1
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Zhao XY, Xu DE, Wu ML, Liu JC, Shi ZL, Ma QH. Regulation and function of endoplasmic reticulum autophagy in neurodegenerative diseases. Neural Regen Res 2025; 20:6-20. [PMID: 38767472 PMCID: PMC11246128 DOI: 10.4103/nrr.nrr-d-23-00995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/09/2023] [Accepted: 12/13/2023] [Indexed: 05/22/2024] Open
Abstract
The endoplasmic reticulum, a key cellular organelle, regulates a wide variety of cellular activities. Endoplasmic reticulum autophagy, one of the quality control systems of the endoplasmic reticulum, plays a pivotal role in maintaining endoplasmic reticulum homeostasis by controlling endoplasmic reticulum turnover, remodeling, and proteostasis. In this review, we briefly describe the endoplasmic reticulum quality control system, and subsequently focus on the role of endoplasmic reticulum autophagy, emphasizing the spatial and temporal mechanisms underlying the regulation of endoplasmic reticulum autophagy according to cellular requirements. We also summarize the evidence relating to how defective or abnormal endoplasmic reticulum autophagy contributes to the pathogenesis of neurodegenerative diseases. In summary, this review highlights the mechanisms associated with the regulation of endoplasmic reticulum autophagy and how they influence the pathophysiology of degenerative nerve disorders. This review would help researchers to understand the roles and regulatory mechanisms of endoplasmic reticulum-phagy in neurodegenerative disorders.
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Affiliation(s)
- Xiu-Yun Zhao
- Department of Neurology and Clinical Research Center of Neurological Disease, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Neuroscience & Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Soochow University, Suzhou, Jiangsu Province, China
| | - De-En Xu
- Department of Neurology, Jiangnan University Medical Center, Wuxi, Jiangsu Province, China
| | - Ming-Lei Wu
- Department of Neurology and Clinical Research Center of Neurological Disease, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Neuroscience & Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Soochow University, Suzhou, Jiangsu Province, China
| | - Ji-Chuan Liu
- Department of Neurology and Clinical Research Center of Neurological Disease, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Neuroscience & Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Soochow University, Suzhou, Jiangsu Province, China
| | - Zi-Ling Shi
- Department of Neurology and Clinical Research Center of Neurological Disease, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Neuroscience & Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Soochow University, Suzhou, Jiangsu Province, China
| | - Quan-Hong Ma
- Department of Neurology and Clinical Research Center of Neurological Disease, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Neuroscience & Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Soochow University, Suzhou, Jiangsu Province, China
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2
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Deolal P, Scholz J, Ren K, Bragulat-Teixidor H, Otsuka S. Sculpting nuclear envelope identity from the endoplasmic reticulum during the cell cycle. Nucleus 2024; 15:2299632. [PMID: 38238284 PMCID: PMC10802211 DOI: 10.1080/19491034.2023.2299632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024] Open
Abstract
The nuclear envelope (NE) regulates nuclear functions, including transcription, nucleocytoplasmic transport, and protein quality control. While the outer membrane of the NE is directly continuous with the endoplasmic reticulum (ER), the NE has an overall distinct protein composition from the ER, which is crucial for its functions. During open mitosis in higher eukaryotes, the NE disassembles during mitotic entry and then reforms as a functional territory at the end of mitosis to reestablish nucleocytoplasmic compartmentalization. In this review, we examine the known mechanisms by which the functional NE reconstitutes from the mitotic ER in the continuous ER-NE endomembrane system during open mitosis. Furthermore, based on recent findings indicating that the NE possesses unique lipid metabolism and quality control mechanisms distinct from those of the ER, we explore the maintenance of NE identity and homeostasis during interphase. We also highlight the potential significance of membrane junctions between the ER and NE.
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Affiliation(s)
- Pallavi Deolal
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Medical University of Vienna, Center for Medical Biochemistry, Department of Molecular Biology, Vienna, Austria
| | - Julia Scholz
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Medical University of Vienna, Center for Medical Biochemistry, Department of Molecular Biology, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Kaike Ren
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Medical University of Vienna, Center for Medical Biochemistry, Department of Molecular Biology, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Helena Bragulat-Teixidor
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Medical University of Vienna, Center for Medical Biochemistry, Department of Molecular Biology, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Shotaro Otsuka
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Medical University of Vienna, Center for Medical Biochemistry, Department of Molecular Biology, Vienna, Austria
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3
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Zhao H, Yang M, Han Y, Jiang N, Liu Y, Liu C, Yang J, Luo S, Liu C, Sun L, Liu F, Liu Y. HIF-1α/BNIP3 mediated endoplasmic reticulum degradation via autophagy protects against ischemia reperfusion-induced acute kidney injury. Antioxid Redox Signal 2024. [PMID: 39099334 DOI: 10.1089/ars.2023.0467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Endoplasmic reticulum (ER) degradation via autophagy is a process that maintains ER homeostasis when cells are in a state of stress and is associated with many diseases; however, the role of hypoxia inducible factor-1α (HIF-1α)-mediated ER degradation and the related regulatory pathway in acute kidney injury (AKI) still needs to be further established. In the present study, an in vivo AKI model was induced in mice via the ischemia‒reperfusion (IR) method. The results revealed that HIF-1α and BNIP3 were increased, and autophagy and ER degradation were activated in the kidneys of AKI mice, whereas HIF-1α knockout significantly inhibited BNIP3, autophagy and ER degradation, accompanied by aggravated kidney injury. Overexpression of HIF-1α in vitro significantly increased BNIP3, autophagy and ER degradation, whereas inhibition of BNIP3 significantly reversed the effects of HIF-1α. In addition, the in vitro inhibition of autophagy with chloroquine significantly reversed the effects of HIF-1α on cell apoptosis. Moreover, selectively overexpressing BNIP3 on the ER membrane significantly increased ER degradation via autophagy and decreased cell apoptosis in vitro. These data indicate that HIF-1α/BNIP3-mediated ER degradation via autophagy in tubular cells protects against IR-induced AKI.
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Affiliation(s)
- Hao Zhao
- The Second Xiangya Hospital of Central South University, Changsha, Hunan, China;
| | - Ming Yang
- Department of Nephrology,The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China;
| | - Yachun Han
- Department of Nephrology,The , Changsha, Hunan 410011, China;
| | - Na Jiang
- The Second Xiangya Hospital, Central South University, changsha, China;
| | - Yan Liu
- The Second Xiangya Hospital of Central South University, Changsha, Hunan, China;
| | - Chenrui Liu
- The Second Xiangya Hospital of Central South University, Changsha, Hunan, China;
| | - Jinfei Yang
- The Second Xiangya Hospital of Central South University, Changsha, Hunan, China;
| | - Shilu Luo
- The Second Xiangya Hospital of Central South University, Changsha, Hunan, China;
| | - Chongbin Liu
- The Second Xiangya Hospital of Central South University, Changsha, Hunan, China;
| | - Lin Sun
- The Second Xiangya Hospital of Central South University, Department of Nephrology, Changsha, Hunan, China;
| | - Fuyou Liu
- The Second Xiangya Hospital of Central South University, Changsha, Hunan, China;
| | - Yu Liu
- The Second Xiangya Hospital of Central South University, Department of Nephrology, Changsha, China, 410011;
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4
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Wright MT, Timalsina B, Garcia Lopez V, Hermanson JN, Garcia S, Plate L. Time-resolved interactome profiling deconvolutes secretory protein quality control dynamics. Mol Syst Biol 2024:10.1038/s44320-024-00058-1. [PMID: 39103653 DOI: 10.1038/s44320-024-00058-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/15/2024] [Accepted: 07/22/2024] [Indexed: 08/07/2024] Open
Abstract
Many cellular processes are governed by protein-protein interactions that require tight spatial and temporal regulation. Accordingly, it is necessary to understand the dynamics of these interactions to fully comprehend and elucidate cellular processes and pathological disease states. To map de novo protein-protein interactions with time resolution at an organelle-wide scale, we developed a quantitative mass spectrometry method, time-resolved interactome profiling (TRIP). We apply TRIP to elucidate aberrant protein interaction dynamics that lead to the protein misfolding disease congenital hypothyroidism. We deconvolute altered temporal interactions of the thyroid hormone precursor thyroglobulin with pathways implicated in hypothyroidism pathophysiology, such as Hsp70-/90-assisted folding, disulfide/redox processing, and N-glycosylation. Functional siRNA screening identified VCP and TEX264 as key protein degradation components whose inhibition selectively rescues mutant prohormone secretion. Ultimately, our results provide novel insight into the temporal coordination of protein homeostasis, and our TRIP method should find broad applications in investigating protein-folding diseases and cellular processes.
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Affiliation(s)
- Madison T Wright
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37240, USA
| | - Bibek Timalsina
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37240, USA
| | - Valeria Garcia Lopez
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37240, USA
| | - Jake N Hermanson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37240, USA
| | - Sarah Garcia
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37240, USA
| | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37240, USA.
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37240, USA.
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
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5
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Pareek G, Kundu M. Physiological functions of ULK1/2. J Mol Biol 2024; 436:168472. [PMID: 38311233 DOI: 10.1016/j.jmb.2024.168472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
UNC-51-like kinases 1 and 2 (ULK1/2) are serine/threonine kinases that are best known for their evolutionarily conserved role in the autophagy pathway. Upon sensing the nutrient status of a cell, ULK1/2 integrate signals from upstream cellular energy sensors such as mTOR and AMPK and relay them to the downstream components of the autophagy machinery. ULK1/2 also play indispensable roles in the selective autophagy pathway, removing damaged mitochondria, invading pathogens, and toxic protein aggregates. Additional functions of ULK1/2 have emerged beyond autophagy, including roles in protein trafficking, RNP granule dynamics, and signaling events impacting innate immunity, axon guidance, cellular homeostasis, and cell fate. Therefore, it is no surprise that alterations in ULK1/2 expression and activity have been linked with pathophysiological processes, including cancer, neurological disorders, and cardiovascular diseases. Growing evidence suggests that ULK1/2 function as biological rheostats, tuning cellular functions to intra and extra-cellular cues. Given their broad physiological relevance, ULK1/2 are candidate targets for small molecule activators or inhibitors that may pave the way for the development of therapeutics for the treatment of diseases in humans.
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Affiliation(s)
- Gautam Pareek
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mondira Kundu
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, TN, USA.
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6
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Zhang M, Wang Z, Zhao Q, Yang Q, Bai J, Yang C, Zhang ZR, Liu Y. USP20 deubiquitinates and stabilizes the reticulophagy receptor RETREG1/FAM134B to drive reticulophagy. Autophagy 2024; 20:1780-1797. [PMID: 38705724 PMCID: PMC11262213 DOI: 10.1080/15548627.2024.2347103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 04/19/2024] [Indexed: 05/07/2024] Open
Abstract
The endoplasmic reticulum (ER) serves as a hub for various cellular processes, and maintaining ER homeostasis is essential for cell function. Reticulophagy is a selective process that removes impaired ER subdomains through autophagy-mediatedlysosomal degradation. While the involvement of ubiquitination in autophagy regulation is well-established, its role in reticulophagy remains unclear. In this study, we screened deubiquitinating enzymes (DUBs) involved in reticulophagy and identified USP20 (ubiquitin specific peptidase 20) as a key regulator of reticulophagy under starvation conditions. USP20 specifically cleaves K48- and K63-linked ubiquitin chains on the reticulophagy receptor RETREG1/FAM134B (reticulophagy regulator 1), thereby stabilizing the substrate and promoting reticulophagy. Remarkably, despite lacking a transmembrane domain, USP20 is recruited to the ER through its interaction with VAPs (VAMP associated proteins). VAPs facilitate the recruitment of early autophagy proteins, including WIPI2 (WD repeat domain, phosphoinositide interacting 2), to specific ER subdomains, where USP20 and RETREG1 are enriched. The recruitment of WIPI2 and other proteins in this process plays a crucial role in facilitating RETREG1-mediated reticulophagy in response to nutrient deprivation. These findings highlight the critical role of USP20 in maintaining ER homeostasis by deubiquitinating and stabilizing RETREG1 at distinct ER subdomains, where USP20 further recruits VAPs and promotes efficient reticulophagy.Abbreviations: ACTB actin beta; ADRB2 adrenoceptor beta 2; AMFR/gp78 autocrine motility factor receptor; ATG autophagy related; ATL3 atlastin GTPase 3; BafA1 bafilomycin A1; BECN1 beclin 1; CALCOCO1 calcium binding and coiled-coil domain 1; CCPG1 cell cycle progression 1; DAPI 4',6-diamidino-2-phenylindole; DTT dithiothreitol; DUB deubiquitinating enzyme; EBSS Earle's Balanced Salt Solution; FFAT two phenylalanines (FF) in an acidic tract; GABARAP GABA type A receptor-associated protein; GFP green fluorescent protein; HMGCR 3-hydroxy-3-methylglutaryl-CoA reductase; IL1B interleukin 1 beta; LIR LC3-interacting region; MAP1LC3/LC3 microtubule associated protein 1 light chain 3; PIK3C3/Vps34 phosphatidylinositol 3-kinase catalytic subunit type 3; RB1CC1/FIP200 RB1 inducible coiled-coil 1; RETREG1/FAM134B reticulophagy regulator 1; RFP red fluorescent protein; RHD reticulon homology domain; RIPK1 receptor interacting serine/threonine kinase 1; RTN3L reticulon 3 long isoform; SEC61B SEC61 translocon subunit beta; SEC62 SEC62 homolog, preprotein translocation factor; SIM super-resolution structured illumination microscopy; SNAI2 snail family transcriptional repressor 2; SQSTM1/p62 sequestosome 1; STING1/MITA stimulator of interferon response cGAMP interactor 1; STX17 syntaxin 17; TEX264 testis expressed 264, ER-phagy receptor; TNF tumor necrosis factor; UB ubiquitin; ULK1 unc-51 like autophagy activating kinase 1; USP20 ubiquitin specific peptidase 20; USP33 ubiquitin specific peptidase 33; VAMP8 vesicle associated membrane protein 8; VAPs VAMP associated proteins; VMP1 vacuole membrane protein 1; WIPI2 WD repeat domain, phosphoinositide interacting 2; ZFYVE1/DFCP1 zinc finger FYVE-type containing 1.
