Baltimore Maryland
| | - Lauren R. DeVine
- Department of Biological Chemistry, Mass Spectrometry and Proteomics FacilityJohns Hopkins University School of Medicine Baltimore Maryland
| | - Honghao Bi
- Department of Neurology, Richard T Johnson Division of Neuroimmunology and Neurological InfectionsJohns Hopkins University School of Medicine Baltimore Maryland
| | - Robert N. Cole
- Department of Biological Chemistry, Mass Spectrometry and Proteomics FacilityJohns Hopkins University School of Medicine Baltimore Maryland
| | - Norman J. Haughey
- Department of Neurology, Richard T Johnson Division of Neuroimmunology and Neurological InfectionsJohns Hopkins University School of Medicine Baltimore Maryland
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Liu X, Abraham JM, Cheng Y, Wang Z, Wang Z, Zhang G, Ashktorab H, Smoot DT, Cole RN, Boronina TN, DeVine LR, Talbot CC, Liu Z, Meltzer SJ. Synthetic Circular RNA Functions as a miR-21 Sponge to Suppress Gastric Carcinoma Cell Proliferation. Mol Ther Nucleic Acids 2018; 13:312-321. [PMID: 30326427 PMCID: PMC6197335 DOI: 10.1016/j.omtn.2018.09.010] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 12/15/2022]
Abstract
MicroRNA (miR) sponges containing miR binding sequences constitute a potentially powerful molecular therapeutic strategy. Recently, naturally occurring circular RNAs (circRNAs) were shown to function as efficient miR sponges in cancer cells. We hypothesized that synthetic circRNA sponges could achieve therapeutic loss-of-function targeted against specific miRs. Linear RNA molecules containing miR-21 binding sites were transcribed in vitro; after dephosphorylation and phosphorylation, circularization was achieved using 5'-3' end-ligation by T4 RNA ligase 1. circRNA stability was assessed using RNase R and fetal bovine serum. Competitive inhibition of miR-21 activity by a synthetic circRNA sponge was assessed using luciferase reporter, cell proliferation, and cell apoptosis assays in three gastric cancer cell lines. circRNA effects on downstream proteins were also delineated by Tandem Mass Tag (TMT) labeling (data available via ProteomeXchange identifier PRIDE: PXD008584), followed by western blotting. We conclude that artificial circRNA sponges resistant to nuclease digestion can be synthesized using simple enzymatic ligation steps. These sponges inhibit cancer cell proliferation and suppress the activity of miR-21 on downstream protein targets, including the cancer protein DAXX. In summary, synthetic circRNA sponges represent a simple, effective, convenient strategy for achieving targeted loss of miR function in vitro, with potential future therapeutic application in human patients.
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Affiliation(s)
- Xi Liu
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an 710061, Shaanxi, China; Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Division of Gastroenterology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - John M Abraham
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Division of Gastroenterology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Yulan Cheng
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Division of Gastroenterology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Zhixiong Wang
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Zhe Wang
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Division of Gastroenterology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Guanjun Zhang
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an 710061, Shaanxi, China
| | - Hassan Ashktorab
- Department of Medicine and Cancer Center, Howard University, Washington, DC, USA
| | - Duane T Smoot
- Department of Internal Medicine, Meharry Medical College, Nashville, TN, USA
| | - Robert N Cole
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tatiana N Boronina
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lauren R DeVine
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - C Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhengwen Liu
- Department of Infectious Diseases, First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an 710061, Shaanxi, China
| | - Stephen J Meltzer
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Division of Gastroenterology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA.
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Wilky BA, Kim C, McCarty G, Montgomery EA, Kammers K, DeVine LR, Cole RN, Raman V, Loeb DM. RNA helicase DDX3: a novel therapeutic target in Ewing sarcoma. Oncogene 2015; 35:2574-83. [PMID: 26364611 DOI: 10.1038/onc.2015.336] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 06/29/2015] [Accepted: 08/03/2015] [Indexed: 02/08/2023]
Abstract
RNA helicase DDX3 has oncogenic activity in breast and lung cancers and is required for translation of complex mRNA transcripts, including those encoding key cell-cycle regulatory proteins. We sought to determine the expression and function of DDX3 in sarcoma cells, and to investigate the antitumor activity of a novel small molecule DDX3 inhibitor, RK-33. Utilizing various sarcoma cell lines, xenografts and human tissue microarrays, we measured DDX3 expression at the mRNA and protein levels, and evaluated cytotoxicity of RK-33 in sarcoma cell lines. To study the role of DDX3 in Ewing sarcoma, we generated stable DDX3-knockdown Ewing sarcoma cell lines using DDX3-specific small hairpin RNA (shRNA), and assessed oncogenic activity. DDX3-knockdown and RK-33-treated Ewing sarcoma cells were compared with wild-type cells using an isobaric mass-tag quantitative proteomics approach to identify target proteins impacted by DDX3 inhibition. Overall, we found high expression of DDX3 in numerous human sarcoma subtypes compared with non-malignant mesenchymal cells, and knockdown of DDX3 by RNA interference inhibited oncogenic activity in Ewing sarcoma cells. Treatment with RK-33 was preferentially cytotoxic to sarcoma cells, including chemotherapy-resistant Ewing sarcoma stem cells, while sparing non-malignant cells. Sensitivity to RK-33 correlated with DDX3 protein expression. Growth of human Ewing sarcoma xenografts expressing high DDX3 was inhibited by RK-33 treatment in mice, without overt toxicity. DDX3 inhibition altered the Ewing sarcoma cellular proteome, especially proteins involved in DNA replication, mRNA translation and proteasome function. These data support further investigation of the role of DDX3 in sarcomas, advancement of RK-33 to Ewing sarcoma clinical trials and development of RNA helicase inhibition as a novel anti-neoplastic strategy.
