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Skvortsova L, Perfilyeva A, Bespalova K, Kuzovleva Y, Kabysheva N, Khamdiyeva O. 7p22.3 microdeletion: a case study of a patient with congenital heart defect, neurodevelopmental delay and epilepsy. Orphanet J Rare Dis 2024; 19:301. [PMID: 39152504 PMCID: PMC11330011 DOI: 10.1186/s13023-024-03321-8] [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: 04/18/2024] [Accepted: 08/08/2024] [Indexed: 08/19/2024] Open
Abstract
BACKGROUND Chromosome 7 has regions enriched with low copy repeats (LCRs), which increase the likelihood of chromosomal microdeletion disorders. Documented microdeletion disorders on chromosome 7 include both well-known Williams syndrome and more rare cases. It is noteworthy that most cases of various microdeletions are characterized by phenotypic signs of neuropsychological developmental disorders, which, however, have a different genetic origin. The localization of the microdeletions, the genes included in the region, as well as the structural features of the sequences of these genes have a cumulative influence on the phenotypic characteristics of the individuals for each specific case and the severity of the manifestations of disorders. The consideration of these features and their detailed analysis is important for a correct and comprehensive assessment of the disease. RESULTS The article describes a clinical case of 7p22.3 microdeletion in a patient with congenital heart defect and neurological abnormalities - epilepsy, combined with moderate mental and motor developmental delay. CONCLUSIONS Through detailed genetic analyses, we are improving the clinical description of the rare 7p22.3 microdeletion and thus creating a basis for future genetic counseling and research into targeted therapies.
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Affiliation(s)
- Liliya Skvortsova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Anastassiya Perfilyeva
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Kira Bespalova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan.
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty, 050040, Kazakhstan.
| | - Yelena Kuzovleva
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Nailya Kabysheva
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Ozada Khamdiyeva
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty, 050040, Kazakhstan
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Siddiqui T, Bhatt LK. Emerging autophagic endo-lysosomal targets in the management of Parkinson's disease. Rev Neurol (Paris) 2024; 180:477-485. [PMID: 37586941 DOI: 10.1016/j.neurol.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 06/26/2023] [Accepted: 07/04/2023] [Indexed: 08/18/2023]
Abstract
Synucleopathies, specifically Parkinson's disease, are still incurable and available therapeutic options are scarce and symptomatic. The autophagy-lysosomal-endosomal system is an indigenous mechanism to manage the proteome. Excess/misfolded protein accumulation activates this system, which degrades the undesired proteins via lysosomes. Cells also eliminate these proteins by releasing them into the extracellular space via exosomes. However, the sutophagy-lysosomal-endosomal system becomes unfunctional in Parkinson's disease and there is accumulation and spread of pathogenic alpha-synuclein. Neuronal degeneration results Owing to pathogenic alpha-synuclein. Thus, the autophagy-lysosomal-endosomal system could be a promising target for neuroprotection. In the present review, we discuss the autophagy-lysosomal-endosomal system as an emerging target for the management of Parkinson's disease. Modulation of these targets associated with the autophagy-lysosomal-endosomal system can aid in clearing pathogenic alpha-synuclein and prevent the degeneration of neurons.
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Affiliation(s)
- T Siddiqui
- Department of Pharmacology, SVKM's Doctor Bhanuben-Nanavati College of Pharmacy, Vile Parle (West), Mumbai, India
| | - L K Bhatt
- Department of Pharmacology, SVKM's Doctor Bhanuben-Nanavati College of Pharmacy, Vile Parle (West), Mumbai, India.
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Hanley SE, Willis SD, Doyle SJ, Strich R, Cooper KF. Ksp1 is an autophagic receptor protein for the Snx4-assisted autophagy of Ssn2/Med13. Autophagy 2024; 20:397-415. [PMID: 37733395 PMCID: PMC10813586 DOI: 10.1080/15548627.2023.2259708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023] Open
Abstract
Ksp1 is a casein II-like kinase whose activity prevents aberrant macroautophagy/autophagy induction in nutrient-rich conditions in yeast. Here, we describe a kinase-independent role of Ksp1 as a novel autophagic receptor protein for Ssn2/Med13, a known cargo of Snx4-assisted autophagy of transcription factors. In this pathway, a subset of conserved transcriptional regulators, Ssn2/Med13, Rim15, and Msn2, are selectively targeted for vacuolar proteolysis following nitrogen starvation, assisted by the sorting nexin heterodimer Snx4-Atg20. Here we show that phagophores also engulf Ksp1 alongside its cargo for vacuolar proteolysis. Ksp1 directly associates with Atg8 following nitrogen starvation at the interface of an Atg8-family interacting motif (AIM)/LC3-interacting region (LIR) in Ksp1 and the LIR/AIM docking site (LDS) in Atg8. Mutating the LDS site prevents the autophagic degradation of Ksp1. However, deletion of the C terminal canonical AIM still permitted Ssn2/Med13 proteolysis, suggesting that additional non-canonical AIMs may mediate the Ksp1-Atg8 interaction. Ksp1 is recruited to the perivacuolar phagophore assembly site by Atg29, a member of the trimeric scaffold complex. This interaction is independent of Atg8 and Snx4, suggesting that Ksp1 is recruited early to phagophores, with Snx4 delivering Ssn2/Med13 thereafter. Finally, normal cell survival following prolonged nitrogen starvation requires Ksp1. Together, these studies define a kinase-independent role for Ksp1 as an autophagic receptor protein mediating Ssn2/Med13 degradation. They also suggest that phagophores built by the trimeric scaffold complex are capable of receptor-mediated autophagy. These results demonstrate the dual functionality of Ksp1, whose kinase activity prevents autophagy while it plays a scaffolding role supporting autophagic degradation.Abbreviations: 3-AT: 3-aminotriazole; 17C: Atg17-Atg31-Atg29 trimeric scaffold complex; AIM: Atg8-family interacting motif; ATG: autophagy related; CKM: CDK8 kinase module; Cvt: cytoplasm-to-vacuole targeting; IDR: intrinsically disordered region; LIR: LC3-interacting region; LDS: LIR/AIM docking site; MoRF: molecular recognition feature; NPC: nuclear pore complex; PAS: phagophore assembly site; PKA: protein kinase A; RBP: RNA-binding protein; UPS: ubiquitin-proteasome system. SAA-TF: Snx4-assisted autophagy of transcription factors; Y2H: yeast two-hybrid.
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Affiliation(s)
- Sara E. Hanley
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Stratford, NJ, USA
| | - Stephen D. Willis
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Stratford, NJ, USA
| | - Steven J. Doyle
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Stratford, NJ, USA
- School of Osteopathic Medicine, Rowan University, Stratford, NJ, USA
| | - Randy Strich
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Stratford, NJ, USA
| | - Katrina F. Cooper
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Stratford, NJ, USA
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Wu D, Wang Y, Xu J, Wang D, Zhang J, Meng L, Hu Y, Wang P, Lin J, Zhou S. SNX10 promoted liver IR injury by facilitating macrophage M1 polarization via NLRP3 inflammasome activation. Mol Immunol 2024; 166:79-86. [PMID: 38271879 DOI: 10.1016/j.molimm.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 12/26/2023] [Accepted: 01/17/2024] [Indexed: 01/27/2024]
Abstract
BACKGROUND Liver ischemia reperfusion (IR) injury is a common cause of liver dysfunction in patients post liver partial resection and liver transplantation. However, the cellular defense mechanisms underlying IR are not well understood. Macrophage mediated sterile inflammation plays critical roles in liver IR injury. Sorting nexin (SNX) 10, a member of the SNX family which functions in regulation of endosomal sorting. This study aimed to explore the role of sorting nexin 10 (SNX10) during liver IR injury with a focus on regulating macrophage function. METHODS Both the gene and protein expression levels of SNX10 were analyzed in human specimens from 10 patients undergoing liver partial resection with ischemic insult and in a mouse model of liver IR. The in vivo effects of SNX10 in liver IR injury and sterile inflammation in mice were investigated. Bone marrow derived macrophages (BMDMs) were used to determine the role of SNX10 in modulating macrophage function in vitro. RESULTS Increased expression of SNX10 was observed both in human specimens and mice livers post IR. SNX10 knockdown alleviated IR induced sterile inflammation and liver damage in mice. SNX10 promoted M1 polarization of macrophage treated with LPS and facilitated inflammatory response by activating NLRP3 inflammasome. CONCLUSIONS We report for the first time that SNX10 is upregulated in IR-stressed livers. SNX10 activation aggravates liver IR injury and sterile inflammation by facilitating macrophage M1 polarization and inflammatory response suggesting SNX10 as a potential therapeutic target for liver IR injury.
