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Li X, Xiang C, Zhu S, Guo J, Liu C, Wang A, Cao J, Lu Y, Neculai D, Xu P, Feng XH. SNX8 enables lysosome reformation and reverses lysosomal storage disorder. Nat Commun 2024; 15:2553. [PMID: 38519472 PMCID: PMC10959956 DOI: 10.1038/s41467-024-46705-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/06/2024] [Indexed: 03/25/2024] Open
Abstract
Lysosomal Storage Disorders (LSDs), which share common phenotypes, including enlarged lysosomes and defective lysosomal storage, are caused by mutations in lysosome-related genes. Although gene therapies and enzyme replacement therapies have been explored, there are currently no effective routine therapies against LSDs. During lysosome reformation, which occurs when the functional lysosome pool is reduced, lysosomal lipids and proteins are recycled to restore lysosome functions. Here we report that the sorting nexin protein SNX8 promotes lysosome tubulation, a process that is required for lysosome reformation, and that loss of SNX8 leads to phenotypes characteristic of LSDs in human cells. SNX8 overexpression rescued features of LSDs in cells, and AAV-based delivery of SNX8 to the brain rescued LSD phenotypes in mice. Importantly, by screening a natural compound library, we identified three small molecules that enhanced SNX8-lysosome binding and reversed LSD phenotypes in human cells and in mice. Altogether, our results provide a potential solution for the treatment of LSDs.
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Affiliation(s)
- Xinran Li
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, Zhejiang, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, 321000, Shaoxing, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, 311200, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Cong Xiang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, Zhejiang, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, 321000, Shaoxing, Zhejiang, China
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Shilei Zhu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, Zhejiang, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, 321000, Shaoxing, Zhejiang, China
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Jiansheng Guo
- Center of Cryo-Electron Microscopy, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chang Liu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, Zhejiang, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, 321000, Shaoxing, Zhejiang, China
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Ailian Wang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, Zhejiang, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, 321000, Shaoxing, Zhejiang, China
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Jin Cao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, Zhejiang, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, 321000, Shaoxing, Zhejiang, China
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Yan Lu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China
- Department of Cell Biology, and Department of General Surgery of Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dante Neculai
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China
- Department of Cell Biology, and Department of General Surgery of Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Pinglong Xu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, Zhejiang, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, 321000, Shaoxing, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, 311200, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Xin-Hua Feng
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, 321000, Shaoxing, Zhejiang, China.
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
- The Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China.
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Fung KYY, Ho TWW, Xu Z, Neculai D, Beauchemin CAA, Lee WL, Fairn GD. Apolipoprotein A1 and high-density lipoprotein limit low-density lipoprotein transcytosis by binding SR-B1. J Lipid Res 2024; 65:100530. [PMID: 38479648 PMCID: PMC11004410 DOI: 10.1016/j.jlr.2024.100530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 04/09/2024] Open
Abstract
Atherosclerosis results from the deposition and oxidation of LDL and immune cell infiltration in the sub-arterial space leading to arterial occlusion. Studies have shown that transcytosis transports circulating LDL across endothelial cells lining blood vessels. LDL transcytosis is initiated by binding to either scavenger receptor B1 (SR-B1) or activin A receptor-like kinase 1 on the apical side of endothelial cells leading to its transit and release on the basolateral side. HDL is thought to partly protect individuals from atherosclerosis due to its ability to remove excess cholesterol and act as an antioxidant. Apolipoprotein A1 (APOA1), an HDL constituent, can bind to SR-B1, raising the possibility that APOA1/HDL can compete with LDL for SR-B1 binding, thereby limiting LDL deposition in the sub-arterial space. To examine this possibility, we used in vitro approaches to quantify the internalization and transcytosis of fluorescent LDL in coronary endothelial cells. Using microscale thermophoresis and affinity capture, we find that SR-B1 and APOA1 interact and that binding is enhanced when using the cardioprotective variant of APOA1 termed Milano (APOA1-Milano). In male mice, transiently increasing the levels of HDL reduced the acute deposition of fluorescently labeled LDL in the atheroprone inner curvature of the aorta. Reduced LDL deposition was also observed when increasing circulating wild-type APOA1 or the APOA1-Milano variant, with a more robust inhibition from the APOA1-Milano. The results suggest that HDL may limit SR-B1-mediated LDL transcytosis and deposition, adding to the mechanisms by which it can act as an atheroprotective particle.
