1
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Chen CW, Guan BJ, Alzahrani MR, Gao Z, Gao L, Bracey S, Wu J, Mbow CA, Jobava R, Haataja L, Zalavadia AH, Schaffer AE, Lee H, LaFramboise T, Bederman I, Arvan P, Mathews CE, Gerling IC, Kaestner KH, Tirosh B, Engin F, Hatzoglou M. Adaptation to chronic ER stress enforces pancreatic β-cell plasticity. Nat Commun 2022; 13:4621. [PMID: 35941159 PMCID: PMC9360004 DOI: 10.1038/s41467-022-32425-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 05/13/2021] [Accepted: 08/01/2022] [Indexed: 11/30/2022] Open
Abstract
Pancreatic β-cells are prone to endoplasmic reticulum (ER) stress due to their role in insulin secretion. They require sustainable and efficient adaptive stress responses to cope with this stress. Whether episodes of chronic stress directly compromise β-cell identity is unknown. We show here under reversible, chronic stress conditions β-cells undergo transcriptional and translational reprogramming associated with impaired expression of regulators of β-cell function and identity. Upon recovery from stress, β-cells regain their identity and function, indicating a high degree of adaptive plasticity. Remarkably, while β-cells show resilience to episodic ER stress, when episodes exceed a threshold, β-cell identity is gradually lost. Single cell RNA-sequencing analysis of islets from type 1 diabetes patients indicates severe deregulation of the chronic stress-adaptation program and reveals novel biomarkers of diabetes progression. Our results suggest β-cell adaptive exhaustion contributes to diabetes pathogenesis.
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Affiliation(s)
- Chien-Wen Chen
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - Bo-Jhih Guan
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Mohammed R Alzahrani
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Zhaofeng Gao
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Long Gao
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Syrena Bracey
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jing Wu
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Cheikh A Mbow
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Raul Jobava
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Leena Haataja
- The Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical Center, Ann Arbor, MI, 48105, USA
| | - Ajay H Zalavadia
- Lerner Research Institute, Cleveland Clinic, 9620 Carnegie Ave N Bldg, Cleveland, OH, 44106, US
| | - Ashleigh E Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Hugo Lee
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, 53706, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Ilya Bederman
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Peter Arvan
- The Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical Center, Ann Arbor, MI, 48105, USA
| | - Clayton E Mathews
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, US
| | - Ivan C Gerling
- Department of Medicine, University of Tennessee, Memphis, TN, US
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Boaz Tirosh
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
- The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Feyza Engin
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, 53706, USA.
- Department of Medicine, Division of Endocrinology, Diabetes & Metabolism, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, 53705, USA.
| | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.
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2
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Krokowski D, Jobava R, Szkop KJ, Chen CW, Fu X, Venus S, Guan BJ, Wu J, Gao Z, Banaszuk W, Tchorzewski M, Mu T, Ropelewski P, Merrick WC, Mao Y, Sevval AI, Miranda H, Qian SB, Manifava M, Ktistakis NT, Vourekas A, Jankowsky E, Topisirovic I, Larsson O, Hatzoglou M. Stress-induced perturbations in intracellular amino acids reprogram mRNA translation in osmoadaptation independently of the ISR. Cell Rep 2022; 40:111092. [PMID: 35858571 PMCID: PMC9491157 DOI: 10.1016/j.celrep.2022.111092] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/26/2022] [Accepted: 06/22/2022] [Indexed: 12/23/2022] Open
Abstract
The integrated stress response (ISR) plays a pivotal role in adaptation of translation machinery to cellular stress. Here, we demonstrate an ISR-independent osmoadaptation mechanism involving reprogramming of translation via coordinated but independent actions of mTOR and plasma membrane amino acid transporter SNAT2. This biphasic response entails reduced global protein synthesis and mTOR signaling followed by translation of SNAT2. Induction of SNAT2 leads to accumulation of amino acids and reactivation of mTOR and global protein synthesis, paralleled by partial reversal of the early-phase, stress-induced translatome. We propose SNAT2 functions as a molecular switch between inhibition of protein synthesis and establishment of an osmoadaptive translation program involving the formation of cytoplasmic condensates of SNAT2-regulated RNA-binding proteins DDX3X and FUS. In summary, we define key roles of SNAT2 in osmotolerance.
