1
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Billing AM, Kim YC, Gullaksen S, Schrage B, Raabe J, Hutzfeldt A, Demir F, Kovalenko E, Lassé M, Dugourd A, Fallegger R, Klampe B, Jaegers J, Li Q, Kravtsova O, Crespo-Masip M, Palermo A, Fenton RA, Hoxha E, Blankenberg S, Kirchhof P, Huber TB, Laugesen E, Zeller T, Chrysopoulou M, Saez-Rodriguez J, Magnussen C, Eschenhagen T, Staruschenko A, Siuzdak G, Poulsen PL, Schwab C, Cuello F, Vallon V, Rinschen MM. Metabolic Communication by SGLT2 Inhibition. Circulation 2024; 149:860-884. [PMID: 38152989 PMCID: PMC10922673 DOI: 10.1161/circulationaha.123.065517] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 11/22/2023] [Indexed: 12/29/2023]
Abstract
BACKGROUND SGLT2 (sodium-glucose cotransporter 2) inhibitors (SGLT2i) can protect the kidneys and heart, but the underlying mechanism remains poorly understood. METHODS To gain insights on primary effects of SGLT2i that are not confounded by pathophysiologic processes or are secondary to improvement by SGLT2i, we performed an in-depth proteomics, phosphoproteomics, and metabolomics analysis by integrating signatures from multiple metabolic organs and body fluids after 1 week of SGLT2i treatment of nondiabetic as well as diabetic mice with early and uncomplicated hyperglycemia. RESULTS Kidneys of nondiabetic mice reacted most strongly to SGLT2i in terms of proteomic reconfiguration, including evidence for less early proximal tubule glucotoxicity and a broad downregulation of the apical uptake transport machinery (including sodium, glucose, urate, purine bases, and amino acids), supported by mouse and human SGLT2 interactome studies. SGLT2i affected heart and liver signaling, but more reactive organs included the white adipose tissue, showing more lipolysis, and, particularly, the gut microbiome, with a lower relative abundance of bacteria taxa capable of fermenting phenylalanine and tryptophan to cardiovascular uremic toxins, resulting in lower plasma levels of these compounds (including p-cresol sulfate). SGLT2i was detectable in murine stool samples and its addition to human stool microbiota fermentation recapitulated some murine microbiome findings, suggesting direct inhibition of fermentation of aromatic amino acids and tryptophan. In mice lacking SGLT2 and in patients with decompensated heart failure or diabetes, the SGLT2i likewise reduced circulating p-cresol sulfate, and p-cresol impaired contractility and rhythm in human induced pluripotent stem cell-derived engineered heart tissue. CONCLUSIONS SGLT2i reduced microbiome formation of uremic toxins such as p-cresol sulfate and thereby their body exposure and need for renal detoxification, which, combined with direct kidney effects of SGLT2i, including less proximal tubule glucotoxicity and a broad downregulation of apical transporters (including sodium, amino acid, and urate uptake), provides a metabolic foundation for kidney and cardiovascular protection.
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Affiliation(s)
- Anja M. Billing
- Departments of Biomedicine (A.M.B., F.D., E.K., J.J., R.A.F., M.C., M.M.R.), Aarhus University, Denmark
| | - Young Chul Kim
- Departments of Medicine and Pharmacology, University of California San Diego, La Jolla (Y.C.K., M.C.-M., V.V.)
- VA San Diego Healthcare System, CA (Y.C.K., M.C.-M., V.V.)
| | - Søren Gullaksen
- Clinical Medicine (S.G., P.L.P.), Aarhus University, Denmark
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Denmark (S.G., E.L.)
| | - Benedikt Schrage
- Department of Cardiology, University Heart and Vascular Center Hamburg, Germany (B.S., S.B., P.K., T.Z., C.M.)
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany (B.S., J.R., S.B., P.K., T.Z., C.M., T.E., F.C.)
| | - Janice Raabe
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany (B.S., J.R., S.B., P.K., T.Z., C.M., T.E., F.C.)
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany (J.R., B.K., T.E., F.C.)
| | - Arvid Hutzfeldt
- III Department of Medicine and Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany (A.H., M.L., E.H., T.B.H., M.M.R.)
| | - Fatih Demir
- Departments of Biomedicine (A.M.B., F.D., E.K., J.J., R.A.F., M.C., M.M.R.), Aarhus University, Denmark
| | - Elina Kovalenko
- Departments of Biomedicine (A.M.B., F.D., E.K., J.J., R.A.F., M.C., M.M.R.), Aarhus University, Denmark
| | - Moritz Lassé
- III Department of Medicine and Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany (A.H., M.L., E.H., T.B.H., M.M.R.)
| | - Aurelien Dugourd
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg, Germany (A.D., R.F., J.S.-R.)
| | - Robin Fallegger
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg, Germany (A.D., R.F., J.S.-R.)
| | - Birgit Klampe
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany (J.R., B.K., T.E., F.C.)
| | - Johannes Jaegers
- Departments of Biomedicine (A.M.B., F.D., E.K., J.J., R.A.F., M.C., M.M.R.), Aarhus University, Denmark
| | - Qing Li
- Engineering (Q.L., C.S.), Aarhus University, Denmark
| | - Olha Kravtsova
- Departments of Biomedicine (A.M.B., F.D., E.K., J.J., R.A.F., M.C., M.M.R.), Aarhus University, Denmark
| | - Maria Crespo-Masip
- Departments of Medicine and Pharmacology, University of California San Diego, La Jolla (Y.C.K., M.C.-M., V.V.)
- VA San Diego Healthcare System, CA (Y.C.K., M.C.-M., V.V.)
| | - Amelia Palermo
- Scripps Research, Center for Metabolomics, San Diego, CA (A.P., G.S., M.M.R.)
