51
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Li L, Chen X, Gu H. The signaling involved in autophagy machinery in keratinocytes and therapeutic approaches for skin diseases. Oncotarget 2018; 7:50682-50697. [PMID: 27191982 PMCID: PMC5226613 DOI: 10.18632/oncotarget.9330] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 04/26/2016] [Indexed: 02/06/2023] Open
Abstract
Autophagy is responsible for the lysosomal degradation of proteins, organelles, microorganisms and exogenous particles. Epidermis primarily consists of keratinocytes which functions as an extremely important barrier. Investigation on autophagy in keratinocytes has been continuously renewing, but is not so systematic due to the complexity of the autophagy machinery. Here we reviewed recent studies on the autophagy in keratinocyte with a focus on interplay between autophagy machinery and keratinocytes biology, and novel autophagy regulators identified in keratinocytes. In this review, we discussed the roles of autophagy in apoptosis, differentiation, immune response, survival and melanin metabolism, trying to reveal the possible involvement of autophagy in skin aging, skin disorders and skin color formation. Since autophagy routinely plays a double-edged sword role in various conditions, its functions in skin homeostasis and potential application as a therapeutic target for skin diseases remains to be clarified. Furthermore, more investigations are needed on optimizing designed strategies to inhibit or enhance autophagy for clinical efficacy.
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Affiliation(s)
- Li Li
- Institute of Dermatology, Chinese Academy of Medical Science & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Xu Chen
- Institute of Dermatology, Chinese Academy of Medical Science & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Heng Gu
- Institute of Dermatology, Chinese Academy of Medical Science & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
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52
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Regulation of selective autophagy: the p62/SQSTM1 paradigm. Essays Biochem 2017; 61:609-624. [PMID: 29233872 DOI: 10.1042/ebc20170035] [Citation(s) in RCA: 456] [Impact Index Per Article: 65.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/19/2017] [Accepted: 10/19/2017] [Indexed: 12/11/2022]
Abstract
In selective autophagy, cytoplasmic components are selected and tagged before being sequestered into an autophagosome by means of selective autophagy receptors such as p62/SQSTM1. In this review, we discuss how selective autophagy is regulated. An important level of regulation is the selection of proteins or organelles for degradation. Components selected for degradation are tagged, often with ubiquitin, to facilitate recognition by autophagy receptors. Another level of regulation is represented by the autophagy receptors themselves. For p62, its ability to co-aggregate with ubiquitinated substrates is strongly induced by post-translational modifications (PTMs). The transcription of p62 is also markedly increased during conditions in which selective autophagy substrates accumulate. For other autophagy receptors, the LC3-interacting region (LIR) motif is regulated by PTMs, inhibiting or stimulating the interaction with ATG8 family proteins. ATG8 proteins are also regulated by PTMs. Regulation of the capacity of the core autophagy machinery also affects selective autophagy. Importantly, autophagy receptors can induce local recruitment and activation of ULK1/2 and PI3KC3 complexes at the site of cargo sequestration.
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53
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Schläfli AM, Isakson P, Garattini E, Simonsen A, Tschan MP. The autophagy scaffold protein ALFY is critical for the granulocytic differentiation of AML cells. Sci Rep 2017; 7:12980. [PMID: 29021535 PMCID: PMC5636880 DOI: 10.1038/s41598-017-12734-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/13/2017] [Indexed: 01/12/2023] Open
Abstract
Acute myeloid leukemia (AML) is a malignancy of myeloid progenitor cells that are blocked in differentiation. Acute promyelocytic leukemia (APL) is a rare form of AML, which generally presents with a t(15;17) translocation causing expression of the fusion protein PML-RARA. Pharmacological doses of all-trans retinoic acid (ATRA) induce granulocytic differentiation of APL cells leading to cure rates of >80% if combined with conventional chemotherapy. Autophagy is a lysosomal degradation pathway for the removal of cytoplasmic content and recycling of macromolecules. ATRA induces autophagy in ATRA-sensitive AML and APL cells and autophagy inhibition attenuates ATRA-triggered differentiation. In this study, we aimed at identifying if the autophagy-linked FYVE-domain containing protein (ALFY/WDFY3) is involved in autophagic degradation of protein aggregates contributes to ATRA therapy-induced autophagy. We found that ALFY mRNA levels increase significantly during the course of ATRA-induced differentiation of APL and AML cell lines. Importantly ALFY depletion impairs ATRA-triggered granulocytic differentiation of these cells. In agreement with its function in aggrephagy, knockdown of ALFY results in reduced ATRA-induced proteolysis. Our data further suggest that PML-RARα is an autophagy substrate degraded with the help of ALFY. In summary, we present a crucial role for ALFY in retinoid triggered maturation of AML cells.
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Affiliation(s)
- Anna M Schläfli
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Pauline Isakson
- Clinical immunology & transfusion medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - E Garattini
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche 'Mario Negri', Milano, Italy
| | - Anne Simonsen
- Department of Molecular Medicine, Institute for Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Mario P Tschan
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland. .,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.
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54
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Tsai TL, Wang HC, Hung CH, Lin PC, Lee YS, Chen HHW, Su WC. Wheat germ agglutinin-induced paraptosis-like cell death and protective autophagy is mediated by autophagy-linked FYVE inhibition. Oncotarget 2017; 8:91209-91222. [PMID: 29207637 PMCID: PMC5710917 DOI: 10.18632/oncotarget.20436] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 07/11/2017] [Indexed: 01/07/2023] Open
Abstract
Wheat germ agglutinin (WGA) is a lectin that specifically binds cell surface glycoproteins and disrupts nuclear pore complex function through its interaction with POM121. Our data indicate WGA induces paraptosis-like cell death without caspase activation. We observed the main features of paraptosis, including cytoplasmic vacuolation, endoplasmic reticulum dilation and increased ER stress, and the unfolded protein response in WGA-treated cervical carcinoma cells. Conversion of microtubule-associated protein I light chain 3 (LC3-I) into LC3-II and punctuate formation suggestive of autophagy were observed in WGA-treated cells. WGA-induced autophagy antagonized paraptosis in HeLa and CaSKi cells, which expressed autophagy-linked FYVE (Alfy) protein, but not in SiHa cells that did not express Alfy. Alfy knockdown in HeLa cells induced paraptosis-like cell death. These data indicate that WGA-induced cell death occurs through paraptosis and that autophagy may exert a protective effect. WGA treatment and Alfy inhibition could be an effective therapeutic strategy for apoptosis-resistant cervical cancer cells.