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Affiliation(s)
- Dawid Krokowski
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland.
| | - Raul Jobava
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Krzysztof J Szkop
- Department of Oncology-Pathology, Science for Life Laboratories, Karolinska Institute, Stockholm, Sweden
| | - Chien-Wen Chen
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Xu Fu
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah Venus
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Bo-Jhih Guan
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jing Wu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Zhaofeng Gao
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Wioleta Banaszuk
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Marek Tchorzewski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland; EcoTech-Complex Centre, Maria Curie-Skłodowska University, Lublin, Poland
| | - Tingwei Mu
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Phil Ropelewski
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - William C Merrick
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Aksoylu Inci Sevval
- Department of Oncology-Pathology, Science for Life Laboratories, Karolinska Institute, Stockholm, Sweden
| | - Helen Miranda
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | | | | | - Anastasios Vourekas
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Eckhard Jankowsky
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Ivan Topisirovic
- The Lady Davis Institute, Jewish General Hospital, Montréal, QC, Canada; Gerald Bronfman Department of Oncology, McGill University, Montréal, QC, Canada; Department of Biochemistry and Division of Experimental Medicine, McGill University, Montréal, QC, Canada.
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratories, Karolinska Institute, Stockholm, Sweden.
| | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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3
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Mathuram TL, Townsend DM, Lynch VJ, Bederman I, Ye ZW, Zhang J, Sigurdson WJ, Prendergast E, Jobava R, Ferruzza JP, D’Angelo MR, Hatzoglou M, Perry Y, Blumental-Perry A. A Synthetic Small RNA Homologous to the D-Loop Transcript of mtDNA Enhances Mitochondrial Bioenergetics. Front Physiol 2022; 13:772313. [PMID: 35464086 PMCID: PMC9020786 DOI: 10.3389/fphys.2022.772313] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial malfunction is a hallmark of many diseases, including neurodegenerative disorders, cardiovascular and lung diseases, and cancers. We previously found that alveolar progenitor cells, which are more resistant to cigarette smoke-induced injury than the other cells of the lung parenchyma, upregulate the mtDNA-encoded small non-coding RNA mito-ncR-805 after exposure to smoke. The mito-ncR-805 acts as a retrograde signal between the mitochondria and the nucleus. Here, we identified a region of mito-ncR-805 that is conserved in the mammalian mitochondrial genomes and generated shorter versions of mouse and human transcripts (mmu-CR805 and hsa-LDL1, respectively), which differ in a few nucleotides and which we refer to as the "functional bit". Overexpression of mouse and human functional bits in either the mouse or the human lung epithelial cells led to an increase in the activity of the Krebs cycle and oxidative phosphorylation, stabilized the mitochondrial potential, conferred faster cell division, and lowered the levels of proapoptotic pseudokinase, TRIB3. Both oligos, mmu-CR805 and hsa-LDL1 conferred cross-species beneficial effects. Our data indicate a high degree of evolutionary conservation of retrograde signaling via a functional bit of the D-loop transcript, mito-ncR-805, in the mammals. This emphasizes the importance of the pathway and suggests a potential to develop this functional bit into a therapeutic agent that enhances mitochondrial bioenergetics.
