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Nie Z, Zhai F, Zhang H, Zheng H, Pei J. The multiple roles of viral 3D pol protein in picornavirus infections. Virulence 2024; 15:2333562. [PMID: 38622757 PMCID: PMC11020597 DOI: 10.1080/21505594.2024.2333562] [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: 12/18/2023] [Accepted: 03/17/2024] [Indexed: 04/17/2024] Open
Abstract
The Picornaviridae are a large group of positive-sense, single-stranded RNA viruses, and most research has focused on the Enterovirus genus, given they present a severe health risk to humans. Other picornaviruses, such as foot-and-mouth disease virus (FMDV) and senecavirus A (SVA), affect agricultural production with high animal mortality to cause huge economic losses. The 3Dpol protein of picornaviruses is widely known to be used for genome replication; however, a growing number of studies have demonstrated its non-polymerase roles, including modulation of host cell biological processes, viral replication complex assembly and localization, autophagy, and innate immune responses. Currently, there is no effective vaccine to control picornavirus diseases widely, and clinical therapeutic strategies have limited efficiency in combating infections. Many efforts have been made to develop different types of drugs to prohibit virus survival; the most important target for drug development is the virus polymerase, a necessary element for virus replication. For picornaviruses, there are also active efforts in targeted 3Dpol drug development. This paper reviews the interaction of 3Dpol proteins with the host and the progress of drug development targeting 3Dpol.
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Affiliation(s)
- Zhenyu Nie
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
| | - Fengge Zhai
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Han Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
| | - Haixue Zheng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Jingjing Pei
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
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Cui Z, Esposito A, Napolitano G, Ballabio A, Hurley JH. Structural basis for growth factor and nutrient signal integration on the lysosomal membrane by mTORC1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.15.623810. [PMID: 39605743 PMCID: PMC11601357 DOI: 10.1101/2024.11.15.623810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Mechanistic target of rapamycin complex 1 (mTORC1), which consists of mTOR, Raptor, and mLST8, receives signaling inputs from growth factor signals and nutrients. These signals are mediated by the Rheb and Rag small GTPases, respectively, which activate mTORC1 on the cytosolic face of the lysosome membrane. We biochemically reconstituted the activation of mTORC1 on membranes by physiological submicromolar concentrations of Rheb, Rags, and Ragulator. We determined the cryo-EM structure and found that Raptor and mTOR directly interact with the membrane at anchor points separated by up to 230 Å across the membrane surface. Full engagement of the membrane anchors is required for maximal activation, which is brought about by alignment of the catalytic residues in the mTOR kinase active site. The observations show at the molecular and atomic scale how converging signals from growth factors and nutrients drive mTORC1 recruitment to and activation on the lysosomal membrane in a three-step process, consisting of (1) Rag-Ragulator-driven recruitment to within ∼100 Å of the lysosomal membrane, (2) Rheb-driven recruitment to within ∼40 Å, and finally (3) direct engagement of mTOR and Raptor with the membrane. The combination of Rheb and membrane engagement leads to full catalytic activation, providing a structural explanation for growth factor and nutrient signal integration at the lysosome.
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Wu B, Huang X, Shi X, Jiang M, Liu H, Zhao L. LAMTOR1 decreased exosomal PD-L1 to enhance immunotherapy efficacy in non-small cell lung cancer. Mol Cancer 2024; 23:184. [PMID: 39223601 PMCID: PMC11367890 DOI: 10.1186/s12943-024-02099-4] [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: 07/03/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
Great progress has been made in utilizing immune checkpoint blockade (ICB) for the treatment of non-small-cell lung cancer (NSCLC). Therapies targeting programmed cell death protein 1 (PD-1) and its ligand PD-L1, expressed on tumor cells, have demonstrated potential in improving patient survival rates. An unresolved issue involves immune suppression induced by exosomal PD-L1 within the tumor microenvironment (TME), particularly regarding CD8+ T cells. Our study unveiled the crucial involvement of LAMTOR1 in suppressing the exosomes of PD-L1 and promoting CD8+ T cell infiltration in NSCLC. Through its interaction with HRS, LAMTOR1 facilitates PD-L1 lysosomal degradation, thereby reducing exosomal PD-L1 release. Notably, the ability of LAMTOR1 to promote PD-L1 lysosomal degradation relies on a specific ubiquitination site and an HRS binding sequence. The findings suggest that employing LAMTOR1 to construct peptides could serve as a promising strategy for bolstering the efficacy of immunotherapy in NSCLC. The discovery and comprehension of how LAMTOR1 inhibits the release of exosomal PD-L1 offer insights into potential therapeutic strategies for improving immunotherapy. It is imperative to conduct further research and clinical trials to investigate the feasibility and efficacy of targeting LAMTOR1 in NSCLC treatment.
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Affiliation(s)
- Bo Wu
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, 110136, China
| | - Xin Huang
- Department of General practice medicine, Shengjing Hospital of China Medical University, Shenyang, 110022, China
| | - Xiang Shi
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, China
| | - Meixi Jiang
- Department of Neurology, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Hongxu Liu
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, China.
| | - Li Zhao
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, 110136, China.
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Liu Y, Wang R, Liu J, Fan M, Ye Z, Hao Y, Xie F, Wang T, Jiang Y, Liu N, Cui X, Lv Q, Yan L. The vacuolar fusion regulated by HOPS complex promotes hyphal initiation and penetration in Candida albicans. Nat Commun 2024; 15:4131. [PMID: 38755250 PMCID: PMC11099166 DOI: 10.1038/s41467-024-48525-5] [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: 10/11/2023] [Accepted: 05/02/2024] [Indexed: 05/18/2024] Open
Abstract
The transition between yeast and hyphae is crucial for regulating the commensalism and pathogenicity in Candida albicans. The mechanisms that affect the invasion of hyphae in solid media, whose deficiency is more related to the pathogenicity of C. albicans, have not been elucidated. Here, we found that the disruption of VAM6 or VPS41 which are components of the homotypic vacuolar fusion and protein sorting (HOPS) complex, or the Rab GTPase YPT72, all responsible for vacuole fusion, led to defects in hyphal growth in both liquid and solid media, but more pronounced on solid agar. The phenotypes of vac8Δ/Δ and GTR1OE-vam6Δ/Δ mutants indicated that these deficiencies are mainly caused by the reduced mechanical forces that drive agar and organs penetration, and confirmed that large vacuoles are required for hyphal mechanical penetration. In summary, our study revealed that large vacuoles generated by vacuolar fusion support hyphal penetration and provided a perspective to refocus attention on the role of solid agar in evaluating C. albicans invasion.
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Affiliation(s)
- Yu Liu
- Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai, 200433, PR China
| | - Ruina Wang
- Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai, 200433, PR China
| | - Jiacun Liu
- Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai, 200433, PR China
| | - Mengting Fan
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, PR China
| | - Zi Ye
- Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai, 200433, PR China
| | - Yumeng Hao
- Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai, 200433, PR China
| | - Fei Xie
- Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai, 200433, PR China
| | - Ting Wang
- Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai, 200433, PR China
| | - Yuanying Jiang
- School of Medicine, Tongji University, Shanghai, 200092, PR China
| | - Ningning Liu
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, PR China.
| | - Xiaoyan Cui
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, PR China.
| | - Quanzhen Lv
- Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai, 200433, PR China.
| | - Lan Yan
- Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai, 200433, PR China.
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Wang X, Hu Z, Zhang W, Wu S, Hao Y, Xiao X, Li J, Yu X, Yang C, Wang J, Zhang H, Ma F, Shi W, Wang J, Lei X, Zhang X, He S. Inhibition of lysosome-tethered Ragulator-Rag-3D complex restricts the replication of Enterovirus 71 and Coxsackie A16. J Cell Biol 2023; 222:e202303108. [PMID: 37906052 PMCID: PMC10619577 DOI: 10.1083/jcb.202303108] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/10/2023] [Accepted: 09/21/2023] [Indexed: 11/02/2023] Open
Abstract
Enterovirus 71 (EV71) and Coxsackie A16 (CVA16) are two major causative agents of hand, foot, and mouth disease (HFMD) in young children. However, the mechanisms regulating the replication and pathogenesis of EV71/CVA16 remain incompletely understood. We performed a genome-wide CRISPR-Cas9 knockout screen and identified Ragulator as a mediator of EV71-induced apoptosis and pyroptosis. The Ragulator-Rag complex is required for EV71 and CVA16 replication. Upon infection, the Ragulator-Rag complex recruits viral 3D protein to the lysosomal surface through the interaction between 3D and RagB. Disruption of the lysosome-tethered Ragulator-Rag-3D complex significantly impairs the replication of EV71/CVA16. We discovered a novel EV71 inhibitor, ZHSI-1, which interacts with 3D and significantly reduces the lysosomal tethering of 3D. ZHSI-1 treatment significantly represses replication of EV71/CVA16 as well as virus-induced pyroptosis associated with viral pathogenesis. Importantly, ZHSI-1 treatment effectively protects against EV71 infection in neonatal and young mice. Thus, our study indicates that targeting lysosome-tethered Ragulator-Rag-3D may be an effective therapeutic strategy for HFMD.
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Affiliation(s)
- Xinhui Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, and Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Zhilin Hu
- Cyrus Tang Hematology Center and Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Wei Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, and Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Shuwei Wu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Yongjin Hao
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Xia Xiao
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Beijing, China
| | - Jingjing Li
- State Key Laboratory of Common Mechanism Research for Major Diseases, and Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Xiaoliang Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, and Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Chengkui Yang
- State Key Laboratory of Common Mechanism Research for Major Diseases, and Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Jingfeng Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, and Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Huiying Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, and Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Feng Ma
- National Key Laboratory of Immunity and Inflammation, and Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Weifeng Shi
- Department of Laboratory Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Jianwei Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaobo Lei
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaohu Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Sudan He
- State Key Laboratory of Common Mechanism Research for Major Diseases, and Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
- Cyrus Tang Hematology Center and Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
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Linde-Garelli KY, Rogala KB. Structural mechanisms of the mTOR pathway. Curr Opin Struct Biol 2023; 82:102663. [PMID: 37572585 DOI: 10.1016/j.sbi.2023.102663] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/01/2023] [Accepted: 07/07/2023] [Indexed: 08/14/2023]
Abstract
The mTOR signaling pathway is essential for regulating cell growth and mammalian metabolism. The mTOR kinase forms two complexes, mTORC1 and mTORC2, which respond to external stimuli and regulate differential downstream targets. Cellular membrane-associated translocation mediates function and assembly of the mTOR complexes, and recent structural studies have begun uncovering the molecular basis by which the mTOR pathway (1) regulates signaling inputs, (2) recruits substrates, (3) localizes to biological membranes, and (4) becomes activated. Moreover, indications of dysregulated mTOR signaling are implicated in a wide range of diseases and an increasingly comprehensive understanding of structural mechanisms is driving novel translational development.
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Affiliation(s)
- Karen Y Linde-Garelli
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Kacper B Rogala
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
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Tettoni SD, Egri SB, Doxsey DD, Veinotte K, Ouch C, Chang JY, Song K, Xu C, Shen K. Structure of the Schizosaccharomyces pombe Gtr-Lam complex reveals evolutionary divergence of mTORC1-dependent amino acid sensing. Structure 2023; 31:1065-1076.e5. [PMID: 37453417 PMCID: PMC10529327 DOI: 10.1016/j.str.2023.06.012] [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: 03/02/2023] [Revised: 05/14/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
mTORC1 is a protein kinase complex that controls cellular growth in response to nutrient availability. Amino acid signals are transmitted toward mTORC1 via the Rag/Gtr GTPases and their upstream regulators. An important regulator is LAMTOR, which localizes Rag/Gtr on the lysosomal/vacuole membrane. In human cells, LAMTOR consists of five subunits, but in yeast, only three or four. Currently, it is not known how variation of the subunit stoichiometry may affect its structural organization and biochemical properties. Here, we report a 3.1 Å-resolution structural model of the Gtr-Lam complex in Schizosaccharomyces pombe. We found that SpGtr shares conserved architecture as HsRag, but the intersubunit communication that coordinates nucleotide loading on the two subunits differs. In contrast, SpLam contains distinctive structural features, but its GTP-specific GEF activity toward SpGtr is evolutionarily conserved. Our results revealed unique evolutionary paths of the protein components of the mTORC1 pathway.
