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Wojtkiewicz M, Subramanian SP, Gundry RL. Multinozzle Emitter for Improved Negative Mode Analysis of Reduced Native N-Glycans by Microflow Porous Graphitized Carbon Liquid Chromatography Mass Spectrometry. Anal Chem 2024; 96:5746-5751. [PMID: 38556995 PMCID: PMC11024887 DOI: 10.1021/acs.analchem.3c03649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/13/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Microflow porous graphitized carbon liquid chromatography (PGC-LC) combined with negative mode ionization mass spectrometry (MS) provides high resolution separation and identification of reduced native N-glycan structural isomers. However, insufficient spray quality and low ionization efficiency of N-glycans present challenges for negative mode electrospray. Here, we evaluated the performance of a recently developed multinozzle electrospray source (MnESI) and accompanying M3 emitter for microflow PGC-LC-MS analysis of N-glycans in negative mode. In comparison to a standard electrospray ionization source, the MnESI with an M3 emitter improves signal intensity, identification, quantification, and resolution of structural isomers to accommodate low-input samples.
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Affiliation(s)
- Melinda Wojtkiewicz
- CardiOmics
Program, Center for Heart and Vascular Research, and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Sabarinath Peruvemba Subramanian
- CardiOmics
Program, Center for Heart and Vascular Research, and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Rebekah L. Gundry
- CardiOmics
Program, Center for Heart and Vascular Research, and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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2
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Berg Luecke L, Mesidor R, Littrell J, Carpenter M, Wojtkiewicz M, Gundry RL. Veneer Is a Webtool for Rapid, Standardized, and Transparent Interpretation, Annotation, and Reporting of Mammalian Cell Surface N-Glycocapture Data. J Proteome Res 2024. [PMID: 38412263 DOI: 10.1021/acs.jproteome.3c00800] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Currently, no consensus exists regarding criteria required to designate a protein within a proteomic data set as a cell surface protein. Most published proteomic studies rely on varied ontology annotations or computational predictions instead of experimental evidence when attributing protein localization. Consequently, standardized approaches for analyzing and reporting cell surface proteome data sets would increase confidence in localization claims and promote data use by other researchers. Recently, we developed Veneer, a web-based bioinformatic tool that analyzes results from cell surface N-glycocapture workflows─the most popular cell surface proteomics method used to date that generates experimental evidence of subcellular location. Veneer assigns protein localization based on defined experimental and bioinformatic evidence. In this study, we updated the criteria and process for assigning protein localization and added new functionality to Veneer. Results of Veneer analysis of 587 cell surface N-glycocapture data sets from 32 published studies demonstrate the importance of applying defined criteria when analyzing cell surface proteomics data sets and exemplify how Veneer can be used to assess experimental quality and facilitate data extraction for informing future biological studies and annotating public repositories.
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Affiliation(s)
- Linda Berg Luecke
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Roneldine Mesidor
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Jack Littrell
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Morgan Carpenter
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Melinda Wojtkiewicz
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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Waknitz M, Berg Luecke L, Mesidor R, Wojtkiewicz M, Castro C, Gundry RL. The GENTIL Method for Isolation of Human Adult Cardiomyocytes from Cryopreserved Tissue for Proteomic Analyses. Methods Mol Biol 2024; 2735:145-167. [PMID: 38038848 DOI: 10.1007/978-1-0716-3527-8_9] [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] [Indexed: 12/02/2023]
Abstract
Heart failure is a serious clinical and economic health care problem, and its clinical progression is linked to pathological cardiac remodeling. Due to the heterogeneity of heart failure, lack of animal models to accurately represent advanced heart failure, and limited access to fresh human cardiac tissue, little is known regarding cell-type-specific mechanisms and context-specific functions of cardiomyocytes during disease development processes. While mass spectrometry has been increasingly applied to unravel changes in the proteome associated with cardiovascular physiology and disease, most studies have used homogenized tissue. Therefore, new studies using isolated cardiomyocytes are necessary to gain a better understanding of the intricate cell-type-specific molecular mechanisms underlying the pathophysiology of heart failure. This chapter describes the GENTIL method, which incorporates recent technological developments in sample handling, for isolation of cardiomyocytes from cryopreserved human cardiac tissues for use in proteomic analyses.
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Affiliation(s)
- Michelle Waknitz
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Linda Berg Luecke
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Roneldine Mesidor
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Melinda Wojtkiewicz
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Chase Castro
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA.
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Yeo CT, Kropp EM, Hansen PA, Pereckas M, Oleson BJ, Naatz A, Stancill JS, Ross KA, Gundry RL, Corbett JA. β-cell-selective inhibition of DNA damage response signaling by nitric oxide is associated with an attenuation in glucose uptake. J Biol Chem 2023; 299:102994. [PMID: 36773802 PMCID: PMC10023961 DOI: 10.1016/j.jbc.2023.102994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
Nitric oxide (NO) plays a dual role in regulating DNA damage response (DDR) signaling in pancreatic β-cells. As a genotoxic agent, NO activates two types of DDR signaling; however, when produced at micromolar levels by the inducible isoform of NO synthase, NO inhibits DDR signaling and DDR-induced apoptosis in a β-cell-selective manner. DDR signaling inhibition by NO correlates with mitochondrial oxidative metabolism inhibition and decreases in ATP and NAD+. Unlike most cell types, β-cells do not compensate for impaired mitochondrial oxidation by increasing glycolytic flux, and this metabolic inflexibility leads to a decrease in ATP and NAD+. Here, we used multiple analytical approaches to determine changes in intermediary metabolites in β-cells and non-β-cells treated with NO or complex I inhibitor rotenone. In addition to ATP and NAD+, glycolytic and tricarboxylic acid cycle intermediates as well as NADPH are significantly decreased in β-cells treated with NO or rotenone. Consistent with glucose-6-phosphate residing at the metabolic branchpoint for glycolysis and the pentose phosphate pathway (NADPH), we show that mitochondrial oxidation inhibitors limit glucose uptake in a β-cell-selective manner. Our findings indicate that the β-cell-selective inhibition of DDR signaling by NO is associated with a decrease in ATP to levels that fall significantly below the KM for ATP of glucokinase (glucose uptake) and suggest that this action places the β-cell in a state of suspended animation where it is metabolically inert until NO is removed, and metabolic function can be restored.
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Affiliation(s)
- Chay Teng Yeo
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Erin M Kropp
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Polly A Hansen
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Michael Pereckas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Bryndon J Oleson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Aaron Naatz
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jennifer S Stancill
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Kyle A Ross
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - John A Corbett
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
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5
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Berg Luecke L, Waas M, Littrell J, Wojtkiewicz M, Castro C, Burkovetskaya M, Schuette EN, Buchberger AR, Churko JM, Chalise U, Waknitz M, Konfrst S, Teuben R, Morrissette-McAlmon J, Mahr C, Anderson DR, Boheler KR, Gundry RL. Surfaceome mapping of primary human heart cells with CellSurfer uncovers cardiomyocyte surface protein LSMEM2 and proteome dynamics in failing hearts. Nat Cardiovasc Res 2023; 2:76-95. [PMID: 36950336 PMCID: PMC10030153 DOI: 10.1038/s44161-022-00200-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 11/29/2022] [Indexed: 01/19/2023]
Abstract
Cardiac cell surface proteins are drug targets and useful biomarkers for discriminating among cellular phenotypes and disease states. Here we developed an analytical platform, CellSurfer, that enables quantitative cell surface proteome (surfaceome) profiling of cells present in limited quantities, and we apply it to isolated primary human heart cells. We report experimental evidence of surface localization and extracellular domains for 1,144 N-glycoproteins, including cell-type-restricted and region-restricted glycoproteins. We identified a surface protein specific for healthy cardiomyocytes, LSMEM2, and validated an anti-LSMEM2 monoclonal antibody for flow cytometry and imaging. Surfaceome comparisons among pluripotent stem cell derivatives and their primary counterparts highlighted important differences with direct implications for drug screening and disease modeling. Finally, 20% of cell surface proteins, including LSMEM2, were differentially abundant between failing and non-failing cardiomyocytes. These results represent a rich resource to advance development of cell type and organ-specific targets for drug delivery, disease modeling, immunophenotyping and in vivo imaging.
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Affiliation(s)
- Linda Berg Luecke
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI USA
| | - Matthew Waas
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
- Present Address: Princess Margaret Cancer Centre, University Health Network, Toronto, ON Canada
| | - Jack Littrell
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
| | - Melinda Wojtkiewicz
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
| | - Chase Castro
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
| | - Maria Burkovetskaya
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
| | - Erin N. Schuette
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
| | - Amanda Rae Buchberger
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI USA
- Present Address: Department of Chemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Jared M. Churko
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ USA
| | - Upendra Chalise
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
| | - Michelle Waknitz
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
| | - Shelby Konfrst
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
| | - Roald Teuben
- Department of Biomedical Engineering, Whiting School of Engineering, The Johns Hopkins University, Baltimore, MD USA
| | - Justin Morrissette-McAlmon
- Department of Biomedical Engineering, Whiting School of Engineering, The Johns Hopkins University, Baltimore, MD USA
| | - Claudius Mahr
- Department of Mechanical Engineering, Division of Cardiology, University of Washington, Seattle, WA USA
| | - Daniel R. Anderson
- Division of Cardiovascular Medicine, University of Nebraska Medical Center, Omaha, NE USA
| | - Kenneth R. Boheler
- Department of Biomedical Engineering, Whiting School of Engineering, The Johns Hopkins University, Baltimore, MD USA
- Department of Medicine, Division of Cardiology, The Johns Hopkins University, Baltimore, MD USA
| | - Rebekah L. Gundry
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
- Division of Cardiovascular Medicine, University of Nebraska Medical Center, Omaha, NE USA
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6
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Medcalf MR, Bantis LE, Shi P, Bhadbhade P, Gundry RL, Mikuls TR, England BR, O'Dell JR, Funk RS. Plasma metabolomic profiling as a tool to identify predictive biomarkers of methotrexate efficacy in rheumatoid arthritis. Semin Arthritis Rheum 2022; 56:152056. [PMID: 35785666 PMCID: PMC10316318 DOI: 10.1016/j.semarthrit.2022.152056] [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: 04/12/2022] [Revised: 06/03/2022] [Accepted: 06/21/2022] [Indexed: 11/23/2022]
Abstract
OBJECTIVE Methotrexate (MTX) remains the first-choice disease-modifying therapy in rheumatoid arthritis (RA). However, clinical response is variable, and no reliable predictive biomarkers of efficacy currently exist. In this study, plasma metabolomic profiling is evaluated as a tool to identify pretreatment biomarkers of MTX response in RA. METHODS Plasma collected from RA patients initiating MTX therapy (n = 20) were analyzed by metabolomic profiling totaling 648 identified metabolites. Pretreatment metabolomic profiles were compared based on clinical response after 16-weeks of MTX therapy. Clinical response to MTX was defined by a clinically meaningful reduction in disease activity score in 28 joints (DAS28-ESR) of greater than 1.2. RESULTS Pretreatment plasma levels of 19 metabolites were found to differ (p < 0.05) between RA patients based on response to MTX at 16-weeks. Spearman's correlation of pretreatment plasma metabolite levels with change in DAS28-ESR over the treatment period further supported three of the identified metabolites as associated with MTX response (p < 0.05). The identified metabolite levels were all found to be lower in RA patients responsive to MTX but were not found to be intercorrelated. Receiver operating characteristic analysis of each of the identified metabolites, alone or in combination, demonstrated an excellent discrimination between responders and non-responders based on pretreatment plasma levels of nornicotine (AUC = 0.84), N-methylisoleucine (AUC = 0.82), 2,3-dihydroxybutanoic acid (AUC = 0.82), and a combination biomarker panel score (AUC = 0.98). CONCLUSION Pretreatment plasma metabolomic profiling identified multiple metabolites associated with early response to MTX therapy in RA and represents a promising approach for the identification of clinical biomarkers of MTX response in RA.
