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Salomonsson SE, Maltos AM, Gill K, Aladesuyi Arogundade O, Brown KA, Sachdev A, Sckaff M, Lam KJK, Fisher IJ, Chouhan RS, Van Laar VS, Marley CB, McLaughlin I, Bankiewicz KS, Tsai YC, Conklin BR, Clelland CD. Validated assays for the quantification of C9orf72 human pathology. Sci Rep 2024; 14:828. [PMID: 38191789 PMCID: PMC10774390 DOI: 10.1038/s41598-023-50667-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/22/2023] [Indexed: 01/10/2024] Open
Abstract
A repeat expansion mutation in the C9orf72 gene is the leading known genetic cause of FTD and ALS. The C9orf72-ALS/FTD field has been plagued by a lack of reliable tools to monitor this genomic locus and its RNA and protein products. We have validated assays that quantify C9orf72 pathobiology at the DNA, RNA and protein levels using knock-out human iPSC lines as controls. Here we show that single-molecule sequencing can accurately measure the repeat expansion and faithfully report on changes to the C9orf72 locus in what has been a traditionally hard to sequence genomic region. This is of particular value to sizing and phasing the repeat expansion and determining changes to the gene locus after gene editing. We developed ddPCR assays to quantify two major C9orf72 transcript variants, which we validated by selective excision of their distinct transcriptional start sites. Using validated knock-out human iPSC lines, we validated 4 commercially available antibodies (of 9 tested) that were specific for C9orf72 protein quantification by Western blot, but none were specific for immunocytochemistry. We tested 15 combinations of antibodies against dipeptide repeat proteins (DPRs) across 66 concentrations using MSD immunoassay, and found two (against poly-GA and poly-GP) that yielded a 1.5-fold or greater signal increase in patient iPSC-motor neurons compared to knock-out control, and validated them in human postmortem and transgenic mouse brain tissue. Our validated DNA, RNA and protein assays are applicable to discovery research as well as clinical trials.
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Affiliation(s)
- S E Salomonsson
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - A M Maltos
- Gladstone Institutes, San Francisco, CA, USA
| | - K Gill
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institutes, San Francisco, CA, USA
| | - O Aladesuyi Arogundade
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - K A Brown
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - A Sachdev
- Gladstone Institutes, San Francisco, CA, USA
| | - M Sckaff
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institutes, San Francisco, CA, USA
| | - K J K Lam
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - I J Fisher
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - R S Chouhan
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - V S Van Laar
- Department of Neurological Surgery, The Ohio State University, Columbus, OH, USA
- The Gene Therapy Institute, The Ohio State University, Columbus, OH, USA
| | - C B Marley
- Gladstone Institutes, San Francisco, CA, USA
| | | | - K S Bankiewicz
- Department of Neurological Surgery, The Ohio State University, Columbus, OH, USA
- The Gene Therapy Institute, The Ohio State University, Columbus, OH, USA
| | - Y-C Tsai
- Pacific Biosciences, Menlo Park, CA, USA
| | - B R Conklin
- Gladstone Institutes, San Francisco, CA, USA
- Departments of Medicine, Ophthalmology, and Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - C D Clelland
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
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2
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Brown KA, Gould TD. Targeting metaplasticity mechanisms to promote sustained antidepressant actions. Mol Psychiatry 2024:10.1038/s41380-023-02397-1. [PMID: 38177353 DOI: 10.1038/s41380-023-02397-1] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024]
Abstract
The discovery that subanesthetic doses of (R, S)-ketamine (ketamine) and (S)-ketamine (esketamine) rapidly induce antidepressant effects and promote sustained actions following drug clearance in depressed patients who are treatment-resistant to other therapies has resulted in a paradigm shift in the conceptualization of how rapidly and effectively depression can be treated. Consequently, the mechanism(s) that next generation antidepressants may engage to improve pathophysiology and resultant symptomology are being reconceptualized. Impaired excitatory glutamatergic synapses in mood-regulating circuits are likely a substantial contributor to the pathophysiology of depression. Metaplasticity is the process of regulating future capacity for plasticity by priming neurons with a stimulation that alters later neuronal plasticity responses. Accordingly, the development of treatment modalities that specifically modulate the duration, direction, or magnitude of glutamatergic synaptic plasticity events such as long-term potentiation (LTP), defined here as metaplastogens, may be an effective approach to reverse the pathophysiology underlying depression and improve depression symptoms. We review evidence that the initiating mechanisms of pharmacologically diverse rapid-acting antidepressants (i.e., ketamine mimetics) converge on consistent downstream molecular mediators that facilitate the expression/maintenance of increased synaptic strength and resultant persisting antidepressant effects. Specifically, while the initiating mechanisms of these therapies may differ (e.g., cell type-specificity, N-methyl-D-aspartate receptor (NMDAR) subtype-selective inhibition vs activation, metabotropic glutamate receptor 2/3 antagonism, AMPA receptor potentiation, 5-HT receptor-activating psychedelics, etc.), the sustained therapeutic mechanisms of putative rapid-acting antidepressants will be mediated, in part, by metaplastic effects that converge on consistent molecular mediators to enhance excitatory neurotransmission and altered capacity for synaptic plasticity. We conclude that the convergence of these therapeutic mechanisms provides the opportunity for metaplasticity processes to be harnessed as a druggable plasticity mechanism by next-generation therapeutics. Further, targeting metaplastic mechanisms presents therapeutic advantages including decreased dosing frequency and associated diminished adverse responses by eliminating the requirement for the drug to be continuously present.
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Affiliation(s)
- Kyle A Brown
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Todd D Gould
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Veterans Affairs Maryland Health Care System, Baltimore, MD, 21201, USA.
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3
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Brown KA, Gould TD. Disassociating drug active ingredients from inactive: ketamine-like synaptic effects of a ketamine excipient. Neuropsychopharmacology 2024; 49:301-302. [PMID: 37488279 PMCID: PMC10700543 DOI: 10.1038/s41386-023-01675-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Affiliation(s)
- Kyle A Brown
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Todd D Gould
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Veterans Affairs Maryland Health Care System, Baltimore, MD, 21201, USA.
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Brown KA, Morris R, Eckhardt SJ, Ge Y, Gellman SH. Phosphorylation Sites of the Gastric Inhibitory Polypeptide Receptor (GIPR) Revealed by Trapped-Ion-Mobility Spectrometry Coupled to Time-of-Flight Mass Spectrometry (TIMS-TOF MS). J Am Chem Soc 2023; 145:28030-28037. [PMID: 38091482 PMCID: PMC10842860 DOI: 10.1021/jacs.3c09078] [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] [Indexed: 12/21/2023]
Abstract
The gastric inhibitory polypeptide receptor (GIPR), a G protein-coupled receptor (GPCR) that regulates glucose metabolism and insulin secretion, is a target for the development of therapeutic agents to address type 2 diabetes and obesity. Signal transduction processes mediated by GPCR activation typically result in receptor phosphorylation, but very little is known about GIPR phosphorylation. Mass spectrometry (MS) is a powerful tool for detecting phosphorylation and other post-translational modifications of proteins and for identifying modification sites. However, applying MS methods to GPCRs is challenging because the native expression levels are low and the hydrophobicity of these proteins complicates isolation and enrichment. Here we use a widely available technique, trapped-ion-mobility spectrometry coupled to time-of-flight mass spectrometry (TIMS-TOF MS), to characterize the phosphorylation status of the GIPR. We identified eight serine residues that are phosphorylated, one in an intracellular loop and the remainder in the C-terminal domain. Stimulation with the native agonist GIP enhanced phosphorylation at four of these sites. For comparison, we evaluated tirzepatide (TZP), a dual agonist of the glucagon-like peptide-1 (GLP-1) receptor and the GIPR that has recently been approved for the treatment of type 2 diabetes. Stimulation with TZP enhanced phosphorylation at the same four sites that were enhanced with GIP; however, TZP also enhanced phosphorylation at a fifth site that is unique to this synthetic agonist. This work establishes an important and accessible tool for the characterization of signal transduction via the GIPR and reveals an unanticipated functional difference between GIP and TZP.
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Affiliation(s)
- Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Rylie Morris
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Samantha J. Eckhardt
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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5
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Brown KA, Gellman SH. Effects of Replacing a Central Glycine Residue in GLP-1 on Receptor Affinity and Signaling Profile. Chembiochem 2023; 24:e202300504. [PMID: 37624685 PMCID: PMC10666649 DOI: 10.1002/cbic.202300504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 08/27/2023]
Abstract
Agonists of the glucagon-like peptide-1 receptor (GLP-1R) are used to treat diabetes and obesity. Cryo-EM structures indicate that GLP-1 is completely α-helical when bound to the GLP-1R. The mature form of this hormone, GLP-1(7-36), contains a glycine residue near the center (Gly22). Since glycine has the second-lowest α-helix propensity among the proteinogenic α-amino acid residues, and Gly22 does not appear to make direct contact with the receptor, we were motivated to explore the impact on agonist activity of altering the α-helix propensity at this position. We examined GLP-1 analogues in which Gly22 was replaced with L-Ala, D-Ala, or β-amino acid residues with varying helix propensities. The results suggest that the receptor is reasonably tolerant of variations in helix propensity, and that the functional receptor-agonist complex may comprise a conformational spectrum rather than a single fixed structure.
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Affiliation(s)
- Kyle A. Brown
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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Maxson IN, Su E, Brown KA, Tcharmtchi MH, Ginsburg S, Bhargava V, Wenger J, Centers GI, Alade KH, Leung SK, Gowda SH, Flores S, Riley A, Thammasitboon S. A Program of Assessment Model for Point-of-Care Ultrasound Training for Pediatric Critical Care Providers: A Comprehensive Approach to Enhance Competency-Based Point-of-Care Ultrasound Training. Pediatr Crit Care Med 2023; 24:e511-e519. [PMID: 37260313 DOI: 10.1097/pcc.0000000000003288] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Point-of-care ultrasound (POCUS) is increasingly accepted in pediatric critical care medicine as a tool for guiding the evaluation and treatment of patients. POCUS is a complex skill that requires user competency to ensure accuracy, reliability, and patient safety. A robust competency-based medical education (CBME) program ensures user competency and mitigates patient safety concerns. A programmatic assessment model provides a longitudinal, holistic, and multimodal approach to teaching, assessing, and evaluating learners. The authors propose a fit-for-purpose and modifiable CBME model that is adaptable for different institutions' resources and needs for any intended competency level. This educational model drives and supports learning, ensures competency attainment, and creates a clear pathway for POCUS education while enhancing patient care and safety.