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Affiliation(s)
- Man Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhangshun Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Qing Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Qian Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jieyun Bai
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Cuiwei Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zai-Rong Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, Beijing, China
| | - Yanfen Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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7
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Wang J, Fan P, Shen P, Fan C, Zhao P, Yao Shen, Dong K, Ling R, Chen S, Zhang J. XBP1s activates METTL3/METTL14 for ER-phagy and paclitaxel sensitivity regulation in breast cancer. Cancer Lett 2024; 596:216846. [PMID: 38582397 DOI: 10.1016/j.canlet.2024.216846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/25/2024] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
Cancer cells employ the unfolded protein response (UPR) or induce autophagy, especially selective removal of certain ER domains via reticulophagy (termed ER-phagy), to mitigate endoplasmic reticulum (ER) stress for ER homeostasis when encountering microenvironmental stress. N6-methyladenosine (m6A) is one of the most abundant epitranscriptional modifications and plays important roles in various biological processes. However, the molecular mechanism of m6A modification in the ER stress response is poorly understood. In this study, we first found that ER stress could dramatically elevate m6A methylation levels through XBP1s-dependent transcriptional upregulation of METTL3/METTL14 in breast cancer (BC) cells. Further MeRIP sequencing and relevant validation results confirmed that ER stress caused m6A methylation enrichment on target genes for ER-phagy. Mechanistically, METTL3/METTL14 increased ER-phagy machinery formation by promoting m6A modification of the ER-phagy regulators CALCOCO1 and p62, thus enhancing their mRNA stability. Of note, we further confirmed that the chemotherapeutic drug paclitaxel (PTX) could induce ER stress and increase m6A methylation for ER-phagy. Furthermore, the combination of METTL3/METTL14 inhibitors with PTX demonstrated a significant synergistic therapeutic effect in both BC cells and xenograft mice. Thus, our data built a novel bridge on the crosstalk between ER stress, m6A methylation and ER-phagy. Most importantly, our work provides novel evidence of METTL3 and METTL14 as potential therapeutic targets for PTX sensitization in breast cancer.
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Affiliation(s)
- Jiajia Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Pengyu Fan
- Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Peng Shen
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Cong Fan
- Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Pan Zhao
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Yao Shen
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Kewei Dong
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Rui Ling
- Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Suning Chen
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China.
| | - Jian Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China.
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8
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De Leonibus C, Maddaluno M, Ferriero R, Besio R, Cinque L, Lim PJ, Palma A, De Cegli R, Gagliotta S, Montefusco S, Iavazzo M, Rohrbach M, Giunta C, Polishchuk E, Medina DL, Di Bernardo D, Forlino A, Piccolo P, Settembre C. Sestrin2 drives ER-phagy in response to protein misfolding. Dev Cell 2024:S1534-5807(24)00441-6. [PMID: 39094564 DOI: 10.1016/j.devcel.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 05/01/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024]
Abstract
Protein biogenesis within the endoplasmic reticulum (ER) is crucial for organismal function. Errors during protein folding necessitate the removal of faulty products. ER-associated protein degradation and ER-phagy target misfolded proteins for proteasomal and lysosomal degradation. The mechanisms initiating ER-phagy in response to ER proteostasis defects are not well understood. By studying mouse primary cells and patient samples as a model of ER storage disorders (ERSDs), we show that accumulation of faulty products within the ER triggers a response involving SESTRIN2, a nutrient sensor controlling mTORC1 signaling. SESTRIN2 induction by XBP1 inhibits mTORC1's phosphorylation of TFEB/TFE3, allowing these transcription factors to enter the nucleus and upregulate the ER-phagy receptor FAM134B along with lysosomal genes. This response promotes ER-phagy of misfolded proteins via FAM134B-Calnexin complex. Pharmacological induction of FAM134B improves clearance of misfolded proteins in ERSDs. Our study identifies the interplay between nutrient signaling and ER quality control, suggesting therapeutic strategies for ERSDs.
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Affiliation(s)
- Chiara De Leonibus
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; Department of Health Sciences, University of Basilicata, Potenza, Italy
| | - Marianna Maddaluno
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy
| | - Rosa Ferriero
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Roberta Besio
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Laura Cinque
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy
| | - Pei Jin Lim
- Division of Metabolism and Children's Research Center, University Hospital of Zurich, Zurich, Switzerland
| | - Alessandro Palma
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Rossella De Cegli
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | - Sandro Montefusco
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Maria Iavazzo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy
| | - Marianne Rohrbach
- Division of Metabolism and Children's Research Center, University Hospital of Zurich, Zurich, Switzerland
| | - Cecilia Giunta
- Division of Metabolism and Children's Research Center, University Hospital of Zurich, Zurich, Switzerland
| | - Elena Polishchuk
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Diego Louis Medina
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Diego Di Bernardo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; Department of Chemical, Materials and Industrial Production Engineering, University of Naples "Federico II", Naples, Italy
| | | | - Pasquale Piccolo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy.
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9
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Li Q, Guo P, Wang S, Su L, Yu W, Guo J, Hu L, Zhang H, Pan J, Tang Z, Liao J. Drp1 Aggravates Copper Nanoparticle-Induced ER-Phagy by Disturbing Mitochondria-Associated Membranes in Chicken Hepatocytes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:16506-16518. [PMID: 38986054 DOI: 10.1021/acs.jafc.4c03978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
As an efficient alternative copper (Cu) source, copper nanoparticles (nano-Cu) have been widely supplemented into animal-producing food. Therefore, it is necessary to assess the effect of nano-Cu exposure on the biological health risk. Recently, the toxic effects of nano-Cu have been confirmed but the underlying mechanism remains unclear. This study reveals the impact of nano-Cu on endoplasmic reticulum autophagy (ER-phagy) in chicken hepatocytes and further identifies Drp1 and its downstream gene FAM134B as crucial regulators of nano-Cu-induced hepatotoxicity. Nano-Cu exposure can induce Cu ion overaccumulation and pathological injury in the liver, trigger excessive mitochondrial fission and mitochondria-associated membrane (MAM) integrity damage, and activate ER-phagy in vivo and in vitro. Interestingly, the knockdown of Drp1 markedly decreases the expression of FAM134B induced by nano-Cu. Furthermore, the expression levels of ATL3, CCPG1, SEC62, TEX264, and LC3II/LC3I induced by nano-Cu exposure are decreased by inhibiting the expression of Drp1. Simultaneously, the inhibition of FAM134B effectively alleviates nano-Cu-induced ER-phagy by downregulating the expression of ATL3, CCPG1, SEC62, TEX264, and LC3II/LC3I. Overall, these results suggest that Drp1-mediated impairment of MAM integrity leads to ER-phagy as a novel molecular mechanism involved in the regulation of nano-Cu-induced hepatotoxicity. These findings provide new ideas for future research on the mechanism of nano-Cu-induced hepatotoxicity.
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Affiliation(s)
- Quanwei Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, Guangdong, P. R. China
| | - Pan Guo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, Guangdong, P. R. China
| | - Shaofeng Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, Guangdong, P. R. China
| | - Luna Su
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, Guangdong, P. R. China
| | - Wenlan Yu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, Guangdong, P. R. China
| | - Jianying Guo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, Guangdong, P. R. China
| | - Liammei Hu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, Guangdong, P. R. China
| | - Hui Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, Guangdong, P. R. China
| | - Jiaqiang Pan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, Guangdong, P. R. China
| | - Zhaoxin Tang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, Guangdong, P. R. China
| | - Jianzhao Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, Guangdong, P. R. China
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10
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Kitta S, Kaminishi T, Higashi M, Shima T, Nishino K, Nakamura N, Kosako H, Yoshimori T, Kuma A. YIPF3 and YIPF4 regulate autophagic turnover of the Golgi apparatus. EMBO J 2024; 43:2954-2978. [PMID: 38822137 PMCID: PMC11250848 DOI: 10.1038/s44318-024-00131-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 04/21/2024] [Accepted: 05/08/2024] [Indexed: 06/02/2024] Open
Abstract
The degradation of organelles by autophagy is essential for cellular homeostasis. The Golgi apparatus has recently been demonstrated to be degraded by autophagy, but little is known about how the Golgi is recognized by the forming autophagosome. Using quantitative proteomic analysis and two novel Golgiphagy reporter systems, we found that the five-pass transmembrane Golgi-resident proteins YIPF3 and YIPF4 constitute a Golgiphagy receptor. The interaction of this complex with LC3B, GABARAP, and GABARAPL1 is dependent on a LIR motif within YIPF3 and putative phosphorylation sites immediately upstream; the stability of the complex is governed by YIPF4. Expression of a YIPF3 protein containing a mutated LIR motif caused an elongated Golgi morphology, indicating the importance of Golgi turnover via selective autophagy. The reporter assays reported here may be readily adapted to different experimental contexts to help deepen our understanding of Golgiphagy.
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Affiliation(s)
- Shinri Kitta
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tatsuya Kaminishi
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Momoko Higashi
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Takayuki Shima
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kohei Nishino
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Nobuhiro Nakamura
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita, Kyoto, 603-8555, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, 565-0871, Japan.
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Akiko Kuma
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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11
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Chen X, Tsvetkov AS, Shen HM, Isidoro C, Ktistakis NT, Linkermann A, Koopman WJ, Simon HU, Galluzzi L, Luo S, Xu D, Gu W, Peulen O, Cai Q, Rubinsztein DC, Chi JT, Zhang DD, Li C, Toyokuni S, Liu J, Roh JL, Dai E, Juhasz G, Liu W, Zhang J, Yang M, Liu J, Zhu LQ, Zou W, Piacentini M, Ding WX, Yue Z, Xie Y, Petersen M, Gewirtz DA, Mandell MA, Chu CT, Sinha D, Eftekharpour E, Zhivotovsky B, Besteiro S, Gabrilovich DI, Kim DH, Kagan VE, Bayir H, Chen GC, Ayton S, Lünemann JD, Komatsu M, Krautwald S, Loos B, Baehrecke EH, Wang J, Lane JD, Sadoshima J, Yang WS, Gao M, Münz C, Thumm M, Kampmann M, Yu D, Lipinski MM, Jones JW, Jiang X, Zeh HJ, Kang R, Klionsky DJ, Kroemer G, Tang D. International consensus guidelines for the definition, detection, and interpretation of autophagy-dependent ferroptosis. Autophagy 2024; 20:1213-1246. [PMID: 38442890 PMCID: PMC11210914 DOI: 10.1080/15548627.2024.2319901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/19/2023] [Indexed: 03/07/2024] Open
Abstract
Macroautophagy/autophagy is a complex degradation process with a dual role in cell death that is influenced by the cell types that are involved and the stressors they are exposed to. Ferroptosis is an iron-dependent oxidative form of cell death characterized by unrestricted lipid peroxidation in the context of heterogeneous and plastic mechanisms. Recent studies have shed light on the involvement of specific types of autophagy (e.g. ferritinophagy, lipophagy, and clockophagy) in initiating or executing ferroptotic cell death through the selective degradation of anti-injury proteins or organelles. Conversely, other forms of selective autophagy (e.g. reticulophagy and lysophagy) enhance the cellular defense against ferroptotic damage. Dysregulated autophagy-dependent ferroptosis has implications for a diverse range of pathological conditions. This review aims to present an updated definition of autophagy-dependent ferroptosis, discuss influential substrates and receptors, outline experimental methods, and propose guidelines for interpreting the results.Abbreviation: 3-MA:3-methyladenine; 4HNE: 4-hydroxynonenal; ACD: accidentalcell death; ADF: autophagy-dependentferroptosis; ARE: antioxidant response element; BH2:dihydrobiopterin; BH4: tetrahydrobiopterin; BMDMs: bonemarrow-derived macrophages; CMA: chaperone-mediated autophagy; CQ:chloroquine; DAMPs: danger/damage-associated molecular patterns; EMT,epithelial-mesenchymal transition; EPR: electronparamagnetic resonance; ER, endoplasmic reticulum; FRET: Försterresonance energy transfer; GFP: green fluorescent protein;GSH: glutathione;IF: immunofluorescence; IHC: immunohistochemistry; IOP, intraocularpressure; IRI: ischemia-reperfusion injury; LAA: linoleamide alkyne;MDA: malondialdehyde; PGSK: Phen Green™ SK;RCD: regulatedcell death; PUFAs: polyunsaturated fatty acids; RFP: red fluorescentprotein;ROS: reactive oxygen species; TBA: thiobarbituricacid; TBARS: thiobarbituric acid reactive substances; TEM:transmission electron microscopy.