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Affiliation(s)
- Matthew R Medcalf
- Department of Pharmacy Practice, University of Kansas, Kansas City, KS, United States
| | - Leonidas E Bantis
- Department of Biostatics & Data Science, University of Kansas Medical Center, Kansas City, KS, United States
| | - Peng Shi
- Department of Biostatics & Data Science, University of Kansas Medical Center, Kansas City, KS, United States
| | - Pooja Bhadbhade
- Department of Internal Medicine, Division of Allergy, Clinical Immunology and Rheumatology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Rebekah L Gundry
- Department of Cellular and Integrative Physiology, CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, University of Nebraska Medical Center, Omaha, NE, United States
| | - Ted R Mikuls
- Department of Internal Medicine, Division of Rheumatology & Immunology, University of Nebraska Medical Center (UNMC), Omaha, NE, United States; VA Nebraska-Western IA Health Care System, Omaha, NE, United States
| | - Bryant R England
- Department of Internal Medicine, Division of Rheumatology & Immunology, University of Nebraska Medical Center (UNMC), Omaha, NE, United States; VA Nebraska-Western IA Health Care System, Omaha, NE, United States
| | - James R O'Dell
- Department of Internal Medicine, Division of Rheumatology & Immunology, University of Nebraska Medical Center (UNMC), Omaha, NE, United States; VA Nebraska-Western IA Health Care System, Omaha, NE, United States
| | - Ryan S Funk
- Department of Pharmacy Practice, University of Kansas, Kansas City, KS, United States.
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Farnoodian M, Bose D, Khristov V, Susaimanickam PJ, Maddileti S, Mariappan I, Abu-Asab M, Campos M, Villasmil R, Wan Q, Maminishkis A, McGaughey D, Barone F, Gundry RL, Riordon DR, Boheler KR, Sharma R, Bharti K. Cell-autonomous lipid-handling defects in Stargardt iPSC-derived retinal pigment epithelium cells. Stem Cell Reports 2022; 17:2438-2450. [DOI: 10.1016/j.stemcr.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
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8
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Abstract
Apolipoproteins, the protein component of lipoproteins, play an important role in lipid transport, lipoprotein assembly, and receptor recognition. Apolipoproteins are glycosylated and the glycan moieties play an integral role in apolipoprotein function. Changes in apolipoprotein glycosylation correlate with several diseases manifesting in dyslipidemias. Despite their relevance in apolipoprotein function and diseases, the total glycan repertoire of most apolipoproteins remains undefined. This review summarizes the current knowledge and knowledge gaps regarding human apolipoprotein glycan composition, structure, glycosylation site, and functions. Given the relevance of glycosylation to apolipoprotein function, we expect that future studies of apolipoprotein glycosylation will contribute new understanding of disease processes and uncover relevant biomarkers and therapeutic targets. Considering these future efforts, we also provide a brief overview of current mass spectrometry based technologies that can be applied to define detailed glycan structures, site-specific compositions, and the role of emerging approaches for clinical applications in biomarker discovery and personalized medicine.
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9
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Jiang X, Wojtkiewicz M, Patwardhan C, Greer S, Kong Y, Kuss M, Huang X, Liao J, Lu Y, Dudley A, Gundry RL, Fuchs M, Streubel P, Duan B. The effects of maturation and aging on the rotator cuff tendon-to-bone interface. FASEB J 2021; 35:e22066. [PMID: 34822203 DOI: 10.1096/fj.202101484r] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/29/2021] [Accepted: 11/10/2021] [Indexed: 12/19/2022]
Abstract
Rotator cuff tendon injuries often occur at the tendon-to-bone interface (i.e., enthesis) area, with a high prevalence for the elderly population, but the underlying reason for this phenomenon is still unknown. The objective of this study is to identify the histological, molecular, and biomechanical alterations of the rotator cuff enthesis with maturation and aging in a mouse model. Four different age groups of mice (newborn, young, adult, and old) were studied. Striking variations of the entheses were observed between the newborn and other matured groups, with collagen content, proteoglycan deposition, collagen fiber dispersion was significantly higher in the newborn group. The compositional and histological features of young, adult, and old groups did not show significant differences, except having increased proteoglycan deposition and thinner collagen fibers at the insertion sites in the old group. Nanoindentation testing showed that the old group had a smaller compressive modulus at the insertion site when compared with other groups. However, tensile mechanical testing reported that the old group demonstrated a significantly higher failure stress when compared with the young and adult groups. The proteomics analysis detected dramatic differences in protein content between newborn and young groups but minor changes among young, adult, and old groups. These results demonstrated: (1) the significant alterations of the enthesis composition and structure occur from the newborn to the young time period; (2) the increased risk of rotator cuff tendon injuries in the elderly population is not solely because of old age alone in the rodent model.
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Affiliation(s)
- Xiping Jiang
- Mary & Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, Nebraska, USA.,Division of Cardiology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA.,Molecular Genetics and Cell Biology Program, Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Melinda Wojtkiewicz
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Chinmay Patwardhan
- Department of Bioengineering, University of Texas at Arlington, Arlington, Texas, USA
| | - Sydney Greer
- Mary & Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, Nebraska, USA.,Molecular Genetics and Cell Biology Program, Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Yunfan Kong
- Mary & Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Mitchell Kuss
- Mary & Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Xi Huang
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jun Liao
- Department of Bioengineering, University of Texas at Arlington, Arlington, Texas, USA
| | - Yongfeng Lu
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Andrew Dudley
- Mary & Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, Nebraska, USA.,Molecular Genetics and Cell Biology Program, Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Matthias Fuchs
- Department of Physics and Astronomy, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Philipp Streubel
- Department of Orthopedic Surgery and Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Bin Duan
- Mary & Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, Nebraska, USA.,Division of Cardiology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA.,Department of Surgery, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA.,Department of Mechanical and Materials Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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10
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Wojtkiewicz M, Berg Luecke L, Castro C, Burkovetskaya M, Mesidor R, Gundry RL. Bottom-up proteomic analysis of human adult cardiac tissue and isolated cardiomyocytes. J Mol Cell Cardiol 2021; 162:20-31. [PMID: 34437879 PMCID: PMC9620472 DOI: 10.1016/j.yjmcc.2021.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/07/2021] [Accepted: 08/04/2021] [Indexed: 12/30/2022]
Abstract
The heart is composed of multiple cell types, each with a specific function. Cell-type-specific approaches are necessary for defining the intricate molecular mechanisms underlying cardiac development, homeostasis, and pathology. While single-cell RNA-seq studies are beginning to define the chamber-specific cellular composition of the heart, our views of the proteome are more limited because most proteomics studies have utilized homogenized human cardiac tissue. To promote future cell-type specific analyses of the human heart, we describe the first method for cardiomyocyte isolation from cryopreserved human cardiac tissue followed by flow cytometry for purity assessment. We also describe a facile method for preparing isolated cardiomyocytes and whole cardiac tissue homogenate for bottom-up proteomic analyses. Prior experience in dissociating cardiac tissue or proteomics is not required to execute these methods. We compare different sample preparation workflows and analysis methods to demonstrate how these can impact the depth of proteome coverage achieved. We expect this how-to guide will serve as a starting point for investigators interested in general and cell-type-specific views of the cardiac proteome.
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Affiliation(s)
- Melinda Wojtkiewicz
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Linda Berg Luecke
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Chase Castro
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Maria Burkovetskaya
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Roneldine Mesidor
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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11
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Abstract
Mass spectrometry (MS) is routinely used to identify, characterize, and quantify biological molecules. For protein analysis, MS‐based workflows can be broadly categorized as top‐down or bottom‐up, depending on whether the proteins are analyzed as intact molecules or first digested into peptides. This article outlines steps for preparing peptide samples for MS as part of a bottom‐up proteomics workflow, providing versatile methods suitable for discovery and targeted analyses in qualitative and quantitative workflows. Resulting samples contain peptides of suitable size for analysis by MS instrumentation generally available to modern research laboratories, including MS coupled to either liquid chromatography (LC) or matrix‐assisted laser desorption/ionization (MALDI) interfaces. This article incorporates recent developments in methodologies and consumables to facilitate sample preparation. The protocols are well‐suited to users without prior experience in proteomics and include methods for universally applicable suspension trap processing and for alternate in‐solution processing to accommodate a range of sample types. Cleanup, quantification, and fractionation procedures are also described. © 2021 The Authors. Basic Protocol: Preparation of high‐complexity peptide samples for mass spectrometry analysis using S‐Trap™ processing Alternate Protocol 1: Preparation of low‐ to moderate‐complexity peptide samples for mass spectrometry analysis using in‐solution processing Alternate Protocol 2: Detergent, polymer, and salt removal from peptide samples before mass spectrometry analysis using SP2 processing Support Protocol 1: Protein quantification using Pierce 660 nm assay Support Protocol 2: Peptide quantification using Pierce quantitative fluorometric peptide assay Support Protocol 3: High‐pH fractionation of complex peptide samples
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Affiliation(s)
- Melinda Wojtkiewicz
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Linda Berg Luecke
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Maia I Kelly
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska
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12
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Berg Luecke L, Gundry RL. Assessment of Streptavidin Bead Binding Capacity to Improve Quality of Streptavidin-based Enrichment Studies. J Proteome Res 2020; 20:1153-1164. [PMID: 33270449 DOI: 10.1021/acs.jproteome.0c00772] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The streptavidin-based enrichment of biotin-tagged molecules is a common methodology that is routinely used across multiple disciplines in biomedical research. Numerous and varied formats of immobilized streptavidin and related proteins are available, but predicting which product is most apt for a given application is complicated by the fact that there are numerous technical considerations and no universal reporting standards for describing the binding capacity of the beads. Here, we define criteria that should be considered when performing a fit-for-purpose evaluation of streptavidin beads. We also describe a colorimetric competitive displacement assay, the streptAVIdin binDing capacITY (AVIDITY) assay, a fast, easy, and inexpensive absorbance-based method to measure the binding capacity of streptavidin beads, which can be used to compare different products and evaluate variation among many of the same product. We expect that the fit-for-purpose criteria and the AVIDITY assay will benefit users across disciplines to make informed decisions regarding the most apt streptavidin bead products for their own experiments.
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Affiliation(s)
- Linda Berg Luecke
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States.,CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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13
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Fehrenbach DJ, Abais-Battad JM, Dasinger JH, Lund H, Keppel T, Zemaj J, Cherian-Shaw M, Gundry RL, Geurts AM, Dwinell MR, Mattson DL. Sexual Dimorphic Role of CD14 (Cluster of Differentiation 14) in Salt-Sensitive Hypertension and Renal Injury. Hypertension 2020; 77:228-240. [PMID: 33249861 DOI: 10.1161/hypertensionaha.120.14928] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Genomic sequence and gene expression association studies in animals and humans have identified genes that may be integral in the pathogenesis of various diseases. CD14 (cluster of differentiation 14)-a cell surface protein involved in innate immune system activation-is one such gene associated with cardiovascular and hypertensive disease. We previously showed that this gene is upregulated in renal macrophages of Dahl salt-sensitive animals fed a high-salt diet; here we test the hypothesis that CD14 contributes to the elevated pressure and renal injury observed in salt-sensitive hypertension. Using CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeat-associated 9), we created a targeted mutation in the CD14 gene on the Dahl SS (SS/JrHSDMcwi) background and validated the absence of CD14 peptides via mass spectrometry. Radiotelemetry was used to monitor blood pressure in wild-type and CD14-/- animals challenged with high salt and identified infiltrating renal immune cells via flow cytometry. Germline knockout of CD14 exacerbated salt-sensitive hypertension and renal injury in female animals but not males. CD14-/- females demonstrated increased infiltrating macrophages but no difference in infiltrating lymphocytes. Transplant of CD14+/+ or CD14-/- bone marrow was used to isolate the effects of CD14 knockout to hematopoietic cells and confirmed that the differential phenotype observed was due to knockout of CD14 in hematopoietic cells. Ovariectomy was used to remove the influence of female sex hormones, which completely abrogated the effect of CD14 knockout. These studies provide a novel treatment target and evidence of a new dichotomy in immune activation between sexes within the context of hypertensive disease where CD14 regulates immune cell activation and renal injury.