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Affiliation(s)
- Ivanna Natasha Maxson
- Department of Pediatrics, Division of Critical Care Medicine, Baylor College of Medicine, Texas Children's Hospital, Houston, TX
| | - Erik Su
- Department of Pediatrics, Division of Critical Care Medicine, Baylor College of Medicine, Texas Children's Hospital, Houston, TX
| | - Kyle A Brown
- Department of Pediatrics, Texas Christian University School of Medicine, Cook Children's Medical Center, Fort Worth, TX
| | - M Hossein Tcharmtchi
- Department of Pediatrics, Division of Critical Care Medicine, Baylor College of Medicine, Texas Children's Hospital, Houston, TX
| | - Sarah Ginsburg
- Department of Pediatrics, Division of Critical Care Medicine, UT Southwestern Medical Center, Dallas, TX
| | - Vidit Bhargava
- Department of Pediatrics, Division of Critical Care Medicine, University of Alabama Children's Hospital of Alabama, Birmingham, AL
| | - Jesse Wenger
- Department of Pediatrics, Division of Critical Care Medicine, University of Washington Seattle Children's Hospital, Seattle, WA
| | - Gabriela I Centers
- Department of Pediatrics, Division of Critical Care Medicine, Indiana University, Riley Children's Hospital, Indianapolis, IN
| | - Kiyetta H Alade
- Department of Pediatrics, Division of Emergency Medicine, Baylor College of Medicine, Texas Children's Hospital, Houston, TX
| | - Stephanie K Leung
- Department of Pediatrics, Division of Emergency Medicine, Baylor College of Medicine, Texas Children's Hospital, Houston, TX
| | - Sharada H Gowda
- Department of Pediatrics, Division of Neonatology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX
| | - Saul Flores
- Department of Pediatrics, Division of Critical Care Medicine and Cardiology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX
| | - Alan Riley
- Department of Pediatrics, Division of Cardiology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX
| | - Satid Thammasitboon
- Department of Pediatrics, Division of Critical Care Medicine, Baylor College of Medicine, Texas Children's Hospital, Houston, TX
- Department of Pediatrics, Center for Research, Innovation, and Scholarship in Medical Education, Baylor College of Medicine, Texas Children's Hospital, Houston, TX
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Rogers HT, Roberts DS, Larson EJ, Melby JA, Rossler KJ, Carr AV, Brown KA, Ge Y. Comprehensive Characterization of Endogenous Phospholamban Proteoforms Enabled by Photocleavable Surfactant and Top-down Proteomics. Anal Chem 2023; 95:13091-13100. [PMID: 37607050 PMCID: PMC10597709 DOI: 10.1021/acs.analchem.3c01618] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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] [Indexed: 08/24/2023]
Abstract
Top-down mass spectrometry (MS)-based proteomics has become a powerful tool for analyzing intact proteins and their associated post-translational modifications (PTMs). In particular, membrane proteins play critical roles in cellular functions and represent the largest class of drug targets. However, the top-down MS characterization of endogenous membrane proteins remains challenging, mainly due to their intrinsic hydrophobicity and low abundance. Phospholamban (PLN) is a regulatory membrane protein located in the sarcoplasmic reticulum and is essential for regulating cardiac muscle contraction. PLN has diverse combinatorial PTMs, and their dynamic regulation has significant influence on cardiac contractility and disease. Herein, we have developed a rapid and robust top-down proteomics method enabled by a photocleavable anionic surfactant, Azo, for the extraction and comprehensive characterization of endogenous PLN from cardiac tissue. We employed a two-pronged top-down MS approach using an online reversed-phase liquid chromatography tandem MS method on a quadrupole time-of-flight MS and a direct infusion method via an ultrahigh-resolution Fourier-transform ion cyclotron resonance MS. We have comprehensively characterized the sequence and combinatorial PTMs of endogenous human cardiac PLN. We have shown the site-specific localization of phosphorylation to Ser16 and Thr17 by MS/MS for the first time and the localization of S-palmitoylation to Cys36. Moreover, we applied our method to characterize PLN in disease and reported the significant reduction of PLN phosphorylation in human failing hearts with ischemic cardiomyopathy. Taken together, we have developed a streamlined top-down targeted proteomics method for comprehensive characterization of combinatorial PTMs in PLN toward better understanding the role of PLN in cardiac contractility.
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Affiliation(s)
- Holden T. Rogers
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Eli J. Larson
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jake A. Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kalina J. Rossler
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Austin V. Carr
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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Larson EJ, Pergande MR, Moss ME, Rossler KJ, Wenger RK, Krichel B, Josyer H, Melby JA, Roberts DS, Pike K, Shi Z, Chan HJ, Knight B, Rogers HT, Brown KA, Ong IM, Jeong K, Marty MT, McIlwain SJ, Ge Y. MASH Native: a unified solution for native top-down proteomics data processing. Bioinformatics 2023; 39:btad359. [PMID: 37294807 PMCID: PMC10283151 DOI: 10.1093/bioinformatics/btad359] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 01/12/2023] [Revised: 04/13/2023] [Accepted: 06/07/2023] [Indexed: 06/11/2023] Open
Abstract
MOTIVATION Native top-down proteomics (nTDP) integrates native mass spectrometry (nMS) with top-down proteomics (TDP) to provide comprehensive analysis of protein complexes together with proteoform identification and characterization. Despite significant advances in nMS and TDP software developments, a unified and user-friendly software package for analysis of nTDP data remains lacking. RESULTS We have developed MASH Native to provide a unified solution for nTDP to process complex datasets with database searching capabilities in a user-friendly interface. MASH Native supports various data formats and incorporates multiple options for deconvolution, database searching, and spectral summing to provide a "one-stop shop" for characterizing both native protein complexes and proteoforms. AVAILABILITY AND IMPLEMENTATION The MASH Native app, video tutorials, written tutorials, and additional documentation are freely available for download at https://labs.wisc.edu/gelab/MASH_Explorer/MASHSoftware.php. All data files shown in user tutorials are included with the MASH Native software in the download .zip file.
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Affiliation(s)
- Eli J Larson
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53705, United States
| | - Melissa R Pergande
- Department of Cell and Regenerative Biology, University of Wisconsin–Madison, Madison, WI 53705, United States
| | - Michelle E Moss
- Department of Cell and Regenerative Biology, University of Wisconsin–Madison, Madison, WI 53705, United States
| | - Kalina J Rossler
- Department of Cell and Regenerative Biology, University of Wisconsin–Madison, Madison, WI 53705, United States
| | - R Kent Wenger
- Department of Cell and Regenerative Biology, University of Wisconsin–Madison, Madison, WI 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705, United States
| | - Boris Krichel
- Department of Cell and Regenerative Biology, University of Wisconsin–Madison, Madison, WI 53705, United States
| | - Harini Josyer
- Department of Cell and Regenerative Biology, University of Wisconsin–Madison, Madison, WI 53705, United States
| | - Jake A Melby
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53705, United States
| | - David S Roberts
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53705, United States
| | - Kyndalanne Pike
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53705, United States
| | - Zhuoxin Shi
- Department of Cell and Regenerative Biology, University of Wisconsin–Madison, Madison, WI 53705, United States
| | - Hsin-Ju Chan
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53705, United States
| | - Bridget Knight
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53705, United States
| | - Holden T Rogers
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53705, United States
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53705, United States
| | - Irene M Ong
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, WI 53705, United States
- University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, United States
- Department of Obstetrics and Gynecology, University of Wisconsin–Madison, Madison, WI 53705, United States
| | - Kyowon Jeong
- Department of Applied Bioinformatics, University of Tübingen, Tübingen 72704, Germany
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85719, United States
| | - Sean J McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, WI 53705, United States
- University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53705, United States
- Department of Cell and Regenerative Biology, University of Wisconsin–Madison, Madison, WI 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705, United States
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Tabb DL, Jeong K, Druart K, Gant MS, Brown KA, Nicora C, Zhou M, Couvillion S, Nakayasu E, Williams JE, Peterson HK, McGuire MK, McGuire MA, Metz TO, Chamot-Rooke J. Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection. J Proteome Res 2023. [PMID: 37235544 DOI: 10.1021/acs.jproteome.2c00673] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Generating top-down tandem mass spectra (MS/MS) from complex mixtures of proteoforms benefits from improvements in fractionation, separation, fragmentation, and mass analysis. The algorithms to match MS/MS to sequences have undergone a parallel evolution, with both spectral alignment and match-counting approaches producing high-quality proteoform-spectrum matches (PrSMs). This study assesses state-of-the-art algorithms for top-down identification (ProSight PD, TopPIC, MSPathFinderT, and pTop) in their yield of PrSMs while controlling false discovery rate. We evaluated deconvolution engines (ThermoFisher Xtract, Bruker AutoMSn, Matrix Science Mascot Distiller, TopFD, and FLASHDeconv) in both ThermoFisher Orbitrap-class and Bruker maXis Q-TOF data (PXD033208) to produce consistent precursor charges and mass determinations. Finally, we sought post-translational modifications (PTMs) in proteoforms from bovine milk (PXD031744) and human ovarian tissue. Contemporary identification workflows produce excellent PrSM yields, although approximately half of all identified proteoforms from these four pipelines were specific to only one workflow. Deconvolution algorithms disagree on precursor masses and charges, contributing to identification variability. Detection of PTMs is inconsistent among algorithms. In bovine milk, 18% of PrSMs produced by pTop and TopMG were singly phosphorylated, but this percentage fell to 1% for one algorithm. Applying multiple search engines produces more comprehensive assessments of experiments. Top-down algorithms would benefit from greater interoperability.
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Affiliation(s)
- David L Tabb
- Université Paris Cité, Institut Pasteur, CNRS UAR 2024, Mass Spectrometry for Biology Unit, Paris 75015, France
| | - Kyowon Jeong
- Applied Bioinformatics, Computer Science Department, University of Tübingen, Tübingen 72076, Germany
| | - Karen Druart
- Université Paris Cité, Institut Pasteur, CNRS UAR 2024, Mass Spectrometry for Biology Unit, Paris 75015, France
| | - Megan S Gant
- Université Paris Cité, Institut Pasteur, CNRS UAR 2024, Mass Spectrometry for Biology Unit, Paris 75015, France
| | - Kyle A Brown
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Carrie Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Sneha Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ernesto Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Janet E Williams
- Department of Animal, Veterinary, and Food Sciences, University of Idaho, Moscow, Idaho 83844, United States
| | - Haley K Peterson
- Department of Animal, Veterinary, and Food Sciences, University of Idaho, Moscow, Idaho 83844, United States
| | - Michelle K McGuire
- Margaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, Idaho 83844, United States
| | - Mark A McGuire
- Department of Animal, Veterinary, and Food Sciences, University of Idaho, Moscow, Idaho 83844, United States
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Julia Chamot-Rooke
- Université Paris Cité, Institut Pasteur, CNRS UAR 2024, Mass Spectrometry for Biology Unit, Paris 75015, France
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10
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Melby JA, Brown KA, Gregorich ZR, Roberts DS, Chapman EA, Ehlers LE, Gao Z, Larson EJ, Jin Y, Lopez JR, Hartung J, Zhu Y, McIlwain SJ, Wang D, Guo W, Diffee GM, Ge Y. High sensitivity top-down proteomics captures single muscle cell heterogeneity in large proteoforms. Proc Natl Acad Sci U S A 2023; 120:e2222081120. [PMID: 37126723 PMCID: PMC10175728 DOI: 10.1073/pnas.2222081120] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 04/05/2023] [Indexed: 05/03/2023] Open
Abstract
Single-cell proteomics has emerged as a powerful method to characterize cellular phenotypic heterogeneity and the cell-specific functional networks underlying biological processes. However, significant challenges remain in single-cell proteomics for the analysis of proteoforms arising from genetic mutations, alternative splicing, and post-translational modifications. Herein, we have developed a highly sensitive functionally integrated top-down proteomics method for the comprehensive analysis of proteoforms from single cells. We applied this method to single muscle fibers (SMFs) to resolve their heterogeneous functional and proteomic properties at the single-cell level. Notably, we have detected single-cell heterogeneity in large proteoforms (>200 kDa) from the SMFs. Using SMFs obtained from three functionally distinct muscles, we found fiber-to-fiber heterogeneity among the sarcomeric proteoforms which can be related to the functional heterogeneity. Importantly, we detected multiple isoforms of myosin heavy chain (~223 kDa), a motor protein that drives muscle contraction, with high reproducibility to enable the classification of individual fiber types. This study reveals single muscle cell heterogeneity in large proteoforms and establishes a direct relationship between sarcomeric proteoforms and muscle fiber types, highlighting the potential of top-down proteomics for uncovering the molecular underpinnings of cell-to-cell variation in complex systems.
