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Will R, Bauer K, Kudla M, Montero-Vergara J, Wiemann S, Jendrossek V, Peña-Llopis S, Vega-Rubín-de-Celis S. A Dual HiBiT-GFP-LC3 Lentiviral Reporter for Autophagy Flux Assessment. Methods Mol Biol 2022; 2445:75-98. [PMID: 34972987 DOI: 10.1007/978-1-0716-2071-7_6] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Autophagy is an intracellular degradation process that maintains the cellular homeostasis and it is regulated in multiple ways, both in health and disease. Assessment of autophagic flux in cells is an important approach for understanding the function of autophagy in biological contexts. Here, we describe a new tool for the qualitative and quantitative determination of autophagic flux using a dual lentiviral reporter system that generates a fusion HiBiT-GFP-LC3B protein suitable for generating stable cell lines.
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Affiliation(s)
- Rainer Will
- Cellular Tools, Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Katja Bauer
- Cellular Tools, Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Kudla
- Institute for Cell Biology, University Hospital Essen, Essen, Germany
| | | | - Stefan Wiemann
- Cellular Tools, Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Verena Jendrossek
- Institute for Cell Biology, University Hospital Essen, Essen, Germany
| | - Samuel Peña-Llopis
- Translational Genomics in Solid Tumors, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) at the University Hospital Essen, Essen, Germany
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Abstract
Autophagy is a dynamic process that can be monitored in multiple ways, both in vitro and in vivo. Studies in mice are a widely used tool to understand multiple diseases and conditions where autophagy plays a role, and therefore autophagic flux measurement in tissues of rodent models are of utmost importance. Here, we present some assays successfully used in determining the autophagy status in the mice mammary gland as well as in xenografts.
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Affiliation(s)
- Zhongju Zou
- Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Álvaro F Fernández
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Verena Jendrossek
- Institute of Cell Biology (Cancer Research), Essen University Hospital, Essen, Germany
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Niersch J, Vega-Rubín-de-Celis S, Bazarna A, Mergener S, Jendrossek V, Siveke JT, Peña-Llopis S. A BAP1 synonymous mutation results in exon skipping, loss of function and worse patient prognosis. iScience 2021; 24:102173. [PMID: 33681728 PMCID: PMC7918674 DOI: 10.1016/j.isci.2021.102173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 05/15/2020] [Revised: 10/11/2020] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Synonymous mutations are generally disregarded by genomic analyses because they are considered non-pathogenic. We identified and characterized a somatic synonymous mutation in the epigenetic modifier and tumor suppressor BAP1, resulting in exon skipping and complete protein inactivation. This radically altered the prognosis of a clear-cell renal cell carcinoma patient from The Cancer Genome Atlas (TCGA) with a PBRM1 mutation (a predictor biomarker for positive responses to immune checkpoint inhibitors) from good (an estimated overall survival of 117 months) to a very bad prognosis (an estimated overall survival of 31 months), emphasizing the importance of scrutinizing synonymous mutations near acceptor splice sites of cancer genes for accurate precision medicine.
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Affiliation(s)
- Jennifer Niersch
- Translational Genomics in Solid Tumors, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) at the University Hospital Essen, Hufelandstrasse 55, 45147 Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | | | - Anna Bazarna
- Translational Genomics in Solid Tumors, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) at the University Hospital Essen, Hufelandstrasse 55, 45147 Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Svenja Mergener
- Translational Genomics in Solid Tumors, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) at the University Hospital Essen, Hufelandstrasse 55, 45147 Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Verena Jendrossek
- Institute of Cell Biology (Cancer Research), University Hospital Essen, Essen, Germany
| | - Jens T. Siveke
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Samuel Peña-Llopis
- Translational Genomics in Solid Tumors, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) at the University Hospital Essen, Hufelandstrasse 55, 45147 Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
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Vega-Rubín-de-Celis S, Kinch L, Peña-Llopis S. Regulation of Beclin 1-Mediated Autophagy by Oncogenic Tyrosine Kinases. Int J Mol Sci 2020; 21:ijms21239210. [PMID: 33287140 PMCID: PMC7729755 DOI: 10.3390/ijms21239210] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [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: 10/30/2020] [Revised: 11/28/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Beclin 1 is a major regulator of autophagy, and it is a core component of the class III PI3K complexes. Beclin 1 is a highly conserved protein and its function is regulated in a number of ways, including post-translational modifications. Several studies indicate that receptor and non-receptor tyrosine kinases regulate autophagy activity in cancer, and some suggest the importance of Beclin 1 tyrosine phosphorylation in this process. Here we summarize the current knowledge of the mechanism whereby some oncogenic tyrosine kinases regulate autophagy through Beclin 1.
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Affiliation(s)
- Silvia Vega-Rubín-de-Celis
- Institute for Cell Biology (Cancer Research), University Hospital Essen, 45147 Essen, Germany
- Correspondence: or
| | - Lisa Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Samuel Peña-Llopis
- Translational Genomics in Solid Tumors, German Cancer Consortium (DKTK) and German Cancer Research Center, University Hospital Essen, 45147 Essen, Germany;
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Vega-Rubín-de-Celis S. The Role of Beclin 1-Dependent Autophagy in Cancer. Biology (Basel) 2019; 9:biology9010004. [PMID: 31877888 PMCID: PMC7168252 DOI: 10.3390/biology9010004] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/20/2022]
Abstract
Autophagy (self-eating) is an intracellular degradation process used by cells to keep a “clean house”; as it degrades abnormal or damaged proteins and organelles, it helps to fight infections and also provides energy in times of fasting or exercising. Autophagy also plays a role in cancer, although its precise function in each cancer type is still obscure, and whether autophagy plays a protecting (through the clearing of damaged organelles and protein aggregates and preventing DNA damage) or a promoting (by fueling the already stablished tumor) role in cancer remains to be fully characterized. Beclin 1, the mammalian ortholog of yeast Atg6/Vps30, is an essential autophagy protein and has been shown to play a role in tumor suppression. Here, an update of the tumorigenesis regulation by Beclin 1-dependent autophagy is provided.
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Affiliation(s)
- Silvia Vega-Rubín-de-Celis
- Institute for Cell Biology (Tumorforschung), University Hospital Essen, 45122 Essen, Germany; ; Tel.: +49-0201-723-3941
- German Cancer Consortium (DKTK) at Essen-Düsseldorf, 445122 Essen, Germany
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