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Affiliation(s)
- Karen Y Y Fung
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Keenan Research Centre, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Tse Wing Winnie Ho
- Keenan Research Centre, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Zizhen Xu
- Department of Cell Biology, and Department of Pathology Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dante Neculai
- Department of Cell Biology, and Department of Pathology Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Catherine A A Beauchemin
- Department of Physics, Toronto Metropolitan University, Toronto, Ontario, Canada; Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS) program, RIKEN, Wako, Saitama, Japan
| | - Warren L Lee
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Keenan Research Centre, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Interdepartmental Division of Critical Care Medicine, University of Toronto, Toronto, Ontario, Canada.
| | - Gregory D Fairn
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Keenan Research Centre, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada.
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3
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Chen Y, Chen H, Wang Y, Liu F, Fan X, Shi C, Su X, Tan M, Yang Y, Lin B, Lei K, Qu L, Yang J, Zhu Z, Yuan Z, Xie S, Sun Q, Neculai D, Liu W, Yan Q, Wang X, Shao J, Liu J, Lin A. LncRNA LINK-A Remodels Tissue Inflammatory Microenvironments to Promote Obesity. Adv Sci (Weinh) 2024; 11:e2303341. [PMID: 38145352 PMCID: PMC10933663 DOI: 10.1002/advs.202303341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/09/2023] [Indexed: 12/26/2023]
Abstract
High-fat diet (HFD)-induced obesity is a crucial risk factor for metabolic syndrome, mainly due to adipose tissue dysfunctions associated with it. However, the underlying mechanism remains unclear. This study has used genetic screening to identify an obesity-associated human lncRNA LINK-A as a critical molecule bridging the metabolic microenvironment and energy expenditure in vivo by establishing the HFD-induced obesity knock-in (KI) mouse model. Mechanistically, HFD LINK-A KI mice induce the infiltration of inflammatory factors, including IL-1β and CXCL16, through the LINK-A/HB-EGF/HIF1α feedback loop axis in a self-amplified manner, thereby promoting the adipose tissue microenvironment remodeling and adaptive thermogenesis disorder, ultimately leading to obesity and insulin resistance. Notably, LINK-A expression is positively correlated with inflammatory factor expression in individuals who are overweight. Of note, targeting LINK-A via nucleic acid drug antisense oligonucleotides (ASO) attenuate HFD-induced obesity and metabolic syndrome, pointing out LINK-A as a valuable and effective therapeutic target for treating HFD-induced obesity. Briefly, the results reveale the roles of lncRNAs (such as LINK-A) in remodeling tissue inflammatory microenvironments to promote HFD-induced obesity.