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Affiliation(s)
- Dongming Wu
- Department of Plastic and Cosmetic Surgery of The Affiliated Friendship Plastic Surgery Hospital & Hepatobiliary Center of The First Affiliated Hospital, Nanjing Medical University, Nanjing, China; NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, China; Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, Nanjing, China
| | - Yong Wang
- Department of Plastic and Cosmetic Surgery of The Affiliated Friendship Plastic Surgery Hospital & Hepatobiliary Center of The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Jian Xu
- Department of Plastic and Cosmetic Surgery of The Affiliated Friendship Plastic Surgery Hospital & Hepatobiliary Center of The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Dong Wang
- Department of Plastic and Cosmetic Surgery of The Affiliated Friendship Plastic Surgery Hospital & Hepatobiliary Center of The First Affiliated Hospital, Nanjing Medical University, Nanjing, China; NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, China; Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, Nanjing, China
| | - Jiawei Zhang
- Department of Plastic and Cosmetic Surgery of The Affiliated Friendship Plastic Surgery Hospital & Hepatobiliary Center of The First Affiliated Hospital, Nanjing Medical University, Nanjing, China; NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, China; Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, Nanjing, China
| | - Lijuan Meng
- Department of Geriatric Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuanchang Hu
- Department of Plastic and Cosmetic Surgery of The Affiliated Friendship Plastic Surgery Hospital & Hepatobiliary Center of The First Affiliated Hospital, Nanjing Medical University, Nanjing, China; NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, China; Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, Nanjing, China
| | - Ping Wang
- Department of Plastic and Cosmetic Surgery of The Affiliated Friendship Plastic Surgery Hospital & Hepatobiliary Center of The First Affiliated Hospital, Nanjing Medical University, Nanjing, China; NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, China; Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, Nanjing, China
| | - Jinde Lin
- Department of Plastic and Cosmetic Surgery of The Affiliated Friendship Plastic Surgery Hospital & Hepatobiliary Center of The First Affiliated Hospital, Nanjing Medical University, Nanjing, China.
| | - Shun Zhou
- Department of Plastic and Cosmetic Surgery of The Affiliated Friendship Plastic Surgery Hospital & Hepatobiliary Center of The First Affiliated Hospital, Nanjing Medical University, Nanjing, China; NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, China; Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, Nanjing, China.
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Bingham R, McCarthy H, Buckley N. Exploring Retrograde Trafficking: Mechanisms and Consequences in Cancer and Disease. Traffic 2024; 25:e12931. [PMID: 38415291 DOI: 10.1111/tra.12931] [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: 11/29/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/29/2024]
Abstract
Retrograde trafficking (RT) orchestrates the intracellular movement of cargo from the plasma membrane, endosomes, Golgi or endoplasmic reticulum (ER)-Golgi intermediate compartment (ERGIC) in an inward/ER-directed manner. RT works as the opposing movement to anterograde trafficking (outward secretion), and the two work together to maintain cellular homeostasis. This is achieved through maintaining cell polarity, retrieving proteins responsible for anterograde trafficking and redirecting proteins that become mis-localised. However, aberrant RT can alter the correct location of key proteins, and thus inhibit or indeed change their canonical function, potentially causing disease. This review highlights the recent advances in the understanding of how upregulation, downregulation or hijacking of RT impacts the localisation of key proteins in cancer and disease to drive progression. Cargoes impacted by aberrant RT are varied amongst maladies including neurodegenerative diseases, autoimmune diseases, bacterial and viral infections (including SARS-CoV-2), and cancer. As we explore the intricacies of RT, it becomes increasingly apparent that it holds significant potential as a target for future therapies to offer more effective interventions in a wide range of pathological conditions.
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Affiliation(s)
- Rachel Bingham
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - Helen McCarthy
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - Niamh Buckley
- School of Pharmacy, Queen's University Belfast, Belfast, UK
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Tang P, Yu Z, Sun H, Liu L, Gong L, Fang T, Sun X, Xie S, An G, Xu Z, Qiu L, Hao M. CRIP1 involves the pathogenesis of multiple myeloma via dual-regulation of proteasome and autophagy. EBioMedicine 2024; 100:104961. [PMID: 38199044 PMCID: PMC10825369 DOI: 10.1016/j.ebiom.2023.104961] [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: 08/01/2023] [Revised: 12/18/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Multiple myeloma (MM) is an incurable hematological malignancy of the plasma cells. The maintenance of protein homeostasis is critical for MM cell survival. Elevated levels of paraproteins in MM cells are cleared by proteasomes or lysosomes, which are independent but inter-connected with each other. Proteasome inhibitors (PIs) work as a backbone agent and successfully improved the outcome of patients; however, the increasing activity of autophagy suppresses the sensitivity to PIs treatment. METHODS The transcription levels of CRIP1 were explored in plasma cells obtained from healthy donors, patients with newly diagnosed multiple myeloma (NDMM), and relapsed/refractory multiple myeloma (RRMM) using Gene expression omnibus datasets. Doxycycline-inducible CRIP1-shRNA and CRIP1 overexpressed MM cell lines were constructed to explore the role of CRIP1 in MM pathogenesis. Proliferation, invasion, migration, proteasome activity and autophagy were examined in MM cells with different CRIP1 levels. Co-immunoprecipitation (Co-IP) with Tandem affinity purification/Mass spectrum (TAP/MS) was performed to identify the binding proteins of CRIP1. The mouse xenograft model was used to determine the role of CRIP1 in the proliferation and drug-resistance of MM cells. FINDINGS High CRIP1 expression was associated with unfavorable clinical outcomes in patients with MM and served as a biomarker for RRMM with shorter overall survival. In vitro and in vivo studies showed that CRIP1 plays a critical role in protein homeostasis via the dual regulation of the activities of proteasome and autophagy in MM cells. A combined analysis of RNA-seq, Co-IP and TAP/MS demonstrated that CRIP1 promotes proteasome inhibitors resistance in MM cells by simultaneously binding to de-ubiquitinase USP7 and proteasome coactivator PA200. CRIP1 promoted proteasome activity and autophagosome maturation by facilitating the dequbiquitination and stabilization of PA200. INTERPRETATION Our findings clarified the pivotal roles of the CRIP1/USP7/PA200 complex in ubiquitin-dependent proteasome degradation and autophagy maturation involved in the pathogenesis of MM. FUNDING A full list of funding sources can be found in the acknowledgements section.
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Affiliation(s)
- Peixia Tang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Tianjin Institutes of Health Science, Tianjin, China
| | - Zhen Yu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Tianjin Institutes of Health Science, Tianjin, China
| | - Hao Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Lanting Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Tianjin Institutes of Health Science, Tianjin, China
| | - Lixin Gong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Teng Fang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Xiyue Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Shiyi Xie
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Gang An
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Zhenshu Xu
- Hematology Department Fujian Medical University Union Hospital, Fujian Institute of Hematology, Fuzhou, Fujian, China.
| | - Lugui Qiu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Tianjin Institutes of Health Science, Tianjin, China; Gobroad Healthcare Group, Beijing, China.
| | - Mu Hao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Tianjin Institutes of Health Science, Tianjin, China.