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Affiliation(s)
- Tsung Lin Tsai
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Radiation Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hao Chen Wang
- Insititue of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chun Hua Hung
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Peng Chan Lin
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi San Lee
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Helen H W Chen
- Department of Radiation Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wu Chou Su
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Insititue of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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55
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Odhams CA, Cortini A, Chen L, Roberts AL, Viñuela A, Buil A, Small KS, Dermitzakis ET, Morris DL, Vyse TJ, Cunninghame Graham DS. Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus. Hum Mol Genet 2017; 26:1003-1017. [PMID: 28062664 PMCID: PMC5409091 DOI: 10.1093/hmg/ddw417] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/05/2016] [Indexed: 12/19/2022] Open
Abstract
Studies attempting to functionally interpret complex-disease susceptibility loci by GWAS and eQTL integration have predominantly employed microarrays to quantify gene-expression. RNA-Seq has the potential to discover a more comprehensive set of eQTLs and illuminate the underlying molecular consequence. We examine the functional outcome of 39 variants associated with Systemic Lupus Erythematosus (SLE) through the integration of GWAS and eQTL data from the TwinsUK microarray and RNA-Seq cohort in lymphoblastoid cell lines. We use conditional analysis and a Bayesian colocalisation method to provide evidence of a shared causal-variant, then compare the ability of each quantification type to detect disease relevant eQTLs and eGenes. We discovered the greatest frequency of candidate-causal eQTLs using exon-level RNA-Seq, and identified novel SLE susceptibility genes (e.g. NADSYN1 and TCF7) that were concealed using microarrays, including four non-coding RNAs. Many of these eQTLs were found to influence the expression of several genes, supporting the notion that risk haplotypes may harbour multiple functional effects. Novel SLE associated splicing events were identified in the T-reg restricted transcription factor, IKZF2, and other candidate genes (e.g. WDFY4) through asQTL mapping using the Geuvadis cohort. We have significantly increased our understanding of the genetic control of gene-expression in SLE by maximising the leverage of RNA-Seq and performing integrative GWAS-eQTL analysis against gene, exon, and splice-junction quantifications. We conclude that to better understand the true functional consequence of regulatory variants, quantification by RNA-Seq should be performed at the exon-level as a minimum, and run in parallel with gene and splice-junction level quantification.
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Affiliation(s)
| | - Andrea Cortini
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Lingyan Chen
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Amy L Roberts
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Ana Viñuela
- Department of Twin Research, King's College London, London, UK
| | | | - Kerrin S Small
- Department of Twin Research, King's College London, London, UK
| | | | - David L Morris
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Timothy J Vyse
- Department of Medical & Molecular Genetics, King's College London, London, UK.,Division of Immunology, Infection and Inflammatory Disease, King's College London, London, UK
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56
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Takayama K, Matsuura A, Itakura E. Dissection of ubiquitinated protein degradation by basal autophagy. FEBS Lett 2017; 591:1199-1211. [PMID: 28369861 PMCID: PMC5435929 DOI: 10.1002/1873-3468.12641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 03/16/2017] [Accepted: 03/25/2017] [Indexed: 11/23/2022]
Abstract
Basal autophagy plays an essential role as a protein quality control system. Although it has been demonstrated that the loss of autophagy results in the accumulation of ubiquitin‐positive aggregates and the development of neurodegenerative diseases, the precise autophagy substrate(s) remain unclear. Here, we determined whether ubiquitinated proteins are direct substrates for basal autophagy using a fluorescent ratiometric probe for ubiquitin. We show that the degradation of polyubiquitinated proteins is not dependent on basal autophagy. Although ubiquitin‐positive aggregates are observed in autophagy knockout cultured cells, the aggregates consist of soluble and mobile polyubiquitinated proteins, which are trapped by p62 without an increase in the total amount of ubiquitinated proteins. These results suggest that ubiquitinated proteins are not major targets for basal autophagy.
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Affiliation(s)
- Kaori Takayama
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University, Inage-ku, Japan
| | - Akira Matsuura
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University, Inage-ku, Japan
| | - Eisuke Itakura
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University, Inage-ku, Japan
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57
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Tranchevent LC, Aubé F, Dulaurier L, Benoit-Pilven C, Rey A, Poret A, Chautard E, Mortada H, Desmet FO, Chakrama FZ, Moreno-Garcia MA, Goillot E, Janczarski S, Mortreux F, Bourgeois CF, Auboeuf D. Identification of protein features encoded by alternative exons using Exon Ontology. Genome Res 2017; 27:1087-1097. [PMID: 28420690 PMCID: PMC5453322 DOI: 10.1101/gr.212696.116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 03/28/2017] [Indexed: 12/16/2022]
Abstract
Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward this end, we developed a computational approach, named “Exon Ontology,” based on terms corresponding to well-characterized protein features organized in an ontology tree. Exon Ontology is conceptually similar to Gene Ontology-based approaches but focuses on exon-encoded protein features instead of gene level functional annotations. Exon Ontology describes the protein features encoded by a selected list of exons and looks for potential Exon Ontology term enrichment. By applying this strategy to exons that are differentially spliced between epithelial and mesenchymal cells and after extensive experimental validation, we demonstrate that Exon Ontology provides support to discover specific protein features regulated by alternative splicing. We also show that Exon Ontology helps to unravel biological processes that depend on suites of coregulated alternative exons, as we uncovered a role of epithelial cell-enriched splicing factors in the AKT signaling pathway and of mesenchymal cell-enriched splicing factors in driving splicing events impacting on autophagy. Freely available on the web, Exon Ontology is the first computational resource that allows getting a quick insight into the protein features encoded by alternative exons and investigating whether coregulated exons contain the same biological information.
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Affiliation(s)
- Léon-Charles Tranchevent
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Fabien Aubé
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Louis Dulaurier
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Clara Benoit-Pilven
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Amandine Rey
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Arnaud Poret
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Emilie Chautard
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, UMR CNRS 5558, INRIA Erable, Villeurbanne, F-69622, France
| | - Hussein Mortada
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - François-Olivier Desmet
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Fatima Zahra Chakrama
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Maira Alejandra Moreno-Garcia
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Evelyne Goillot
- Institut NeuroMyoGène, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, F-69007 France
| | - Stéphane Janczarski
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Franck Mortreux
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Cyril F Bourgeois
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Didier Auboeuf
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
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58
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59
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Lippai M, Szatmári Z. Autophagy-from molecular mechanisms to clinical relevance. Cell Biol Toxicol 2016; 33:145-168. [PMID: 27957648 DOI: 10.1007/s10565-016-9374-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/02/2016] [Indexed: 12/14/2022]
Abstract
Autophagy is a lysosomal degradation pathway of eukaryotic cells that is highly conserved from yeast to mammals. During this process, cooperating protein complexes are recruited in a hierarchic order to the phagophore assembly site (PAS) to mediate the elongation and closure of double-membrane vesicles called autophagosomes, which sequester cytosolic components and deliver their content to the endolysosomal system for degradation. As a major cytoprotective mechanism, autophagy plays a key role in the stress response against nutrient starvation, hypoxia, and infections. Although numerous studies reported that impaired function of core autophagy proteins also contributes to the development and progression of various human diseases such as neurodegenerative disorders, cardiovascular and muscle diseases, infections, and different types of cancer, the function of this process in human diseases remains unclear. Evidence often suggests a controversial role for autophagy in the pathomechanisms of these severe disorders. Here, we provide an overview of the molecular mechanisms of autophagy and summarize the recent advances on its function in human health and disease.
