1
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Chapman EA, Li BH, Krichel B, Chan HJ, Buck KM, Roberts DS, Ge Y. Native Top-Down Mass Spectrometry for Characterizing Sarcomeric Proteins Directly from Cardiac Tissue Lysate. J Am Soc Mass Spectrom 2024; 35:738-745. [PMID: 38422011 PMCID: PMC11098619 DOI: 10.1021/jasms.3c00430] [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] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Native top-down mass spectrometry (nTDMS) has emerged as a powerful structural biology tool that can localize post-translational modifications (PTMs), explore ligand-binding interactions, and elucidate the three-dimensional structure of proteins and protein complexes in the gas-phase. Fourier-transform ion cyclotron resonance (FTICR) MS offers distinct capabilities for nTDMS, owing to its ultrahigh resolving power, mass accuracy, and robust fragmentation techniques. Previous nTDMS studies using FTICR have mainly been applied to overexpressed recombinant proteins and protein complexes. Here, we report the first nTDMS study that directly analyzes human heart tissue lysate by direct infusion FTICR MS without prior chromatographic separation strategies. We have achieved comprehensive nTDMS characterization of cardiac contractile proteins that play critical roles in heart contraction and relaxation. Specifically, our results reveal structural insights into ventricular myosin light chain 2 (MLC-2v), ventricular myosin light chain 1 (MLC-1v), and alpha-tropomyosin (α-Tpm) in the sarcomere, the basic contractile unit of cardiac muscle. Furthermore, we verified the calcium (Ca2+) binding domain in MLC-2v. In summary, our nTDMS platform extends the application of FTICR MS to directly characterize the structure, PTMs, and metal-binding of endogenous proteins from heart tissue lysate without prior separation methods.
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Affiliation(s)
- Emily A. Chapman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Brad H. Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Boris Krichel
- School of Life Sciences, University of Siegen, 57076, Germany
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Hsin-Ju Chan
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kevin M. Buck
- 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
| | - 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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2
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Yang JL, Yamada-Hunter SA, Labanieh L, Sotillo E, Cheah JS, Roberts DS, Mackall CL, Bertozzi CR, Ting AY. Directed evolution of genetically encoded LYTACs for cell-mediated delivery. Proc Natl Acad Sci U S A 2024; 121:e2320053121. [PMID: 38513100 PMCID: PMC10990137 DOI: 10.1073/pnas.2320053121] [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: 11/15/2023] [Accepted: 02/20/2024] [Indexed: 03/23/2024] Open
Abstract
Lysosome-targeting chimeras (LYTACs) are a promising therapeutic modality to drive the degradation of extracellular proteins. However, early versions of LYTAC contain synthetic glycopeptides that cannot be genetically encoded. Here, we present our designs for a fully genetically encodable LYTAC (GELYTAC), making our tool compatible with integration into therapeutic cells for targeted delivery at diseased sites. To achieve this, we replaced the glycopeptide portion of LYTACs with the protein insulin-like growth factor 2 (IGF2). After showing initial efficacy with wild-type IGF2, we increased the potency of GELYTAC using directed evolution. Subsequently, we demonstrated that our engineered GELYTAC construct not only secretes from HEK293T cells but also from human primary T-cells to drive the uptake of various targets into receiver cells. Immune cells engineered to secrete GELYTAC thus represent a promising avenue for spatially selective targeted protein degradation.
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Affiliation(s)
- Jonathan Lee Yang
- Department of Chemistry, Stanford University, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Sean A. Yamada-Hunter
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA94305
| | - Louai Labanieh
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Bioengineering, Stanford University, Stanford, CA94305
- Parker Institute for Cancer Immunotherapy, San Francisco, CA94305
| | - Elena Sotillo
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Bioengineering, Stanford University, Stanford, CA94305
| | - Joleen S. Cheah
- Department of Biology, Stanford University, Stanford, CA94305
| | - David S. Roberts
- Department of Chemistry, Stanford University, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Crystal L. Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA94305
- Parker Institute for Cancer Immunotherapy, San Francisco, CA94305
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA94305
- Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- HHMI, Stanford University, Stanford, CA94305
| | - Alice Y. Ting
- Department of Chemistry, Stanford University, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Biology, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA94158
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3
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Peltan EL, Riley NM, Flynn RA, Roberts DS, Bertozzi CR. Galectin-3 does not interact with RNA directly. Glycobiology 2024; 34:cwad076. [PMID: 37815932 DOI: 10.1093/glycob/cwad076] [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: 04/28/2023] [Revised: 09/08/2023] [Accepted: 09/09/2023] [Indexed: 10/12/2023] Open
Abstract
Galectin-3, well characterized as a glycan binding protein, has been identified as a putative RNA binding protein, possibly through participation in pre-mRNA maturation through interactions with splicosomes. Given recent developments with cell surface RNA biology, the putative dual-function nature of galectin-3 evokes a possible non-classical connection between glycobiology and RNA biology. However, with limited functional evidence of a direct RNA interaction, many molecular-level observations rely on affinity reagents and lack appropriate genetic controls. Thus, evidence of a direct interaction remains elusive. We demonstrate that antibodies raised to endogenous human galectin-3 can isolate RNA-protein crosslinks, but this activity remains insensitive to LGALS3 knock-out. Proteomic characterization of anti-galectin-3 IPs revealed enrichment of galectin-3, but high abundance of hnRNPA2B1, an abundant, well-characterized RNA-binding protein with weak homology to the N-terminal domain of galectin-3, in the isolate. Genetic ablation of HNRNPA2B1, but not LGALS3, eliminates the ability of the anti-galectin-3 antibodies to isolate RNA-protein crosslinks, implying either an indirect interaction or cross-reactivity. To address this, we introduced an epitope tag to the endogenous C-terminal locus of LGALS3. Isolation of the tagged galectin-3 failed to reveal any RNA-protein crosslinks. This result suggests that the galectin-3 does not directly interact with RNA and may be misidentified as an RNA-binding protein, at least in HeLa where the putative RNA associations were first identified. We encourage further investigation of this phenomenon employ gene deletions and, when possible, endogenous epitope tags to achieve the specificity required to evaluate potential interactions.
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Affiliation(s)
- Egan L Peltan
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 269 Campus Drive CCSR 4145 Stanford, CA 94305, United States
- Sarafan ChEM-H, Stanford University, Stanford ChEM-H Building 290 Jane Stanford Way Stanford, CA 94305, United States
| | - Nicholas M Riley
- Sarafan ChEM-H, Stanford University, Stanford ChEM-H Building 290 Jane Stanford Way Stanford, CA 94305, United States
- Department of Chemistry, Stanford University, 333 Campus Drive Stanford, CA 94305, United States
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, 1 Blackfan Circle, Boston, MA 02445, United States
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave, Cambridge, MA 02138, United States
| | - David S Roberts
- Sarafan ChEM-H, Stanford University, Stanford ChEM-H Building 290 Jane Stanford Way Stanford, CA 94305, United States
- Department of Chemistry, Stanford University, 333 Campus Drive Stanford, CA 94305, United States
| | - Carolyn R Bertozzi
- Sarafan ChEM-H, Stanford University, Stanford ChEM-H Building 290 Jane Stanford Way Stanford, CA 94305, United States
- Department of Chemistry, Stanford University, 333 Campus Drive Stanford, CA 94305, United States
- Howard Hughes Medical Institute, Stanford University, 279 Campus Drive Room B202 Stanford, CA 94305-5323, United States
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4
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Donnelly J, Kamber RA, Wisnovsky S, Roberts DS, Peltan EL, Bassik MC, Bertozzi CR. A Genome-Wide CRISPR Screen Identifies Sortilin as the Receptor Responsible for Galectin-1 Lysosomal Trafficking. bioRxiv 2024:2024.01.03.574113. [PMID: 38260508 PMCID: PMC10802331 DOI: 10.1101/2024.01.03.574113] [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: 01/24/2024]
Abstract
Galectins are a family of mammalian glycan-binding proteins that have been implicated as regulators of myriad cellular processes including cell migration, apoptosis, and immune modulation. Several members of this family, such as galectin-1, exhibit both cell-surface and intracellular functions. Interestingly, galectin-1 can be found in the endomembrane system, nucleus, or cytosol, as well as on the cell surface. The mechanisms by which galectin-1 traffics between cellular compartments, including its unconventional secretion and internalization processes, are poorly understood. Here, we determined the pathways by which exogenous galectin-1 enters cells and explored its capacity as a delivery vehicle for protein and siRNA therapeutics. We used a galectin-1-toxin conjugate, modelled on antibody-drug conjugates, as a selection tool in a genome-wide CRISPR screen. We discovered that galectin-1 interacts with the endosome-lysosome trafficking receptor sortilin in a glycan-dependent manner, which regulates galectin-1 trafficking to the lysosome. Further, we show that this pathway can be exploited for delivery of a functional siRNA. This study sheds light on the mechanisms by which galectin-1 is internalized by cells and suggests a new strategy for intracellular drug delivery via galectin-1 conjugation.