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Affiliation(s)
- Daniel J Fehrenbach
- Department of Physiology (D.J.F., H.L., J.Z., A.M.G., M.R.D.), Medical College of Wisconsin, Wauwatosa, WI.,Department of Physiology, Augusta University and the Medical College of Georgia, Augusta, GA (D.J.F., J.M.A.-B., J.H.D., M.C.-S., D.L.M.)
| | - Justine M Abais-Battad
- Department of Physiology, Augusta University and the Medical College of Georgia, Augusta, GA (D.J.F., J.M.A.-B., J.H.D., M.C.-S., D.L.M.)
| | - John Henry Dasinger
- Department of Physiology, Augusta University and the Medical College of Georgia, Augusta, GA (D.J.F., J.M.A.-B., J.H.D., M.C.-S., D.L.M.)
| | - Hayley Lund
- Department of Physiology (D.J.F., H.L., J.Z., A.M.G., M.R.D.), Medical College of Wisconsin, Wauwatosa, WI
| | - Theodore Keppel
- Center for Biomedical Mass Spectrometry Research (T.K., R.L.G.), Medical College of Wisconsin, Wauwatosa, WI
| | - Jeylan Zemaj
- Department of Physiology (D.J.F., H.L., J.Z., A.M.G., M.R.D.), Medical College of Wisconsin, Wauwatosa, WI
| | - Mary Cherian-Shaw
- Department of Physiology, Augusta University and the Medical College of Georgia, Augusta, GA (D.J.F., J.M.A.-B., J.H.D., M.C.-S., D.L.M.)
| | - Rebekah L Gundry
- Center for Biomedical Mass Spectrometry Research (T.K., R.L.G.), Medical College of Wisconsin, Wauwatosa, WI.,CardiOmics Program, Center for Heart and Vascular Research (R.L.G.), University of Nebraska Medical Center, Omaha, NE.,Division of Cardiovascular Medicine (R.L.G.), University of Nebraska Medical Center, Omaha, NE.,Department of Cellular and Integrative Physiology (R.L.G.), University of Nebraska Medical Center, Omaha, NE
| | - Aron M Geurts
- Department of Physiology (D.J.F., H.L., J.Z., A.M.G., M.R.D.), Medical College of Wisconsin, Wauwatosa, WI.,Genomic Sciences and Precision Medicine Center (A.M.G., M.R.D.), Medical College of Wisconsin, Wauwatosa, WI
| | - Melinda R Dwinell
- Department of Physiology (D.J.F., H.L., J.Z., A.M.G., M.R.D.), Medical College of Wisconsin, Wauwatosa, WI.,Genomic Sciences and Precision Medicine Center (A.M.G., M.R.D.), Medical College of Wisconsin, Wauwatosa, WI
| | - David L Mattson
- Department of Physiology, Augusta University and the Medical College of Georgia, Augusta, GA (D.J.F., J.M.A.-B., J.H.D., M.C.-S., D.L.M.)
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14
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Adhikari S, Nice EC, Deutsch EW, Lane L, Omenn GS, Pennington SR, Paik YK, Overall CM, Corrales FJ, Cristea IM, Van Eyk JE, Uhlén M, Lindskog C, Chan DW, Bairoch A, Waddington JC, Justice JL, LaBaer J, Rodriguez H, He F, Kostrzewa M, Ping P, Gundry RL, Stewart P, Srivastava S, Srivastava S, Nogueira FCS, Domont GB, Vandenbrouck Y, Lam MPY, Wennersten S, Vizcaino JA, Wilkins M, Schwenk JM, Lundberg E, Bandeira N, Marko-Varga G, Weintraub ST, Pineau C, Kusebauch U, Moritz RL, Ahn SB, Palmblad M, Snyder MP, Aebersold R, Baker MS. A high-stringency blueprint of the human proteome. Nat Commun 2020; 11:5301. [PMID: 33067450 PMCID: PMC7568584 DOI: 10.1038/s41467-020-19045-9] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 09/25/2020] [Indexed: 02/07/2023] Open
Abstract
The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases.
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Affiliation(s)
- Subash Adhikari
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Edouard C Nice
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
- Faculty of Medicine, Nursing and Health Sciences, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Eric W Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Lydie Lane
- Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA
| | - Stephen R Pennington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Young-Ki Paik
- Yonsei Proteome Research Center, 50 Yonsei-ro, Sudaemoon-ku, Seoul, 120-749, South Korea
| | | | - Fernando J Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, 28049, Madrid, Spain
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Jennifer E Van Eyk
- Cedars Sinai Medical Center, Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Los Angeles, CA, 90048, USA
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Cecilia Lindskog
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 75185, Uppsala, Sweden
| | - Daniel W Chan
- Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA
| | - Amos Bairoch
- Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland
| | - James C Waddington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Joshua L Justice
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Joshua LaBaer
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Markus Kostrzewa
- Bruker Daltonik GmbH, Microbiology and Diagnostics, Fahrenheitstrasse, 428359, Bremen, Germany
| | - Peipei Ping
- Cardiac Proteomics and Signaling Laboratory, Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Peter Stewart
- Department of Chemical Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | | | - Sudhir Srivastava
- Cancer Biomarkers Research Branch, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Suite 5E136, Rockville, MD, 20852, USA
| | - Fabio C S Nogueira
- Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Gilberto B Domont
- Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Yves Vandenbrouck
- University of Grenoble Alpes, Inserm, CEA, IRIG-BGE, U1038, 38000, Grenoble, France
| | - Maggie P Y Lam
- Departments of Medicine-Cardiology and Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Consortium for Fibrosis Research and Translation, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Sara Wennersten
- Division of Cardiology, Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Juan Antonio Vizcaino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Marc Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, Mail Code 0404, La Jolla, CA, 92093-0404, USA
| | | | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center San Antonio, UT Health, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Charles Pineau
- University of Rennes, Inserm, EHESP, IREST, UMR_S 1085, F-35042, Rennes, France
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Seong Beom Ahn
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Magnus Palmblad
- Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Ruedi Aebersold
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Mark S Baker
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia.
- Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA.
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15
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Berg Luecke L, Waas M, Gundry RL. Reliable Protocols for Flow Cytometry Analysis of Intracellular Proteins in Pluripotent Stem Cell Derivatives: A Fit-For-Purpose Approach. ACTA ACUST UNITED AC 2020; 50:e94. [PMID: 31479597 DOI: 10.1002/cpsc.94] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Human pluripotent stem cell (hPSC) derivatives are valuable for a variety of research applications and have the potential to revolutionize approaches to personalized medicine. However, differentiation efficiency varies among cell lines and protocols. Therefore, methods to reliably determine cell type identity in cultures of hPSC derivatives in a manner that is consistent among laboratories are needed. While flow cytometry is apt for routine assessment of population heterogeneity, standardized protocols are not available for most cell types. This article describes a workflow for establishing a fit-for-purpose protocol for flow cytometric analysis of hPSC derivatives. Based on the application of this workflow, a standard operating procedure (SOP) was developed for the analysis of cardiac troponin in hPSC-derived cardiomyocytes (hPSC-CM). Throughout the article, important concepts related to antibody validation and gating strategies are presented to enable users to properly validate any antibody of interest and develop a rigorous SOP for their experimental needs. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Linda Berg Luecke
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin.,Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, Wisconsin
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16
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Oldham RAA, Faber ML, Keppel TR, Buchberger AR, Waas M, Hari P, Gundry RL, Medin JA. Discovery and validation of surface N-glycoproteins in MM cell lines and patient samples uncovers immunotherapy targets. J Immunother Cancer 2020; 8:e000915. [PMID: 32771993 PMCID: PMC7418848 DOI: 10.1136/jitc-2020-000915] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Multiple myeloma (MM) is characterized by clonal expansion of malignant plasma cells in the bone marrow. While recent advances in treatment for MM have improved patient outcomes, the 5-year survival rate remains ~50%. A better understanding of the MM cell surface proteome could facilitate development of new directed therapies and assist in stratification and monitoring of patient outcomes. METHODS In this study, we first used a mass spectrometry (MS)-based discovery-driven cell surface capture (CSC) approach to map the cell surface N-glycoproteome of MM cell lines. Next, we developed targeted MS assays, and applied these to cell lines and primary patient samples to refine the list of candidate tumor markers. Candidates of interest detected by MS on MM patient samples were further validated using flow cytometry (FCM). RESULTS We identified 696 MM cell surface N-glycoproteins by CSC, and developed 73 targeted MS detection assays. MS-based validation using primary specimens detected 30 proteins with significantly higher abundance in patient MM cells than controls. Nine of these proteins were identified as potential immunotherapeutic targets, including five that were validated by FCM, confirming their expression on the cell surface of primary MM patient cells. CONCLUSIONS This MM surface N-glycoproteome will be a valuable resource in the development of biomarkers and therapeutics. Further, we anticipate that our targeted MS assays will have clinical benefit for the diagnosis, stratification, and treatment of MM patients.
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Affiliation(s)
- Robyn A A Oldham
- Medical Biophysics, University of Toronto Faculty of Medicine, Toronto, Ontario, Canada
- Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Mary L Faber
- Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Theodore R Keppel
- Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Amanda R Buchberger
- Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Matthew Waas
- Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Parameswaran Hari
- Division of Hematology Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Rebekah L Gundry
- Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jeffrey A Medin
- Medical Biophysics, University of Toronto Faculty of Medicine, Toronto, Ontario, Canada
- Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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17
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Ashwood C, Berg Luecke L, Gundry RL. Abstract MP143: Harnessing Glycomics to Understand Cardiac Biology and Disease. Circ Res 2020. [DOI: 10.1161/res.127.suppl_1.mp143] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cell surface glycoproteins play critical roles in maintaining cardiac structure and function, and the glycan-moiety attached to a protein is critical for proper protein folding, stability, and signaling. Despite mounting evidence that glycan structures are key modulators of heart function and must be considered when developing cardiac biomarkers, we currently do not have a comprehensive view of the glycans present in the normal human heart. Here, we used an innovative mass spectrometry approach to generate the first glycan structure libraries for primary human heart tissue, cardiomyocytes (CM) enriched from human heart tissue, and human induced pluripotent stem cell derived CM (hiPSC-CM), containing >260
N-
and
O-
glycans. Comparing the glycome of CM enriched from primary heart tissue to that of heart tissue homogenate, 21 structures significantly differed, and the high mannose class is increased in enriched CM. Moreover, >30% of the glycome significantly changed across 20-100 days of
in vitro
differentiation, and only 23% of the
N
-glycan structures were shared between hiPSC-CM and primary CM. Overall, these observations are an important complement to genomic, transcriptomic, and proteomic profiling and reveal new considerations for the use and interpretation of hiPSC-CM models for studies of human development, disease, and drug testing. These data are also expected to aid in the evaluation of the immunogenic potential of hiPSC-CM for transplantation. Finally, harnessing differences observed between immature, proliferative hiPSC-CM and adult primary CM may be exploited to drive
in vitro
differentiation towards a more mature phenotype. Building on these data, current efforts are underway to develop chamber- and cell-type specific views (
e.g.
cardiomyocytes, fibroblasts) of the glycome in the healthy and failing human heart. Such analyses provide a key link to understand the role glycosylation plays in cell-type specific functions and cardiac disease. The structural differences observed here, either among cell types or stages of differentiation, require complex regulation of multiple enzymes in the biosynthetic pathway, and therefore would be challenging to measure with antibody arrays, RNAseq, or proteomics. Therefore, continued application of structure-based glycomics approaches, such as the method used here, will be essential for elucidating the roles that glycans and glycoproteins play during developmental and disease processes in the human heart.