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Affiliation(s)
- Steven D Tettoni
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Shawn B Egri
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Dylan D Doxsey
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Kristen Veinotte
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Christna Ouch
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Jeng-Yih Chang
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Kangkang Song
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Chen Xu
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Kuang Shen
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, 373 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA.
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Xu J, Quan G, Huang W, Jiang J. VSIG2 promotes malignant progression of pancreatic ductal adenocarcinoma by enhancing LAMTOR2-mediated mTOR activation. Cell Commun Signal 2023; 21:223. [PMID: 37626304 PMCID: PMC10463957 DOI: 10.1186/s12964-023-01209-x] [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: 04/05/2023] [Accepted: 06/30/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is one of the most intractable malignancies to overcome clinically due to its insidious onset as well as rapid progression. It is urgent to seek new diagnostic markers and therapeutic targets in order to furthest ameliorate the prognosis of patients with PDAC. V-set and immunoglobulin domain containing 2 (VSIG2) belongs to immunoglobulin superfamily (IgSF), which function as coinhibitory molecule to mediate immune evasion of tumors. Nevertheless, the role of VSIG2 in PDAC and related mechanism still keep unclear. METHODS Different expression of VSIG2 in PDAC tissues and cells were detected by bioinformatic analysis, immunohistochemistry, real-time quantitative PCR as well as western blotting. CCK-8, colony formation, Transwell assay, and scratch experiment were utilized to assess proliferation, invasion and migration properties of PDAC cells. The relationship of VSIG2 with late endosomal/lysosomal adaptor, MAPK and MTOR activator 2 (LAMTOR2) and mechanistic target of rapamycin (mTOR) was identified using mass spectrometry, co-immunoprecipitation and immunofluorescence. GO and KEGG enrichment analysis were performed for further pathway verification using western blotting. Additionally, subcutaneous xenograft tumor model and clinical samples analysis were implemented to further elucidate the oncogenic effect of VSIG2 on PDAC in vivo and clinically. RESULTS VSIG2 was highly expressed in PDAC tissues and cells. Overexpression of VSIG2 facilitated the proliferation, invasion and migration abilities of PDAC cells, while VSIG2-inhibition exerted opposite effects. Mechanistically, VSIG2 could simultaneously bind to LAMTOR2 and mTOR, thereby enhancing interaction between two molecules, which resulted in elevated phosphorylation-modificatory activation of mTOR and downstream key molecules. Clinically, up-regulation of VSIG2 was positively associated with advanced stage, overall survival and disease-free survival of PDAC patients. CONCLUSIONS Our study disclosed that VSIG2 was overexpressed in PDAC, which promoted the proliferation, invasion and metastasis. Mechanically, VSIG2 acted as a scaffold to recruit LAMTOR2 and mTOR simultaneously, stabilize the interaction between them, thus enhancing LAMTOR2-mediated mTOR phosphorylated activation. Collectively, VSIG2 could be exploited as a biomarker for diagnosis and prognosis monitor of PDAC in the future, meanwhile, targeting VSIG2 in PDAC management is expected to be a novel strategy. Video Abstract. Video Abstract.
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Affiliation(s)
- Jichuan Xu
- Department of Hepatobiliary, Pancreatic and Splenic Surgery, Affiliated Dongguan Hospital, Southern Medical University (Dongguan People's Hospital), 78 Wandao Road, Wanjiang Street, Dongguan City, Guangdong Province, 523058, People's Republic of China
| | - Gang Quan
- Department of Hepatobiliary, Pancreatic and Splenic Surgery, Affiliated Dongguan Hospital, Southern Medical University (Dongguan People's Hospital), 78 Wandao Road, Wanjiang Street, Dongguan City, Guangdong Province, 523058, People's Republic of China
- Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Wei Huang
- Department of Hepatobiliary, Pancreatic and Splenic Surgery, Affiliated Dongguan Hospital, Southern Medical University (Dongguan People's Hospital), 78 Wandao Road, Wanjiang Street, Dongguan City, Guangdong Province, 523058, People's Republic of China
| | - Jianxin Jiang
- Department of Hepatobiliary, Pancreatic and Splenic Surgery, Affiliated Dongguan Hospital, Southern Medical University (Dongguan People's Hospital), 78 Wandao Road, Wanjiang Street, Dongguan City, Guangdong Province, 523058, People's Republic of China.
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Chhuon C, Herrera-Marcos LV, Zhang SY, Charrière-Bertrand C, Jung V, Lipecka J, Savas B, Nasser N, Pawlak A, Boulmerka H, Audard V, Sahali D, Guerrera IC, Ollero M. Proteomics of Plasma and Plasma-Treated Podocytes: Application to Focal and Segmental Glomerulosclerosis. Int J Mol Sci 2023; 24:12124. [PMID: 37569500 PMCID: PMC10418338 DOI: 10.3390/ijms241512124] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Focal and segmental glomerulosclerosis (FSGS) is a severe form of idiopathic nephrotic syndrome (INS), a glomerulopathy of presumably immune origin that is attributed to extrarenal pathogenic circulating factors. The recurrence of FSGS (rFSGS) after transplant occurs in 30% to 50% of cases. The direct analysis of patient plasma proteome has scarcely been addressed to date, mainly due to the methodological difficulties associated with plasma complexity and dynamic range. In this study, first, we compared different methods of plasma preparation, second, we compared the plasma proteomes of rFSGS and controls using two preparation methods, and third, we analyzed the early proximal signaling events in podocytes subjected to patient plasma, through a combination of phosphoproteomics and lipid-raft proteomics (raftomics). By combining immunodepletion and high pH fractionation, we performed a differential proteomic analysis of soluble plasma proteins and of extracellular vesicles (EV) obtained from healthy controls, non-INS patient controls, and rFSGS patients (n = 4). In both the soluble- and the EV-protein sets from the rFSGS patients, we found a statistically significant increase in a cluster of proteins involved in neutrophil degranulation. A group of lipid-binding proteins, generally associated with lipoproteins, was found to be decreased in the soluble set from the rFSGS patients. In addition, three amino acid transporters involved in mTORC1 activation were found to be significantly increased in the EV from the rFSGS. Next, we incubated human podocytes for 30 min with 10% plasma from both groups of patients. The phosphoproteomics and raftomics of the podocytes revealed profound differences in the proteins involved in the mTOR pathway, in autophagy, and in cytoskeleton organization. We analyzed the correlation between the abundance of plasma and plasma-regulated podocyte proteins. The observed changes highlight some of the mechanisms involved in FSGS recurrence and could be used as specific early markers of circulating-factor activity in podocytes.
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Affiliation(s)
- Cerina Chhuon
- Proteomic Platform Necker, Université Paris Cité Structure Fédérative de Recherche SFR Necker US24, 75015 Paris, France; (C.C.); (V.J.); (J.L.)
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (L.V.H.-M.); (S.-Y.Z.); (C.C.-B.); (B.S.); (N.N.); (A.P.); (H.B.); (V.A.); (D.S.)
| | - Luis Vicente Herrera-Marcos
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (L.V.H.-M.); (S.-Y.Z.); (C.C.-B.); (B.S.); (N.N.); (A.P.); (H.B.); (V.A.); (D.S.)
| | - Shao-Yu Zhang
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (L.V.H.-M.); (S.-Y.Z.); (C.C.-B.); (B.S.); (N.N.); (A.P.); (H.B.); (V.A.); (D.S.)
| | - Cécile Charrière-Bertrand
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (L.V.H.-M.); (S.-Y.Z.); (C.C.-B.); (B.S.); (N.N.); (A.P.); (H.B.); (V.A.); (D.S.)
| | - Vincent Jung
- Proteomic Platform Necker, Université Paris Cité Structure Fédérative de Recherche SFR Necker US24, 75015 Paris, France; (C.C.); (V.J.); (J.L.)
| | - Joanna Lipecka
- Proteomic Platform Necker, Université Paris Cité Structure Fédérative de Recherche SFR Necker US24, 75015 Paris, France; (C.C.); (V.J.); (J.L.)
| | - Berkan Savas
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (L.V.H.-M.); (S.-Y.Z.); (C.C.-B.); (B.S.); (N.N.); (A.P.); (H.B.); (V.A.); (D.S.)
| | - Nour Nasser
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (L.V.H.-M.); (S.-Y.Z.); (C.C.-B.); (B.S.); (N.N.); (A.P.); (H.B.); (V.A.); (D.S.)
| | - André Pawlak
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (L.V.H.-M.); (S.-Y.Z.); (C.C.-B.); (B.S.); (N.N.); (A.P.); (H.B.); (V.A.); (D.S.)
| | - Hocine Boulmerka
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (L.V.H.-M.); (S.-Y.Z.); (C.C.-B.); (B.S.); (N.N.); (A.P.); (H.B.); (V.A.); (D.S.)
| | - Vincent Audard
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (L.V.H.-M.); (S.-Y.Z.); (C.C.-B.); (B.S.); (N.N.); (A.P.); (H.B.); (V.A.); (D.S.)
- AP-HP, Hôpitaux Universitaires Henri Mondor, Service de Néphrologie, F-94010 Creteil, France
| | - Dil Sahali
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (L.V.H.-M.); (S.-Y.Z.); (C.C.-B.); (B.S.); (N.N.); (A.P.); (H.B.); (V.A.); (D.S.)
- AP-HP, Hôpitaux Universitaires Henri Mondor, Service de Néphrologie, F-94010 Creteil, France
| | - Ida Chiara Guerrera
- Proteomic Platform Necker, Université Paris Cité Structure Fédérative de Recherche SFR Necker US24, 75015 Paris, France; (C.C.); (V.J.); (J.L.)
| | - Mario Ollero
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (L.V.H.-M.); (S.-Y.Z.); (C.C.-B.); (B.S.); (N.N.); (A.P.); (H.B.); (V.A.); (D.S.)
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10
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Zhang H, Bai L, Wu XQ, Tian X, Feng J, Wu X, Shi GH, Pei X, Lyu J, Yang G, Liu Y, Xu W, Anwaier A, Zhu Y, Cao DL, Xu F, Wang Y, Gan HL, Sun MH, Zhao JY, Qu Y, Ye D, Ding C. Proteogenomics of clear cell renal cell carcinoma response to tyrosine kinase inhibitor. Nat Commun 2023; 14:4274. [PMID: 37460463 DOI: 10.1038/s41467-023-39981-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 07/04/2023] [Indexed: 07/20/2023] Open
Abstract
The tyrosine kinase inhibitor (TKI) Sunitinib is one the therapies approved for advanced renal cell carcinoma. Here, we undertake proteogenomic profiling of 115 tumors from patients with clear cell renal cell carcinoma (ccRCC) undergoing Sunitinib treatment and reveal the molecular basis of differential clinical outcomes with TKI therapy. We find that chromosome 7q gain-induced mTOR signaling activation is associated with poor therapeutic outcomes with Sunitinib treatment, whereas the aristolochic acid signature and VHL mutation synergistically caused enhanced glycolysis is correlated with better prognosis. The proteomic and phosphoproteomic analysis further highlights the responsibility of mTOR signaling for non-response to Sunitinib. Immune landscape characterization reveals diverse tumor microenvironment subsets in ccRCC. Finally, we construct a multi-omics classifier that can detect responder and non-responder patients (receiver operating characteristic-area under the curve, 0.98). Our study highlights associations between ccRCC molecular characteristics and the response to TKI, which can facilitate future improvement of therapeutic responses.
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Affiliation(s)
- Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Lin Bai
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
| | - Xin-Qiang Wu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Jinwen Feng
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
| | - Xiaohui Wu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
| | - Guo-Hai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Xiaoru Pei
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
| | - Jiacheng Lyu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
| | - Guojian Yang
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
| | - Yang Liu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
| | - Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Aihetaimujiang Anwaier
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Yu Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Da-Long Cao
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Fujiang Xu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
| | - Yue Wang
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Hua-Lei Gan
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
- Tissue Bank & Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Meng-Hong Sun
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
- Tissue Bank & Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Jian-Yuan Zhao
- Institute for Developmental and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
- Department of Anatomy and Neuroscience Research Institute, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Yuanyuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China.
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China.
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China.
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China.
| | - Chen Ding
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Qingdao Institute, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China.
