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Goldstein SI, Fan AC, Wang Z, Naineni SK, Lengqvist J, Chernobrovkin A, Garcia-Gutierrez SB, Cencic R, Patel K, Huang S, Brown LE, Emili A, Porco JA. Proteomic Discovery of RNA-Protein Molecular Clamps Using a Thermal Shift Assay with ATP and RNA (TSAR). bioRxiv 2024:2024.04.19.590252. [PMID: 38659867 PMCID: PMC11042367 DOI: 10.1101/2024.04.19.590252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Uncompetitive inhibition is an effective strategy for suppressing dysregulated enzymes and their substrates, but discovery of suitable ligands depends on often-unavailable structural knowledge and serendipity. Hence, despite surging interest in mass spectrometry-based target identification, proteomic studies of substrate-dependent target engagement remain sparse. Herein, we describe the Thermal Shift Assay with ATP and RNA (TSAR) as a template for proteome-wide discovery of substrate-dependent ligand binding. Using proteomic thermal shift assays, we show that simple biochemical additives can facilitate detection of target engagement in native cell lysates. We apply our approach to rocaglates, a family of molecules that specifically clamp RNA to eukaryotic translation initiation factor 4A (eIF4A), DEAD-box helicase 3X (DDX3X), and potentially other members of the DEAD-box (DDX) family of RNA helicases. To identify unexpected interactions, we optimized a target class-specific thermal denaturation window and evaluated ATP analog and RNA probe dependencies for key rocaglate-DDX interactions. We report novel DDX targets of the rocaglate clamping spectrum, confirm that DDX3X is a common target of several widely studied analogs, and provide structural insights into divergent DDX3X affinities between synthetic rocaglates. We independently validate novel targets of high-profile rocaglates, including the clinical candidate Zotatifin (eFT226), using limited proteolysis-mass spectrometry and fluorescence polarization experiments. Taken together, our study provides a model for screening uncompetitive inhibitors using a systematic chemical-proteomics approach to uncover actionable DDX targets, clearing a path towards characterization of novel molecular clamps and associated RNA helicase targets.
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Affiliation(s)
- Stanley I. Goldstein
- BU Target Discovery Laboratory (BU-TDL), Boston University, Boston, MA, USA
- Department of Chemistry, Boston University, Boston, MA, USA
- Department of Pharmacology, Physiology, and Biophysics, Boston University, Boston, MA, USA
| | - Alice C. Fan
- BU Target Discovery Laboratory (BU-TDL), Boston University, Boston, MA, USA
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Zihao Wang
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Sai K. Naineni
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | | | | | | | - Regina Cencic
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Kesha Patel
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | | | - Andrew Emili
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - John A. Porco
- BU Target Discovery Laboratory (BU-TDL), Boston University, Boston, MA, USA
- Department of Chemistry, Boston University, Boston, MA, USA
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Cook BE, Archbold J, Nasr K, Girmay S, Goldstein SI, Li P, Dandapani S, Genung NE, Tang SP, McClusky S, Plisson C, Afetian ME, Dwyer CA, Fazio M, Drury WJ, Rigo F, Martarello L, Kaliszczak M. Non-invasive Imaging of Antisense Oligonucleotides in the Brain via In Vivo Click Chemistry. Mol Imaging Biol 2022; 24:940-949. [PMID: 35655109 DOI: 10.1007/s11307-022-01744-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 04/27/2022] [Revised: 05/10/2022] [Accepted: 05/22/2022] [Indexed: 12/29/2022]
Abstract
PURPOSE The treatment of complex neurological diseases often requires the administration of large therapeutic drugs, such as antisense oligonucleotide (ASO), by lumbar puncture into the intrathecal space in order to bypass the blood-brain barrier. Despite the growing number of ASOs in clinical development, there are still uncertainties regarding their dosing, primarily around their distribution and kinetics in the brain following intrathecal injection. The challenge of taking measurements within the delicate structures of the central nervous system (CNS) necessitates the use of non-invasive nuclear imaging, such as positron emission tomography (PET). Herein, an emergent strategy known as "pretargeted imaging" is applied to image the distribution of an ASO in the brain by developing a novel PET tracer, [18F]F-537-Tz. This tracer is able to undergo an in vivo "click" reaction, covalently binding to a trans-cyclooctene conjugated ASO. PROCEDURES A novel small molecule tracer for pretargeted PET imaging of ASOs in the CNS is developed and tested in a series of in vitro and in vivo experiments, including biodistribution in rats and non-human primates. RESULTS In vitro data and extensive in vivo rat data demonstrated delivery of the tracer to the CNS, and its successful ligation to its ASO target in the brain. In an NHP study, the slow tracer kinetics did not allow for specific binding to be determined by PET. CONCLUSION A CNS-penetrant radioligand for pretargeted imaging was successfully demonstrated in a proof-of-concept study in rats, laying the groundwork for further optimization.