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles (A.P.)
| | - Robert A. Fenton
- Departments of Biomedicine (A.M.B., F.D., E.K., J.J., R.A.F., M.C., M.M.R.), Aarhus University, Denmark
| | - Elion Hoxha
- III Department of Medicine and Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany (A.H., M.L., E.H., T.B.H., M.M.R.)
| | - Stefan Blankenberg
- Department of Cardiology, University Heart and Vascular Center Hamburg, Germany (B.S., S.B., P.K., T.Z., C.M.)
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany (B.S., J.R., S.B., P.K., T.Z., C.M., T.E., F.C.)
| | - Paulus Kirchhof
- Department of Cardiology, University Heart and Vascular Center Hamburg, Germany (B.S., S.B., P.K., T.Z., C.M.)
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany (B.S., J.R., S.B., P.K., T.Z., C.M., T.E., F.C.)
- Institute of Cardiovascular Sciences, University of Birmingham, United Kingdom (P.K.)
| | - Tobias B. Huber
- III Department of Medicine and Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany (A.H., M.L., E.H., T.B.H., M.M.R.)
| | - Esben Laugesen
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Denmark (S.G., E.L.)
- Diagnostic Centre, Silkeborg Regional Hospital, Denmark (E.L.)
| | - Tanja Zeller
- Department of Cardiology, University Heart and Vascular Center Hamburg, Germany (B.S., S.B., P.K., T.Z., C.M.)
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany (B.S., J.R., S.B., P.K., T.Z., C.M., T.E., F.C.)
| | - Maria Chrysopoulou
- Departments of Biomedicine (A.M.B., F.D., E.K., J.J., R.A.F., M.C., M.M.R.), Aarhus University, Denmark
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg, Germany (A.D., R.F., J.S.-R.)
| | - Christina Magnussen
- Department of Cardiology, University Heart and Vascular Center Hamburg, Germany (B.S., S.B., P.K., T.Z., C.M.)
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany (B.S., J.R., S.B., P.K., T.Z., C.M., T.E., F.C.)
| | - Thomas Eschenhagen
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany (B.S., J.R., S.B., P.K., T.Z., C.M., T.E., F.C.)
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany (J.R., B.K., T.E., F.C.)
| | - Alexander Staruschenko
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa (O.K., A.S.)
| | - Gary Siuzdak
- Scripps Research, Center for Metabolomics, San Diego, CA (A.P., G.S., M.M.R.)
| | - Per L. Poulsen
- Clinical Medicine (S.G., P.L.P.), Aarhus University, Denmark
- Steno Diabetes Center (P.L.P.), Aarhus University, Denmark
| | | | - Friederike Cuello
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany (B.S., J.R., S.B., P.K., T.Z., C.M., T.E., F.C.)
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany (J.R., B.K., T.E., F.C.)
| | - Volker Vallon
- Departments of Medicine and Pharmacology, University of California San Diego, La Jolla (Y.C.K., M.C.-M., V.V.)
- VA San Diego Healthcare System, CA (Y.C.K., M.C.-M., V.V.)
| | - Markus M. Rinschen
- Departments of Biomedicine (A.M.B., F.D., E.K., J.J., R.A.F., M.C., M.M.R.), Aarhus University, Denmark
- Aarhus Institute of Advanced Studies (M.M.R.), Aarhus University, Denmark
- III Department of Medicine and Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany (A.H., M.L., E.H., T.B.H., M.M.R.)
- Scripps Research, Center for Metabolomics, San Diego, CA (A.P., G.S., M.M.R.)
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2
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Lassé M, El Saghir J, Berthier CC, Eddy S, Fischer M, Laufer SD, Kylies D, Hutzfeldt A, Bonin LL, Dumoulin B, Menon R, Vega-Warner V, Eichinger F, Alakwaa F, Fermin D, Billing AM, Minakawa A, McCown PJ, Rose MP, Godfrey B, Meister E, Wiech T, Noriega M, Chrysopoulou M, Brandts P, Ju W, Reinhard L, Hoxha E, Grahammer F, Lindenmeyer MT, Huber TB, Schlüter H, Thiel S, Mariani LH, Puelles VG, Braun F, Kretzler M, Demir F, Harder JL, Rinschen MM. An integrated organoid omics map extends modeling potential of kidney disease. Nat Commun 2023; 14:4903. [PMID: 37580326 PMCID: PMC10425428 DOI: 10.1038/s41467-023-39740-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 06/27/2023] [Indexed: 08/16/2023] Open
Abstract
Kidney organoids are a promising model to study kidney disease, but their use is constrained by limited knowledge of their functional protein expression profile. Here, we define the organoid proteome and transcriptome trajectories over culture duration and upon exposure to TNFα, a cytokine stressor. Older organoids increase deposition of extracellular matrix but decrease expression of glomerular proteins. Single cell transcriptome integration reveals that most proteome changes localize to podocytes, tubular and stromal cells. TNFα treatment of organoids results in 322 differentially expressed proteins, including cytokines and complement components. Transcript expression of these 322 proteins is significantly higher in individuals with poorer clinical outcomes in proteinuric kidney disease. Key TNFα-associated protein (C3 and VCAM1) expression is increased in both human tubular and organoid kidney cell populations, highlighting the potential for organoids to advance biomarker development. By integrating kidney organoid omic layers, incorporating a disease-relevant cytokine stressor and comparing with human data, we provide crucial evidence for the functional relevance of the kidney organoid model to human kidney disease.