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Affiliation(s)
- Xin Chen
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Andrey S. Tsvetkov
- Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, USA
| | - Han-Ming Shen
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau, China
| | - Ciro Isidoro
- Department of Health Sciences, University of Piemonte Orientale, Novara, Italy
| | | | - Andreas Linkermann
- Division of Nephrology, Department of Internal Medicine 3, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Germany
- Division of Nephrology, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Werner J.H. Koopman
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Hans-Uwe Simon
- Institute of Pharmacology, University of Bern, Bern, Switzerland
- Institute of Biochemistry, Brandenburg Medical School, Neuruppin, Germany
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA
| | - Shouqing Luo
- Peninsula Medical School, University of Plymouth, Plymouth, UK
| | - Daqian Xu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Wei Gu
- Institute for Cancer Genetics, and Department of Pathology and Cell Biology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Olivier Peulen
- Metastasis Research Laboratory, GIGA Cancer-University of Liège, Liège, Belgium
| | - Qian Cai
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - David C. Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - Jen-Tsan Chi
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Donna D. Zhang
- Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson, AZ, USA
| | - Changfeng Li
- Department of Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Shinya Toyokuni
- Department of Pathology and Biological Response, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Center for Low-temperature Plasma Sciences, Nagoya University, Nagoya, Japan
| | - Jinbao Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Jong-Lyel Roh
- Department of Otorhinolaryngology-Head and Neck Surgery, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea
| | - Enyong Dai
- The Second Department of Hematology and Oncology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Gabor Juhasz
- Biological Research Center, Institute of Genetics, Szeged, Hungary
- Department of Anatomy, Cell and Developmental Biology, Eotvos Lorand University, Budapest, Hungary
| | - Wei Liu
- Department of Orthopedics, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Jianhua Zhang
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Minghua Yang
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Clinical Research Center of Pediatric Cancer, Changsha, China
| | - Jiao Liu
- DAMP Laboratory, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ling-Qiang Zhu
- Department of Pathophysiology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weiping Zou
- Departments of Surgery and Pathology, University of Michigan Medical School, Ann Arbor, USA
| | - Mauro Piacentini
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
- National Institute for Infectious Diseases IRCCS “Lazzaro Spallanzani”, Rome, Italy
| | - Wen-Xing Ding
- Department of Pharmacology, Toxicology and Therapeutics, The University of Kansas Medical Center, Kansas City, KS, USA
| | - Zhenyu Yue
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yangchun Xie
- Department of Oncology, Central South University, Changsha, Hunan, China
| | - Morten Petersen
- Functional genomics, Department of Biology, Copenhagen University, Denmark
| | - David A. Gewirtz
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Massey Cancer Center, Richmond, VA, USA
| | - Michael A. Mandell
- Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, USA
| | - Charleen T. Chu
- Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Debasish Sinha
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Wilmer Eye lnstitute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eftekhar Eftekharpour
- Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Canada
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer, Villejuif, France; Gustave Roussy Cancer, Villejuif, France
| | - Boris Zhivotovsky
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden, Europe
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Moscow, Russia
| | - Sébastien Besteiro
- LPHI, University Montpellier, CNRS, Montpellier, France
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | | | - Do-Hyung Kim
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Valerian E. Kagan
- Department of Environmental Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hülya Bayir
- Department of Pediatrics, Columbia University, New York, USA
| | - Guang-Chao Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Scott Ayton
- Florey Institute, University of Melbourne, Parkville, Australia
| | - Jan D. Lünemann
- Department of Neurology with Institute of Translational Neurology, University of Münster, Münster, Germany
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University School of Medicine, Bunkyo-ku Tokyo, Japan
| | - Stefan Krautwald
- Department of Nephrology and Hypertension, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Ben Loos
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Eric H. Baehrecke
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jiayi Wang
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Thoracic Oncology Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Medical Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jon D. Lane
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Junichi Sadoshima
- Rutgers New Jersey Medical School, Department of Cell Biology and Molecular Medicine, Newark, USA
| | - Wan Seok Yang
- Department of Biological Sciences, St. John’s University, New York City, NY, USA
| | - Minghui Gao
- The HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Christian Münz
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Michael Thumm
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Martin Kampmann
- Department of Biochemistry & Biophysics, University of California, San Francisco, USA
- Institute for Neurodegenerative Diseases, University of California, San Francisco, USA
| | - Di Yu
- Faculty of Medicine, Frazer Institute, University of Queensland, Brisbane, Australia
- Faculty of Medicine, Ian Frazer Centre for Children’s Immunotherapy Research, Child Health Research Centre, University of Queensland, Brisbane, Australia
| | - Marta M. Lipinski
- Department of Anesthesiology & Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jace W. Jones
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Xuejun Jiang
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Herbert J. Zeh
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| | - Daniel J. Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer, Villejuif, France; Gustave Roussy Cancer, Villejuif, France
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA
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12
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Chen J, Zhao H, Liu M, Chen L. A new perspective on the autophagic and non-autophagic functions of the GABARAP protein family: a potential therapeutic target for human diseases. Mol Cell Biochem 2024; 479:1415-1441. [PMID: 37440122 DOI: 10.1007/s11010-023-04800-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/24/2023] [Indexed: 07/14/2023]
Abstract
Mammalian autophagy-related protein Atg8, including the LC3 subfamily and GABARAP subfamily. Atg8 proteins play a vital role in autophagy initiation, autophagosome formation and transport, and autophagy-lysosome fusion. GABARAP subfamily proteins (GABARAPs) share a high degree of homology with LC3 family proteins, and their unique roles are often overlooked. GABARAPs are as indispensable as LC3 in autophagy. Deletion of GABARAPs fails autophagy flux induction and autophagy lysosomal fusion, which leads to the failure of autophagy. GABARAPs are also involved in the transport of selective autophagy receptors. They are engaged in various particular autophagy processes, including mitochondrial autophagy, endoplasmic reticulum autophagy, Golgi autophagy, centrosome autophagy, and dorphagy. Furthermore, GABARAPs are closely related to the transport and delivery of the inhibitory neurotransmitter γ-GABAA and the angiotensin II AT1 receptor (AT1R), tumor growth, metastasis, and prognosis. GABARAPs also have been confirmed to be involved in various diseases, such as cancer, cardiovascular disease, and neurodegenerative diseases. In order to better understand the role and therapeutic potential of GABARAPs, this article comprehensively reviews the autophagic and non-autophagic functions of GABARAPs, as well as the research progress of the role and mechanism of GABARAPs in cancer, cardiovascular diseases and neurodegenerative diseases. It emphasizes the significance of GABARAPs in the clinical prevention and treatment of diseases, and may provide new therapeutic ideas and targets for human diseases. GABARAP and GABARAPL1 in the serum of cancer patients are positively correlated with the prognosis of patients, which can be used as a clinical biomarker, predictor and potential therapeutic target.
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Affiliation(s)
- Jiawei Chen
- Central Laboratory of Yan'nan Hospital Affiliated to Kunming, Medical University, Key Laboratory of Cardiovascular Diseases of Yunnan Province, Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, No. 245, Renmin East Road, Kunming, 650000, Yunnan, China
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Hong Zhao
- Central Laboratory of Yan'nan Hospital Affiliated to Kunming, Medical University, Key Laboratory of Cardiovascular Diseases of Yunnan Province, Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, No. 245, Renmin East Road, Kunming, 650000, Yunnan, China
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
- School of Nursing, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Meiqing Liu
- Central Laboratory of Yan'nan Hospital Affiliated to Kunming, Medical University, Key Laboratory of Cardiovascular Diseases of Yunnan Province, Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, No. 245, Renmin East Road, Kunming, 650000, Yunnan, China.
| | - Linxi Chen
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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13
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Mou W, Tang Y, Huang Y, Wu Z, Cui Y. Upregulation of neuronal ER-phagy improves organismal fitness and alleviates APP toxicity. Cell Rep 2024; 43:114255. [PMID: 38761376 DOI: 10.1016/j.celrep.2024.114255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/31/2024] [Accepted: 05/04/2024] [Indexed: 05/20/2024] Open
Abstract
ER-phagy, a selective autophagy targeting the endoplasmic reticulum (ER) for lysosomal degradation through cargo receptors, plays a critical role in ER quality control and is linked to various diseases. However, its physiological and pathological roles remain largely unclear due to a lack of animal model studies. This study establishes Drosophila as an in vivo ER-phagy model. Starvation triggers ER-phagy across multiple fly tissues. Disturbing ER-phagy by either globally upregulating or downregulating ER-phagy receptors, Atl or Rtnl1, harms the fly. Notably, moderate upregulation of ER-phagy in fly brains by overexpressing Atl or Rtnl1 significantly attenuates age-associated neurodegenerations. Furthermore, in a Drosophila model of Alzheimer's disease expressing human amyloid precursor protein (APP), impaired ER-phagy is observed. Enhancing ER-phagy in the APP-expressing fly brain facilitates APP degradation, significantly alleviating disease symptoms. Therefore, our findings suggest that modulating ER-phagy may offer a therapeutic strategy to treat aging and diseases associated with ER protein aggregation.
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Affiliation(s)
- Wenqing Mou
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Yinglu Tang
- Department of Biological Sciences, Dedman College of Humanities and Sciences, Southern Methodist University, Dallas, TX 75275, USA
| | - Yunpeng Huang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Zhihao Wu
- Department of Biological Sciences, Dedman College of Humanities and Sciences, Southern Methodist University, Dallas, TX 75275, USA.
| | - Yixian Cui
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China.
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14
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Zhou X, Lee YK, Li X, Kim H, Sanchez-Priego C, Han X, Tan H, Zhou S, Fu Y, Purtell K, Wang Q, Holstein GR, Tang B, Peng J, Yang N, Yue Z. Integrated proteomics reveals autophagy landscape and an autophagy receptor controlling PKA-RI complex homeostasis in neurons. Nat Commun 2024; 15:3113. [PMID: 38600097 PMCID: PMC11006854 DOI: 10.1038/s41467-024-47440-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/02/2024] [Indexed: 04/12/2024] Open
Abstract
Autophagy is a conserved, catabolic process essential for maintaining cellular homeostasis. Malfunctional autophagy contributes to neurodevelopmental and neurodegenerative diseases. However, the exact role and targets of autophagy in human neurons remain elusive. Here we report a systematic investigation of neuronal autophagy targets through integrated proteomics. Deep proteomic profiling of multiple autophagy-deficient lines of human induced neurons, mouse brains, and brain LC3-interactome reveals roles of neuronal autophagy in targeting proteins of multiple cellular organelles/pathways, including endoplasmic reticulum (ER), mitochondria, endosome, Golgi apparatus, synaptic vesicle (SV) for degradation. By combining phosphoproteomics and functional analysis in human and mouse neurons, we uncovered a function of neuronal autophagy in controlling cAMP-PKA and c-FOS-mediated neuronal activity through selective degradation of the protein kinase A - cAMP-binding regulatory (R)-subunit I (PKA-RI) complex. Lack of AKAP11 causes accumulation of the PKA-RI complex in the soma and neurites, demonstrating a constant clearance of PKA-RI complex through AKAP11-mediated degradation in neurons. Our study thus reveals the landscape of autophagy degradation in human neurons and identifies a physiological function of autophagy in controlling homeostasis of PKA-RI complex and specific PKA activity in neurons.
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Affiliation(s)
- Xiaoting Zhou
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - You-Kyung Lee
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Xianting Li
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Henry Kim
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carlos Sanchez-Priego
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Institute for Regenerative Medicine, Alper Center for Neural Development and Regeneration, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Xian Han
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Haiyan Tan
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Suiping Zhou
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yingxue Fu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kerry Purtell
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Qian Wang
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gay R Holstein
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Nan Yang
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Institute for Regenerative Medicine, Alper Center for Neural Development and Regeneration, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Zhenyu Yue
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Center of Parkinson's Disease Neurobiology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA.
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15
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González A, Dikić I. Decoding Golgiphagy: selective recycling under stress. Cell Res 2024; 34:277-278. [PMID: 38012262 PMCID: PMC10978888 DOI: 10.1038/s41422-023-00905-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Affiliation(s)
- Alexis González
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Ivan Dikić
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Straße 15, 60438, Frankfurt am Main, Germany.
- Fraunhofer Institute of Translational Medicine and Pharmacology, Carl-von-Noorden-Platz 9, 60596, Frankfurt am Main, Germany.
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16
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Zhang M, Wang Y, Gong X, Wang Y, Zhang Y, Tang Y, Zhou X, Liu H, Huang Y, Zhang J, Pan L. Mechanistic insights into the interactions of TAX1BP1 with RB1CC1 and mammalian ATG8 family proteins. Proc Natl Acad Sci U S A 2024; 121:e2315550121. [PMID: 38437556 PMCID: PMC10945755 DOI: 10.1073/pnas.2315550121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/02/2024] [Indexed: 03/06/2024] Open
Abstract
TAX1BP1, a multifunctional autophagy adaptor, plays critical roles in different autophagy processes. As an autophagy receptor, TAX1BP1 can interact with RB1CC1, NAP1, and mammalian ATG8 family proteins to drive selective autophagy for relevant substrates. However, the mechanistic bases underpinning the specific interactions of TAX1BP1 with RB1CC1 and mammalian ATG8 family proteins remain elusive. Here, we find that there are two distinct binding sites between TAX1BP1 and RB1CC1. In addition to the previously reported TAX1BP1 SKICH (skeletal muscle and kidney enriched inositol phosphatase (SKIP) carboxyl homology)/RB1CC1 coiled-coil interaction, the first coiled-coil domain of TAX1BP1 can directly bind to the extreme C-terminal coiled-coil and Claw region of RB1CC1. We determine the crystal structure of the TAX1BP1 SKICH/RB1CC1 coiled-coil complex and unravel the detailed binding mechanism of TAX1BP1 SKICH with RB1CC1. Moreover, we demonstrate that RB1CC1 and NAP1 are competitive in binding to the TAX1BP1 SKICH domain, but the presence of NAP1's FIP200-interacting region (FIR) motif can stabilize the ternary TAX1BP1/NAP1/RB1CC1 complex formation. Finally, we elucidate the molecular mechanism governing the selective interactions of TAX1BP1 with ATG8 family members by solving the structure of GABARAP in complex with the non-canonical LIR (LC3-interacting region) motif of TAX1BP1, which unveils a unique binding mode between LIR and ATG8 family protein. Collectively, our findings provide mechanistic insights into the interactions of TAX1BP1 with RB1CC1 and mammalian ATG8 family proteins and are valuable for further understanding the working mode and function of TAX1BP1 in autophagy.
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Affiliation(s)
- Mingfang Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Yingli Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Xinyu Gong
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Yaru Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou310024, China
| | - Yuchao Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Yubin Tang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Xindi Zhou
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Haobo Liu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Yichao Huang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Jing Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, Sichuan610068, China
| | - Lifeng Pan
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou310024, China
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, Sichuan610068, China
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17
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Eguchi T, Sakurai M, Wang Y, Saito C, Yoshii G, Wileman T, Mizushima N, Kuwahara T, Iwatsubo T. The V-ATPase-ATG16L1 axis recruits LRRK2 to facilitate the lysosomal stress response. J Cell Biol 2024; 223:e202302067. [PMID: 38227290 PMCID: PMC10791558 DOI: 10.1083/jcb.202302067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 10/13/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024] Open
Abstract
Leucine-rich repeat kinase 2 (LRRK2), a Rab kinase associated with Parkinson's disease and several inflammatory diseases, has been shown to localize to stressed lysosomes and get activated to regulate lysosomal homeostasis. However, the mechanisms of LRRK2 recruitment and activation have not been well understood. Here, we found that the ATG8 conjugation system regulates the recruitment of LRRK2 as well as LC3 onto single membranes of stressed lysosomes/phagosomes. This recruitment did not require FIP200-containing autophagy initiation complex, nor did it occur on double-membrane autophagosomes, suggesting independence from canonical autophagy. Consistently, LRRK2 recruitment was regulated by the V-ATPase-ATG16L1 axis, which requires the WD40 domain of ATG16L1 and specifically mediates ATG8 lipidation on single membranes. This mechanism was also responsible for the lysosomal stress-induced activation of LRRK2 and the resultant regulation of lysosomal secretion and enlargement. These results indicate that the V-ATPase-ATG16L1 axis serves a novel non-autophagic role in the maintenance of lysosomal homeostasis by recruiting LRRK2.