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Affiliation(s)
| | | | - Khaled Nasr
- Invicro, A Konica Minolta Company, Boston, MA, 02210, USA
| | | | | | - Pei Li
- , Biogen, Cambridge, MA, 02142, USA
| | | | | | - Sac-Pham Tang
- Invicro, A Konica Minolta Company, Boston, MA, 02210, USA
| | | | | | | | | | | | | | - Frank Rigo
- Ionis Pharmaceuticals Inc, Carlsbad, CA, 92010, USA
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Beierle JA, Yao EJ, Goldstein SI, Lynch WB, Scotellaro JL, Shah AA, Sena KD, Wong AL, Linnertz CL, Averin O, Moody DE, Reilly CA, Peltz G, Emili A, Ferris MT, Bryant CD. Zhx2 Is a Candidate Gene Underlying Oxymorphone Metabolite Brain Concentration Associated with State-Dependent Oxycodone Reward. J Pharmacol Exp Ther 2022; 382:167-180. [PMID: 35688478 PMCID: PMC9341249 DOI: 10.1124/jpet.122.001217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/17/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022] Open
Abstract
Understanding the pharmacogenomics of opioid metabolism and behavior is vital to therapeutic success, as mutations can dramatically alter therapeutic efficacy and addiction liability. We found robust, sex-dependent BALB/c substrain differences in oxycodone behaviors and whole brain concentration of oxycodone metabolites. BALB/cJ females showed robust state-dependent oxycodone reward learning as measured via conditioned place preference when compared with the closely related BALB/cByJ substrain. Accordingly, BALB/cJ females also showed a robust increase in brain concentration of the inactive metabolite noroxycodone and the active metabolite oxymorphone compared with BALB/cByJ mice. Oxymorphone is a highly potent, full agonist at the mu opioid receptor that could enhance drug-induced interoception and state-dependent oxycodone reward learning. Quantitative trait locus (QTL) mapping in a BALB/c F2 reduced complexity cross revealed one major QTL on chromosome 15 underlying brain oxymorphone concentration that explained 32% of the female variance. BALB/cJ and BALB/cByJ differ by fewer than 10,000 variants, which can greatly facilitate candidate gene/variant identification. Hippocampal and striatal cis-expression QTL (eQTL) and exon-level eQTL analysis identified Zhx2, a candidate gene coding for a transcriptional repressor with a private BALB/cJ retroviral insertion that reduces Zhx2 expression and sex-dependent dysregulation of cytochrome P450 enzymes. Whole brain proteomics corroborated the Zhx2 eQTL and identified upregulated CYP2D11 that could increase brain oxymorphone in BALB/cJ females. To summarize, Zhx2 is a highly promising candidate gene underlying brain oxycodone metabolite levels. Future studies will validate Zhx2 and its site of action using reciprocal gene editing and tissue-specific viral manipulations in BALB/c substrains. SIGNIFICANCE STATEMENT: Our findings show that genetic variation can result in sex-specific alterations in whole brain concentration of a bioactive opioid metabolite after oxycodone administration, reinforcing the need for sex as a biological factor in pharmacogenomic studies. The cooccurrence of female-specific increased oxymorphone and state-dependent reward learning suggests that this minor yet potent and efficacious metabolite of oxycodone could increase opioid interoception and drug-cue associative learning of opioid reward, which has implications for cue-induced relapse of drug-seeking behavior and for precision pharmacogenetics.