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Chapman EA, Roberts DS, Tiambeng TN, Andrews J, Wang MD, Reasoner EA, Melby JA, Li BH, Kim D, Alpert AJ, Jin S, Ge Y. Structure and dynamics of endogenous cardiac troponin complex in human heart tissue captured by native nanoproteomics. Nat Commun 2023; 14:8400. [PMID: 38110393 PMCID: PMC10728164 DOI: 10.1038/s41467-023-43321-z] [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: 07/04/2023] [Accepted: 11/07/2023] [Indexed: 12/20/2023] Open
Abstract
Protein complexes are highly dynamic entities that display substantial diversity in their assembly, post-translational modifications, and non-covalent interactions, allowing them to play critical roles in various biological processes. The heterogeneity, dynamic nature, and low abundance of protein complexes in their native states present challenges to study using conventional structural biology techniques. Here we develop a native nanoproteomics strategy for the enrichment and subsequent native top-down mass spectrometry (nTDMS) analysis of endogenous cardiac troponin (cTn) complex directly from human heart tissue. The cTn complex is enriched and purified using peptide-functionalized superparamagnetic nanoparticles under non-denaturing conditions to enable the isotopic resolution of cTn complex, revealing their complex structure and assembly. Moreover, nTDMS elucidates the stoichiometry and composition of the cTn complex, localizes Ca2+ binding domains, defines cTn-Ca2+ binding dynamics, and provides high-resolution mapping of the proteoform landscape. This native nanoproteomics strategy opens a paradigm for structural characterization of endogenous native protein complexes.
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Affiliation(s)
- Emily A Chapman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Timothy N Tiambeng
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jãán Andrews
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Man-Di Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Emily A Reasoner
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jake A Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Brad H Li
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Donguk Kim
- Department of Chemical and Biological Engineering, 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, 53705, USA.
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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6
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Pergande MR, Osterbauer KJ, Buck KM, Roberts DS, Wood NN, Balasubramanian P, Mann MW, Rossler KJ, Diffee GM, Colman RJ, Anderson RM, Ge Y. Mass Spectrometry-Based Multiomics Identifies Metabolic Signatures of Sarcopenia in Rhesus Monkey Skeletal Muscle. J Proteome Res 2023:10.1021/acs.jproteome.3c00474. [PMID: 37991985 PMCID: PMC11109024 DOI: 10.1021/acs.jproteome.3c00474] [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] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Sarcopenia is a progressive disorder characterized by age-related loss of skeletal muscle mass and function. Although significant progress has been made over the years to identify the molecular determinants of sarcopenia, the precise mechanisms underlying the age-related loss of contractile function remains unclear. Advances in "omics" technologies, including mass spectrometry-based proteomic and metabolomic analyses, offer great opportunities to better understand sarcopenia. Herein, we performed mass spectrometry-based analyses of the vastus lateralis from young, middle-aged, and older rhesus monkeys to identify molecular signatures of sarcopenia. In our proteomic analysis, we identified proteins that change with age, including those involved in adenosine triphosphate and adenosine monophosphate metabolism as well as fatty acid beta oxidation. In our untargeted metabolomic analysis, we identified metabolites that changed with age largely related to energy metabolism including fatty acid beta oxidation. Pathway analysis of age-responsive proteins and metabolites revealed changes in muscle structure and contraction as well as lipid, carbohydrate, and purine metabolism. Together, this study discovers new metabolic signatures and offers new insights into the molecular mechanisms underlying sarcopenia for the evaluation and monitoring of a therapeutic treatment of sarcopenia.
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Affiliation(s)
- Melissa R. Pergande
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Katie J. Osterbauer
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Kevin M. Buck
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nina N. Wood
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - Morgan W. Mann
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Kalina J. Rossler
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Gary M. Diffee
- Department of Kinesiology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ricki J. Colman
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Rozalyn M. Anderson
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
- Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53705, USA
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7
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Yang JL, Yamada-Hunter SA, Labanieh L, Sotillo E, Cheah JS, Roberts DS, Mackall CL, Ting AY, Bertozzi CR. Directed Evolution of Genetically Encoded LYTACs for Cell-Mediated Delivery. bioRxiv 2023:2023.11.14.567117. [PMID: 38014030 PMCID: PMC10680704 DOI: 10.1101/2023.11.14.567117] [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] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Lysosome-targeting chimeras (LYTACs) are a promising therapeutic modality to drive the degradation of extracellular proteins. However, early versions of LYTAC contain synthetic glycopeptides that cannot be genetically encoded. Here we present our designs for a fully genetically encodable LYTAC (GELYTAC), making our tool compatible with integration into therapeutic cells for targeted delivery at diseased sites. To achieve this, we replaced the glycopeptide portion of LYTACs with the protein insulin like growth factor 2 (IGF2). After showing initial efficacy with wild type IGF2, we increased the potency of GELYTAC using directed evolution. Subsequently, we demonstrated that our engineered GELYTAC construct not only secretes from HEK293T cells but also from human primary T-cells to drive the uptake of various targets into receiver cells. Immune cells engineered to secrete GELYTAC thus represent a promising avenue for spatially-selective targeted protein degradation.
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Affiliation(s)
- Jonathan Lee Yang
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Sean A. Yamada-Hunter
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Louai Labanieh
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elena Sotillo
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joleen S. Cheah
- Departments of Biology, and Genetics Stanford University, Stanford, CA 94305, USA
| | - David S. Roberts
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Crystal L. Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94305, USA
| | - Alice Y. Ting
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Departments of Biology, and Genetics Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA 94158, USA
| | - Carolyn R. Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
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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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9
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Bayne EF, Rossler KJ, Gregorich ZR, Aballo TJ, Roberts DS, Chapman EA, Guo W, Palecek SP, Ralphe JC, Kamp TJ, Ge Y. Top-down proteomics of myosin light chain isoforms define chamber-specific expression in the human heart. J Mol Cell Cardiol 2023; 181:89-97. [PMID: 37327991 PMCID: PMC10528938 DOI: 10.1016/j.yjmcc.2023.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 05/27/2023] [Accepted: 06/13/2023] [Indexed: 06/18/2023]
Abstract
Myosin functions as the "molecular motor" of the sarcomere and generates the contractile force necessary for cardiac muscle contraction. Myosin light chains 1 and 2 (MLC-1 and -2) play important functional roles in regulating the structure of the hexameric myosin molecule. Each of these light chains has an 'atrial' and 'ventricular' isoform, so called because they are believed to exhibit chamber-restricted expression in the heart. However, recently the chamber-specific expression of MLC isoforms in the human heart has been questioned. Herein, we analyzed the expression of MLC-1 and -2 atrial and ventricular isoforms in each of the four cardiac chambers in adult non-failing donor hearts using top-down mass spectrometry (MS)-based proteomics. Strikingly, we detected an isoform thought to be ventricular, MLC-2v (gene: MYL2), in the atria and confirmed the protein sequence using tandem MS (MS/MS). For the first time, a putative deamidation post-translation modification (PTM) located on MLC-2v in atrial tissue was localized to amino acid N13. MLC-1v (MYL3) and MLC-2a (MYL7) were the only MLC isoforms exhibiting chamber-restricted expression patterns across all donor hearts. Importantly, our results unambiguously show that MLC-1v, not MLC-2v, is ventricle-specific in adult human hearts. Moreover, we found elevated MLC-2 phosphorylation in male hearts compared to female hearts across each cardiac chamber. Overall, top-down proteomics allowed an unbiased analysis of MLC isoform expression throughout the human heart, uncovering previously unexpected isoform expression patterns and PTMs.
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Affiliation(s)
- Elizabeth F Bayne
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kalina J Rossler
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zachery R Gregorich
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Timothy J Aballo
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Emily A Chapman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wei Guo
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sean P Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - J Carter Ralphe
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Timothy J Kamp
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA; Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.