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Affiliation(s)
- Tomoya Eguchi
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Maria Sakurai
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yingxue Wang
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Chieko Saito
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Gen Yoshii
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Thomas Wileman
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoki Kuwahara
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeshi Iwatsubo
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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18
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Hoyer MJ, Capitanio C, Smith IR, Paoli JC, Bieber A, Jiang Y, Paulo JA, Gonzalez-Lozano MA, Baumeister W, Wilfling F, Schulman BA, Harper JW. Combinatorial selective ER-phagy remodels the ER during neurogenesis. Nat Cell Biol 2024; 26:378-392. [PMID: 38429475 PMCID: PMC10940164 DOI: 10.1038/s41556-024-01356-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 01/11/2024] [Indexed: 03/03/2024]
Abstract
The endoplasmic reticulum (ER) employs a diverse proteome landscape to orchestrate many cellular functions, ranging from protein and lipid synthesis to calcium ion flux and inter-organelle communication. A case in point concerns the process of neurogenesis, where a refined tubular ER network is assembled via ER shaping proteins into the newly formed neuronal projections to create highly polarized dendrites and axons. Previous studies have suggested a role for autophagy in ER remodelling, as autophagy-deficient neurons in vivo display axonal ER accumulation within synaptic boutons, and the membrane-embedded ER-phagy receptor FAM134B has been genetically linked with human sensory and autonomic neuropathy. However, our understanding of the mechanisms underlying selective removal of the ER and the role of individual ER-phagy receptors is limited. Here we combine a genetically tractable induced neuron (iNeuron) system for monitoring ER remodelling during in vitro differentiation with proteomic and computational tools to create a quantitative landscape of ER proteome remodelling via selective autophagy. Through analysis of single and combinatorial ER-phagy receptor mutants, we delineate the extent to which each receptor contributes to both the magnitude and selectivity of ER protein clearance. We define specific subsets of ER membrane or lumenal proteins as preferred clients for distinct receptors. Using spatial sensors and flux reporters, we demonstrate receptor-specific autophagic capture of ER in axons, and directly visualize tubular ER membranes within autophagosomes in neuronal projections by cryo-electron tomography. This molecular inventory of ER proteome remodelling and versatile genetic toolkit provide a quantitative framework for understanding the contributions of individual ER-phagy receptors for reshaping ER during cell state transitions.
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Affiliation(s)
- Melissa J Hoyer
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Cristina Capitanio
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ian R Smith
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Velia Therapeutics, San Diego, CA, USA
| | - Julia C Paoli
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Anna Bieber
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Yizhi Jiang
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Miguel A Gonzalez-Lozano
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Wolfgang Baumeister
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Wilfling
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Brenda A Schulman
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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19
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Zalon AJ, Quiriconi DJ, Pitcairn C, Mazzulli JR. α-Synuclein: Multiple pathogenic roles in trafficking and proteostasis pathways in Parkinson's disease. Neuroscientist 2024:10738584241232963. [PMID: 38420922 DOI: 10.1177/10738584241232963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Parkinson's disease (PD) is a common age-related neurodegenerative disorder characterized by the loss of dopaminergic neurons in the midbrain. A hallmark of both familial and sporadic PD is the presence of Lewy body inclusions composed mainly of aggregated α-synuclein (α-syn), a presynaptic protein encoded by the SNCA gene. The mechanisms driving the relationship between α-syn accumulation and neurodegeneration are not completely understood, although recent evidence indicates that multiple branches of the proteostasis pathway are simultaneously perturbed when α-syn aberrantly accumulates within neurons. Studies from patient-derived midbrain cultures that develop α-syn pathology through the endogenous expression of PD-causing mutations show that proteostasis disruption occurs at the level of synthesis/folding in the endoplasmic reticulum (ER), downstream ER-Golgi trafficking, and autophagic-lysosomal clearance. Here, we review the fundamentals of protein transport, highlighting the specific steps where α-syn accumulation may intervene and the downstream effects on proteostasis. Current therapeutic efforts are focused on targeting single pathways or proteins, but the multifaceted pathogenic role of α-syn throughout the proteostasis pathway suggests that manipulating several targets simultaneously will provide more effective disease-modifying therapies for PD and other synucleinopathies.
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Affiliation(s)
- Annie J Zalon
- The Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Drew J Quiriconi
- The Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Caleb Pitcairn
- The Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Joseph R Mazzulli
- The Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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20
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Jang W, Haucke V. ER remodeling via lipid metabolism. Trends Cell Biol 2024:S0962-8924(24)00023-0. [PMID: 38395735 DOI: 10.1016/j.tcb.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/22/2023] [Accepted: 01/24/2024] [Indexed: 02/25/2024]
Abstract
Unlike most other organelles found in multiple copies, the endoplasmic reticulum (ER) is a unique singular organelle within eukaryotic cells. Despite its continuous membrane structure, encompassing more than half of the cellular endomembrane system, the ER is subdivided into specialized sub-compartments, including morphological, membrane contact site (MCS), and de novo organelle biogenesis domains. In this review, we discuss recent emerging evidence indicating that, in response to nutrient stress, cells undergo a reorganization of these sub-compartmental ER domains through two main mechanisms: non-destructive remodeling of morphological ER domains via regulation of MCS and organelle hitchhiking, and destructive remodeling of specialized domains by ER-phagy. We further highlight and propose a critical role of membrane lipid metabolism in this ER remodeling during starvation.
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Affiliation(s)
- Wonyul Jang
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany; Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
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21
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Mohapatra G, Dachet F, Coleman LJ, Gillis B, Behm FG. Identification of unique genomic signatures in patients with fibromyalgia and chronic pain. Sci Rep 2024; 14:3949. [PMID: 38366049 PMCID: PMC10873305 DOI: 10.1038/s41598-024-53874-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
Fibromyalgia (FM) is a chronic pain syndrome characterized by widespread pain. The pathophysiology of fibromyalgia is not clearly understood and there are no specific biomarkers available for accurate diagnosis. Here we define genomic signatures using high throughput RNA sequencing on 96 fibromyalgia and 93 control cases. Our findings revealed three major fibromyalgia-associated expression signatures. The first group included 43 patients with a signature enriched for gene expression associated with extracellular matrix and downregulation of RhoGDI signaling pathway. The second group included 30 patients and showed a profound reduction in the expression of inflammatory mediators with an increased expression of genes involved in the CLEAR signaling pathway. These results suggest defective tissue homeostasis associated with the extra-cellular matrix and cellular program that regulates lysosomal biogenesis and participates in macromolecule clearance in fibromyalgia. The third group of 17 FM patients showed overexpression of pathways that control acute inflammation and dysfunction of the global transcriptional process. The result of this study indicates that FM is a heterogeneous and complex disease. Further elucidation of these pathways will lead to the development of accurate diagnostic markers, and effective therapeutic options for fibromyalgia.
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Affiliation(s)
- Gayatry Mohapatra
- Laboratory of Genomic Medicine, Department of Pathology, University of Illinois at Chicago (UIC) College of Medicine, 840 S. Wood St., Chicago, IL, 60612, USA.
| | - Fabien Dachet
- Laboratory of Genomic Medicine, Department of Pathology, University of Illinois at Chicago (UIC) College of Medicine, 840 S. Wood St., Chicago, IL, 60612, USA
| | - Louis J Coleman
- Laboratory of Genomic Medicine, Department of Pathology, University of Illinois at Chicago (UIC) College of Medicine, 840 S. Wood St., Chicago, IL, 60612, USA
| | - Bruce Gillis
- Department of Medicine, University of Illinois at Chicago (UIC) College of Medicine, Chicago, USA
| | - Frederick G Behm
- Laboratory of Genomic Medicine, Department of Pathology, University of Illinois at Chicago (UIC) College of Medicine, 840 S. Wood St., Chicago, IL, 60612, USA
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22
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Li J, Moretti F, Hidvegi T, Sviben S, Fitzpatrick JAJ, Sundaramoorthi H, Pak SC, Silverman GA, Knapp B, Filipuzzi I, Alford J, Reece-Hoyes J, Nigsch F, Murphy LO, Nyfeler B, Perlmutter DH. Multiple Genes Core to ERAD, Macroautophagy and Lysosomal Degradation Pathways Participate in the Proteostasis Response in α1-Antitrypsin Deficiency. Cell Mol Gastroenterol Hepatol 2024; 17:1007-1024. [PMID: 38336172 PMCID: PMC11053228 DOI: 10.1016/j.jcmgh.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/05/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND & AIMS In the classic form of α1-antitrypsin deficiency (ATD), the misfolded α1-antitrypsin Z (ATZ) variant accumulates in the endoplasmic reticulum (ER) of liver cells. A gain-of-function proteotoxic mechanism is responsible for chronic liver disease in a subgroup of homozygotes. Proteostatic response pathways, including conventional endoplasmic reticulum-associated degradation and autophagy, have been proposed as the mechanisms that allow cellular adaptation and presumably protection from the liver disease phenotype. Recent studies have concluded that a distinct lysosomal pathway called endoplasmic reticulum-to-lysosome completely supplants the role of the conventional macroautophagy pathway in degradation of ATZ. Here, we used several state-of-the-art approaches to characterize the proteostatic responses more fully in cellular systems that model ATD. METHODS We used clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing coupled to a cell selection step by fluorescence-activated cell sorter to perform screening for proteostasis genes that regulate ATZ accumulation and combined that with selective genome editing in 2 other model systems. RESULTS Endoplasmic reticulum-associated degradation genes are key early regulators and multiple autophagy genes, from classic as well as from ER-to-lysosome and other newly described ER-phagy pathways, participate in degradation of ATZ in a manner that is temporally regulated and evolves as ATZ accumulation persists. Time-dependent changes in gene expression are accompanied by specific ultrastructural changes including dilation of the ER, formation of globular inclusions, budding of autophagic vesicles, and alterations in the overall shape and component parts of mitochondria. CONCLUSIONS Macroautophagy is a critical component of the proteostasis response to cellular ATZ accumulation and it becomes more important over time as ATZ synthesis continues unabated. Multiple subtypes of macroautophagy and nonautophagic lysosomal degradative pathways are needed to respond to the high concentrations of misfolded protein that characterizes ATD and these pathways are attractive candidates for genetic variants that predispose to the hepatic phenotype.
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Affiliation(s)
- Jie Li
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | | | - Tunda Hidvegi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Sanja Sviben
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, Missouri
| | - James A J Fitzpatrick
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, Missouri; Department of Cell Biology, Washington University School of Medicine, St. Louis, Missouri; Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri
| | | | - Stephen C Pak
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Gary A Silverman
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Britta Knapp
- Novartis Biomedical Research, Basel, Switzerland
| | | | - John Alford
- Novartis Biomedical Research, Cambridge, Massachusetts
| | | | | | - Leon O Murphy
- Novartis Biomedical Research, Cambridge, Massachusetts
| | - Beat Nyfeler
- Novartis Biomedical Research, Basel, Switzerland
| | - David H Perlmutter
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri.
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23
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Liu J, Wu Y, Meng S, Xu P, Li S, Li Y, Hu X, Ouyang L, Wang G. Selective autophagy in cancer: mechanisms, therapeutic implications, and future perspectives. Mol Cancer 2024; 23:22. [PMID: 38262996 PMCID: PMC10807193 DOI: 10.1186/s12943-024-01934-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/05/2024] [Indexed: 01/25/2024] Open
Abstract
Eukaryotic cells engage in autophagy, an internal process of self-degradation through lysosomes. Autophagy can be classified as selective or non-selective depending on the way it chooses to degrade substrates. During the process of selective autophagy, damaged and/or redundant organelles like mitochondria, peroxisomes, ribosomes, endoplasmic reticulum (ER), lysosomes, nuclei, proteasomes, and lipid droplets are selectively recycled. Specific cargo is delivered to autophagosomes by specific receptors, isolated and engulfed. Selective autophagy dysfunction is closely linked with cancers, neurodegenerative diseases, metabolic disorders, heart failure, etc. Through reviewing latest research, this review summarized molecular markers and important signaling pathways for selective autophagy, and its significant role in cancers. Moreover, we conducted a comprehensive analysis of small-molecule compounds targeting selective autophagy for their potential application in anti-tumor therapy, elucidating the underlying mechanisms involved. This review aims to supply important scientific references and development directions for the biological mechanisms and drug discovery of anti-tumor targeting selective autophagy in the future.
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Affiliation(s)
- Jiaxi Liu
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Yongya Wu
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Sha Meng
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Ping Xu
- Emergency Department, Zigong Fourth People's Hospital, Zigong, 643000, China
| | - Shutong Li
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Yong Li
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Xiuying Hu
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China.
| | - Liang Ouyang
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China.
| | - Guan Wang
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China.