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Affiliation(s)
- Jacob A Beierle
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Emily J Yao
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Stanley I Goldstein
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - William B Lynch
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Julia L Scotellaro
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Anyaa A Shah
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Katherine D Sena
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Alyssa L Wong
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Colton L Linnertz
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Olga Averin
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - David E Moody
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Christopher A Reilly
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Gary Peltz
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Andrew Emili
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Martin T Ferris
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
| | - Camron D Bryant
- Ph.D. Program in Biomolecular Pharmacology (J.A.B., S.I.G.), Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry (J.A.B., E.J.Y., W.B.L., J.L.S., A.A.S., K.D.S., A.L.W., C.D.B.), Department of Biology and Biochemistry, Center for Network Systems Biology (S.I.G., A.E.), and Graduate Program in Neuroscience (W.B.L), Boston University School of Medicine, Boston, Massachusetts; Transformative Training Program in Addiction Science (TTPAS) (J.A.B., W.B.L.) and Undergraduate Research Opportunity Program (J.L.S., K.D.S.), Boston University, Boston, Massachusetts; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.L.L., M.T.F.); Department of Pharmacology and Toxicity, Center for Human Toxicology, University of Utah, Salt Lake City, Utah (O.A., D.E.M., C.A.R.); and Department of Anesthesiology, Pain, and Preoperative Medicine Stanford University School of Medicine, Stanford, California (G.P.)
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Kenney DJ, O’Connell AK, Turcinovic J, Montanaro P, Hekman RM, Tamura T, Berneshawi AR, Cafiero TR, Al Abdullatif S, Blum B, Goldstein SI, Heller BL, Gertje HP, Bullitt E, Trachtenberg AJ, Chavez E, Nono ET, Morrison C, Tseng AE, Sheikh A, Kurnick S, Grosz K, Bosmann M, Ericsson M, Huber BR, Saeed M, Balazs AB, Francis KP, Klose A, Paragas N, Campbell JD, Connor JH, Emili A, Crossland NA, Ploss A, Douam F. Humanized mice reveal a macrophage-enriched gene signature defining human lung tissue protection during SARS-CoV-2 infection. Cell Rep 2022; 39:110714. [PMID: 35421379 PMCID: PMC8977517 DOI: 10.1016/j.celrep.2022.110714] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/17/2022] [Accepted: 03/29/2022] [Indexed: 01/11/2023] Open
Abstract
The human immunological mechanisms defining the clinical outcome of SARS-CoV-2 infection remain elusive. This knowledge gap is mostly driven by the lack of appropriate experimental platforms recapitulating human immune responses in a controlled human lung environment. Here, we report a mouse model (i.e., HNFL mice) co-engrafted with human fetal lung xenografts (fLX) and a myeloid-enhanced human immune system to identify cellular and molecular correlates of lung protection during SARS-CoV-2 infection. Unlike mice solely engrafted with human fLX, HNFL mice are protected against infection, severe inflammation, and histopathological phenotypes. Lung tissue protection from infection and severe histopathology associates with macrophage infiltration and differentiation and the upregulation of a macrophage-enriched signature composed of 11 specific genes mainly associated with the type I interferon signaling pathway. Our work highlights the HNFL model as a transformative platform to investigate, in controlled experimental settings, human myeloid immune mechanisms governing lung tissue protection during SARS-CoV-2 infection.
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Affiliation(s)
- Devin J. Kenney
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Aoife K. O’Connell
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Jacquelyn Turcinovic
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA,Bioinformatics Program, Boston University, Boston, MA, USA
| | - Paige Montanaro
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Ryan M. Hekman
- Center for Network Systems Biology, Boston University, Boston, MA, USA,Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Tomokazu Tamura
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - Thomas R. Cafiero
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Salam Al Abdullatif
- Single Cell RNA Sequencing Core, Boston University, Boston, MA, USA,Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Benjamin Blum
- Center for Network Systems Biology, Boston University, Boston, MA, USA,Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Stanley I. Goldstein
- Center for Network Systems Biology, Boston University, Boston, MA, USA,Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Brigitte L. Heller
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Hans P. Gertje
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Esther Bullitt
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Alexander J. Trachtenberg
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Elizabeth Chavez
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Evans Tuekam Nono
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Catherine Morrison
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Anna E. Tseng
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Amira Sheikh
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Susanna Kurnick
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA,Animal Science Center, Boston University, Boston, MA, USA
| | - Kyle Grosz
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA,Animal Science Center, Boston University, Boston, MA, USA
| | - Markus Bosmann
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA,Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
| | - Maria Ericsson