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Affiliation(s)
- Moritz Lassé
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jamal El Saghir
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Celine C Berthier
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Sean Eddy
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Matthew Fischer
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Sandra D Laufer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dominik Kylies
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Arvid Hutzfeldt
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Bernhard Dumoulin
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Virginia Vega-Warner
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Felix Eichinger
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Fadhl Alakwaa
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Damian Fermin
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Anja M Billing
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Akihiro Minakawa
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Phillip J McCown
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Michael P Rose
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Bradley Godfrey
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Elisabeth Meister
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Wiech
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pathology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Mercedes Noriega
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pathology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | | | - Paul Brandts
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Wenjun Ju
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Linda Reinhard
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Elion Hoxha
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Florian Grahammer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maja T Lindenmeyer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Steffen Thiel
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Laura H Mariani
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Victor G Puelles
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Fabian Braun
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Kretzler
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Fatih Demir
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jennifer L Harder
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA.
| | - Markus M Rinschen
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
- Aarhus Institute of Advanced Studies (AIAS), Aarhus, Denmark.
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3
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Bubis JA, Gorshkov V, Billing AM, Kjeldsen F. HUMOS: How to Understand My Orbitrap Spectrum?-An Interactive Web-Based Tool to Teach the Basics of Mass-Spectrometry-Based Proteomics. J Proteome Res 2020; 19:3910-3918. [PMID: 32813527 DOI: 10.1021/acs.jproteome.0c00395] [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: 11/29/2022]
Abstract
The Orbitrap mass analyzer can provide high mass accuracy and throughput, which has significantly improved proteome research and made this type of instrumentation one of the most frequently applied in proteomics. The efficient use of Orbitrap mass spectrometers requires training. Students in the field of proteomics can benefit from a deeper understanding of the Orbitrap technology to comprehend mass spectral interpretation, troubleshooting, and judgment of experimental settings. Unfortunately, the cost of high-end mass spectrometers limits the implementation of this type of equipment in educational laboratories. Guided by these concerns, we developed an eLearning web application called HUMOS aimed to help teach Orbitrap mass spectrometry. Although a typical proteomics experiment includes the use of several different technologies, such as liquid chromatography, mass spectrometry, and bioinformatics, the learning objectives of HUMOS are focused on mass spectrometry. HUMOS models a mass spectrum of a peptide mixture, allowing us to investigate the influence of mass spectral acquisition parameters. By changing the parameters and observing the differences, students can learn more about the mass spectral resolution, duty cycle, throughput of the analysis, ion accumulation, and spectral dynamic range and get familiar with advanced spectral acquisition methods, such as BoxCar. HUMOS is an open-source software published under the Apache license; the live installation is available at http://humos.bmb.sdu.dk.
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Affiliation(s)
- Julia A Bubis
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia.,Moscow Institute of Physics and Technology (State University), 141700 Dolgoprudny, Russia.,Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Vladimir Gorshkov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Anja M Billing
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Frank Kjeldsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
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4
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Billing AM, Knudsen KB, Chetwynd AJ, Ellis LJA, Tang SVY, Berthing T, Wallin H, Lynch I, Vogel U, Kjeldsen F. Fast and Robust Proteome Screening Platform Identifies Neutrophil Extracellular Trap Formation in the Lung in Response to Cobalt Ferrite Nanoparticles. ACS Nano 2020; 14:4096-4110. [PMID: 32167280 PMCID: PMC7498156 DOI: 10.1021/acsnano.9b08818] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/13/2020] [Indexed: 05/28/2023]
Abstract
Despite broad application of magnetic nanoparticles in biomedicine and electronics, only a few in vivo studies on biocompatibility are available. In this study, toxicity of magnetic metal oxide nanoparticles on the respiratory system was examined in vivo by single intratracheal instillation in mice. Bronchoalveolar lavage fluid (BALF) samples were collected for proteome analyses by LC-MS/MS, testing Fe3O4 nanoparticles doped with increasing amounts of cobalt (Fe3O4, CoFe2O4 with an iron to cobalt ratio 5:1, 3:1, 1:3, Co3O4) at two doses (54 μg, 162 μg per animal) and two time points (day 1 and 3 days postinstillation). In discovery phase, in-depth proteome profiling of a few representative samples allowed for comprehensive pathway analyses. Clustering of the 681 differentially expressed proteins (FDR < 0.05) revealed general as well as metal oxide specific responses with an overall strong induction of innate immunity and activation of the complement system. The highest expression increase could be found for a cluster of 39 proteins, which displayed strong dose-dependency to iron oxide and can be attributed to neutrophil extracellular trap (NET) formation. In-depth proteome analysis expanded the knowledge of in vivo NET formation. During screening, all BALF samples of the study (n = 166) were measured label-free as single-injections after a short gradient (21 min) LC separation using the Evosep One system, validating the findings from the discovery and defining protein signatures which enable discrimination of lung inflammation. We demonstrate a proteomics-based toxicity screening with high sample throughput easily transferrable to other nanoparticle types. Data are available via ProteomeXchange with identifier PXD016148.