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24
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Jin H, Yang Y, Zhu X, Zhou Y, Xu Y, Li J, Qi C, Shao X, Wu J, Wu S, Cai H, Gu L, Mou S, Ni Z, Li S, Lin Q. DDRGK1-mediated ER-phagy attenuates acute kidney injury through ER-stress and apoptosis. Cell Death Dis 2024; 15:63. [PMID: 38233375 PMCID: PMC10794694 DOI: 10.1038/s41419-024-06449-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/19/2024]
Abstract
Acute kidney injury (AKI) constitutes a prevalent clinical syndrome characterized by elevated morbidity and mortality rates, emerging as a significant public health issue. This study investigates the interplay between endoplasmic reticulum (ER) stress, unfolded protein response (UPR), and ER-associated degradation (ER-phagy) in the pathogenesis of AKI. We employed four distinct murine models of AKI-induced by contrast media, ischemia-reperfusion injury, cisplatin, and folic acid-to elucidate the relationship between ER-phagy, ER stress, and apoptosis. Our findings reveal a marked decrease in ER-phagy coinciding with an accumulation of damaged ER, elevated ER stress, and increased apoptosis across all AKI models. Importantly, overexpression of DDRGK1 in HK-2 cells enhanced ER-phagy levels, ameliorating contrast-induced ER stress and apoptosis. These findings unveil a novel protective mechanism in AKI, wherein DDRGK1-UFL1-mediated ER-phagy mitigates ER stress and apoptosis in renal tubular epithelial cells. Our results thereby contribute to understanding the molecular underpinnings of AKI and offer potential therapeutic targets for its treatment.
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Affiliation(s)
- Haijiao Jin
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yuanting Yang
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Xuying Zhu
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yin Zhou
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yao Xu
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Jialin Li
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Chaojun Qi
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Xinghua Shao
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Jingkui Wu
- Department of Nephrology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201200, China
| | - Shan Wu
- Department of Endoscopy, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Hong Cai
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Leyi Gu
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Shan Mou
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Zhaohui Ni
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
| | - Shu Li
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
| | - Qisheng Lin
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
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Liang Y, Meng F, Zhao X, He X, Liu J. OsHLP1 is an endoplasmic-reticulum-phagy receptor in rice plants. Cell Rep 2023; 42:113480. [PMID: 38019652 DOI: 10.1016/j.celrep.2023.113480] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 09/21/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Abstract
The endoplasmic reticulum (ER) is the largest intracellular endomembrane system; it shows dynamic changes upon environmental stress. To maintain ER morphology and homeostasis under stress, the excessive ER membrane and the associated unwanted proteins can be removed via ER-phagy. Although a few ER-phagy receptors have been reported in mammals and yeast, their functional counterparts in plants remain largely unexplored. Here, we report that the HVA22 family protein OsHLP1 is an uncharacterized ER-phagy receptor in rice (Oryza sativa L.). OsHLP1 interacts with OsATG8b and recruits ER subdomains and the cargo protein OsNTL6, a negative immune regulator, to autophagosomes upon infection with the fungus Magnaporthe oryzae, which substantially activates disease resistance in rice. AtHVA22J, an Arabidopsis thaliana OsHLP1 ortholog, induced similar ER-phagy in plants. Altogether, we unraveled a conservative protein family that may act as ER-phagy receptors in higher plants, and in particular, we highlighted their roles in rice immune responses.
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Affiliation(s)
- Yingbo Liang
- College of Plant Protection, China Agricultural University, Beijing 100193, China; State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Fanwei Meng
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xia Zhao
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xinyi He
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jun Liu
- College of Plant Protection, China Agricultural University, Beijing 100193, China.
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26
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Berkane R, Ho-Xuan H, Glogger M, Sanz-Martinez P, Brunello L, Glaesner T, Kuncha SK, Holzhüter K, Cano-Franco S, Buonomo V, Cabrerizo-Poveda P, Balakrishnan A, Tascher G, Husnjak K, Juretschke T, Misra M, González A, Dötsch V, Grumati P, Heilemann M, Stolz A. The function of ER-phagy receptors is regulated through phosphorylation-dependent ubiquitination pathways. Nat Commun 2023; 14:8364. [PMID: 38102139 PMCID: PMC10724265 DOI: 10.1038/s41467-023-44101-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Selective autophagy of the endoplasmic reticulum (ER), known as ER-phagy, is an important regulator of ER remodeling and essential to maintain cellular homeostasis during environmental changes. We recently showed that members of the FAM134 family play a critical role during stress-induced ER-phagy. However, the mechanisms on how they are activated remain largely unknown. In this study, we analyze phosphorylation of FAM134 as a trigger of FAM134-driven ER-phagy upon mTOR (mechanistic target of rapamycin) inhibition. An unbiased screen of kinase inhibitors reveals CK2 to be essential for FAM134B- and FAM134C-driven ER-phagy after mTOR inhibition. Furthermore, we provide evidence that ER-phagy receptors are regulated by ubiquitination events and that treatment with E1 inhibitor suppresses Torin1-induced ER-phagy flux. Using super-resolution microscopy, we show that CK2 activity is essential for the formation of high-density FAM134B and FAM134C clusters. In addition, dense clustering of FAM134B and FAM134C requires phosphorylation-dependent ubiquitination of FAM134B and FAM134C. Treatment with the CK2 inhibitor SGC-CK2-1 or mutation of FAM134B and FAM134C phosphosites prevents ubiquitination of FAM134 proteins, formation of high-density clusters, as well as Torin1-induced ER-phagy flux. Therefore, we propose that CK2-dependent phosphorylation of ER-phagy receptors precedes ubiquitin-dependent activation of ER-phagy flux.
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Affiliation(s)
- Rayene Berkane
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Hung Ho-Xuan
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Marius Glogger
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Pablo Sanz-Martinez
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Lorène Brunello
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Tristan Glaesner
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Santosh Kumar Kuncha
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Katharina Holzhüter
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Sara Cano-Franco
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Viviana Buonomo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Paloma Cabrerizo-Poveda
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Ashwin Balakrishnan
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Georg Tascher
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Koraljka Husnjak
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | | | - Mohit Misra
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Alexis González
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Paolo Grumati
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Alexandra Stolz
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany.
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27
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Knupp J, Pletan ML, Arvan P, Tsai B. Autophagy of the ER: the secretome finds the lysosome. FEBS J 2023; 290:5656-5673. [PMID: 37920925 PMCID: PMC11044768 DOI: 10.1111/febs.16986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023]
Abstract
Lysosomal degradation of the endoplasmic reticulum (ER) and its components through the autophagy pathway has emerged as a major regulator of ER proteostasis. Commonly referred to as ER-phagy and ER-to-lysosome-associated degradation (ERLAD), how the ER is targeted to the lysosome has been recently clarified by a growing number of studies. Here, we summarize the discoveries of the molecular components required for lysosomal degradation of the ER and their proposed mechanisms of action. Additionally, we discuss how cells employ these machineries to create the different routes of ER-lysosome-associated degradation. Further, we review the role of ER-phagy in viral infection pathways, as well as the implication of ER-phagy in human disease. In sum, we provide a comprehensive overview of the current field of ER-phagy.
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Affiliation(s)
- Jeffrey Knupp
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Madison L Pletan
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Peter Arvan
- Division of Metabolism, Endocrinology & Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Billy Tsai
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA
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28
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Qian X, He L, Yang J, Sun J, Peng X, Zhang Y, Mao Y, Zhang Y, Cui Y. UVRAG cooperates with cargo receptors to assemble the ER-phagy site. EMBO J 2023; 42:e113625. [PMID: 37902287 PMCID: PMC10690450 DOI: 10.15252/embj.2023113625] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 10/04/2023] [Accepted: 10/11/2023] [Indexed: 10/31/2023] Open
Abstract
ER-phagy is a selective autophagy process that targets specific regions of the endoplasmic reticulum (ER) for removal via lysosomal degradation. During cellular stress induced by starvation, cargo receptors concentrate at distinct ER-phagy sites (ERPHS) to recruit core autophagy proteins and initiate ER-phagy. However, the molecular mechanism responsible for ERPHS formation remains unclear. In our study, we discovered that the autophagy regulator UV radiation Resistance-Associated Gene (UVRAG) plays a crucial role in orchestrating the assembly of ERPHS. Upon starvation, UVRAG localizes to ERPHS and interacts with specific ER-phagy cargo receptors, such as FAM134B, ATL3, and RTN3L. UVRAG regulates the oligomerization of cargo receptors and facilitates the recruitment of Atg8 family proteins. Consequently, UVRAG promotes efficient ERPHS assembly and turnover of both ER sheets and tubules. Importantly, UVRAG-mediated ER-phagy contributes to the clearance of pathogenic proinsulin aggregates. Remarkably, the involvement of UVRAG in ER-phagy initiation is independent of its canonical function as a subunit of class III phosphatidylinositol 3-kinase complex II.
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Affiliation(s)
- Xuehong Qian
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center for Immunology and MetabolismZhongnan Hospital of Wuhan University, Wuhan UniversityWuhanChina
| | - Lingang He
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center for Immunology and MetabolismZhongnan Hospital of Wuhan University, Wuhan UniversityWuhanChina
| | - Jiejie Yang
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center for Immunology and MetabolismZhongnan Hospital of Wuhan University, Wuhan UniversityWuhanChina
| | - Jiajia Sun
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center for Immunology and MetabolismZhongnan Hospital of Wuhan University, Wuhan UniversityWuhanChina
| | - Xueying Peng
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center for Immunology and MetabolismZhongnan Hospital of Wuhan University, Wuhan UniversityWuhanChina
| | - Yuting Zhang
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center for Immunology and MetabolismZhongnan Hospital of Wuhan University, Wuhan UniversityWuhanChina
| | - Yizhou Mao
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and MetabolismZhongnan Hospital of Wuhan University, Wuhan UniversityWuhanChina
| | - Ying Zhang
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and MetabolismZhongnan Hospital of Wuhan University, Wuhan UniversityWuhanChina
| | - Yixian Cui
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center for Immunology and MetabolismZhongnan Hospital of Wuhan University, Wuhan UniversityWuhanChina
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29
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Wang TT, Zhang LC, Qin Z, Chen SJ, Zeng JM, Li JY, An L, Wang CY, Gao Y, Wang LM, Zhao ZX, Liu ZQ, Wang SG. Decreased syntaxin17 expression contributes to the pathogenesis of acute pancreatitis in murine models by impairing autophagic degradation. Acta Pharmacol Sin 2023; 44:2445-2454. [PMID: 37580492 PMCID: PMC10692237 DOI: 10.1038/s41401-023-01139-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 07/09/2023] [Indexed: 08/16/2023] Open
Abstract
Acute pancreatitis (AP) is an inflammatory disease of the exocrine pancreas. Disruptions in organelle homeostasis, including macroautophagy/autophagy dysfunction and endoplasmic reticulum (ER) stress, have been implicated in human and rodent pancreatitis. Syntaxin 17 (STX17) belongs to the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) subfamily. The Qa-SNARE STX17 is an autophagosomal SNARE protein that interacts with SNAP29 (Qbc-SNARE) and the lysosomal SNARE VAMP8 (R-SNARE) to drive autophagosome-lysosome fusion. In this study, we investigated the role of STX17 in the pathogenesis of AP in male mice or rats induced by repeated intraperitoneal injections of cerulein. We showed that cerulein hyperstimulation induced AP in mouse and rat models, which was characterized by increased serum amylase and lipase activities, pancreatic edema, necrotic cell death and the infiltration of inflammatory cells, as well as markedly decreased pancreatic STX17 expression. A similar reduction in STX17 levels was observed in primary and AR42J pancreatic acinar cells treated with CCK (100 nM) in vitro. By analyzing autophagic flux, we found that the decrease in STX17 blocked autophagosome-lysosome fusion and autophagic degradation, as well as the activation of ER stress. Pancreas-specific STX17 knockdown using adenovirus-shSTX17 further exacerbated pancreatic edema, inflammatory cell infiltration and necrotic cell death after cerulein injection. These data demonstrate a critical role of STX17 in maintaining pancreatic homeostasis and provide new evidence that autophagy serves as a protective mechanism against AP.
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Affiliation(s)
- Tian-Tian Wang
- International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Li-Chun Zhang
- International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Zhen Qin
- International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Shu-Jun Chen
- International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Jing-Min Zeng
- International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Jing-Yan Li
- International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Lin An
- International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Cai-Yan Wang
- International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Yong Gao
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Li-Ming Wang
- School of Biomedical Science, Hunan University, Changsha, 410082, China
| | - Zhong-Xiang Zhao
- International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
- Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
| | - Zhong-Qiu Liu
- International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
- Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
| | - Shao-Gui Wang
- International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
- Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
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30
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Hayashi Y, Takatori S, Warsame WY, Tomita T, Fujisawa T, Ichijo H. TOLLIP acts as a cargo adaptor to promote lysosomal degradation of aberrant ER membrane proteins. EMBO J 2023; 42:e114272. [PMID: 37929762 PMCID: PMC10690474 DOI: 10.15252/embj.2023114272] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023] Open
Abstract
Endoplasmic reticulum (ER) proteostasis is maintained by various catabolic pathways. Lysosomes clear entire ER portions by ER-phagy, while proteasomes selectively clear misfolded or surplus aberrant proteins by ER-associated degradation (ERAD). Recently, lysosomes have also been implicated in the selective clearance of aberrant ER proteins, but the molecular basis remains unclear. Here, we show that the phosphatidylinositol-3-phosphate (PI3P)-binding protein TOLLIP promotes selective lysosomal degradation of aberrant membrane proteins, including an artificial substrate and motoneuron disease-causing mutants of VAPB and Seipin. These cargos are recognized by TOLLIP through its misfolding-sensing intrinsically disordered region (IDR) and ubiquitin-binding CUE domain. In contrast to ER-phagy receptors, which clear both native and aberrant proteins by ER-phagy, TOLLIP selectively clears aberrant cargos by coupling them with the PI3P-dependent lysosomal trafficking without promoting bulk ER turnover. Moreover, TOLLIP depletion augments ER stress after ERAD inhibition, indicating that TOLLIP and ERAD cooperatively safeguard ER proteostasis. Our study identifies TOLLIP as a unique type of cargo-specific adaptor dedicated to the clearance of aberrant ER cargos and provides insights into molecular mechanisms underlying lysosome-mediated quality control of membrane proteins.