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Affiliation(s)
- Jake A. Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Zachery R. Gregorich
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI53706
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Emily A. Chapman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Lauren E. Ehlers
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Zhan Gao
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI53705
| | - Eli J. Larson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Yutong Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Justin R. Lopez
- Department of Kinesiology, University of Wisconsin-Madison, Madison, WI53706
| | - Jared Hartung
- Department of Kinesiology, University of Wisconsin-Madison, Madison, WI53706
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI53705
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53705
| | - Sean J. McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI53705
| | | | - Wei Guo
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI53706
| | - Gary M. Diffee
- Department of Kinesiology, University of Wisconsin-Madison, Madison, WI53706
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI53705
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53705
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11
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Rogers HT, Roberts DS, Larson EJ, Melby JA, Rossler KJ, Carr AV, Brown KA, Ge Y. Comprehensive Characterization of Endogenous Phospholamban Proteoforms Enabled by Photocleavable Surfactant and Top-down Proteomics. bioRxiv 2023:2023.04.12.536120. [PMID: 37090578 PMCID: PMC10120617 DOI: 10.1101/2023.04.12.536120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Top-down mass spectrometry (MS)-based proteomics has become a powerful tool for analyzing intact proteins and their associated post-translational modification (PTMs). In particular, membrane proteins play critical roles in cellular functions and represent the largest class of drug targets. However, the top-down MS characterization of endogenous membrane proteins remains challenging, mainly due to their intrinsic hydrophobicity and low abundance. Phospholamban (PLN) is a regulatory membrane protein located in the sarcoplasmic reticulum and is essential for regulating cardiac muscle contraction. PLN has diverse combinatorial PTMs and their dynamic regulation has significant influence on cardiac contractility and disease. Herein, we have developed a rapid and robust top-down proteomics method enabled by a photocleavable anionic surfactant, Azo, for the extraction and comprehensive characterization of endogenous PLN from cardiac tissue. We employed a two-pronged top-down MS approach using an online reversed-phase liquid chromatography tandem MS (LC-MS/MS) method on a quadrupole time-of-flight (Q-TOF) MS and a direct infusion method via an ultrahigh-resolution Fourier-transform ion cyclotron resonance (FTICR) MS. We have comprehensively characterized the sequence and combinatorial PTMs of endogenous human cardiac PLN. We have shown the site-specific localization of phosphorylation to Ser16 and Thr17 by MS/MS for the first time and the localization of S-palmitoylation to Cys36. Taken together, we have developed a streamlined top-down targeted proteomics method for comprehensive characterization of combinatorial PTMs in PLN toward better understanding the role of PLN in cardiac contractility.
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12
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Brown KA, Zanos P, Powels CF, Fix CJ, Michaelides M, Pereira EFR, Moaddel R, Gould TD. Ketamine preservative benzethonium chloride potentiates hippocampal synaptic transmission and binds neurotransmitter receptors and transporters. Neuropharmacology 2023; 225:109403. [PMID: 36565852 PMCID: PMC9867909 DOI: 10.1016/j.neuropharm.2022.109403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
Benzethonium chloride (BZT) is an excipient used in numerous products including (R,S)-ketamine (ketamine) drug formulations for human and veterinary use. Emerging evidence indicates BZT is pharmacologically active. BZT may therefore contribute to some of the clinical or preclinical effects observed with ketamine. In the present study, we evaluated: (i) the affinity of BZT for neurotransmitter receptors and transporters, (ii) the effects of BZT on hippocampal synaptic transmission in vitro, and (iii) plasma and brain concentrations of BZT following its intraperitoneal administration to male CD1 mice. Radioligand binding assays determined the affinity of BZT for neurotransmitter targets. Effects of BZT on field excitatory postsynaptic potentials (fEPSPs) were established via electrophysiological recordings from slices collected from male C57BL/6J mice. The binding assays revealed that BZT binds to numerous receptors (e.g., σ2 Ki = 7 nM) and transporters (e.g., dopamine transporter Ki = 545 nM). Bath application of BZT potentiated hippocampal fEPSPs in mouse hippocampal slices with an EC50 of 2.03 nM. Following intraperitoneal administration, BZT was detected in the plasma, but not in the brain of mice. These data highlight that studies measuring peripheral endpoints or directly exposing systems, in vitro, intracerebroventricularly, or intracortically, to BZT-containing formulations should account for the direct effects of BZT. Our findings also suggest that earlier data attributing pharmacological effects to ketamine may be confounded by BZT and that additional investigation into the functional impact of BZT is warranted. This article is part of the Special Issue on 'Ketamine and its Metabolites'.
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Affiliation(s)
- Kyle A Brown
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Panos Zanos
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, 21201, USA; Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA; Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Chris F Powels
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Connor J Fix
- Biomedical Research Center, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Michael Michaelides
- Biobehavioral Imaging and Molecular Neuropsychopharmacology Unit, National Institute on Drug Abuse Intramural Research Program, Baltimore, MD, 21224, USA; Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Edna F R Pereira
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA; Department of Epidemiology and Public Health, Division of Translational Toxicology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Ruin Moaddel
- Biomedical Research Center, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Todd D Gould
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, 21201, USA; Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA; Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA; Veterans Affairs Maryland Health Care System, Baltimore, MD, 21201, USA.
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13
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Zanos P, Brown KA, Georgiou P, Yuan P, Zarate CA, Thompson SM, Gould TD. NMDA Receptor Activation-Dependent Antidepressant-Relevant Behavioral and Synaptic Actions of Ketamine. J Neurosci 2023; 43:1038-1050. [PMID: 36596696 PMCID: PMC9908316 DOI: 10.1523/jneurosci.1316-22.2022] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 11/30/2022] [Accepted: 12/18/2022] [Indexed: 01/05/2023] Open
Abstract
Ketamine is a well-characterized NMDA receptor (NMDAR) antagonist, although the relevance of this pharmacology to its rapid (within hours of administration) antidepressant actions, which depend on mechanisms convergent with strengthening of excitatory synapses, is unclear. Activation of synaptic NMDARs is necessary for the induction of canonical long-term potentiation (LTP) leading to a sustained expression of increased synaptic strength. We tested the hypothesis that induction of rapid antidepressant effects requires NMDAR activation, by using behavioral pharmacology, western blot quantification of hippocampal synaptoneurosomal protein levels, and ex vivo hippocampal slice electrophysiology in male mice. We found that ketamine exerts an inverted U-shaped dose-response in antidepressant-sensitive behavioral tests, suggesting that an excessive NMDAR inhibition can prevent ketamine's antidepressant effects. Ketamine's actions to induce antidepressant-like behavioral effects, up-regulation of hippocampal AMPAR subunits GluA1 and GluA2, as well as metaplasticity measured ex vivo using electrically-stimulated LTP, were abolished by pretreatment with other non-antidepressant NMDAR antagonists, including MK-801 and CPP. Similarly, the antidepressant-like actions of other putative rapid-acting antidepressant drugs (2R,6R)-hydroxynorketamine (ketamine metabolite), MRK-016 (GABAAα5 negative allosteric modulator), and LY341495 (mGlu2/3 receptor antagonist) were blocked by NMDAR inhibition. Ketamine acted synergistically with an NMDAR positive allosteric modulator to exert antidepressant-like behavioral effects and activation of the NMDAR subunit GluN2A was necessary and sufficient for such relevant effects. We conclude rapid-acting antidepressant compounds share a common downstream NMDAR-activation dependent effector mechanism, despite variation in initial pharmacological targets. Promoting NMDAR signaling or other approaches that enhance NMDAR-dependent LTP-like synaptic potentiation may be an effective antidepressant strategy.SIGNIFICANCE STATEMENT The anesthetic and antidepressant drug ketamine is well-characterized as an NMDA receptor (NMDAR) antagonist; though, the relevance and full impact of this pharmacology to its antidepressant actions is unclear. We found that NMDAR activation, which occurs downstream of their initial actions, is necessary for the beneficial effects of ketamine and several other putative antidepressant compounds. As such, promoting NMDAR signaling, or other approaches that enhance NMDAR-dependent long-term potentiation (LTP)-like synaptic potentiation in vivo may be an effective antidepressant strategy directly, or acting synergistically with other drug or interventional treatments.
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Affiliation(s)
- Panos Zanos
- Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Maryland 21201
- Department of Psychology, University of Cyprus, Nicosia 2109, Cyprus
- Department of Physiology, School of Medicine, University of Maryland, Baltimore, Maryland 21201
| | - Kyle A Brown
- Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Maryland 21201
| | - Polymnia Georgiou
- Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Maryland 21201
- Department of Biology, University of Cyprus, Nicosia 2109, Cyprus
| | - Peixiong Yuan
- Experimental Therapeutics and Pathophysiology Branch, Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892
| | - Carlos A Zarate
- Experimental Therapeutics and Pathophysiology Branch, Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892
| | - Scott M Thompson
- Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Maryland 21201
- Department of Physiology, School of Medicine, University of Maryland, Baltimore, Maryland 21201
| | - Todd D Gould
- Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Maryland 21201
- Department of Pharmacology, School of Medicine, University of Maryland, Baltimore, Maryland 21201
- Department of Anatomy & Neurobiology, School of Medicine, University of Maryland, Baltimore, Maryland 21201
- Veterans Affairs Maryland Health Care System, Baltimore, Maryland 21201
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14
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Brown KA, Gugger MK, Roberts DS, Moreno D, Chae PS, Ge Y, Jin S. Synthesis, Self-Assembly Properties, and Degradation Characterization of a Nonionic Photocleavable Azo-Sulfide Surfactant Family. Langmuir 2023; 39:1465-1473. [PMID: 36638323 PMCID: PMC10164600 DOI: 10.1021/acs.langmuir.2c02820] [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: 05/09/2023]
Abstract
We report the synthesis and characterization of a new family of maltose-derived nonionic surfactants that contain a photocleavable azo-sulfide linker (mAzo). The self-assembly properties of these surfactants were investigated using surface tension measurements to determine the critical micelle concentration (CMC), dynamic light scattering (DLS) to reveal the hydrodynamic radius of their self-assemblies, and transmission electron microscopy (TEM) to elucidate the micelle morphology. Ultraviolet-visible (UV-visible) spectroscopy confirmed the rapid photodegradation of these surfactants, but surface tension measurements of the surfactant solutions before and after degradation showed unusual degradation products. The photodegradation process was further studied using online liquid chromatography coupled with mass spectrometry (LC-MS),which revealed that these surfactants can form another photo-stable surfactant post-degradation. Finally, traditionally challenging proteins from heart tissue were solubilized using the mAzo surfactants to demonstrate their potential in biological applications.
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Affiliation(s)
- Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Morgan K. Gugger
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - David Moreno
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Pil Seok Chae
- Department of Bionano Engineering, Hanyang University, Ansan, 15588, South Korea
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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15
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Abstract
Nonionic surfactants are often used as general reagents for cell lysis enabling protein extraction, stabilization, and purification under nondenaturing conditions for downstream analysis in structural biology. However, the presence of surfactants in the sample matrix often has a deleterious effect on electrospray ionization (ESI)-mass spectrometry (MS) analysis of proteins and complexes. Here, we report a nonionic, cleavable surfactant, n-decyl-disulfide-β-D-maltoside (DSSM), for top-down proteomics. DSSM was designed to mimic the properties of one of the most common surfactants used in structural biology, n-dodecyl-β-D-maltoside (DDM), but contains a disulfide bond that allows for facile cleavage and surfactant removal before or during MS analysis. We have shown that DSSM is compatible with direct electrospray ionization (ESI)-MS analysis and reversed-phase liquid chromatography (RPLC)-MS analysis of proteins and protein complexes. We have demonstrated that DSSM can facilitate top-down proteomic characterization of membrane proteins such as a model ion channel protein and a G protein-coupled receptor as well as endogenous proteins from cell lysates for the determination of sequence variations and posttranslational modifications (PTMs). Conceivably, DSSM could serve as a general replacement for DDM in proteomic experiments and structural biology studies.