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Affiliation(s)
- Mónika Lippai
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Pázmány Péter stny. 1/C, Budapest, 1117, Hungary
| | - Zsuzsanna Szatmári
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Pázmány Péter stny. 1/C, Budapest, 1117, Hungary.
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60
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Shin JH, Min SH. Novel functional roles of caspase-related genes in the regulation of apoptosis and autophagy. THE KOREAN JOURNAL OF PHYSIOLOGY & PHARMACOLOGY : OFFICIAL JOURNAL OF THE KOREAN PHYSIOLOGICAL SOCIETY AND THE KOREAN SOCIETY OF PHARMACOLOGY 2016; 20:573-580. [PMID: 27847434 PMCID: PMC5106391 DOI: 10.4196/kjpp.2016.20.6.573] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 07/04/2016] [Accepted: 07/20/2016] [Indexed: 11/22/2022]
Abstract
Caspases, a family of cysteine proteases, cleave substrates and play significant roles in apoptosis, autophagy, and development. Recently, our group identified 72 genes that interact with Death Caspase-1 (DCP-1) proteins in Drosophila by genetic screening of 15,000 EP lines. However, the cellular functions and molecular mechanisms of the screened genes, such as their involvement in apoptosis and autophagy, are poorly understood in mammalian cells. In order to study the functional characterizations of the genes in human cells, we investigated 16 full-length human genes in mammalian expression vectors and tested their effects on apoptosis and autophagy in human cell lines. Our studies revealed that ALFY, BIRC4, and TAK1 induced autophagy, while SEC61A2, N-PAC, BIRC4, WIPI1, and FALZ increased apoptotic cell death. BIRC4 was involved in both autophagy and apoptosis. Western blot analysis and luciferase reporter activity indicated that ALFY, BIRC4, PDGFA, and TAK1 act in a p53-dependent manner, whereas CPSF1, SEC61A2, N-PAC, and WIPI1 appear to be p53-independent. Overexpression of BIRC4 and TAK1 caused upregulation of p53 and accumulation of its target proteins as well as an increase in p53 mRNA levels, suggesting that these genes are involved in p53 transcription and expression of its target genes followed by p53 protein accumulation. In conclusion, apoptosis and/or autophagy mediated by BIRC4 and TAK1 may be regulated by p53 and caspase activity. These novel findings may provide valuable information that will aid in a better understanding of the roles of caspase-related genes in human cell lines and be useful for the process of drug discovery.
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Affiliation(s)
- Ju-Hyun Shin
- Biomedical Research Center, KAIST, Daejeon 34141, Korea.; LegoChem Biosciences, Inc., Daejeon 34302, Korea
| | - Sang-Hyun Min
- New Drug Development Center, DGMIF, Daegu 41061, Korea
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61
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Dragich JM, Kuwajima T, Hirose-Ikeda M, Yoon MS, Eenjes E, Bosco JR, Fox LM, Lystad AH, Oo TF, Yarygina O, Mita T, Waguri S, Ichimura Y, Komatsu M, Simonsen A, Burke RE, Mason CA, Yamamoto A. Autophagy linked FYVE (Alfy/WDFY3) is required for establishing neuronal connectivity in the mammalian brain. eLife 2016; 5. [PMID: 27648578 PMCID: PMC5030082 DOI: 10.7554/elife.14810] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 08/25/2016] [Indexed: 12/23/2022] Open
Abstract
The regulation of protein degradation is essential for maintaining the appropriate environment to coordinate complex cell signaling events and to promote cellular remodeling. The Autophagy linked FYVE protein (Alfy), previously identified as a molecular scaffold between the ubiquitinated cargo and the autophagic machinery, is highly expressed in the developing central nervous system, indicating that this pathway may have yet unexplored roles in neurodevelopment. To examine this possibility, we used mouse genetics to eliminate Alfy expression. We report that this evolutionarily conserved protein is required for the formation of axonal tracts throughout the brain and spinal cord, including the formation of the major forebrain commissures. Consistent with a phenotype reflecting a failure in axon guidance, the loss of Alfy in mice disrupts localization of glial guidepost cells, and attenuates axon outgrowth in response to Netrin-1. These findings further support the growing indication that macroautophagy plays a key role in the developing CNS.
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Affiliation(s)
- Joanna M Dragich
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Takaaki Kuwajima
- Department of Pathology, College of Physicians and Surgeons, Columbia University, New York, United States.,Department of Cell Biology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Megumi Hirose-Ikeda
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Michael S Yoon
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Evelien Eenjes
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Joan R Bosco
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Leora M Fox
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States.,Doctoral Program in Neurobiology and Behavior, Columbia University, New York, United States
| | - Alf H Lystad
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Tinmarla F Oo
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Olga Yarygina
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Tomohiro Mita
- The Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Satoshi Waguri
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Yoshinobu Ichimura
- The Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Masaaki Komatsu
- The Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Anne Simonsen
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Robert E Burke
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States.,Department of Pathology, College of Physicians and Surgeons, Columbia University, New York, United States.,Department of Cell Biology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Carol A Mason
- Department of Pathology, College of Physicians and Surgeons, Columbia University, New York, United States.,Department of Cell Biology, College of Physicians and Surgeons, Columbia University, New York, United States.,Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, United States.,Department of Ophthalmology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Ai Yamamoto
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States.,Department of Pathology, College of Physicians and Surgeons, Columbia University, New York, United States.,Department of Cell Biology, College of Physicians and Surgeons, Columbia University, New York, United States
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62
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Wu DJ, Gu R, Sarin R, Zavodovskaya R, Chen CP, Christiansen BA, Zarbalis KS, Adamopoulos IE. Autophagy-linked FYVE containing protein WDFY3 interacts with TRAF6 and modulates RANKL-induced osteoclastogenesis. J Autoimmun 2016; 73:73-84. [PMID: 27330028 PMCID: PMC5003737 DOI: 10.1016/j.jaut.2016.06.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 06/07/2016] [Accepted: 06/13/2016] [Indexed: 12/20/2022]
Abstract
Recently, autophagy-related proteins were shown to regulate osteoclast mediated bone resorption, a critical process in autoimmune diseases such as rheumatoid arthritis. However, the role of autophagy-linked FYVE containing protein, WDFY3, in osteoclast biology remains elusive. WDFY3 is a master regulator in selective autophagy for clearing ubiquitinated protein aggregates and has been linked with rheumatoid arthritis. Herein, we used a series of WDFY3 transgenic mice (Wdfy3(lacZ) and Wdfy3(loxP)) to investigate the function of WDFY3 in osteoclast development and function. Our data demonstrate that WDFY3 is highly expressed at the growth plate of neonatal mice and is expressed in osteoclasts in vitro cultures. Osteoclasts derived from WDFY3 conditional knockout mice (Wdfy3(loxP/loxP)-LysM-Cre(+)) demonstrated increased osteoclast differentiation as evidenced by higher number and enlarged size of TRAP(+) multinucleated cells. Western blot analysis also revealed up-regulation of TRAF6 and an increase in RANKL-induced NF-κB signaling in WDFY3-deficient bone marrow-derived macrophages compared to wild type cultures. Consistent with these observations WDFY3-deficient cells also demonstrated an increase in osteoclast-related genes Ctsk, Acp5, Mmp9 and an increase of dentine resorption in in vitro assays. Importantly, in vivo RANKL gene transfer exacerbated bone loss in WDFY3 conditional knockout mice, as evidenced by elevated serum TRAP, CTX-I and micro-CT analysis of distal femurs compared to wild type littermates. Taken together, our data highlight a novel role for WDFY3 in osteoclast development and function, which can be exploited for the treatment of musculoskeletal diseases.