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Affiliation(s)
- Yu Chen
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Hui Chen
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Ying Wang
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Fangzhou Liu
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Xiao Fan
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Chengyu Shi
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Xinwan Su
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Manman Tan
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Yebin Yang
- The Fourth School of Clinical MedicineZhejiang Chinese Medical UniversityHangzhouZhejiang310053China
| | - Bangxing Lin
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang ProvinceAffiliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhouZhejiang310006China
| | - Kai Lei
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Lei Qu
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Jiecheng Yang
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Zhipeng Zhu
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Zengzhuang Yuan
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute)University School of MedicineInternational CampusZhejiang UniversityHainingZhejiang314400China
| | - Shanshan Xie
- The Children's HospitalNational Clinical Research Center for Child HealthZhejiang University School of MedicineHangzhouZhejiang310003China
- Department of Cell BiologyZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Qinming Sun
- Department of BiochemistryDepartment of Cardiology of Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang313000China
- International School of MedicineInternational Institutes of MedicineThe 4th Affiliated Hospital of Zhejiang University School of MedicineYiwuZhejiang322000China
| | - Dante Neculai
- International School of MedicineInternational Institutes of MedicineThe 4th Affiliated Hospital of Zhejiang University School of MedicineYiwuZhejiang322000China
- Department of Cell BiologyDepartment of General Surgery of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouZhejiang310016China
| | - Wei Liu
- Department of BiochemistryDepartment of Cardiology of Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang313000China
- International School of MedicineInternational Institutes of MedicineThe 4th Affiliated Hospital of Zhejiang University School of MedicineYiwuZhejiang322000China
| | - Qingfeng Yan
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Xiang Wang
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang ProvinceAffiliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhouZhejiang310006China
- Department of Central LaboratoryThe First People's Hospital of HuzhouHuzhouZhejiang313000China
| | - Jianzhong Shao
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Jian Liu
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute)University School of MedicineInternational CampusZhejiang UniversityHainingZhejiang314400China
- Cancer CenterZhejiang UniversityHangzhouZhejiang310058China
- Hangzhou Cancer InstitutionAffiliated Hangzhou Cancer HospitalZhejiang University School of MedicineZhejiang UniversityHangzhouZhejiang310002China
- College of Medicine and Veterinary MedicineThe University of EdinburghEdinburghEH16 4SBUK
| | - Aifu Lin
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
- International School of MedicineInternational Institutes of MedicineThe 4th Affiliated Hospital of Zhejiang University School of MedicineYiwuZhejiang322000China
- Cancer CenterZhejiang UniversityHangzhouZhejiang310058China
- Key Laboratory for Cell and Gene Engineering of Zhejiang ProvinceHangzhouZhejiang310058China
- Future Health LaboratoryInnovation Center of Yangtze River DeltaZhejiang UniversityJiaxingZhejiang314100China
- Key Laboratory of Cancer Prevention and InterventionChina National Ministry of EducationHangzhouZhejiang310009China
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4
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Wang A, Chen C, Mei C, Liu S, Xiang C, Fang W, Zhang F, Xu Y, Chen S, Zhang Q, Bai X, Lin A, Neculai D, Xia B, Ye C, Zou J, Liang T, Feng XH, Li X, Shen C, Xu P. Innate immune sensing of lysosomal dysfunction drives multiple lysosomal storage disorders. Nat Cell Biol 2024; 26:219-234. [PMID: 38253667 DOI: 10.1038/s41556-023-01339-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/15/2023] [Indexed: 01/24/2024]
Abstract
Lysosomal storage disorders (LSDs), which are characterized by genetic and metabolic lysosomal dysfunctions, constitute over 60 degenerative diseases with considerable health and economic burdens. However, the mechanisms driving the progressive death of functional cells due to lysosomal defects remain incompletely understood, and broad-spectrum therapeutics against LSDs are lacking. Here, we found that various gene abnormalities that cause LSDs, including Hexb, Gla, Npc1, Ctsd and Gba, all shared mutual properties to robustly autoactivate neuron-intrinsic cGAS-STING signalling, driving neuronal death and disease progression. This signalling was triggered by excessive cytoplasmic congregation of the dsDNA and DNA sensor cGAS in neurons. Genetic ablation of cGAS or STING, digestion of neuronal cytosolic dsDNA by DNase, and repair of neuronal lysosomal dysfunction alleviated symptoms of Sandhoff disease, Fabry disease and Niemann-Pick disease, with substantially reduced neuronal loss. We therefore identify a ubiquitous mechanism mediating the pathogenesis of a variety of LSDs, unveil an inherent connection between lysosomal defects and innate immunity, and suggest a uniform strategy for curing LSDs.