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Affiliation(s)
- Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Morgan K. Gugger
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Zhen Yu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - David Moreno
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
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16
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Larson EJ, Pergande MR, Moss ME, Rossler KJ, Wenger RK, Krichel B, Josyer H, Melby JA, Roberts DS, Pike K, Shi Z, Chan HJ, Knight B, Rogers HT, Brown KA, Ong IM, Jeong K, Marty M, McIlwain SJ, Ge Y. MASH Native: A Unified Solution for Native Top-Down Proteomics Data Processing. bioRxiv 2023:2023.01.02.522513. [PMID: 36711733 PMCID: PMC9881860 DOI: 10.1101/2023.01.02.522513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Native top-down proteomics (nTDP) integrates native mass spectrometry (nMS) with top-down proteomics (TDP) to provide comprehensive analysis of protein complexes together with proteoform identification and characterization. Despite significant advances in nMS and TDP software developments, a unified and user-friendly software package for analysis of nTDP data remains lacking. Herein, we have developed MASH Native to provide a unified solution for nTDP to process complex datasets with database searching capabilities in a user-friendly interface. MASH Native supports various data formats and incorporates multiple options for deconvolution, database searching, and spectral summing to provide a one-stop shop for characterizing both native protein complexes and proteoforms. The MASH Native app, video tutorials, written tutorials and additional documentation are freely available for download at https://labs.wisc.edu/gelab/MASH_Explorer/MASHNativeSoftware.php . All data files shown in user tutorials are included with the MASH Native software in the download .zip file.
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17
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Carpenter JM, Brown KA, Veltmaat L, Ludwig HD, Clay KB, Norberg T, Harn DA, Wagner JJ, Filipov NM. Evaluation of delayed LNFPIII treatment initiation protocol on improving long-term behavioral and neuroinflammatory pathology in a mouse model of Gulf War Illness. Brain Behav Immun Health 2022; 26:100553. [DOI: 10.1016/j.bbih.2022.100553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/29/2022] [Accepted: 11/06/2022] [Indexed: 11/09/2022] Open
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18
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Gupta K, Brown KA, Hsieh ML, Hoover BM, Wang J, Khoury MK, Pilli VSS, Beyer RSH, Voruganti NR, Chaudhary S, Roberts DS, Murphy RM, Hong S, Ge Y, Liu B. Necroptosis is associated with Rab27-independent expulsion of extracellular vesicles containing RIPK3 and MLKL. J Extracell Vesicles 2022; 11:e12261. [PMID: 36063142 PMCID: PMC9443950 DOI: 10.1002/jev2.12261] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/23/2022] [Accepted: 08/13/2022] [Indexed: 11/30/2022] Open
Abstract
Extracellular vesicle (EV) secretion is an important mechanism used by cells to release biomolecules. A common necroptosis effector—mixed lineage kinase domain like (MLKL)—was recently found to participate in the biogenesis of small and large EVs independent of its function in necroptosis. The objective of the current study is to gain mechanistic insights into EV biogenesis during necroptosis. Assessing EV number by nanoparticle tracking analysis revealed an increased number of EVs released during necroptosis. To evaluate the nature of such vesicles, we performed a newly adapted, highly sensitive mass spectrometry‐based proteomics on EVs released by healthy or necroptotic cells. Compared to EVs released by healthy cells, EVs released during necroptosis contained a markedly higher number of unique proteins. Receptor interacting protein kinase‐3 (RIPK3) and MLKL were among the proteins enriched in EVs released during necroptosis. Further, mouse embryonic fibroblasts (MEFs) derived from mice deficient of Rab27a and Rab27b showed diminished basal EV release but responded to necroptosis with enhanced EV biogenesis as the wildtype MEFs. In contrast, necroptosis‐associated EVs were sensitive to Ca2+ depletion or lysosomal disruption. Neither treatment affected the RIPK3‐mediated MLKL phosphorylation. An unbiased screen using RIPK3 immunoprecipitation‐mass spectrometry on necroptotic EVs led to the identification of Rab11b in RIPK3 immune‐complexes. Our data suggests that necroptosis switches EV biogenesis from a Rab27a/b dependent mechanism to a lysosomal mediated mechanism.
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Affiliation(s)
- Kartik Gupta
- Division of Vascular Surgery, Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Kyle A Brown
- Division of Vascular Surgery, Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Marvin L Hsieh
- Division of Vascular Surgery, Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Brandon M Hoover
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Jianxin Wang
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Mitri K Khoury
- Division of Vascular Surgery, Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Vijaya Satish Sekhar Pilli
- Division of Vascular Surgery, Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Reagan S H Beyer
- Division of Vascular Surgery, Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Nihal R Voruganti
- Division of Vascular Surgery, Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Sahil Chaudhary
- Division of Vascular Surgery, Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Regina M Murphy
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Seungpyo Hong
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA.,Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA.,Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Bo Liu
- Division of Vascular Surgery, Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
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19
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Buck KM, Roberts DS, Aballo TJ, Inman DR, Jin S, Ponik S, Brown KA, Ge Y. One-Pot Exosome Proteomics Enabled by a Photocleavable Surfactant. Anal Chem 2022; 94:7164-7168. [PMID: 35543580 DOI: 10.1021/acs.analchem.2c01252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Exosomes are small extracellular vesicles (EVs) secreted by all cells and found in biological fluids, which can serve as minimally invasive liquid biopsies with extremely high therapeutic and diagnostic potential. Mass spectrometry (MS)-based proteomics is a powerful technique to profile and quantify the protein content in exosomes, but the current methods require laborious and time-consuming multistep sample preparation that significantly limit throughput. Herein, we report a one-pot exosome proteomics method enabled by a photocleavable surfactant, Azo, to simplify exosomal lysis, effectively extract proteins, and expedite digestion. We have applied this method to exosomes derived from isolated mammary fibroblasts and confidently identified 3466 proteins and quantified 2288 proteins using a reversed-phase liquid chromatography coupled to trapped ion mobility spectrometry (TIMS) quadrupole time-of-flight mass spectrometer. Here, 3166 (91%) of the identified proteins are annotated in the exosome/EVs databases, ExoCarta and Vesiclepedia, including important exosomal markers, CD63, PDCD6IP, and SDCBP. This method is fast, simple, and highly effective at extracting exosomal proteins with high reproducibility for deep exosomal proteome coverage. We envision that this method could be generally applicable for exosome proteomics applications in biomedical research, therapeutic interventions, and clinical diagnostics.
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Affiliation(s)
- Kevin M Buck
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Timothy J Aballo
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - David R Inman
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Suzanne Ponik
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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20
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Brown KA, Anderson C, Reilly L, Sondhi K, Ge Y, Eckhardt LL. Proteomic Analysis of the Functional Inward Rectifier Potassium Channel (Kir) 2.1 Reveals Several Novel Phosphorylation Sites. Biochemistry 2021; 60:3292-3301. [PMID: 34676745 DOI: 10.1021/acs.biochem.1c00555] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Membrane proteins represent a large family of proteins that perform vital physiological roles and represent key drug targets. Despite their importance, bioanalytical methods aiming to comprehensively characterize the post-translational modification (PTM) of membrane proteins remain challenging compared to other classes of proteins in part because of their inherent low expression and hydrophobicity. The inward rectifier potassium channel (Kir) 2.1, an integral membrane protein, is critical for the maintenance of the resting membrane potential and phase-3 repolarization of the cardiac action potential in the heart. The importance of this channel to cardiac physiology is highlighted by the recognition of several sudden arrhythmic death syndromes, Andersen-Tawil and short QT syndromes, which are associated with loss or gain of function mutations in Kir2.1, often triggered by changes in the β-adrenergic tone. Therefore, understanding the PTMs of this channel (particularly β-adrenergic tone-driven phosphorylation) is important for arrhythmia prevention. Here, we developed a proteomic method, integrating both top-down (intact protein) and bottom-up (after enzymatic digestion) proteomic analyses, to characterize the PTMs of recombinant wild-type and mutant Kir2.1, successfully mapping five novel sites of phosphorylation and confirming a sixth site. Our study provides a framework for future work to assess the role of PTMs in regulating Kir2.1 functions.
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Affiliation(s)
- Kyle A Brown
- Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Corey Anderson
- Cellular and Molecular Arrhythmia Research Program, Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Louise Reilly
- Cellular and Molecular Arrhythmia Research Program, Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kunal Sondhi
- Cellular and Molecular Arrhythmia Research Program, Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Lee L Eckhardt
- Cellular and Molecular Arrhythmia Research Program, Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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21
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Tiribocchi A, Montessori A, Lauricella M, Bonaccorso F, Brown KA, Succi S. Microscale modelling of dielectrophoresis assembly processes. Philos Trans A Math Phys Eng Sci 2021; 379:20200407. [PMID: 34455845 DOI: 10.1098/rsta.2020.0407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/04/2021] [Indexed: 06/13/2023]
Abstract
This work presents a microscale approach for simulating the dielectrophoresis assembly of polarizable particles under an external electric field. The model is shown to capture interesting dynamical and topological features, such as the formation of chains of particles and their incipient aggregation into hierarchical structures. A quantitative characterization in terms of the number and size of these structures is also discussed. This computational model could represent a viable numerical tool to study the mechanical properties of particle-based hierarchical materials and suggest new strategies for enhancing their design and manufacture. This article is part of the theme issue 'Progress in mesoscale methods for fluid dynamics simulation'.
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Affiliation(s)
- A Tiribocchi
- Center for Life Nano Science@La Sapienza, Istituto Italiano di Tecnologia, 00161 Roma, Italy
- Istituto per le Applicazioni del Calcolo CNR, via dei Taurini, 19, 00185 Rome, Italy
| | - A Montessori
- Istituto per le Applicazioni del Calcolo CNR, via dei Taurini, 19, 00185 Rome, Italy
| | - M Lauricella
- Istituto per le Applicazioni del Calcolo CNR, via dei Taurini, 19, 00185 Rome, Italy
| | - F Bonaccorso
- Center for Life Nano Science@La Sapienza, Istituto Italiano di Tecnologia, 00161 Roma, Italy
- Istituto per le Applicazioni del Calcolo CNR, via dei Taurini, 19, 00185 Rome, Italy
- Department of Physics and INFN, University of Rome 'Tor Vergata', Via della Ricerca Scientifica, 1 00133 Rome, Italy
| | - K A Brown
- Department of Mechanical Engineering, Boston University, Boston, MA 02215, USA
| | - S Succi
- Center for Life Nano Science@La Sapienza, Istituto Italiano di Tecnologia, 00161 Roma, Italy
- Istituto per le Applicazioni del Calcolo CNR, via dei Taurini, 19, 00185 Rome, Italy
- Institute for Applied Computational Science, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
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22
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Carpenter JM, Brown KA, Diaz AN, Dockman RL, Benbow RA, Harn DA, Norberg T, Wagner JJ, Filipov NM. Delayed treatment with the immunotherapeutic LNFPIII ameliorates multiple neurological deficits in a pesticide-nerve agent prophylactic mouse model of Gulf War Illness. Neurotoxicol Teratol 2021; 87:107012. [PMID: 34256162 DOI: 10.1016/j.ntt.2021.107012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 03/03/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/20/2022]
Abstract
Residual effects of the 1990-1991 Gulf War (GW) still plague veterans 30 years later as Gulf War Illness (GWI). Thought to stem mostly from deployment-related chemical overexposures, GWI is a disease with multiple neurological symptoms with likely immunological underpinnings. Currently, GWI remains untreatable, and the long-term neurological disease manifestation is not characterized fully. The present study sought to expand and evaluate the long-term implications of prior GW chemicals exposure on neurological function 6-8 months post GWI-like symptomatology induction. Additionally, the beneficial effects of delayed treatment with the glycan immunotherapeutic lacto-N-fucopentaose III (LNFPIII) were evaluated. Male C57BL/6J mice underwent a 10-day combinational exposure (i.p.) to GW chemicals, the nerve agent prophylactic pyridostigmine bromide (PB) and the insecticide permethrin (PM; 0.7 and 200 mg/kg, respectively). Beginning 4 months after PB/PM exposure, a subset of the mice were treated twice a week until study completion with LNFPIII. Evaluation of cognition/memory, motor function, and mood was performed beginning 1 month after LNFPIII treatment initiation. Prior exposure to PB/PM produced multiple locomotor, neuromuscular, and sensorimotor deficits across several motor tests. Subtle anxiety-like behavior was also present in PB/PM mice in mood tests. Further, PB/PM-exposed mice learned at a slower rate, mostly during early phases of the learning and memory tests employed. LNFPIII treatment restored or improved many of these behaviors, particularly in motor and cognition/memory domains. Electrophysiology data collected from hippocampal slices 8 months post PB/PM exposure revealed modest aberrations in basal synaptic transmission and long-term potentiation in the dorsal or ventral hippocampus that were improved by LNFPIII treatment. Immunohistochemical analysis of tyrosine hydroxylase (TH), a dopaminergic marker, did not detect major PB/PM effects along the nigrostriatal pathway, but LNFPIII increased striatal TH. Additionally, neuroinflammatory cells were increased in PB/PM mice, an effect reduced by LNFPIII. Collectively, long-term neurobehavioral and neurobiological dysfunction associated with prior PB/PM exposure was characterized; delayed LNFPIII treatment provided multiple behavioral and biological beneficial effects in the context of GWI, highlighting its potential as a GWI therapeutic.