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Affiliation(s)
- B A Wilky
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - C Kim
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - G McCarty
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - E A Montgomery
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - K Kammers
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - L R DeVine
- Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - R N Cole
- Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - V Raman
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Department of Radiology, Johns Hopkins University, Baltimore, MD, USA
| | - D M Loeb
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
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Cole RN, Ruczinski I, Schulze K, Christian P, Herbrich S, Wu L, DeVine LR, O'Meally RN, Shrestha S, Boronina TN, Yager JD, Groopman J, West KP. The plasma proteome identifies expected and novel proteins correlated with micronutrient status in undernourished Nepalese children. J Nutr 2013; 143:1540-8. [PMID: 23966331 PMCID: PMC6879017 DOI: 10.3945/jn.113.175018] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Micronutrient deficiencies are common in undernourished societies yet remain inadequately assessed due to the complexity and costs of existing assays. A plasma proteomics-based approach holds promise in quantifying multiple nutrient:protein associations that reflect biological function and nutritional status. To validate this concept, in plasma samples of a cohort of 500 6- to 8-y-old Nepalese children, we estimated cross-sectional correlations between vitamins A (retinol), D (25-hydroxyvitamin D), and E (α-tocopherol), copper, and selenium, measured by conventional assays, and relative abundance of their major plasma-bound proteins, measured by quantitative proteomics using 8-plex iTRAQ mass tags. The prevalence of low-to-deficient status was 8.8% (<0.70 μmol/L) for retinol, 19.2% (<50 nmol/L) for 25-hydroxyvitamin D, 17.6% (<9.3 μmol/L) for α-tocopherol, 0% (<10 μmol/L) for copper, and 13.6% (<0.6 μmol/L) for selenium. We identified 4705 proteins, 982 in >50 children. Employing a linear mixed effects model, we observed the following correlations: retinol:retinol-binding protein 4 (r = 0.88), 25-hydroxyvitamin D:vitamin D-binding protein (r = 0.58), α-tocopherol:apolipoprotein C-III (r = 0.64), copper:ceruloplasmin (r = 0.65), and selenium:selenoprotein P isoform 1 (r = 0.79) (all P < 0.0001), passing a false discovery rate threshold of 1% (based on P value-derived q values). Individual proteins explained 34-77% (R(2)) of variation in their respective nutrient concentration. Adding second proteins to models raised R(2) to 48-79%, demonstrating a potential to explain additional variation in nutrient concentration by this strategy. Plasma proteomics can identify and quantify protein biomarkers of micronutrient status in undernourished children. The maternal micronutrient supplementation trial, from which data were derived as a follow-up activity, was registered at clinicaltrials.gov as NCT00115271.
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Affiliation(s)
- Robert N. Cole
- Mass Spectrometry and Proteomics Core Facility, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD,Center for Human Nutrition, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD,Department of Biological Chemistry, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Kerry Schulze
- Center for Human Nutrition, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD,Department of International Health, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Parul Christian
- Center for Human Nutrition, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD,Department of International Health, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Shelley Herbrich
- Department of Biostatistics, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Lee Wu
- Center for Human Nutrition, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD,Department of International Health, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Lauren R. DeVine
- Mass Spectrometry and Proteomics Core Facility, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD,Department of Biological Chemistry, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Robert N. O'Meally
- Mass Spectrometry and Proteomics Core Facility, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD,Department of Biological Chemistry, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Sudeep Shrestha
- Center for Human Nutrition, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD,Department of International Health, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Tatiana N. Boronina
- Mass Spectrometry and Proteomics Core Facility, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD,Department of Biological Chemistry, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD
| | - James D. Yager
- Center for Human Nutrition, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD,Department of Environmental Health Sciences, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD
| | - John Groopman
- Center for Human Nutrition, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD,Department of Environmental Health Sciences, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Keith P. West
- Center for Human Nutrition, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD,Department of International Health, Bloomberg School of Public Health and School of Medicine, Johns Hopkins University, Baltimore, MD,To whom correspondence should be addressed. E-mail:
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