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11
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Tsujimoto K, Takamatsu H, Kumanogoh A. The Ragulator complex: delving its multifunctional impact on metabolism and beyond. Inflamm Regen 2023; 43:28. [PMID: 37173755 PMCID: PMC10175929 DOI: 10.1186/s41232-023-00278-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023] Open
Abstract
Our understanding of lysosomes has undergone a significant transformation in recent years, from the view that they are static organelles primarily responsible for the disposal and recycling of cellular waste to their recognition as highly dynamic structures. Current research posits that lysosomes function as a signaling hub that integrates both extracellular and intracellular stimuli, thereby regulating cellular homeostasis. The dysregulation of lysosomal function has been linked to a wide range of diseases. Of note, lysosomes contribute to the activation of mammalian target of rapamycin complex 1 (mTORC1), a key regulator of cellular metabolism. The Ragulator complex, a protein complex anchored on the lysosomal membrane, was initially shown to tether the mTORC1 complex to lysosomes. Recent research has substantially expanded our understanding of the roles of the Ragulator complex in lysosomes, including roles in the regulation of metabolism, inflammation, cell death, cell migration, and the maintenance of homeostasis, via interactions with various proteins. This review summarizes our current knowledge on the diverse functions of the Ragulator complex, highlighting important protein interactions.
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Affiliation(s)
- Kohei Tsujimoto
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Department of Immunopathology, Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Hyota Takamatsu
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan.
- Department of Immunopathology, Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan.
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Department of Immunopathology, Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
- Center for Infectious Diseases Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
- Japan Agency for Medical Research and Development - Core Research for Evolutional Science and Technology (AMED-CREST), Osaka University, Osaka, Japan
- Center for Advanced Modalities and DDS (CAMaD), Osaka University, Osaka, Japan
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12
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Regulation of mTORC1 by the Rag GTPases. Biochem Soc Trans 2023; 51:655-664. [PMID: 36929165 DOI: 10.1042/bst20210038] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/18/2023]
Abstract
The Rag GTPases are an evolutionarily conserved family that play a crucial role in amino acid sensing by the mammalian target of rapamycin complex 1 (mTORC1). mTORC1 is often referred to as the master regulator of cell growth. mTORC1 hyperactivation is observed in multiple diseases such as cancer, obesity, metabolic disorders, and neurodegeneration. The Rag GTPases sense amino acid levels and form heterodimers, where RagA or RagB binds to RagC or RagD, to recruit mTORC1 to the lysosome where it becomes activated. Here, we review amino acid signaling to mTORC1 through the Rag GTPases.
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13
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Romero‐Gavilán F, Cerqueira A, García‐Arnáez I, Azkargorta M, Elortza F, Gurruchaga M, Goñi I, Suay J. Proteomic evaluation of human osteoblast responses to titanium implants over time. J Biomed Mater Res A 2023; 111:45-59. [PMID: 36054528 PMCID: PMC9804409 DOI: 10.1002/jbm.a.37444] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/13/2022] [Accepted: 08/18/2022] [Indexed: 01/05/2023]
Abstract
Titanium is widely used in bone prostheses due to its excellent biocompatibility and osseointegration capacity. To understand the effect of sandblasted acid-etched (SAE) Ti implants on the biological responses of human osteoblast (HOb), their proteomic profiles were analyzed using nLC-MS/MS. The cells were cultured with the implant materials, and 2544 distinct proteins were detected in samples taken after 1, 3, and 7 days. Comparative analyses of proteomic data were performed using Perseus software. The expression of proteins related to EIF2, mTOR, insulin-secretion and IGF pathways showed marked differences in cells grown with SAE-Ti in comparison with cells cultured without Ti. Moreover, the proteomic profiles obtained with SAE-Ti were compared over time. The affected proteins were related to adhesion, immunity, oxidative stress, coagulation, angiogenesis, osteogenesis, and extracellular matrix formation functions. The proliferation, mineralization and osteogenic gene expression in HObs cultured with SAE-Ti were characterized in vitro. The results showed that the osteoblasts exposed to this material increase their mineralization rate and expression of COLI, RUNX2, SP7, CTNNB1, CAD13, IGF2, MAPK2, and mTOR. Overall, the observed proteomic profiles can explain the SAE-Ti osteogenic properties, widening our knowledge of key signaling pathways taking part in the early stages of the osseointegration process in this type of implantations.
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Affiliation(s)
- Francisco Romero‐Gavilán
- Department of Industrial Systems Engineering and DesignUniversitat Jaume ICastellón de la PlanaSpain
| | - Andreia Cerqueira
- Department of Industrial Systems Engineering and DesignUniversitat Jaume ICastellón de la PlanaSpain
| | - Iñaki García‐Arnáez
- Department of Polymers and Advanced Materials: Physics, Chemistry and TechnologyUniversidad del País VascoSan SebastiánSpain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, ProteoRed‐ISCIIIBizkaia Science and Technology ParkDerioSpain
| | - Félix Elortza
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, ProteoRed‐ISCIIIBizkaia Science and Technology ParkDerioSpain
| | - Mariló Gurruchaga
- Department of Polymers and Advanced Materials: Physics, Chemistry and TechnologyUniversidad del País VascoSan SebastiánSpain
| | - Isabel Goñi
- Department of Polymers and Advanced Materials: Physics, Chemistry and TechnologyUniversidad del País VascoSan SebastiánSpain
| | - Julio Suay
- Department of Industrial Systems Engineering and DesignUniversitat Jaume ICastellón de la PlanaSpain
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14
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Napolitano G, Di Malta C, Ballabio A. Non-canonical mTORC1 signaling at the lysosome. Trends Cell Biol 2022; 32:920-931. [PMID: 35654731 DOI: 10.1016/j.tcb.2022.04.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/21/2023]
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) signaling hub integrates multiple environmental cues to modulate cell growth and metabolism. Over the past decade considerable knowledge has been gained on the mechanisms modulating mTORC1 lysosomal recruitment and activation. However, whether and how mTORC1 is able to elicit selective responses to diverse signals has remained elusive until recently. We discuss emerging evidence for a 'non-canonical' mTORC1 signaling pathway that controls the function of microphthalmia/transcription factor E (MiT-TFE) transcription factors, key regulators of cell metabolism. This signaling pathway is mediated by a specific mechanism of substrate recruitment, and responds to stimuli that appear to converge on the lysosomal surface. We discuss the relevance of this pathway in physiological and disease conditions.
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Affiliation(s)
- Gennaro Napolitano
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Via Pansini 5, 80131 Naples, Italy.
| | - Chiara Di Malta
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Via Pansini 5, 80131 Naples, Italy.
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Via Pansini 5, 80131 Naples, Italy; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA.
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15
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Bea-Mascato B, Neira-Goyanes E, Iglesias-Rodríguez A, Valverde D. Depletion of ALMS1 affects TGF-β signalling pathway and downstream processes such as cell migration and adhesion capacity. Front Mol Biosci 2022; 9:992313. [PMID: 36325276 PMCID: PMC9621122 DOI: 10.3389/fmolb.2022.992313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/13/2022] [Indexed: 12/23/2023] Open
Abstract
Background: ALMS1 is a ubiquitous gene associated with Alström syndrome (ALMS). The main symptoms of ALMS affect multiple organs and tissues, generating at last, multi-organic fibrosis in the lungs, kidneys and liver. TGF-β is one of the main pathways implicated in fibrosis, controlling the cell cycle, apoptosis, cell migration, cell adhesion and epithelial-mesenchymal transition (EMT). Nevertheless, the role of ALMS1 gene in fibrosis generation and other implicated processes such as cell migration or cell adhesion via the TGF- β pathway has not been elucidated yet. Methods: Initially, we evaluated how depletion of ALMS1 affects different processes like apoptosis, cell cycle and mitochondrial activity in HeLa cells. Then, we performed proteomic profiling with TGF-β stimuli in HeLa ALMS1 -/- cells and validated the results by examining different EMT biomarkers using qPCR. The expression of these EMT biomarkers were also studied in hTERT-BJ-5ta ALMS1 -/-. Finally, we evaluated the SMAD3 and SMAD2 phosphorylation and cell migration capacity in both models. Results: Depletion of ALMS1 generated apoptosis resistance to thapsigargin (THAP) and C2-Ceramide (C2-C), and G2/M cell cycle arrest in HeLa cells. For mitochondrial activity, results did not show significant differences between ALMS1 +/+ and ALMS1 -/-. Proteomic results showed inhibition of downstream pathways regulated by TGF-β. The protein-coding genes (PCG) were associated with processes like focal adhesion or cell-substrate adherens junction in HeLa. SNAI1 showed an opposite pattern to what would be expected when activating the EMT in HeLa and BJ-5ta. Finally, in BJ-5ta model a reduced activation of SMAD3 but not SMAD2 were also observed. In HeLa model no alterations in the canonical TGF-β pathway were observed but both cell lines showed a reduction in migration capacity. Conclusion: ALMS1 has a role in controlling the cell cycle and the apoptosis processes. Moreover, the depletion of ALMS1 affects the signal transduction through the TGF-β and other processes like the cell migration and adhesion capacity.
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Affiliation(s)
- Brais Bea-Mascato
- CINBIO, Universidad de Vigo, Vigo, Spain
- Grupo de Investigación en Enfermedades Raras y Medicina Pediátrica, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Elena Neira-Goyanes
- CINBIO, Universidad de Vigo, Vigo, Spain
- Grupo de Investigación en Enfermedades Raras y Medicina Pediátrica, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Antía Iglesias-Rodríguez
- CINBIO, Universidad de Vigo, Vigo, Spain
- Grupo de Investigación en Enfermedades Raras y Medicina Pediátrica, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Diana Valverde
- CINBIO, Universidad de Vigo, Vigo, Spain
- Grupo de Investigación en Enfermedades Raras y Medicina Pediátrica, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
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16
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Yue S, Li G, He S, Li T. The central role of mTORC1 in amino acid sensing. Cancer Res 2022; 82:2964-2974. [PMID: 35749594 DOI: 10.1158/0008-5472.can-21-4403] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/28/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022]
Abstract
The mechanistic target of rapamycin (mTOR) is a master regulator of cell growth that controls cell homeostasis in response to nutrients, growth factors, and other environmental cues. Recent studies have emphasized the importance of lysosomes as a hub for nutrient sensing, especially amino acid sensing by mTORC1. This review highlights recent advances in understanding the amino acid-mTORC1 signaling axis and the role of mTORC1 in cancer.
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17
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Liu JT, Yao QP, Chen Y, Lv F, Liu Z, Bao H, Han Y, Zhang ML, Jiang ZL, Qi YX. Arterial cyclic stretch regulates Lamtor1 and promotes neointimal hyperplasia via circSlc8a1/miR-20a-5p axis in vein grafts. Am J Cancer Res 2022; 12:4851-4865. [PMID: 35836818 PMCID: PMC9274756 DOI: 10.7150/thno.69551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/03/2022] [Indexed: 01/12/2023] Open
Abstract
Rationale: Neointimal hyperplasia caused by dedifferentiation and proliferation of venous smooth muscle cells (SMCs) is the major challenge for restenosis after coronary artery bypass graft. Herein, we investigated the role of Lamtor1 in neointimal formation and the regulatory mechanism of non-coding RNA underlying this process. Methods: Using a "cuff" model, veins were grafted into arterial system and Lamtor1 expression which was correlated with the activation of mTORC1 signaling and dedifferentiation of SMCs, were measured by Western blot. Whole transcriptome deep sequencing (RNA-seq) of the grafted veins combined with bioinformatic analysis identified highly conserved circSlc8a1 and its interaction with miR-20a-5p, which may target Lamtor1. CircSlc8a1 was biochemically characterized by Sanger sequencing and resistant to RNase R digestion. The cytoplasmic location of circSlc8a1 was shown by fluorescence in situ hybridization (FISH). RNA pull-down, luciferase assays and RNA immunoprecipitation (RIP) with Ago2 assays were used to identify the interaction circSlc8a1 with miR-20a-5p. Furthermore, arterial mechanical stretch (10% elongation) was applied in vitro. Results:In vivo, Lamtor1 was significantly enhanced in grafted vein and activated mTORC1 signaling to promote dedifferentiation of SMCs. Arterial mechanical stretch (10% elongation) induced circSlc8a1 expression and positively regulated Lamtor1, activated mTORC1 and promoted SMC dedifferentiation and proliferation. Local injection of circSlc8a1 siRNA or SMC-specific Lamtor1 knockout mice prevented neointimal hyperplasia in vein grafts in vivo. Conclusions: Our study reveals a novel mechanobiological mechanism underlying the dedifferentiation and proliferation of venous SMCs in neointimal hyperplasia. CircSlc81/miR-20a-5p/Lamtor1 axis induced by arterial cyclic stretch may be a potential clinical target that attenuates neointimal hyperplasia in grafted vessels.
