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Ng MYW, Charsou C, Lapao A, Singh S, Trachsel-Moncho L, Schultz SW, Nakken S, Munson MJ, Simonsen A. The cholesterol transport protein GRAMD1C regulates autophagy initiation and mitochondrial bioenergetics. Nat Commun 2022; 13:6283. [PMID: 36270994 PMCID: PMC9586981 DOI: 10.1038/s41467-022-33933-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/05/2022] [Indexed: 12/25/2022] Open
Abstract
During autophagy, cytosolic cargo is sequestered into double-membrane vesicles called autophagosomes. The contributions of specific lipids, such as cholesterol, to the membranes that form the autophagosome, remain to be fully characterized. Here, we demonstrate that short term cholesterol depletion leads to a rapid induction of autophagy and a corresponding increase in autophagy initiation events. We further show that the ER-localized cholesterol transport protein GRAMD1C functions as a negative regulator of starvation-induced autophagy and that both its cholesterol transport VASt domain and membrane binding GRAM domain are required for GRAMD1C-mediated suppression of autophagy initiation. Similar to its yeast orthologue, GRAMD1C associates with mitochondria through its GRAM domain. Cells lacking GRAMD1C or its VASt domain show increased mitochondrial cholesterol levels and mitochondrial oxidative phosphorylation, suggesting that GRAMD1C may facilitate cholesterol transfer at ER-mitochondria contact sites. Finally, we demonstrate that expression of GRAMD family proteins is linked to clear cell renal carcinoma survival, highlighting the pathophysiological relevance of cholesterol transport proteins.
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Affiliation(s)
- Matthew Yoke Wui Ng
- grid.5510.10000 0004 1936 8921Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway ,grid.5510.10000 0004 1936 8921Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0450 Oslo, Norway
| | - Chara Charsou
- grid.5510.10000 0004 1936 8921Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway ,grid.5510.10000 0004 1936 8921Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0450 Oslo, Norway
| | - Ana Lapao
- grid.5510.10000 0004 1936 8921Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway ,grid.5510.10000 0004 1936 8921Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0450 Oslo, Norway
| | - Sakshi Singh
- grid.5510.10000 0004 1936 8921Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway ,grid.5510.10000 0004 1936 8921Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0450 Oslo, Norway
| | - Laura Trachsel-Moncho
- grid.5510.10000 0004 1936 8921Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway ,grid.5510.10000 0004 1936 8921Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0450 Oslo, Norway
| | - Sebastian W. Schultz
- grid.5510.10000 0004 1936 8921Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0450 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital Montebello, 0379 Oslo, Norway
| | - Sigve Nakken
- grid.5510.10000 0004 1936 8921Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0450 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital Montebello, 0379 Oslo, Norway
| | - Michael J. Munson
- grid.5510.10000 0004 1936 8921Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway ,grid.5510.10000 0004 1936 8921Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0450 Oslo, Norway ,grid.418151.80000 0001 1519 6403Present Address: Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anne Simonsen
- grid.5510.10000 0004 1936 8921Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway ,grid.5510.10000 0004 1936 8921Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0450 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital Montebello, 0379 Oslo, Norway
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Abstract
Mitochondria are dynamic, multifunctional cellular organelles that play a fundamental role in maintaining cellular homeostasis. Keeping the quality of mitochondria in check is of essential importance for functioning and survival of the cells. Selective autophagic clearance of flawed mitochondria, a process termed mitophagy, is one of the most prominent mechanisms through which cells maintain a healthy mitochondrial pool. The best-studied pathway through which mitophagy is exerted is the PINK1-PRKN pathway. However, an increasing number of studies have shown an existence of alternative pathways, where different proteins and lipids are able to recruit autophagic machinery independently of PINK1 and PRKN. The significance of PRKN-independent mitophagy pathways is reflected in various physiological and pathophysiological processes, but many questions regarding the regulation and the interplay between these pathways remain open. Here we review the current knowledge and recent progress made in the field of PRKN-independent mitophagy. Particularly we focus on the regulation of various receptors that participate in targeting impaired mitochondria to autophagosomes independently of PRKN.AbbreviationsAMPK: AMP-activated protein kinase; ATP: adenosine triphosphate; BCL2: BCL2 apoptosis regulator; BH: BCL2 homology; CCCP: Carbonyl cyanide m-chlorophenylhydrazone; CL: cardiolipin; ER: endoplasmic reticulum; FCCP: carbonyl cyanide p-trifluoromethoxyphenylhydrazone; IMM: inner mitochondrial membrane; IMS: mitochondrial intermembrane space; LIR: LC3-interacting region; MDVs: mitochondrial-derived vesicles; MTORC1: mechanistic target of rapamycin kinase complex 1; OMM: outer mitochondrial membrane; OXPHOS: oxidative phosphorylation; PD: Parkinson disease; PtdIns3K: phosphatidylinositol 3-kinase; RGC: retinal ganglion cell; RING: really interesting new gene; ROS: reactive oxygen species; SUMO: small ubiquitin like modifier; TBI: traumatic brain injury; TM: transmembrane.