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Affiliation(s)
- Anja M. Billing
- Department
of Biochemistry and Molecular Biology, University
of Southern Denmark, Odense 5230, Denmark
| | - Kristina B. Knudsen
- National
Research Centre for the Working Environment, Copenhagen 2100, Denmark
| | - Andrew J. Chetwynd
- School
of Geography Earth and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, United Kingdom
| | - Laura-Jayne A. Ellis
- School
of Geography Earth and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, United Kingdom
| | | | - Trine Berthing
- National
Research Centre for the Working Environment, Copenhagen 2100, Denmark
| | - Håkan Wallin
- National
Research Centre for the Working Environment, Copenhagen 2100, Denmark
| | - Iseult Lynch
- School
of Geography Earth and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, United Kingdom
| | - Ulla Vogel
- National
Research Centre for the Working Environment, Copenhagen 2100, Denmark
- Department
of Health Technology, Technical University
of Denmark, Lyngby 2800, Denmark
| | - Frank Kjeldsen
- Department
of Biochemistry and Molecular Biology, University
of Southern Denmark, Odense 5230, Denmark
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5
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Billing AM, Dib SS, Bhagwat AM, da Silva IT, Drummond RD, Hayat S, Al-Mismar R, Ben-Hamidane H, Goswami N, Engholm-Keller K, Larsen MR, Suhre K, Rafii A, Graumann J. A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells. Mol Cell Proteomics 2019; 18:1950-1966. [PMID: 31332097 PMCID: PMC6773553 DOI: 10.1074/mcp.ra119.001356] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 07/12/2019] [Indexed: 12/22/2022] Open
Abstract
Mesenchymal stem/stromal cells (MSCs) are self-renewing multipotent cells with regenerative, secretory and immunomodulatory capabilities that are beneficial for the treatment of various diseases. To avoid the issues that come with using tissue-derived MSCs in therapy, MSCs may be generated by the differentiation of human embryonic stems cells (hESCs) in culture. However, the changes that occur during the differentiation process have not been comprehensively characterized. Here, we combined transcriptome, proteome and phosphoproteome profiling to perform an in-depth, multi-omics study of the hESCs-to-MSCs differentiation process. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation. Among the earliest and strongest induced proteins with extensive differential phosphorylation was AHNAK, which we hypothesized to be a defining factor in MSC biology. We observed two distinct expression waves of developmental HOX genes and an AGO2-to-AGO3 switch in gene silencing. Exploring the kinetic of noncoding ORFs during differentiation, we mapped new functions to well annotated long noncoding RNAs (CARMN, MALAT, NEAT1, LINC00152) as well as new candidates which we identified to be important to the differentiation process. Phosphoproteome analysis revealed ESC and MSC-specific phosphorylation motifs with PAK2 and RAF1 as top predicted upstream kinases in MSCs. Our data represent a rich systems-level resource on ESC-to-MSC differentiation that will be useful for the study of stem cell biology.
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Affiliation(s)
- Anja M Billing
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar.
| | - Shaima S Dib
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Aditya M Bhagwat
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Israel T da Silva
- Laboratory of Bioinformatics and Computational Biology, A. C., Camargo Cancer Center, São Paulo 01508-010, Brazil; Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065
| | - Rodrigo D Drummond
- Laboratory of Bioinformatics and Computational Biology, A. C., Camargo Cancer Center, São Paulo 01508-010, Brazil
| | - Shahina Hayat
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Rasha Al-Mismar
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Hisham Ben-Hamidane
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Neha Goswami
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Kasper Engholm-Keller
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark; Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Karsten Suhre
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Arash Rafii
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar; Department of Gynecology and Obstetrics, Hôpital Foch, 92100 Suresnes, France
| | - Johannes Graumann
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar.
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6
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Silva CNS, McFarlane SE, Hagen IJ, Rönnegård L, Billing AM, Kvalnes T, Kemppainen P, Rønning B, Ringsby TH, Sæther BE, Qvarnström A, Ellegren H, Jensen H, Husby A. Insights into the genetic architecture of morphological traits in two passerine bird species. Heredity (Edinb) 2017; 119:197-205. [PMID: 28613280 DOI: 10.1038/hdy.2017.29] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 04/08/2017] [Accepted: 05/04/2017] [Indexed: 01/15/2023] Open
Abstract
Knowledge about the underlying genetic architecture of phenotypic traits is needed to understand and predict evolutionary dynamics. The number of causal loci, magnitude of the effects and location in the genome are, however, still largely unknown. Here, we use genome-wide single-nucleotide polymorphism (SNP) data from two large-scale data sets on house sparrows and collared flycatchers to examine the genetic architecture of different morphological traits (tarsus length, wing length, body mass, bill depth, bill length, total and visible badge size and white wing patches). Genomic heritabilities were estimated using relatedness calculated from SNPs. The proportion of variance captured by the SNPs (SNP-based heritability) was lower in house sparrows compared with collared flycatchers, as expected given marker density (6348 SNPs in house sparrows versus 38 689 SNPs in collared flycatchers). Indeed, after downsampling to similar SNP density and sample size, this estimate was no longer markedly different between species. Chromosome-partitioning analyses demonstrated that the proportion of variance explained by each chromosome was significantly positively related to the chromosome size for some traits and, generally, that larger chromosomes tended to explain proportionally more variation than smaller chromosomes. Finally, we found two genome-wide significant associations with very small-effect sizes. One SNP on chromosome 20 was associated with bill length in house sparrows and explained 1.2% of phenotypic variation (VP), and one SNP on chromosome 4 was associated with tarsus length in collared flycatchers (3% of VP). Although we cannot exclude the possibility of undetected large-effect loci, our results indicate a polygenic basis for morphological traits.