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18
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Waas M, Littrell J, Gundry RL. CIRFESS: An Interactive Resource for Querying the Set of Theoretically Detectable Peptides for Cell Surface and Extracellular Enrichment Proteomic Studies. J Am Soc Mass Spectrom 2020; 31:1389-1397. [PMID: 32212654 PMCID: PMC8116119 DOI: 10.1021/jasms.0c00021] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Cell surface transmembrane, extracellular, and secreted proteins are high value targets for immunophenotyping, drug development, and studies related to intercellular communication in health and disease. As the number of specific and validated affinity reagents that target this subproteome are limited, mass spectrometry (MS)-based approaches will continue to play a critical role in enabling discovery and quantitation of these molecules. Given the technical considerations that make MS-based cell surface proteome studies uniquely challenging, it can be difficult to select an appropriate experimental approach. To this end, we have integrated multiple prediction strategies and annotations into a single online resource, Compiled Interactive Resource for Extracellular and Surface Studies (CIRFESS). CIRFESS enables rapid interrogation of the human proteome to reveal the cell surface proteome theoretically detectable by current approaches and highlights where current prediction strategies provide concordant and discordant information. We applied CIRFESS to identify the percentage of various subsets of the proteome which are expected to be captured by targeted enrichment strategies, including two established methods and one that is possible but not yet demonstrated. These results will inform the selection of available proteomic strategies and development of new strategies to enhance coverage of the cell surface and extracellular proteome. CIRFESS is available at www.cellsurfer.net/cirfess.
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Affiliation(s)
- Matthew Waas
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Jack Littrell
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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19
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Bates ML, Gundry RL, Lindsey ML. Using an Investigative Journalism Approach to Design Mechanistic Experiments in Physiology. Physiology (Bethesda) 2020; 35:218-219. [PMID: 32490747 DOI: 10.1152/physiol.00006.2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
| | | | - Merry L Lindsey
- University of Nebraska Medical Center, Omaha, Nebraska.,Nebraska-Western Iowa Health Care System, Omaha, Nebraska
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20
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Waas M, Snarrenberg ST, Littrell J, Jones Lipinski RA, Hansen PA, Corbett JA, Gundry RL. SurfaceGenie: a web-based application for prioritizing cell-type-specific marker candidates. Bioinformatics 2020; 36:3447-3456. [PMID: 32053146 PMCID: PMC7267825 DOI: 10.1093/bioinformatics/btaa092] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 06/29/2019] [Revised: 12/16/2019] [Accepted: 02/05/2020] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Cell-type-specific surface proteins can be exploited as valuable markers for a range of applications including immunophenotyping live cells, targeted drug delivery and in vivo imaging. Despite their utility and relevance, the unique combination of molecules present at the cell surface are not yet described for most cell types. A significant challenge in analyzing 'omic' discovery datasets is the selection of candidate markers that are most applicable for downstream applications. RESULTS Here, we developed GenieScore, a prioritization metric that integrates a consensus-based prediction of cell surface localization with user-input data to rank-order candidate cell-type-specific surface markers. In this report, we demonstrate the utility of GenieScore for analyzing human and rodent data from proteomic and transcriptomic experiments in the areas of cancer, stem cell and islet biology. We also demonstrate that permutations of GenieScore, termed IsoGenieScore and OmniGenieScore, can efficiently prioritize co-expressed and intracellular cell-type-specific markers, respectively. AVAILABILITY AND IMPLEMENTATION Calculation of GenieScores and lookup of SPC scores is made freely accessible via the SurfaceGenie web application: www.cellsurfer.net/surfacegenie. CONTACT Rebekah.gundry@unmc.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shana T Snarrenberg
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jack Littrell
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Polly A Hansen
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - John A Corbett
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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21
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Kanack A, Vittal V, Haver H, Keppel T, Gundry RL, Klevit RE, Scaglione KM. UbcH5 Interacts with Substrates to Participate in Lysine Selection with the E3 Ubiquitin Ligase CHIP. Biochemistry 2020; 59:2078-2088. [PMID: 32401531 DOI: 10.1021/acs.biochem.0c00084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The E3 ubiquitin ligase C-terminus of Hsc70 interacting protein (CHIP) plays a critical role in regulating the ubiquitin-dependent degradation of misfolded proteins. CHIP mediates the ubiquitination of the α-amino-terminus of substrates with the E2 Ube2w and facilitates the ubiquitination of lysine residues with the E2 UbcH5. While it is known that Ube2w directly interacts with the disordered regions at the N-terminus of its substrates, it is unclear how CHIP and UbcH5 mediate substrate lysine selection. Here, we have decoupled the contributions of the E2, UbcH5, and the E3, CHIP, in ubiquitin transfer. We show that UbcH5 selects substrate lysine residues independent of CHIP, and that CHIP participates in lysine selection by fine-tuning the subset of substrate lysines that are ubiquitinated. We also identify lysine 128 near the C-terminus of UbcH5 as a critical residue for the efficient ubiquitin transfer by UbcH5 in both the presence and absence of CHIP. Together, these data demonstrate an important role of the UbcH5/substrate interactions in mediating the efficient ubiquitin transfer by the CHIP/UbcH5 complex.
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Affiliation(s)
- Adam Kanack
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States.,Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Vinayak Vittal
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Holly Haver
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27710, United States
| | - Theodore Keppel
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Kenneth Matthew Scaglione
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States.,Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States.,Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27710, United States.,Department of Neurology, Duke University, Durham, North Carolina 27710, United States.,Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, North Carolina 27710, United States
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22
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Lindsey ML, Gundry RL. Secrets of Cardiac Remodeling Revealed in the Secretome. Circulation 2020; 141:1645-1647. [PMID: 32421415 DOI: 10.1161/circulationaha.120.046042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Merry L Lindsey
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha (M.L.L., R.L.G.).,Research Service, Nebraska-Western Iowa Health Care System, Omaha, NE (M.L.L.)
| | - Rebekah L Gundry
- Research Service, Nebraska-Western Iowa Health Care System, Omaha, NE (M.L.L.)
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23
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Boheler KR, Gundry RL. Cutting edge technologies in cardiovascular research. J Mol Cell Cardiol 2020; 142:154. [PMID: 32339568 DOI: 10.1016/j.yjmcc.2020.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 11/16/2022]
Affiliation(s)
- Kenneth R Boheler
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, USA
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA.
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24
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Dhawan R, Gundry RL, Brett-Major DM, Mahr C, Thiele GM, Lindsey ML, Anderson DR. COVID-19 and cardiovascular disease: What we know, what we think we know, and what we need to know. J Mol Cell Cardiol 2020; 144:12-14. [PMID: 32339565 PMCID: PMC7180349 DOI: 10.1016/j.yjmcc.2020.04.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 04/21/2020] [Indexed: 01/19/2023]
Affiliation(s)
- Rahul Dhawan
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Rebekah L Gundry
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America; Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - David M Brett-Major
- Department of Epidemiology, College of Public Health, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Claudius Mahr
- Division of Cardiology, University of Washington, Seattle, WA, United States of America
| | - Geoffrey M Thiele
- Department of Internal Medicine, Division of Rheumatology, University of Nebraska Medical Center, Omaha, NE, United States of America; Research Service, Nebraska-Western Iowa Health Care System, Omaha, NE, United States of America
| | - Merry L Lindsey
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, United States of America; Research Service, Nebraska-Western Iowa Health Care System, Omaha, NE, United States of America
| | - Daniel R Anderson
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America.
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25
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Wu PK, Hong SK, Chen W, Becker AE, Gundry RL, Lin CW, Shao H, Gestwicki JE, Park JI. Mortalin (HSPA9) facilitates BRAF-mutant tumor cell survival by suppressing ANT3-mediated mitochondrial membrane permeability. Sci Signal 2020; 13:13/622/eaay1478. [PMID: 32156782 DOI: 10.1126/scisignal.aay1478] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mortalin [also known as heat shock protein family A (HSP70) member 9 (HSPA9) or glucose-regulated protein 75 (GRP75)] is a mitochondrial molecular chaperone that is often up-regulated and mislocalized in tumors with abnormal activation of the kinases MEK and ERK. Here, we found that mortalin depletion was selectively lethal to tumor and immortalized normal cells expressing the mutant kinase B-RafV600E or the chimeric protein ΔRaf-1:ER and that MEK-ERK-sensitive regulation of the peptide-binding domain in mortalin was critical to cell survival or death. Proteomics screening identified adenine nucleotide translocase 3 (ANT3) as a previously unknown mortalin substrate and cell survival/death effector. Mechanistically, increased MEK-ERK signaling activity and mortalin function converged opposingly on the regulation of mitochondrial permeability. Specifically, whereas MEK-ERK activity increased mitochondrial permeability by promoting the interaction between ANT3 and the peptidyl-prolyl isomerase cyclophilin D (CypD), mortalin decreased mitochondrial permeability by inhibiting this interaction. Hence, mortalin depletion increased mitochondrial permeability in MEK-ERK-deregulated cells to an extent that triggered cell death. HSP70 inhibitor derivatives that effectively inhibited mortalin suppressed the proliferation of B-RafV600E tumor cells in culture and in vivo, including their B-Raf inhibitor-resistant progenies. These findings suggest that targeting mortalin has potential as a selective therapeutic strategy in B-Raf-mutant or MEK-ERK-driven tumors.
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Affiliation(s)
- Pui-Kei Wu
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Seung-Keun Hong
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wenjing Chen
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Andrew E Becker
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Hao Shao
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jong-In Park
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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26
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Poon ENY, Luo XL, Webb SE, Yan B, Zhao R, Wu SCM, Yang Y, Zhang P, Bai H, Shao J, Chan CM, Chan GCF, Tsang SY, Gundry RL, Yang HT, Boheler KR. The cell surface marker CD36 selectively identifies matured, mitochondria-rich hPSC-cardiomyocytes. Cell Res 2020; 30:626-629. [PMID: 32157205 PMCID: PMC7343859 DOI: 10.1038/s41422-020-0292-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 02/06/2020] [Indexed: 11/09/2022] Open
Affiliation(s)
- Ellen Ngar-Yun Poon
- Department of Medicine and Therapeutics, and Centre for Cardiovascular Genomics and Medicine, The Chinese University of Hong Kong (CUHK), HKSAR, China.
| | - Xiao-Ling Luo
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences (CAS), CAS, Shanghai, China
| | - Sarah E Webb
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, HKSAR, China
| | - Bin Yan
- Department of Computer Science, The University of Hong Kong (HKU), HKSAR, China.,Intervention and Cell Therapy Center, Peking University Shenzhen Hospital, Shenzhen, China
| | - Rui Zhao
- School of Life Sciences, CUHK, HKSAR, China
| | | | - Yong Yang
- School of Biomedical Sciences, HKU, HKSAR, China.,SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Peng Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences (CAS), CAS, Shanghai, China
| | - Huajun Bai
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences (CAS), CAS, Shanghai, China
| | - Jiaofang Shao
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ching Man Chan
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, HKSAR, China
| | | | - Suk Ying Tsang
- School of Life Sciences, CUHK, HKSAR, China.,State Key Laboratory of Agrobiotechnology, CUHK, HKSAR, China
| | - Rebekah L Gundry
- Department of Biochemistry and Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, WI, USA.,CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Huang-Tian Yang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences (CAS), CAS, Shanghai, China.,Institute for Stem Cell and Regeneration Medicine, CAS, Beijing, China
| | - Kenneth R Boheler
- School of Biomedical Sciences, HKU, HKSAR, China. .,Division of Cardiology, Department of Medicine, and Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, USA.