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Yang W, Li L, Zhang J, Wu J, Kang W, Wang Y, Ding H, Li D, Zheng H. SNX32 is a host restriction factor that degrades African swine fever virus CP204L via the RAB1B-dependent autophagy pathway. J Virol 2024; 98:e0159923. [PMID: 38169281 PMCID: PMC10804981 DOI: 10.1128/jvi.01599-23] [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: 10/28/2023] [Accepted: 11/13/2023] [Indexed: 01/05/2024] Open
Abstract
African swine fever virus (ASFV) causes a highly contagious and deadly disease in domestic pigs and European wild boars, posing a severe threat to the global pig industry. ASFV CP204L, a highly immunogenic protein, is produced during the early stages of ASFV infection. However, the impact of CP204L protein-interacting partners on the outcome of ASFV infection is poorly understood. To accomplish this, coimmunoprecipitation and mass spectrometry analysis were conducted in ASFV-infected porcine alveolar macrophages (PAMs). We have demonstrated that sorting nexin 32 (SNX32) is a CP204L-binding protein and that CP204L interacted and colocalized with SNX32 in ASFV-infected PAMs. ASFV growth and replication were promoted by silencing SNX32 and suppressed by overexpressing SNX32. SNX32 degraded CP204L by recruiting the autophagy-related protein Ras-related protein Rab-1b (RAB1B). RAB1B overexpression inhibited ASFV replication, while knockdown of RAB1B had the opposite effect. Additionally, RAB1B, SNX32, and CP204L formed a complex upon ASFV infection. Taken together, this study demonstrates that SNX32 antagonizes ASFV growth and replication by recruiting the autophagy-related protein RAB1B. This finding extends our understanding of the interaction between ASFV CP204L and its host and provides new insights into exploring the relationship between ASFV infection and autophagy.IMPORTANCEAfrican swine fever (ASF) is a highly contagious and acute hemorrhagic viral disease with a high mortality near 100% in domestic pigs. ASF virus (ASFV), which is the only member of the family Asfarviridae, is a dsDNA virus of great complexity and size, encoding more than 150 proteins. Currently, there are no available vaccines against ASFV. ASFV CP204L represents the most abundantly expressed viral protein early in infection and plays an important role in regulating ASFV replication. However, the mechanism by which the interaction between ASFV CP204L and host proteins affects ASFV replication remains unclear. In this study, we demonstrated that the cellular protein SNX32 interacted with CP204L and degraded CP204L by upregulating the autophagy-related protein RAB1B. In summary, this study will help us understand the interaction mechanism between CP204L and its host upon infection and provide new insights for the development of vaccines and antiviral drugs.
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Affiliation(s)
- Wenping Yang
- 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
| | - Lingxia Li
- 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
| | - Jing 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
| | - Junhuang Wu
- 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
| | - Weifang Kang
- 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
| | - Yue Wang
- 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
| | - Haiyan Ding
- 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
| | - Dan Li
- 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
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Rouskas K, Katsareli EA, Amerikanou C, Dimopoulos AC, Glentis S, Kalantzi A, Skoulakis A, Panousis N, Ongen H, Bielser D, Planchon A, Romano L, Harokopos V, Reczko M, Moulos P, Griniatsos I, Diamantis T, Dermitzakis ET, Ragoussis J, Dedoussis G, Dimas AS. Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population. BMC Genomics 2023; 24:442. [PMID: 37543566 PMCID: PMC10403965 DOI: 10.1186/s12864-023-09532-w] [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] [Accepted: 07/25/2023] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND Expression quantitative trait loci (eQTL) studies provide insights into regulatory mechanisms underlying disease risk. Expanding studies of gene regulation to underexplored populations and to medically relevant tissues offers potential to reveal yet unknown regulatory variants and to better understand disease mechanisms. Here, we performed eQTL mapping in subcutaneous (S) and visceral (V) adipose tissue from 106 Greek individuals (Greek Metabolic study, GM) and compared our findings to those from the Genotype-Tissue Expression (GTEx) resource. RESULTS We identified 1,930 and 1,515 eGenes in S and V respectively, over 13% of which are not observed in GTEx adipose tissue, and that do not arise due to different ancestry. We report additional context-specific regulatory effects in genes of clinical interest (e.g. oncogene ST7) and in genes regulating responses to environmental stimuli (e.g. MIR21, SNX33). We suggest that a fraction of the reported differences across populations is due to environmental effects on gene expression, driving context-specific eQTLs, and suggest that environmental effects can determine the penetrance of disease variants thus shaping disease risk. We report that over half of GM eQTLs colocalize with GWAS SNPs and of these colocalizations 41% are not detected in GTEx. We also highlight the clinical relevance of S adipose tissue by revealing that inflammatory processes are upregulated in individuals with obesity, not only in V, but also in S tissue. CONCLUSIONS By focusing on an understudied population, our results provide further candidate genes for investigation regarding their role in adipose tissue biology and their contribution to disease risk and pathogenesis.
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Affiliation(s)
- Konstantinos Rouskas
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
- Institute of Applied Biosciences, Centre for Research & Technology Hellas, Thessaloniki, Greece
| | - Efthymia A Katsareli
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Charalampia Amerikanou
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Alexandros C Dimopoulos
- Institute for Fundamental Biomedical Science, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
- Hellenic Naval Academy, Hatzikyriakou Avenue, Pireaus, Greece
| | - Stavros Glentis
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
- Pediatric Hematology/Oncology Unit (POHemU), First Department of Pediatrics, University of Athens, Aghia Sophia Children's Hospital, Athens, Greece
| | - Alexandra Kalantzi
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
| | - Anargyros Skoulakis
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
| | | | - Halit Ongen
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Swiss Institute of Bioinformatics, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Deborah Bielser
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Alexandra Planchon
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Luciana Romano
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Vaggelis Harokopos
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
| | - Martin Reczko
- Institute for Fundamental Biomedical Science, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
| | - Panagiotis Moulos
- Institute for Fundamental Biomedical Science, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
- Center of New Biotechnologies & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis Griniatsos
- First Department of Surgery, National and Kapodistrian University of Athens, Medical School, Laiko Hospital, Athens, Greece
| | - Theodoros Diamantis
- First Department of Surgery, National and Kapodistrian University of Athens, Medical School, Laiko Hospital, Athens, Greece
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
- Department of Bioengineering, McGill University, Montréal, QC, Canada
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Antigone S Dimas
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece.
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9
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Wang H, Zhou R, Xu F, Yang K, Zheng L, Zhao P, Shi G, Dai L, Xu C, Yu L, Li Z, Wang J, Wang J. Beyond canonical PROTAC: biological targeted protein degradation (bioTPD). Biomater Res 2023; 27:72. [PMID: 37480049 PMCID: PMC10362593 DOI: 10.1186/s40824-023-00385-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/21/2023] [Indexed: 07/23/2023] Open
Abstract
Targeted protein degradation (TPD) is an emerging therapeutic strategy with the potential to modulate disease-associated proteins that have previously been considered undruggable, by employing the host destruction machinery. The exploration and discovery of cellular degradation pathways, including but not limited to proteasomes and lysosome pathways as well as their degraders, is an area of active research. Since the concept of proteolysis-targeting chimeras (PROTACs) was introduced in 2001, the paradigm of TPD has been greatly expanded and moved from academia to industry for clinical translation, with small-molecule TPD being particularly represented. As an indispensable part of TPD, biological TPD (bioTPD) technologies including peptide-, fusion protein-, antibody-, nucleic acid-based bioTPD and others have also emerged and undergone significant advancement in recent years, demonstrating unique and promising activities beyond those of conventional small-molecule TPD. In this review, we provide an overview of recent advances in bioTPD technologies, summarize their compositional features and potential applications, and briefly discuss their drawbacks. Moreover, we present some strategies to improve the delivery efficacy of bioTPD, addressing their challenges in further clinical development.