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Affiliation(s)
- C N S Silva
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, Helsinki, Finland
| | - S E McFarlane
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - I J Hagen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - L Rönnegård
- School of Technology and Business Studies, Dalarna University, Falun, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - A M Billing
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - T Kvalnes
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - P Kemppainen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - B Rønning
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - T H Ringsby
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - B-E Sæther
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - A Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - H Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - H Jensen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - A Husby
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, Helsinki, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
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7
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Billing AM, Ben Hamidane H, Bhagwat AM, Cotton RJ, Dib SS, Kumar P, Hayat S, Goswami N, Suhre K, Rafii A, Graumann J. Complementarity of SOMAscan to LC-MS/MS and RNA-seq for quantitative profiling of human embryonic and mesenchymal stem cells. J Proteomics 2016; 150:86-97. [PMID: 27613379 DOI: 10.1016/j.jprot.2016.08.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [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: 06/07/2016] [Revised: 08/01/2016] [Accepted: 08/29/2016] [Indexed: 11/16/2022]
Abstract
Dynamic range limitations are challenging to proteomics, particularly in clinical samples. Affinity proteomics partially overcomes this, yet suffers from dependence on reagent quality. SOMAscan, an aptamer-based platform for over 1000 proteins, avoids that issue using nucleic acid binders. Targets include low expressed proteins not easily accessible by other approaches. Here we report on the potential of SOMAscan for the study of differently sourced mesenchymal stem cells (MSC) in comparison to LC-MS/MS and RNA sequencing. While targeting fewer analytes, SOMAscan displays high precision and dynamic range coverage, allowing quantification of proteins not measured by the other platforms. Expression between cell types (ESC and MSC) was compared across techniques and uncovered the expected large differences. Sourcing was investigated by comparing subtypes: bone marrow-derived, standard in clinical studies, and ESC-derived MSC, thought to hold similar potential but devoid of inter-donor variability and proliferating faster in vitro. We confirmed subtype-equivalency, as well as vesicle and extracellular matrix related processes in MSC. In contrast, the proliferative nature of ESC was captured less by SOMAscan, where nuclear proteins are underrepresented. The complementary of SOMAscan allowed the comprehensive exploration of CD markers and signaling molecules, not readily accessible otherwise and offering unprecedented potential in subtype characterization. SIGNIFICANCE Mesenchymal stem cells (MSC) represent promising stem cell-derived therapeutics as indicated by their application in >500 clinical trials currently registered with the NIH. Tissue-derived MSC require invasive harvesting and imply donor-to-donor differences, to which embryonic stem cell (ESC)-derived MSC may provide an alternative and thus warrant thorough characterization. In continuation of our previous study where we compared in depth embryonic stem cells (ESC) and MSC from two sources (bone marrow and ESC-derived), we included the aptamer-based SOMAscan assay, complementing LC-MS/MS and RNA-seq data. Furthermore, SOMAscan, a targeted proteomics platform developed for analyzing clinical samples, has been benchmarked against established analytical platforms (LC-MS/MS and RNA-seq) using stem cell comparisons as a model.
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Affiliation(s)
- Anja M Billing
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | | | - Aditya M Bhagwat
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Richard J Cotton
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Shaima S Dib
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Pankaj Kumar
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Shahina Hayat
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Neha Goswami
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Karsten Suhre
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Arash Rafii
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Johannes Graumann
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
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Abdesselem H, Madani A, Hani A, Al-Noubi M, Goswami N, Ben Hamidane H, Billing AM, Pasquier J, Bonkowski MS, Halabi N, Dalloul R, Sheriff MZ, Mesaeli N, ElRayess M, Sinclair DA, Graumann J, Mazloum NA. SIRT1 Limits Adipocyte Hyperplasia through c-Myc Inhibition. J Biol Chem 2015; 291:2119-35. [PMID: 26655722 PMCID: PMC4732199 DOI: 10.1074/jbc.m115.675645] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [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: 06/30/2015] [Indexed: 01/14/2023] Open
Abstract
The expansion of fat mass in the obese state is due to increased adipocyte hypertrophy and hyperplasia. The molecular mechanism that drives adipocyte hyperplasia remains unknown. The NAD(+)-dependent protein deacetylase sirtuin 1 (SIRT1), a key regulator of mammalian metabolism, maintains proper metabolic functions in many tissues, counteracting obesity. Here we report that differentiated adipocytes are hyperplastic when SIRT1 is knocked down stably in mouse 3T3-L1 preadipocytes. This phenotype is associated with dysregulated adipocyte metabolism and enhanced inflammation. We also demonstrate that SIRT1 is a key regulator of proliferation in preadipocytes. Quantitative proteomics reveal that the c-Myc pathway is altered to drive enhanced proliferation in SIRT1-silenced 3T3-L1 cells. Moreover, c-Myc is hyperacetylated, levels of p27 are reduced, and cyclin-dependent kinase 2 (CDK2) is activated upon SIRT1 reduction. Remarkably, differentiating SIRT1-silenced preadipocytes exhibit enhanced mitotic clonal expansion accompanied by reduced levels of p27 as well as elevated levels of CCAAT/enhancer-binding protein β (C/EBPβ) and c-Myc, which is also hyperacetylated. c-Myc activation and enhanced proliferation phenotype are also found to be SIRT1-dependent in proliferating mouse embryonic fibroblasts and differentiating human SW872 preadipocytes. Reducing both SIRT1 and c-Myc expression in 3T3-L1 cells simultaneously does not induce the adipocyte hyperplasia phenotype, confirming that SIRT1 controls adipocyte hyperplasia through c-Myc regulation. A better understanding of the molecular mechanisms of adipocyte hyperplasia will open new avenues toward understanding obesity.