- Electron Microscopy Core Facility, Harvard Medical School, Boston, MA, USA
| | - Bertrand R. Huber
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Mohsan Saeed
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA,Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | | | | | | | - Neal Paragas
- In Vivo Analytics, Inc., New York, NY, USA,Department of Radiology Imaging Research Lab, University of Washington, Seattle, WA, USA
| | - Joshua D. Campbell
- Single Cell RNA Sequencing Core, Boston University, Boston, MA, USA,Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - John H. Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA, USA,Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA,Department of Biology, Boston University School of Medicine, Boston, MA, USA
| | - Nicholas A. Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA,Corresponding author
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA,Corresponding author
| | - Florian Douam
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA,Corresponding author
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5
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Beierle JA, Yao EJ, Goldstein SI, Scotellaro JL, Sena KD, Linnertz CA, Willits AB, Kader L, Young EE, Peltz G, Emili A, Ferris MT, Bryant CD. Genetic basis of thermal nociceptive sensitivity and brain weight in a BALB/c reduced complexity cross. Mol Pain 2022; 18:17448069221079540. [PMID: 35088629 PMCID: PMC8891926 DOI: 10.1177/17448069221079540] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 12/13/2021] [Accepted: 01/20/2022] [Indexed: 11/30/2022] Open
Abstract
Thermal nociception involves the transmission of temperature-related noxious information from the periphery to the CNS and is a heritable trait that could predict transition to persistent pain. Rodent forward genetics complement human studies by controlling genetic complexity and environmental factors, analysis of end point tissue, and validation of variants on appropriate genetic backgrounds. Reduced complexity crosses between nearly identical inbred substrains with robust trait differences can greatly facilitate unbiased discovery of novel genes and variants. We found BALB/cByJ mice showed enhanced sensitivity on the 53.5°C hot plate and mechanical stimulation in the von Frey test compared to BALB/cJ mice and replicated decreased gross brain weight in BALB/cByJ versus BALB/cJ. We then identified a quantitative trait locus (QTL) on chromosome 13 for hot plate sensitivity (LOD = 10.7; p < 0.001; peak = 56 Mb) and a QTL for brain weight on chromosome 5 (LOD = 8.7; p < 0.001). Expression QTL mapping of brain tissues identified H2afy (56.07 Mb) as the top transcript with the strongest association at the hot plate locus (FDR = 0.0002) and spliceome analysis identified differential exon usage within H2afy associated with the same locus. Whole brain proteomics further supported decreased H2AFY expression could underlie enhanced hot plate sensitivity, and identified ACADS as a candidate for reduced brain weight. To summarize, a BALB/c reduced complexity cross combined with multiple-omics approaches facilitated identification of candidate genes underlying thermal nociception and brain weight. These substrains provide a powerful, reciprocal platform for future validation of candidate variants.
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Affiliation(s)
- Jacob A Beierle
- Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, MA, USA
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Emily J Yao
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Stanley I Goldstein
- Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, MA, USA
- Department of Biology and Biochemistry, Center for Network Systems Biology, Boston University School of Medicine, Boston, MA, USA
| | - Julia L Scotellaro
- Department of Biology and Biochemistry, Center for Network Systems Biology, Boston University School of Medicine, Boston, MA, USA
- Undergraduate Research Opportunity Program, Boston University, Boston, MA, USA
| | - Katherine D Sena
- Department of Biology and Biochemistry, Center for Network Systems Biology, Boston University School of Medicine, Boston, MA, USA
- Undergraduate Research Opportunity Program, Boston University, Boston, MA, USA
| | - Colton A Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adam B Willits
- Neuroscience Program, University of Kansas Medical Center, Kansas City, KS, USA
| | - Leena Kader
- Neuroscience Program, University of Kansas Medical Center, Kansas City, KS, USA
| | - Erin E Young
- Department of Anesthesiology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Gary Peltz
- Department of Anesthesiology, Pain, and Preoperative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrew Emili
- Department of Biology and Biochemistry, Center for Network Systems Biology, Boston University School of Medicine, Boston, MA, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Camron D Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
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6
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Evans CA, Liu T, Lescarbeau A, Nair SJ, Grenier L, Pradeilles JA, Glenadel Q, Tibbitts T, Rowley AM, DiNitto JP, Brophy EE, O’Hearn EL, Ali JA, Winkler DG, Goldstein SI, O’Hearn P, Martin CM, Hoyt JG, Soglia JR, Cheung C, Pink MM, Proctor JL, Palombella VJ, Tremblay MR, Castro AC. Discovery of a Selective Phosphoinositide-3-Kinase (PI3K)-γ Inhibitor (IPI-549) as an Immuno-Oncology Clinical Candidate. ACS Med Chem Lett 2016; 7:862-7. [PMID: 27660692 DOI: 10.1021/acsmedchemlett.6b00238] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [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: 06/16/2016] [Accepted: 07/22/2016] [Indexed: 01/01/2023] Open
Abstract
Optimization of isoquinolinone PI3K inhibitors led to the discovery of a potent inhibitor of PI3K-γ (26 or IPI-549) with >100-fold selectivity over other lipid and protein kinases. IPI-549 demonstrates favorable pharmacokinetic properties and robust inhibition of PI3K-γ mediated neutrophil migration in vivo and is currently in Phase 1 clinical evaluation in subjects with advanced solid tumors.