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Affiliation(s)
- Dennis J Wu
- Graduate Group in Immunology, University of California at Davis, United States; Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis, United States
| | - Ran Gu
- Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis, United States
| | - Ritu Sarin
- Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis, United States
| | - Regina Zavodovskaya
- Department of Anatomy, Physiology and Cell Biology, University of California at Davis, United States
| | - Chia-Pei Chen
- Department of Statistics, University of California at Davis, United States
| | | | | | - Iannis E Adamopoulos
- Graduate Group in Immunology, University of California at Davis, United States; Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis, United States; Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children, Northern California, United States.
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Cecarini V, Bonfili L, Cuccioloni M, Mozzicafreddo M, Angeletti M, Keller JN, Eleuteri AM. The fine-tuning of proteolytic pathways in Alzheimer's disease. Cell Mol Life Sci 2016; 73:3433-51. [PMID: 27120560 PMCID: PMC11108445 DOI: 10.1007/s00018-016-2238-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/31/2016] [Accepted: 04/21/2016] [Indexed: 11/28/2022]
Abstract
Several integrated proteolytic systems contribute to the maintenance of cellular homeostasis through the continuous removal of misfolded, aggregated or oxidized proteins and damaged organelles. Among these systems, the proteasome and autophagy play the major role in protein quality control, which is a fundamental issue in non-proliferative cells such as neurons. Disturbances in the functionality of these two pathways are frequently observed in neurodegenerative diseases, like Alzheimer's disease, and reflect the accumulation of protease-resistant, deleterious protein aggregates. In this review, we explored the sophisticated crosstalk between the ubiquitin-proteasome system and autophagy in the removal of the harmful structures that characterize Alzheimer's disease neurons. We also dissected the role of the numerous shuttle factors and chaperones that, directly or indirectly interacting with ubiquitin and LC3, are used for cargo selection and delivery to one pathway or the other.
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Affiliation(s)
- Valentina Cecarini
- Department of Biosciences and Veterinary Medicine, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy.
| | - Laura Bonfili
- Department of Biosciences and Veterinary Medicine, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Massimiliano Cuccioloni
- Department of Biosciences and Veterinary Medicine, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Matteo Mozzicafreddo
- Department of Biosciences and Veterinary Medicine, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Mauro Angeletti
- Department of Biosciences and Veterinary Medicine, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Jeffrey N Keller
- Pennington Biomedical Research Centre, Louisiana State University System, Baton Rouge, LA, 70808, USA
| | - Anna Maria Eleuteri
- Department of Biosciences and Veterinary Medicine, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
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Ni HM, McGill MR, Chao X, Du K, Williams JA, Xie Y, Jaeschke H, Ding WX. Removal of acetaminophen protein adducts by autophagy protects against acetaminophen-induced liver injury in mice. J Hepatol 2016; 65:354-62. [PMID: 27151180 PMCID: PMC4955750 DOI: 10.1016/j.jhep.2016.04.025] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 03/16/2016] [Accepted: 04/11/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Acetaminophen (APAP)-induced liver injury is the most frequent cause of acute liver failure in the US and many other countries. Metabolism of APAP results in formation of APAP protein adducts (APAP-AD) in hepatocytes and triggers mitochondrial dysfunction and necrosis. However, the mechanisms for how APAP-AD are removed from hepatocytes remain unknown. METHODS Mice or primary hepatocytes were treated with APAP. APAP-AD were determined by immunoblot, immunostaining and high pressure liquid chomatography with electrochemical detection analysis. RESULTS We found that APAP-AD were detected at 1h, peaked at approximately 2h, declined at 6h and almost full removed at 24h post treatment with APAP in mouse livers and in primary mouse hepatocytes. APAP-AD displayed a punctate pattern and were colocalized with GFP-LC3 positive autophagosomes and Lamp1 positive lysosomes in APAP-treated primary hepatocytes. Moreover, isolated autophagosomes and autolysosomes from APAP-treated mouse livers contained APAP-AD, suggesting autophagy may selectively remove APAP-AD. APAP-AD were detected in both detergent soluble and insoluble pools in APAP-treated mouse livers and hepatocytes. More importantly, pharmacological inhibition of autophagy by leupeptin or chloroquine increased whereas induction of autophagy by Torin 1 decreased serum APAP-AD levels in APAP-treated mice, which correlated with alanine aminotransferase levels and liver necrosis. Furthermore, SQSTM1/p62, an autophagy receptor protein, was recruited to APAP-AD. Adenovirus-mediated shRNA knockdown of SQSTM1/p62 led to increased APAP-AD and necrosis in primary hepatocytes. CONCLUSIONS Our data indicate that APAP-AD are removed though selective autophagy. Pharmacological induction of autophagy may be a novel promising approach for treating APAP-induced liver injury. LAY SUMMARY Acetaminophen overdose can form acetaminophen protein adducts and mitochondria damage in hepatocytes resulting in liver injury. Activation of autophagy-lysosomal degradation pathway can help to remove acetaminophen protein adducts. Pharmacological induction of autophagy may be a novel promising approach for treating APAP-induced liver injury.
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Affiliation(s)
| | | | | | | | | | | | | | - Wen-Xing Ding
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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TSC but not PTEN loss in starving cones of retinitis pigmentosa mice leads to an autophagy defect and mTORC1 dissociation from the lysosome. Cell Death Dis 2016; 7:e2279. [PMID: 27362797 PMCID: PMC5108335 DOI: 10.1038/cddis.2016.182] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/13/2016] [Accepted: 05/31/2016] [Indexed: 02/08/2023]
Abstract
Understanding the mechanisms that contribute to secondary cone photoreceptor loss in retinitis pigmentosa (RP) is critical to devise strategies to prolong vision in this neurodegenerative disease. We previously showed that constitutive activation of the mammalian target of rapamycin complex 1 (mTORC1), by loss of its negative regulator the tuberous sclerosis complex protein 1 (Tsc1; also known as Hamartin), was sufficient to promote robust survival of nutrient-stressed cones in two mouse models of RP by improving glucose uptake and utilization. However, while cone protection remained initially stable for several weeks, eventually cone loss resumed. Here we show that loss of Tsc1 in the cones of RP mice causes a defect in autophagy, leading to the accumulation of ubiquitinated aggregates. We demonstrate that this defect was not due to an inhibition of autophagy initiation, but due to an accumulation of autolysosomes, suggesting a defect in the end-stage of the process causing an amino-acid shortage in cones, thereby hampering long-term cone survival. Because cells with TSC loss fail to completely inhibit mTORC1 and properly activate autophagy in the absence of amino acids, we sporadically administered the mTORC1 inhibitor rapamycin, which was sufficient to correct the defects seen in cones, further enhancing the efficiency of cone survival mediated by Tsc1 loss. Concordantly, activation of mTORC1 by loss of the phosphatase and tensin homolog (Pten) did not affect autophagy and amino-acid metabolism, leading to a more sustained long-term protection of cones. As loss of Pten, which in cones results in less robust mTORC1 activation when compared with loss of Tsc1, still affords long-term cone survival, therapeutic interventions with mTORC1 activators or gene therapy with selected mTORC1 targets that improve glucose metabolism are potential strategies to delay vision loss in patients with RP.