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Affiliation(s)
| | - Aisha Madani
- From the Departments of Microbiology and Immunology
| | - Ahmad Hani
- From the Departments of Microbiology and Immunology
| | | | | | | | | | - Jennifer Pasquier
- Genetic Medicine, Weill Cornell Medicine Qatar, Qatar Foundation, Education City, P.O. Box 24144, Doha, Qatar
| | - Michael S Bonkowski
- the Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, and
| | - Najeeb Halabi
- Genetic Medicine, Weill Cornell Medicine Qatar, Qatar Foundation, Education City, P.O. Box 24144, Doha, Qatar
| | | | | | | | - Mohamed ElRayess
- the Life Sciences Research Division, Anti-Doping Lab Qatar, P.O. Box 27775, Doha, Qatar
| | - David A Sinclair
- the Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, and
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9
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Billing AM, Ben Hamidane H, Graumann J. Quantitative Proteomic Approaches in Mouse: Stable Isotope Incorporation by Metabolic (SILAC) or Chemical Labeling (Reductive Dimethylation) Combined with High-Resolution Mass Spectrometry. ACTA ACUST UNITED AC 2015; 5:1-20. [DOI: 10.1002/9780470942390.mo140156] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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10
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Blanc V, Park E, Schaefer S, Miller M, Lin Y, Kennedy S, Billing AM, Ben Hamidane H, Graumann J, Mortazavi A, Nadeau JH, Davidson NO. Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver. Genome Biol 2014; 15:R79. [PMID: 24946870 PMCID: PMC4197816 DOI: 10.1186/gb-2014-15-6-r79] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 06/19/2014] [Indexed: 01/10/2023] Open
Abstract
Background RNA editing encompasses a post-transcriptional process in which the genomically templated sequence is enzymatically altered and introduces a modified base into the edited transcript. Mammalian C-to-U RNA editing represents a distinct subtype of base modification, whose prototype is intestinal apolipoprotein B mRNA, mediated by the catalytic deaminase Apobec-1. However, the genome-wide identification, tissue-specificity and functional implications of Apobec-1-mediated C-to-U RNA editing remain incompletely explored. Results Deep sequencing, data filtering and Sanger-sequence validation of intestinal and hepatic RNA from wild-type and Apobec-1-deficient mice revealed 56 novel editing sites in 54 intestinal mRNAs and 22 novel sites in 17 liver mRNAs, all within 3′ untranslated regions. Eleven of 17 liver RNAs shared editing sites with intestinal RNAs, while 6 sites are unique to liver. Changes in RNA editing lead to corresponding changes in intestinal mRNA and protein levels for 11 genes. Analysis of RNA editing in vivo following tissue-specific Apobec-1 adenoviral or transgenic Apobec-1 overexpression reveals that a subset of targets identified in wild-type mice are restored in Apobec-1-deficient mouse intestine and liver following Apobec-1 rescue. We find distinctive polysome profiles for several RNA editing targets and demonstrate novel exonic editing sites in nuclear preparations from intestine but not hepatic apolipoprotein B RNA. RNA editing is validated using cell-free extracts from wild-type but not Apobec-1-deficient mice, demonstrating that Apobec-1 is required. Conclusions These studies define selective, tissue-specific targets of Apobec-1-dependent RNA editing and show the functional consequences of editing are both transcript- and tissue-specific.
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11
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Billing AM, Kessler JR, Revets D, Sausy A, Schmitz S, Barra C, Muller CP. Proteome profiling of virus-host interactions of wild type and attenuated measles virus strains. J Proteomics 2014; 108:325-36. [PMID: 24914991 DOI: 10.1016/j.jprot.2014.05.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 05/12/2014] [Accepted: 05/14/2014] [Indexed: 11/18/2022]
Abstract
UNLABELLED Quantitative gel-based proteomics (2D DIGE coupled to MALDI-TOF/TOF MS) has been used to investigate the effects of different measles virus (MV) strains on the host cell proteome. A549/hSLAM cells were infected either with wild type MV strains, an attenuated vaccine or a multiple passaged Vero cell adapted strain. By including interferon beta treatment as a control it was possible to distinguish between the classical antiviral response and changes induced specifically by the different strains. Of 38 differentially expressed proteins in total (p-value ≤0.05, fold change ≥2), 18 proteins were uniquely modulated following MV infection with up to 9 proteins specific per individual strain. Interestingly, wt strains displayed distinct protein patterns particularly during the late phase of infection. Proteins were grouped into cytoskeleton, metabolism, transcription/translation, immune response and mitochondrial proteins. Bioinformatics analysis revealed mostly changes in proteins regulating cell death and apoptosis. Surprisingly, wt strains affected the cytokeratin system much stronger than the vaccine strain. To our knowledge, this is the first study on the MV-host proteome addressing interstrain differences. BIOLOGICAL SIGNIFICANCE In the present study we investigated the host cell proteome upon measles virus (MV) infection. The novelty about this study is the side-by side comparison of different strains from the same virus, which has not been done at the proteome level for any other virus including MV. We used different virus strains including a vaccine strain, wild type isolates derived from MV-infected patients as well as a Vero cell adapted strain, which serves as an intermediate between vaccine and wild type strain. We observed differences between vaccine and wild type strains as well as common features between different wild type strains. Perhaps one of the most surprising findings was that differences did not only occur between wild type and vaccine or Vero cell adapted strains but also between different wild type strains. In fact our study suggests that besides the cytokeratin and the IFN system wild type viruses seem to differ as much among each other than from vaccine strains. Thus our results are suggestive of complex and diverse virus-host interactions which differ considerably between different wild type strains. Our data indicate that interstrain differences are prominent and have so far been neglected by proteomics studies.
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Affiliation(s)
- Anja M Billing
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, 20A rue Auguste Lumière, L-1950 Luxembourg, Luxembourg
| | - Julia R Kessler
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, 20A rue Auguste Lumière, L-1950 Luxembourg, Luxembourg
| | - Dominique Revets
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, 20A rue Auguste Lumière, L-1950 Luxembourg, Luxembourg
| | - Aurélie Sausy
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, 20A rue Auguste Lumière, L-1950 Luxembourg, Luxembourg
| | - Stephanie Schmitz
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, 20A rue Auguste Lumière, L-1950 Luxembourg, Luxembourg
| | - Claire Barra
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, 20A rue Auguste Lumière, L-1950 Luxembourg, Luxembourg
| | - Claude P Muller
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, 20A rue Auguste Lumière, L-1950 Luxembourg, Luxembourg.