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27
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Anderson DR, Duryee M, Walker J, Hall JH, Thiele GM, Klassen L, Zimmerman M, Gundry RL, Clemens DL. INACTIVATION OF MANGANESE SUPEROXIDE DISMUTASE BY IRREVERSIBLE COVALENT OXIDATIVE MODIFICATION IN CARDIOVASCULAR DISEASE. J Am Coll Cardiol 2020. [DOI: 10.1016/s0735-1097(20)31665-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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28
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Ashwood C, Waas M, Weerasekera R, Gundry RL. Reference glycan structure libraries of primary human cardiomyocytes and pluripotent stem cell-derived cardiomyocytes reveal cell-type and culture stage-specific glycan phenotypes. J Mol Cell Cardiol 2020; 139:33-46. [PMID: 31972267 DOI: 10.1016/j.yjmcc.2019.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/23/2019] [Accepted: 12/27/2019] [Indexed: 12/16/2022]
Abstract
Cell surface glycoproteins play critical roles in maintaining cardiac structure and function in health and disease and the glycan-moiety attached to the protein is critical for proper protein folding, stability and signaling [1]. However, despite mounting evidence that glycan structures are key modulators of heart function and must be considered when developing cardiac biomarkers, we currently do not have a comprehensive view of the glycans present in the normal human heart. In the current study, we used porous graphitized carbon liquid chromatography interfaced with mass spectrometry (PGC-LC-MS) to generate glycan structure libraries for primary human heart tissue homogenate, cardiomyocytes (CM) enriched from human heart tissue, and human induced pluripotent stem cell derived CM (hiPSC-CM). Altogether, we established the first reference structure libraries of the cardiac glycome containing 265 N- and O-glycans. Comparing the N-glycome of CM enriched from primary heart tissue to that of heart tissue homogenate, the same pool of N-glycan structures was detected in each sample type but the relative signal of 21 structures significantly differed between samples, with the high mannose class increased in enriched CM. Moreover, by comparing primary CM to hiPSC-CM collected during 20-100 days of differentiation, dynamic changes in the glycan profile throughout in vitro differentiation were observed and differences between primary and hiPSC-CM were revealed. Namely, >30% of the N-glycome significantly changed across these time-points of differentiation and only 23% of the N-glycan structures were shared between hiPSC-CM and primary CM. These observations are an important complement to current genomic, transcriptomic, and proteomic profiling and reveal new considerations for the use and interpretation of hiPSC-CM models for studies of human development, disease, and drug testing. Finally, these data are expected to support future regenerative medicine efforts by informing targets for evaluating the immunogenic potential of hiPSC-CM and harnessing differences between immature, proliferative hiPSC-CM and adult primary CM.
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Affiliation(s)
- Christopher Ashwood
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ranjuna Weerasekera
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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29
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Young JB, Keppel TR, Waas M, Salmon AE, Buchberger AR, Skumatz CM, Gundry RL, Kassem IS. Quantitative proteomic analysis of aqueous humor after rabbit lensectomy reveals differences in coagulation and immunomodulatory proteins. Mol Omics 2020; 16:126-137. [DOI: 10.1039/c9mo00169g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Proteomics of juvenile rabbit aqueous humor was evaluated before and after surgery to determine proteins responsible for postoperative outcomes.
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Affiliation(s)
- Jonathon B. Young
- Cell Biology, Neurobiology, & Anatomy
- Medical College of Wisconsin
- The Eye Institute
- Milwaukee
- USA
| | - Theodore R. Keppel
- Center for Biomedical Mass Spectrometry Research
- Medical College of Wisconsin
- Milwaukee
- USA
| | - Matthew Waas
- Biochemistry, Medical College of Wisconsin
- Milwaukee
- USA
| | - Alexander E. Salmon
- Cell Biology, Neurobiology, & Anatomy
- Medical College of Wisconsin
- The Eye Institute
- Milwaukee
- USA
| | - Amanda Rae Buchberger
- Center for Biomedical Mass Spectrometry Research
- Medical College of Wisconsin
- Milwaukee
- USA
| | | | - Rebekah L. Gundry
- Center for Biomedical Mass Spectrometry Research
- Medical College of Wisconsin
- Milwaukee
- USA
- Biochemistry, Medical College of Wisconsin
| | - Iris S. Kassem
- Cell Biology, Neurobiology, & Anatomy
- Medical College of Wisconsin
- The Eye Institute
- Milwaukee
- USA
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30
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Waas M, Gundry RL. A call to adopt a "fit for purpose" approach to antibody validation for flow cytometry analyses of stem cell models and beyond. Am J Physiol Heart Circ Physiol 2019; 317:H954-H957. [PMID: 31559827 DOI: 10.1152/ajpheart.00347.2019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) can be exploited as models for a wide range of research applications and numerous protocols for generating hPSC-CMs have been described. However, it is currently not possible to direct differentiation to a single, homogeneous end point, and the resulting heterogeneity may be variable among laboratories, cell lines, and protocols. Consequently, the ability to assess phenotypic heterogeneity of the cell population is critical to the interpretation, repeatability, and reproduction of hPSC-CM studies. While flow cytometry is well suited for this purpose, a review of published literature reveals there is currently no consensus regarding which marker, antibody, or protocol is best suited to enable comparisons of hPSC-CM culture heterogeneity. Moreover, the lack of available experimental detail, combined with the variability in the approaches used for hPSC-CM evaluation, makes it challenging to reproduce, interpret, and compare published data. Consequently, this article calls for an alignment of the way researchers approach the routine use and documentation of the antibodies and controls used during flow cytometry-based assessment of hPSC-CM cultures. We advocate for the adoption of a "fit for purpose" validation mindset, whereby antibodies and experimental conditions are demonstrated as specific within a defined experimental design and biological context. Overall, we expect that by adhering to rigorous standards for antibody validation and use, reporting of experimental details, and presentation of data, the concepts emphasized here will promote enhanced utility and dialogue regarding hPSC-CM for a variety of research and translational applications by enabling more accurate comparisons of results among studies.
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Affiliation(s)
- Matthew Waas
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska
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31
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Fehrenbach DJ, Abais-Battad JM, Dasinger JH, Lund H, Keppel T, Zemaj J, Gundry RL, Geurts AM, Dwinell MR, Mattson DL. Abstract P164: Sexual Dimorphic Role of CD14 in Dahl SS Hypertension. Hypertension 2019. [DOI: 10.1161/hyp.74.suppl_1.p164] [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: 11/16/2022]
Abstract
Previous work has implicated the immune system in potentiating salt-sensitive (SS) hypertension and kidney damage in the Dahl SS rat model. The innate immunity protein Cluster of Differentiation 14 (CD14), normally involved in bacterial responses of macrophages, has been associated with hypertension in humans. The present study tests the hypothesis that CD14 influences the extent of high-salt diet induced renal damage and hypertension in the Dahl SS rat, by modulating activation of the innate immune system. CD14 was mutated in the Dahl SS background using CRISPR-Cas9 technology, leading to the loss of CD14 protein in peritoneal macrophages (pMacs) as evidenced by mass spectrometry-based parallel reaction monitoring. pMac stimulation
in vitro
demonstrated altered IL-1β production in CD14-/- animals. To monitor SS phenotypes
in vivo
, male and female CD14+/+ and CD14-/- animals maintained on a 0.4% NaCl diet underwent carotid catheter telemetry implantation at 7 weeks of age (n=12/14). After recovery and baseline recordings, animals were switched to a 4.0% NaCl diet for 21 days. There was no significant difference in the SS increase in blood pressure or albuminuria between genotypes of males. However, female CD14-/- animals demonstrated exacerbated salt-sensitivity of blood pressure (+45mmHg) compared to wild types (+31mmHg). To determine what may mediate this difference, immune cells were isolated from the kidneys of these animals. Accordingly, males showed no difference in immune cell infiltration; whereas, female CD14-/- animals showed an elevation in the infiltration of CD11b/c+ macrophages. To determine whether knockout of CD14 in immune cells specifically was responsible for this phenotypic difference, a lethal dose of total body irradiation (11Gy) of CD14+/+ recipient animals followed by either CD14-/- or CD14+/+ bone marrow transfer experiment was done in female animals (n=6/7). Remarkably, even though all host tissue cells were wildtype, transfer of CD14-/- bone marrow recapitulated the exacerbated SS phenotypes, including increased renal infiltration of macrophages. Together, these data demonstrate that CD14 signaling in hematopoietic cells of females modulates the full extent of the immune response and blunts SS hypertension.
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32
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Berg Luecke L, Buchberger AR, Waas M, Mahr C, Gundry RL. Abstract 246: Applying a Quantitative, Cell Surface Glycoproteomic Approach to Understanding the Role of Human Cardiac Fibroblasts in Advanced Heart Failure. Circ Res 2019. [DOI: 10.1161/res.125.suppl_1.246] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Heart Failure (HF) is a complex clinical syndrome defined by the heart’s inability to adequately perfuse the human body. The clinical progression of HF has been linked to the pathological activation of CF, which contributes to adverse remodeling and cardiac fibrosis. Previous studies have shown that unloading the failing heart
via
mechanical circulatory support devices contributes to reverse remodeling, improving both cardiac structure and function. However, despite the importance of CF in biology and disease, little is known regarding CF-specific mechanisms and functions during cardiac remodeling and reverse remodeling. Moreover, most human studies have relied on
in vitro
culture systems to investigate CF function, despite the fact that extended culturing leads to phenotypic changes in CF. Here, we apply state-of-the-art mass spectrometry approaches to discover and quantify cell surface and extracellular matrix (ECM) proteins to 1) develop an optimized CF culture system that allows for the preservation of their
in situ
phenotype and 2) study CF isolated from failing hearts, including failing hearts treated with mechanical circulatory support to identify novel targets for tracking and studying disease. To date, we have identified >600 surface
N-
glycoproteins on primary human CF (n=12), including those with known relevance to CF (
e.g.
BGN, BSG, FBN1) and those not previously described within CF (
e.g.
HHIP, NFACS, GPNMB). In CF samples that were passaged
ex vivo
, cell surface and ECM
N-
glycoproteins that are associated with a phenotype switch (
e.g.
COL5A1, ECM1, FBLN5, LAMB2) were detected and changes in their abundance correlated with increased expression of α-SMA. Our studies also identified cell surface and ECM proteins that have not been previously associated with the heart and those with known relevance to HF, cardiac remodeling and fibrosis (
e.g.
BGN, GLUT8, ITGA11). Current efforts are underway to quantify surface proteins of interest to determine how their abundance changes during reverse remodeling in the context of HF. Overall, this work allowed for the development of an optimized CF culture system and revealed new cell-type specific molecular targets to study and track reverse remodeling in the context of advanced HF.
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33
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Abstract
Porous graphitized carbon (PGC) based chromatography achieves high-resolution separation of glycan structures released from glycoproteins. This approach is especially valuable when resolving structurally similar isomers and for discovery of novel and/or sample-specific glycan structures. However, the implementation of PGC-based separations in glycomics studies has been limited because system-independent retention values have not been established to normalize technical variation. To address this limitation, this study combined the use of hydrolyzed dextran as an internal standard and Skyline software for post-acquisition normalization to reduce retention time and peak area technical variation in PGC-based glycan analyses. This approach allowed assignment of system-independent retention values that are applicable to typical PGC-based glycan separations and supported the construction of a library containing >300 PGC-separated glycan structures with normalized glucose unit (GU) retention values. To enable the automation of this normalization method, a spectral MS/MS library was developed of the dextran ladder, achieving confident discrimination against isomeric glycans. The utility of this approach is demonstrated in two ways. First, to inform the search space for bioinformatically predicted but unobserved glycan structures, predictive models for two structural modifications, core-fucosylation and bisecting GlcNAc, were developed based on the GU library. Second, the applicability of this method for the analysis of complex biological samples is evidenced by the ability to discriminate between cell culture and tissue sample types by the normalized intensity of N-glycan structures alone. Overall, the methods and data described here are expected to support the future development of more automated approaches to glycan identification and quantitation.