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Affiliation(s)
- Petra Terešak
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ana Lapao
- Department of Molecular Medicine, Institute of Basic Medical Sciences and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Nemanja Subic
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Patricia Boya
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Zvulun Elazar
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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Lekomtsev S, Aligianni S, Lapao A, Bürckstümmer T. Efficient generation and reversion of chromosomal translocations using CRISPR/Cas technology. BMC Genomics 2016; 17:739. [PMID: 27640184 PMCID: PMC5027121 DOI: 10.1186/s12864-016-3084-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 09/14/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Chromosomal translocations are a hallmark of cancer cells and give rise to fusion oncogenes. To gain insight into the mechanisms governing tumorigenesis, adequate model cell lines are required. RESULTS We employ the versatile CRISPR/Cas system to engineer cell lines in which chromosomal translocations are either generated de novo (CD74-ROS1) or existing translocations are reverted back to the original configuration (BCR-ABL1). To this end, we co-apply two guide RNAs to artificially generate two breakpoints and screen for spontaneous fusion events by PCR. CONCLUSIONS The approach we use is efficient and delivers clones bearing translocationsin a predictable fashion. Detailed analysis suggests that the clones display no additional undesired alterations, implying that the approach is robust and precise.
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Affiliation(s)
- Sergey Lekomtsev
- Horizon Discovery Ltd, Cambridge Research Park, Waterbeach, Cambridge, United Kingdom
| | - Sofia Aligianni
- Horizon Genomics GmbH, Campus Vienna Biocenter, Vienna, Austria
| | - Ana Lapao
- Horizon Genomics GmbH, Campus Vienna Biocenter, Vienna, Austria
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Bürckstümmer T, Banning C, Hainzl P, Schobesberger R, Kerzendorfer C, Pauler FM, Chen D, Them N, Schischlik F, Rebsamen M, Smida M, Fece de la Cruz F, Lapao A, Liszt M, Eizinger B, Guenzl PM, Blomen VA, Konopka T, Gapp B, Parapatics K, Maier B, Stöckl J, Fischl W, Salic S, Taba Casari MR, Knapp S, Bennett KL, Bock C, Colinge J, Kralovics R, Ammerer G, Casari G, Brummelkamp TR, Superti-Furga G, Nijman SMB. A reversible gene trap collection empowers haploid genetics in human cells. Nat Methods 2013; 10:965-71. [PMID: 24161985 DOI: 10.1038/nmeth.2609] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 07/22/2013] [Indexed: 11/09/2022]
Abstract
Knockout collections are invaluable tools for studying model organisms such as yeast. However, there are no large-scale knockout collections of human cells. Using gene-trap mutagenesis in near-haploid human cells, we established a platform to generate and isolate individual 'gene-trapped cells' and used it to prepare a collection of human cell lines carrying single gene-trap insertions. In most cases, the insertion can be reversed. This growing library covers 3,396 genes, one-third of the expressed genome, is DNA-barcoded and allows systematic screens for a wide variety of cellular phenotypes. We examined cellular responses to TNF-α, TGF-β, IFN-γ and TNF-related apoptosis-inducing ligand (TRAIL), to illustrate the value of this unique collection of isogenic human cell lines.
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