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12
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Liberski AR, Al-Noubi MN, Rahman ZH, Halabi NM, Dib SS, Al-Mismar R, Billing AM, Krishnankutty R, Ahmad FS, Raynaud CM, Rafii A, Engholm-Keller K, Graumann J. Adaptation of a commonly used, chemically defined medium for human embryonic stem cells to stable isotope labeling with amino acids in cell culture. J Proteome Res 2013; 12:3233-45. [PMID: 23734825 DOI: 10.1021/pr400099j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metabolic labeling with stable isotopes is a prominent technique for comparative quantitative proteomics, and stable isotope labeling with amino acids in cell culture (SILAC) is the most commonly used approach. SILAC is, however, traditionally limited to simple tissue culture regimens and only rarely employed in the context of complex culturing conditions as those required for human embryonic stem cells (hESCs). Classic hESC culture is based on the use of mouse embryonic fibroblasts (MEFs) as a feeder layer, and as a result, possible xenogeneic contamination, contribution of unlabeled amino acids by the feeders, interlaboratory variability of MEF preparation, and the overall complexity of the culture system are all of concern in conjunction with SILAC. We demonstrate a feeder-free SILAC culture system based on a customized version of a commonly used, chemically defined hESC medium developed by Ludwig et al. and commercially available as mTeSR1 [mTeSR1 is a trade mark of WiCell (Madison, WI) licensed to STEMCELL Technologies (Vancouver, Canada)]. This medium, together with adjustments to the culturing protocol, facilitates reproducible labeling that is easily scalable to the protein amounts required by proteomic work flows. It greatly enhances the usability of quantitative proteomics as a tool for the study of mechanisms underlying hESCs differentiation and self-renewal. Associated data have been deposited to the ProteomeXchange with the identifier PXD000151.
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13
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Vernocchi S, Battello N, Schmitz S, Revets D, Billing AM, Turner JD, Muller CP. Membrane glucocorticoid receptor activation induces proteomic changes aligning with classical glucocorticoid effects. Mol Cell Proteomics 2013; 12:1764-79. [PMID: 23339905 DOI: 10.1074/mcp.m112.022947] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Glucocorticoids exert rapid nongenomic effects by several mechanisms including the activation of a membrane-bound glucocorticoid receptor (mGR). Here, we report the first proteomic study on the effects of mGR activation by BSA-conjugated cortisol (Cort-BSA). A subset of target proteins in the proteomic data set was validated by Western blot and we found them responding to mGR activation by BSA-conjugated cortisol in three additional cell lines, indicating a conserved effect in cells originating from different tissues. Changes in the proteome of BSA-conjugated cortisol treated CCRF-CEM leukemia cells were associated with early and rapid pro-apoptotic, immune-modulatory and metabolic effects aligning with and possibly "priming" classical activities of the cytosolic glucocorticoid receptor (cGR). PCR arrays investigating target genes of the major signaling pathways indicated that the mGR does not exert its effects through the transcriptional activity of any of the most common kinases in these leukemic cells, but RhoA signaling emerged from our pathway analysis. All cell lines tested displayed very low levels of mGR on their surface. Highly sensitive and specific in situ proximity ligation assay visualized low numbers of mGR even in cells previously thought to be mGR negative. We obtained similar results when using three distinct anti-GR monoclonal antibodies directed against the N-terminal half of the cGR. This strongly suggests that the mGR and the cGR have a high sequence homology and most probably originate from the same gene. Furthermore, the mGR appears to reside in caveolae and its association with caveolin-1 (Cav-1) was clearly detected in two of the four cell lines investigated using double recognition proximity ligation assay. Our results indicate however that Cav-1 is not necessary for membrane localization of the GR since CCRF-CEM and Jurkat cells have a functional mGR, but did not express this caveolar protein. However, if expressed, this membrane protein dimerizes with the mGR modulating its function.
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Affiliation(s)
- Sara Vernocchi
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, Luxembourg, Grand-Duchy of Luxembourg
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14
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Teiten MH, Gaigneaux A, Chateauvieux S, Billing AM, Planchon S, Fack F, Renaut J, Mack F, Muller CP, Dicato M, Diederich M. Identification of differentially expressed proteins in curcumin-treated prostate cancer cell lines. OMICS 2012; 16:289-300. [PMID: 22475723 DOI: 10.1089/omi.2011.0136] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Due to high prevalence and slow progression of prostate cancer, primary prevention appears to be attractive strategy for its eradication. During the last decade, curcumin (diferuloylmethane), a natural compound from the root of turmeric (Curcuma longa), was described as a potent chemopreventive agent. Curcumin exhibits anti-inflammatory, anticarcinogenic, antiproliferative, antiangiogenic, and antioxidant properties in various cancer cell models. This study was designed to identify proteins involved in the anticancer activity of curcumin in androgen-dependent (22Rv1) and -independent (PC-3) human prostate cancer cell lines using two-dimensional difference in gel electrophoresis (2D-DIGE). Out of 425 differentially expressed spots, we describe here the MALDI-TOF-MS analysis of 192 spots of interest, selected by their expression profile. This approach allowed the identification of 60 differentially expressed proteins (32 in 22Rv1 cells and 47 in PC-3 cells). Nineteen proteins are regulated in both cell lines. Further bioinformatic analysis shows that proteins modulated by curcumin are implicated in protein folding (such as heat-shock protein PPP2R1A; RNA splicing proteins RBM17, DDX39; cell death proteins HMGB1 and NPM1; proteins involved in androgen receptor signaling, NPM1 and FKBP4/FKBP52), and that this compound could have an impact on miR-141, miR-152, and miR-183 expression. Taken together, these data support the hypothesis that curcumin is an interesting chemopreventive agent as it modulates the expression of proteins that potentially contribute to prostate carcinogenesis.