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Affiliation(s)
- Huifang Wang
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Runhua Zhou
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China
| | - Fushan Xu
- The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Kongjun Yang
- The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Liuhai Zheng
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Pan Zhao
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Guangwei Shi
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China
| | - Lingyun Dai
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Chengchao Xu
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
| | - Le Yu
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China.
| | - Zhijie Li
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China.
| | - Jianhong Wang
- Shenzhen Mental Health Center, Shenzhen Kangning Hospital, Shenzhen, 518020, Guangdong, P. R. China.
| | - Jigang Wang
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China.
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China.
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China.
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10
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Tornero-Écija A, Zapata-Del-Baño A, Antón-Esteban L, Vincent O, Escalante R. The association of lipid transfer protein VPS13A with endosomes is mediated by sorting nexin SNX5. Life Sci Alliance 2023; 6:e202201852. [PMID: 36977596 PMCID: PMC10053439 DOI: 10.26508/lsa.202201852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/17/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Human VPS13 proteins are implicated in severe neurological diseases. These proteins play an important role in lipid transport at membrane contact sites between different organelles. Identification of adaptors that regulate the subcellular localization of these proteins at specific membrane contact sites is essential to understand their function and role in disease. We have identified the sorting nexin SNX5 as an interactor of VPS13A that mediates its association with endosomal subdomains. As for the yeast sorting nexin and Vps13 endosomal adaptor Ypt35, this association involves the VPS13 adaptor-binding (VAB) domain in VPS13A and a PxP motif in SNX5. Notably, this interaction is impaired by mutation of a conserved asparagine residue in the VAB domain, which is also required for Vps13-adaptor binding in yeast and is pathogenic in VPS13D. VPS13A fragments containing the VAB domain co-localize with SNX5, whereas the more C-terminal part of VPS13A directs its localization to the mitochondria. Overall, our results suggest that a fraction of VPS13A localizes to junctions between the endoplasmic reticulum, mitochondria, and SNX5-containing endosomes.
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Affiliation(s)
- Alba Tornero-Écija
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
| | | | - Laura Antón-Esteban
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
| | - Olivier Vincent
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
| | - Ricardo Escalante
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
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11
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Hakim S, Woolf CJ. Macrophages set the bar for acute pain sensitivity. Nat Immunol 2023; 24:382-384. [PMID: 36823407 DOI: 10.1038/s41590-023-01438-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- Sara Hakim
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Clifford J Woolf
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
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12
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Feng H, Tan J, Wang Q, Zhou T, Li L, Sun D, Fan M, Cheng H, Shen W. α-hederin regulates glucose metabolism in intestinal epithelial cells by increasing SNX10 expression. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 111:154677. [PMID: 36724620 DOI: 10.1016/j.phymed.2023.154677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/31/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Sorting nexin 10 (SNX10) has recently been identified as a critical regulator of colorectal carcinogenesis, whose deletion promoted cell proliferation and survival in human CRC cells, and promoted colorectal tumor growth and upregulated amino-acid metabolism in mice. However, what happens when silencing SNX10 in normal human intestinal epithelial cells (IECs) remains unknown, and no drugs targeting SNX10 have been reported. Here, we first investigated the biological function and underlying mechanisms of SNX10 in normal human IECs, and found that α-hederin, a pentacyclic triterpenoid saponin, has a regulatory effect on SNX10 expression. PURPOSE This study aimed to explore the function of SNX10 in IECs to provide a new target for the prevention and treatment of malignant transformation and the intervention mechanism of α-hederin for further development of potential novel agents targeting SNX10. METHODS The transfection approach was used to construct SNX10 stable knockdown cells. Cell proliferation was detected by CCK8, clone formation, EdU, flow cytometry, and wound healing assays. Enzyme activity assays for glucose metabolism, qRT-PCR, western blotting, and immunofluorescence staining were performed to investigate the protein expression of signaling pathways. RESULTS Silencing SNX10 promoted cell proliferation and cycle transition in IECs and increased the activity of key enzymes involved in glucose metabolism. Moreover, DEPDC5 expression was significantly decreased following SNX10 knockdown, followed by activation of the mTORC1 pathway. α-hederin reversed the accelerated cell proliferation, cycle progression, and glucose metabolic activity, as well as the activated mTORC1 pathway caused by SNX10 knockdown, by notably increasing SNX10 expression in a dose-dependent manner. CONCLUSION We first reported that knockdown of SNX10 in normal human IECs promoted cell proliferation and activated glucose metabolism by activating the mTORC1 pathway. Meanwhile, we first found that α-hederin down-regulated glucose metabolism activity and slowed cell proliferation by increasing SNX10 expression in IECs.
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Affiliation(s)
- Hui Feng
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China
| | - Jiani Tan
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China; Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing 210023, Jiangsu, China; Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China
| | - Qijuan Wang
- Zhenjiang Hospital of Integrated Traditional Chinese and Western Medicine, Zhenjiang 212000, Jiangsu, China
| | - Tingting Zhou
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China
| | - Liu Li
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China; Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing 210023, Jiangsu, China; Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China
| | - Dongdong Sun
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China; Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing 210023, Jiangsu, China; Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China
| | - Minmin Fan
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China; Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing 210023, Jiangsu, China; Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China
| | - Haibo Cheng
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China; Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing 210023, Jiangsu, China; Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China.
| | - Weixing Shen
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China; Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing 210023, Jiangsu, China; Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China.
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13
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Xu C, Li F, Liu Z, Yan C, Xiao J. Pan-cancer analysis of the prognostic and immunological role of SNX29: a potential target for survival and immunotherapy. BMC Med Genomics 2023; 16:34. [PMID: 36829159 PMCID: PMC9951530 DOI: 10.1186/s12920-023-01466-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND There is growing evidence that the SNX family is critical for clinical prognosis, immune infiltration and drug sensitivity in many types of tumors. The relationships between the SNX29 gene and clinical prognosis as well as pan-cancer cell infiltration and drug sensitivity have not been fully elucidated. METHODS In the current study, we explored the correlation between SNX29 expression and 33 types of malignancies via TCGA and GTEx. The relationship between SNX29 expression and prognostic outcome in the pan-caner cohort was also analyzed. Immune infiltration, microsatellite instability, tumor mutational burden and potential therapeutic targets of SNX29 were investigated by analyzing public databases. RESULTS The expression of SNX29 was found to be significantly upregulated in most tumor tissues compared to normal tissues. SNX29 expression was associated with prognosis and clinical stage. In the immune infiltration analysis, a significant relationship was found between SNX29 expression and the level of immune infiltration. In addition, we found associations between the SNX29 gene and tumor mutation burden, microsatellite instability, immunoinhibition-related genes and autophagy-related genes. Finally, the expression of SNX29 was significantly associated with the sensitivity of various tumor cell lines to 8 antitumor drugs. These results suggest that SNX29 expression is important in determining the progression, immune infiltration and drug sensitivity of various cancers. CONCLUSION This study provides novel insights into the potential pan-cancer targets of SNX29.
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Affiliation(s)
- Chengfei Xu
- Department of Gastrointestinal Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China.,School of Clinical Medicine, Chengdu Medical College, Chengdu, 610500, People's Republic of China.,First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China
| | - Fanghan Li
- Department of Gastrointestinal Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China.,School of Clinical Medicine, Chengdu Medical College, Chengdu, 610500, People's Republic of China
| | - Zilin Liu
- Department of Gastrointestinal Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China.,School of Clinical Medicine, Chengdu Medical College, Chengdu, 610500, People's Republic of China.,First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China
| | - Chuanjing Yan
- Department of Gastrointestinal Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China. .,School of Clinical Medicine, Chengdu Medical College, Chengdu, 610500, People's Republic of China. .,First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China.
| | - Jiangwei Xiao
- Department of Gastrointestinal Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China. .,School of Clinical Medicine, Chengdu Medical College, Chengdu, 610500, People's Republic of China. .,First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China.