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Affiliation(s)
- Yuki Hayashi
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Sho Takatori
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | | | - Taisuke Tomita
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Takao Fujisawa
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Hidenori Ichijo
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
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31
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Hoyer MJ, Capitanio C, Smith IR, Paoli JC, Bieber A, Jiang Y, Paulo JA, Gonzalez-Lozano MA, Baumeister W, Wilfling F, Schulman BA, Harper JW. Combinatorial selective ER-phagy remodels the ER during neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546565. [PMID: 37425907 PMCID: PMC10326971 DOI: 10.1101/2023.06.26.546565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The endoplasmic reticulum (ER) employs a diverse proteome landscape to orchestrate many cellular functions ranging from protein and lipid synthesis to calcium ion flux and inter-organelle communication. A case in point concerns the process of neurogenesis: a refined tubular ER network is assembled via ER shaping proteins into the newly formed neuronal projections to create highly polarized dendrites and axons. Previous studies have suggested a role for autophagy in ER remodeling, as autophagy-deficient neurons in vivo display axonal ER accumulation within synaptic boutons, and the membrane-embedded ER-phagy receptor FAM134B has been genetically linked with human sensory and autonomic neuropathy. However, our understanding of the mechanisms underlying selective removal of ER and the role of individual ER-phagy receptors is limited. Here, we combine a genetically tractable induced neuron (iNeuron) system for monitoring ER remodeling during in vitro differentiation with proteomic and computational tools to create a quantitative landscape of ER proteome remodeling via selective autophagy. Through analysis of single and combinatorial ER-phagy receptor mutants, we delineate the extent to which each receptor contributes to both magnitude and selectivity of ER protein clearance. We define specific subsets of ER membrane or lumenal proteins as preferred clients for distinct receptors. Using spatial sensors and flux reporters, we demonstrate receptor-specific autophagic capture of ER in axons, and directly visualize tubular ER membranes within autophagosomes in neuronal projections by cryo-electron tomography. This molecular inventory of ER proteome remodeling and versatile genetic toolkit provides a quantitative framework for understanding contributions of individual ER-phagy receptors for reshaping ER during cell state transitions.
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32
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Sigrist SJ, Haucke V. Orchestrating vesicular and nonvesicular membrane dynamics by intrinsically disordered proteins. EMBO Rep 2023; 24:e57758. [PMID: 37680133 PMCID: PMC10626433 DOI: 10.15252/embr.202357758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023] Open
Abstract
Compartmentalization by membranes is a common feature of eukaryotic cells and serves to spatiotemporally confine biochemical reactions to control physiology. Membrane-bound organelles such as the endoplasmic reticulum (ER), the Golgi complex, endosomes and lysosomes, and the plasma membrane, continuously exchange material via vesicular carriers. In addition to vesicular trafficking entailing budding, fission, and fusion processes, organelles can form membrane contact sites (MCSs) that enable the nonvesicular exchange of lipids, ions, and metabolites, or the secretion of neurotransmitters via subsequent membrane fusion. Recent data suggest that biomolecule and information transfer via vesicular carriers and via MCSs share common organizational principles and are often mediated by proteins with intrinsically disordered regions (IDRs). Intrinsically disordered proteins (IDPs) can assemble via low-affinity, multivalent interactions to facilitate membrane tethering, deformation, fission, or fusion. Here, we review our current understanding of how IDPs drive the formation of multivalent protein assemblies and protein condensates to orchestrate vesicular and nonvesicular transport with a special focus on presynaptic neurotransmission. We further discuss how dysfunction of IDPs causes disease and outline perspectives for future research.
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Affiliation(s)
- Stephan J Sigrist
- Department of Biology, Chemistry, PharmacyFreie Universität BerlinBerlinGermany
| | - Volker Haucke
- Department of Biology, Chemistry, PharmacyFreie Universität BerlinBerlinGermany
- Department of Molecular Pharmacology and Cell BiologyLeibniz Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
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Pham TNM, Perumal N, Manicam C, Basoglu M, Eimer S, Fuhrmann DC, Pietrzik CU, Clement AM, Körschgen H, Schepers J, Behl C. Adaptive responses of neuronal cells to chronic endoplasmic reticulum (ER) stress. Redox Biol 2023; 67:102943. [PMID: 37883843 PMCID: PMC10618786 DOI: 10.1016/j.redox.2023.102943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023] Open
Abstract
Accumulation of misfolded proteins or perturbation of calcium homeostasis leads to endoplasmic reticulum (ER) stress and is linked to the pathogenesis of neurodegenerative diseases. Hence, understanding the ability of neuronal cells to cope with chronic ER stress is of fundamental interest. Interestingly, several brain areas uphold functions that enable them to resist challenges associated with neurodegeneration. Here, we established novel clonal mouse hippocampal (HT22) cell lines that are resistant to prolonged (chronic) ER stress induced by thapsigargin (TgR) or tunicamycin (TmR) as in vitro models to study the adaption to ER stress. Morphologically, we observed a significant increase in vesicular und autophagosomal structures in both resistant lines and 'giant lysosomes', especially striking in TgR cells. While autophagic activity increased under ER stress, lysosomal function appeared slightly impaired; in both cell lines, we observed enhanced ER-phagy. However, proteomic analyses revealed that various protein clusters and signaling pathways were differentially regulated in TgR versus TmR cells in response to chronic ER stress. Additionally, bioenergetic analyses in both resistant cell lines showed a shift toward aerobic glycolysis ('Warburg effect') and a defective complex I of the oxidative phosphorylation (OXPHOS) machinery. Furthermore, ER stress-resistant cells differentially activated the unfolded protein response (UPR) comprising IRE1α and ATF6 pathways. These findings display the wide portfolio of adaptive responses of neuronal cells to chronic ER stress. ER stress-resistant neuronal cells could be the basis to uncover molecular modulators of adaptation, resistance, and neuroprotection as potential pharmacological targets for preventing neurodegeneration.
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Affiliation(s)
- Thu Nguyen Minh Pham
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Natarajan Perumal
- Department of Ophthalmology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Caroline Manicam
- Department of Ophthalmology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Marion Basoglu
- Department of Structural Cell Biology, Institute for Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
| | - Stefan Eimer
- Department of Structural Cell Biology, Institute for Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
| | - Dominik C Fuhrmann
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt, Germany
| | - Claus U Pietrzik
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Albrecht M Clement
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Hagen Körschgen
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Jana Schepers
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Christian Behl
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany.
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Tetenborg S, Liss V, Breitsprecher L, Timonina K, Kotova A, Acevedo Harnecker AJ, Yuan C, Shihabeddin E, Ariakia F, Qin G, Chengzhi C, Dedek K, Zoidl G, Hensel M, O'Brien J. Intralumenal docking of connexin 36 channels in the ER isolates mistrafficked protein. J Biol Chem 2023; 299:105282. [PMID: 37742923 PMCID: PMC10637963 DOI: 10.1016/j.jbc.2023.105282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/26/2023] Open
Abstract
The intracellular domains of connexins are essential for the assembly of gap junctions. For connexin 36 (Cx36), the major neuronal connexin, it has been shown that a dysfunctional PDZ-binding motif interferes with electrical synapse formation. However, it is still unknown how this motif coordinates the transport of Cx36. In the present study, we characterize a phenotype of Cx36 mutants that lack a functional PDZ-binding motif using HEK293T cells as an expression system. We provide evidence that an intact PDZ-binding motif is critical for proper endoplasmic reticulum (ER) export of Cx36. Removing the PDZ-binding motif of Cx36 results in ER retention and the formation of multimembrane vesicles containing gap junction-like connexin aggregates. Using a combination of site-directed mutagenesis and electron micrographs, we reveal that these vesicles consist of Cx36 channels that docked prematurely in the ER. Our data suggest a model in which ER-retained Cx36 channels reshape the ER membrane into concentric whorls that are released into the cytoplasm.
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Affiliation(s)
| | - Viktoria Liss
- Department of Biology/Chemistry, iBiOs-Integrated Bioimaging Facility, CellNanOs - Center of Cellular Nanoanalytics, Osnabrück, Germany; Department of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - Leonhard Breitsprecher
- Department of Biology/Chemistry, iBiOs-Integrated Bioimaging Facility, CellNanOs - Center of Cellular Nanoanalytics, Osnabrück, Germany; Department of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - Ksenia Timonina
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Anna Kotova
- Department of Biology, York University, Toronto, Ontario, Canada
| | | | - Chunxu Yuan
- Animal Navigation/Neurosensorics, Institute for Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
| | - Eyad Shihabeddin
- College of Optometry, University of Houston, Houston, Texas, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Fatemeh Ariakia
- College of Optometry, University of Houston, Houston, Texas, USA
| | - Guoting Qin
- College of Optometry, University of Houston, Houston, Texas, USA
| | - Cai Chengzhi
- Department of Chemistry, University of Houston, Houston, Texas, USA
| | - Karin Dedek
- Animal Navigation/Neurosensorics, Institute for Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany; Research Center Neurosensory Science, University of Oldenburg, Oldenburg, Germany
| | - Georg Zoidl
- Department of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - Michael Hensel
- Department of Biology/Chemistry, iBiOs-Integrated Bioimaging Facility, CellNanOs - Center of Cellular Nanoanalytics, Osnabrück, Germany; Department of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - John O'Brien
- College of Optometry, University of Houston, Houston, Texas, USA.
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35
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Hickey KL, Swarup S, Smith IR, Paoli JC, Miguel Whelan E, Paulo JA, Harper JW. Proteome census upon nutrient stress reveals Golgiphagy membrane receptors. Nature 2023; 623:167-174. [PMID: 37757899 PMCID: PMC10620096 DOI: 10.1038/s41586-023-06657-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023]
Abstract
During nutrient stress, macroautophagy degrades cellular macromolecules, thereby providing biosynthetic building blocks while simultaneously remodelling the proteome1,2. Although the machinery responsible for initiation of macroautophagy has been well characterized3,4, our understanding of the extent to which individual proteins, protein complexes and organelles are selected for autophagic degradation, and the underlying targeting mechanisms, is limited. Here we use orthogonal proteomic strategies to provide a spatial proteome census of autophagic cargo during nutrient stress in mammalian cells. We find that macroautophagy has selectivity for recycling membrane-bound organelles (principally Golgi and endoplasmic reticulum). Through autophagic cargo prioritization, we identify a complex of membrane-embedded proteins, YIPF3 and YIPF4, as receptors for Golgiphagy. During nutrient stress, YIPF3 and YIPF4 interact with ATG8 proteins through LIR motifs and are mobilized into autophagosomes that traffic to lysosomes in a process that requires the canonical autophagic machinery. Cells lacking YIPF3 or YIPF4 are selectively defective in elimination of a specific cohort of Golgi membrane proteins during nutrient stress. Moreover, YIPF3 and YIPF4 play an analogous role in Golgi remodelling during programmed conversion of stem cells to the neuronal lineage in vitro. Collectively, the findings of this study reveal prioritization of membrane protein cargo during nutrient-stress-dependent proteome remodelling and identify a Golgi remodelling pathway that requires membrane-embedded receptors.
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Affiliation(s)
- Kelsey L Hickey
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Sharan Swarup
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Casma Therapeutics, Cambridge, MA, USA
| | - Ian R Smith
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Velia Therapeutics, San Diego, CA, USA
| | - Julia C Paoli
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | | | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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36
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Popelka H, Lahiri V, Hawkins WD, da Veiga Leprevost F, Nesvizhskii AI, Klionsky DJ. The Intrinsically Disordered N Terminus in Atg12 from Yeast Is Necessary for the Functional Structure of the Protein. Int J Mol Sci 2023; 24:15036. [PMID: 37894717 PMCID: PMC10606595 DOI: 10.3390/ijms242015036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
The Atg12 protein in yeast is an indispensable polypeptide in the highly conserved ubiquitin-like conjugation system operating in the macroautophagy/autophagy pathway. Atg12 is covalently conjugated to Atg5 through the action of Atg7 and Atg10; the Atg12-Atg5 conjugate binds Atg16 to form an E3 ligase that functions in a separate conjugation pathway involving Atg8. Atg12 is comprised of a ubiquitin-like (UBL) domain preceded at the N terminus by an intrinsically disordered protein region (IDPR), a domain that comprises a major portion of the protein but remains elusive in its conformation and function. Here, we show that the IDPR in unconjugated Atg12 is positioned in proximity to the UBL domain, a configuration that is important for the functional structure of the protein. A major deletion in the IDPR disrupts intactness of the UBL domain at the unconjugated C terminus, and a mutation in the predicted α0 helix in the IDPR prevents Atg12 from binding to Atg7 and Atg10, which ultimately affects the protein function in the ubiquitin-like conjugation cascade. These findings provide evidence that the IDPR is an indispensable part of the Atg12 protein from yeast.
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Affiliation(s)
- Hana Popelka
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; (V.L.); (W.D.H.); (D.J.K.)
| | - Vikramjit Lahiri
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; (V.L.); (W.D.H.); (D.J.K.)
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wayne D. Hawkins
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; (V.L.); (W.D.H.); (D.J.K.)
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Felipe da Veiga Leprevost
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA; (F.d.V.L.); (A.I.N.)
| | - Alexey I. Nesvizhskii
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA; (F.d.V.L.); (A.I.N.)
| | - Daniel J. Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; (V.L.); (W.D.H.); (D.J.K.)
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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37
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Linnert J, Güler BE, Krzysko J, Wolfrum U. The adhesion G protein-coupled receptor VLGR1/ADGRV1 controls autophagy. Basic Clin Pharmacol Toxicol 2023; 133:313-330. [PMID: 37002809 DOI: 10.1111/bcpt.13869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
VLGR1/ADGRV1 (very large G protein-coupled receptor-1) is the largest known adhesion G protein-coupled receptor. Mutations in VLGR1/ADGRV1 cause Usher syndrome (USH), the most common form of hereditary deaf-blindness, and have been additionally linked to epilepsy. Although VLGR1/ADGRV1 is almost ubiquitously expressed, little is known about the subcellular function and signalling of the VLGR1 protein and thus about mechanisms underlying the development of diseases. Using affinity proteomics, we identified key components of autophagosomes as putative interacting proteins of VLGR1. In addition, whole transcriptome sequencing of the retinae of the Vlgr1/del7TM mouse model revealed altered expression profiles of gene-related autophagy. Monitoring autophagy by immunoblotting and immunocytochemistry of the LC3 and p62 as autophagy marker proteins revealed evoked autophagy in VLGR1-deficient hTERT-RPE1 cells and USH2C patient-derived fibroblasts. Our data demonstrate the molecular and functional interaction of VLGR1 with key components of the autophagy process and point to an essential role of VLGR1 in the regulation of autophagy at internal membranes. The close association of VLGR1 with autophagy helps to explain the pathomechanisms underlying human USH and epilepsy related to VLGR1 defects.