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10
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Pergande MR, Osterbauer KJ, Buck KM, Roberts DS, Wood NN, Balasubramanian P, Mann MW, Rossler K, Diffee GM, Colman RJ, Anderson RM, Ge Y. Mass spectrometry-based multi-omics identifies metabolic signatures of sarcopenia in rhesus monkey skeletal muscle. bioRxiv 2023:2023.07.31.551315. [PMID: 37577600 PMCID: PMC10418093 DOI: 10.1101/2023.07.31.551315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Sarcopenia is a progressive disorder characterized by age-related loss of skeletal muscle mass and function. Although significant progress has been made over the years to identify the molecular determinants of sarcopenia, the precise mechanisms underlying the age-related loss of contractile function remains unclear. Advances in omics technologies, including mass spectrometry-based proteomic and metabolomic analyses, offer great opportunities to better understand sarcopenia. Herein, we performed mass spectrometry-based analyses of the vastus lateralis from young, middle-aged, and older rhesus monkeys to identify molecular signatures of sarcopenia. In our proteomic analysis, we identified numerous proteins that change with age, including those involved in adenosine triphosphate and adenosine monophosphate metabolism as well as fatty acid beta oxidation. In our untargeted metabolomic analysis, we identified multiple metabolites that changed with age largely related to energy metabolism including fatty acid beta oxidation. Pathway analysis of age-responsive proteins and metabolites revealed changes in muscle structure and contraction as well as lipid, carbohydrate, and purine metabolism. Together, this study discovers new metabolic signatures and offer new insights into the molecular mechanism underlying sarcopenia for the evaluation and monitoring of therapeutic treatment of sarcopenia.
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Chapman EA, Roberts DS, Tiambeng TN, Andrews J, Wang MD, Reasoner EA, Melby JA, Li BH, Kim D, Alpert AJ, Jin S, Ge Y. Structure and dynamics of endogenous protein complexes in human heart tissue captured by native nanoproteomics. Res Sq 2023:rs.3.rs-3108087. [PMID: 37461709 PMCID: PMC10350235 DOI: 10.21203/rs.3.rs-3108087/v1] [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: 07/25/2023]
Abstract
Protein complexes are highly dynamic entities that display substantial diversity in their assembly, post-translational modifications, and non-covalent interactions, allowing them to play critical roles in various biological processes. The heterogeneity, dynamic nature, and low abundance of protein complexes in their native states present tremendous challenges to study using conventional structural biology techniques. Here we develop a "native nanoproteomics" strategy for the native enrichment and subsequent native top-down mass spectrometry (nTDMS) of low-abundance protein complexes. Specifically, we demonstrate the first comprehensive characterization of the structure and dynamics of cardiac troponin (cTn) complexes directly from human heart tissue. The endogenous cTn complex is effectively enriched and purified using peptide-functionalized superparamagnetic nanoparticles under non-denaturing conditions to enable the isotopic resolution of cTn complexes, revealing their complex structure and assembly. Moreover, nTDMS elucidates the stoichiometry and composition of the heterotrimeric cTn complex, localizes Ca2+ binding domains (II-IV), defines cTn-Ca2+ binding dynamics, and provides high-resolution mapping of the proteoform landscape. This native nanoproteomics strategy opens a new paradigm for structural characterization of low-abundance native protein complexes.
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Affiliation(s)
- Emily A. Chapman
- 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
| | - Timothy N. Tiambeng
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Jãán Andrews
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Man-Di Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Emily A. Reasoner
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Jake A. Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Brad H. Li
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Donguk Kim
- Department of Chemical and Biological Engineering, 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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12
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Chapman EA, Roberts DS, Tiambeng TN, Andrews J, Wang MD, Reasoner EA, Melby JA, Li BH, Kim D, Alpert AJ, Jin S, Ge Y. Structure and dynamics of endogenous protein complexes in human heart tissue captured by native nanoproteomics. bioRxiv 2023:2023.06.13.544817. [PMID: 37398031 PMCID: PMC10312745 DOI: 10.1101/2023.06.13.544817] [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: 07/04/2023]
Abstract
Protein complexes are highly dynamic entities that display substantial diversity in their assembly, post-translational modifications, and non-covalent interactions, allowing them to play critical roles in various biological processes. The heterogeneity, dynamic nature, and low abundance of protein complexes in their native states present tremendous challenges to study using conventional structural biology techniques. Here we develop a "native nanoproteomics" strategy for the native enrichment and subsequent native top-down mass spectrometry (nTDMS) of low-abundance protein complexes. Specifically, we demonstrate the first comprehensive characterization of the structure and dynamics of cardiac troponin (cTn) complexes directly from human heart tissue. The endogenous cTn complex is effectively enriched and purified using peptide-functionalized superparamagnetic nanoparticles under non-denaturing conditions to enable the isotopic resolution of cTn complexes, revealing their complex structure and assembly. Moreover, nTDMS elucidates the stoichiometry and composition of the heterotrimeric cTn complex, localizes Ca2+ binding domains (II-IV), defines cTn-Ca2+ binding dynamics, and provides high-resolution mapping of the proteoform landscape. This native nanoproteomics strategy opens a new paradigm for structural characterization of low-abundance native protein complexes.
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13
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Mann MW, Fu Y, Gearhart RL, Xu X, Roberts DS, Li Y, Zhou J, Ge Y, Brasier AR. Bromodomain-containing Protein 4 regulates innate inflammation via modulation of alternative splicing. Front Immunol 2023; 14:1212770. [PMID: 37435059 PMCID: PMC10331468 DOI: 10.3389/fimmu.2023.1212770] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/05/2023] [Indexed: 07/13/2023] Open
Abstract
Introduction Bromodomain-containing Protein 4 (BRD4) is a transcriptional regulator which coordinates gene expression programs controlling cancer biology, inflammation, and fibrosis. In the context of airway viral infection, BRD4-specific inhibitors (BRD4i) block the release of pro-inflammatory cytokines and prevent downstream epithelial plasticity. Although the chromatin modifying functions of BRD4 in inducible gene expression have been extensively investigated, its roles in post-transcriptional regulation are not well understood. Given BRD4's interaction with the transcriptional elongation complex and spliceosome, we hypothesize that BRD4 is a functional regulator of mRNA processing. Methods To address this question, we combine data-independent analysis - parallel accumulation-serial fragmentation (diaPASEF) with RNA-sequencing to achieve deep and integrated coverage of the proteomic and transcriptomic landscapes of human small airway epithelial cells exposed to viral challenge and treated with BRD4i. Results We discover that BRD4 regulates alternative splicing of key genes, including Interferon-related Developmental Regulator 1 (IFRD1) and X-Box Binding Protein 1 (XBP1), related to the innate immune response and the unfolded protein response (UPR). We identify requirement of BRD4 for expression of serine-arginine splicing factors, splicosome components and the Inositol-Requiring Enzyme 1 IREα affecting immediate early innate response and the UPR. Discussion These findings extend the transcriptional elongation-facilitating actions of BRD4 in control of post-transcriptional RNA processing via modulating splicing factor expression in virus-induced innate signaling.
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Affiliation(s)
- Morgan W. Mann
- Department of Medicine, University of Wisconsin – Madison, Madison, WI, United States
| | - Yao Fu
- Department of Medicine, University of Wisconsin – Madison, Madison, WI, United States
| | - Robert L. Gearhart
- Department of Chemistry, University of Wisconsin – Madison, Madison, WI, United States
| | - Xiaofang Xu
- Department of Medicine, University of Wisconsin – Madison, Madison, WI, United States
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin – Madison, Madison, WI, United States
| | - Yi Li
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, United States
| | - Jia Zhou
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin – Madison, Madison, WI, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, United States
| | - Allan R. Brasier
- Department of Medicine, University of Wisconsin – Madison, Madison, WI, United States
- Institute for Clinical and Translational Research, University of Wisconsin-Madison, Madison, WI, United States
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14
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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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15
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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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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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Aballo TJ, Roberts DS, Bayne EF, Zhu W, Walcott G, Mahmoud AI, Zhang J, Ge Y. Integrated proteomics reveals alterations in sarcomere composition and developmental processes during postnatal swine heart development. J Mol Cell Cardiol 2023; 176:33-40. [PMID: 36657638 PMCID: PMC10006350 DOI: 10.1016/j.yjmcc.2023.01.004] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/20/2022] [Accepted: 01/13/2023] [Indexed: 01/18/2023]
Abstract
The neonatal swine heart possesses an endogenous ability to regenerate injured myocardium through the proliferation of pre-existing cardiomyocyte (CM) populations. However, this regenerative capacity is lost shortly after birth. Normal postnatal developmental processes and the regenerative capacity of mammalian hearts are tightly linked, but not much is known about how the swine cardiac proteome changes throughout postnatal development. Herein, we integrated robust and quantitative targeted "top-down" and global "bottom-up" proteomic workflows to comprehensively define the dynamic landscape of the swine cardiac proteome throughout postnatal maturation. Using targeted top-down proteomics, we were able to identify significant alterations in sarcomere composition, providing new insight into the proteoform landscape of sarcomeres that can disassemble, a process necessary for productive CM proliferation. Furthermore, we quantified global changes in protein abundance using bottom-up proteomics, identified over 700 differentially expressed proteins throughout postnatal development, and mapped these proteins to changes in developmental and metabolic processes. We envision these results will help guide future investigations to comprehensively understand endogenous cardiac regeneration toward the development of novel therapeutic strategies for heart failure.