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Affiliation(s)
- Jessica M Carpenter
- Department of Physiology and Pharmacology, University of Georgia, Athens, GA, United States; Neuroscience Program, University of Georgia, Athens, GA, United States
| | - Kyle A Brown
- Department of Physiology and Pharmacology, University of Georgia, Athens, GA, United States; Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States
| | - Alexa N Diaz
- Department of Physiology and Pharmacology, University of Georgia, Athens, GA, United States
| | - Rachel L Dockman
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - Robert A Benbow
- Department of Physiology and Pharmacology, University of Georgia, Athens, GA, United States
| | - Donald A Harn
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States; Center for Tropical and Emerging Infectious Diseases, University of Georgia, Athens, GA, United States
| | - Thomas Norberg
- Department of Chemistry, University of Uppsala, Uppsala, Sweden
| | - John J Wagner
- Department of Physiology and Pharmacology, University of Georgia, Athens, GA, United States; Neuroscience Program, University of Georgia, Athens, GA, United States; Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States.
| | - Nikolay M Filipov
- Department of Physiology and Pharmacology, University of Georgia, Athens, GA, United States; Neuroscience Program, University of Georgia, Athens, GA, United States; Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States.
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23
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Aballo TJ, Roberts DS, Melby JA, Buck KM, Brown KA, Ge Y. Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro. J Proteome Res 2021; 20:4203-4211. [PMID: 34236868 PMCID: PMC8349881 DOI: 10.1021/acs.jproteome.1c00446] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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] [Indexed: 01/25/2023]
Abstract
Global bottom-up mass spectrometry (MS)-based proteomics is widely used for protein identification and quantification to achieve a comprehensive understanding of the composition, structure, and function of the proteome. However, traditional sample preparation methods are time-consuming, typically including overnight tryptic digestion, extensive sample cleanup to remove MS-incompatible surfactants, and offline sample fractionation to reduce proteome complexity prior to online liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Thus, there is a need for a fast, robust, and reproducible method for protein identification and quantification from complex proteomes. Herein, we developed an ultrafast bottom-up proteomics method enabled by Azo, a photocleavable, MS-compatible surfactant that effectively solubilizes proteins and promotes rapid tryptic digestion, combined with the Bruker timsTOF Pro, which enables deeper proteome coverage through trapped ion mobility spectrometry (TIMS) and parallel accumulation-serial fragmentation (PASEF) of peptides. We applied this method to analyze the complex human cardiac proteome and identified nearly 4000 protein groups from as little as 1 mg of human heart tissue in a single one-dimensional LC-TIMS-MS/MS run with high reproducibility. Overall, we anticipate this ultrafast, robust, and reproducible bottom-up method empowered by both Azo and the timsTOF Pro will be generally applicable and greatly accelerate the throughput of large-scale quantitative proteomic studies. Raw data are available via the MassIVE repository with identifier MSV000087476.
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Affiliation(s)
- Timothy J Aballo
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jake A Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kevin M Buck
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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24
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Hayes KN, He N, Brown KA, Cheung AM, Juurlink DN, Cadarette SM. Over half of seniors who start oral bisphosphonate therapy are exposed for 3 or more years: novel rolling window approach and patterns of use. Osteoporos Int 2021; 32:1413-1420. [PMID: 33415374 DOI: 10.1007/s00198-020-05794-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/10/2020] [Indexed: 12/17/2022]
Abstract
UNLABELLED Most adherence studies only consider treatment following a first prescription. Using an extended follow-up, we found that 60% of seniors starting oral bisphosphonate therapy were exposed for ≥ 3 years (48% for ≥ 5 years). Studies are needed to examine the benefits and harms of continuing bisphosphonate therapy beyond 3 years. INTRODUCTION The purpose of this study was to identify and describe patterns of long-term oral bisphosphonate use among seniors using a novel methodological approach that considers extended follow-up. METHODS Among Ontarians aged 66 years or older, we identified subjects with a first dispensing of alendronate or risedronate between November 2000 and December 2016. We followed them until death or December 2019 to identify patients with ≥ 3 years of bisphosphonate use, defined as a proportion of days covered ≥ 80%, using 3-year rolling windows. We calculated the proportion of patients with long-term therapy (≥ 3 years of use) using Kaplan-Meier estimates. We described patterns of long-term use and compared patient characteristics between patients with and without long-term therapy. RESULTS We identified 260,784 eligible seniors initiating bisphosphonate therapy. Of these, 60% continued therapy ≥ 3 years (77% women), and 48% continued ≥ 5 years. Characteristics did not meaningfully differ between patients with or without long-term therapy. The median length of long-term therapy was 7.0 (IQR 5.1) years for women and 6.1 (IQR 4.3) years for men. Only 20% experienced a treatment gap before long-term therapy, yet 50% experienced a treatment gap of ≥ 120 days after a median 5.3 years of therapy. Eighty-one percent who returned to therapy following a treatment gap re-initiated an oral bisphosphonate, with 18% switching to denosumab. CONCLUSIONS Among seniors initiating oral bisphosphonates, we found that 60% receive at least 3 years of therapy when using an extended follow-up. Studies are needed to examine the benefits and harms of continuing bisphosphonate therapy beyond 3 years.
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Affiliation(s)
- K N Hayes
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, ON, M5S 3M2, Canada.
| | - N He
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, ON, M5S 3M2, Canada
- ICES, Toronto, ON, Canada
| | - K A Brown
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- ICES, Toronto, ON, Canada
- Public Health Ontario, Toronto, ON, Canada
| | - A M Cheung
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Department of Medicine, University Health Network, University of Toronto, Toronto, ON, Canada
| | - D N Juurlink
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- ICES, Toronto, ON, Canada
- Sunnybrook Research Institute, Toronto, ON, Canada
| | - S M Cadarette
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, ON, M5S 3M2, Canada
- ICES, Toronto, ON, Canada
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
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25
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Brown KA, Carpenter JM, Preston CJ, Ludwig HD, Clay KB, Harn DA, Norberg T, Wagner JJ, Filipov NM. Lacto-N-fucopentaose-III ameliorates acute and persisting hippocampal synaptic plasticity and transmission deficits in a Gulf War Illness mouse model. Life Sci 2021; 279:119707. [PMID: 34102195 DOI: 10.1016/j.lfs.2021.119707] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/19/2021] [Accepted: 06/01/2021] [Indexed: 12/12/2022]
Abstract
AIMS The present study investigated if treatment with the immunotherapeutic, lacto-N-fucopentaose-III (LNFPIII), resulted in amelioration of acute and persisting deficits in synaptic plasticity and transmission as well as trophic factor expression along the hippocampal dorsoventral axis in a mouse model of Gulf War Illness (GWI). MAIN METHODS Mice received either coadministered or delayed LNFPIII treatment throughout or following, respectively, exposure to a 15-day GWI induction paradigm. Subsets of animals were subsequently sacrificed 48 h, seven months, or 11 months post GWI-related (GWIR) exposure for hippocampal qPCR or in vitro electrophysiology experiments. KEY FINDINGS Progressively worsened impairments in hippocampal synaptic plasticity, as well as a biphasic effect on hippocampal synaptic transmission, were detected in GWIR-exposed animals. Dorsoventral-specific impairments in hippocampal synaptic responses became more pronounced over time, particularly in the dorsal hippocampus. Notably, delayed LNFPIII treatment ameliorated GWI-related aberrations in hippocampal synaptic plasticity and transmission seven and 11 months post-exposure, an effect that was consistent with enhanced hippocampal trophic factor expression and absence of increased interleukin 6 (IL-6) in animals treated with LNFPIII. SIGNIFICANCE Approximately a third of Gulf War Veterans have GWI; however, GWI therapeutics are presently limited to targeted and symptomatic treatments. As increasing evidence underscores the substantial role of persisting neuroimmune dysfunction in GWI, efficacious neuroactive immunotherapeutics hold substantial promise in yielding GWI remission. The findings in the present report indicate that LNFPIII may be an efficacious candidate for ameliorating persisting neurological abnormalities presented in GWI.
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Affiliation(s)
- Kyle A Brown
- Department of Physiology and Pharmacology, University of Georgia, Athens, GA, United States; Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States
| | - Jessica M Carpenter
- Department of Physiology and Pharmacology, University of Georgia, Athens, GA, United States; Neuroscience Program, University of Georgia, Athens, GA, United States
| | - Collin J Preston
- Department of Physiology and Pharmacology, University of Georgia, Athens, GA, United States; Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States
| | - Helaina D Ludwig
- Department of Physiology and Pharmacology, University of Georgia, Athens, GA, United States; Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States
| | - Kendall B Clay
- Neuroscience Program, University of Georgia, Athens, GA, United States
| | - Donald A Harn
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States; Center for Tropical and Emerging Diseases, University of Georgia, Athens, GA, United States
| | - Thomas Norberg
- Department of Chemistry, University of Uppsala, Uppsala, Sweden
| | - John J Wagner
- Department of Physiology and Pharmacology, University of Georgia, Athens, GA, United States; Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States; Neuroscience Program, University of Georgia, Athens, GA, United States.
| | - Nikolay M Filipov
- Department of Physiology and Pharmacology, University of Georgia, Athens, GA, United States; Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States; Neuroscience Program, University of Georgia, Athens, GA, United States.
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26
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Melby JA, Roberts DS, Larson EJ, Brown KA, Bayne EF, Jin S, Ge Y. Novel Strategies to Address the Challenges in Top-Down Proteomics. J Am Soc Mass Spectrom 2021; 32:1278-1294. [PMID: 33983025 PMCID: PMC8310706 DOI: 10.1021/jasms.1c00099] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Top-down mass spectrometry (MS)-based proteomics is a powerful technology for comprehensively characterizing proteoforms to decipher post-translational modifications (PTMs) together with genetic variations and alternative splicing isoforms toward a proteome-wide understanding of protein functions. In the past decade, top-down proteomics has experienced rapid growth benefiting from groundbreaking technological advances, which have begun to reveal the potential of top-down proteomics for understanding basic biological functions, unraveling disease mechanisms, and discovering new biomarkers. However, many challenges remain to be comprehensively addressed. In this Account & Perspective, we discuss the major challenges currently facing the top-down proteomics field, particularly in protein solubility, proteome dynamic range, proteome complexity, data analysis, proteoform-function relationship, and analytical throughput for precision medicine. We specifically review the major technology developments addressing these challenges with an emphasis on our research group's efforts, including the development of top-down MS-compatible surfactants for protein solubilization, functionalized nanoparticles for the enrichment of low-abundance proteoforms, strategies for multidimensional chromatography separation of proteins, and a new comprehensive user-friendly software package for top-down proteomics. We have also made efforts to connect proteoforms with biological functions and provide our visions on what the future holds for top-down proteomics.