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14
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Berlin I, Sapmaz A, Stévenin V, Neefjes J. Ubiquitin and its relatives as wizards of the endolysosomal system. J Cell Sci 2023; 136:288517. [PMID: 36825571 PMCID: PMC10022685 DOI: 10.1242/jcs.260101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The endolysosomal system comprises a dynamic constellation of vesicles working together to sense and interpret environmental cues and facilitate homeostasis. Integrating extracellular information with the internal affairs of the cell requires endosomes and lysosomes to be proficient in decision-making: fusion or fission; recycling or degradation; fast transport or contacts with other organelles. To effectively discriminate between these options, the endolysosomal system employs complex regulatory strategies that crucially rely on reversible post-translational modifications (PTMs) with ubiquitin (Ub) and ubiquitin-like (Ubl) proteins. The cycle of conjugation, recognition and removal of different Ub- and Ubl-modified states informs cellular protein stability and behavior at spatial and temporal resolution and is thus well suited to finetune macromolecular complex assembly and function on endolysosomal membranes. Here, we discuss how ubiquitylation (also known as ubiquitination) and its biochemical relatives orchestrate endocytic traffic and designate cargo fate, influence membrane identity transitions and support formation of membrane contact sites (MCSs). Finally, we explore the opportunistic hijacking of Ub and Ubl modification cascades by intracellular bacteria that remodel host trafficking pathways to invade and prosper inside cells.
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Affiliation(s)
- Ilana Berlin
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Aysegul Sapmaz
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Virginie Stévenin
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Jacques Neefjes
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
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15
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Huang J, Tiu AC, Jose PA, Yang J. Sorting nexins: role in the regulation of blood pressure. FEBS J 2023; 290:600-619. [PMID: 34847291 PMCID: PMC9149145 DOI: 10.1111/febs.16305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 10/13/2021] [Accepted: 11/29/2021] [Indexed: 02/06/2023]
Abstract
Sorting nexins (SNXs) are a family of proteins that regulate cellular cargo sorting and trafficking, maintain intracellular protein homeostasis, and participate in intracellular signaling. SNXs are also important in the regulation of blood pressure via several mechanisms. Aberrant expression and dysfunction of SNXs participate in the dysregulation of blood pressure. Genetic studies show a correlation between SNX gene variants and the response to antihypertensive drugs. In this review, we summarize the progress in SNX-mediated regulation of blood pressure, discuss the potential role of SNXs in the pathophysiology and treatment of hypertension, and propose novel strategies for the medical therapy of hypertension.
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Affiliation(s)
- Juan Huang
- Department of Clinical Nutrition, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 410020, P.R. China
| | - Andrew C. Tiu
- Department of Medicine, Einstein Medical Center Philadelphia, Philadelphia, PA 19141, USA
| | - Pedro A. Jose
- Division of Renal Diseases & Hypertension, Department of Medicine, and Department of Physiology and Pharmacology, The George Washington University School of Medicine & Health Sciences, Washington, DC 20052, USA
| | - Jian Yang
- Department of Clinical Nutrition, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 410020, P.R. China
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16
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Li JG, Blass BE, Praticò D. Beneficial Effect of a Small Pharmacologic Chaperone on the Established Alzheimer's Disease Phenotype. J Alzheimers Dis 2023; 91:463-469. [PMID: 36442197 DOI: 10.3233/jad-220869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND The endosomal retromer complex system is a key controller for trafficking of proteins. Downregulation of its recognition core proteins, such as VPS35, is present in Alzheimer's disease (AD) brain, whereas its normalization prevents the development of AD pathology in a transgenic model with amyloid-β deposits and tau tangles. OBJECTIVE Assess the effect of targeting VPS35 after the AD pathology and memory impairments have developed. METHODS Twelve-month-old triple transgenic mice were treated with a small pharmacological chaperone, TPT-172, or vehicle for 14 weeks. At the end of this period, the effect of the drug on their phenotype was evaluated. RESULTS While control mice had a decline of learning and memory, the group receiving the chaperone did not. Moreover, when compared with controls the treated mice had significantly less amyloid-β peptides and phosphorylated tau, elevation of post-synaptic protein, and reduction in astrocytes activation. CONCLUSION Taken together, our findings demonstrate that pharmacologic stabilization of the retromer recognition core is beneficial also after the AD-like pathologic phenotype is established.
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Affiliation(s)
- Jian-Guo Li
- Alzheimer's Center at Temple, Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Benjamin E Blass
- Alzheimer's Center at Temple, Lewis Katz School of Medicine, Philadelphia, PA, USA.,Moulder Center for Drug Discovery Research, School of Pharmacy, Temple University, Philadelphia, PA, USA
| | - Domenico Praticò
- Alzheimer's Center at Temple, Lewis Katz School of Medicine, Philadelphia, PA, USA
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17
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Da Graça J, Morel E. Canonical and Non-Canonical Roles of SNX1 and SNX2 in Endosomal Membrane Dynamics. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231217867. [PMID: 38033809 PMCID: PMC10683387 DOI: 10.1177/25152564231217867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023]
Abstract
Sorting nexins (SNXs) are a family of membrane-binding proteins known to play a critical role in regulating endocytic pathway sorting and endosomal membrane trafficking. Among them, SNX1 and SNX2 are members of the SNX-BAR subfamily and possess a membrane-curvature domain and a phosphoinositide-binding domain, which enables their stabilization at the phosphatidylinositol-3-phosphate (PI3P)-positive surface of endosomes. While their binding to PI3P-positive platforms facilitates interaction with endosomal partners and stabilization at the endosomal membrane, their SNX-BAR region is pivotal for generating membrane tubulation from endosomal compartments. In this context, their primary identified biological roles-and their partnership-are tightly associated with the retromer and endosomal SNX-BAR sorting complex for promoting exit 1 complex trafficking, facilitating the transport of cargoes from early endosomes to the secretory pathway. However, recent literature indicates that these proteins also possess biological functions in other aspects of endosomal features and sorting processes. Notably, SNX2 has been found to regulate endosome-endoplasmic reticulum (ER) contact sites through its interaction with VAP proteins at the ER membrane. Furthermore, data from our laboratory show that SNX1 and SNX2 are involved in the tubulation of early endosomes toward ER sites associated with autophagy initiation during starvation. These findings shed light on a novel role of SNXs in inter-organelle tethering and communication. In this concise review, we will explore the non-retromer functions of SNX1 and SNX2, specifically focusing on their involvement in endosomal membrane dynamics during stress sensing and autophagy-associated processes.
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Affiliation(s)
- Juliane Da Graça
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Paris, France
| | - Etienne Morel
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Paris, France
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18
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Yarmohammadi F, Hayes AW, Karimi G. Sorting nexins as a promising therapeutic target for cardiovascular disorders: An updated overview. Exp Cell Res 2022; 419:113304. [PMID: 35931142 DOI: 10.1016/j.yexcr.2022.113304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022]
Abstract
Sorting nexins (SNXs) are involved in sorting the protein cargo within the endolysosomal system. Recently, several studies have shown the role of SNXs in cardiovascular pathology. SNXs exert both physiologic and pathologic functions in the cardiovascular system by regulating protein sorting and trafficking, maintaining protein homeostasis, and participating in multiple signaling pathways. SNX deficiency results in blood pressure response to dopamine 5 receptor [D5R] stimulation. SNX knockout protected against atherosclerosis lesions by suppressing foam cell formation. Moreover, SNXs can act as endogenous anti-arrhythmic agents via maintenance of calcium homeostasis. Overexpression SNXs also can reduce cardiac fibrosis in atrial fibrillation. The SNX-STAT3 interaction in cardiac cells promoted heart failure. SNXs may have the potential to act as a pharmacological target against specific cardiovascular diseases.