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Affiliation(s)
- Timothy J Aballo
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA; Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Elizabeth F Bayne
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wuqiang Zhu
- Department of Cardiovascular Diseases, Mayo Clinic Arizona, Scottsdale, AZ 85259, USA
| | - Gregory Walcott
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35205, USA
| | - Ahmed I Mahmoud
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jianyi Zhang
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35205, USA
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.
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18
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Bayne EF, Rossler KJ, Gregorich ZR, Aballo TJ, Roberts DS, Chapman EA, Guo W, Ralphe JC, Kamp TJ, Ge Y. Top-down Proteomics of Myosin Light Chain Isoforms Define Chamber-Specific Expression in the Human Heart. bioRxiv 2023:2023.01.26.525767. [PMID: 36747670 PMCID: PMC9900887 DOI: 10.1101/2023.01.26.525767] [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: 01/29/2023]
Abstract
Myosin functions as the "molecular motor" of the sarcomere and generates the contractile force necessary for cardiac muscle contraction. Myosin light chains 1 and 2 (MLC-1 and -2) play important functional roles in regulating the structure of the hexameric myosin molecule. Each of these light chains has an "atrial" and "ventricular" isoform, so called because they are believed to exhibit chamber-restricted expression in the heart. However, recently the chamber-specific expression of MLC isoforms in the human heart has been questioned. Herein, we analyzed the expression of MLC-1 and -2 atrial and ventricular isoforms in each of the four cardiac chambers in adult non-failing donor hearts using top-down mass spectrometry (MS)-based proteomics. Strikingly, we detected an isoform thought to be ventricular, MLC-2v, in the atria and confirmed the protein sequence using tandem MS (MS/MS). For the first time, a putative deamidation post-translation modification (PTM) located on MLC-2v in atrial tissue was localized to amino acid N13. MLC-1v and MLC-2a were the only MLC isoforms exhibiting chamber-restricted expression patterns across all donor hearts. Importantly, our results unambiguously show that MLC-1v, not MLC-2v, is ventricle-specific in adult human hearts. Overall, top-down proteomics allowed us an unbiased analysis of MLC isoform expression throughout the human heart, uncovering previously unexpected isoform expression patterns and PTMs.
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19
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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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20
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Mann M, Fu Y, Xu X, Roberts DS, Li Y, Zhou J, Ge Y, Brasier AR. Bromodomain-containing Protein 4 Regulates Innate Inflammation in Airway Epithelial Cells via Modulation of Alternative Splicing. bioRxiv 2023:2023.01.17.524257. [PMID: 36711789 PMCID: PMC9882210 DOI: 10.1101/2023.01.17.524257] [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] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Bromodomain-containing Protein 4 (BRD4) is a transcriptional regulator which coordinates gene expression programs controlling cancer biology, inflammation, and fibrosis. In airway viral infection, non-toxic BRD4-specific inhibitors (BRD4i) block the release of pro-inflammatory cytokines and prevent downstream remodeling. Although the chromatin modifying functions of BRD4 in inducible gene expression have been extensively investigated, its roles in post-transcriptional regulation are not as well understood. Based on its interaction with the transcriptional elongation complex and spliceosome, we hypothesize that BRD4 is a functional regulator of mRNA processing. To address this question, we combine data-independent analysis - parallel accumulation-serial fragmentation (diaPASEF) with RNA-sequencing to achieve deep and integrated coverage of the proteomic and transcriptomic landscapes of human small airway epithelial cells exposed to viral challenge and treated with BRD4i. The transcript-level data was further interrogated for alternative splicing analysis, and the resulting data sets were correlated to identify pathways subject to post-transcriptional regulation. We discover that BRD4 regulates alternative splicing of key genes, including Interferon-related Developmental Regulator 1 ( IFRD1 ) and X-Box Binding Protein 1 ( XBP1 ), related to the innate immune response and the unfolded protein response, respectively. These findings extend the transcriptional elongation-facilitating actions of BRD4 in control of post-transcriptional RNA processing in innate signaling.
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Affiliation(s)
- Morgan Mann
- Department of Medicine, University of Wisconsin – Madison, Madison, 53705, Wisconsin, USA
| | - Yao Fu
- Department of Medicine, University of Wisconsin – Madison, Madison, 53705, Wisconsin, USA
| | - Xiaofang Xu
- Department of Medicine, University of Wisconsin – Madison, Madison, 53705, Wisconsin, USA
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin – Madison, Madison, 53705, Wisconsin, USA
| | - Yi Li
- Department of Pharmacology and Toxicology, University of Texas, Medical Branch, Galveston, 77550, Texas, USA
| | - Jia Zhou
- Department of Pharmacology and Toxicology, University of Texas, Medical Branch, Galveston, 77550, Texas, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin – Madison, Madison, 53705, Wisconsin, USA,Human Proteomics Program, University of Wisconsin – Madison, Madison, 53705, Wisconsin, USA,Department of Cell and Regenerative Biology, University of Wisconsin – Madison, Madison, 53705, Wisconsin, USA
| | - Allan R. Brasier
- Institute for Clinical and Translational Research (ICTR), University of Wisconsin – Madison, Madison, 53705, Wisconsin, USA
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21
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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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22
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Roberts DS, Mann M, Li BH, Kim D, Braiser AR, Jin S, Ge Y. Distinct core glycan and O-glycoform utilization of SARS-CoV-2 Omicron variant Spike protein RBD revealed by top-down mass spectrometry. Chem Sci 2022; 13:10944-10949. [PMID: 36320702 PMCID: PMC9491206 DOI: 10.1039/d2sc02132c] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/30/2022] [Indexed: 09/21/2023] Open
Abstract
The SARS-CoV-2 Omicron (B.1.1.529) variant possesses numerous spike (S) mutations particularly in the S receptor-binding domain (S-RBD) that significantly improve transmissibility and evasion of neutralizing antibodies. But exactly how the mutations in the Omicron variant enhance viral escape from immunological protection remains to be understood. The S-RBD remains the principal target for neutralizing antibodies and therapeutics, thus new structural insights into the Omicron S-RBD and characterization of the post-translational glycosylation changes can inform rational design of vaccines and therapeutics. Here we report the molecular variations and O-glycoform changes of the Omicron S-RBD variant as compared to wild-type (WA1/2020) and Delta (B.1.617.2) variants using high-resolution top-down mass spectrometry (MS). A novel O-glycosite (Thr376) unique to the Omicron variant is identified. Moreover, we have directly quantified the Core 1 and Core 2 O-glycan structures and characterized the O-glycoform structural heterogeneity of the three variants. Our findings reveal high resolution detail of Omicron O-glycoforms and their utilization to provide direct molecular evidence of proteoform alterations in the Omicron variant which could shed light on how this variant escapes immunological protection.