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Affiliation(s)
- Ailian Wang
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Institute of Intelligent Medicine, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, University School of Medicine, Zhejiang University, Hangzhou, China
| | - Chen Chen
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Chen Mei
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Institute of Intelligent Medicine, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, University School of Medicine, Zhejiang University, Hangzhou, China
| | - Shengduo Liu
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Institute of Intelligent Medicine, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Cong Xiang
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Wen Fang
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Fei Zhang
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, University School of Medicine, Zhejiang University, Hangzhou, China
| | - Yifan Xu
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Shasha Chen
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, University School of Medicine, Zhejiang University, Hangzhou, China
| | - Xueli Bai
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, University School of Medicine, Zhejiang University, Hangzhou, China
| | - Aifu Lin
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Dante Neculai
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Bing Xia
- Department of Thoracic Cancer, Affiliated Hangzhou Cancer Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Cunqi Ye
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jian Zou
- Eye Center of the Second Affiliated Hospital, Institutes of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, University School of Medicine, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Xin-Hua Feng
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Xinran Li
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
- Institute of Intelligent Medicine, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China.
| | - Chengyong Shen
- Department of Neurobiology of The First Affiliated Hospital, Institute of Translational Medicine, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Medicine, Zhejiang University, Hangzhou, China.
| | - Pinglong Xu
- MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
- Institute of Intelligent Medicine, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China.
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, University School of Medicine, Zhejiang University, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
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5
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Zhang G, Jiang P, Tang W, Wang Y, Qiu F, An J, Zheng Y, Wu D, Zhou J, Neculai D, Shi Y, Sheng W. CPT1A induction following epigenetic perturbation promotes MAVS palmitoylation and activation to potentiate antitumor immunity. Mol Cell 2023; 83:4370-4385.e9. [PMID: 38016475 DOI: 10.1016/j.molcel.2023.10.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/31/2023] [Accepted: 10/31/2023] [Indexed: 11/30/2023]
Abstract
Targeting epigenetic regulators to potentiate anti-PD-1 immunotherapy converges on the activation of type I interferon (IFN-I) response, mimicking cellular response to viral infection, but how its strength and duration are regulated to impact combination therapy efficacy remains largely unknown. Here, we show that mitochondrial CPT1A downregulation following viral infection restrains, while its induction by epigenetic perturbations sustains, a double-stranded RNA-activated IFN-I response. Mechanistically, CPT1A recruits the endoplasmic reticulum-localized ZDHHC4 to catalyze MAVS Cys79-palmitoylation, which promotes MAVS stabilization and activation by inhibiting K48- but facilitating K63-linked ubiquitination. Further elevation of CPT1A incrementally increases MAVS palmitoylation and amplifies the IFN-I response, which enhances control of viral infection and epigenetic perturbation-induced antitumor immunity. Moreover, CPT1A chemical inducers augment the therapeutic effect of combined epigenetic treatment with PD-1 blockade in refractory tumors. Our study identifies CPT1A as a stabilizer of MAVS activation, and its link to epigenetic perturbation can be exploited for cancer immunotherapy.
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Affiliation(s)
- Guiheng Zhang
- Institute of Immunology, and Department of Respiratory Disease of The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, Zhejiang, China
| | - Peishan Jiang
- Institute of Immunology, and Department of Respiratory Disease of The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, Zhejiang, China
| | - Wen Tang
- Department of Human Anatomy, Histology and Embryology, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China
| | - Yunyi Wang
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX3 7DQ, UK
| | - Fengqi Qiu
- Department of Respiratory Disease of The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang, China
| | - Jie An
- Institute of Immunology, and Department of Respiratory Disease of The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, Zhejiang, China
| | - Yuping Zheng
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu 322000, Zhejiang, China
| | - Dandan Wu
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu 322000, Zhejiang, China
| | - Jianya Zhou
- Department of Respiratory Disease of The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang, China
| | - Dante Neculai
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu 322000, Zhejiang, China
| | - Yang Shi
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX3 7DQ, UK.
| | - Wanqiang Sheng
- Institute of Immunology, and Department of Respiratory Disease of The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, Zhejiang, China.