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Affiliation(s)
- Fatemeh Yarmohammadi
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - A Wallace Hayes
- Center for Environmental Occupational Risk Analysis and Management, College of Public Health, University of South Florida, Tampa, FL,, USA; Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, USA
| | - Gholamreza Karimi
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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19
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Mahmutefendić Lučin H, Blagojević Zagorac G, Marcelić M, Lučin P. Host Cell Signatures of the Envelopment Site within Beta-Herpes Virions. Int J Mol Sci 2022; 23:9994. [PMID: 36077391 PMCID: PMC9456339 DOI: 10.3390/ijms23179994] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/26/2022] Open
Abstract
Beta-herpesvirus infection completely reorganizes the membrane system of the cell. This system is maintained by the spatiotemporal arrangement of more than 3000 cellular proteins that continuously adapt the configuration of membrane organelles according to cellular needs. Beta-herpesvirus infection establishes a new configuration known as the assembly compartment (AC). The AC membranes are loaded with virus-encoded proteins during the long replication cycle and used for the final envelopment of the newly formed capsids to form infectious virions. The identity of the envelopment membranes is still largely unknown. Electron microscopy and immunofluorescence studies suggest that the envelopment occurs as a membrane wrapping around the capsids, similar to the growth of phagophores, in the area of the AC with the membrane identities of early/recycling endosomes and the trans-Golgi network. During wrapping, host cell proteins that define the identity and shape of these membranes are captured along with the capsids and incorporated into the virions as host cell signatures. In this report, we reviewed the existing information on host cell signatures in human cytomegalovirus (HCMV) virions. We analyzed the published proteomes of the HCMV virion preparations that identified a large number of host cell proteins. Virion purification methods are not yet advanced enough to separate all of the components of the rich extracellular material, including the large amounts of non-vesicular extracellular particles (NVEPs). Therefore, we used the proteomic data from large and small extracellular vesicles (lEVs and sEVs) and NVEPs to filter out the host cell proteins identified in the viral proteomes. Using these filters, we were able to narrow down the analysis of the host cell signatures within the virions and determine that envelopment likely occurs at the membranes derived from the tubular recycling endosomes. Many of these signatures were also found at the autophagosomes, suggesting that the CMV-infected cell forms membrane organelles with phagophore growth properties using early endosomal host cell machinery that coordinates endosomal recycling.
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Affiliation(s)
| | | | | | - Pero Lučin
- Department of Physiology, Immunology and Pathophysiology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
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Parihar K, Nukpezah J, Iwamoto DV, Janmey PA, Radhakrishnan R. Data driven and biophysical insights into the regulation of trafficking vesicles by extracellular matrix stiffness. iScience 2022; 25:104721. [PMID: 35865140 PMCID: PMC9293776 DOI: 10.1016/j.isci.2022.104721] [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: 03/03/2022] [Revised: 05/30/2022] [Accepted: 06/28/2022] [Indexed: 11/19/2022] Open
Abstract
Biomechanical signals from remodeled extracellular matrix (ECM) promote tumor progression. Here, we show that cell-matrix and cell-cell communication may be inherently linked and tuned through mechanisms of mechanosensitive biogenesis of trafficking vesicles. Pan-cancer analysis of cancer cells' mechanical properties (focusing primarily on cell stiffness) on substrates of varied stiffness and composition elucidated a heterogeneous cellular response to mechanical stimuli. Through machine learning, we identified a fingerprint of cytoskeleton-related proteins that accurately characterize cell stiffness in different ECM conditions. Expression of their respective genes correlates with patient prognosis across different tumor types. The levels of selected cytoskeleton proteins indicated that cortical tension mirrors the increase (or decrease) in cell stiffness with a change in ECM stiffness. A mechanistic biophysical model shows that the tendency for curvature generation by curvature-inducing proteins has an ultrasensitive dependence on cortical tension. This study thus highlights the effect of ECM stiffness, mediated by cortical tension, in modulating vesicle biogenesis.
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Affiliation(s)
- Kshitiz Parihar
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan Nukpezah
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel V. Iwamoto
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paul A. Janmey
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
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A novel RARA-SNX15 fusion in PML-RARA-positive acute promyelocytic leukemia with t(11;17;15)(q13;q21.2;q24.1). Int J Hematol 2022; 116:956-960. [PMID: 35854096 DOI: 10.1007/s12185-022-03421-w] [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: 05/07/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 10/17/2022]
Abstract
Acute promyelocytic leukemia (APL) is characterized by a series of retinoic acid receptor (RAR) fusion genes that lead to the dysregulation of RAR signaling and onset of APL. PML-RARA is the most common fusion generated from t(15;17)(q24;q21). In addition, the reciprocal fusion RARA-PML is present in over 80% of t(15;17) APL cases. The bcr3 types of RARA-PML and RARA-PLZF in particular are reciprocal fusions that contribute to leukemogenesis. Here, we report a variant APL case with t(11;17;15)(q13;q21.2;q24.1). Massive parallel sequencing of patient RNA detected the novel fusion transcripts RARA-SNX15 and SNX15-LINC02255 along with the bcr3 type of PML-RARA. Genetic analysis revealed that RARA-SNX15L is an in-frame fusion due to intron retention caused by RNA mis-splicing. RARA-SNX15L consisted mainly of SNX15 domains, including the Phox-homology domain, which has a critical role in protein-protein interactions among sorting nexins and with other partners. Co-immunoprecipitation analysis revealed that RARA-SNX15L is directly associated with SNX15 and with itself. Further studies are needed to evaluate the biological significance of RARA-SNX15L in APL. In conclusion, this is the first report of APL with a complex chromosomal rearrangement involving SNX15.
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Liang C, Li C, Wu J, Zhao M, Chen D, Liu C, Chu J, Zhang W, Hwang I, Wang M. SORTING NEXIN2 proteins mediate stomatal movement and the response to drought stress by modulating trafficking and protein levels of the ABA exporter ABCG25. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1603-1618. [PMID: 35384109 DOI: 10.1111/tpj.15758] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 03/23/2022] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
The phytohormone abscisic acid (ABA) regulates ion channel activity and stomatal movement in response to drought stress. Cellular ABA levels change depending on cellular and environmental conditions via modulation of its biosynthesis, catabolism and transport. Although factors involved in ABA biosynthesis and degradation have been studied extensively, how ABA transporters are modulated to fine-tune ABA levels, especially under drought stress, remains elusive. Here, we show that Arabidopsis thaliana SORTING NEXIN 2 (SNX2) proteins play a critical role in endosomal trafficking of the ABA exporter ATP BINDING CASETTE G25 (ABCG25) via direct interaction at endosomes, leading to its degradation in the vacuole. In agreement, snx2a and snx2b mutant plants showed enhanced recycling of GFP-ABCG25 from early endosomes to the plasma membrane and higher accumulation of GFP-ABCG25. Phenotypically, snx2a and snx2b plants were highly sensitive to exogenous ABA and displayed enhanced ABA-mediated inhibition of inward K+ currents and ABA-mediated activation of slow anion currents in guard cells, resulting in an increased tolerance to drought stress. Based on these results, we propose that SNX2 proteins play a crucial role in stomatal movement and tolerance to drought stress by modulating the endosomal trafficking of ABCG25 and thus cellular ABA levels.
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Affiliation(s)
- Chaochao Liang
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Chunlong Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Jing Wu
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Min Zhao
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Donghua Chen
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Cuimei Liu
- National Centre for Plant Gene Research (Beijing), Innovation Academy for Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, P.R. China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Innovation Academy for Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, P.R. China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, P.R. China
| | - Wei Zhang
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
| | - Inhwan Hwang
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, 790-784, South Korea
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Mei Wang
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, P.R. China
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Obita T, Inaka K, Kohda D, Maita N. Crystal structure of the PX domain of Vps17p from Saccharomyces cerevisiae. Acta Crystallogr F Struct Biol Commun 2022; 78:210-216. [PMID: 35506766 PMCID: PMC9067373 DOI: 10.1107/s2053230x22004472] [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: 03/24/2022] [Accepted: 04/27/2022] [Indexed: 11/10/2022] Open
Abstract
The structure determination of the PX (phox homology) domain of the Saccharomyces cerevisiae Vps17p protein presented a challenging case for molecular replacement because it has noncrystallographic symmetry close to a crystallographic axis. The combination of diffraction-quality crystals grown under microgravity on the International Space Station and a highly accurate template structure predicted by AlphaFold2 provided the key to successful crystal structure determination. Although the structure of the Vps17p PX domain is seen in many PX domains, no basic residues are found around the canonical phosphatidylinositol phosphate (PtdIns-P) binding site, suggesting an inability to bind PtdIns-P molecules.