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Affiliation(s)
- David S Roberts
- Department of Chemistry, University of Wisconsin-Madison WI 53706 USA
| | - Morgan Mann
- Department of Medicine, School of Medicine and Public Health University of Wisconsin-Madison WI 53705 USA
| | - Brad H Li
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison WI 53705 USA
| | - Donguk Kim
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison WI 53705 USA
| | - Allan R Braiser
- Department of Medicine, School of Medicine and Public Health University of Wisconsin-Madison WI 53705 USA
- Institute for Clinical and Translational Research, University of Wisconsin-Madison WI 53705 USA
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison WI 53706 USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison WI 53706 USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison WI 53705 USA
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23
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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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24
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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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25
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Roberts DS, Mann M, Li BH, Kim D, Brasier AR, Jin S, Ge Y. Distinct Core Glycan and O-Glycoform Utilization of SARS-CoV-2 Omicron Variant Spike Protein RBD Revealed by Top-Down Mass Spectrometry. bioRxiv 2022:2022.02.09.479776. [PMID: 35475171 PMCID: PMC9040677 DOI: 10.1101/2022.02.09.479776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The SARS-CoV-2 Omicron (B.1.1.529) variant possesses numerous spike (S) mutations particularly in the S receptor-binding domain (S-RBD) that significantly improve transmissibility and evasion of neutralizing antibodies. But exactly how the mutations in the Omicron variant enhance viral escape from immunological protection remains to be understood. The S-RBD remains the principal target for neutralizing antibodies and therapeutics, thus new structural insights into the Omicron S-RBD and characterization of the post-translational glycosylation changes can inform rational design of vaccines and therapeutics. Here we report the molecular variations and O-glycoform changes of the Omicron S-RBD variant as compared to wild-type (WA1/2020) and Delta (B.1.617.2) variants using high-resolution top-down mass spectrometry (MS). A novel O-glycosite (Thr376) unique to the Omicron variant is identified. Moreover, we have directly quantified the Core 1 and Core 2 O-glycan structures and characterized the O-glycoform structural heterogeneity of the three variants. Our findings reveal high resolution detail of Omicron O-glycoforms and their utilization to provide direct molecular evidence of proteoform alterations in the Omicron variant which could shed light on how this variant escapes immunological protection.
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26
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Wang R, Sheng H, Wang F, Li W, Roberts DS, Jin S. Sustainable Coproduction of Two Disinfectants via Hydroxide-Balanced Modular Electrochemical Synthesis Using a Redox Reservoir. ACS Cent Sci 2021; 7:2083-2091. [PMID: 34963900 PMCID: PMC8704031 DOI: 10.1021/acscentsci.1c01157] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Indexed: 06/14/2023]
Abstract
Challenges posed by the sacrificial auxiliary reactions and expensive ion-exchange membranes in conventional electrosynthesis necessitate developing new electrochemical processes to enable efficient and sustainable distributed electrochemical manufacturing. Modular electrochemical synthesis (ModES) using a redox reservoir (RR) offers a promising membrane-free approach to improve energy efficiency and reduce waste through the pairing of multiple independent oxidative and reductive half-reactions; however, undesired ion-imbalance and induced pH changes in the existing ModES process limit sustained production. Here we present Ni(OH)2 as a heterogeneous RR that can selectively store and transport the hydroxide ions involved in the target half-reactions by reversible conversion with NiOOH to enable an ion-balanced ModES of two common disinfectants, hydrogen peroxide (H2O2) and sodium hypochlorite (NaClO). This hydroxide-balanced ModES realizes stable operation without appreciable pH swing to accumulate practically useful concentrations of H2O2 and NaClO up to 251 and 481 ppm, respectively. These results illustrate additional design principles for electrosynthesis without sacrificial auxiliary reactions and the need for ion-selective RRs for modular electrochemical manufacturing.
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Affiliation(s)
- Rui Wang
- Department
of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Hongyuan Sheng
- Department
of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Fengmei Wang
- Department
of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- CAS
Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Wenjie Li
- Department
of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - David S. Roberts
- Department
of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Song Jin
- Department
of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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27
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Bayne EF, Simmons AD, Roberts DS, Zhu Y, Aballo TJ, Wancewicz B, Palecek SP, Ge Y. Multiomics Method Enabled by Sequential Metabolomics and Proteomics for Human Pluripotent Stem-Cell-Derived Cardiomyocytes. J Proteome Res 2021; 20:4646-4654. [PMID: 34499502 PMCID: PMC8714023 DOI: 10.1021/acs.jproteome.1c00611] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human pluripotent stem-cell-derived cardiomyocytes (hPSC-CMs) show immense promise for patient-specific disease modeling, cardiotoxicity screening, and regenerative therapy development. However, thus far, hPSC-CMs in culture have not recapitulated the structural or functional properties of adult CMs in vivo. To gain global insight into hPSC-CM biology, we established a multiomics method for analyzing the hPSC-CM metabolome and proteome from the same cell culture, creating multidimensional profiles of hPSC-CMs. Specifically, we developed a sequential extraction to capture metabolites and proteins from the same hPSC-CM monolayer cultures and analyzed these extracts using high-resolution mass spectrometry. Using this method, we annotated 205 metabolites/lipids and 4319 proteins from 106 cells with high reproducibility. We further integrated the proteome and metabolome measurements to create network profiles of molecular phenotypes for hPSC-CMs. Out of 310 pathways identified using metabolomics and proteomics, 40 pathways were considered significantly overrepresented (false-discovery-rate-corrected p ≤ 0.05). Highly populated pathways included those involved in protein synthesis (ribosome, spliceosome), ATP generation (oxidative phosphorylation), and cardiac muscle contraction. This multiomics method achieves a deep coverage of metabolites and proteins, creating a multidimensional view of the hPSC-CM phenotype, which provides a strong technological foundation to advance the understanding of hPSC-CM biology. Raw data are available in the MassIVE repository with identifier MSV000088010.
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Affiliation(s)
- Elizabeth F. Bayne
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aaron D. Simmons
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David S. Roberts
- 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 53705, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Timothy J. Aballo
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Benjamin Wancewicz
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sean P. Palecek
- Department of Chemical and Biological Engineering, 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 53705, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
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28
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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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29
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Roberts DS, Mann M, Melby JA, Larson EJ, Zhu Y, Brasier AR, Jin S, Ge Y. Structural O-Glycoform Heterogeneity of the SARS-CoV-2 Spike Protein Receptor-Binding Domain Revealed by Top-Down Mass Spectrometry. J Am Chem Soc 2021; 143:12014-12024. [PMID: 34328324 PMCID: PMC8353889 DOI: 10.1021/jacs.1c02713] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes an extensively glycosylated surface spike (S) protein to mediate host cell entry, and the S protein glycosylation plays key roles in altering the viral binding/function and infectivity. However, the molecular structures and glycan heterogeneity of the new O-glycans found on the S protein regional-binding domain (S-RBD) remain cryptic because of the challenges in intact glycoform analysis by conventional bottom-up glycoproteomic approaches. Here, we report the complete structural elucidation of intact O-glycan proteoforms through a hybrid native and denaturing top-down mass spectrometry (MS) approach employing both trapped ion mobility spectrometry (TIMS) quadrupole time-of-flight and ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR)-MS. Native top-down TIMS-MS/MS separates the protein conformers of the S-RBD to reveal their gas-phase structural heterogeneity, and top-down FTICR-MS/MS provides in-depth glycoform analysis for unambiguous identification of the glycan structures and their glycosites. A total of eight O-glycoforms and their relative molecular abundance are structurally elucidated for the first time. These findings demonstrate that this hybrid top-down MS approach can provide a high-resolution proteoform-resolved mapping of diverse O-glycoforms of the S glycoprotein, which lays a strong molecular foundation to uncover the functional roles of their O-glycans. This proteoform-resolved approach can be applied to reveal the structural O-glycoform heterogeneity of emergent SARS-CoV-2 S-RBD variants as well as other O-glycoproteins in general.
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Affiliation(s)
- David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Morgan Mann
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Jake A Melby
- 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
| | - Yanlong Zhu
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Allan R Brasier
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Institute for Clinical and Translational Research, University of Wisconsin-Madison, Madison, Wisconsin 53705, 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 Medicine, School of Medicine and Public Health, 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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30
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Larson EJ, Roberts DS, Melby JA, Buck KM, Zhu Y, Zhou S, Han L, Zhang Q, Ge Y. High-Throughput Multi-attribute Analysis of Antibody-Drug Conjugates Enabled by Trapped Ion Mobility Spectrometry and Top-Down Mass Spectrometry. Anal Chem 2021; 93:10013-10021. [PMID: 34258999 PMCID: PMC8319120 DOI: 10.1021/acs.analchem.1c00150] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antibody-drug conjugates (ADCs) are one of the fastest growing classes of anticancer therapies. Combining the high targeting specificity of monoclonal antibodies (mAbs) with cytotoxic small molecule drugs, ADCs are complex molecular entities that are intrinsically heterogeneous. Primary sequence variants, varied drug-to-antibody ratio (DAR) species, and conformational changes in the starting mAb structure upon drug conjugation must be monitored to ensure the safety and efficacy of ADCs. Herein, we have developed a high-throughput method for the analysis of cysteine-linked ADCs using trapped ion mobility spectrometry (TIMS) combined with top-down mass spectrometry (MS) on a Bruker timsTOF Pro. This method can analyze ADCs (∼150 kDa) by TIMS followed by a three-tiered top-down MS characterization strategy for multi-attribute analysis. First, the charge state distribution and DAR value of the ADC are monitored (MS1). Second, the intact mass of subunits dissociated from the ADC by low-energy collision-induced dissociation (CID) is determined (MS2). Third, the primary sequence for the dissociated subunits is characterized by CID fragmentation using elevated collisional energies (MS3). We further automate this workflow by directly injecting the ADC and using MS segmentation to obtain all three tiers of MS information in a single 3-min run. Overall, this work highlights a multi-attribute top-down MS characterization method that possesses unparalleled speed for high-throughput characterization of ADCs.