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Affiliation(s)
- Jake A Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Eli J Larson
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Elizabeth F Bayne
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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Kurgan KW, Chen B, Brown KA, Falco Cobra P, Ye X, Ge Y, Gellman SH. Stable Picodisc Assemblies from Saposin Proteins and Branched Detergents. Biochemistry 2021; 60:1108-1119. [PMID: 33755420 DOI: 10.1021/acs.biochem.0c00924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methods for maintaining membrane proteins in their native state after removal from the lipid bilayer are essential for the study of this important class of biomacromolecules. Common solubilization strategies range from the use of detergents to more complex systems that involve a polypeptide working in concert with lipids or detergents, such as nanodiscs, picodiscs, and peptidiscs, in which an engineered protein or synthetic peptide surrounds the membrane protein along with a lipid sheath. Picodiscs employ the protein saposin A, which naturally functions to facilitate lipid degradation in the lysozome. Saposin A-amphiphile complexes therefore tend to be most stable at acidic pH, which is not optimal for most membrane protein applications. In search of new picodisc assemblies, we have explored pairings of saposin A or other saposin proteins with a range of detergents, and we have identified a number of combinations that spontaneously co-assemble at neutral pH. The resulting picodiscs are stable for weeks and have been characterized by size-exclusion chromatography, native mass spectrometry, and small angle X-ray scattering. The new assemblies are formed by double-tail detergents rather than more traditional single-tail detergents; the double-tail detergents can be seen as structurally intermediate between single-tail detergents and common lipids. In addition to saposin A, an engineered variant of saposin B (designated saposin BW) forms picodisc assemblies. These findings provide a framework for future efforts to solubilize membrane proteins with multiple picodisc systems that were previously unknown.
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Brown KA, Tucholski T, Alpert AJ, Eken C, Wesemann L, Kyrvasilis A, Jin S, Ge Y. Top-Down Proteomics of Endogenous Membrane Proteins Enabled by Cloud Point Enrichment and Multidimensional Liquid Chromatography-Mass Spectrometry. Anal Chem 2020; 92:15726-15735. [PMID: 33231430 PMCID: PMC7968110 DOI: 10.1021/acs.analchem.0c02533] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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] [Indexed: 01/31/2023]
Abstract
Although top-down proteomics has emerged as a powerful strategy to characterize proteins in biological systems, the analysis of endogenous membrane proteins remains challenging due to their low solubility, low abundance, and the complexity of the membrane subproteome. Here, we report a simple but effective enrichment and separation strategy for top-down proteomics of endogenous membrane proteins enabled by cloud point extraction and multidimensional liquid chromatography coupled to high-resolution mass spectrometry (MS). The cloud point extraction efficiently enriched membrane proteins using a single extraction, eliminating the need for time-consuming ultracentrifugation steps. Subsequently, size-exclusion chromatography (SEC) with an MS-compatible mobile phase (59% water, 40% isopropanol, 1% formic acid) was used to remove the residual surfactant and fractionate intact proteins (6-115 kDa). The fractions were separated further by reversed-phase liquid chromatography (RPLC) coupled with MS for protein characterization. This method was applied to human embryonic kidney cells and cardiac tissue lysates to enable the identification of 188 and 124 endogenous integral membrane proteins, respectively, some with as many as 19 transmembrane domains.
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Affiliation(s)
- Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Andrew J. Alpert
- PolyLC Inc., Columbia, Maryland 21045, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Christian Eken
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Lucas Wesemann
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Andreas Kyrvasilis
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
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29
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Knott SJ, Brown KA, Josyer H, Carr A, Inman D, Jin S, Friedl A, Ponik SM, Ge Y. Photocleavable Surfactant-Enabled Extracellular Matrix Proteomics. Anal Chem 2020; 92:15693-15698. [PMID: 33232116 DOI: 10.1021/acs.analchem.0c03104] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The extracellular matrix (ECM) provides an architectural meshwork that surrounds and supports cells. The dysregulation of heavily post-translationally modified ECM proteins directly contributes to various diseases. Mass spectrometry (MS)-based proteomics is an ideal tool to identify ECM proteins and characterize their post-translational modifications, but ECM proteomics remains challenging owing to the extremely low solubility of the ECM. Herein, enabled by effective solubilization of ECM proteins using our recently developed photocleavable surfactant, Azo, we have developed a streamlined ECM proteomic strategy that allows fast tissue decellularization, efficient extraction and enrichment of ECM proteins, and rapid digestion prior to reversed-phase liquid chromatography (RPLC)-MS analysis. A total of 173 and 225 unique ECM proteins from mouse mammary tumors have been identified using 1D and 2D RPLC-MS/MS, respectively. Moreover, 87 (from 1DLC-MS/MS) and 229 (from 2DLC-MS/MS) post-translational modifications of ECM proteins, including glycosylation, phosphorylation, and hydroxylation, were identified and localized. This Azo-enabled ECM proteomics strategy will streamline the analysis of ECM proteins and promote the study of ECM biology.
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Affiliation(s)
- Samantha J Knott
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Harini Josyer
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Austin Carr
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - David Inman
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Andreas Friedl
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 1685 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Suzanne M Ponik
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, United States.,Human Proteomics Program, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, United States
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Zhou M, Lantz C, Brown KA, Ge Y, Paša-Tolić L, Loo JA, Lermyte F. Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry. Chem Sci 2020; 11:12918-12936. [PMID: 34094482 PMCID: PMC8163214 DOI: 10.1039/d0sc04392c] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022] Open
Abstract
In biology, it can be argued that if the genome contains the script for a cell's life cycle, then the proteome constitutes an ensemble cast of actors that brings these instructions to life. Their interactions with each other, co-factors, ligands, substrates, and so on, are key to understanding nearly any biological process. Mass spectrometry is well established as the method of choice to determine protein primary structure and location of post-translational modifications. In recent years, top-down fragmentation of intact proteins has been increasingly combined with ionisation of noncovalent assemblies under non-denaturing conditions, i.e., native mass spectrometry. Sequence, post-translational modifications, ligand/metal binding, protein folding, and complex stoichiometry can thus all be probed directly. Here, we review recent developments in this new and exciting field of research. While this work is written primarily from a mass spectrometry perspective, it is targeted to all bioanalytical scientists who are interested in applying these methods to their own biochemistry and chemical biology research.
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Affiliation(s)
- Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | - Carter Lantz
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles Los Angeles CA 90095 USA
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Madison WI 53706 USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles Los Angeles CA 90095 USA
| | - Frederik Lermyte
- Department of Chemistry, Institute of Chemistry and Biochemistry, Technical University of Darmstadt 64287 Darmstadt Germany
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège 4000 Liège Belgium
- School of Engineering, University of Warwick Coventry CV4 7AL UK
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31
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Brown KA, Melby JA, Roberts DS, Ge Y. Top-down proteomics: challenges, innovations, and applications in basic and clinical research. Expert Rev Proteomics 2020; 17:719-733. [PMID: 33232185 PMCID: PMC7864889 DOI: 10.1080/14789450.2020.1855982] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022]
Abstract
Introduction- A better understanding of the underlying molecular mechanism of diseases is critical for developing more effective diagnostic tools and therapeutics toward precision medicine. However, many challenges remain to unravel the complex nature of diseases. Areas covered- Changes in protein isoform expression and post-translation modifications (PTMs) have gained recognition for their role in underlying disease mechanisms. Top-down mass spectrometry (MS)-based proteomics is increasingly recognized as an important method for the comprehensive characterization of proteoforms that arise from alternative splicing events and/or PTMs for basic and clinical research. Here, we review the challenges, technological innovations, and recent studies that utilize top-down proteomics to elucidate changes in the proteome with an emphasis on its use to study heart diseases. Expert opinion- Proteoform-resolved information can substantially contribute to the understanding of the molecular mechanisms underlying various diseases and for the identification of novel proteoform targets for better therapeutic development . Despite the challenges of sequencing intact proteins, top-down proteomics has enabled a wealth of information regarding protein isoform switching and changes in PTMs. Continuous developments in sample preparation, intact protein separation, and instrumentation for top-down MS have broadened its capabilities to characterize proteoforms from a range of samples on an increasingly global scale.
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Affiliation(s)
- Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Jake A. Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin, United States
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32
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Tiambeng TN, Roberts DS, Brown KA, Zhu Y, Chen B, Wu Z, Mitchell SD, Guardado-Alvarez TM, Jin S, Ge Y. Nanoproteomics enables proteoform-resolved analysis of low-abundance proteins in human serum. Nat Commun 2020; 11:3903. [PMID: 32764543 PMCID: PMC7411019 DOI: 10.1038/s41467-020-17643-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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: 03/19/2020] [Accepted: 07/02/2020] [Indexed: 12/17/2022] Open
Abstract
Top-down mass spectrometry (MS)-based proteomics provides a comprehensive analysis of proteoforms to achieve a proteome-wide understanding of protein functions. However, the MS detection of low-abundance proteins from blood remains an unsolved challenge due to the extraordinary dynamic range of the blood proteome. Here, we develop an integrated nanoproteomics method coupling peptide-functionalized superparamagnetic nanoparticles (NPs) with top-down MS for the enrichment and comprehensive analysis of cardiac troponin I (cTnI), a gold-standard cardiac biomarker, directly from serum. These NPs enable the sensitive enrichment of cTnI (<1 ng/mL) with high specificity and reproducibility, while simultaneously depleting highly abundant proteins such as human serum albumin (>1010 more abundant than cTnI). We demonstrate that top-down nanoproteomics can provide high-resolution proteoform-resolved molecular fingerprints of diverse cTnI proteoforms to establish proteoform-pathophysiology relationships. This scalable and reproducible antibody-free strategy can generally enable the proteoform-resolved analysis of low-abundance proteins directly from serum to reveal previously unachievable molecular details.
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Affiliation(s)
- Timothy N Tiambeng
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53719, USA
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53719, USA
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53719, USA
| | - Yanlong Zhu
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53719, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53719, USA
| | - Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53719, USA
| | - Zhijie Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53719, USA
| | - Stanford D Mitchell
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53719, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI, 53719, USA
| | | | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53719, USA.
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53719, USA.
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53719, USA.
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53719, USA.
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Brown KA, Tucholski T, Eken C, Knott S, Zhu Y, Jin S, Ge Y. High-Throughput Proteomics Enabled by a Photocleavable Surfactant. Angew Chem Int Ed Engl 2020; 59:8406-8410. [PMID: 32097521 PMCID: PMC7230032 DOI: 10.1002/anie.201915374] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 12/03/2019] [Revised: 02/07/2020] [Indexed: 11/10/2022]
Abstract
Mass spectrometry (MS)-based proteomics provides unprecedented opportunities for understanding the structure and function of proteins in complex biological systems; however, protein solubility and sample preparation before MS remain a bottleneck preventing high-throughput proteomics. Herein, we report a high-throughput bottom-up proteomic method enabled by a newly developed MS-compatible photocleavable surfactant, 4-hexylphenylazosulfonate (Azo) that facilitates robust protein extraction, rapid enzymatic digestion (30 min compared to overnight), and subsequent MS-analysis following UV degradation. Moreover, we developed an Azo-aided bottom-up method for analysis of integral membrane proteins, which are key drug targets and are generally underrepresented in global proteomic studies. Furthermore, we demonstrated the ability of Azo to serve as an "all-in-one" MS-compatible surfactant for both top-down and bottom-up proteomics, with streamlined workflows for high-throughput proteomics amenable to clinical applications.