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Affiliation(s)
- Theodore L. Mathuram
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, United States
| | - Danyelle M. Townsend
- Department of Drug Discovery & Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, Charleston, SC, United States
| | - Vincent J. Lynch
- Department of Biological Sciences, College of Arts and Sciences, University at Buffalo, State University of New York, Buffalo, NY, United States
| | - Ilya Bederman
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Zhi-Wei Ye
- Department of Drug Discovery & Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, Charleston, SC, United States
| | - Jie Zhang
- Department of Drug Discovery & Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, Charleston, SC, United States
| | - Wade J. Sigurdson
- Department of Medicine, Confocal Microscope and Flow Cytometry Facility, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, United States
| | - Erin Prendergast
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Raul Jobava
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Jonathan P. Ferruzza
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, United States
| | - Mary R. D’Angelo
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, United States
| | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Yaron Perry
- Division of Thoracic Surgery, Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, United States
| | - Anna Blumental-Perry
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, United States
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4
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Jobava R, Mao Y, Guan BJ, Hu D, Krokowski D, Chen CW, Shu XE, Chukwurah E, Wu J, Gao Z, Zagore LL, Merrick WC, Trifunovic A, Hsieh AC, Valadkhan S, Zhang Y, Qi X, Jankowsky E, Topisirovic I, Licatalosi DD, Qian SB, Hatzoglou M. Adaptive translational pausing is a hallmark of the cellular response to severe environmental stress. Mol Cell 2021; 81:4191-4208.e8. [PMID: 34686314 PMCID: PMC8559772 DOI: 10.1016/j.molcel.2021.09.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 01/27/2021] [Revised: 05/27/2021] [Accepted: 09/28/2021] [Indexed: 12/12/2022]
Abstract
To survive, mammalian cells must adapt to environmental challenges. While the cellular response to mild stress has been widely studied, how cells respond to severe stress remains unclear. We show here that under severe hyperosmotic stress, cells enter a transient hibernation-like state in anticipation of recovery. We demonstrate this adaptive pausing response (APR) is a coordinated cellular response that limits ATP supply and consumption through mitochondrial fragmentation and widespread pausing of mRNA translation. This pausing is accomplished by ribosome stalling at translation initiation codons, which keeps mRNAs poised to resume translation upon recovery. We further show that recovery from severe stress involves ISR (integrated stress response) signaling that permits cell cycle progression, resumption of growth, and reversal of mitochondria fragmentation. Our findings indicate that cells can respond to severe stress via a hibernation-like mechanism that preserves vital elements of cellular function under harsh environmental conditions.
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Affiliation(s)
- Raul Jobava
- Department of Biochemistry, CWRU, Cleveland, OH 44106, USA; Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Bo-Jhih Guan
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Di Hu
- Department of Physiology & Biophysics, CWRU, Cleveland, OH 44106, USA
| | - Dawid Krokowski
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA; Department of Molecular Biology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Lublin 20-033, Poland
| | - Chien-Wen Chen
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Xin Erica Shu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Evelyn Chukwurah
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Jing Wu
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Zhaofeng Gao
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Leah L Zagore
- Department of Biochemistry, CWRU, Cleveland, OH 44106, USA; Center for RNA Science and Therapeutics, CWRU, Cleveland, OH 44106, USA
| | | | - Aleksandra Trifunovic
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Medical Faculty, University of Cologne, 50931 Cologne, Germany; Institute for Mitochondrial Diseases and Ageing, Medical Faculty and Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Andrew C Hsieh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Saba Valadkhan
- Department of Molecular Biology and Microbiology, CWRU, Cleveland, OH 44106, USA
| | - Youwei Zhang
- Department of Pharmacology, CWRU, Cleveland, OH 44106, USA
| | - Xin Qi
- Department of Physiology & Biophysics, CWRU, Cleveland, OH 44106, USA
| | - Eckhard Jankowsky
- Department of Biochemistry, CWRU, Cleveland, OH 44106, USA; Center for RNA Science and Therapeutics, CWRU, Cleveland, OH 44106, USA
| | - Ivan Topisirovic
- Gerald Bronfman Department of Oncology, Departments of Biochemistry and Experimental Medicine and Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, QC H3T 1E2, Canada
| | - Donny D Licatalosi
- Department of Biochemistry, CWRU, Cleveland, OH 44106, USA; Center for RNA Science and Therapeutics, CWRU, Cleveland, OH 44106, USA.