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Affiliation(s)
- Christopher Ashwood
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia. and ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, NSW, Australia and Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian Pratt
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Brendan X MacLean
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA and Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nicolle H Packer
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia. and ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, NSW, Australia
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34
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Abstract
Peptide cleanup is essential for the removal of contaminating substances that may be introduced during sample preparation steps in bottom-up proteomic workflows. Recent studies have described benefits of carboxylate-modified paramagnetic particles over traditional reversed-phase methods for detergent and polymer removal, but challenges with reproducibility have limited the widespread implementation of this approach among laboratories. To overcome these challenges, the current study systematically evaluated key experimental parameters regarding the use of carboxylate-modified paramagnetic particles and determined those that are critical for maximum performance and peptide recovery and those for which the protocol is tolerant to deviation. These results supported the development of a detailed, easy-to-use standard operating protocol, termed SP2, which can be applied to remove detergents and polymers from peptide samples while concentrating the sample in solvent that is directly compatible with typical LC-MS workflows. We demonstrate that SP2 can be applied to phosphopeptides and glycopeptides and that the approach is compatible with robotic liquid handling for automated sample processing. Altogether, the results of this study and accompanying detailed operating protocols for both manual and automated processing are expected to facilitate reproducible implementation of SP2 for various proteomics applications and will especially benefit core or shared resource facilities where unknown or unexpected contaminants may be particularly problematic.
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Affiliation(s)
- Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Michael Pereckas
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Christopher Ashwood
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Rebekah L. Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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35
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Fujinaka CM, Waas M, Gundry RL. Mass Spectrometry-Based Identification of Extracellular Domains of Cell Surface N-Glycoproteins: Defining the Accessible Surfaceome for Immunophenotyping Stem Cells and Their Derivatives. Methods Mol Biol 2018; 1722:57-78. [PMID: 29264798 DOI: 10.1007/978-1-4939-7553-2_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Human stem cells and their progeny are valuable for a variety of research applications and have the potential to revolutionize approaches to regenerative medicine. However, we currently have limited tools to permit live isolation of homogeneous populations of cells apt for mechanistic studies or cellular therapies. While these challenges can be overcome through the use of immunophenotyping based on accessible cell surface markers, the success of this process depends on the availability of reliable antibodies and well-characterized markers, which are lacking for most stem cell lineages. This chapter outlines an iterative process for the development of new cell surface marker barcodes for identifying and selecting stem cell derived progeny of specific cell types, subtypes, and maturation stages, where antibody-independent identification of cell surface proteins is achieved using a modern chemoproteomic approach to specifically identify N-glycoproteins localized to the cell surface. By taking advantage of a large repository of available cell surfaceome data, proteins that are unlikely to confer cell type specificity can be rapidly eliminated from consideration. Subsequently, targeted quantitation by mass spectrometry can be used to refine candidates of interest, and a bioinformatic visualization tool is key to mapping experimental data to candidate protein sequences for the purpose of epitope selection during the antibody development phase. Overall, the process of developing cell surface barcodes for immunophenotyping is iterative and can include multiple rounds of discovery, refinement, and validation depending on the phenotypic resolution required.
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Affiliation(s)
- Chelsea M Fujinaka
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA.
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Waas M, Weerasekera R, Kropp EM, Romero M, Poon E, Boheler KR, Burridge PW, Gundry RL. Abstract 346: A Standard Flow Cytometry Protocol for Assessing Human Pluripotent Stem Cell-derived Cardiomyocyte Identity by Troponin Positivity. Circ Res 2018. [DOI: 10.1161/res.123.suppl_1.346] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Directed differentiation of human pluripotent stem cells (hPSC) into cardiomyocytes (hPSC-CM) offers an inexhaustible supply of cells for basic science research and translational applications. However, despite significant advancements in defining the factors most critical for differentiation, the resulting cultures remain a heterogeneous mixture of cells. Ultimately, as heterogeneity can pose challenges to interpreting functional data, the ability to accurately and precisely assess cell identity in differentiation cultures is paramount to well-defined and reproducible studies. To date, a standardized flow cytometry protocol that is broadly accepted among laboratories has not been established for assessing cell type heterogeneity within hPSC-CM cultures, posing challenges to evaluating outcomes generated among laboratories and studies. A survey of studies published over the past seven years (1/2010-10/2017) reveals the wide range of antibodies and experimental conditions reported for flow cytometry-based assessment of hPSC-CM. Although our literature survey revealed that a preponderance of studies relied on TNNT2 as a marker of cardiomyocyte identity, TNNI3 is more specific to cardiomyocytes than TNNT2 throughout development. We applied targeted mass spectrometry to confirm the presence of TNNI3 in our hPSC-CM. We then investigated five commercially available anti-TNNI3 and three sample preparation techniques for use in the assessment of heterogeneity of hPSC-CM cultures by flow cytometry. Results demonstrate two of the five anti-TNNI3 clones appear suitable for marking hPSC-CM and reveal differential susceptibility of antibody clones to sample preparation conditions. To further test the rigor and utility of our flow cytometry protocol, it was shared with two collaborating laboratories and applied to heterogeneous mixtures of positive and negative cell types. Results from these two laboratories demonstrate the protocol successfully distinguishes positive and negative cell types similarly, despite using different cell lines and differentiation protocols. We propose a workflow for establishing the fit-for-purpose use of antibodies and a standard protocol for assessing hPSC-CM identity by troponin positivity.
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Moehring F, Waas M, Keppel TR, Rathore D, Cowie AM, Stucky CL, Gundry RL. Quantitative Top-Down Mass Spectrometry Identifies Proteoforms Differentially Released during Mechanical Stimulation of Mouse Skin. J Proteome Res 2018; 17:2635-2648. [PMID: 29925238 DOI: 10.1021/acs.jproteome.8b00109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mechanotransduction refers to the processes whereby mechanical stimuli are converted into electrochemical signals that allow for the sensation of our surrounding environment through touch. Despite its fundamental role in our daily lives, the molecular and cellular mechanisms of mechanotransduction are not yet well-defined. Previous data suggest that keratinocytes may release factors that activate or modulate cutaneous sensory neuron terminals, including small molecules, lipids, peptides, proteins, and oligosaccharides. This study presents a first step toward identifying soluble mediators of keratinocyte-sensory neuron communication by evaluating the potential for top-down mass spectrometry to identify proteoforms released during 1 min of mechanical stimulation of mouse skin from naı̈ve animals. Overall, this study identified 47 proteoforms in the secretome of mouse hind paw skin, of which 14 were differentially released during mechanical stimulation, and includes proteins with known and previously unknown relevance to mechanotransduction. Finally, this study outlines a bioinformatic workflow that merges output from two complementary analysis platforms for top-down data and demonstrates the utility of this workflow for integrating quantitative and qualitative data.
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Affiliation(s)
- Francie Moehring
- Department of Cell Biology, Neurobiology, and Anatomy , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States
| | - Matthew Waas
- Department of Biochemistry , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States
| | - Theodore R Keppel
- Department of Biochemistry , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States.,Center for Biomedical Mass Spectrometry Research , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States
| | - Deepali Rathore
- Center for Biomedical Mass Spectrometry Research , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States
| | - Ashley M Cowie
- Department of Cell Biology, Neurobiology, and Anatomy , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States
| | - Cheryl L Stucky
- Department of Cell Biology, Neurobiology, and Anatomy , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States
| | - Rebekah L Gundry
- Department of Biochemistry , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States.,Center for Biomedical Mass Spectrometry Research , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States
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Haverland NA, Waas M, Ntai I, Keppel T, Gundry RL, Kelleher NL. Cell Surface Proteomics of N-Linked Glycoproteins for Typing of Human Lymphocytes. Proteomics 2018; 17. [PMID: 28834292 DOI: 10.1002/pmic.201700156] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/27/2017] [Indexed: 11/12/2022]
Abstract
Lymphocytes are immune cells that are critical for the maintenance of adaptive immunity. Differentiation of lymphoid progenitors yields B-, T-, and NK-cell subtypes that individually correlate with specific forms of leukemia or lymphoma. Therefore, it is imperative a precise method of cell categorization is utilized to detect differences in distinct disease states present in patients. One viable means of classification involves evaluation of the cell surface proteome of lymphoid malignancies. Specifically, this manuscript details the use of an antibody independent approach known as Cell Surface Capture Technology, to assess the N-glycoproteome of four human lymphocyte cell lines. Altogether, 404 cell surface N-glycoproteins were identified as markers for specific cell types involved in lymphocytic malignancies, including 82 N-glycoproteins that had not been previously been described for B or T cells within the Cell Surface Protein Atlas. Comparative analysis, hierarchical clustering techniques, and label-free quantitation were used to reveal proteins most informative for each cell type. Undoubtedly, the characterization of the cell surface proteome of lymphoid malignancies is a first step toward improving personalized diagnosis and treatment of leukemia and lymphoma.
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Affiliation(s)
- Nicole A Haverland
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ioanna Ntai
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Theodore Keppel
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
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Haverland NA, Waas M, Ntai I, Keppel T, Gundry RL, Kelleher NL. Front Cover: Cell Surface Proteomics of N-Linked Glycoproteins for Typing of Human Lymphocytes. Proteomics 2017. [DOI: 10.1002/pmic.201770141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Kropp EM, Broniowska KA, Waas M, Nycz A, Corbett JA, Gundry RL. Cardiomyocyte Differentiation Promotes Cell Survival During Nicotinamide Phosphoribosyltransferase Inhibition Through Increased Maintenance of Cellular Energy Stores. Stem Cells Transl Med 2017; 6:1191-1201. [PMID: 28224719 PMCID: PMC5442850 DOI: 10.1002/sctm.16-0151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 10/02/2016] [Accepted: 11/07/2016] [Indexed: 12/13/2022] Open
Abstract
To address concerns regarding the tumorigenic potential of undifferentiated human pluripotent stem cells (hPSC) that may remain after in vitro differentiation and ultimately limit the broad use of hPSC‐derivatives for therapeutics, we recently described a method to selectively eliminate tumorigenic hPSC from their progeny by inhibiting nicotinamide phosphoribosyltransferase (NAMPT). Limited exposure to NAMPT inhibitors selectively removes hPSC from hPSC‐derived cardiomyocytes (hPSC‐CM) and spares a wide range of differentiated cell types; yet, it remains unclear when and how cells acquire resistance to NAMPT inhibition during differentiation. In this study, we examined the effects of NAMPT inhibition among multiple time points of cardiomyocyte differentiation. Overall, these studies show that in vitro cardiomyogenic commitment and continued culturing provides resistance to NAMPT inhibition and cell survival is associated with the ability to maintain cellular ATP pools despite depletion of NAD levels. Unlike cells at earlier stages of differentiation, day 28 hPSC‐CM can survive longer periods of NAMPT inhibition and maintain ATP generation by glycolysis and/or mitochondrial respiration. This is distinct from terminally differentiated fibroblasts, which maintain mitochondrial respiration during NAMPT inhibition. Overall, these results provide new mechanistic insight into how regulation of cellular NAD and energy pools change with hPSC‐CM differentiation and further inform how NAMPT inhibition strategies could be implemented within the context of cardiomyocyte differentiation. Stem Cells Translational Medicine2017;6:1191–1201
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Affiliation(s)
- Erin M Kropp
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | | | - Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Alyssa Nycz
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - John A Corbett
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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Mallanna SK, Waas M, Duncan SA, Gundry RL. N-glycoprotein surfaceome of human induced pluripotent stem cell derived hepatic endoderm. Proteomics 2017; 17. [PMID: 27966262 DOI: 10.1002/pmic.201600397] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/02/2016] [Accepted: 12/09/2016] [Indexed: 12/20/2022]
Abstract
Using cell surface capture technology, the cell surface N-glycoproteome of human-induced pluripotent stem cell derived hepatic endoderm cells was assessed. Altogether, 395 cell surface N-glycoproteins were identified, represented by 1273 N-glycopeptides. This study identified N-glycoproteins that are not predicted to be localized to the cell surface and provides experimental data that assist in resolving ambiguous or incorrectly annotated transmembrane topology annotations. In a proof-of-concept analysis, combining these data with other cell surface proteome datasets is useful for identifying potentially cell type and lineage restricted markers and drug targets to advance the use of stem cell technologies for mechanistic developmental studies, disease modeling, drug discovery, and regenerative medicine.