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Affiliation(s)
- Takayuki Obita
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Koji Inaka
- Maruwa Foods and Biosciences Inc., Yamatokoriyama, Nara 639-1123, Japan
| | - Daisuke Kohda
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Nobuo Maita
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
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Targeted protein degradation: mechanisms, strategies and application. Signal Transduct Target Ther 2022; 7:113. [PMID: 35379777 PMCID: PMC8977435 DOI: 10.1038/s41392-022-00966-4] [Citation(s) in RCA: 207] [Impact Index Per Article: 103.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/21/2022] [Accepted: 03/15/2022] [Indexed: 12/11/2022] Open
Abstract
Traditional drug discovery mainly focuses on direct regulation of protein activity. The development and application of protein activity modulators, particularly inhibitors, has been the mainstream in drug development. In recent years, PROteolysis TArgeting Chimeras (PROTAC) technology has emerged as one of the most promising approaches to remove specific disease-associated proteins by exploiting cells’ own destruction machinery. In addition to PROTAC, many different targeted protein degradation (TPD) strategies including, but not limited to, molecular glue, Lysosome-Targeting Chimaera (LYTAC), and Antibody-based PROTAC (AbTAC), are emerging. These technologies have not only greatly expanded the scope of TPD, but also provided fresh insights into drug discovery. Here, we summarize recent advances of major TPD technologies, discuss their potential applications, and hope to provide a prime for both biologists and chemists who are interested in this vibrant field.
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Zhou Y, Fu HC, Wang YY, Huang HZ, Fu XZ, Li NQ. The dynamic immune responses of Mandarin fish (Siniperca chuatsi) to ISKNV in early infection based on full-length transcriptome analysis and weighted gene co-expression network analysis. FISH & SHELLFISH IMMUNOLOGY 2022; 122:191-205. [PMID: 35158068 DOI: 10.1016/j.fsi.2022.02.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 05/26/2023]
Abstract
Mandarin fish (Siniperca chuatsi) been seriously harmed by infectious spleen and kidney necrosis virus (ISKNV) in recent years, but the early immune response mechanism of infection is still unknown. Here, we performed RNA sequencing on the spleens of mandarin fish infected with ISKNV at 0, 12, 24, 48, and 72 h post-infection (hpi) using short-read Illumina RNA sequencing and long-read Pacific Biosciences isoform sequencing to generate a full-length transcriptome. The immune responses of mandarin fish infected with ISKNV at the molecular level were characterized by RNA-seq analysis and weighted gene co-expression network analysis (WGCNA). A total of 26,528 full-length transcript sequences were obtained. There were 2,729 (1,680 up-regulated and 1,112 down-regulated), 1,874 (1,136 up-regulated and 738 down-regulated), 2,032 (1,158 up-regulated and 847 down-regulated), and 4,176 (2,233 up-regulated and 1,943 down-regulated) differentially expressed genes (DEGs) in mandarin fish at 12, 24, 48, and 72 hpi, compared with uninfected fish, respectively. A total of four modules of co-expressed DEGs identified by WGCNA were significantly positively correlated to the four time points after infection, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the immune-related DEGs in all these modules were mainly enriched in Phagosome, Endocytosis, Herpes simplex infection, and Cytokine-cytokine receptor interaction pathways. Further analysis showed that oher signaling pathways, including CAMs, NOD-like receptor and ER protein processing, Intestinal immune network for IgA production, TLR pathway, and Apoptosis significantly enriched in four modules corresponding to 12, 24, 48, and 72 hpi respectively, had specifically participated in the immune response. Hub genes identified based on the high-degree nodes in the WGCN, including CAM3, IL-8, CCL21, STING, SNX1, PFR and TBK1, and some DEGs such as MHCI, MHCII, TfR, STING, TNF α, TBK1, IRF1, and NF-kB, BCR, IgA and Bcl-XL had involved in dynamic molecular response of mandarin fish to ISKNV infection. In sum, this study provides a set of full-length transcriptome of the spleen tissue of mandarin fish for the first time and revealed a group of immune genes and pathways involved in different temporal responses to ISKNV infection, which has implications for resource conservation and aiding the development of strategies to prevent virus early infection for mandarin fish.
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Affiliation(s)
- Yu Zhou
- School of Basic Medicine and Biological Sciences, Fisheries Research Institute, Soochow University, Suzhou, 215123, China
| | - Huang-Cui Fu
- School of Basic Medicine and Biological Sciences, Fisheries Research Institute, Soochow University, Suzhou, 215123, China
| | - Ying-Ying Wang
- School of Basic Medicine and Biological Sciences, Fisheries Research Institute, Soochow University, Suzhou, 215123, China
| | - He-Zhong Huang
- School of Basic Medicine and Biological Sciences, Fisheries Research Institute, Soochow University, Suzhou, 215123, China.
| | - Xiao-Zhe Fu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquatic Animal Immune Technology, Guangdong Provinces, Guangzhou, 510380, China
| | - Ning-Qiu Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquatic Animal Immune Technology, Guangdong Provinces, Guangzhou, 510380, China
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Lacey J, Webster SJ, Heath PR, Hill CJ, Nicholson-Goult L, Wagner BE, Khan AO, Morgan NV, Makris M, Daly ME. Sorting nexin 24 is required for α-granule biogenesis and cargo delivery in megakaryocytes. Haematologica 2022; 107:1902-1913. [PMID: 35021601 PMCID: PMC9335091 DOI: 10.3324/haematol.2021.279636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Indexed: 01/06/2023] Open
Abstract
Germline defects affecting the DNA-binding domain of the transcription factor FLI1 are associated with a bleeding disorder that is characterized by the presence of large, fused α-granules in platelets. We investigated whether the genes showing abnormal expression in FLI1-deficient platelets could be involved in platelet α-granule biogenesis by undertaking transcriptome analysis of control platelets and platelets harboring a DNA-binding variant of FLI1. Our analysis identified 2,276 transcripts that were differentially expressed in FLI1-deficient platelets. Functional annotation clustering of the coding transcripts revealed significant enrichment for gene annotations relating to protein transport, and identified Sorting nexin 24 (SNX24) as a candidate for further investigation. Using an induced pluripotent stem cell-derived megakaryocyte model, SNX24 expression was found to be increased during the early stages of megakaryocyte differentiation and downregulated during proplatelet formation, indicating tight regulatory control during megakaryopoiesis. CRISPR-Cas9 mediated knockout (KO) of SNX24 led to decreased expression of immature megakaryocyte markers, CD41 and CD61, and increased expression of the mature megakaryocyte marker CD42b (P=0.0001), without affecting megakaryocyte polyploidisation, or proplatelet formation. Electron microscopic analysis revealed an increase in empty membrane-bound organelles in SNX24 KO megakaryocytes, a reduction in α-granules and an absence of immature and mature multivesicular bodies, consistent with a defect in the intermediate stage of α-granule maturation. Co-localization studies showed that SNX24 associates with each compartment of α-granule maturation. Reduced expression of CD62P and VWF was observed in SNX24 KO megakaryocytes. We conclude that SNX24 is required for α-granule biogenesis and intracellular trafficking of α-granule cargo within megakaryocytes.