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Affiliation(s)
- Eli J Larson
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - David S Roberts
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jake A Melby
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Kevin M Buck
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin - Madison, 1111 Highland Avenue., Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin, 1111 Highland Avenue., Madison, Wisconsin 53705, United States
| | - Shiyue Zhou
- Analytical R&D, AbbVie Inc., 1 Waukegan Rd, North Chicago, Illinois 60064, United States
| | - Linjie Han
- Analytical R&D, AbbVie Inc., 1 Waukegan Rd, North Chicago, Illinois 60064, United States
| | - Qunying Zhang
- Analytical R&D, AbbVie Inc., 1 Waukegan Rd, North Chicago, Illinois 60064, 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, School of Medicine and Public Health, University of Wisconsin, 1111 Highland Avenue., Madison, Wisconsin 53705, United States
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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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Mann M, Roberts DS, Zhu Y, Li Y, Zhou J, Ge Y, Brasier AR. Discovery of RSV-Induced BRD4 Protein Interactions Using Native Immunoprecipitation and Parallel Accumulation-Serial Fragmentation (PASEF) Mass Spectrometry. Viruses 2021; 13:v13030454. [PMID: 33799525 PMCID: PMC8000986 DOI: 10.3390/v13030454] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 01/29/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/19/2022] Open
Abstract
Respiratory Syncytial Virus (RSV) causes severe inflammation and airway pathology in children and the elderly by infecting the epithelial cells of the upper and lower respiratory tract. RSV replication is sensed by intracellular pattern recognition receptors upstream of the IRF and NF-κB transcription factors. These proteins coordinate an innate inflammatory response via Bromodomain-containing protein 4 (BRD4), a protein that functions as a scaffold for unknown transcriptional regulators. To better understand the pleiotropic regulatory function of BRD4, we examine the BRD4 interactome and identify how RSV infection dynamically alters it. To accomplish these goals, we leverage native immunoprecipitation and Parallel Accumulation—Serial Fragmentation (PASEF) mass spectrometry to examine BRD4 complexes isolated from human alveolar epithelial cells in the absence or presence of RSV infection. In addition, we explore the role of BRD4’s acetyl-lysine binding bromodomains in mediating these interactions by using a highly selective competitive bromodomain inhibitor. We identify 101 proteins that are significantly enriched in the BRD4 complex and are responsive to both RSV-infection and BRD4 inhibition. These proteins are highly enriched in transcription factors and transcriptional coactivators. Among them, we identify members of the AP1 transcription factor complex, a complex important in innate signaling and cell stress responses. We independently confirm the BRD4/AP1 interaction in primary human small airway epithelial cells. We conclude that BRD4 recruits multiple transcription factors during RSV infection in a manner dependent on acetyl-lysine binding domain interactions. This data suggests that BRD4 recruits transcription factors to target its RNA processing complex to regulate gene expression in innate immunity and inflammation.
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Affiliation(s)
- Morgan Mann
- Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health (SMPH), Madison, WI 53705, USA;
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (D.S.R.); (Y.G.)
| | - Yanlong Zhu
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA;
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Yi Li
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77550, USA; (Y.L.); (J.Z.)
| | - Jia Zhou
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77550, USA; (Y.L.); (J.Z.)
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (D.S.R.); (Y.G.)
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA;
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Allan R. Brasier
- Institute for Clinical and Translational Research (ICTR), University of Wisconsin-Madison, Madison, WI 53705, USA
- Correspondence: ; Tel.: +1-608-263-7371
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Roberts DS, Mann MW, Melby JA, Larson EJ, Zhu Y, Brasier AR, Jin S, Ge Y. Structural O-Glycoform Heterogeneity of the SARS-CoV-2 Spike Protein Receptor-Binding Domain Revealed by Native Top-Down Mass Spectrometry. bioRxiv 2021. [PMID: 33688648 DOI: 10.1101/2021.02.28.433291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes an extensively glycosylated surface spike (S) protein to mediate host cell entry and the S protein glycosylation is strongly implicated in altering viral binding/function and infectivity. However, the structures and relative abundance of the new O-glycans found on the S protein regional-binding domain (S-RBD) remain cryptic because of the challenges in intact glycoform analysis. Here, we report the complete structural characterization of intact O-glycan proteoforms using native top-down mass spectrometry (MS). By combining trapped ion mobility spectrometry (TIMS), which can separate the protein conformers of S-RBD and analyze their gas phase structural variants, with ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR) MS analysis, the O-glycoforms of the S-RBD are comprehensively characterized, so that seven O-glycoforms and their relative molecular abundance are structurally elucidated for the first time. These findings demonstrate that native top-down MS can provide a high-resolution proteoform-resolved mapping of diverse O-glycoforms of the S glycoprotein, which lays a strong molecular foundation to uncover the functional roles of their O-glycans. This proteoform-resolved approach can be applied to reveal the structural O-glycoform heterogeneity of emergent SARS-CoV-2 S-RBD variants, as well as other O-glycoproteins in general.
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Melby JA, de Lange WJ, Zhang J, Roberts DS, Mitchell SD, Tucholski T, Kim G, Kyrvasilis A, McIlwain SJ, Kamp TJ, Ralphe JC, Ge Y. Functionally Integrated Top-Down Proteomics for Standardized Assessment of Human Induced Pluripotent Stem Cell-Derived Engineered Cardiac Tissues. J Proteome Res 2021; 20:1424-1433. [PMID: 33395532 DOI: 10.1021/acs.jproteome.0c00830] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three-dimensional (3D) human induced pluripotent stem cell-derived engineered cardiac tissues (hiPSC-ECTs) have emerged as a promising alternative to two-dimensional hiPSC-cardiomyocyte monolayer systems because hiPSC-ECTs are a closer representation of endogenous cardiac tissues and more faithfully reflect the relevant cardiac pathophysiology. The ability to perform functional and molecular assessments using the same hiPSC-ECT construct would allow for more reliable correlation between observed functional performance and underlying molecular events, and thus is critically needed. Herein, for the first time, we have established an integrated method that permits sequential assessment of functional properties and top-down proteomics from the same single hiPSC-ECT construct. We quantitatively determined the differences in isometric twitch force and the sarcomeric proteoforms between two groups of hiPSC-ECTs that differed in the duration of time of 3D-ECT culture. Importantly, by using this integrated method we discovered a new and strong correlation between the measured contractile parameters and the phosphorylation levels of alpha-tropomyosin between the two groups of hiPSC-ECTs. The integration of functional assessments together with molecular characterization by top-down proteomics in the same hiPSC-ECT construct enables a holistic analysis of hiPSC-ECTs to accelerate their applications in disease modeling, cardiotoxicity, and drug discovery. Data are available via ProteomeXchange with identifier PXD022814.
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Affiliation(s)
- Jake A Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Willem J de Lange
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Jianhua Zhang
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Stanford D Mitchell
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Gina Kim
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Andreas Kyrvasilis
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Sean J McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Timothy J Kamp
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - J Carter Ralphe
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin 53705, 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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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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Wu Z, Roberts DS, Melby JA, Wenger K, Wetzel M, Gu Y, Ramanathan SG, Bayne EF, Liu X, Sun R, Ong IM, McIlwain SJ, Ge Y. MASH Explorer: A Universal Software Environment for Top-Down Proteomics. J Proteome Res 2020; 19:3867-3876. [PMID: 32786689 DOI: 10.1021/acs.jproteome.0c00469] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [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: 12/18/2022]
Abstract
Top-down mass spectrometry (MS)-based proteomics enable a comprehensive analysis of proteoforms with molecular specificity to achieve a proteome-wide understanding of protein functions. However, the lack of a universal software for top-down proteomics is becoming increasingly recognized as a major barrier, especially for newcomers. Here, we have developed MASH Explorer, a universal, comprehensive, and user-friendly software environment for top-down proteomics. MASH Explorer integrates multiple spectral deconvolution and database search algorithms into a single, universal platform which can process top-down proteomics data from various vendor formats, for the first time. It addresses the urgent need in the rapidly growing top-down proteomics community and is freely available to all users worldwide. With the critical need and tremendous support from the community, we envision that this MASH Explorer software package will play an integral role in advancing top-down proteomics to realize its full potential for biomedical research.