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Affiliation(s)
- Joshua Linnert
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Baran E Güler
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jacek Krzysko
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
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38
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Hill MA, Sykes AM, Mellick GD. ER-phagy in neurodegeneration. J Neurosci Res 2023; 101:1611-1623. [PMID: 37334842 DOI: 10.1002/jnr.25225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/11/2023] [Accepted: 05/31/2023] [Indexed: 06/21/2023]
Abstract
There are many cellular mechanisms implicated in the initiation and progression of neurodegenerative disorders. However, age and the accumulation of unwanted cellular products are a common theme underlying many neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, and Niemann-Pick type C. Autophagy has been studied extensively in these diseases and various genetic risk factors have implicated disruption in autophagy homoeostasis as a major pathogenic mechanism. Autophagy is essential in the maintenance of neuronal homeostasis, as their postmitotic nature makes them particularly susceptible to the damage caused by accumulation of defective or misfolded proteins, disease-prone aggregates, and damaged organelles. Recently, autophagy of the endoplasmic reticulum (ER-phagy) has been identified as a novel cellular mechanism for regulating ER morphology and response to cellular stress. As neurodegenerative diseases are generally precipitated by cellular stressors such as protein accumulation and environmental toxin exposure the role of ER-phagy has begun to be investigated. In this review we discuss the current research in ER-phagy and its involvement in neurodegenerative diseases.
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Affiliation(s)
- Melissa A Hill
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Alex M Sykes
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - George D Mellick
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
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Walther J, Kirsch EM, Hellwig L, Schmerbeck SS, Holloway PM, Buchan AM, Mergenthaler P. Reinventing the Penumbra - the Emerging Clockwork of a Multi-modal Mechanistic Paradigm. Transl Stroke Res 2023; 14:643-666. [PMID: 36219377 PMCID: PMC10444697 DOI: 10.1007/s12975-022-01090-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 11/25/2022]
Abstract
The concept of the ischemic penumbra was originally defined as the area around a necrotic stroke core and seen as the tissue at imminent risk of further damage. Today, the penumbra is generally considered as time-sensitive hypoperfused brain tissue with decreased oxygen and glucose availability, salvageable tissue as treated by intervention, and the potential target for neuroprotection in focal stroke. The original concept entailed electrical failure and potassium release but one short of neuronal cell death and was based on experimental stroke models, later confirmed in clinical imaging studies. However, even though the basic mechanisms have translated well, conferring brain protection, and improving neurological outcome after stroke based on the pathophysiological mechanisms in the penumbra has yet to be achieved. Recent findings shape the modern understanding of the penumbra revealing a plethora of molecular and cellular pathophysiological mechanisms. We now propose a new model of the penumbra, one which we hope will lay the foundation for future translational success. We focus on the availability of glucose, the brain's central source of energy, and bioenergetic failure as core pathophysiological concepts. We discuss the relation of mitochondrial function in different cell types to bioenergetics and apoptotic cell death mechanisms, autophagy, and neuroinflammation, to glucose metabolism in what is a dynamic ischemic penumbra.
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Affiliation(s)
- Jakob Walther
- Charité - Universitätsmedizin Berlin, Department of Neurology with Experimental Neurology, Charitéplatz 1, 10117, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Center for Stroke Research Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Elena Marie Kirsch
- Charité - Universitätsmedizin Berlin, Department of Neurology with Experimental Neurology, Charitéplatz 1, 10117, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Center for Stroke Research Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Lina Hellwig
- Charité - Universitätsmedizin Berlin, Department of Neurology with Experimental Neurology, Charitéplatz 1, 10117, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Center for Stroke Research Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Sarah S Schmerbeck
- Charité - Universitätsmedizin Berlin, Department of Neurology with Experimental Neurology, Charitéplatz 1, 10117, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Center for Stroke Research Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Paul M Holloway
- Acute Stroke Programme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | - Alastair M Buchan
- Charité - Universitätsmedizin Berlin, Center for Stroke Research Berlin, Charitéplatz 1, 10117, Berlin, Germany.
- Acute Stroke Programme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK.
| | - Philipp Mergenthaler
- Charité - Universitätsmedizin Berlin, Department of Neurology with Experimental Neurology, Charitéplatz 1, 10117, Berlin, Germany.
- Charité - Universitätsmedizin Berlin, Center for Stroke Research Berlin, Charitéplatz 1, 10117, Berlin, Germany.
- Charité - Universitätsmedizin Berlin, NeuroCure Clinical Research Center, Charitéplatz 1, 10117, Berlin, Germany.
- Acute Stroke Programme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK.
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40
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Nakagama S, Maejima Y, Fan Q, Shiheido-Watanabe Y, Tamura N, Ihara K, Sasano T. Endoplasmic Reticulum Selective Autophagy Alleviates Anthracycline-Induced Cardiotoxicity. JACC CardioOncol 2023; 5:656-670. [PMID: 37969644 PMCID: PMC10635891 DOI: 10.1016/j.jaccao.2023.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 11/17/2023] Open
Abstract
Background The administration of anthracycline drugs induces progressive and dose-related cardiac damage through several cytotoxic mechanisms, including endoplasmic reticulum (ER) stress. The unfolded protein response plays a crucial role for mitigating misfolded protein accumulation induced by excessive ER stress. Objectives We aimed to clarify whether endoplasmic reticulum-selective autophagy machinery (ER-phagy) serves as an alternative system to protect cardiomyocytes from ER stress caused by anthracycline drugs. Methods Primary cultured cardiomyocytes, H9c2 cell lines, and cardiomyocyte-specific transgenic mice, all expressing ss-RFP-GFP-KDEL proteins, were used as ER-phagy reporter models. We generated loss-of-function models using RNA interference or gene-trap mutagenesis techniques. We assessed phenotypes and molecular signaling pathways using immunoblotting, quantitative polymerase chain reaction, cell viability assays, immunocytochemical and histopathological analyses, and cardiac ultrasonography. Results The administration of doxorubicin (Dox) activated ER-phagy in ss-RFP-GFP-KDEL-transduced cardiomyocytes. In addition, Dox-induced cardiomyopathy models of ER-phagy reporter mice showed marked activation of ER-phagy in the myocardium compared to those of saline-treated mice. Quantitative polymerase chain reaction analyses revealed that Dox enhanced the expression of cell-cycle progression gene 1 (CCPG1), one of the ER-phagy receptors, in H9c2 cells. Ablation of CCPG1 in H9c2 cells resulted in the reduced ER-phagy activity, accumulation of proapoptotic proteins, and deterioration of cell survival against Dox administration. CCPG1-hypomorphic mice developed more severe deterioration in systolic function in response to Dox compared to wild-type mice. Conclusions Our findings highlight a compensatory role of CCPG1-driven ER-phagy in reducing Dox toxicity. With further study, ER-phagy may be a potential therapeutic target to mitigate Dox-induced cardiomyopathy.
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Affiliation(s)
- Shun Nakagama
- Department of Cardiovascular Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yasuhiro Maejima
- Department of Cardiovascular Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Qintao Fan
- Department of Cardiovascular Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yuka Shiheido-Watanabe
- Department of Cardiovascular Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Natsuko Tamura
- Department of Cardiovascular Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kensuke Ihara
- Department of Cardiovascular Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Bio-informational Pharmacology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tetsuo Sasano
- Department of Cardiovascular Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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41
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Cui B, Song L, Wang Q, Li K, He Q, Wu X, Gao F, Liu M, An C, Gao Q, Hu C, Hao X, Dong F, Zhou J, Liu D, Song Z, Yan X, Zhang J, Bai Y, Mao Q, Yang X, Liang Z. Non-small cell lung cancers (NSCLCs) oncolysis using coxsackievirus B5 and synergistic DNA-damage response inhibitors. Signal Transduct Target Ther 2023; 8:366. [PMID: 37743418 PMCID: PMC10518312 DOI: 10.1038/s41392-023-01603-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 07/18/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023] Open
Abstract
With the continuous in-depth study of the interaction mechanism between viruses and hosts, the virus has become a promising tool in cancer treatment. In fact, many oncolytic viruses with selectivity and effectiveness have been used in cancer therapy. Human enterovirus is one of the most convenient sources to generate oncolytic viruses, however, the high seroprevalence of some enteroviruses limits its application which urges to exploit more oncolytic enteroviruses. In this study, coxsackievirus B5/Faulkner (CV-B5/F) was screened for its potential oncolytic effect against non-small cell lung cancers (NSCLCs) through inducing apoptosis and autophagy. For refractory NSCLCs, DNA-dependent protein kinase (DNA-PK) or ataxia telangiectasia mutated protein (ATM) inhibitors can synergize with CV-B5/F to promote refractory cell death. Here, we showed that viral infection triggered endoplasmic reticulum (ER) stress-related pro-apoptosis and autophagy signals, whereas repair for double-stranded DNA breaks (DSBs) contributed to cell survival which can be antagonized by inhibitor-induced cell death, manifesting exacerbated DSBs, apoptosis, and autophagy. Mechanistically, PERK pathway was activated by the combination of CV-B5/F and inhibitor, and the irreversible ER stress-induced exacerbated cell death. Furthermore, the degradation of activated STING by ERphagy promoted viral replication. Meanwhile, no treatment-related deaths due to CV-B5/F and/or inhibitors occurred. Conclusively, our study identifies an oncolytic CV-B5/F and the synergistic effects of inhibitors of DNA-PK or ATM, which is a potential therapy for NSCLCs.
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Affiliation(s)
- Bopei Cui
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, China
| | - Lifang Song
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, China
| | - Qian Wang
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Kelei Li
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
- Beijing Minhai Biotechnology Co., Ltd, Beijing, China
| | - Qian He
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Xing Wu
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Fan Gao
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Mingchen Liu
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Chaoqiang An
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
- Beijing Minhai Biotechnology Co., Ltd, Beijing, China
| | - Qiushuang Gao
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Chaoying Hu
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Xiaotian Hao
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Fangyu Dong
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
- Taibang Biologic Group, Beijing, China
| | | | - Dong Liu
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
- Changchun Institute of Biological Products Co., Ltd, Changchun, China
| | - Ziyang Song
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
- Shanghai Institute of Biological Products Co., Ltd, Shanghai, China
| | - Xujia Yan
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
- Changchun Institute of Biological Products Co., Ltd, Changchun, China
| | - Jialu Zhang
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Yu Bai
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Qunying Mao
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China.
| | - Xiaoming Yang
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, China.
- China National Biotec Group Company Limited, Beijing, China.
| | - Zhenglun Liang
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China.
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42
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Wang R, Fortier TM, Chai F, Miao G, Shen JL, Restrepo LJ, DiGiacomo JJ, Velentzas PD, Baehrecke EH. PINK1, Keap1, and Rtnl1 regulate selective clearance of endoplasmic reticulum during development. Cell 2023; 186:4172-4188.e18. [PMID: 37633267 PMCID: PMC10530463 DOI: 10.1016/j.cell.2023.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/27/2023] [Accepted: 08/07/2023] [Indexed: 08/28/2023]
Abstract
Selective clearance of organelles, including endoplasmic reticulum (ER) and mitochondria, by autophagy plays an important role in cell health. Here, we describe a developmentally programmed selective ER clearance by autophagy. We show that Parkinson's disease-associated PINK1, as well as Atl, Rtnl1, and Trp1 receptors, regulate ER clearance by autophagy. The E3 ubiquitin ligase Parkin functions downstream of PINK1 and is required for mitochondrial clearance while having the opposite function in ER clearance. By contrast, Keap1 and the E3 ubiquitin ligase Cullin3 function downstream of PINK1 to regulate ER clearance by influencing Rtnl1 and Atl. PINK1 regulates a change in Keap1 localization and Keap1-dependent ubiquitylation of the ER-phagy receptor Rtnl1 to facilitate ER clearance. Thus, PINK1 regulates the selective clearance of ER and mitochondria by influencing the balance of Keap1- and Parkin-dependent ubiquitylation of substrates that determine which organelle is removed by autophagy.
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Affiliation(s)
- Ruoxi Wang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Tina M Fortier
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Fei Chai
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Guangyan Miao
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - James L Shen
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Lucas J Restrepo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jeromy J DiGiacomo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Panagiotis D Velentzas
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Eric H Baehrecke
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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43
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Shapiro D, Lee K, Asmussen J, Bourquard T, Lichtarge O. Evolutionary Action-Machine Learning Model Identifies Candidate Genes Associated With Early-Onset Coronary Artery Disease. J Am Heart Assoc 2023; 12:e029103. [PMID: 37642027 PMCID: PMC10547338 DOI: 10.1161/jaha.122.029103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 07/11/2023] [Indexed: 08/31/2023]
Abstract
Background Coronary artery disease is a primary cause of death around the world, with both genetic and environmental risk factors. Although genome-wide association studies have linked >100 unique loci to its genetic basis, these only explain a fraction of disease heritability. Methods and Results To find additional gene drivers of coronary artery disease, we applied machine learning to quantitative evolutionary information on the impact of coding variants in whole exomes from the Myocardial Infarction Genetics Consortium. Using ensemble-based supervised learning, the Evolutionary Action-Machine Learning framework ranked each gene's ability to classify case and control samples and identified 79 significant associations. These were connected to known risk loci; enriched in cardiovascular processes like lipid metabolism, blood clotting, and inflammation; and enriched for cardiovascular phenotypes in knockout mouse models. Among them, INPP5F and MST1R are examples of potentially novel coronary artery disease risk genes that modulate immune signaling in response to cardiac stress. Conclusions We concluded that machine learning on the functional impact of coding variants, based on a massive amount of evolutionary information, has the power to suggest novel coronary artery disease risk genes for mechanistic and therapeutic discoveries in cardiovascular biology, and should also apply in other complex polygenic diseases.