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Affiliation(s)
- Ji-Ting Liu
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qing-Ping Yao
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Chen
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fan Lv
- Department of Pediatric Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Ze Liu
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Han Bao
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Han
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ming-Liang Zhang
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Key Clinical Center for Metabolic Disease, Shanghai, China.,✉ Corresponding authors: Dr. Ying-Xin Qi, Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang, Shanghai 200240, China. Tel.: +86-21-34204863, Fax: +86-21-34204118, E-mail: ; Dr. Zong-Lai Jiang, Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang, Shanghai 200240, China. Tel.: +86-21-34204863, Fax: +86-21-34204118, E-mail: ; Dr. Ming-Liang Zhang, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Key Clinical Center for Metabolic Disease, 600 Yishan Road, Xuhui, Shanghai 200233 China. Tel.: +86-21-24058337, Fax: +86-21-24058337, E-mail:
| | - Zong-Lai Jiang
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,✉ Corresponding authors: Dr. Ying-Xin Qi, Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang, Shanghai 200240, China. Tel.: +86-21-34204863, Fax: +86-21-34204118, E-mail: ; Dr. Zong-Lai Jiang, Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang, Shanghai 200240, China. Tel.: +86-21-34204863, Fax: +86-21-34204118, E-mail: ; Dr. Ming-Liang Zhang, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Key Clinical Center for Metabolic Disease, 600 Yishan Road, Xuhui, Shanghai 200233 China. Tel.: +86-21-24058337, Fax: +86-21-24058337, E-mail:
| | - Ying-Xin Qi
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,✉ Corresponding authors: Dr. Ying-Xin Qi, Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang, Shanghai 200240, China. Tel.: +86-21-34204863, Fax: +86-21-34204118, E-mail: ; Dr. Zong-Lai Jiang, Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang, Shanghai 200240, China. Tel.: +86-21-34204863, Fax: +86-21-34204118, E-mail: ; Dr. Ming-Liang Zhang, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Key Clinical Center for Metabolic Disease, 600 Yishan Road, Xuhui, Shanghai 200233 China. Tel.: +86-21-24058337, Fax: +86-21-24058337, E-mail:
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Annesley SJ, Allan CY, Sanislav O, Evans A, Fisher PR. Dysregulated Gene Expression in Lymphoblasts from Parkinson’s Disease. Proteomes 2022; 10:proteomes10020020. [PMID: 35736800 PMCID: PMC9230639 DOI: 10.3390/proteomes10020020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 02/01/2023] Open
Abstract
Parkinson’s disease is the second largest neurodegenerative disease worldwide and is caused by a combination of genetics and environment. It is characterized by the death of neurons in the substantia nigra of the brain but is not solely a disease of the brain, as it affects multiple tissues and organs. Studying Parkinson’s disease in accessible tissues such as skin and blood has increased our understanding of the disease’s pathogenesis. Here, we used lymphoblast cell lines generated from Parkinson’s disease patient and healthy age- and sex-matched control groups and obtained their whole-cell transcriptomes and proteomes. Our analysis revealed, in both the transcriptomes and the proteomes of PD cells, a global downregulation of genes involved in protein synthesis, as well as the upregulation of immune processes and sphingolipid metabolism. In contrast, we discovered an uncoupling of mRNA and protein expression in processes associated with mitochondrial respiration in the form of a general downregulation in associated transcripts and an upregulation in proteins. Complex V was different to the other oxidative phosphorylation complexes in that the levels of its associated transcripts were also lower, but the levels of their encoded polypeptides were not elevated. This may suggest that further layers of regulation specific to Complex V are in play.
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Affiliation(s)
- Sarah Jane Annesley
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Melbourne, VIC 3086, Australia; (C.Y.A.); (O.S.); (P.R.F.)
- Correspondence: ; Tel.: +61-394791412
| | - Claire Yvonne Allan
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Melbourne, VIC 3086, Australia; (C.Y.A.); (O.S.); (P.R.F.)
| | - Oana Sanislav
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Melbourne, VIC 3086, Australia; (C.Y.A.); (O.S.); (P.R.F.)
| | - Andrew Evans
- Department of Neurology, Royal Melbourne Hospital, Parkville, VIC 3052, Australia;
| | - Paul Robert Fisher
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Melbourne, VIC 3086, Australia; (C.Y.A.); (O.S.); (P.R.F.)
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19
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Egri SB, Ouch C, Chou HT, Yu Z, Song K, Xu C, Shen K. Cryo-EM structures of the human GATOR1-Rag-Ragulator complex reveal a spatial-constraint regulated GAP mechanism. Mol Cell 2022; 82:1836-1849.e5. [PMID: 35338845 PMCID: PMC9133170 DOI: 10.1016/j.molcel.2022.03.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/09/2021] [Accepted: 02/28/2022] [Indexed: 12/20/2022]
Abstract
mTORC1 controls cellular metabolic processes in response to nutrient availability. Amino acid signals are transmitted to mTORC1 through the Rag GTPases, which are localized on the lysosomal surface by the Ragulator complex. The Rag GTPases receive amino acid signals from multiple upstream regulators. One negative regulator, GATOR1, is a GTPase activating protein (GAP) for RagA. GATOR1 binds to the Rag GTPases via two modes: an inhibitory mode and a GAP mode. How these two binding interactions coordinate to process amino acid signals is unknown. Here, we resolved three cryo-EM structural models of the GATOR1-Rag-Ragulator complex, with the Rag-Ragulator subcomplex occupying the inhibitory site, the GAP site, and both binding sites simultaneously. When the Rag GTPases bind to GATOR1 at the GAP site, both Rag subunits contact GATOR1 to coordinate their nucleotide loading states. These results reveal a potential GAP mechanism of GATOR1 during the mTORC1 inactivation process.
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Affiliation(s)
- Shawn B Egri
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, 373 Plantation St, Worcester, MA 01605, USA
| | - Christna Ouch
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Chan Medical School, 364 Plantation St, Worcester, MA 01605, USA
| | - Hui-Ting Chou
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Zhiheng Yu
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Kangkang Song
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Chan Medical School, 364 Plantation St, Worcester, MA 01605, USA
| | - Chen Xu
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Chan Medical School, 364 Plantation St, Worcester, MA 01605, USA
| | - Kuang Shen
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, 373 Plantation St, Worcester, MA 01605, USA.
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20
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Deyssenroth MA, Peng S, Hao K, Marsit CJ, Chen J. Placental Gene Transcript Proportions are Altered in the Presence of In Utero Arsenic and Cadmium Exposures, Genetic Variants, and Birth Weight Differences. Front Genet 2022; 13:865449. [PMID: 35646058 PMCID: PMC9136297 DOI: 10.3389/fgene.2022.865449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/07/2022] [Indexed: 11/26/2022] Open
Abstract
Background: In utero arsenic and cadmium exposures are linked with reduced birth weight as well as alterations in placental molecular features. However, studies thus far have focused on summarizing transcriptional activity at the gene level and do not capture transcript specification, an important resource during fetal development to enable adaptive responses to the rapidly changing in utero physiological conditions. In this study, we conducted a genome-wide analysis of the placental transcriptome to evaluate the role of differential transcript usage (DTU) as a potential marker of in utero arsenic and cadmium exposure and fetal growth restriction. Methods: Transcriptome-wide RNA sequencing was performed in placenta samples from the Rhode Island Child Health Study (RICHS, n = 199). Arsenic and cadmium levels were measured in maternal toenails using ICP-MS. Differential transcript usage (DTU) contrasting small (SGA) and appropriate (AGA) for gestational age infants as well as above vs. below median exposure to arsenic and cadmium were assessed using the DRIMSeq R package. Genetic variants that influence transcript usage were determined using the sQTLseeker R package. Results: We identified 82 genes demonstrating DTU in association with SGA status at an FDR <0.05. Among these, one gene, ORMDL1, also demonstrated DTU in association with arsenic exposure, and fifteen genes (CSNK1E, GBA, LAMTOR4, MORF4L1, PIGO, PSG1, PSG3, PTMA, RBMS1, SLC38A2, SMAD4, SPCS2, TUBA1B, UBE2A, YIPF5) demonstrated DTU in association with cadmium exposure. In addition to cadmium exposure and SGA status, proportions of the LAMTOR4 transcript ENST00000474141.5 also differed by genetic variants (rs10231604, rs12878, and rs3736591), suggesting a pathway by which an in utero exposure and genetic variants converge to impact fetal growth through perturbations of placental processes. Discussion: We report the first genome-wide characterization of placental transcript usage and associations with intrauterine metal exposure and fetal growth restriction. These results highlight the utility of interrogating the transcriptome at finer-scale transcript-level resolution to identify novel placental biomarkers of exposure-induced outcomes.
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Affiliation(s)
- Maya A. Deyssenroth
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Shouneng Peng
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Carmen J. Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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21
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Nowosad A, Besson A. Lysosomes at the Crossroads of Cell Metabolism, Cell Cycle, and Stemness. Int J Mol Sci 2022; 23:ijms23042290. [PMID: 35216401 PMCID: PMC8879101 DOI: 10.3390/ijms23042290] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 02/07/2023] Open
Abstract
Initially described as lytic bodies due to their degradative and recycling functions, lysosomes play a critical role in metabolic adaptation to nutrient availability. More recently, the contribution of lysosomal proteins to cell signaling has been established, and lysosomes have emerged as signaling hubs that regulate diverse cellular processes, including cell proliferation and cell fate. Deciphering these signaling pathways has revealed an extensive crosstalk between the lysosomal and cell cycle machineries that is only beginning to be understood. Recent studies also indicate that a number of lysosomal proteins are involved in the regulation of embryonic and adult stem cell fate and identity. In this review, we will focus on the role of the lysosome as a signaling platform with an emphasis on its function in integrating nutrient sensing with proliferation and cell cycle progression, as well as in stemness-related features, such as self-renewal and quiescence.
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Affiliation(s)
- Ada Nowosad
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France;
- Department of Oncology, KULeuven, Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium
| | - Arnaud Besson
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France;
- Correspondence: ; Tel.: +33-561558486
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22
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Nuciferine protects against high-fat diet-induced hepatic steatosis and insulin resistance via activating TFEB-mediated autophagy–lysosomal pathway. Acta Pharm Sin B 2021; 12:2869-2886. [PMID: 35755273 PMCID: PMC9214335 DOI: 10.1016/j.apsb.2021.12.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/10/2021] [Accepted: 11/17/2021] [Indexed: 12/30/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is characterized by hepatic steatosis and insulin resistance and there are currently no approved drugs for its treatment. Hyperactivation of mTOR complex 1 (mTORC1) and subsequent impairment of the transcription factor EB (TFEB)-mediated autophagy–lysosomal pathway (ALP) are implicated in the development of NAFLD. Accordingly, agents that augment hepatic TFEB transcriptional activity may have therapeutic potential against NAFLD. The objective of this study was to investigate the effects of nuciferine, a major active component from lotus leaf, on NAFLD and its underlying mechanism of action. Here we show that nuciferine activated ALP and alleviated steatosis, insulin resistance in the livers of NAFLD mice and palmitic acid-challenged hepatocytes in a TFEB-dependent manner. Mechanistic investigation revealed that nuciferine interacts with the Ragulator subunit hepatitis B X-interacting protein and impairs the interaction of the Ragulator complex with Rag GTPases, thereby suppressing lysosomal localization and activity of mTORC1, which activates TFEB-mediated ALP and further ameliorates hepatic steatosis and insulin resistance. Our present results indicate that nuciferine may be a potential agent for treating NAFLD and that regulation of the mTORC1–TFEB–ALP axis could represent a novel pharmacological strategy to combat NAFLD.