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Affiliation(s)
- Zhijie Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Jake A Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Kent Wenger
- 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
| | - Molly Wetzel
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Yiwen Gu
- 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
| | | | - Elizabeth F Bayne
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States.,Center for Computational Biology and Bioinformatics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Ruixiang Sun
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Irene M Ong
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Sean J McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, 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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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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Hollett G, Roberts DS, Sewell M, Wensley E, Wagner J, Murray W, Krotz A, Toth B, Vijayakumar V, Sailor MJ. Quantum Ensembles of Silicon Nanoparticles: Discrimination of Static and Dynamic Photoluminescence Quenching Processes. J Phys Chem C Nanomater Interfaces 2019; 123:17976-17986. [PMID: 32489514 PMCID: PMC7266134 DOI: 10.1021/acs.jpcc.9b04334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Porous silicon photoluminescence is characterized by a broad emission band that displays unusually long (tens to hundreds of micro-seconds), wavelength-dependent emissive lifetimes. The photoluminescence is associated with quantum confinement of excitons in silicon nanocrystallites contained within the porous matrix, and the broad emission spectrum derives from the wide distribution of nanocrystallite sizes in the material. The longer emissive lifetimes in the ensemble of quantum-confined emitters correspond to the larger nanocrystallites, with their longer wavelengths of emission. The quenching of this photoluminescence by aromatic, redox-active molecules aminochrome (AMC), dopamine, adrenochrome, sodium anthraquinone-2-sulfonate, benzyl viologen dichloride, methyl viologen dichloride hydrate, and ethyl viologen dibromide is studied, and dynamic and static quenching mechanisms are distinguished by the emission lifetime analysis. Because of the dependence of the emission lifetime on emission wavelength from the silicon nanocrystallite ensemble, a pronounced blue shift is observed in the steady-state emission spectrum upon exposure to dynamic-type quenchers. Conversely, static-type quenching systems show uniform quenching across all emission wavelengths. Thus, the difference between static and dynamic quenching mechanisms is readily distinguished by ratiometric photoluminescence spectroscopy. The application of this concept to imaging of AMC, the oxidized form of the neurotransmitter dopamine that is of interest for its role in neurodegenerative diseases, is demonstrated. It is found that static electron acceptors result in no ratiometric contrast, while AMC shows a strong contrast, allowing ready visualization in a 2-D imaging experiment.
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Affiliation(s)
- Geoffrey Hollett
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
| | - David S. Roberts
- Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Mollie Sewell
- Bioengineering, North Carolina A&T State University, Greensboro, North Carolina 27412, United States
| | - Emma Wensley
- Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Julia Wagner
- Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - William Murray
- Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Alex Krotz
- Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Bryan Toth
- Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Vibha Vijayakumar
- Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Michael J. Sailor
- Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
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39
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Roberts DS, Chen B, Tiambeng TN, Wu Z, Ge Y, Jin S. Reproducible Large-Scale Synthesis of Surface Silanized Nanoparticles as an Enabling Nanoproteomics Platform: Enrichment of the Human Heart Phosphoproteome. Nano Res 2019; 12:1473-1481. [PMID: 31341559 PMCID: PMC6656398 DOI: 10.1007/s12274-019-2418-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
A reproducible synthetic strategy was developed for facile large-scale (200 mg) synthesis of surface silanized magnetite (Fe3O4) nanoparticles (NPs) for biological applications. After further coupling a phosphate-specific affinity ligand, these functionalized magnetic NPs were used for the highly specific enrichment of phosphoproteins from a complex biological mixture. Moreover, correlating the surface silane density of the silanized magnetite NPs to their resultant enrichment performance established a simple and reliable quality assurance control to ensure reproducible synthesis of these NPs routinely in large scale and optimal phosphoprotein enrichment performance from batch-to-batch. Furthermore, by successful exploitation of a top-down phosphoproteomics strategy that integrates this high throughput nanoproteomics platform with online liquid chromatography (LC) and tandem mass spectrometry (MS/MS), we were able to specifically enrich, identify, and characterize endogenous phosphoproteins from highly complex human cardiac tissue homogenate. This nanoproteomics platform possesses a unique combination of scalability, specificity, reproducibility, and efficiency for the capture and enrichment of low abundance proteins in general, thereby enabling downstream proteomics applications.
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Affiliation(s)
- David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Timothy N. Tiambeng
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Zhijie Wu
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706, USA
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Zuidema JM, Kumeria T, Kim D, Kang J, Wang J, Hollett G, Zhang X, Roberts DS, Chan N, Dowling C, Blanco-Suarez E, Allen NJ, Tuszynski MH, Sailor MJ. Oriented Nanofibrous Polymer Scaffolds Containing Protein-Loaded Porous Silicon Generated by Spray Nebulization. Adv Mater 2018; 30:e1706785. [PMID: 29363828 PMCID: PMC6475500 DOI: 10.1002/adma.201706785] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 12/13/2017] [Indexed: 06/07/2023]
Abstract
Oriented composite nanofibers consisting of porous silicon nanoparticles (pSiNPs) embedded in a polycaprolactone or poly(lactide-co-glycolide) matrix are prepared by spray nebulization from chloroform solutions using an airbrush. The nanofibers can be oriented by an appropriate positioning of the airbrush nozzle, and they can direct growth of neurites from rat dorsal root ganglion neurons. When loaded with the model protein lysozyme, the pSiNPs allow the generation of nanofiber scaffolds that carry and deliver the protein under physiologic conditions (phosphate-buffered saline (PBS), at 37 °C) for up to 60 d, retaining 75% of the enzymatic activity over this time period. The mass loading of protein in the pSiNPs is 36%, and in the resulting polymer/pSiNP scaffolds it is 3.6%. The use of pSiNPs that display intrinsic photoluminescence (from the quantum-confined Si nanostructure) allows the polymer/pSiNP composites to be definitively identified and tracked by time-gated photoluminescence imaging. The remarkable ability of the pSiNPs to protect the protein payload from denaturation, both during processing and for the duration of the long-term aqueous release study, establishes a model for the generation of biodegradable nanofiber scaffolds that can load and deliver sensitive biologics.
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Affiliation(s)
| | | | - Dokyoung Kim
- Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, 26 Kyungheedae-Ro, Dongdaemun-Gu, Seoul 02447, Republic of Korea
| | - Jinyoung Kang
- Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
| | - Joanna Wang
- Materials Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093 (USA)
| | - Geoffrey Hollett
- Materials Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093 (USA)
| | - Xuan Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093 (USA)
| | - David S. Roberts
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093 (USA)
| | - Nicole Chan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093 (USA)
| | - Cari Dowling
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, 10010 N Torrey Pines, La Jolla, CA, 92037 (USA)
| | - Elena Blanco-Suarez
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, 10010 N Torrey Pines, La Jolla, CA, 92037 (USA)
| | - Nicola J. Allen
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, 10010 N Torrey Pines, La Jolla, CA, 92037 (USA)
| | - Mark H. Tuszynski
- Veterans Administration Medical Center, 3350 La Jolla Village Drive, San Diego, CA, 92161 (USA), Department of Neurosciences, University of California, San Diego, 9500 Gilman, La Jolla, CA 92093 (USA)
| | - Michael J. Sailor
- Department of Chemistry and BiochemistryUniversity of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093 (USA)
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Roberts DS, Faquin WC, Deschler DG. Temporal bone giant cell tumour: report of a second primary giant cell tumour of the temporal bone and infratemporal fossa. B-ENT 2011; 7:301-303. [PMID: 22338246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
Abstract
OBJECTIVE To report a second primary giant cell tumour (GCT) of the temporal bone and infratemporal fossa. METHODOLOGY Medical records were analyzed in the context of the available literature. RESULTS A 30 year-old male developed a temporal bone GCT with infratemporal fossa extension 12 years after undergoing successful surgical treatment of a GCT of the femur. These tumours were histologically distinct, suggesting the development of a second primary GCT rather than metastatic disease. This case differs from prior reported cases by surgical approach. Complete removal was achieved but required resection of the zygomatic arch and dissection of all upper facial nerve branches. The patient is disease free after 3 years with acceptable functional and cosmetic results. CONCLUSION Complete resection of GCTs of the temporal bone and infratemporal fossa is advocated. Surgical techniques that allow for visualization of the facial nerve and increase surgical access can enhance overall clinical success.