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
| | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA.
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5
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Blumental-Perry A, Jobava R, Bederman I, Degar AJ, Kenche H, Guan BJ, Pandit K, Perry NA, Molyneaux ND, Wu J, Prendergas E, Ye ZW, Zhang J, Nelson CE, Ahangari F, Krokowski D, Guttentag SH, Linden PA, Townsend DM, Miron A, Kang MJ, Kaminski N, Perry Y, Hatzoglou M. Retrograde signaling by a mtDNA-encoded non-coding RNA preserves mitochondrial bioenergetics. Commun Biol 2020; 3:626. [PMID: 33127975 PMCID: PMC7603330 DOI: 10.1038/s42003-020-01322-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 06/22/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022] Open
Abstract
Alveolar epithelial type II (AETII) cells are important for lung epithelium maintenance and function. We demonstrate that AETII cells from mouse lungs exposed to cigarette smoke (CS) increase the levels of the mitochondria-encoded non-coding RNA, mito-RNA-805, generated by the control region of the mitochondrial genome. The protective effects of mito-ncR-805 are associated with positive regulation of mitochondrial energy metabolism, and respiration. Levels of mito-ncR-805 do not relate to steady-state transcription or replication of the mitochondrial genome. Instead, CS-exposure causes the redistribution of mito-ncR-805 from mitochondria to the nucleus, which correlated with the increased expression of nuclear-encoded genes involved in mitochondrial function. These studies reveal an unrecognized mitochondria stress associated retrograde signaling, and put forward the idea that mito-ncRNA-805 represents a subtype of small non coding RNAs that are regulated in a tissue- or cell-type specific manner to protect cells under physiological stress.
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Affiliation(s)
- A Blumental-Perry
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA.
| | - R Jobava
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - I Bederman
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - A J Degar
- College of Pharmacology, Mercer University, Atlanta, GA, USA
| | - H Kenche
- Biomedical Sciences, Mercer University School of Medicine, Savannah Campus, Savannah, GA, USA
- Savannah State University, Savannah, GA, USA
| | - B J Guan
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - K Pandit
- Sekusui XenoTech, LLC, Kansas City, KS, USA
| | - N A Perry
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - N D Molyneaux
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - J Wu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - E Prendergas
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Z-W Ye
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
| | - J Zhang
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
| | - C E Nelson
- Biomedical Sciences, Mercer University School of Medicine, Savannah Campus, Savannah, GA, USA
| | - F Ahangari
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, and Center for RNA Science and Medicine, Yale School of Medicine, New Haven, CT, USA
| | - D Krokowski
- Department of Molecular Biology, Maria Curie-Skłodowska University, Lublin, Poland
| | - S H Guttentag
- Division of Neonatology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - P A Linden
- Department of Surgery, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - D M Townsend
- College of Pharmacy, Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - A Miron
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - M-J Kang
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, and Center for RNA Science and Medicine, Yale School of Medicine, New Haven, CT, USA
| | - N Kaminski
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, and Center for RNA Science and Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Y Perry
- Division of Thoracic Surgery, Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA.