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23
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Comparison of the transcriptome in circulating leukocytes in early lactation between primiparous and multiparous cows provides evidence for age-related changes. BMC Genomics 2021; 22:693. [PMID: 34563126 PMCID: PMC8466696 DOI: 10.1186/s12864-021-07977-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 09/06/2021] [Indexed: 12/18/2022] Open
Abstract
Background Previous studies have identified many immune pathways which are consistently altered in humans and model organisms as they age. Dairy cows are often culled at quite young ages due to an inability to cope adequately with metabolic and infectious diseases, resulting in reduced milk production and infertility. Improved longevity is therefore a desirable trait which would benefit both farmers and their cows. This study analysed the transcriptome derived from RNA-seq data of leukocytes obtained from Holstein cows in early lactation with respect to lactation number. Results Samples were divided into three lactation groups for analysis: i) primiparous (PP, n = 53), ii) multiparous in lactations 2–3 (MP 2–3, n = 121), and iii) MP in lactations 4–7 (MP > 3, n = 55). Leukocyte expression was compared between PP vs MP > 3 cows with MP 2–3 as background using DESeq2 followed by weighted gene co-expression network analysis (WGCNA). Seven modules were significantly correlated (r ≥ 0.25) to the trait lactation number. Genes from the modules which were more highly expressed in either the PP or MP > 3 cows were pooled, and the gene lists subjected to David functional annotation cluster analysis. The top three clusters from modules more highly expressed in the PP cows all involved regulation of gene transcription, particularly zinc fingers. Another cluster included genes encoding enzymes in the mitochondrial beta-oxidation pathway. Top clusters up-regulated in MP > 3 cows included the terms Glycolysis/Gluconeogenesis, C-type lectin, and Immunity. Differentially expressed candidate genes for ageing previously identified in the human blood transcriptome up-regulated in PP cows were mainly associated with T-cell function (CCR7, CD27, IL7R, CAMK4, CD28), mitochondrial ribosomal proteins (MRPS27, MRPS9, MRPS31), and DNA replication and repair (WRN). Those up-regulated in MP > 3 cows encoded immune defence proteins (LYZ, CTSZ, SREBF1, GRN, ANXA5, ADARB1). Conclusions Genes and pathways associated with lactation number in cows were identified for the first time to date, and we found that many were comparable to those known to be associated with ageing in humans and model organisms. We also detected changes in energy utilization and immune responses in leukocytes from older cows. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07977-5.
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24
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Cayo A, Segovia R, Venturini W, Moore-Carrasco R, Valenzuela C, Brown N. mTOR Activity and Autophagy in Senescent Cells, a Complex Partnership. Int J Mol Sci 2021; 22:ijms22158149. [PMID: 34360912 PMCID: PMC8347619 DOI: 10.3390/ijms22158149] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
Cellular senescence is a form of proliferative arrest triggered in response to a wide variety of stimuli and characterized by unique changes in cell morphology and function. Although unable to divide, senescent cells remain metabolically active and acquire the ability to produce and secrete bioactive molecules, some of which have recognized pro-inflammatory and/or pro-tumorigenic actions. As expected, this “senescence-associated secretory phenotype (SASP)” accounts for most of the non-cell-autonomous effects of senescent cells, which can be beneficial or detrimental for tissue homeostasis, depending on the context. It is now evident that many features linked to cellular senescence, including the SASP, reflect complex changes in the activities of mTOR and other metabolic pathways. Indeed, the available evidence indicates that mTOR-dependent signaling is required for the maintenance or implementation of different aspects of cellular senescence. Thus, depending on the cell type and biological context, inhibiting mTOR in cells undergoing senescence can reverse senescence, induce quiescence or cell death, or exacerbate some features of senescent cells while inhibiting others. Interestingly, autophagy—a highly regulated catabolic process—is also commonly upregulated in senescent cells. As mTOR activation leads to repression of autophagy in non-senescent cells (mTOR as an upstream regulator of autophagy), the upregulation of autophagy observed in senescent cells must take place in an mTOR-independent manner. Notably, there is evidence that autophagy provides free amino acids that feed the mTOR complex 1 (mTORC1), which in turn is required to initiate the synthesis of SASP components. Therefore, mTOR activation can follow the induction of autophagy in senescent cells (mTOR as a downstream effector of autophagy). These functional connections suggest the existence of autophagy regulatory pathways in senescent cells that differ from those activated in non-senescence contexts. We envision that untangling these functional connections will be key for the generation of combinatorial anti-cancer therapies involving pro-senescence drugs, mTOR inhibitors, and/or autophagy inhibitors.
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Affiliation(s)
- Angel Cayo
- Center for Medical Research, University of Talca School of Medicine, Talca 346000, Chile; (A.C.); (R.S.); (W.V.); (C.V.)
| | - Raúl Segovia
- Center for Medical Research, University of Talca School of Medicine, Talca 346000, Chile; (A.C.); (R.S.); (W.V.); (C.V.)
| | - Whitney Venturini
- Center for Medical Research, University of Talca School of Medicine, Talca 346000, Chile; (A.C.); (R.S.); (W.V.); (C.V.)
- Department of Clinical Biochemistry and Immunohematology, Faculty of Health Sciences, University of Talca, Talca 346000, Chile;
| | - Rodrigo Moore-Carrasco
- Department of Clinical Biochemistry and Immunohematology, Faculty of Health Sciences, University of Talca, Talca 346000, Chile;
| | - Claudio Valenzuela
- Center for Medical Research, University of Talca School of Medicine, Talca 346000, Chile; (A.C.); (R.S.); (W.V.); (C.V.)
| | - Nelson Brown
- Center for Medical Research, University of Talca School of Medicine, Talca 346000, Chile; (A.C.); (R.S.); (W.V.); (C.V.)
- Correspondence:
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Fernandez-Guerra P, Gonzalez-Ebsen AC, Boonen SE, Courraud J, Gregersen N, Mehlsen J, Palmfeldt J, Olsen RKJ, Brinth LS. Bioenergetic and Proteomic Profiling of Immune Cells in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Patients: An Exploratory Study. Biomolecules 2021; 11:961. [PMID: 34209852 PMCID: PMC8301912 DOI: 10.3390/biom11070961] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 01/22/2023] Open
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a heterogeneous, debilitating, and complex disease. Along with disabling fatigue, ME/CFS presents an array of other core symptoms, including autonomic nervous system (ANS) dysfunction, sustained inflammation, altered energy metabolism, and mitochondrial dysfunction. Here, we evaluated patients' symptomatology and the mitochondrial metabolic parameters in peripheral blood mononuclear cells (PBMCs) and plasma from a clinically well-characterised cohort of six ME/CFS patients compared to age- and gender-matched controls. We performed a comprehensive cellular assessment using bioenergetics (extracellular flux analysis) and protein profiles (quantitative mass spectrometry-based proteomics) together with self-reported symptom measures of fatigue, ANS dysfunction, and overall physical and mental well-being. This ME/CFS cohort presented with severe fatigue, which correlated with the severity of ANS dysfunction and overall physical well-being. PBMCs from ME/CFS patients showed significantly lower mitochondrial coupling efficiency. They exhibited proteome alterations, including altered mitochondrial metabolism, centred on pyruvate dehydrogenase and coenzyme A metabolism, leading to a decreased capacity to provide adequate intracellular ATP levels. Overall, these results indicate that PBMCs from ME/CFS patients have a decreased ability to fulfill their cellular energy demands.
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Affiliation(s)
- Paula Fernandez-Guerra
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, 8200 Aarhus, Denmark; (A.C.G.-E.); (N.G.); (J.P.)
- KMEB, Department of Endocrinology, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Ana C. Gonzalez-Ebsen
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, 8200 Aarhus, Denmark; (A.C.G.-E.); (N.G.); (J.P.)
| | - Susanne E. Boonen
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark;
| | - Julie Courraud
- Section for Clinical Mass Spectrometry, Danish Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institute, 2300 Copenhagen, Denmark;
| | - Niels Gregersen
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, 8200 Aarhus, Denmark; (A.C.G.-E.); (N.G.); (J.P.)
| | - Jesper Mehlsen
- Section for Surgical Pathophysiology, Juliane Marie Center, Rigshospitalet, 2100 Copenhagen, Denmark;
| | - Johan Palmfeldt
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, 8200 Aarhus, Denmark; (A.C.G.-E.); (N.G.); (J.P.)
| | - Rikke K. J. Olsen
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, 8200 Aarhus, Denmark; (A.C.G.-E.); (N.G.); (J.P.)
| | - Louise Schouborg Brinth
- Department of Clinical Physiology and Nuclear Medicine, Nordsjaellands Hospital, 2400 Hilleroed, Denmark;
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26
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Sciarretta S, Forte M, Frati G, Sadoshima J. The complex network of mTOR signaling in the heart. Cardiovasc Res 2021; 118:424-439. [PMID: 33512477 DOI: 10.1093/cvr/cvab033] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/13/2020] [Accepted: 01/26/2021] [Indexed: 12/13/2022] Open
Abstract
The mechanistic target of rapamycin (mTOR) integrates several intracellular and extracellular signals involved in the regulation of anabolic and catabolic processes. mTOR assembles into two macromolecular complexes, named mTORC1 and mTORC2, which have different regulators, substrates and functions. Studies of gain- and loss-of-function animal models of mTOR signaling revealed that mTORC1/2 elicit both adaptive and maladaptive functions in the cardiovascular system. Both mTORC1 and mTORC2 are indispensable for driving cardiac development and cardiac adaption to stress, such as pressure overload. However, persistent and deregulated mTORC1 activation in the heart is detrimental during stress and contributes to the development and progression of cardiac remodeling and genetic and metabolic cardiomyopathies. In this review, we discuss the latest findings regarding the role of mTOR in the cardiovascular system, both under basal conditions and during stress, such as pressure overload, ischemia and metabolic stress. Current data suggest that mTOR modulation may represent a potential therapeutic strategy for the treatment of cardiac diseases.
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Affiliation(s)
- Sebastiano Sciarretta
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy.,IRCCS Neuromed, Pozzilli (IS), Italy
| | | | - Giacomo Frati
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy.,IRCCS Neuromed, Pozzilli (IS), Italy
| | - Junichi Sadoshima
- Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers New Jersey Medical School, Newark, NJ, USA
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27
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Nesterov SV, Yaguzhinsky LS, Podoprigora GI, Nartsissov YR. Amino Acids as Regulators of Cell Metabolism. BIOCHEMISTRY (MOSCOW) 2021; 85:393-408. [PMID: 32569548 DOI: 10.1134/s000629792004001x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In this review, we discuss the principles of regulation and synchronization of metabolic processes in mammalian cells using a two-component model of cell metabolism consisting of a controlling signaling system that regulates major enzymatic cascades and executive metabolic system that directly performs biosynthetic reactions. This approach has allowed us to distinguish two transitional metabolic states (from catabolism to anabolism and vice versa) accompanied by major rearrangements in the signaling system. The signaling system of natural amino acids was selected, because amino acids are involved in both signaling and executive metabolic subsystems of general cell metabolism. We have developed a graphical representation of metabolic events that allowed us to demonstrate the succession of processes occurring in both metabolic subsystems during complete metabolic cycle in a non-dividing cell. An important revealed feature of the amino acid signaling system is that the signaling properties of amino acid are determined not only by their molecular structure, but also by the location within the cell. Four major signaling groups of amino acids have been identified that localize to lysosomes, mitochondria, cytosol, and extracellular space adjacent to the plasma membrane. Although these amino acids groups are similar in the composition, they have different receptors. We also proposed a scheme for the metabolism regulation by amino acids signaling that can serve as a basis for developing more complete spatio-temporal picture of metabolic regulation involving a wide variety of intracellular signaling cascades.
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Affiliation(s)
- S V Nesterov
- Institute of Cytochemistry and Molecular Pharmacology, Moscow, 115404, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - L S Yaguzhinsky
- Institute of Cytochemistry and Molecular Pharmacology, Moscow, 115404, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - G I Podoprigora
- Institute of Cytochemistry and Molecular Pharmacology, Moscow, 115404, Russia
| | - Ya R Nartsissov
- Institute of Cytochemistry and Molecular Pharmacology, Moscow, 115404, Russia
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Takahara T, Amemiya Y, Sugiyama R, Maki M, Shibata H. Amino acid-dependent control of mTORC1 signaling: a variety of regulatory modes. J Biomed Sci 2020; 27:87. [PMID: 32799865 PMCID: PMC7429791 DOI: 10.1186/s12929-020-00679-2] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/30/2020] [Indexed: 01/10/2023] Open
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) is an essential regulator of cell growth and metabolism through the modulation of protein and lipid synthesis, lysosome biogenesis, and autophagy. The activity of mTORC1 is dynamically regulated by several environmental cues, including amino acid availability, growth factors, energy levels, and stresses, to coordinate cellular status with environmental conditions. Dysregulation of mTORC1 activity is closely associated with various diseases, including diabetes, cancer, and neurodegenerative disorders. The discovery of Rag GTPases has greatly expanded our understanding of the regulation of mTORC1 activity by amino acids, especially leucine and arginine. In addition to Rag GTPases, other factors that also contribute to the modulation of mTORC1 activity have been identified. In this review, we discuss the mechanisms of regulation of mTORC1 activity by particular amino acids.