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Affiliation(s)
- Dillon Shapiro
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Kwanghyuk Lee
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Jennifer Asmussen
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Thomas Bourquard
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Olivier Lichtarge
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
- Computational & Integrative Biomedical Research CenterBaylor College of MedicineHoustonTXUSA
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44
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Bi T, Lu Q, Pan X, Dong F, Hu Y, Xu Z, Xiu P, Liu Z, Li J. circFAM134B is a key factor regulating reticulophagy-mediated ferroptosis in hepatocellular carcinoma. Cell Cycle 2023; 22:1900-1920. [PMID: 37603831 PMCID: PMC10599178 DOI: 10.1080/15384101.2023.2249302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/25/2023] [Accepted: 08/04/2023] [Indexed: 08/23/2023] Open
Abstract
Ferroptosis is an important mode of regulated cell death (RCD). Its inhibition is closely related to therapeutic resistance and poor prognosis in hepatocellular carcinoma (HCC). Previous reports have demonstrated ferroptosis as a biological process highly dependent on selective autophagy, such as ferritinophagy, lipophagy, and clockophagy. Our study also revealed a role for ER-phagy-mediated ferroptosis in HCC cells treated with multi-targeted tyrosine kinase inhibitors (TKIs). In the current study, we found that the homologous circular RNA (circRNA) of the family with sequence similarity 134, member B (FAM134B), hsa_circ_0128505 (was abbreviated as circFAM134B in the present study), was identified to specifically target ER-phagy to promote lenvatinib (LV)-induced ferroptosis using reactive oxygen species (ROS), Fe2+, malondialdehyde (MDA), and western blot (WB) assays in HCC cells. RNA pull-down and mass spectrometry analyses suggested that circFAM134B and FAM134B mRNA were enriched with several common interacting proteins. Among them, poly (A) binding protein cytoplasmic 4 (PABPC4) was identified as the most enriched binding partner. It was proven to be a novel antagonist against the nonsense-mediated mRNA decay (NMD) mechanism. We then applied RNA immunoprecipitation (RIP), RNA pull-down, luciferase reporter, and NMD reporter gene assays to further explore the exact role and underlying mechanism of circFAM134B-PABPC4-FAM134B axis in HCC cells. circFAM134B was confirmed as a sponge that competitively interacted with PABPC4, thereby influencing FAM134B mRNA nonsense decay. Our results provide novel evidences and strategies for the comprehensive treatment of HCC.
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Affiliation(s)
- Tao Bi
- Department of Hepatobiliary Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
- Department of Gastrointestinal Surgery, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Qianqian Lu
- Department of Oncology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Xiaohong Pan
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Fenglin Dong
- Department of Hepatobiliary Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
| | - Yejia Hu
- Department of Pathophysiology, School of Basic Medicine, Binzhou Medical University, Yantai, China
| | - Zongzhen Xu
- Department of Hepatobiliary Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
| | - Peng Xiu
- Department of Hepatobiliary Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
| | - Zhiqian Liu
- Department of Hepatobiliary Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
| | - Jie Li
- Department of Hepatobiliary Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
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45
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Zou X, Shi Y, Zhang S, Quan J, Han J, Han S. Fluorescence-On Imaging of Reticulophagy Enabled by an Acidity-Reporting Solvatochromic Probe. Anal Chem 2023. [PMID: 37463355 DOI: 10.1021/acs.analchem.3c02016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Aberrant autophagy of the endoplasmic reticulum (reticulophagy) is engaged in diverse pathological disorders. Herein, we reported sensitive imaging of reticulophagy with ER-Green-proRed, a diad combining a solvatochromic entity of trifluoromethylated naphthalimide for long-term ER tracking by green fluorescence and an entity of rhodamine-lactam fluorogenic to lysosomal acidity. Stringently accumulated in the ER to give green fluorescence, ER-Green-proRed exhibits robust red fluorescence upon codelivery with the ER subdomain into lysosomes. The relevance of turn-on red fluorescence to reticulophagy was validated by reticulophagy modulated by starvation, reticulophagic receptors, and autophagy inhibition. This imaging method was successfully employed to discern reticulophagy induced by various pharmacological agents. These results show the potential of ER-targeted pH probes, as exemplified by ER-Green-proRed, to image reticulophagy and to identify reticulophagy inducers.
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Affiliation(s)
- Xiaoxue Zou
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory for Physical Chemistry of Solid Surfaces, the Key Laboratory for Chemical Biology of Fujian Province, the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Xiamen University, Xiamen 361005, China
| | - Yilong Shi
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Shuo Zhang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory for Physical Chemistry of Solid Surfaces, the Key Laboratory for Chemical Biology of Fujian Province, the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Xiamen University, Xiamen 361005, China
| | - Jialiang Quan
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory for Physical Chemistry of Solid Surfaces, the Key Laboratory for Chemical Biology of Fujian Province, the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Xiamen University, Xiamen 361005, China
| | - Jiahuai Han
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Shoufa Han
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory for Physical Chemistry of Solid Surfaces, the Key Laboratory for Chemical Biology of Fujian Province, the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Xiamen University, Xiamen 361005, China
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46
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Shi Y, Zou X, Zheng X, Wu Y, Han J, Han S. Sensitive imaging of Endoplasmic reticulum (ER) autophagy with an acidity-reporting ER-Tracker. Autophagy 2023; 19:2015-2025. [PMID: 36625032 PMCID: PMC10283422 DOI: 10.1080/15548627.2023.2165759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
Macroautophagic/autophagic turnover of endoplasmic reticulum (reticulophagy) is critical for cell health. Herein we reported a sensitive fluorescence-on imaging of reticulophagy using a small molecule probe (ER-proRed) comprised of green-emissive fluorinated rhodol for ER targeting and nonfluorescent rhodamine-lactam prone to lysosome-triggered red fluorescence. Partitioned in ER to exhibit green fluorescence, ER-proRed gives intense red fluorescence upon co-delivery with ER into acidic lysosomes. Serving as the signal of reticulophagy, the turning on of red fluorescence enables discernment of reticulophagy induced by starvation, varied levels of reticulophagic receptors, and chemical agents such as etoposide and sodium butyrate. These results show ER probes optically activatable in lysosomes, such as ER-proRed, offer a sensitive and simplified tool for studying reticulophagy in biology and diseases.Abbreviations: Baf-A1, bafilomycin A1; CCCP, carbonyl cyanide m-chlorophenyl hydrazone; CQ, chloroquine diphosphate; ER, endoplasmic reticulum; FHR, fluorinated hydrophobic rhodol; GFP, green fluorescent protein; Reticulophagy, selective autophagy of ER; RFP, red fluorescent protein; ROX, X-rhodamine; UPR, unfolded protein response.
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Affiliation(s)
- Yilong Shi
- State Key Laboratory for Physical Chemistry of Solid Surfaces, the Key Laboratory for Chemical Biology of Fujian Province, the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Xiaoxue Zou
- State Key Laboratory for Physical Chemistry of Solid Surfaces, the Key Laboratory for Chemical Biology of Fujian Province, the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | | | - Yimin Wu
- State Key Laboratory for Physical Chemistry of Solid Surfaces, the Key Laboratory for Chemical Biology of Fujian Province, the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Jiahuai Han
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signalling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shoufa Han
- State Key Laboratory for Physical Chemistry of Solid Surfaces, the Key Laboratory for Chemical Biology of Fujian Province, the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
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47
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Kucińska MK, Fedry J, Galli C, Morone D, Raimondi A, Soldà T, Förster F, Molinari M. TMX4-driven LINC complex disassembly and asymmetric autophagy of the nuclear envelope upon acute ER stress. Nat Commun 2023; 14:3497. [PMID: 37311770 DOI: 10.1038/s41467-023-39172-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 05/31/2023] [Indexed: 06/15/2023] Open
Abstract
The endoplasmic reticulum (ER) is an organelle of nucleated cells that produces proteins, lipids and oligosaccharides. ER volume and activity are increased upon induction of unfolded protein responses (UPR) and are reduced upon activation of ER-phagy programs. A specialized domain of the ER, the nuclear envelope (NE), protects the cell genome with two juxtaposed lipid bilayers, the inner and outer nuclear membranes (INM and ONM) separated by the perinuclear space (PNS). Here we report that expansion of the mammalian ER upon homeostatic perturbations results in TMX4 reductase-driven disassembly of the LINC complexes connecting INM and ONM and in ONM swelling. The physiologic distance between ONM and INM is restored, upon resolution of the ER stress, by asymmetric autophagy of the NE, which involves the LC3 lipidation machinery, the autophagy receptor SEC62 and the direct capture of ONM-derived vesicles by degradative LAMP1/RAB7-positive endolysosomes in a catabolic pathway mechanistically defined as micro-ONM-phagy.
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Affiliation(s)
- Marika K Kucińska
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, CH-6500, Bellinzona, Switzerland
- Department of Biology, Swiss Federal Institute of Technology, CH-8093, Zurich, Switzerland
| | - Juliette Fedry
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Carmela Galli
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, CH-6500, Bellinzona, Switzerland
| | - Diego Morone
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, CH-6500, Bellinzona, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3000, Bern, Switzerland
| | - Andrea Raimondi
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, CH-6500, Bellinzona, Switzerland
- Experimental Imaging Center, San Raffaele Scientific Institute, I-20132, Milan, Italy
| | - Tatiana Soldà
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, CH-6500, Bellinzona, Switzerland
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Maurizio Molinari
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, CH-6500, Bellinzona, Switzerland.
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
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48
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Mitchell DC, Kuljanin M, Li J, Van Vranken JG, Bulloch N, Schweppe DK, Huttlin EL, Gygi SP. A proteome-wide atlas of drug mechanism of action. Nat Biotechnol 2023; 41:845-857. [PMID: 36593396 PMCID: PMC11069389 DOI: 10.1038/s41587-022-01539-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 09/30/2022] [Indexed: 01/03/2023]
Abstract
Defining the cellular response to pharmacological agents is critical for understanding the mechanism of action of small molecule perturbagens. Here, we developed a 96-well-plate-based high-throughput screening infrastructure for quantitative proteomics and profiled 875 compounds in a human cancer cell line with near-comprehensive proteome coverage. Examining the 24-h proteome changes revealed ligand-induced changes in protein expression and uncovered rules by which compounds regulate their protein targets while identifying putative dihydrofolate reductase and tankyrase inhibitors. We used protein-protein and compound-compound correlation networks to uncover mechanisms of action for several compounds, including the adrenergic receptor antagonist JP1302, which we show disrupts the FACT complex and degrades histone H1. By profiling many compounds with overlapping targets covering a broad chemical space, we linked compound structure to mechanisms of action and highlighted off-target polypharmacology for molecules within the library.
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Affiliation(s)
- Dylan C Mitchell
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Miljan Kuljanin
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Jiaming Li
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | | | - Nathan Bulloch
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
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49
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González A, Covarrubias-Pinto A, Bhaskara RM, Glogger M, Kuncha SK, Xavier A, Seemann E, Misra M, Hoffmann ME, Bräuning B, Balakrishnan A, Qualmann B, Dötsch V, Schulman BA, Kessels MM, Hübner CA, Heilemann M, Hummer G, Dikić I. Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum. Nature 2023:10.1038/s41586-023-06089-2. [PMID: 37225996 DOI: 10.1038/s41586-023-06089-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/14/2023] [Indexed: 05/26/2023]
Abstract
The endoplasmic reticulum (ER) undergoes continuous remodelling via a selective autophagy pathway, known as ER-phagy1. ER-phagy receptors have a central role in this process2, but the regulatory mechanism remains largely unknown. Here we report that ubiquitination of the ER-phagy receptor FAM134B within its reticulon homology domain (RHD) promotes receptor clustering and binding to lipidated LC3B, thereby stimulating ER-phagy. Molecular dynamics (MD) simulations showed how ubiquitination perturbs the RHD structure in model bilayers and enhances membrane curvature induction. Ubiquitin molecules on RHDs mediate interactions between neighbouring RHDs to form dense receptor clusters that facilitate the large-scale remodelling of lipid bilayers. Membrane remodelling was reconstituted in vitro with liposomes and ubiquitinated FAM134B. Using super-resolution microscopy, we discovered FAM134B nanoclusters and microclusters in cells. Quantitative image analysis revealed a ubiquitin-mediated increase in FAM134B oligomerization and cluster size. We found that the E3 ligase AMFR, within multimeric ER-phagy receptor clusters, catalyses FAM134B ubiquitination and regulates the dynamic flux of ER-phagy. Our results show that ubiquitination enhances RHD functions via receptor clustering, facilitates ER-phagy and controls ER remodelling in response to cellular demands.
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Affiliation(s)
- Alexis González
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Adriana Covarrubias-Pinto
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ramachandra M Bhaskara
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Marius Glogger
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Santosh K Kuncha
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Audrey Xavier
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Eric Seemann
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Mohit Misra
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marina E Hoffmann
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Bastian Bräuning
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ashwin Balakrishnan
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Britta Qualmann
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Michael M Kessels
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Christian A Hübner
- Institute of Human Genetics, University Hospital Jena, Friedrich Schiller University, Jena, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ivan Dikić
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany.
- Fraunhofer Institute of Translational Medicine and Pharmacology, Frankfurt am Main, Germany.
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50
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Themistokleous C, Bagnoli E, Parulekar R, M K Muqit M. Role of autophagy pathway in Parkinson's disease and related Genetic Neurological disorders. J Mol Biol 2023:168144. [PMID: 37182812 DOI: 10.1016/j.jmb.2023.168144] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/16/2023]
Abstract
The elucidation of the function of the PINK1 protein kinase and Parkin ubiquitin E3 ligase in the elimination of damaged mitochondria by autophagy (mitophagy) has provided unprecedented understanding of the mechanistic pathways underlying Parkinson's disease (PD). We provide a comprehensive overview of the general importance of autophagy in Parkinson's disease and related disorders of the central nervous system. This reveals a critical link between autophagy and neurodegenerative and neurodevelopmental disorders and suggests that strategies to modulate mitophagy may have greater relevance in the CNS beyond PD.
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Affiliation(s)
- Christos Themistokleous
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK of Dundee, Dundee, DD1 5EH, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Enrico Bagnoli
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK of Dundee, Dundee, DD1 5EH, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Ramaa Parulekar
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK of Dundee, Dundee, DD1 5EH, UK
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK of Dundee, Dundee, DD1 5EH, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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