| | - M Hatzoglou
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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6
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Farabaugh KT, Krokowski D, Guan BJ, Gao Z, Gao XH, Wu J, Jobava R, Ray G, de Jesus TJ, Bianchi MG, Chukwurah E, Bussolati O, Kilberg M, Buchner DA, Sen GC, Cotton C, McDonald C, Longworth M, Ramakrishnan P, Hatzoglou M. PACT-mediated PKR activation acts as a hyperosmotic stress intensity sensor weakening osmoadaptation and enhancing inflammation. eLife 2020; 9:e52241. [PMID: 32175843 PMCID: PMC7145421 DOI: 10.7554/elife.52241] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 09/27/2019] [Accepted: 03/14/2020] [Indexed: 12/15/2022] Open
Abstract
The inability of cells to adapt to increased environmental tonicity can lead to inflammatory gene expression and pathogenesis. The Rel family of transcription factors TonEBP and NF-κB p65 play critical roles in the switch from osmoadaptive homeostasis to inflammation, respectively. Here we identified PACT-mediated PKR kinase activation as a marker of the termination of adaptation and initiation of inflammation in Mus musculus embryonic fibroblasts. We found that high stress-induced PACT-PKR activation inhibits the interaction between NF-κB c-Rel and TonEBP essential for the increased expression of TonEBP-dependent osmoprotective genes. This resulted in enhanced formation of TonEBP/NF-κB p65 complexes and enhanced proinflammatory gene expression. These data demonstrate a novel role of c-Rel in the adaptive response to hyperosmotic stress, which is inhibited via a PACT/PKR-dependent dimer redistribution of the Rel family transcription factors. Our results suggest that inhibiting PACT-PKR signaling may prove a novel target for alleviating stress-induced inflammatory diseases.
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Affiliation(s)
- Kenneth T Farabaugh
- Department of Pharmacology, Case Western Reserve UniversityClevelandUnited States
| | - Dawid Krokowski
- Department of Genetics and Genome Sciences, Case Western Reserve UniversityClevelandUnited States
- Department of Molecular Biology, Maria Curie-Sklodowska UniversityLublinPoland
| | - Bo-Jhih Guan
- Department of Genetics and Genome Sciences, Case Western Reserve UniversityClevelandUnited States
| | - Zhaofeng Gao
- Department of Genetics and Genome Sciences, Case Western Reserve UniversityClevelandUnited States
| | - Xing-Huang Gao
- Department of Genetics and Genome Sciences, Case Western Reserve UniversityClevelandUnited States
| | - Jing Wu
- Department of Genetics and Genome Sciences, Case Western Reserve UniversityClevelandUnited States
| | - Raul Jobava
- Department of Biochemistry, Case Western Reserve UniversityClevelandUnited States
| | - Greeshma Ray
- Department of Inflammation and Immunity, Cleveland Clinic FoundationClevelandUnited States
| | - Tristan J de Jesus
- Department of Pathology, Case Western Reserve UniversityClevelandUnited States
| | | | - Evelyn Chukwurah
- Department of Genetics and Genome Sciences, Case Western Reserve UniversityClevelandUnited States
| | - Ovidio Bussolati
- Department of Medicine and Surgery, Universita degli Studi di ParmaParmaItaly
| | - Michael Kilberg
- Department of Biochemistry and Molecular Biology, University of FloridaGainesvilleUnited States
| | - David A Buchner
- Department of Genetics and Genome Sciences, Case Western Reserve UniversityClevelandUnited States
- Department of Biochemistry, Case Western Reserve UniversityClevelandUnited States
| | - Ganes C Sen
- Department of Inflammation and Immunity, Cleveland Clinic FoundationClevelandUnited States
| | - Calvin Cotton
- Department of Physiology and Biophysics, Case Western Reserve UniversityClevelandUnited States
| | - Christine McDonald
- Department of Inflammation and Immunity, Cleveland Clinic FoundationClevelandUnited States
| | - Michelle Longworth
- Department of Inflammation and Immunity, Cleveland Clinic FoundationClevelandUnited States
| | | | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, Case Western Reserve UniversityClevelandUnited States
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7
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Zagore LL, Sweet TJ, Hannigan MM, Weyn-Vanhentenryck SM, Jobava R, Hatzoglou M, Zhang C, Licatalosi DD. DAZL Regulates Germ Cell Survival through a Network of PolyA-Proximal mRNA Interactions. Cell Rep 2019; 25:1225-1240.e6. [PMID: 30380414 PMCID: PMC6878787 DOI: 10.1016/j.celrep.2018.10.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 07/26/2018] [Accepted: 10/01/2018] [Indexed: 01/25/2023] Open
Abstract