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Affiliation(s)
- Terunao Takahara
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan.
| | - Yuna Amemiya
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Risa Sugiyama
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Masatoshi Maki
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Hideki Shibata
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
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Costales-Carrera A, Fernández-Barral A, Bustamante-Madrid P, Domínguez O, Guerra-Pastrián L, Cantero R, del Peso L, Burgos A, Barbáchano A, Muñoz A. Comparative Study of Organoids from Patient-Derived Normal and Tumor Colon and Rectal Tissue. Cancers (Basel) 2020; 12:2302. [PMID: 32824266 PMCID: PMC7465167 DOI: 10.3390/cancers12082302] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
Colon and rectal tumors, often referred to as colorectal cancer, show different gene expression patterns in studies that analyze whole tissue biopsies containing a mix of tumor and non-tumor cells. To better characterize colon and rectal tumors, we investigated the gene expression profile of organoids generated from endoscopic biopsies of rectal tumors and adjacent normal colon and rectum mucosa from therapy-naive rectal cancer patients. We also studied the effect of vitamin D on these organoid types. Gene profiling was performed by RNA-sequencing. Organoids from a normal colon and rectum had a shared gene expression profile that profoundly differed from that of rectal tumor organoids. We identified a group of genes of the biosynthetic machinery as rectal tumor organoid-specific, including those encoding the RNA polymerase II subunits POLR2H and POLR2J. The active vitamin D metabolite 1α,25-dihydroxyvitamin D3/calcitriol upregulated stemness-related genes (LGR5, LRIG1, SMOC2, and MSI1) in normal rectum organoids, while it downregulated differentiation marker genes (TFF2 and MUC2). Normal colon and rectum organoids share similar gene expression patterns and respond similarly to calcitriol. Rectal tumor organoids display distinct and heterogeneous gene expression profiles, with differences with respect to those of colon tumor organoids, and respond differently to calcitriol than normal rectum organoids.
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Affiliation(s)
- Alba Costales-Carrera
- Departamento de Biología del Cáncer, Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (A.C.-C.); (A.F.-B.); (P.B.-M.); (L.d.P.); (A.B.)
- Instituto de Investigación del Hospital Universitario La Paz (IdiPAZ), 28029 Madrid, Spain; (L.G.-P.); (R.C.)
- Centro de Investigaciones Biomédicas en Red-Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Asunción Fernández-Barral
- Departamento de Biología del Cáncer, Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (A.C.-C.); (A.F.-B.); (P.B.-M.); (L.d.P.); (A.B.)
- Instituto de Investigación del Hospital Universitario La Paz (IdiPAZ), 28029 Madrid, Spain; (L.G.-P.); (R.C.)
- Centro de Investigaciones Biomédicas en Red-Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Pilar Bustamante-Madrid
- Departamento de Biología del Cáncer, Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (A.C.-C.); (A.F.-B.); (P.B.-M.); (L.d.P.); (A.B.)
- Instituto de Investigación del Hospital Universitario La Paz (IdiPAZ), 28029 Madrid, Spain; (L.G.-P.); (R.C.)
- Centro de Investigaciones Biomédicas en Red-Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Orlando Domínguez
- Unidad de Genómica, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029 Madrid, Spain;
| | - Laura Guerra-Pastrián
- Instituto de Investigación del Hospital Universitario La Paz (IdiPAZ), 28029 Madrid, Spain; (L.G.-P.); (R.C.)
- Departamento de Patología, Hospital Universitario La Paz, 28029 Madrid, Spain
| | - Ramón Cantero
- Instituto de Investigación del Hospital Universitario La Paz (IdiPAZ), 28029 Madrid, Spain; (L.G.-P.); (R.C.)
- Unidad Colorrectal, Departamento de Cirugía, Hospital Universitario La Paz, 28029 Madrid, Spain
| | - Luis del Peso
- Departamento de Biología del Cáncer, Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (A.C.-C.); (A.F.-B.); (P.B.-M.); (L.d.P.); (A.B.)
- Centro de Investigaciones Biomédicas en Red-Enfermedades Respiratorias (CIBERES), 28029 Madrid, Spain
| | - Aurora Burgos
- Unidad de Endoscopia, Departamento de Digestivo, Hospital Universitario La Paz, 28029 Madrid, Spain;
| | - Antonio Barbáchano
- Departamento de Biología del Cáncer, Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (A.C.-C.); (A.F.-B.); (P.B.-M.); (L.d.P.); (A.B.)
- Instituto de Investigación del Hospital Universitario La Paz (IdiPAZ), 28029 Madrid, Spain; (L.G.-P.); (R.C.)
- Centro de Investigaciones Biomédicas en Red-Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Alberto Muñoz
- Departamento de Biología del Cáncer, Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (A.C.-C.); (A.F.-B.); (P.B.-M.); (L.d.P.); (A.B.)
- Instituto de Investigación del Hospital Universitario La Paz (IdiPAZ), 28029 Madrid, Spain; (L.G.-P.); (R.C.)
- Centro de Investigaciones Biomédicas en Red-Cáncer (CIBERONC), 28029 Madrid, Spain
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Garcia de la Serrana D, Pérez M, Nande M, Hernández-Urcera J, Pérez E, Coll-Lladó C, Hollenbeck C. Regulation of growth-related genes by nutrition in paralarvae of the common octopus (Octopus vulgaris). Gene 2020; 747:144670. [PMID: 32298760 DOI: 10.1016/j.gene.2020.144670] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 03/26/2020] [Accepted: 04/12/2020] [Indexed: 02/07/2023]
Abstract
The common octopus (Octopus vulgaris) is a species of great interest to the aquaculture industry. However, the high mortalities registered during different phases of the octopus lifecycle, particularly the paralarvae stage, present a challenge for commercial aquaculture. Improvement of diet formulation is seen as one way to reduce mortality and improve growth. Molecular growth-markers could help to improve rearing protocols and increase survival and growth performance; therefore, over a hundred orthologous genes related to protein balance and muscle growth in vertebrates were identified for the common octopus and their suitability as molecular markers for growth in octopus paralarvae explored. We successfully amplified 14 of those genes and studied their transcription in paralarvae either fed with artemia, artemia + zoea diets or submitted to a short fasting-refeeding procedure. Paralarvae fed with artemia + zoea had higher growth rates compared to those fed only with artemia, as well as a significant increase in octopus mtor (mtor-L) and hsp90 (hsp90-L) transcription, with both genes also up-regulated during refeeding. Our results suggest that at least mtor-L and hsp90-L are likely linked to somatic growth in octopus paralarvae. Conversely, ckip1-L, crk-L, src-L and srf-L had expression patterns that did not match to periods of growth as would be expected based on similar studies in vertebrates, indicating that further research is needed to understand their function during growth and in a muscle specific context.
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Affiliation(s)
- D Garcia de la Serrana
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain; Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, UK.
| | - M Pérez
- AQUACOV. Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, Vigo, Spain
| | - M Nande
- AQUACOV. Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, Vigo, Spain; CIMAR/CIIMAR - Interdisciplinary Centre for Marine and Environmental Research, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - J Hernández-Urcera
- AQUACOV. Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, Vigo, Spain; Department of Ecology and Marine Resources, Instituto de Investigaciones Marinas (CSIC), Vigo, Spain
| | - E Pérez
- AQUACOV. Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, Vigo, Spain
| | - C Coll-Lladó
- Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, UK
| | - C Hollenbeck
- Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, UK
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Palušová V, Renzová T, Verlande A, Vaclová T, Medková M, Cetlová L, Sedláčková M, Hříbková H, Slaninová I, Krutá M, Rotrekl V, Uhlířová H, Křížová A, Chmelík R, Veselý P, Krafčíková M, Trantírek L, Schink KO, Uldrijan S. Dual Targeting of BRAF and mTOR Signaling in Melanoma Cells with Pyridinyl Imidazole Compounds. Cancers (Basel) 2020; 12:cancers12061516. [PMID: 32531927 PMCID: PMC7352453 DOI: 10.3390/cancers12061516] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 12/19/2022] Open
Abstract
BRAF inhibitors can delay the progression of metastatic melanoma, but resistance usually emerges, leading to relapse. Drugs simultaneously targeting two or more pathways essential for cancer growth could slow or prevent the development of resistant clones. Here, we identified pyridinyl imidazole compounds SB202190, SB203580, and SB590885 as dual inhibitors of critical proliferative pathways in human melanoma cells bearing the V600E activating mutation of BRAF kinase. We found that the drugs simultaneously disrupt the BRAF V600E-driven extracellular signal-regulated kinase (ERK) mitogen-activated protein kinase (MAPK) activity and the mechanistic target of rapamycin complex 1 (mTORC1) signaling in melanoma cells. Pyridinyl imidazole compounds directly inhibit BRAF V600E kinase. Moreover, they interfere with the endolysosomal compartment, promoting the accumulation of large acidic vacuole-like vesicles and dynamic changes in mTOR signaling. A transient increase in mTORC1 activity is followed by the enrichment of the Ragulator complex protein p18/LAMTOR1 at contact sites of large vesicles and delocalization of mTOR from the lysosomes. The induced disruption of the endolysosomal pathway not only disrupts mTORC1 signaling, but also renders melanoma cells sensitive to endoplasmic reticulum (ER) stress. Our findings identify new activities of pharmacologically relevant small molecule compounds and provide a biological rationale for the development of anti-melanoma therapeutics based on the pyridinyl imidazole core.
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Affiliation(s)
- Veronika Palušová
- Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (V.P.); (T.R.); (A.V.); (T.V.); (M.M.); (L.C.); (M.S.); (H.H.); (I.S.); (M.K.); (V.R.)
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekařská 664/53, 656 91 Brno, Czech Republic
| | - Tereza Renzová
- Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (V.P.); (T.R.); (A.V.); (T.V.); (M.M.); (L.C.); (M.S.); (H.H.); (I.S.); (M.K.); (V.R.)
| | - Amandine Verlande
- Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (V.P.); (T.R.); (A.V.); (T.V.); (M.M.); (L.C.); (M.S.); (H.H.); (I.S.); (M.K.); (V.R.)
| | - Tereza Vaclová
- Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (V.P.); (T.R.); (A.V.); (T.V.); (M.M.); (L.C.); (M.S.); (H.H.); (I.S.); (M.K.); (V.R.)
| | - Michaela Medková
- Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (V.P.); (T.R.); (A.V.); (T.V.); (M.M.); (L.C.); (M.S.); (H.H.); (I.S.); (M.K.); (V.R.)
| | - Linda Cetlová
- Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (V.P.); (T.R.); (A.V.); (T.V.); (M.M.); (L.C.); (M.S.); (H.H.); (I.S.); (M.K.); (V.R.)
| | - Miroslava Sedláčková
- Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (V.P.); (T.R.); (A.V.); (T.V.); (M.M.); (L.C.); (M.S.); (H.H.); (I.S.); (M.K.); (V.R.)
| | - Hana Hříbková
- Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (V.P.); (T.R.); (A.V.); (T.V.); (M.M.); (L.C.); (M.S.); (H.H.); (I.S.); (M.K.); (V.R.)
| | - Iva Slaninová
- Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (V.P.); (T.R.); (A.V.); (T.V.); (M.M.); (L.C.); (M.S.); (H.H.); (I.S.); (M.K.); (V.R.)
| | - Miriama Krutá
- Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (V.P.); (T.R.); (A.V.); (T.V.); (M.M.); (L.C.); (M.S.); (H.H.); (I.S.); (M.K.); (V.R.)
| | - Vladimír Rotrekl
- Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (V.P.); (T.R.); (A.V.); (T.V.); (M.M.); (L.C.); (M.S.); (H.H.); (I.S.); (M.K.); (V.R.)
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekařská 664/53, 656 91 Brno, Czech Republic
| | - Hana Uhlířová
- Institute of Physical Engineering, Faculty of Mechanical Engineering, Brno University of Technology, Technická 2896/2, 616 69 Brno, Czech Republic; (H.U.); (R.C.)
- CEITEC—Central European Institute of Technology, Brno University of Technology, Purkyňova 656/123, 612 00 Brno, Czech Republic; (A.K.); (P.V.)
| | - Aneta Křížová
- CEITEC—Central European Institute of Technology, Brno University of Technology, Purkyňova 656/123, 612 00 Brno, Czech Republic; (A.K.); (P.V.)
| | - Radim Chmelík
- Institute of Physical Engineering, Faculty of Mechanical Engineering, Brno University of Technology, Technická 2896/2, 616 69 Brno, Czech Republic; (H.U.); (R.C.)