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Hudnall SD, Meng H, Lozovatsky L, Li P, Strout M, Kleinstein SH. Recurrent genetic defects in classical Hodgkin lymphoma cell lines. Leuk Lymphoma 2016; 57:2890-2900. [PMID: 27121023 DOI: 10.1080/10428194.2016.1177179] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Genetic analysis of classical Hodgkin lymphoma (cHL) has been hampered by the paucity of Hodgkin cells in biopsies and their poor growth in vitro. However, a wealth of information has been obtained from cHL cell lines. Here we report results of whole-exome sequencing and karyotypic analysis of five cHL cell lines. Four genes with potentially pathogenic single nucleotide variants (SNV) were detected in three cell lines. SNV were also detected in seventeen HL-related genes and three mitosis-related genes. Copy number variants were detected in four HL-related genes in all five cell lines. Given the high degree of aneuploidy in HL, mitosis-related genes were screened for defects. One mitotic gene (NCAPD2) was amplified in all five HL cell lines, and two genes (FAM190A, PLK4) were amplified in four cell lines. These results suggest that genomic instability of HL may be due to defects in genes involved in chromosome duplication and segregation.
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Affiliation(s)
- S David Hudnall
- a Department of Pathology, Yale School of Medicine , New Haven , CT , USA
| | - Hailong Meng
- a Department of Pathology, Yale School of Medicine , New Haven , CT , USA
| | - Larissa Lozovatsky
- a Department of Pathology, Yale School of Medicine , New Haven , CT , USA
| | - Peining Li
- b Department of Genetics, Yale School of Medicine , New Haven , CT , USA
| | - Matthew Strout
- c Yale Cancer Center, Yale School of Medicine , New Haven , CT , USA.,d Department of Medicine (Hematology), Yale School of Medicine , New Haven , CT , USA
| | - Steven H Kleinstein
- a Department of Pathology, Yale School of Medicine , New Haven , CT , USA.,e Interdepartmental Program in Computational Biology and Bioinformatics , Yale University , New Haven , CT , USA.,f Department of Immunobiology, Yale School of Medicine , New Haven , CT , USA
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67
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Yang RY, Xue H, Yu L, Velayos-Baeza A, Monaco AP, Liu FT. Identification of VPS13C as a Galectin-12-Binding Protein That Regulates Galectin-12 Protein Stability and Adipogenesis. PLoS One 2016; 11:e0153534. [PMID: 27073999 PMCID: PMC4830523 DOI: 10.1371/journal.pone.0153534] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 03/30/2016] [Indexed: 01/13/2023] Open
Abstract
Galectin-12, a member of the galectin family of β-galactoside-binding animal lectins, is preferentially expressed in adipocytes and required for adipocyte differentiation in vitro. This protein was recently found to regulate lipolysis, whole body adiposity, and glucose homeostasis in vivo. Here we identify VPS13C, a member of the VPS13 family of vacuolar protein sorting-associated proteins highly conserved throughout eukaryotic evolution, as a major galectin-12-binding protein. VPS13C is upregulated during adipocyte differentiation, and is required for galectin-12 protein stability. Knockdown of Vps13c markedly reduces the steady-state levels of galectin-12 by promoting its degradation through primarily the lysosomal pathway, and impairs adipocyte differentiation. Our studies also suggest that VPS13C may have a broader role in protein quality control. The regulation of galectin-12 stability by VPS13C could potentially be exploited for therapeutic intervention of obesity and related metabolic diseases.
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Affiliation(s)
- Ri-Yao Yang
- Department of Dermatology, School of Medicine, University of California-Davis, Sacramento, California, 95817, United States of America
| | - Huiting Xue
- Department of Dermatology, School of Medicine, University of California-Davis, Sacramento, California, 95817, United States of America
- School of Life Sciences, Northeast Normal University, Changchun, 130024, People’s Republic of China
| | - Lan Yu
- Department of Dermatology, School of Medicine, University of California-Davis, Sacramento, California, 95817, United States of America
| | | | - Anthony P. Monaco
- Wellcome Trust Centre for Human Genetics, OX3 7BN, Oxford, United Kingdom
| | - Fu-Tong Liu
- Department of Dermatology, School of Medicine, University of California-Davis, Sacramento, California, 95817, United States of America
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei, 115, Taiwan
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Barrett A, Hermann GJ. A Caenorhabditis elegans Homologue of LYST Functions in Endosome and Lysosome-Related Organelle Biogenesis. Traffic 2016; 17:515-35. [PMID: 26822177 DOI: 10.1111/tra.12381] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 01/25/2016] [Accepted: 01/25/2016] [Indexed: 01/20/2023]
Abstract
LYST-1 is a Caenorhabditis elegans BEACH domain containing protein (BDCP) homologous to LYST and NBEAL2, BDCPs controlling organelle biogenesis that are implicated in human disease. Unlike the three other BDCPs encoded by C. elegans, mutations in lyst-1 lead to smaller lysosome-related organelles (LROs), smaller lysosomes, increased numbers of LROs and decreased numbers of early endosomes. lyst-1(-) mutations do not obviously disrupt protein trafficking to lysosomes or LROs, however, the formation of gut granules is diminished.
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Affiliation(s)
- Alec Barrett
- Department of Biology, Lewis & Clark College, 0615 SW Palatine Hill Rd., Portland, OR, 97219, USA
| | - Greg J Hermann
- Department of Biology, Lewis & Clark College, 0615 SW Palatine Hill Rd., Portland, OR, 97219, USA
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69
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Chaurasia M, Bhatt AN, Das A, Dwarakanath BS, Sharma K. Radiation-induced autophagy: mechanisms and consequences. Free Radic Res 2016; 50:273-90. [DOI: 10.3109/10715762.2015.1129534] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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70
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Cho GW, Altamirano F, Hill JA. Chronic heart failure: Ca(2+), catabolism, and catastrophic cell death. Biochim Biophys Acta Mol Basis Dis 2016; 1862:763-777. [PMID: 26775029 DOI: 10.1016/j.bbadis.2016.01.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 12/28/2015] [Accepted: 01/06/2016] [Indexed: 12/12/2022]
Abstract
Robust successes have been achieved in recent years in conquering the acutely lethal manifestations of heart disease. Many patients who previously would have died now survive to enjoy happy and productive lives. Nevertheless, the devastating impact of heart disease continues unabated, as the spectrum of disease has evolved with new manifestations. In light of this ever-evolving challenge, insights that culminate in novel therapeutic targets are urgently needed. Here, we review fundamental mechanisms of heart failure, both with reduced (HFrEF) and preserved (HFpEF) ejection fraction. We discuss pathways that regulate cardiomyocyte remodeling and turnover, focusing on Ca(2+) signaling, autophagy, and apoptosis. In particular, we highlight recent insights pointing to novel connections among these events. We also explore mechanisms whereby potential therapeutic approaches targeting these processes may improve morbidity and mortality in the devastating syndrome of heart failure.