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Affiliation(s)
- Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Christian Eken
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Samantha Knott
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
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34
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Affiliation(s)
- Kyle A. Brown
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Trisha Tucholski
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Christian Eken
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Samantha Knott
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology University of Wisconsin-Madison Madison WI 53706 USA
| | - Song Jin
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Ying Ge
- Department of Chemistry University of Wisconsin-Madison Madison WI 53706 USA
- Department of Cell and Regenerative Biology University of Wisconsin-Madison Madison WI 53706 USA
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Brown KA, Filipov NM, Wagner JJ. Dorsoventral-Specific Effects of Nerve Agent Surrogate Diisopropylfluorophosphate on Synaptic Transmission in the Mouse Hippocampus. J Pharmacol Exp Ther 2020; 373:10-23. [DOI: 10.1124/jpet.119.263053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/16/2019] [Indexed: 11/22/2022] Open
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Adler AC, Brown KA, Conlin FT, Thammasitboon S, Chandrakantan A. Cardiac and lung point-of-care ultrasound in pediatric anesthesia and critical care medicine: Uses, pitfalls, and future directions to optimize pediatric care. Paediatr Anaesth 2019; 29:790-798. [PMID: 31211472 DOI: 10.1111/pan.13684] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/09/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022]
Abstract
Point-of-care ultrasound (POCUS) has found many relevant applications in pediatric anesthesia and critical care medicine. Specifically, the cardiac and pulmonary POCUS examinations provide a wealth of information from physical examination assistance to diagnostic evaluation and assessment of treatment response. However, as with any adjunct, potentially dangerous pitfalls exist when POCUS is performed, interpreted, and applied by the novice sonographer. Using case illustrations, we highlight the clinical application of POCUS in addition to potential dangers. Additionally, suggestions for learning POCUS, assessing competency and credentialing are reviewed.
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Affiliation(s)
- Adam C Adler
- Department of Anesthesiology, Perioperative and Pain Medicine, Texas Children's Hospital, Houston, Texas.,Section of Pediatric Critical Care Medicine, Department of Pediatrics, Texas Children's Hospital, Houston, Texas
| | - Kyle A Brown
- Section of Pediatric Critical Care Medicine, Department of Pediatrics, Texas Children's Hospital, Houston, Texas.,Baylor College of Medicine, Houston, Texas
| | - Frederick T Conlin
- Department of Anesthesiology and Pain Medicine, Baystate Medical Center, Springfield, Massachusetts.,University of Massachusetts School of Medicine, Worcester, Massachusetts
| | - Satid Thammasitboon
- Section of Pediatric Critical Care Medicine, Department of Pediatrics, Texas Children's Hospital, Houston, Texas.,Baylor College of Medicine, Houston, Texas
| | - Arvind Chandrakantan
- Department of Anesthesiology, Perioperative and Pain Medicine, Texas Children's Hospital, Houston, Texas.,Section of Pediatric Critical Care Medicine, Department of Pediatrics, Texas Children's Hospital, Houston, Texas
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37
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Preston CJ, Brown KA, Wagner JJ. Cocaine conditioning induces persisting changes in ventral hippocampus synaptic transmission, long-term potentiation, and radial arm maze performance in the mouse. Neuropharmacology 2019; 150:27-37. [DOI: 10.1016/j.neuropharm.2019.02.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/29/2019] [Accepted: 02/25/2019] [Indexed: 10/27/2022]
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Brown KA, Chen B, Guardado-Alvarez TM, Lin Z, Hwang L, Ayaz-Guner S, Jin S, Ge Y. A photocleavable surfactant for top-down proteomics. Nat Methods 2019; 16:417-420. [PMID: 30988469 PMCID: PMC6532422 DOI: 10.1038/s41592-019-0391-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 03/13/2019] [Indexed: 01/21/2023]
Abstract
We report the identification of a photo-cleavable anionic surfactant, 4-hexylphenylazosulfonate (Azo) that can be rapidly degraded upon UV irradiation, for top-down proteomics. Azo can effectively solubilize proteins with performance comparable to SDS and is mass spectrometry (MS)-compatible. Importantly, Azo-aided top-down proteomics enables the solubilization of membrane proteins for comprehensive characterization of post-translational modifications. Moreover, Azo is simple to synthesize and can be used as a general SDS replacement in SDS-PAGE.
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Affiliation(s)
- Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Ziqing Lin
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.,Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Leekyoung Hwang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Serife Ayaz-Guner
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA. .,Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
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39
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Brown KA, Filipov NM, Wagner JJ. Septotemporal‐specific Effects of a Gulf War Illness Sarin Surrogate, Diisopropylfluorophosphate, on Synaptic Transmission in the Mouse Hippocampus. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.813.1] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kyle A Brown
- Department of Physiology and PharmacologyUniversity of GeorgiaAthensGA
- Interdisciplinary Toxicology ProgramUniversity of GeorgiaAthensGA
| | - Nikolay M Filipov
- Department of Physiology and PharmacologyUniversity of GeorgiaAthensGA
- Interdisciplinary Toxicology ProgramUniversity of GeorgiaAthensGA
| | - John J Wagner
- Department of Physiology and PharmacologyUniversity of GeorgiaAthensGA
- Interdisciplinary Toxicology ProgramUniversity of GeorgiaAthensGA
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Liang Y, Jin Y, Wu Z, Tucholski T, Brown KA, Zhang L, Zhang Y, Ge Y. Bridged Hybrid Monolithic Column Coupled to High-Resolution Mass Spectrometry for Top-Down Proteomics. Anal Chem 2019; 91:1743-1747. [PMID: 30668094 DOI: 10.1021/acs.analchem.8b05817] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Top-down mass spectrometry (MS)-based proteomics has become a powerful tool for comprehensive characterization of intact proteins. However, because of the high complexity of the proteome, highly effective separation of intact proteins from complex mixtures prior to MS analysis remains challenging. Monolithic columns have shown great promise for intact protein separation due to their high permeability, low backpressure, and fast mass transfer. Herein, for the first time, we developed bridged hybrid bis(triethoxysilyl)ethylene (BTSEY) monolith with C8 functional groups (C8@BTSEY) for highly effective protein separation and coupled it to high-resolution MS for identification of intact proteins from complex protein mixtures. We have optimized mobile phase conditions of our monolith-based reverse-phase chromatography (RPC) for online liquid chromatography (LC)-MS analysis and evaluated separation reproducibility of the C8@BTSEY column. We further assessed the chromatographic performance of this column by separating a complex protein mixture extracted from swine heart tissue. Using our monolithic column (i.d. 100 μm × 35 cm), we separated over 300 proteoforms (up to 104 kDa) from 360 ng of protein mixture in an 80 min one-dimensional (1D) LC run. The highly effective separation and recovery of intact proteins from this monolithic column allowed unambiguous identification of ∼100 proteoforms including a large protein, αactinin2 (103.77 kDa), by online 1D LC-MS/MS analysis for the first time. As demonstrated, this C8@BTSEY column is reproducible and effective in separation of intact proteins, which shows high promise for top-down proteomics.
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Affiliation(s)
- Yu Liang
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States.,CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , Liaoning 116023 , China
| | - Yutong Jin
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Zhijie Wu
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Trisha Tucholski
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Kyle A Brown
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , Liaoning 116023 , China
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , Liaoning 116023 , China
| | - Ying Ge
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States.,Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program, School of Medicine and Public Health , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
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Preston CJ, Brown KA, Wagner JJ. Cocaine exposure results in persisting impairment of hippocampal long‐term potentiation and reduced performance in a spatial working memory task in C57BL/6J mice. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.551.5] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Kyle A. Brown
- Physiology and PharmacologyUniversity of GeorgiaAthensGA
| | - John J. Wagner
- Physiology and PharmacologyUniversity of GeorgiaAthensGA
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43
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Kelty ML, Morris W, Gallagher AT, Anderson JS, Brown KA, Mirkin CA, Harris TD. High-throughput synthesis and characterization of nanocrystalline porphyrinic zirconium metal-organic frameworks. Chem Commun (Camb) 2018; 52:7854-7. [PMID: 27247981 DOI: 10.1039/c6cc03264h] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We describe and employ a high-throughput screening method to accelerate the synthesis and identification of pure-phase, nanocrystalline metal-organic frameworks (MOFs). We demonstrate the efficacy of this method through its application to a series of porphyrinic zirconium MOFs, resulting in the isolation of MOF-525, MOF-545, and PCN-223 on the nanoscale.
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Affiliation(s)
- M L Kelty
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - W Morris
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - A T Gallagher
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - J S Anderson
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - K A Brown
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA. and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - C A Mirkin
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA. and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA and Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, IL 60208, USA
| | - T D Harris
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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Affiliation(s)
- Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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45
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Yang X, Wu X, Brown KA, Le T, Stice SL, Bartlett MG. Determination of chlorpyrifos and its metabolites in cells and culture media by liquid chromatography-electrospray ionization tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1063:112-117. [PMID: 28858752 DOI: 10.1016/j.jchromb.2017.08.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 03/08/2017] [Revised: 07/17/2017] [Accepted: 08/07/2017] [Indexed: 01/01/2023]
Abstract
A sensitive method to simultaneously quantitate chlorpyrifos, chlorpyrifos oxon and the detoxified product 3,5,6-trichloro-2-pyridinol (TCP) was developed using either liquid-liquid extraction for culture media samples, or protein precipitation for cell samples. Multiple reaction monitoring in positive ion mode was applied for the detection of chlorpyrifos and chlorpyrifos oxon, and selected ion recording in negative mode was applied to detect TCP. The method provided linear ranges from 5 to 500, 0.2-20 and 20-2000ng/mL for media samples and from 0.5-50, 0.02-2 and 2-200ng/million cells for CPF, CPO and TCP, respectively. The method was validated using selectivity, linearity, precision, accuracy, recovery, stability and dilution tests. All relative standard deviations (RSDs) and relative errors (REs) for QC samples were within 15% (except for LLOQ, within 20%). This method has been successfully applied to study the neurotoxicity and metabolism of chlorpyrifos in a human neuronal model.
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Affiliation(s)
- Xiangkun Yang
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, GA 30602-2352, United States
| | - Xian Wu
- Regenerative Bioscience Center, University of Georgia, Athens, GA 30602, United States
| | - Kyle A Brown
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, GA 30602-2352, United States
| | - Thao Le
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, GA 30602-2352, United States
| | - Steven L Stice
- Regenerative Bioscience Center, University of Georgia, Athens, GA 30602, United States
| | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, GA 30602-2352, United States.
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Khanafer N, Daneman N, Greene T, Simor A, Vanhems P, Samore M, Brown KA. Susceptibilities of clinical Clostridium difficile isolates to antimicrobials: a systematic review and meta-analysis of studies since 1970. Clin Microbiol Infect 2017; 24:110-117. [PMID: 28750918 DOI: 10.1016/j.cmi.2017.07.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/10/2017] [Accepted: 07/13/2017] [Indexed: 12/29/2022]
Abstract
OBJECTIVES Although exposure to antibiotics can cause Clostridium difficile infection, certain antibiotics are used to treat C. difficile. Measurements of antimicrobial C. difficile activity could help to identify antibiotic risk and emergent resistance. Here, we describe publication patterns relating to C. difficile susceptibilities and estimate minimum inhibitory concentrations (MIC) for antibiotic classes in the published literature between January 1970 and June 2014. METHODS We queried PUBMED and EMBASE for studies reporting antibiotic C. difficile MIC in English or French. We used mixed-effects models to obtain pooled estimates of antibiotic class median MIC (MIC50), 90th percentile of MIC (MIC90), and MIC90:MIC50 ratio. RESULTS Our search identified 182 articles that met our inclusion criteria, of which 27 were retained for meta-analysis. Aminoglycosides (MIC50 120 mg/L, 95% CI 62-250), 3rd (MIC50 75 mg/L, 95% CI 39-130) and 2nd generation cephalosporins (MIC50 64 mg/L, 95% CI 27-140) had the least C. difficile activity. Rifamycins (MIC50 0.034 mg/L, 95% CI 0.012-0.099) and tetracyclines (MIC50 0.29 mg/L, 95% CI 0.054-1.7) had the highest level of activity. The activity of 3rd generation cephalosporins was more than three times lower than that of 1st generation agents (MIC50 19 mg/L, 95% CI 7.0-54). Time-trends in MIC50 were increasing for carbapenems (70% increase per 10 years) while decreasing for tetracyclines (51% decrease per 10 years). CONCLUSIONS We found a 3500-fold variation in antibiotic C. difficile MIC50, with aminoglycosides as the least active agents and rifamycins as the most active. Further research is needed to determine how in vitro measures can help assess patient C. difficile risk and guide antimicrobial stewardship.