The RNA binding protein DAZL is essential for gametogenesis, but its direct in vivo functions, RNA targets, and the molecular basis for germ cell loss in Dazl-null mice are unknown. Here, we mapped transcriptome-wide DAZL-RNA interactions in vivo, revealing DAZL binding to thousands of mRNAs via polyA-proximal 3′ UTR interactions. In parallel, fluorescence-activated cell sorting and RNA-seq identified mRNAs sensitive to DAZL deletion in male germ cells. Despite binding a broad set of mRNAs, integrative analyses indicate that DAZL post-transcriptionally controls only a subset of its mRNA targets, namely those corresponding to a network of genes that are critical for germ cell proliferation and survival. In addition, we provide evidence that polyA sequences have key roles in specifying DAZL-RNA interactions across the transcriptome. Our results reveal a mechanism for DAZL-RNA binding and illustrate that DAZL functions as a master regulator of a post-transcriptional mRNA program essential for germ cell survival. Combining transgenic mice, FACS, and multiple RNA-profiling methods, Zagore et al. show that DAZL binds thousands of mRNAs via GUU sites upstream of polyA tails. Loss of DAZL results in decreased mRNA levels for a network of genes that are essential for germ cell proliferation and differentiation.
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Affiliation(s)
- Leah L Zagore
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Thomas J Sweet
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Molly M Hannigan
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | - Raul Jobava
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Chaolin Zhang
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Donny D Licatalosi
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA.
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8
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Danielpour D, Gao Z, Zmina PM, Shankar E, Shultes BC, Jobava R, Welford SM, Hatzoglou M. Author Correction: Early Cellular Responses of Prostate Carcinoma Cells to Sepantronium Bromide (YM155) Involve Suppression of mTORC1 by AMPK. Sci Rep 2019; 9:14826. [PMID: 31597941 PMCID: PMC6785556 DOI: 10.1038/s41598-019-51007-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- David Danielpour
- Case Comprehensive Cancer Center Research Laboratories, The Division of General Medical Sciences-Oncology, Case Western Reserve University, Cleveland, OH, 44106, USA. .,Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106, USA. .,Department of Urology, University Hospitals of Cleveland, Cleveland, OH, 44106, USA.
| | - Zhaofeng Gao
- Department of Genetics and Genomic Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Patrick M Zmina
- Case Comprehensive Cancer Center Research Laboratories, The Division of General Medical Sciences-Oncology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Eswar Shankar
- Case Comprehensive Cancer Center Research Laboratories, The Division of General Medical Sciences-Oncology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Benjamin C Shultes
- Case Comprehensive Cancer Center Research Laboratories, The Division of General Medical Sciences-Oncology, Case Western Reserve University, Cleveland, OH, 44106, USA.,Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Raul Jobava
- Department of Genetics and Genomic Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Scott M Welford
- Department of Radiation Oncology, Case Western Reserve University, Cleveland, OH, 44106, USA.,Department of Radiation Oncology, University of Miami, Coral Gables, FL, 33136, USA
| | - Maria Hatzoglou
- Department of Genetics and Genomic Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
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9
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Krokowski D, Guan BJ, Wu J, Zheng Y, Pattabiraman PP, Jobava R, Gao XH, Di XJ, Snider MD, Mu TW, Liu S, Storrie B, Pearlman E, Blumental-Perry A, Hatzoglou M. GADD34 Function in Protein Trafficking Promotes Adaptation to Hyperosmotic Stress in Human Corneal Cells. Cell Rep 2018; 21:2895-2910. [PMID: 29212034 DOI: 10.1016/j.celrep.2017.11.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 09/01/2017] [Accepted: 11/06/2017] [Indexed: 12/14/2022] Open
Abstract
GADD34, a stress-induced regulatory subunit of the phosphatase PP1, is known to function in hyperosmotic stress through its well-known role in the integrated stress response (ISR) pathway. Adaptation to hyperosmotic stress is important for the health of corneal epithelial cells exposed to changes in extracellular osmolarity, with maladaptation leading to dry eye syndrome. This adaptation includes induction of SNAT2, an endoplasmic reticulum (ER)-Golgi-processed protein, which helps to reverse the stress-induced loss of cell volume and promote homeostasis through amino acid uptake. Here, we show that GADD34 promotes the processing of proteins synthesized on the ER during hyperosmotic stress independent of its action in the ISR. We show that GADD34/PP1 phosphatase activity reverses hyperosmotic-stress-induced Golgi fragmentation and is important for cis- to trans-Golgi trafficking of SNAT2, thereby promoting SNAT2 plasma membrane localization and function. These results suggest that GADD34 is a protective molecule for ocular diseases such as dry eye syndrome.