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Affiliation(s)
- Geoffrey W Cho
- Department of Internal Medicine (Cardiology), University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Francisco Altamirano
- Department of Internal Medicine (Cardiology), University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joseph A Hill
- Department of Internal Medicine (Cardiology), University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Abstract
Autophagosomes are double-membrane sequestering vesicles that are the hallmark of the intracellular catabolic process called macroautophagy. They are formed by the orchestrated interplay of the AuTophaGy-related (ATG) proteins. The cargo molecules targeted by autophagosomes ranges from long-lived proteins and superfluous or excess organelles to invading pathogens. Autophagosomes finally fuse with lysosomes delivering the sequestered material in the interior of these organelles where it is degraded by resident hydrolases. Autophagy represents a key survival mechanism because it clears the cytoplasm from unwanted and potentially toxic structures, and the autophagosomes are the central stage of it.
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72
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Rashid HO, Yadav RK, Kim HR, Chae HJ. ER stress: Autophagy induction, inhibition and selection. Autophagy 2015; 11:1956-1977. [PMID: 26389781 DOI: 10.1080/15548627.2015.1091141] [Citation(s) in RCA: 561] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
An accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) leads to stress conditions. To mitigate such circumstances, stressed cells activate a homeostatic intracellular signaling network cumulatively called the unfolded protein response (UPR), which orchestrates the recuperation of ER function. Macroautophagy (hereafter autophagy), an intracellular lysosome-mediated bulk degradation pathway for recycling and eliminating wornout proteins, protein aggregates, and damaged organelles, has also emerged as an essential protective mechanism during ER stress. These 2 systems are dynamically interconnected, and recent investigations have revealed that ER stress can either stimulate or inhibit autophagy. However, the stress-associated molecular cues that control the changeover switch between induction and inhibition of autophagy are largely obscure. This review summarizes the crosstalk between ER stress and autophagy and their signaling networks mainly in mammalian-based systems. Additionally, we highlight current knowledge on selective autophagy and its connection to ER stress.
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Affiliation(s)
- Harun-Or Rashid
- a Department of Pharmacology ; Medical School; Chonbuk National University
| | - Raj Kumar Yadav
- a Department of Pharmacology ; Medical School; Chonbuk National University
| | - Hyung-Ryong Kim
- b Department of Dental Pharmacology ; College of Dentistry; Wonkwang University
| | - Han-Jung Chae
- a Department of Pharmacology ; Medical School; Chonbuk National University
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73
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Kenney DL, Benarroch EE. The autophagy-lysosomal pathway: General concepts and clinical implications. Neurology 2015. [PMID: 26203091 DOI: 10.1212/wnl.0000000000001860] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Daniel L Kenney
- From the Departments of Child and Adolescent Neurology (D.L.K.) and Neurology (E.E.B.), Mayo Clinic, Rochester, MN
| | - Eduardo E Benarroch
- From the Departments of Child and Adolescent Neurology (D.L.K.) and Neurology (E.E.B.), Mayo Clinic, Rochester, MN.
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74
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Schönenberger MJ, Kovacs WJ. Hypoxia signaling pathways: modulators of oxygen-related organelles. Front Cell Dev Biol 2015; 3:42. [PMID: 26258123 PMCID: PMC4508581 DOI: 10.3389/fcell.2015.00042] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/15/2015] [Indexed: 01/09/2023] Open
Abstract
Oxygen (O2) is an essential substrate in cellular metabolism, bioenergetics, and signaling and as such linked to the survival and normal function of all metazoans. Low O2 tension (hypoxia) is a fundamental feature of physiological processes as well as pathophysiological conditions such as cancer and ischemic diseases. Central to the molecular mechanisms underlying O2 homeostasis are the hypoxia-inducible factors-1 and -2 alpha (HIF-1α and EPAS1/HIF-2α) that function as master regulators of the adaptive response to hypoxia. HIF-induced genes promote characteristic tumor behaviors, including angiogenesis and metabolic reprogramming. The aim of this review is to critically explore current knowledge of how HIF-α signaling regulates the abundance and function of major O2-consuming organelles. Abundant evidence suggests key roles for HIF-1α in the regulation of mitochondrial homeostasis. An essential adaptation to sustained hypoxia is repression of mitochondrial respiration and induction of glycolysis. HIF-1α activates several genes that trigger mitophagy and represses regulators of mitochondrial biogenesis. Several lines of evidence point to a strong relationship between hypoxia, the accumulation of misfolded proteins in the endoplasmic reticulum, and activation of the unfolded protein response. Surprisingly, although peroxisomes depend highly on molecular O2 for their function, there has been no evidence linking HIF signaling to peroxisomes. We discuss our recent findings that establish HIF-2α as a negative regulator of peroxisome abundance and suggest a mechanism by which cells attune peroxisomal function with O2 availability. HIF-2α activation augments peroxisome turnover by pexophagy and thereby changes lipid composition reminiscent of peroxisomal disorders. We discuss potential mechanisms by which HIF-2α might trigger pexophagy and place special emphasis on the potential pathological implications of HIF-2α-mediated pexophagy for human health.
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Affiliation(s)
- Miriam J Schönenberger
- Department of Biology, Institute of Molecular Health Sciences ETH Zurich, Zurich, Switzerland
| | - Werner J Kovacs
- Department of Biology, Institute of Molecular Health Sciences ETH Zurich, Zurich, Switzerland
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75
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Abstract
Proteostasis is maintained by multiple cellular pathways, including protein synthesis, quality control, and degradation. An imbalance of neuronal proteostasis, associated with protein misfolding and aggregation, leads to proteinopathies or neurodegeneration. While genetic variations and protein modifications contribute to aggregate formation, components of the proteostasis network dictate the fate of protein aggregates. Here we provide an overview of proteostasis pathways and their interplay (particularly autophagy) with the metabolism of disease-related proteins. We review recent studies on neuronal activity-mediated regulation of proteostasis and transcellular propagation of protein aggregates in the nervous system. Targeting proteostasis pathways therapeutically remains an attractive but challenging task.