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Affiliation(s)
- Marie-Hélène Teiten
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, Luxembourg
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15
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Billing AM, Revets D, Hoffmann C, Turner JD, Vernocchi S, Muller CP. Proteomic profiling of rapid non-genomic and concomitant genomic effects of acute restraint stress on rat thymocytes. J Proteomics 2012; 75:2064-79. [PMID: 22270012 DOI: 10.1016/j.jprot.2012.01.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 12/16/2011] [Accepted: 01/07/2012] [Indexed: 02/06/2023]
Abstract
In order to investigate rapid non-genomic effects of acute stress, rats were restrained for 15 min which was sufficient to activate the hypothalamus-pituitary-adrenal (HPA) axis but too short to induce massive genomic effects of cortisol. Subcellular fractions of thymocytes (cytosol, nucleus, membrane) were investigated using quantitative 2D DIGE with MALDI-TOF/TOF mass spectrometry. In total, 108 proteins with differential subcellular localizations were identified. The specificity of the changes induced by psychological stress was reflected by the prominent modulation of proteins involved in the HPA and sympathoadrenal medullar (SAM) axis such as HMGB1 and NHERF1. Intracellular trafficking was characterized by a dominant protein exodus from the cytosol. Real translocation was observed for 9 proteins with 6 that shuttled from the cytosol to the nucleus (HYOU1, HNRPF, HNRPC, STRAP, PSA1, PPA1) and 3 from the nucleus to the cytosol (HMGB1, NHERF1, PSMA1). Proteins showing subcellular reshuffling were largely involved in transcription and translation processes (39 of 108) with a significant enrichment of RNA splicing factors. Bioinformatics analysis revealed significant enrichment for protein kinase A and 14-3-3 signaling, probably reflecting real non-genomic effects. This is the first study investigating rapid effects of stress-induced HPA activation in vivo at the proteome level.
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Affiliation(s)
- Anja M Billing
- Institute of Immunology, Centre de Recherche Public de la Santé/National Public Health Laboratory, 20A, rue Auguste Lumière, L-1950 Luxembourg, Luxembourg
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16
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Billing AM, Fack F, Turner JD, Muller CP. Cortisol is a potent modulator of lipopolysaccharide-induced interferon signaling in macrophages. Innate Immun 2010; 17:302-20. [PMID: 20501517 DOI: 10.1177/1753425910369269] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The effects of cortisol (CORT) on resting and lipopolysaccharide (LPS)-activated monocyte-derived THP-1 macrophages were investigated by proteomics. Forty-seven proteins were found to be modulated, 20 by CORT, 11 by LPS, and 16 by CORT and LPS. Cortisol-sensitive chaperones and cytoskeletal proteins were mostly repressed. HCLS1, MGN, and MX1 were new proteins identified to be under the transcriptional control of this steroid and new CORT-sensitive variants of MX1, SYWC and IFIT3 were found. FKBP51, a known CORT target gene, showed the strongest response to CORT and synergism with LPS. In resting THP-1 macrophages, 18 proteins were modulated by CORT, with 15 being down-regulated. Activation of macrophages by LPS was associated with enhanced expression of immune response and metabolic proteins. In activated macrophages, CORT had a more equilibrated effect and almost all metabolism-related proteins were up-regulated, whereas immune response proteins were mostly down-regulated. The majority of the LPS up-regulated immune response-related proteins are known interferon (IFN) target genes (IFIT3, MX1, SYWC, PSME2) suggesting activation of the IRF3 signaling pathway. They were all suppressed by CORT. This is the first proteomics study to investigate the effects of CORT on activated immune cells.
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Affiliation(s)
- Anja M Billing
- Institute of Immunology, CRP-Santé/National Public Health Laboratory, 20A rue Auguste Lumiére, Luxembourg, Grand Duchy of Luxembourg
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Billing AM, Fack F, Renaut J, Olinger CM, Schote AB, Turner JD, Muller CP. Proteomic analysis of the cortisol-mediated stress response in THP-1 monocytes using DIGE technology. J Mass Spectrom 2007; 42:1433-1444. [PMID: 17960574 DOI: 10.1002/jms.1270] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The glucocorticoid (GC) cortisol, the main mediator of the hypothalamic-pituitary-adrenal axis has many implications in metabolism, stress response and the immune system. Its function is mediated via binding to the glucocorticoid receptor (GR), a member of the superfamily of ligand-activated nuclear hormone receptors. The activity of the ligated GR results from its binding as a transcription factor to glucocorticoid response elements (GREs). Two-dimensional gel electrophoresis with DIGE (fluorescence difference gel electrophoresis) technology was applied to study the effects of cortisol on the human THP-1 monocytic cell line. A total of 28 cortisol-modulated proteins were identified belonging to five functional groups: cytoskeleton (8), chaperones (9), immune response (4), metabolism (3) and transcription/translation (4). Their corresponding genes were screened for putative GREs in their + 10 kb/- 0.2 kb promoter regions including all alternative promoters available within the Database for Transcription Start Sites (DBTSS). FKBP51, known to be induced by cortisol, was identified as the strongest differentially expressed protein, and contains the highest number of strict GREs. Genomic analysis of five alternative FKBP5 promoter regions suggests GC inducibility of all transcripts. Additionally, proteomics (2D DIGE and 2D immunoblotting) revealed the existence of several FKBP51 isoforms, which were not previously described. To our knowledge this is the first proteomic study that addresses the effects of cortisol on immune cells. FKBP51 isoforms found on the gel map were linked to alternative promoter usage on the genetic level, successfully correlating both the specific proteomic and genomic findings.
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Affiliation(s)
- Anja M Billing
- Institute of Immunology, National Public Health Laboratory, 20A, rue Auguste Lumière, L-1950 Luxembourg, Grand Duchy of Luxembourg
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