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Affiliation(s)
- Joanne Lacey
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield
| | - Simon J. Webster
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield
| | - Paul R. Heath
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield
| | - Chris J. Hill
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield
| | | | - Bart E. Wagner
- Histopathology Department, Royal Hallamshire Hospital, Sheffield
| | - Abdullah O. Khan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Neil V. Morgan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Michael Makris
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield
| | - Martina E. Daly
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield,Martina E. Daly
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27
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Ohashi Y. Activation Mechanisms of the VPS34 Complexes. Cells 2021; 10:cells10113124. [PMID: 34831348 PMCID: PMC8624279 DOI: 10.3390/cells10113124] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 01/18/2023] Open
Abstract
Phosphatidylinositol-3-phosphate (PtdIns(3)P) is essential for cell survival, and its intracellular synthesis is spatially and temporally regulated. It has major roles in two distinctive cellular pathways, namely, the autophagy and endocytic pathways. PtdIns(3)P is synthesized from phosphatidylinositol (PtdIns) by PIK3C3C/VPS34 in mammals or Vps34 in yeast. Pathway-specific VPS34/Vps34 activity is the consequence of the enzyme being incorporated into two mutually exclusive complexes: complex I for autophagy, composed of VPS34/Vps34-Vps15/Vps15-Beclin 1/Vps30-ATG14L/Atg14 (mammals/yeast), and complex II for endocytic pathways, in which ATG14L/Atg14 is replaced with UVRAG/Vps38 (mammals/yeast). Because of its involvement in autophagy, defects in which are closely associated with human diseases such as cancer and neurodegenerative diseases, developing highly selective drugs that target specific VPS34/Vps34 complexes is an essential goal in the autophagy field. Recent studies on the activation mechanisms of VPS34/Vps34 complexes have revealed that a variety of factors, including conformational changes, lipid physicochemical parameters, upstream regulators, and downstream effectors, greatly influence the activity of these complexes. This review summarizes and highlights each of these influences as well as clarifying key questions remaining in the field and outlining future perspectives.
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Affiliation(s)
- Yohei Ohashi
- MRC Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Francis Crick Avenue, Cambridge CB2 0QH, UK
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28
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Hanley SE, Willis SD, Cooper KF. Snx4-assisted vacuolar targeting of transcription factors defines a new autophagy pathway for controlling ATG expression. Autophagy 2021; 17:3547-3565. [PMID: 33678121 PMCID: PMC8632336 DOI: 10.1080/15548627.2021.1877934] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/14/2021] [Indexed: 12/18/2022] Open
Abstract
Autophagy, in part, is controlled by the repression and activation of autophagy-related (ATG) genes. Here, we describe a new selective autophagy pathway that targets functional transcriptional regulators to control their activity. This pathway is activated in response to nitrogen starvation and recycles transcriptional activators (Msn2 and Rim15) and a repressor (Ssn2/Med13) of ATG expression. Further analysis of Ssn2/Med13 vacuolar proteolysis revealed that this pathway utilizes the core autophagic machinery. However, it is independent of known nucleophagy mechanisms, receptor proteins, and the scaffold protein Atg11. Instead, Ssn2/Med13 exits the nucleus through the nuclear pore complex (NPC) and associates with the cytoplasmic nucleoporin Gle1, a member of the RNA remodeling complex. Dbp5 and Nup159, that act in concert with Gle1, are also required for Ssn2/Med13 clearance. Ssn2/Med13 is retrieved from the nuclear periphery and degraded by Atg17-initiated phagophores anchored to the vacuole. Efficient transfer to phagophores depends on the sorting nexin heterodimer Snx4/Atg24-Atg20, which binds to Atg17, and relocates to the perinucleus following nitrogen starvation. To conclude, this pathway defines a previously undescribed autophagy mechanism that targets select transcriptional regulators for rapid vacuolar proteolysis, utilizing the RNA remodeling complex, the sorting nexin heterodimer Snx4-Atg20, Atg17, and the core autophagic machinery. It is physiologically relevant as this Snx4-assisted vacuolar targeting pathway permits cells to fine-tune the autophagic response by controlling the turnover of both positive and negative regulators of ATG transcription.Abbreviations: AIM: Atg8 interacting motif; ATG: autophagy-related; CKM: CDK8 kinase module; IDR: intrinsically disordered region; IP6: phosphoinositide inositol hexaphosphate; NPC: nuclear pore complex; PAS: phagophore assembly site; UPS: ubiquitin-proteasomal system.
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Affiliation(s)
- Sara E. Hanley
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, USA
| | - Stephen D. Willis
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, USA
| | - Katrina F. Cooper
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, USA
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Cdk8 Kinase Module: A Mediator of Life and Death Decisions in Times of Stress. Microorganisms 2021; 9:microorganisms9102152. [PMID: 34683473 PMCID: PMC8540245 DOI: 10.3390/microorganisms9102152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 01/18/2023] Open
Abstract
The Cdk8 kinase module (CKM) of the multi-subunit mediator complex plays an essential role in cell fate decisions in response to different environmental cues. In the budding yeast S. cerevisiae, the CKM consists of four conserved subunits (cyclin C and its cognate cyclin-dependent kinase Cdk8, Med13, and Med12) and predominantly negatively regulates a subset of stress responsive genes (SRG’s). Derepression of these SRG’s is accomplished by disassociating the CKM from the mediator, thus allowing RNA polymerase II-directed transcription. In response to cell death stimuli, cyclin C translocates to the mitochondria where it induces mitochondrial hyper-fission and promotes regulated cell death (RCD). The nuclear release of cyclin C requires Med13 destruction by the ubiquitin-proteasome system (UPS). In contrast, to protect the cell from RCD following SRG induction induced by nutrient deprivation, cyclin C is rapidly destroyed by the UPS before it reaches the cytoplasm. This enables a survival response by two mechanisms: increased ATP production by retaining reticular mitochondrial morphology and relieving CKM-mediated repression on autophagy genes. Intriguingly, nitrogen starvation also stimulates Med13 destruction but through a different mechanism. Rather than destruction via the UPS, Med13 proteolysis occurs in the vacuole (yeast lysosome) via a newly identified Snx4-assisted autophagy pathway. Taken together, these findings reveal that the CKM regulates cell fate decisions by both transcriptional and non-transcriptional mechanisms, placing it at a convergence point between cell death and cell survival pathways.
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30
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Kervin TA, Wiseman BC, Overduin M. Phosphoinositide Recognition Sites Are Blocked by Metabolite Attachment. Front Cell Dev Biol 2021; 9:690461. [PMID: 34368138 PMCID: PMC8340361 DOI: 10.3389/fcell.2021.690461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/18/2021] [Indexed: 12/16/2022] Open
Abstract
Membrane readers take part in trafficking and signaling processes by localizing proteins to organelle surfaces and transducing molecular information. They accomplish this by engaging phosphoinositides (PIs), a class of lipid molecules which are found in different proportions in various cellular membranes. The prototypes are the PX domains, which exhibit a range of specificities for PIs. Our meta-analysis indicates that recognition of membranes by PX domains is specifically controlled by modification of lysine and arginine residues including acetylation, hydroxyisobutyrylation, glycation, malonylation, methylation and succinylation of sidechains that normally bind headgroups of phospholipids including organelle-specific PI signals. Such metabolite-modulated residues in lipid binding elements are named MET-stops here to highlight their roles as erasers of membrane reader functions. These modifications are concentrated in the membrane binding sites of half of all 49 PX domains in the human proteome and correlate with phosphoregulatory sites, as mapped using the Membrane Optimal Docking Area (MODA) algorithm. As these motifs are mutated and modified in various cancers and the responsible enzymes serve as potential drug targets, the discovery of MET-stops as a widespread inhibitory mechanism may aid in the development of diagnostics and therapeutics aimed at the readers, writers and erasers of the PI code.
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Affiliation(s)
- Troy A Kervin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Brittany C Wiseman
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.,Molecular and Cellular Biology, MacEwan University, Edmonton, AB, Canada.,SMALP Network, Edmonton, AB, Canada
| | - Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.,SMALP Network, Edmonton, AB, Canada
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Nazarko TY. Special Issue on "Ubiquitin and Autophagy". Cells 2021; 10:cells10010116. [PMID: 33435134 PMCID: PMC7827787 DOI: 10.3390/cells10010116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 01/05/2021] [Indexed: 11/16/2022] Open
Affiliation(s)
- Taras Y Nazarko
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
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