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Affiliation(s)
- Dawid Krokowski
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Bo-Jhih Guan
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jing Wu
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Yuke Zheng
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Padmanabhan P Pattabiraman
- Department of Ophthalmology and Visual Science, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Raul Jobava
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Xing-Huang Gao
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Xiao-Jing Di
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Martin D Snider
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ting-Wei Mu
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Shijie Liu
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Brian Storrie
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Eric Pearlman
- Institute for Immunology, University of California, Irvine, Irvine, CA 92697, USA
| | - Anna Blumental-Perry
- Department of Surgery, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA.
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10
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Krokowski D, Jobava R, Guan BJ, Farabaugh K, Wu J, Majumder M, Bianchi MG, Snider MD, Bussolati O, Hatzoglou M. Coordinated Regulation of the Neutral Amino Acid Transporter SNAT2 and the Protein Phosphatase Subunit GADD34 Promotes Adaptation to Increased Extracellular Osmolarity. J Biol Chem 2015; 290:17822-17837. [PMID: 26041779 DOI: 10.1074/jbc.m114.636217] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Indexed: 02/04/2023] Open
Abstract
Cells respond to shrinkage induced by increased extracellular osmolarity via programmed changes in gene transcription and mRNA translation. The immediate response to this stress includes the induction of expression of the neutral amino acid transporter SNAT2. Increased SNAT2-mediated uptake of neutral amino acids is an essential adaptive mechanism for restoring cell volume. In contrast, stress-induced phosphorylation of the α subunit of the translation initiation factor eIF2 (eIF2α) can promote apoptosis. Here we show that the response to mild hyperosmotic stress involves regulation of the phosphorylation of eIF2α by increased levels of GADD34, a regulatory subunit of protein phosphatase 1 (PP1). The induction of GADD34 was dependent on transcriptional control by the c-Jun-binding cAMP response element in the GADD34 gene promoter and posttranscriptional stabilization of its mRNA. This mechanism differs from the regulation of GADD34 expression by other stresses that involve activating transcription factor 4 (ATF4). ATF4 was not translated during hyperosmotic stress despite an increase in eIF2α phosphorylation. The SNAT2-mediated increase in amino acid uptake was enhanced by increased GADD34 levels in a manner involving decreased eIF2α phosphorylation. It is proposed that the induction of the SNAT2/GADD34 axis enhances cell survival by promoting the immediate adaptive response to stress.
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Affiliation(s)
- Dawid Krokowski
- Departments of Pharmacology, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106.
| | - Raul Jobava
- Departments of Pharmacology, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106
| | - Bo-Jhih Guan
- Departments of Pharmacology, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106
| | - Kenneth Farabaugh
- Departments of Pharmacology, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106
| | - Jing Wu
- Departments of Pharmacology, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106
| | - Mithu Majumder
- Departments of Pharmacology, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106
| | - Massimiliano G Bianchi
- Department of Biomedical, Biotechnological, and Translational Sciences, University of Parma, 43100 Parma, Italy
| | - Martin D Snider
- Departments of Biochemistry, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106
| | - Ovidio Bussolati
- Department of Biomedical, Biotechnological, and Translational Sciences, University of Parma, 43100 Parma, Italy
| | - Maria Hatzoglou
- Departments of Pharmacology, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106.
