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Russo S, Kwiatkowski M, Wolters JC, Gerding A, Hermans J, Govorukhina N, Bischoff R, Melgert BN. Effects of lysine deacetylase inhibitor treatment on LPS responses of alveolar-like macrophages. J Leukoc Biol 2024; 115:435-449. [PMID: 37811856 DOI: 10.1093/jleuko/qiad121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/10/2023] Open
Abstract
Macrophages are key immune cells that can adapt their metabolic phenotype in response to different stimuli. Lysine deacetylases are important enzymes regulating inflammatory gene expression and lysine deacetylase inhibitors have been shown to exert anti-inflammatory effects in models of chronic obstructive pulmonary disease. We hypothesized that these anti-inflammatory effects may be associated with metabolic changes in macrophages. To validate this hypothesis, we used an unbiased and a targeted proteomic approach to investigate metabolic enzymes, as well as liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry, to quantify metabolites in combination with the measurement of functional parameters in primary murine alveolar-like macrophages after lipopolysaccharide-induced activation in the presence or absence of lysine deacetylase inhibition. We found that lysine deacetylase inhibition resulted in reduced production of inflammatory mediators such as tumor necrosis factor α and interleukin 1β. However, only minor changes in macrophage metabolism were observed, as only one of the lysine deacetylase inhibitors slightly increased mitochondrial respiration while no changes in metabolite levels were seen. However, lysine deacetylase inhibition specifically enhanced expression of proteins involved in ubiquitination, which may be a driver of the anti-inflammatory effects of lysine deacetylase inhibitors. Our data illustrate that a multiomics approach provides novel insights into how macrophages interact with cues from their environment. More detailed studies investigating ubiquitination as a potential driver of lysine deacetylase inhibition will help developing novel anti-inflammatory drugs for difficult-to-treat diseases such as chronic obstructive pulmonary disease.
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Affiliation(s)
- Sara Russo
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Marcel Kwiatkowski
- Functional Proteo-Metabolomics, Department of Biochemistry, University of Innsbruck, Innrain 80-82, Innsbruck 6020, Austria
| | - Justina C Wolters
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
| | - Albert Gerding
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
| | - Jos Hermans
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Natalia Govorukhina
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Barbro N Melgert
- Department of Molecular Pharmacology, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
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Zappacosta F, Wagner CD, Della Pietra A, Gerhart SV, Keenan K, Korenchuck S, Quinn CJ, Barbash O, McCabe MT, Annan RS. A Chemical Acetylation-Based Mass Spectrometry Platform for Histone Methylation Profiling. Mol Cell Proteomics 2021; 20:100067. [PMID: 33775892 PMCID: PMC8138768 DOI: 10.1016/j.mcpro.2021.100067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 12/18/2022] Open
Abstract
Histones are highly posttranslationally modified proteins that regulate gene expression by modulating chromatin structure and function. Acetylation and methylation are the most abundant histone modifications, with methylation occurring on lysine (mono-, di-, and trimethylation) and arginine (mono- and dimethylation) predominately on histones H3 and H4. In addition, arginine dimethylation can occur either symmetrically (SDMA) or asymmetrically (ADMA) conferring different biological functions. Despite the importance of histone methylation on gene regulation, characterization and quantitation of this modification have proven to be quite challenging. Great advances have been made in the analysis of histone modification using both bottom-up and top-down mass spectrometry (MS). However, MS-based analysis of histone posttranslational modifications (PTMs) is still problematic, due both to the basic nature of the histone N-terminal tails and to the combinatorial complexity of the histone PTMs. In this report, we describe a simplified MS-based platform for histone methylation analysis. The strategy uses chemical acetylation with d0-acetic anhydride to collapse all the differently acetylated histone forms into one form, greatly reducing the complexity of the peptide mixture and improving sensitivity for the detection of methylation via summation of all the differently acetylated forms. We have used this strategy for the robust identification and relative quantitation of H4R3 methylation, for which stoichiometry and symmetry status were determined, providing an antibody-independent evidence that H4R3 is a substrate for both Type I and Type II PRMTs. Additionally, this approach permitted the robust detection of H4K5 monomethylation, a very low stoichiometry methylation event (0.02% methylation). In an independent example, we developed an in vitro assay to profile H3K27 methylation and applied it to an EZH2 mutant xenograft model following small-molecule inhibition of the EZH2 methyltransferase. These specific examples highlight the utility of this simplified MS-based approach to quantify histone methylation profiles. Simplification of histone complexity for analysis of lysine and arginine methylation. Improved sensitivity for the analysis of dimethylarginine symmetry. Accurate ratio of symmetric and asymmetric H4R3 dimethylarginine in cancer cells. Catalog of accessible histone methyl marks to facilitate assay development.