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Affiliation(s)
- Junghyun Lim
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhenyu Yue
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Affiliation(s)
- Nicholas J. Lennemann
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Carolyn B. Coyne
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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77
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Lystad AH, Simonsen A. Assays to monitor aggrephagy. Methods 2015; 75:112-9. [DOI: 10.1016/j.ymeth.2014.12.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/12/2014] [Accepted: 12/22/2014] [Indexed: 12/15/2022] Open
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79
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Hyttinen JM, Amadio M, Viiri J, Pascale A, Salminen A, Kaarniranta K. Clearance of misfolded and aggregated proteins by aggrephagy and implications for aggregation diseases. Ageing Res Rev 2014; 18:16-28. [PMID: 25062811 DOI: 10.1016/j.arr.2014.07.002] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/02/2014] [Accepted: 07/14/2014] [Indexed: 12/19/2022]
Abstract
Processing of misfolded proteins is important in order for the cell to maintain its normal functioning and homeostasis. Three systems control the quality of proteins: chaperone-mediated refolding, proteasomal degradation of ubiquitinated proteins, and finally, when the two others fail, aggrephagy, as selective form of autophagy, degrades ubiquitin-labelled aggregated cargos. In this route misfolded proteins gradually form larger aggregates, aggresomes and they eventually become double membrane-wrapped organelles called autophagosomes, which become degraded when they fuse to lysosomes, for reuse by the cell. The stages, the main molecules participating in the process, and the regulation of aggrephagy are discussed here, as is the role of protein aggregation in protein accumulation diseases. In particular, we emphasize that both Alzheimer's disease and age-related macular degeneration, two of the most common pathologies in the aged, are characterized by altered protein clearance and deposits. Based on the hypothesis that manipulations of autophagy may be potentially useful in these and other aggregation-related diseases, we will discuss some promising therapeutic strategies to counteract protein aggregates-induced cellular toxicity.
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80
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Holland P, Torgersen ML, Sandvig K, Simonsen A. LYST Affects Lysosome Size and Quantity, but not Trafficking or Degradation Through Autophagy or Endocytosis. Traffic 2014; 15:1390-405. [DOI: 10.1111/tra.12227] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 09/08/2014] [Accepted: 09/10/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Petter Holland
- Department of Biochemistry, Institute of Basic Medical Sciences; University of Oslo; PB 1112 Blindern, 0317 Oslo Norway
| | - Maria L. Torgersen
- Department of Biochemistry, Institute of Basic Medical Sciences; University of Oslo; PB 1112 Blindern, 0317 Oslo Norway
- Department of Biochemistry, Institute for Cancer Research; Oslo University Hospital - The Norwegian Radium Hospital; 0379 Osloa Norway
| | - Kirsten Sandvig
- Department of Biochemistry, Institute for Cancer Research; Oslo University Hospital - The Norwegian Radium Hospital; 0379 Osloa Norway
| | - Anne Simonsen
- Department of Biochemistry, Institute of Basic Medical Sciences; University of Oslo; PB 1112 Blindern, 0317 Oslo Norway
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81
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Martin DDO, Ladha S, Ehrnhoefer DE, Hayden MR. Autophagy in Huntington disease and huntingtin in autophagy. Trends Neurosci 2014; 38:26-35. [PMID: 25282404 DOI: 10.1016/j.tins.2014.09.003] [Citation(s) in RCA: 225] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/08/2014] [Accepted: 09/09/2014] [Indexed: 01/20/2023]
Abstract
Autophagy is an important biological process that is essential for the removal of damaged organelles and toxic or aggregated proteins by delivering them to the lysosome for degradation. Consequently, autophagy has become a primary target for the treatment of neurodegenerative diseases that involve aggregating proteins. In Huntington disease (HD), an expansion of the polyglutamine (polyQ) tract in the N-terminus of the huntingtin (HTT) protein leads to protein aggregation. However, HD is unique among the neurodegenerative proteinopathies in that autophagy is not only dysfunctional but wild type (wt) HTT also appears to play several roles in regulating the dynamics of autophagy. Herein, we attempt to integrate the recently described novel roles of wtHTT and altered autophagy in HD.
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Affiliation(s)
- Dale D O Martin
- Centre for Molecular Medicine and Therapeutics (CMMT), Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada.
| | - Safia Ladha
- Centre for Molecular Medicine and Therapeutics (CMMT), Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Dagmar E Ehrnhoefer
- Centre for Molecular Medicine and Therapeutics (CMMT), Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Michael R Hayden
- Centre for Molecular Medicine and Therapeutics (CMMT), Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada.
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Abstract
Autophagy is the main cellular catabolic process responsible for degrading organelles and large protein aggregates. It is initiated by the formation of a unique membrane structure, the phagophore, which engulfs part of the cytoplasm and forms a double-membrane vesicle termed the autophagosome. Fusion of the outer autophagosomal membrane with the lysosome and degradation of the inner membrane contents complete the process. The extent of autophagy must be tightly regulated to avoid destruction of proteins and organelles essential for cell survival. Autophagic activity is thus regulated by external and internal cues, which initiate the formation of well-defined autophagy-related protein complexes that mediate autophagosome formation and selective cargo recruitment into these organelles. Autophagosome formation and the signaling pathways that regulate it have recently attracted substantial attention. In this review, we analyze the different signaling pathways that regulate autophagy and discuss recent progress in our understanding of autophagosome biogenesis.
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Affiliation(s)
- Adi Abada
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Zvulun Elazar
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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Abstract
Autophagy is a conserved catabolic process that delivers the cytosol and cytosolic constituents to the lysosome. Its fundamental role is to maintain cellular homeostasis and to protect cells from varying insults, including misfolded proteins and damaged organelles. Beyond these roles, the highly specialized cells of the brain have further adapted autophagic pathways to suit their distinct needs. In this review, we briefly summarize our current understanding of the different forms of autophagy and then offer a closer look at how these pathways impact neuronal and glial functions. The emerging evidence indicates that not only are autophagy pathways essential for neural health, but they have a direct impact on developmental and neurodegenerative processes. Taken together, as we unravel the complex roles autophagy pathways play, we will gain the necessary insight to modify these pathways to protect the human brain and treat neurodegenerative diseases.
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Affiliation(s)
- Ai Yamamoto
- Departments of Neurology, Pathology, and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032;
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84
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Abstract
SIGNIFICANCE Autophagy is a highly conserved eukaryotic cellular recycling process. Through the degradation of cytoplasmic organelles, proteins, and macromolecules, and the recycling of the breakdown products, autophagy plays important roles in cell survival and maintenance. Accordingly, dysfunction of this process contributes to the pathologies of many human diseases. RECENT ADVANCES Extensive research is currently being done to better understand the process of autophagy. In this review, we describe current knowledge of the morphology, molecular mechanism, and regulation of mammalian autophagy. CRITICAL ISSUES At the mechanistic and regulatory levels, there are still many unanswered questions and points of confusion that have yet to be resolved. FUTURE DIRECTIONS Through further research, a more complete and accurate picture of the molecular mechanism and regulation of autophagy will not only strengthen our understanding of this significant cellular process, but will aid in the development of new treatments for human diseases in which autophagy is not functioning properly.