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Affiliation(s)
- D S Roberts
- Department of Otolaryngology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
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Roberts DS, Raol YH, Bandyopadhyay S, Lund IV, Budreck EC, Passini MA, Passini MJ, Wolfe JH, Brooks-Kayal AR, Russek SJ. Egr3 stimulation of GABRA4 promoter activity as a mechanism for seizure-induced up-regulation of GABA(A) receptor alpha4 subunit expression. Proc Natl Acad Sci U S A 2005; 102:11894-9. [PMID: 16091474 PMCID: PMC1187961 DOI: 10.1073/pnas.0501434102] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [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: 11/18/2022] Open
Abstract
GABA is the major inhibitory transmitter at CNS synapses. Changes in subunit composition of the pentameric GABA(A) receptor, including increased levels of alpha4 subunit in dentate granule cells and associated functional alterations such as increased zinc blockade of GABA currents, are hypothesized to be critical components of epileptogenesis. Here, we report that the minimal promoter of the human alpha4 subunit gene (GABRA4p), when used to drive reporter gene expression from adeno-associated viral vectors, controls condition-specific up-regulation in response to status epilepticus, defining a transcriptional mechanism for seizure-induced changes in levels of alpha4 subunit containing GABA(A) receptors. Transfection studies in primary hippocampal neurons show that inducible early growth response factor 3 (Egr3) up-regulates GABRA4p activity as well as the levels of endogenous alpha4 subunits. Given that Egr3 knockout mice display approximately 50% less GABRA4 mRNAs in the hippocampus and that increases in alpha4 and Egr3 mRNAs in response to pilocarpine-induced status epilepticus are accompanied by increased binding of Egr3 to GABRA4 in dentate granule cells, our findings support a role for Egr3 as a major regulator of GABRA4 in developing neurons and in epilepsy.
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Affiliation(s)
- D S Roberts
- Laboratory of Molecular Neurobiology, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
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Abstract
The purpose of the present investigation was to examine how measures of imagery, creativity, and socioeconomic status relate to performance in a stock-market trading game. The 368 participants were students enrolled in an administration studies curriculum. A multiple regression analysis showed imaging scores to be a predictor of stock-trading performance as were creativity and socioeconomic status to a lesser extent. High imagers and high scorers on creativity and socioeconomic status made several times more profit with their portfolios. Results are discussed in terms of imagery having multiple repercussions on learning, e.g., memory and problem-solving. It is concluded that scores on imagery, creativity, and socioeconomic status, being weakly correlated, are interdependent and likely associated with personality traits shaped within a stimulating home or social environment.
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Affiliation(s)
- D S Roberts
- Department of Psychology, Concordia University, 7141 Sherbrooke Street West, Montreal, PQ Canada H4B 1R6
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Abstract
Mesenchyme cells surround early ossicles in the developing middle ear, then are replaced by space that is created by what has been described as an expansion of the pharyngeal pouch. Cell death has not been considered important in cavitation of chick middle ear (Jaskoll and Maderson [1978] Anat. Rec., 190:177-200), but an uncharacterized form of cell death has been reported to play a major role in cavitation of mouse middle ear (Jaskoll [1977] PhD thesis, CUNY). We investigated whether this uncharacterized cell death is the non-random form known as apoptosis. We examined the middle ear cavitation process using an in situ immunomarker for apoptosis. CBy RF mice during prenatal days 15-20 and postnatal days 1-3 and chick embryos representing HH stages 33-38 were investigated. Apoptotic cells were marked in mouse postnatal day 1. No indication of apoptosis was present in other prenatal and postnatal days of development included in this study, although morphology showed that cavitation proceeds over several perinatal days in the mouse. Apoptosis was not marked in the chick middle ear. Previously observed cell death in murine middle ear is the non-random form of cell death known as apoptosis. Cell death has not been reported in avian middle ear, and lack of apoptotic marker supports those observations. The limited occurrence of apoptosis in mice and apparent absence of apoptosis in chicks suggest that several mechanisms contribute to cavitation of vertebrate middle ear space.
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Affiliation(s)
- D S Roberts
- Department of Biology, Hamilton College, Clinton, New York 13323, USA
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Abstract
Recent reports suggest that children under 3 years of age are best operated on by a specialist pediatric surgeon. In the United Kingdom, hypertrophic pyloric stenosis traditionally has been treated by adult general surgeons. Should this change? In 1991, a retrospective review of 10 years' experience with pyloric stenosis, managed by general surgeons in a large district general hospital, was published. In 1969, an accredited pediatric surgeon, who largely took over the management of pyloric stenosis, was appointed to the staff. His results with 70 children over a 5-year period (series 2) were reviewed retrospectively and compared with the previously published general surgical series of 170 children (series 1). There was no significant difference in the gender, age, or weight distribution between the two series. There was a marked difference in the rates of wound infection (15.5% in series 1; 2.8% in series 2; P < .05), wound dehiscence (6.7% in series 1; 0% in series 2; P < .05), and breach of the duodenal mucosa (12.8% in series 1; 0% in series 2; P < .01). The lower morbidity rate resulted in a shorter hospital stay, with emotional and financial savings. This supports the recommendation that children with this condition should be managed by a pediatric surgeon.
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Affiliation(s)
- A J Brain
- Jenny Lind Children's Department, Norfolk and Norwich Hospital, England
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Affiliation(s)
- D S Roberts
- Virginia Polytechnic Institute and State University, Blacksburg
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Roberts DS. Self-administration of stimulants and serotonergic systems. NIDA Res Monogr 1992; 119:136-40. [PMID: 1359416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Affiliation(s)
- D S Roberts
- Dept. of Psychology, Carleton University, Ottawa, Canada
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Abstract
Twenty-one babies of 34-41 weeks' gestational age with birth asphyxia (5 minute Apgar score less than or equal to 5 or umbilical artery pH less than or equal to 7.2) were studied during the first two days of life to find out whether the urinary excretion of tubular markers of renal function is of value in the early diagnosis of acute renal failure. Urinary retinol binding protein, myoglobin, and N-acetyl-beta-D-glucosaminidase (NAG), expressed as a ratio with urinary creatinine, were measured and excretion profiles repeated at 3-6 days in 15 infants and at 7-14 days in 11 infants. Plasma creatinine concentration, creatinine clearance, plasma myoglobin concentration, and fractional sodium excretion were measured where possible in asphyxiated infants. Control data were obtained from 50 healthy infants: 28 gave urine samples alone, 17 urine and blood, and five blood alone. Normal urinary values were derived from 17, 25, and three infants, respectively, for the three time periods. The number of control samples was limited for ethical reasons. Four asphyxiated infants had acute renal failure (group 1), four had tubular dysfunction without glomerular disturbance (group 2) and 13 had normal renal function (group 3). Group 1 were clearly identified by greatly increased urinary retinol binding protein (greater than 27,000 micrograms/mmol creatinine) and myoglobin (greater than 1500 micrograms/mmol creatinine) excretion measured in the first two days of life. In control infants the range of excretion of retinol binding protein within the same time period was 3 to 967 micrograms/mmol creatinine and urinary myoglobin was undetectable. Excretion of NAG failed to discriminate between groups 1 and 2. Acute renal failure occurred only in infants who had heavy myoglobinaemia. Tubular dysfunction in group 2 was transient and not accompanied by plasma electrolyte disturbances. We conclude that measurement of urinary excretion of retinol binding protein or myoglobin after birth is helpful in the early diagnosis of acute renal failure.
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Affiliation(s)
- D S Roberts
- Department of Paediatrics, United Medical School, St Thomas's Hospital, London
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Abstract
Thirty eight assessments of postmicturition residual volume were undertaken in 34 babies of various gestational and postnatal ages using abdominal ultrasonography. Twenty one (54%) babies had no detectable residual bladder volume. In all cases manual expression of the bladder failed to eliminate the residual volume. The formula widely used in the estimation of fetal bladder size and urine output is not applicable in the newborn infant.
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Affiliation(s)
- D S Roberts
- Department of Paediatrics, St Thomas's Hospital, London
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