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Affiliation(s)
- Francesca Zappacosta
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Craig D Wagner
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - Sarah V Gerhart
- Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Kathryn Keenan
- Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - Chad J Quinn
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Olena Barbash
- Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - Roland S Annan
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA.
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3
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Shah AK, Wali G, Sue CM, Mackay-Sim A, Hill MM. Antibody-Free Targeted Proteomics Assay for Absolute Measurement of α-Tubulin Acetylation. Anal Chem 2020; 92:11204-11212. [PMID: 32639142 DOI: 10.1021/acs.analchem.0c01683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acetylation of α-tubulin at conserved lysine 40 (K40) amino acid residue regulates microtubule dynamics and controls a wide range of cellular activities. Dysregulated microtubule dynamics characterized by differential α-tubulin acetylation is a hallmark of cancer, neurodegeneration, and other complex disorders. Hence, accurate quantitation of α-tubulin acetylation is required in human disease and animal model studies. We developed a novel antibody-free proteomics assay to measure α-tubulin acetylation targeting protease AspN-generated peptides harboring K40 site. Using the synthetic unmodified and acetylated stable isotope labeled peptides DKTIGGG and DKTIGGGD, we demonstrate assay linearity across 4 log magnitude and reproducibility of <10% coefficient of variation. The assay accuracy was validated by titration of 10-80% mixture of acetylated/nonacetylated α-tubulin peptides in the background of human olfactory neurosphere-derived stem (ONS) cell matrix. Furthermore, in agreement with antibody-based high content microscopy analysis, the targeted proteomics assay reported an induction of α-tubulin K40 acetylation upon Trichostatin A stimulation of ONS cells. Independently, we found 35.99% and 16.11% α-tubulin acetylation for mouse spinal cord and brain homogenate tissue, respectively, as measured by our assay. In conclusion, this simple, antibody-free proteomics assay enables quantitation of α-tubulin acetylation, and is applicable across various fields of biology and medicine.
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Affiliation(s)
- Alok K Shah
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Queensland 4006, Australia
| | - Gautam Wali
- Department of Neurogenetics, Kolling Institute, Sydney Medical School, University of Sydney, Sydney, New South Wales 2065, Australia
| | - Carolyn M Sue
- Department of Neurogenetics, Kolling Institute, Sydney Medical School, University of Sydney, Sydney, New South Wales 2065, Australia
| | - Alan Mackay-Sim
- Department of Neurogenetics, Kolling Institute, Sydney Medical School, University of Sydney, Sydney, New South Wales 2065, Australia.,Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Rd, Nathan, Queensland 4111, Australia
| | - Michelle M Hill
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Queensland 4006, Australia.,Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Queensland 4006, Australia
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van Pijkeren A, Bischoff R, Kwiatkowski M. Mass spectrometric analysis of PTM dynamics using stable isotope labeled metabolic precursors in cell culture. Analyst 2019; 144:6812-6833. [PMID: 31650141 DOI: 10.1039/c9an01258c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biological organisms represent highly dynamic systems, which are continually exposed to environmental factors and always strive to restore steady-state homeostasis. Posttranslational modifications are key regulators with which biological systems respond to external stimuli. To understand how homeostasis is restored, it is important to study the kinetics of posttranslational modifications. In this review we discuss proteomic approaches using stable isotope labeled metabolic precursors to study dynamics of posttranslational modifications in cell culture.
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Affiliation(s)
- Alienke van Pijkeren
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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Gianazza E, Banfi C. Post-translational quantitation by SRM/MRM: applications in cardiology. Expert Rev Proteomics 2018; 15:477-502. [DOI: 10.1080/14789450.2018.1484283] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Erica Gianazza
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
| | - Cristina Banfi
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
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