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Affiliation(s)
- Katherine R Parzych
- Department of Molecular, Cellular and Developmental Biology, Life Sciences Institute, University of Michigan , Ann Arbor, Michigan
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85
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Shapiro IM, Layfield R, Lotz M, Settembre C, Whitehouse C. Boning up on autophagy: the role of autophagy in skeletal biology. Autophagy 2013; 10:7-19. [PMID: 24225636 DOI: 10.4161/auto.26679] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
From an evolutionary perspective, the major function of bone is to provide stable sites for muscle attachment and affording protection of vital organs, especially the heart and lungs (ribs) and spinal cord (vertebrae and intervertebral discs). However, bone has a considerable number of other functions: serving as a store for mineral ions, providing a site for blood cell synthesis and participating in a complex system-wide endocrine system. Not surprisingly, bone and cartilage cell homeostasis is tightly controlled, as is the maintenance of tissue structure and mass. While a great deal of new information is accruing concerning skeletal cell homeostasis, one relatively new observation is that the cells of bone (osteoclasts osteoblasts and osteocytes) and cartilage (chondrocytes) exhibit autophagy. The focus of this review is to examine the significance of this process in terms of the functional demands of the skeleton in health and during growth and to provide evidence that dysregulation of the autophagic response is involved in the pathogenesis of diseases of bone (Paget disease of bone) and cartilage (osteoarthritis and the mucopolysaccharidoses). Delineation of molecular changes in the autophagic process is uncovering new approaches for the treatment of diseases that affect the axial and appendicular skeleton.
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Affiliation(s)
- Irving M Shapiro
- Jefferson Medical College; Thomas Jefferson University; Philadelphia, PA USA
| | - Robert Layfield
- School of Life Sciences; University of Nottingham Medical School; Nottingham UK
| | - Martin Lotz
- Arthritis Research; The Scripps Research Institute; La Jolla, CA USA
| | - Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM); Naples, Italy; Department of Molecular and Human Genetics; Baylor College of Medicine, Houston, TXUSA and Jan and Dan Duncan Neurological Research Institute; Texas Children's Hospital; Houston, TX USA; Medical Genetics; Department of Translational and Medical Science; Federico II University; Naples, Italy
| | - Caroline Whitehouse
- Department of Medical and Molecular Genetics; Kings College London; London UK
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Cullinane AR, Schäffer AA, Huizing M. The BEACH is hot: a LYST of emerging roles for BEACH-domain containing proteins in human disease. Traffic 2013; 14:749-66. [PMID: 23521701 DOI: 10.1111/tra.12069] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/18/2013] [Accepted: 03/23/2013] [Indexed: 12/19/2022]
Abstract
BEACH (named after 'Beige and Chediak-Higashi') is a conserved ∼280 residue domain, present in nine human BEACH domain containing proteins (BDCPs). Most BDCPs are large, containing a PH-like domain for membrane association preceding their BEACH domain, and containing WD40 and other domains for ligand binding. Recent studies found that mutations in individual BDCPs cause several human diseases. BDCP alterations affect lysosome size (LYST and NSMAF), apoptosis (NSMAF), autophagy (LYST, WDFY3, LRBA), granule size (LYST, NBEAL2, NBEA) or synapse formation (NBEA). However, the roles of each BDCP in these membrane events remain controversial. After reviewing studies on individual BDCPs, we propose a unifying hypothesis that BDCPs act as scaffolding proteins that facilitate membrane events, including both fission and fusion, determined by their binding partners. BDCPs may also bind each other, enabling fusion or fission of vesicles that are not necessarily of the same type. Such mechanisms explain why different BDCPs may have roles in autophagy; each BDCP is specific for the cell type or the cargo, but not necessarily specific for attaching to the autophagosome. Further elucidation of these mechanisms, preferably carrying out the same experiment on multiple BDCPs, and possibly using patients' cells, may identify potential targets for therapy.
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Affiliation(s)
- Andrew R Cullinane
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
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Gaugel A, Bakula D, Hoffmann A, Proikas-Cezanne T. Defining regulatory and phosphoinositide-binding sites in the human WIPI-1 β-propeller responsible for autophagosomal membrane localization downstream of mTORC1 inhibition. J Mol Signal 2012; 7:16. [PMID: 23088497 PMCID: PMC3543385 DOI: 10.1186/1750-2187-7-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 09/24/2012] [Indexed: 12/15/2022] Open
Abstract
UNLABELLED BACKGROUND Autophagy is a cytoprotective, lysosomal degradation system regulated upon induced phosphatidylinositol 3-phosphate (PtdIns(3)P) generation by phosphatidylinositol 3-kinase class III (PtdIns3KC3) downstream of mTORC1 inhibition. The human PtdIns(3)P-binding β-propeller protein WIPI-1 accumulates at the initiation site for autophagosome formation (phagophore), functions upstream of the Atg12 and LC3 conjugation systems, and localizes at both the inner and outer membrane of generated autophagosomes. In addition, to a minor degree WIPI-1 also binds PtdIns(3,5)P2. By homology modelling we earlier identified 24 evolutionarily highly conserved amino acids that cluster at two opposite sites of the open Velcro arranged WIPI-1 β-propeller. RESULTS By alanine scanning mutagenesis of 24 conserved residues in human WIPI-1 we define the PtdIns-binding site of human WIPI-1 to critically include S203, S205, G208, T209, R212, R226, R227, G228, S251, T255, H257. These amino acids confer PtdIns(3)P or PtdIns(3,5)P2 binding. In general, WIPI-1 mutants unable to bind PtdIns(3)P/PtdIns(3,5)P2 lost their potential to localize at autophagosomal membranes, but WIPI-1 mutants that retained PtdIns(3)P/PtdIns(3,5)P2 binding localized at Atg12-positive phagophores upon mTORC1 inhibition. Both, downregulation of mTOR by siRNA or cellular PtdIns(3)P elevation upon PIKfyve inhibition by YM201636 significantly increased the localization of WIPI-1 at autophagosomal membranes. Further, we identified regulatory amino acids that influence the membrane recruitment of WIPI-1. Exceptional, WIPI-1 R110A localization at Atg12-positive membranes was independent of autophagy stimulation and insensitive to wortmannin. R112A and H185A mutants were unable to bind PtdIns(3)P/PtdIns(3,5)P2 but localized at autophagosomal membranes, although in a significant reduced number of cells when compared to wild-type WIPI-1. CONCLUSIONS We identified amino acids of the WIPI-1 β-propeller that confer PtdIns(3)P or PtdIns(3,5)P2 binding (S203, S205, G208, T209, R212, R226, R227, G228, S251, T255, H257), and that regulate the localization at autophagosomal membranes (R110, R112, H185) downstream of mTORC1 inhibition.
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Affiliation(s)
- Anja Gaugel
- From the Autophagy Laboratory, Department of Molecular Biology, Interfaculty Institute of Cell Biology, Eberhard Karls University Tuebingen, Auf der Morgenstelle 15, 72076, Tuebingen, Germany.
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