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Affiliation(s)
- Sunil K Mallanna
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA.,Present address: National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Stephen A Duncan
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
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Mallanna SK, Cayo MA, Twaroski K, Gundry RL, Duncan SA. Mapping the Cell-Surface N-Glycoproteome of Human Hepatocytes Reveals Markers for Selecting a Homogeneous Population of iPSC-Derived Hepatocytes. Stem Cell Reports 2016; 7:543-556. [PMID: 27569060 PMCID: PMC5032032 DOI: 10.1016/j.stemcr.2016.07.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [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] [Received: 05/09/2016] [Revised: 07/18/2016] [Accepted: 07/20/2016] [Indexed: 02/07/2023] Open
Abstract
When comparing hepatic phenotypes between iPSC-derived hepatocyte-like cells from different liver disease patients, cell heterogeneity can confound interpretation. We proposed that homogeneous cell populations could be generated by fluorescence-activated cell sorting (FACS). Using cell-surface capture proteomics, we identified a total of 300 glycoproteins on hepatocytes. Analyses of the expression profiles during the differentiation of iPSCs revealed that SLC10A1, CLRN3, and AADAC were highly enriched during the final stages of hepatocyte differentiation. FACS purification of hepatocyte-like cells expressing SLC10A1, CLRN3, or AADAC demonstrated enrichment of cells with hepatocyte characteristics. Moreover, transcriptome analyses revealed that cells expressing the liver gene regulatory network were enriched while cells expressing a pluripotent stem cell network were depleted. In conclusion, we report an extensive catalog of cell-surface N-linked glycoproteins expressed in primary hepatocytes and identify cell-surface proteins that facilitate the purification of homogeneous populations of iPSC-derived hepatocyte-like cells. Identified N-linked glycoproteins occupying surface of primary human hepatocytes SLC10A1, CLRN3, and AADAC are expressed on ∼25% of iPSC-derived hepatocytes FACS with these markers enriches hepatic character in iPSC-derived hepatocytes SLC10A1 sorted cells provide homogeneous populations of hepatocyte-like cells
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Affiliation(s)
- Sunil K Mallanna
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Max A Cayo
- Department of Cell Biology, Neurobiology and Anatomy, Program in Regenerative Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kirk Twaroski
- Department of Cell Biology, Neurobiology and Anatomy, Program in Regenerative Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55454, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stephen A Duncan
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA.
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Boheler KR, Gundry RL. Concise Review: Cell Surface N-Linked Glycoproteins as Potential Stem Cell Markers and Drug Targets. Stem Cells Transl Med 2016; 6:131-138. [PMID: 28170199 PMCID: PMC5442750 DOI: 10.5966/sctm.2016-0109] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 03/01/2016] [Accepted: 06/13/2016] [Indexed: 12/28/2022] Open
Abstract
Stem cells and their derivatives hold great promise to advance regenerative medicine. Critical to the progression of this field is the identification and utilization of antibody‐accessible cell‐surface proteins for immunophenotyping and cell sorting—techniques essential for assessment and isolation of defined cell populations with known functional and therapeutic properties. Beyond their utility for cell identification and selection, cell‐surface proteins are also major targets for pharmacological intervention. Although comprehensive cell‐surface protein maps are highly valuable, they have been difficult to define until recently. In this review, we discuss the application of a contemporary targeted chemoproteomic‐based technique for defining the cell‐surface proteomes of stem and progenitor cells. In applying this approach to pluripotent stem cells (PSCs), these studies have improved the biological understanding of these cells, led to the enhanced use and development of antibodies suitable for immunophenotyping and sorting, and contributed to the repurposing of existing drugs without the need for high‐throughput screening. The utility of this latter approach was first demonstrated with human PSCs (hPSCs) through the identification of small molecules that are selectively toxic to hPSCs and have the potential for eliminating confounding and tumorigenic cells in hPSC‐derived progeny destined for research and transplantation. Overall, the cutting‐edge technologies reviewed here will accelerate the development of novel cell‐surface protein targets for immunophenotyping, new reagents to improve the isolation of therapeutically qualified cells, and pharmacological studies to advance the treatment of intractable diseases amenable to cell‐replacement therapies. Stem Cells Translational Medicine2017;6:131–138
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Affiliation(s)
- Kenneth R. Boheler
- Stem Cell and Regenerative Medicine Consortium, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China
| | - Rebekah L. Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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Bausch-Fluck D, Hofmann A, Bock T, Frei AP, Cerciello F, Jacobs A, Moest H, Omasits U, Gundry RL, Yoon C, Schiess R, Schmidt A, Mirkowska P, Härtlová A, Van Eyk JE, Bourquin JP, Aebersold R, Boheler KR, Zandstra P, Wollscheid B. A mass spectrometric-derived cell surface protein atlas. PLoS One 2015; 10:e0121314. [PMID: 25894527 PMCID: PMC4404347 DOI: 10.1371/journal.pone.0121314] [Citation(s) in RCA: 264] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 01/30/2015] [Indexed: 01/08/2023] Open
Abstract
Cell surface proteins are major targets of biomedical research due to their utility as cellular markers and their extracellular accessibility for pharmacological intervention. However, information about the cell surface protein repertoire (the surfaceome) of individual cells is only sparsely available. Here, we applied the Cell Surface Capture (CSC) technology to 41 human and 31 mouse cell types to generate a mass-spectrometry derived Cell Surface Protein Atlas (CSPA) providing cellular surfaceome snapshots at high resolution. The CSPA is presented in form of an easy-to-navigate interactive database, a downloadable data matrix and with tools for targeted surfaceome rediscovery (http://wlab.ethz.ch/cspa). The cellular surfaceome snapshots of different cell types, including cancer cells, resulted in a combined dataset of 1492 human and 1296 mouse cell surface glycoproteins, providing experimental evidence for their cell surface expression on different cell types, including 136 G-protein coupled receptors and 75 membrane receptor tyrosine-protein kinases. Integrated analysis of the CSPA reveals that the concerted biological function of individual cell types is mainly guided by quantitative rather than qualitative surfaceome differences. The CSPA will be useful for the evaluation of drug targets, for the improved classification of cell types and for a better understanding of the surfaceome and its concerted biological functions in complex signaling microenvironments.
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Affiliation(s)
- Damaris Bausch-Fluck
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Health Sciences and Technology, BMPP, ETH Zurich, Zurich, Switzerland
| | - Andreas Hofmann
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Thomas Bock
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Andreas P. Frei
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ferdinando Cerciello
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Molecular Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Andrea Jacobs
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Hansjoerg Moest
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ulrich Omasits
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Health Sciences and Technology, BMPP, ETH Zurich, Zurich, Switzerland
| | - Rebekah L. Gundry
- Department of Biochemistry, Medical College of Wisconsin, Wisconsin, Milwaukee, United States of America
| | - Charles Yoon
- Institute for Biomaterials & Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Ralph Schiess
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Alexander Schmidt
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Paulina Mirkowska
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Oncology Research Laboratory, University Children Hospital Zurich, Zurich, Switzerland
| | - Anetta Härtlová
- Centre of Advanced Studies, Faculty of Military Health Sciences, University of Defense, Hradec Kralove, Czech Republic
| | - Jennifer E. Van Eyk
- Department of Medicine, Biological Chemistry and Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jean-Pierre Bourquin
- Oncology Research Laboratory, University Children Hospital Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Kenneth R. Boheler
- SCRMC, LKS Faculty of Medicine, Hong Kong University, Hong Kong, Hong Kong SAR
- Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Peter Zandstra
- Institute for Biomaterials & Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Bernd Wollscheid
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Health Sciences and Technology, BMPP, ETH Zurich, Zurich, Switzerland
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Kropp EM, Bhattacharya S, Waas M, Chuppa SL, Hadjantonakis AK, Boheler KR, Gundry RL. N-glycoprotein surfaceomes of four developmentally distinct mouse cell types. Proteomics Clin Appl 2015; 8:603-9. [PMID: 24920426 DOI: 10.1002/prca.201400021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/06/2014] [Accepted: 06/06/2014] [Indexed: 11/12/2022]
Abstract
PURPOSE Detailed knowledge of cell surface proteins present during early embryonic development remains limited for most cell lineages. Due to the relevance of cell surface proteins in their functional roles controlling cell signaling and their utility as accessible, nongenetic markers for cell identification and sorting, the goal of this study was to provide new information regarding the cell surface proteins present during early mouse embryonic development. EXPERIMENTAL DESIGN Using the cell surface capture technology, the cell surface N-glycoproteomes of three cell lines and one in vitro differentiated cell type representing distinct cell fates and stages in mouse embryogenesis were assessed. RESULTS Altogether, more than 600 cell surface N-glycoproteins were identified represented by >5500 N-glycopeptides. CONCLUSIONS AND CLINICAL RELEVANCE The development of new, informative cell surface markers for the reliable identification and isolation of functionally defined subsets of cells from early developmental stages will advance the use of stem cell technologies for mechanistic developmental studies, including disease modeling and drug discovery.
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Affiliation(s)
- Erin M Kropp
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
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Olson LJ, Jensen DR, Volkman BF, Kim JJP, Peterson FC, Gundry RL, Dahms NM. Bacterial expression of the phosphodiester-binding site of the cation-independent mannose 6-phosphate receptor for crystallographic and NMR studies. Protein Expr Purif 2015; 111:91-7. [PMID: 25863146 DOI: 10.1016/j.pep.2015.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 03/30/2015] [Accepted: 04/02/2015] [Indexed: 12/21/2022]
Abstract
The cation-independent mannose 6-phosphate receptor (CI-MPR) is a multifunctional protein that interacts with diverse ligands and plays central roles in autophagy, development, and tumor suppression. By delivering newly synthesized phosphomannosyl-containing acid hydrolases from the Golgi to endosomal compartments, CI-MPR is an essential component in the generation of lysosomes that are critical for the maintenance of cellular homeostasis. The ability of CI-MPR to interact with ∼60 different acid hydrolases is facilitated by its large extracellular region, with four out of its 15 domains binding phosphomannosyl residues. Although the glycan specificity of CI-MPR has been elucidated, the molecular basis of carbohydrate binding has not been determined for two out of these four carbohydrate recognition domains (CRD). Here we report expression of CI-MPR's CRD located in domain 5 that preferentially binds phosphodiester-containing glycans. Domain 5 of CI-MPR was expressed in Escherichia coli BL21 (DE3) cells as a fusion protein containing an N-terminal histidine tag and the small ubiquitin-like modifier (SUMO) protein. The His6-SUMO-CRD construct was recovered from inclusion bodies, refolded in buffer to facilitate disulfide bond formation, and subjected to Ni-NTA affinity chromatography and size exclusion chromatography. Surface plasmon resonance analyses demonstrated that the purified protein was active and bound phosphorylated glycans. Characterization by NMR spectroscopy revealed high quality (1)H-(15)N HSQC spectra. Additionally, crystallization conditions were identified and a crystallographic data set of the CRD was collected to 1.8Å resolution. Together, these studies demonstrate the feasibility of producing CI-MPR's CRD suitable for three-dimensional structure determination by NMR spectroscopic and X-ray crystallographic approaches.
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Affiliation(s)
- Linda J Olson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, United States
| | - Davin R Jensen
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, United States
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, United States
| | - Jung-Ja P Kim
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, United States
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, United States
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, United States
| | - Nancy M Dahms
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, United States.
