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Schmitt D, Bozkurt S, Henning-Domres P, Huesmann H, Eimer S, Bindila L, Behrends C, Boyle E, Wilfling F, Tascher G, Münch C, Behl C, Kern A. FACS-mediated isolation of native autophagic vesicles. Autophagy 2023; 19:2146-2147. [PMID: 36416088 PMCID: PMC10283435 DOI: 10.1080/15548627.2022.2151188] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Autophagosome isolation enables the thorough investigation of structural components and engulfed materials. Recently, we introduced a novel antibody-based FACS-mediated method for isolation of native macroautophagic/autophagic vesicles and confirmed the quality of the preparations. We performed phospholipidomic and proteomic analyses to characterize autophagic vesicle-associated phospholipids and protein cargoes under different autophagy conditions. Lipidomic analyses identified phosphoglycerides and sphingomyelins within autophagic vesicles and revealed that the lipid composition was unaffected by different rates of autophagosome formation. Proteomic analyses identified more than 4500 potential autophagy substrates and showed that in comparison to autophagic vesicles isolated under basal autophagy conditions, starvation only marginally affected the cargo profile. Proteasome inhibition, however, resulted in the enhanced degradation of ubiquitin-proteasome system components. Taken together, the novel isolation method enriched large quantities of autophagic vesicles and enabled detailed analyses of their lipid and cargo composition.
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Affiliation(s)
- Daniel Schmitt
- Institute of Pathobiochemistry, The Autophagy Lab, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Süleyman Bozkurt
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Pascale Henning-Domres
- Institute of Pathobiochemistry, The Autophagy Lab, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Heike Huesmann
- Institute of Pathobiochemistry, The Autophagy Lab, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Stefan Eimer
- Department of Structural Cell Biology, Institute for Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
| | - Laura Bindila
- Institute of Physiological Chemistry, Clinical Lipidomics Unit, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Christian Behrends
- Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians- University, Munich, Germany
| | - Emily Boyle
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Florian Wilfling
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Georg Tascher
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Christian Behl
- Institute of Pathobiochemistry, The Autophagy Lab, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Andreas Kern
- Institute of Pathobiochemistry, The Autophagy Lab, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
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Schmitt D, Bozkurt S, Henning‐Domres P, Huesmann H, Eimer S, Bindila L, Behrends C, Boyle E, Wilfling F, Tascher G, Münch C, Behl C, Kern A. Lipid and protein content profiling of isolated native autophagic vesicles. EMBO Rep 2022; 23:e53065. [PMID: 36215690 PMCID: PMC9724672 DOI: 10.15252/embr.202153065] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022] Open
Abstract
Autophagy is responsible for clearance of an extensive portfolio of cargoes, which are sequestered into vesicles, called autophagosomes, and are delivered to lysosomes for degradation. The pathway is highly dynamic and responsive to several stress conditions. However, the phospholipid composition and protein contents of human autophagosomes under changing autophagy rates are elusive so far. Here, we introduce an antibody-based FACS-mediated approach for the isolation of native autophagic vesicles and ensured the quality of the preparations. Employing quantitative lipidomics, we analyze phospholipids present within human autophagic vesicles purified upon basal autophagy, starvation, and proteasome inhibition. Importantly, besides phosphoglycerides, we identify sphingomyelin within autophagic vesicles and show that the phospholipid composition is unaffected by the different conditions. Employing quantitative proteomics, we obtain cargo profiles of autophagic vesicles isolated upon the different treatment paradigms. Interestingly, starvation shows only subtle effects, while proteasome inhibition results in the enhanced presence of ubiquitin-proteasome pathway factors within autophagic vesicles. Thus, here we present a powerful method for the isolation of native autophagic vesicles, which enabled profound phospholipid and cargo analyses.
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Affiliation(s)
- Daniel Schmitt
- The Autophagy Lab, Institute of PathobiochemistryUniversity Medical Center of the Johannes Gutenberg UniversityMainzGermany
| | - Süleyman Bozkurt
- Institute of Biochemistry II, Faculty of MedicineGoethe UniversityFrankfurt am MainGermany
| | - Pascale Henning‐Domres
- The Autophagy Lab, Institute of PathobiochemistryUniversity Medical Center of the Johannes Gutenberg UniversityMainzGermany
| | - Heike Huesmann
- The Autophagy Lab, Institute of PathobiochemistryUniversity Medical Center of the Johannes Gutenberg UniversityMainzGermany
| | - Stefan Eimer
- Department of Structural Cell BiologyInstitute for Cell Biology and Neuroscience, Goethe UniversityFrankfurt am MainGermany
| | - Laura Bindila
- Clinical Lipidomics Unit, Institute of Physiological ChemistryUniversity Medical Center of the Johannes Gutenberg UniversityMainzGermany
| | - Christian Behrends
- Munich Cluster for Systems Neurology (SyNergy)Ludwig‐Maximilians‐UniversityMunichGermany
| | - Emily Boyle
- Mechanisms of Cellular Quality ControlMax Planck Institute of BiophysicsFrankfurt am MainGermany
| | - Florian Wilfling
- Mechanisms of Cellular Quality ControlMax Planck Institute of BiophysicsFrankfurt am MainGermany
| | - Georg Tascher
- Institute of Biochemistry II, Faculty of MedicineGoethe UniversityFrankfurt am MainGermany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of MedicineGoethe UniversityFrankfurt am MainGermany
| | - Christian Behl
- The Autophagy Lab, Institute of PathobiochemistryUniversity Medical Center of the Johannes Gutenberg UniversityMainzGermany
| | - Andreas Kern
- The Autophagy Lab, Institute of PathobiochemistryUniversity Medical Center of the Johannes Gutenberg UniversityMainzGermany
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