- CEITEC—Central European Institute of Technology, Brno University of Technology, Purkyňova 656/123, 612 00 Brno, Czech Republic; (A.K.); (P.V.)
| | - Pavel Veselý
- CEITEC—Central European Institute of Technology, Brno University of Technology, Purkyňova 656/123, 612 00 Brno, Czech Republic; (A.K.); (P.V.)
| | - Michaela Krafčíková
- National Centre for Biomolecular Research, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic;
| | - Lukáš Trantírek
- CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic;
| | - Kay Oliver Schink
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Montebello, N-0379 Oslo, Norway;
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, N-0379 Oslo, Norway
| | - Stjepan Uldrijan
- Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (V.P.); (T.R.); (A.V.); (T.V.); (M.M.); (L.C.); (M.S.); (H.H.); (I.S.); (M.K.); (V.R.)
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekařská 664/53, 656 91 Brno, Czech Republic
- Correspondence:
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de Martín Garrido N, Aylett CHS. Nutrient Signaling and Lysosome Positioning Crosstalk Through a Multifunctional Protein, Folliculin. Front Cell Dev Biol 2020; 8:108. [PMID: 32195250 PMCID: PMC7063858 DOI: 10.3389/fcell.2020.00108] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 02/10/2020] [Indexed: 12/16/2022] Open
Abstract
FLCN was identified as the gene responsible for Birt-Hogg-Dubé (BHD) syndrome, a hereditary syndrome associated with the appearance of familiar renal oncocytomas. Most mutations affecting FLCN result in the truncation of the protein, and therefore loss of its associated functions, as typical for a tumor suppressor. FLCN encodes the protein folliculin (FLCN), which is involved in numerous biological processes; mutations affecting this protein thus lead to different phenotypes depending on the cellular context. FLCN forms complexes with two large interacting proteins, FNIP1 and FNIP2. Structural studies have shown that both FLCN and FNIPs contain longin and differentially expressed in normal versus neoplastic cells (DENN) domains, typically involved in the regulation of small GTPases. Accordingly, functional studies show that FLCN regulates both the Rag and the Rab GTPases depending on nutrient availability, which are respectively involved in the mTORC1 pathway and lysosomal positioning. Although recent structural studies shed light on the precise mechanism by which FLCN regulates the Rag GTPases, which in turn regulate mTORC1, how FLCN regulates membrane trafficking through the Rab GTPases or the significance of the intriguing FLCN-FNIP-AMPK complex formation are questions that still remain unanswered. We discuss the recent progress in our understanding of FLCN regulation of both growth signaling and lysosomal positioning, as well as future approaches to establish detailed mechanisms to explain the disparate phenotypes caused by the loss of FLCN function and the development of BHD-associated and other tumors.
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Affiliation(s)
| | - Christopher H. S. Aylett
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
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Verghese S, Moberg K. Roles of Membrane and Vesicular Traffic in Regulation of the Hippo Pathway. Front Cell Dev Biol 2020; 7:384. [PMID: 32010696 PMCID: PMC6971369 DOI: 10.3389/fcell.2019.00384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/19/2019] [Indexed: 12/12/2022] Open
Abstract
The Hippo pathway is a well conserved signaling cascade that modulates cell proliferation and survival in response to external cues such as cell:cell contact, injury, and nutritional status. Models of the Hippo pathway have evolved from a series of genetic interactions defined in the fruit fly Drosophila melanogaster into a complex series of biochemical mechanisms in which transmembrane and cytoskeletal proteins modulate cytoplasmic phosphatase and kinase activities that converge on the serine/threonine kinase Warts (Wts) to regulate nuclear entry of the co-activator protein Yorkie (Yki; vertebrate Yap1). This pathway is well conserved in human cells and broadly implicated in cancer. Progress in understanding biochemical events within the Hippo pathway highlights a need for improved understanding of the cell biological contexts in which these molecular interactions occur. A significant body of data linking Hippo signaling to membranes and proteins involved in intracellular membrane trafficking raise the possibility that some molecular regulatory events occur on the cytoplasmic face of vesicles. In Drosophila, a Yki-vesicle link was solidified by discoveries that cytoplasmic Yki concentrates at late-endosomes and physically interacts with two endosomal adaptor proteins, Myopic (Mop) and Leash. These two proteins are required for Yki to transit the endolysosomal pathway and be turned over in lysosomes. Molecules involved in recruiting and tethering Yki along this endosomal route are not defined but are predicted to play key roles in regulating Yki levels and thus Hippo-responsiveness of cells. As Wts is recruited to the apical membrane by upstream Hippo components, endosomal internalization could also affect complexes involved in Yki phosphorylation events that alter nucleocytoplasmic shuttling. Recent work has revealed an unexpected, non-transcriptional role of membrane-associated Yki in triggering actinomyosin contractility via the myosin-regulatory light chain Spaghetti squash (Sqh). How Yki interacts with the membrane and controls Sqh is unclear, but this mechanism represents a novel regulatory mechanism based on induced localization of Yki to a specific membrane compartment. These and other data will be discussed as we review data linking Yki to membrane and vesicular traffic in development and homeostasis and speculate on missing elements of these membrane-linked Yki regulatory mechanisms.
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Affiliation(s)
- Shilpi Verghese
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, United States
| | - Ken Moberg
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, United States
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Shen K, Rogala KB, Chou HT, Huang RK, Yu Z, Sabatini DM. Cryo-EM Structure of the Human FLCN-FNIP2-Rag-Ragulator Complex. Cell 2019; 179:1319-1329.e8. [PMID: 31704029 PMCID: PMC7008705 DOI: 10.1016/j.cell.2019.10.036] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/08/2019] [Accepted: 10/28/2019] [Indexed: 12/22/2022]
Abstract
mTORC1 controls anabolic and catabolic processes in response to nutrients through the Rag GTPase heterodimer, which is regulated by multiple upstream protein complexes. One such regulator, FLCN-FNIP2, is a GTPase activating protein (GAP) for RagC/D, but despite its important role, how it activates the Rag GTPase heterodimer remains unknown. We used cryo-EM to determine the structure of FLCN-FNIP2 in a complex with the Rag GTPases and Ragulator. FLCN-FNIP2 adopts an extended conformation with two pairs of heterodimerized domains. The Longin domains heterodimerize and contact both nucleotide binding domains of the Rag heterodimer, while the DENN domains interact at the distal end of the structure. Biochemical analyses reveal a conserved arginine on FLCN as the catalytic arginine finger and lead us to interpret our structure as an on-pathway intermediate. These data reveal features of a GAP-GTPase interaction and the structure of a critical component of the nutrient-sensing mTORC1 pathway.
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Affiliation(s)
- Kuang Shen
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA; Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, 01605, USA
| | - Kacper B Rogala
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Hui-Ting Chou
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Rick K Huang
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Zhiheng Yu
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA.
| | - David M Sabatini
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA.
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Abstract
The mechanistic target of rapamycin (mTOR) signaling pathway coordinates environmental and intracellular cues to control eukaryotic cell growth. As a pivot point between anabolic and catabolic processes, mTOR complex 1 (mTORC1) signaling has established roles in regulating metabolism, translation and autophagy. Hyperactivity of the mTOR pathway is associated with numerous human diseases, including diabetes, cancer and epilepsy. Pharmacological inhibition of the mTOR pathway can extend lifespan in a variety of model organisms. Given its broad control of essential cellular processes and clear relevance to human health, there is extensive interest in elucidating how upstream inputs regulate mTORC1 activation. In this Cell Science at a Glance article and accompanying poster, we summarize our understanding of how extracellular and intracellular signals feed into the mTOR pathway, how the lysosome acts as an mTOR signaling hub, and how downstream signaling controls autophagy and lysosome biogenesis.
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Affiliation(s)
- Kendall J Condon
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute, Cambridge, MA 02142, USA.,The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA .,Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute, Cambridge, MA 02142, USA.,The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
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36
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Chichger H, Rounds S, Harrington EO. Endosomes and Autophagy: Regulators of Pulmonary Endothelial Cell Homeostasis in Health and Disease. Antioxid Redox Signal 2019; 31:994-1008. [PMID: 31190562 PMCID: PMC6765061 DOI: 10.1089/ars.2019.7817] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 06/07/2019] [Indexed: 12/12/2022]
Abstract
Significance: Alterations in oxidant/antioxidant balance injure pulmonary endothelial cells and are important in the pathogenesis of lung diseases, such as Acute Respiratory Distress Syndrome (ARDS), ischemia/reperfusion injury, pulmonary arterial hypertension (PAH), and emphysema. Recent Advances: The endosomal and autophagic pathways regulate cell homeostasis. Both pathways support recycling or degradation of macromolecules or organelles, targeted to endosomes or lysosomes, respectively. Thus, both processes promote cell survival. However, with environmental stress or injury, imbalance in endosomal and autophagic pathways may enhance macromolecular or organelle degradation, diminish biosynthetic processes, and cause cell death. Critical Issues: While the role of autophagy in cellular homeostasis in pulmonary disease has been investigated, the role of the endosome in the lung vasculature is less known. Furthermore, autophagy can either decrease or exacerbate endothelial injury, depending upon inciting insult and disease process. Future Directions: Diseases affecting the pulmonary endothelium, such as emphysema, ARDS, and PAH, are linked to altered endosomal or autophagic processing, leading to enhanced degradation of macromolecules and potential cell death. Efforts to target this imbalance have yielded limited success as treatments for lung injuries, which may be due to the complexity of both processes. It is possible that endosomal trafficking proteins, such as Rab GTPases and late endosomal/lysosomal adaptor, MAPK and MTOR activator 1, may be novel therapeutic targets. While endocytosis or autophagy have been linked to improved function of the pulmonary endothelium in vitro and in vivo, further studies are needed to identify targets for modulating cellular homeostasis in the lung.
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Affiliation(s)
- Havovi Chichger
- Biomedical Research Group, Department of Biomedical and Forensic Sciences, Anglia Ruskin University, Cambridge, United Kingdom
| | - Sharon Rounds
- Vascular Research Laboratory, Providence Veterans Affairs Medical Center, Providence, Rhode Island
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Alpert Medical School of Brown University, Providence, Rhode Island
| | - Elizabeth O. Harrington
- Vascular Research Laboratory, Providence Veterans Affairs Medical Center, Providence, Rhode Island
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Alpert Medical School of Brown University, Providence, Rhode Island
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37
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Rogala KB, Gu X, Kedir JF, Abu-Remaileh M, Bianchi LF, Bottino AMS, Dueholm R, Niehaus A, Overwijn D, Fils ACP, Zhou SX, Leary D, Laqtom NN, Brignole EJ, Sabatini DM. Structural basis for the docking of mTORC1 on the lysosomal surface. Science 2019; 366:468-475. [PMID: 31601708 PMCID: PMC7176403 DOI: 10.1126/science.aay0166] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022]
Abstract
The mTORC1 (mechanistic target of rapamycin complex 1) protein kinase regulates growth in response to nutrients and growth factors. Nutrients promote its translocation to the lysosomal surface, where its Raptor subunit interacts with the Rag guanosine triphosphatase (GTPase)-Ragulator complex. Nutrients switch the heterodimeric Rag GTPases among four different nucleotide-binding states, only one of which (RagA/B•GTP-RagC/D•GDP) permits mTORC1 association. We used cryo-electron microscopy to determine the structure of the supercomplex of Raptor with Rag-Ragulator at a resolution of 3.2 angstroms. Our findings indicate that the Raptor α-solenoid directly detects the nucleotide state of RagA while the Raptor "claw" threads between the GTPase domains to detect that of RagC. Mutations that disrupted Rag-Raptor binding inhibited mTORC1 lysosomal localization and signaling. By comparison with a structure of mTORC1 bound to its activator Rheb, we developed a model of active mTORC1 docked on the lysosome.