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47
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Kropp EM, Oleson BJ, Broniowska KA, Bhattacharya S, Chadwick AC, Diers AR, Hu Q, Sahoo D, Hogg N, Boheler KR, Corbett JA, Gundry RL. Inhibition of an NAD⁺ salvage pathway provides efficient and selective toxicity to human pluripotent stem cells. Stem Cells Transl Med 2015; 4:483-93. [PMID: 25834119 DOI: 10.5966/sctm.2014-0163] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 02/16/2015] [Indexed: 11/16/2022] Open
Abstract
The tumorigenic potential of human pluripotent stem cells (hPSCs) is a major limitation to the widespread use of hPSC derivatives in the clinic. Here, we demonstrate that the small molecule STF-31 is effective at eliminating undifferentiated hPSCs across a broad range of cell culture conditions with important advantages over previously described methods that target metabolic processes. Although STF-31 was originally described as an inhibitor of glucose transporter 1, these data support the reclassification of STF-31 as a specific NAD⁺ salvage pathway inhibitor through the inhibition of nicotinamide phosphoribosyltransferase (NAMPT). These findings demonstrate the importance of an NAD⁺ salvage pathway in hPSC biology and describe how inhibition of NAMPT can effectively eliminate hPSCs from culture. These results will advance and accelerate the development of safe, clinically relevant hPSC-derived cell-based therapies.
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Affiliation(s)
- Erin M Kropp
- Department of Biochemistry, Department of Biophysics, Redox Biology Program, and Department of Medicine, Division of Endocrinology, Metabolism and Clinical Nutrition, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Physiology, Stem Cell and Regenerative Medicine Consortium, Li Ka Shing Faculty of Medicine, Hong Kong University, Hong Kong, Special Administrative Region of the People's Republic of China; Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Bryndon J Oleson
- Department of Biochemistry, Department of Biophysics, Redox Biology Program, and Department of Medicine, Division of Endocrinology, Metabolism and Clinical Nutrition, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Physiology, Stem Cell and Regenerative Medicine Consortium, Li Ka Shing Faculty of Medicine, Hong Kong University, Hong Kong, Special Administrative Region of the People's Republic of China; Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Katarzyna A Broniowska
- Department of Biochemistry, Department of Biophysics, Redox Biology Program, and Department of Medicine, Division of Endocrinology, Metabolism and Clinical Nutrition, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Physiology, Stem Cell and Regenerative Medicine Consortium, Li Ka Shing Faculty of Medicine, Hong Kong University, Hong Kong, Special Administrative Region of the People's Republic of China; Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Subarna Bhattacharya
- Department of Biochemistry, Department of Biophysics, Redox Biology Program, and Department of Medicine, Division of Endocrinology, Metabolism and Clinical Nutrition, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Physiology, Stem Cell and Regenerative Medicine Consortium, Li Ka Shing Faculty of Medicine, Hong Kong University, Hong Kong, Special Administrative Region of the People's Republic of China; Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alexandra C Chadwick
- Department of Biochemistry, Department of Biophysics, Redox Biology Program, and Department of Medicine, Division of Endocrinology, Metabolism and Clinical Nutrition, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Physiology, Stem Cell and Regenerative Medicine Consortium, Li Ka Shing Faculty of Medicine, Hong Kong University, Hong Kong, Special Administrative Region of the People's Republic of China; Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Anne R Diers
- Department of Biochemistry, Department of Biophysics, Redox Biology Program, and Department of Medicine, Division of Endocrinology, Metabolism and Clinical Nutrition, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Physiology, Stem Cell and Regenerative Medicine Consortium, Li Ka Shing Faculty of Medicine, Hong Kong University, Hong Kong, Special Administrative Region of the People's Republic of China; Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Qinghui Hu
- Department of Biochemistry, Department of Biophysics, Redox Biology Program, and Department of Medicine, Division of Endocrinology, Metabolism and Clinical Nutrition, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Physiology, Stem Cell and Regenerative Medicine Consortium, Li Ka Shing Faculty of Medicine, Hong Kong University, Hong Kong, Special Administrative Region of the People's Republic of China; Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daisy Sahoo
- Department of Biochemistry, Department of Biophysics, Redox Biology Program, and Department of Medicine, Division of Endocrinology, Metabolism and Clinical Nutrition, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Physiology, Stem Cell and Regenerative Medicine Consortium, Li Ka Shing Faculty of Medicine, Hong Kong University, Hong Kong, Special Administrative Region of the People's Republic of China; Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Neil Hogg
- Department of Biochemistry, Department of Biophysics, Redox Biology Program, and Department of Medicine, Division of Endocrinology, Metabolism and Clinical Nutrition, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Physiology, Stem Cell and Regenerative Medicine Consortium, Li Ka Shing Faculty of Medicine, Hong Kong University, Hong Kong, Special Administrative Region of the People's Republic of China; Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kenneth R Boheler
- Department of Biochemistry, Department of Biophysics, Redox Biology Program, and Department of Medicine, Division of Endocrinology, Metabolism and Clinical Nutrition, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Physiology, Stem Cell and Regenerative Medicine Consortium, Li Ka Shing Faculty of Medicine, Hong Kong University, Hong Kong, Special Administrative Region of the People's Republic of China; Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John A Corbett
- Department of Biochemistry, Department of Biophysics, Redox Biology Program, and Department of Medicine, Division of Endocrinology, Metabolism and Clinical Nutrition, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Physiology, Stem Cell and Regenerative Medicine Consortium, Li Ka Shing Faculty of Medicine, Hong Kong University, Hong Kong, Special Administrative Region of the People's Republic of China; Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Department of Biophysics, Redox Biology Program, and Department of Medicine, Division of Endocrinology, Metabolism and Clinical Nutrition, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Physiology, Stem Cell and Regenerative Medicine Consortium, Li Ka Shing Faculty of Medicine, Hong Kong University, Hong Kong, Special Administrative Region of the People's Republic of China; Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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48
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Thomas MA, Buelow BJ, Nevins AM, Jones SE, Peterson FC, Gundry RL, Grayson MH, Volkman BF. Structure-function analysis of CCL28 in the development of post-viral asthma. J Biol Chem 2015; 290:4528-36. [PMID: 25556652 DOI: 10.1074/jbc.m114.627786] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
CCL28 is a human chemokine constitutively expressed by epithelial cells in diverse mucosal tissues and is known to attract a variety of immune cell types including T-cell subsets and eosinophils. Elevated levels of CCL28 have been found in the airways of individuals with asthma, and previous studies have indicated that CCL28 plays a vital role in the acute development of post-viral asthma. Our study builds on this, demonstrating that CCL28 is also important in the chronic post-viral asthma phenotype. In the absence of a viral infection, we also demonstrate that CCL28 is both necessary and sufficient for induction of asthma pathology. Additionally, we present the first effort aimed at elucidating the structural features of CCL28. Chemokines are defined by a conserved tertiary structure composed of a three-stranded β-sheet and a C-terminal α-helix constrained by two disulfide bonds. In addition to the four disulfide bond-forming cysteine residues that define the traditional chemokine fold, CCL28 possesses two additional cysteine residues that form a third disulfide bond. If all disulfide bonds are disrupted, recombinant human CCL28 is no longer able to drive mouse CD4+ T-cell chemotaxis or in vivo airway hyper-reactivity, indicating that the conserved chemokine fold is necessary for its biologic activity. Due to the intimate relationship between CCL28 and asthma pathology, it is clear that CCL28 presents a novel target for the development of alternative asthma therapeutics.
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Affiliation(s)
- Monica A Thomas
- From the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226 and
| | - Becky J Buelow
- Department of Pediatrics, Section of Allergy and Immunology, Medical College of Wisconsin, Milwaukee, Milwaukee 53226
| | - Amanda M Nevins
- From the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226 and
| | - Stephanie E Jones
- Department of Pediatrics, Section of Allergy and Immunology, Medical College of Wisconsin, Milwaukee, Milwaukee 53226
| | - Francis C Peterson
- From the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226 and
| | - Rebekah L Gundry
- From the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226 and
| | - Mitchell H Grayson
- Department of Pediatrics, Section of Allergy and Immunology, Medical College of Wisconsin, Milwaukee, Milwaukee 53226
| | - Brian F Volkman
- From the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226 and
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49
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Mahr C, Gundry RL. Hold or fold--proteins in advanced heart failure and myocardial recovery. Proteomics Clin Appl 2014; 9:121-33. [PMID: 25331159 DOI: 10.1002/prca.201400100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/17/2014] [Accepted: 10/14/2014] [Indexed: 12/14/2022]
Abstract
Advanced heart failure (AHF) describes the subset of heart failure patients refractory to conventional medical therapy. For some AHF patients, the use of mechanical circulatory support (MCS) provides an intermediary "bridge" step for transplant-eligible patients or an alternative therapy for transplant-ineligible patients. Over the past 20 years, clinical observations have revealed that approximately 1% of patients with MCS undergo significant reverse remodeling to the point where the device can be explanted. Unfortunately, it is unclear why some patients experience durable, sustained myocardial remission, while others redevelop heart failure (i.e. which hearts "hold" and which hearts "fold"). In this review, we outline unmet clinical needs related to treating patients with MCS, provide an overview of protein dynamics in the reverse-remodeling process, and propose specific areas where we expect MS and proteomic analyses will have significant impact on our understanding of disease progression, molecular mechanisms of recovery, and provide new markers with prognostic value that can positively impact patient care. Complimentary perspectives are provided with the goal of making this important topic accessible and relevant to both a clinical and basic science audience, as the intersection of these disciplines is required to advance the field.
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Affiliation(s)
- Claudius Mahr
- Division of Cardiology, University of Washington, Seattle, WA, USA
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50
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Bhattacharya S, Burridge PW, Kropp EM, Chuppa SL, Kwok WM, Wu JC, Boheler KR, Gundry RL. High efficiency differentiation of human pluripotent stem cells to cardiomyocytes and characterization by flow cytometry. J Vis Exp 2014:52010. [PMID: 25286293 DOI: 10.3791/52010] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
There is an urgent need to develop approaches for repairing the damaged heart, discovering new therapeutic drugs that do not have toxic effects on the heart, and improving strategies to accurately model heart disease. The potential of exploiting human induced pluripotent stem cell (hiPSC) technology to generate cardiac muscle "in a dish" for these applications continues to generate high enthusiasm. In recent years, the ability to efficiently generate cardiomyogenic cells from human pluripotent stem cells (hPSCs) has greatly improved, offering us new opportunities to model very early stages of human cardiac development not otherwise accessible. In contrast to many previous methods, the cardiomyocyte differentiation protocol described here does not require cell aggregation or the addition of Activin A or BMP4 and robustly generates cultures of cells that are highly positive for cardiac troponin I and T (TNNI3, TNNT2), iroquois-class homeodomain protein IRX-4 (IRX4), myosin regulatory light chain 2, ventricular/cardiac muscle isoform (MLC2v) and myosin regulatory light chain 2, atrial isoform (MLC2a) by day 10 across all human embryonic stem cell (hESC) and hiPSC lines tested to date. Cells can be passaged and maintained for more than 90 days in culture. The strategy is technically simple to implement and cost-effective. Characterization of cardiomyocytes derived from pluripotent cells often includes the analysis of reference markers, both at the mRNA and protein level. For protein analysis, flow cytometry is a powerful analytical tool for assessing quality of cells in culture and determining subpopulation homogeneity. However, technical variation in sample preparation can significantly affect quality of flow cytometry data. Thus, standardization of staining protocols should facilitate comparisons among various differentiation strategies. Accordingly, optimized staining protocols for the analysis of IRX4, MLC2v, MLC2a, TNNI3, and TNNT2 by flow cytometry are described.
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Affiliation(s)
| | - Paul W Burridge
- Stanford Cardiovascular Institute, Stanford University School of Medicine
| | - Erin M Kropp
- Department of Biochemistry, Medical College of Wisconsin
| | | | - Wai-Meng Kwok
- Department of Anesthesiology, Medical College of Wisconsin
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine
| | - Kenneth R Boheler
- Stem Cell and Regenerative Medicine Consortium, LKS Faculty of Medicine, Hong Kong University; Division of Cardiology, Johns Hopkins University School of Medicine
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin; Cardiovascular Research Center, Biotechnology and Bioengineering Center, Medical College of Wisconsin;
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