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11
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Kambara H, Gunawardane L, Zebrowski E, Kostadinova L, Jobava R, Krokowski D, Hatzoglou M, Anthony DD, Valadkhan S. Regulation of Interferon-Stimulated Gene BST2 by a lncRNA Transcribed from a Shared Bidirectional Promoter. Front Immunol 2015; 5:676. [PMID: 25688240 PMCID: PMC4311693 DOI: 10.3389/fimmu.2014.00676] [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] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/15/2014] [Indexed: 01/30/2023] Open
Abstract
Recent genome-wide studies have revealed the presence of thousands of long non-protein-coding RNAs (lncRNAs), some of which may play critical roles in the cell. We have previously shown that a large number of lncRNAs show differential expression in response to interferon (IFN)α stimulation in primary human cells. Here, we show that a subset of IFN-induced lncRNAs are positioned in proximity of protein-coding IFN-stimulated genes (ISGs). The majority of gene pairs originated from bidirectional promoters and showed positively correlated expression. We focused our analysis on a pair consisting of the known protein-coding ISG, BST2, and an un-studied putative lncRNA originating from the promoter region of BST2 in a divergent orientation. We showed that this transcript was a multi-exonic, polyadenylated long RNA that lacked protein-coding capacity. BST2 and the lncRNA were both induced in response to IFNα in diverse cell types. The induction of both genes was mediated through the JAK-STAT pathway, suggesting that IFN-stimulated response elements within the shared promoter activated the transcription of both genes. RNAi-mediated knock-down of the lncRNA resulted in down-regulation of BST2, and we could show that this down-regulation occurred at the level of transcription. Forced overexpression of this lncRNA, which we named BST2 IFN-Stimulated Positive Regulator (BISPR), resulted in up-regulation of BST2, indicating that the regulation of expression of BST2 by BISPR is mediated through interactions involving BISPR RNA itself, rather than the impact of its transcription from an adjacent locus. Importantly, upon IFN stimulation, transcriptional activation of BISPR preceded the induction of BST2, suggesting that expression of BISPR facilitated the initiation of transcription in its paired protein-coding gene. The lncRNA-mediated transcriptional regulation described in this study may help govern the expression of additional protein-coding RNAs involved in IFN response and other cellular processes.
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Affiliation(s)
- Hiroto Kambara
- Department of Biochemistry, Case Western Reserve University School of Medicine , Cleveland, OH , USA
| | - Lalith Gunawardane
- Department of Biochemistry, Case Western Reserve University School of Medicine , Cleveland, OH , USA
| | - Elizabeth Zebrowski
- Divisions of Infectious and Rheumatic Diseases, Department of Medicine, Case Western Reserve University School of Medicine , Cleveland, OH , USA
| | - Lenche Kostadinova
- Divisions of Infectious and Rheumatic Diseases, Department of Medicine, Case Western Reserve University School of Medicine , Cleveland, OH , USA
| | - Raul Jobava
- Department of Nutrition, Case Western Reserve University School of Medicine , Cleveland, OH , USA
| | - Dawid Krokowski
- Department of Nutrition, Case Western Reserve University School of Medicine , Cleveland, OH , USA
| | - Maria Hatzoglou
- Department of Nutrition, Case Western Reserve University School of Medicine , Cleveland, OH , USA
| | - Donald D Anthony
- Divisions of Infectious and Rheumatic Diseases, Department of Medicine, Case Western Reserve University School of Medicine , Cleveland, OH , USA
| | - Saba Valadkhan
- Department of Biochemistry, Case Western Reserve University School of Medicine , Cleveland, OH , USA
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