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Affiliation(s)
- Kacper B Rogala
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xin Gu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jibril F Kedir
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Monther Abu-Remaileh
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Laura F Bianchi
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Rikke Dueholm
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Anna Niehaus
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Daan Overwijn
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Sherry X Zhou
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Daniel Leary
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Nouf N Laqtom
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Edward J Brignole
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- MIT.nano, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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38
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Zhang T, Péli-Gulli MP, Zhang Z, Tang X, Ye J, De Virgilio C, Ding J. Structural insights into the EGO-TC-mediated membrane tethering of the TORC1-regulatory Rag GTPases. SCIENCE ADVANCES 2019; 5:eaax8164. [PMID: 31579828 PMCID: PMC6760929 DOI: 10.1126/sciadv.aax8164] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
The Rag/Gtr GTPases serve as a central module in the nutrient-sensing signaling network upstream of TORC1. In yeast, the anchoring of Gtr1-Gtr2 to membranes depends on the Ego1-Ego2-Ego3 ternary complex (EGO-TC), resulting in an EGO-TC-Gtr1-Gtr2 complex (EGOC). EGO-TC and human Ragulator share no obvious sequence similarities and also differ in their composition with respect to the number of known subunits, which raises the question of how the EGO-TC fulfills its function in recruiting Gtr1-Gtr2. Here, we report the structure of EGOC, in which Ego1 wraps around Ego2, Ego3, and Gtr1-Gtr2. In addition, Ego3 interacts with Gtr1-Gtr2 to stabilize the complex. The functional roles of key residues involved in the assembly are validated by in vivo assays. Our structural and functional data combined demonstrate that EGOC and Ragulator-Rag complex are structurally conserved and that EGO-TC is essential and sufficient to recruit Gtr1-Gtr2 to membranes to ensure appropriate TORC1 signaling.
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Affiliation(s)
- Tianlong Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | | | - Zhen Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, 393 Hua-Xia Zhong Road, Shanghai 201210, China
| | - Xin Tang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, 393 Hua-Xia Zhong Road, Shanghai 201210, China
| | - Jie Ye
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Claudio De Virgilio
- Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, 393 Hua-Xia Zhong Road, Shanghai 201210, China
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39
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Rasheed N, Lima TB, Mercaldi GF, Nascimento AF, Silva AL, Righetto GL, Bar‐Peled L, Shen K, Sabatini DM, Gozzo FC, Aparicio R, Smetana JH. C7orf59/LAMTOR4 phosphorylation and structural flexibility modulate Ragulator assembly. FEBS Open Bio 2019; 9:1589-1602. [PMID: 31314152 PMCID: PMC6722880 DOI: 10.1002/2211-5463.12700] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/28/2019] [Accepted: 07/15/2019] [Indexed: 01/09/2023] Open
Abstract
Ragulator is a pentamer composed of p18, MP1, p14, C7orf59, and hepatitis B virus X-interacting protein (HBXIP; LAMTOR 1-5) which acts as a lysosomal scaffold of the Rag GTPases in the amino acid sensitive branch of TORC1 signaling. Here, we present the crystal structure of human HBXIP-C7orf59 dimer (LAMTOR 4/5) at 2.9 Å and identify a phosphorylation site on C7orf59 which modulates its interaction with p18. Additionally, we demonstrate the requirement of HBXIP-C7orf59 to stabilize p18 and allow further binding of MP1-p14. The structure of the dimer revealed an unfolded N terminus in C7orf59 (residues 1-15) which was shown to be essential for p18 binding. Full-length p18 does not interact stably with MP1-p14 in the absence of HBXIP-C7orf59, but deletion of p18 residues 108-161 rescues MP1-p14 binding. C7orf59 was phosphorylated by protein kinase A (PKA) in vitro and mutation of the conserved Ser67 residue to aspartate prevented phosphorylation and negatively affected the C7orf59 interaction with p18 both in cell culture and in vitro. C7orf59 Ser67 was phosphorylated in human embryonic kidney 293T cells. PKA activation with forskolin induced dissociation of p18 from C7orf59, which was prevented by the PKA inhibitor H-89. Our results highlight the essential role of HBXIP-C7orf59 dimer as a nucleator of pentameric Ragulator and support a sequential model of Ragulator assembly in which HBXIP-C7orf59 binds and stabilizes p18 which allows subsequent binding of MP1-p14.
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Affiliation(s)
- Nadia Rasheed
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasBrazil
- Institute of BiologyUniversity of CampinasBrazil
| | - Tatiani B. Lima
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasBrazil
- Institute of ChemistryUniversity of CampinasBrazil
| | - Gustavo F. Mercaldi
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasBrazil
| | - Andrey F.Z. Nascimento
- Brazilian Synchrotron Light Laboratory (LNLS)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasBrazil
| | - Ana L.S. Silva
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasBrazil
| | - Germanna L. Righetto
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasBrazil
| | | | - Kuang Shen
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Whitehead Institute for Biomedical ResearchCambridgeMAUSA
- Howard Hughes Medical InstituteCambridgeMAUSA
- Koch Institute for Integrative Cancer ResearchCambridgeMAUSA
- Broad Institute of Harvard and Massachusetts Institute of TechnologyCambridgeMAUSA
| | - David M. Sabatini
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Whitehead Institute for Biomedical ResearchCambridgeMAUSA
- Howard Hughes Medical InstituteCambridgeMAUSA
- Koch Institute for Integrative Cancer ResearchCambridgeMAUSA
- Broad Institute of Harvard and Massachusetts Institute of TechnologyCambridgeMAUSA
| | | | | | - Juliana H.C. Smetana
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasBrazil
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40
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Kim E, Dede M, Lenoir WF, Wang G, Srinivasan S, Colic M, Hart T. A network of human functional gene interactions from knockout fitness screens in cancer cells. Life Sci Alliance 2019; 2:2/2/e201800278. [PMID: 30979825 PMCID: PMC6464042 DOI: 10.26508/lsa.201800278] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 12/12/2022] Open
Abstract
The function of human genes can be strongly inferred from their knockout fitness profiles across hundreds of CRISPR screens, illuminating the modular organization of the cell. Genetic interactions mediate the emergence of phenotype from genotype. The systematic survey of genetic interactions in yeast showed that genes operating in the same biological process have highly correlated genetic interaction profiles, and this observation has been exploited to infer gene function in model organisms. Such assays of digenic perturbations in human cells are also highly informative, but are not scalable, even with CRISPR-mediated methods. As an alternative, we developed an indirect method of deriving functional interactions. We show that genes having correlated knockout fitness profiles across diverse, non-isogenic cell lines are analogous to genes having correlated genetic interaction profiles across isogenic query strains and similarly imply shared biological function. We constructed a network of genes with correlated fitness profiles across 276 high-quality CRISPR knockout screens in cancer cell lines into a “coessentiality network,” with up to 500-fold enrichment for co-functional gene pairs, enabling strong inference of gene function and highlighting the modular organization of the cell.
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Affiliation(s)
- Eiru Kim
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Merve Dede
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Walter F Lenoir
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gang Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sanjana Srinivasan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Medina Colic
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA .,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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41
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Prediction of intracellular targets of a small compound by analyzing peptides presented on MHC class I. Biochem Biophys Res Commun 2019; 508:480-486. [PMID: 30503339 DOI: 10.1016/j.bbrc.2018.11.089] [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: 11/07/2018] [Accepted: 11/14/2018] [Indexed: 11/21/2022]
Abstract
In chemical biology, the elucidation of chemical target is crucial for successful drug development. Because MHC class I molecules present peptides from intracellular damaged proteins, it might be possible to identify targets of a chemical by analyzing peptide sequences on MHC class I. Therefore, we treated cells with the autophagy-inducing chemical TMD-457 and identified the peptides presented on MHC class I. Many of the peptides were derived from molecules involved in ER trafficking and ER stress, which were confirmed by morphological and biochemical analyses. Therefore, our results demonstrate that analyzing MHC class I peptides is useful for the detection of chemical targets.
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42
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Amino acids stimulate the endosome-to-Golgi trafficking through Ragulator and small GTPase Arl5. Nat Commun 2018; 9:4987. [PMID: 30478271 PMCID: PMC6255761 DOI: 10.1038/s41467-018-07444-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/31/2018] [Indexed: 11/22/2022] Open
Abstract
The endosome-to-Golgi or endocytic retrograde trafficking pathway is an important post-Golgi recycling route. Here we show that amino acids (AAs) can stimulate the retrograde trafficking and regulate the cell surface localization of certain Golgi membrane proteins. By testing components of the AA-stimulated mTORC1 signaling pathway, we demonstrate that SLC38A9, v-ATPase and Ragulator, but not Rag GTPases and mTORC1, are essential for the AA-stimulated trafficking. Arl5, an ARF-like family small GTPase, interacts with Ragulator in an AA-regulated manner and both Arl5 and its effector, the Golgi-associated retrograde protein complex (GARP), are required for the AA-stimulated trafficking. We have therefore identified a mechanistic connection between the nutrient signaling and the retrograde trafficking pathway, whereby SLC38A9 and v-ATPase sense AA-sufficiency and Ragulator might function as a guanine nucleotide exchange factor to activate Arl5, which, together with GARP, a tethering factor, probably facilitates the endosome-to-Golgi trafficking. Amino acid levels are known to regulate anabolic and catabolic pathways. Here, the authors report that amino acids also affect membrane trafficking by stimulating endosome-to-Golgi retrograde trafficking and regulating cell surface localization of certain Golgi proteins through Ragulator and Arl5.
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43
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Bonvini A, Coqueiro AY, Tirapegui J, Calder PC, Rogero MM. Immunomodulatory role of branched-chain amino acids. Nutr Rev 2018; 76:840-856. [PMID: 30124936 DOI: 10.1093/nutrit/nuy037] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2025] Open
Abstract
Branched-chain amino acids (BCAAs) have been associated with immunomodulation since the mid-1970s and 1980s and have been used in the nutritional therapy of critically ill patients. Evidence shows that BCAAs can directly contribute to immune cell function, aiding recovery of an impaired immune system, as well as improving the nutritional status in cancer and liver diseases. Branched-chain amino acids may also play a role in treatment of patients with sepsis or trauma, contributing to improved clinical outcomes and survival. Branched-chain amino acids, especially leucine, are activators of the mammalian target of rapamycin (mTOR), which, in turn, interacts with several signaling pathways involved in biological mechanisms of insulin action, protein synthesis, mitochondrial biogenesis, inflammation, and lipid metabolism. Although many in vitro and human and animal model studies have provided evidence for the biological activity of BCAAs, findings have been conflicting, and the mechanisms of action of these amino acids are still poorly understood. This review addresses several aspects related to BCAAs, including their transport, oxidation, and mechanisms of action, as well as their role in nutritional therapy and immunomodulation.
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Affiliation(s)
- Andrea Bonvini
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Audrey Y Coqueiro
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Julio Tirapegui
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Philip C Calder
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, Southampton, United Kingdom
| | - Marcelo M Rogero
- Department of Nutrition, Faculty of Public Health, University of São Paulo, São Paulo, Brazil
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44
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Abstract
Background The protein kinase Target Of Rapamycin (TOR) is a nexus for the regulation of eukaryotic cell growth. TOR assembles into one of two distinct signalling complexes, TOR complex 1 (TORC1) and TORC2 (mTORC1/2 in mammals), with a set of largely non-overlapping protein partners. (m)TORC1 activation occurs in response to a series of stimuli relevant to cell growth, including nutrient availability, growth factor signals and stress, and regulates much of the cell's biosynthetic activity, from proteins to lipids, and recycling through autophagy. mTORC1 regulation is of great therapeutic significance, since in humans many of these signalling complexes, alongside subunits of mTORC1 itself, are implicated in a wide variety of pathophysiologies, including multiple types of cancer, neurological disorders, neurodegenerative diseases and metabolic disorders including diabetes. Methodology Recent years have seen numerous structures determined of (m)TOR, which have provided mechanistic insight into (m)TORC1 activation in particular, however the integration of cellular signals occurs upstream of the kinase and remains incompletely understood. Here we have collected and analysed in detail as many as possible of the molecular and structural studies which have shed light on (m)TORC1 repression, activation and signal integration. Conclusions A molecular understanding of this signal integration pathway is required to understand how (m)TORC1 activation is reconciled with the many diverse and contradictory stimuli affecting cell growth. We discuss the current level of molecular understanding of the upstream components of the (m)TORC1 signalling pathway, recent progress on this key biochemical frontier, and the future studies necessary to establish a mechanistic understanding of this master-switch for eukaryotic cell growth.
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Affiliation(s)
- Kailash Ramlaul
- Section of Structural Biology, Department of Medicine, Imperial College London, SW7 2AZ, UK
| | - Christopher H S Aylett
- Section of Structural Biology, Department of Medicine, Imperial College London, SW7 2AZ, UK
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