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Affiliation(s)
- N Khanafer
- Service d'Hygiène, Épidémiologie et Prévention, Hôpital Edouard Herriot, Hospices civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie, Institut national de la santé et de la recherche médicale U1111, Centre National de la Recherche Scientifique UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard 1, Lyon, France.
| | - N Daneman
- Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Canada
| | - T Greene
- Division of Epidemiology, University of Utah, UT, USA
| | - A Simor
- Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Canada
| | - P Vanhems
- Service d'Hygiène, Épidémiologie et Prévention, Hôpital Edouard Herriot, Hospices civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie, Institut national de la santé et de la recherche médicale U1111, Centre National de la Recherche Scientifique UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard 1, Lyon, France
| | - M Samore
- Division of Epidemiology, University of Utah, UT, USA; Salt Lake City Veterans Affairs Health Care System, Salt Lake City, UT, USA
| | - K A Brown
- Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Canada; Division of Epidemiology, University of Utah, UT, USA; Salt Lake City Veterans Affairs Health Care System, Salt Lake City, UT, USA; Public Health Ontario, Ontario, Canada.
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Iyengar NM, Brown KA, Zhou XK, Subbaramaiah K, Giri DD, Gucalp A, Howe LR, Zahid H, Bhardwaj P, Wendel NK, Falcone DJ, Morrow M, Wang H, Williams S, Pollak M, Hudis CA, Dannenberg AJ. Abstract PD5-05: Metabolic obesity, adipose inflammation and aromatase: Potential drivers of breast cancer risk in women with normal body mass index. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-pd5-05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Elevated body mass index (BMI) is associated with increased risk of postmenopausal breast cancer, which may be partly attributable to an inflammation-aromatase axis. Most individuals with elevated BMI harbor white adipose tissue inflammation (WATi), defined by the presence of crown-like structures in the breast (CLS-B). CLS-B are composed of a dead/dying adipocyte surrounded by CD68+ macrophages. This inflammation is associated with activation of NF-κB and elevated expression of aromatase, which could contribute to tumor development. Additionally, WATi correlates with several circulating changes, including hyperinsulinemia, which increase breast cancer risk. Although breast WATi correlates with rising BMI, it is also present in some normal BMI individuals. Beyond inherited germline syndromes, the etiology of breast cancer in individuals with normal BMI is not well understood. Here we examined the impact of breast WATi on breast aromatase expression and circulating factors in women with normal BMI.
Methods: Non-tumorous breast tissue and fasting blood were collected from 72 women with BMI < 25 kg/m2 undergoing mastectomy at MSKCC. Breast inflammation was detected by the presence of CLS-B using CD68 immunohistochemistry. The primary objective was to determine if breast WATi in normal BMI individuals correlates with elevated aromatase levels in the breast, measured by qPCR, western blotting, immunofluorescence and enzyme activity. Secondary objectives included assessment of breast adipocyte size and circulating metabolic and inflammatory factors.
Results: Breast inflammation was present in 39% of women. Median BMI was 23.0 (range 18.4 to 24.9) in women with breast WATi versus 21.8 (range 17.3 to 24.6) in those without inflammation (P=0.04). Aromatase mRNA expression was positively correlated with WATi (CLS-B/cm2; P=0.002). Those with severe WATi had highest aromatase mRNA levels, compared to those with no or mild WATi (P=0.005). Aromatase protein, assessed by measuring adipose stromal cell-specific immunofluorescence or western blotting, and activity were also higher in CLS-B+ cases compared to CLS-B- (P<0.001). Breast WATi correlated with larger adipocytes (P=0.01) and higher circulating levels of C-reactive protein, leptin, insulin, and triglycerides (P<0.05). Insulin resistance, characterized by the homeostasis model (HOMA2-IR), correlated with breast WATi (P=0.004). Finally, leptin, a known inducer of aromatase and driver of cancer growth, correlated with higher breast aromatase levels (P=0.02) and larger adipocytes (P<0.01).
Conclusions: A metabolically unhealthy state occurs in women with inflamed breast adipose despite having a normal BMI. This subclinical inflammatory state is characterized by elevated aromatase in the breast, insulin resistance, and dysplipidemia. The presence of enlarged adipocytes in the breasts of normal BMI women with inflammation suggests a state of hyperadiposity which could not be predicted based on BMI alone. These findings indicate that normal BMI metabolic obesity may be associated with increased cancer risk. Our results suggest that objective measurements of adiposity rather than BMI may help to identify individuals at increased risk for disease.
Citation Format: Iyengar NM, Brown KA, Zhou XK, Subbaramaiah K, Giri DD, Gucalp A, Howe LR, Zahid H, Bhardwaj P, Wendel NK, Falcone DJ, Morrow M, Wang H, Williams S, Pollak M, Hudis CA, Dannenberg AJ. Metabolic obesity, adipose inflammation and aromatase: Potential drivers of breast cancer risk in women with normal body mass index [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr PD5-05.
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Affiliation(s)
- NM Iyengar
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - KA Brown
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - XK Zhou
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - K Subbaramaiah
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - DD Giri
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - A Gucalp
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - LR Howe
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - H Zahid
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - P Bhardwaj
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - NK Wendel
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - DJ Falcone
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - M Morrow
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - H Wang
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - S Williams
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - M Pollak
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - CA Hudis
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - AJ Dannenberg
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
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Junker A, Balasubramanian R, Ciancetta A, Uliassi E, Kiselev E, Martiriggiano C, Trujillo K, Mtchedlidze G, Birdwell L, Brown KA, Harden TK, Jacobson KA. Structure-Based Design of 3-(4-Aryl-1H-1,2,3-triazol-1-yl)-Biphenyl Derivatives as P2Y14 Receptor Antagonists. J Med Chem 2016; 59:6149-68. [PMID: 27331270 PMCID: PMC4947982 DOI: 10.1021/acs.jmedchem.6b00044] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
UDP and UDP-glucose activate the P2Y14 receptor (P2Y14R) to modulate processes related to inflammation, diabetes, and asthma. A computational pipeline suggested alternatives to naphthalene of a previously reported P2Y14R antagonist (3, PPTN) using docking and molecular dynamics simulations on a hP2Y14R homology model based on P2Y12R structures. By reevaluating the binding of 3 to P2Y14R computationally, two alternatives, i.e., alkynyl and triazolyl derivatives, were identified. Improved synthesis of fluorescent antagonist 4 enabled affinity quantification (IC50s, nM) using flow cytometry of P2Y14R-expressing CHO cells. p-F3C-phenyl-triazole 65 (32) was more potent than a corresponding alkyne 11. Thus, additional triazolyl derivatives were prepared, as guided by docking simulations, with nonpolar aryl substituents favored. Although triazoles were less potent than 3 (6), simpler synthesis facilitated further structural optimization. Additionally, relative P2Y14R affinities agreed with predicted binding of alkynyl and triazole analogues. These triazoles, designed through a structure-based approach, can be assessed in disease models.
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Affiliation(s)
- Anna Junker
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0810, United States
| | - Ramachandran Balasubramanian
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0810, United States
| | - Antonella Ciancetta
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0810, United States
| | - Elisa Uliassi
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0810, United States
| | - Evgeny Kiselev
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0810, United States
| | - Chiara Martiriggiano
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0810, United States
| | - Kevin Trujillo
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0810, United States
| | - Giorgi Mtchedlidze
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0810, United States
| | - Leah Birdwell
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0810, United States
| | - Kyle A Brown
- Department of Pharmacology, University of North Carolina, School of Medicine , Chapel Hill, North Carolina 27599, United States
| | - T Kendall Harden
- Department of Pharmacology, University of North Carolina, School of Medicine , Chapel Hill, North Carolina 27599, United States
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0810, United States
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Brown KA, Jones M, Adler F, Leecaster M, Nechodom K, Stevens V, Samore M, Mayer J. The determinants of C. difficile infection in long-term care facilities: a portrait of patient- and facility-level factors across 90 care regions in the veterans affairs health care system. Antimicrob Resist Infect Control 2015. [PMCID: PMC4474708 DOI: 10.1186/2047-2994-4-s1-o36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Lewis SM, Treacher DF, Edgeworth J, Mahalingam G, Brown CS, Mare TA, Stacey M, Beale R, Brown KA. Expression of CD11c and EMR2 on neutrophils: potential diagnostic biomarkers for sepsis and systemic inflammation. Clin Exp Immunol 2015; 182:184-94. [PMID: 26153037 DOI: 10.1111/cei.12679] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2015] [Indexed: 12/26/2022] Open
Abstract
There is a need for cellular biomarkers to differentiate patients with sepsis from those with the non-infectious systemic inflammatory response syndrome (SIRS). In this double-blind study we determined whether the expression of known (CD11a/b/c, CD62L) and putative adhesion molecules [CD64, CD97 and epidermal growth factor (EGF)-like molecule containing mucin-like hormone receptor (EMR2)] on blood neutrophils could serve as useful biomarkers of infection and of non-infectious SIRS in critically ill patients. We studied 103 patients with SIRS, 83 of whom had sepsis, and 50 healthy normal subjects, using flow cytometry to characterize neutrophils phenotypically in whole blood samples. Patients with SIRS had an increased prevalence of neutrophils expressing CD11c, CD64 and EMR2 in comparison with healthy subjects (P < 0.001), but normal expression of CD11a, CD11b, CD62L and CD97. An increase in the percentage of neutrophils bearing CD11c was associated with sepsis, EMR2 with SIRS and CD64 with sepsis and SIRS. Neutrophils expressing CD11c had the highest sensitivity (81%) and specificity (80%) for the detection of sepsis, and there was an association between the percentage of neutrophils expressing EMR2 and the extent of organ failure (P < 0.05). Contrary to other reports, we did not observe an abnormal expression of CD11b or CD62L on neutrophils from patients with SIRS, and suggest that this discrepancy is due to differences in cell processing protocols. We propose that blood neutrophils expressing CD11c and EMR2 be considered as potential biomarkers for sepsis and SIRS, respectively.
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Affiliation(s)
- S M Lewis
- Intensive Care Unit, Guy's and St Thomas' NHS Foundation Trust, London.,Department of Vascular Immunology, Division of Asthma, Allergy and Lung Biology, King's College London
| | - D F Treacher
- Intensive Care Unit, Guy's and St Thomas' NHS Foundation Trust, London
| | - J Edgeworth
- Department of Infection, Guy's and St Thomas' NHS Foundation Trust, University of Leeds, London, UK
| | - G Mahalingam
- Department of Vascular Immunology, Division of Asthma, Allergy and Lung Biology, King's College London
| | - C S Brown
- Intensive Care Unit, Guy's and St Thomas' NHS Foundation Trust, London
| | - T A Mare
- Intensive Care Unit, Guy's and St Thomas' NHS Foundation Trust, London.,Department of Vascular Immunology, Division of Asthma, Allergy and Lung Biology, King's College London
| | - M Stacey
- School of Molecular and Cellular Biology, University of Leeds, London, UK
| | - R Beale
- Intensive Care Unit, Guy's and St Thomas' NHS Foundation Trust, London.,Department of Vascular Immunology, Division of Asthma, Allergy and Lung Biology, King's College London
| | - K A Brown
- Intensive Care Unit, Guy's and St Thomas' NHS Foundation Trust, London.,Department of Vascular Immunology, Division of Asthma, Allergy and Lung Biology, King's College London
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