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Affiliation(s)
- Catherine A. Evans
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Tao Liu
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - André Lescarbeau
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Somarajan J. Nair
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Louis Grenier
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Johan A. Pradeilles
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Quentin Glenadel
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Thomas Tibbitts
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Ann M. Rowley
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Jonathan P. DiNitto
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Erin E. Brophy
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Erin L. O’Hearn
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Janid A. Ali
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - David G. Winkler
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Stanley I. Goldstein
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Patrick O’Hearn
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Christian M. Martin
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Jennifer G. Hoyt
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - John R. Soglia
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Culver Cheung
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Melissa M. Pink
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Jennifer L. Proctor
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Vito J. Palombella
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Martin R. Tremblay
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Alfredo C. Castro
- Infinity Pharmaceuticals, Inc., 784 Memorial Drive, Cambridge, Massachusetts 02139, United States
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7
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Daniello NJ, Goldstein SI. Retropharyngeal hematoma secondary to minor blunt head and neck trauma. Ear Nose Throat J 1994; 73:41-3. [PMID: 8162871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Retropharyngeal hematomas are relatively rare. They are clinically important because of the close proximity of the retropharyngeal space to the upper airway. Any swelling in the space may cause the posterior pharyngeal wall to bulge anteriorly into the airway and cause airway obstruction. Management starts with securing and maintaining the patient's airway. Diagnosis rests upon clinical examination and radiographic studies. Treatment depends upon the size of the hematoma as well as the clinical course of the patient. Smaller hematomas may be observed. Larger hematomas and those that fail to reabsorb should undergo drainage. A case of retropharyngeal hematoma following minor blunt head and neck trauma is presented. We review the literature and present management and treatment principles for this group of patients.
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Affiliation(s)
- N J Daniello
- Department of Otolaryngology, Westchester Square Medical Center, Bronx, New York
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8
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Abstract
The prognosis of metastatic thyroid carcinoma is dependent on the age of the patient, the histologic characteristics of the neoplasm, and the site of metastasis. A more favorable prognosis is found in patients less than 40 years old with follicular carcinoma and without any bony metastases. Metastatic thyroid carcinoma presenting as distal spinal cord compression is extremely rare. We report one such case and review the literature. As reported in the literature, the combination of decompressive laminectomy followed by total thyroidectomy and radioactive iodine therapy has proved to be effective in the treatment of patients with thyroid carcinoma metastatic to the distal vertebral bodies.
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Affiliation(s)
- S I Goldstein
- Department of Otolaryngology, New York University Medical Center, New York
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9
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Abstract
A prospective analysis of 124 consecutive adult patients undergoing tracheotomy was performed to examine the incidence of resulting complications. All tracheotomies were performed by a junior otolaryngology resident under the supervision of a member of the attending staff or a chief resident. The vast majority were performed at the bedside in an intensive care unit. The complications were divided into two groups: early (within 2 days) and late (2 to 14 days). Seven patients had complications directly related to tracheotomy. Four of these complications occurred in three patients and were considered significant. There were no mortalities. Despite the fact that our tracheotomies were routinely performed by residents at the bedside, our complication rate was comparable to those reported from other centers. We believe that bedside tracheotomy, properly supervised and performed, is a safe procedure.
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Affiliation(s)
- S I Goldstein
- Department of Otolaryngology, New York University Medical Center, New York 10016
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10
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