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6
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Huang X, Yao J, Liu L, Chen J, Mei L, Huangfu J, Luo D, Wang X, Lin C, Chen X, Yang Y, Ouyang S, Wei F, Wang Z, Zhang S, Xiang T, Neculai D, Sun Q, Kong E, Tate EW, Yang A. S-acylation of p62 promotes p62 droplet recruitment into autophagosomes in mammalian autophagy. Mol Cell 2023; 83:3485-3501.e11. [PMID: 37802024 PMCID: PMC10552648 DOI: 10.1016/j.molcel.2023.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 06/22/2023] [Accepted: 09/07/2023] [Indexed: 10/08/2023]
Abstract
p62 is a well-characterized autophagy receptor that recognizes and sequesters specific cargoes into autophagosomes for degradation. p62 promotes the assembly and removal of ubiquitinated proteins by forming p62-liquid droplets. However, it remains unclear how autophagosomes efficiently sequester p62 droplets. Herein, we report that p62 undergoes reversible S-acylation in multiple human-, rat-, and mouse-derived cell lines, catalyzed by zinc-finger Asp-His-His-Cys S-acyltransferase 19 (ZDHHC19) and deacylated by acyl protein thioesterase 1 (APT1). S-acylation of p62 enhances the affinity of p62 for microtubule-associated protein 1 light chain 3 (LC3)-positive membranes and promotes autophagic membrane localization of p62 droplets, thereby leading to the production of small LC3-positive p62 droplets and efficient autophagic degradation of p62-cargo complexes. Specifically, increasing p62 acylation by upregulating ZDHHC19 or by genetic knockout of APT1 accelerates p62 degradation and p62-mediated autophagic clearance of ubiquitinated proteins. Thus, the protein S-acylation-deacylation cycle regulates p62 droplet recruitment to the autophagic membrane and selective autophagic flux, thereby contributing to the control of selective autophagic clearance of ubiquitinated proteins.
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Affiliation(s)
- Xue Huang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Jia Yao
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Lu Liu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Jing Chen
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ligang Mei
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Jingjing Huangfu
- Institute of Psychiatry and Neuroscience, Xinxiang Key Laboratory of Protein Palmitoylation and Major Human Diseases, Xinxiang Medical University, Xinxiang, China
| | - Dong Luo
- School of Pharmacy, Chongqing University, Chongqing 401331, China
| | - Xinyi Wang
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China; Department of Biochemistry and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Changhai Lin
- School of Life Sciences, Chongqing University, Chongqing 401331, China; Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Xiaorong Chen
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Yi Yang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Sheng Ouyang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Fujing Wei
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Zhuolin Wang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Shaolin Zhang
- School of Pharmacy, Chongqing University, Chongqing 401331, China
| | - Tingxiu Xiang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Dante Neculai
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Qiming Sun
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China; Department of Biochemistry and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Eryan Kong
- Institute of Psychiatry and Neuroscience, Xinxiang Key Laboratory of Protein Palmitoylation and Major Human Diseases, Xinxiang Medical University, Xinxiang, China
| | - Edward W Tate
- Department of Chemistry, Imperial College London, 82 Wood Lane, London W12 0BZ, UK
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing 401331, China.
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7
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Pu M, Zheng W, Zhang H, Wan W, Peng C, Chen X, Liu X, Xu Z, Zhou T, Sun Q, Neculai D, Liu W. ORP8 acts as a lipophagy receptor to mediate lipid droplet turnover. Protein Cell 2023; 14:653-667. [PMID: 37707322 PMCID: PMC10501187 DOI: 10.1093/procel/pwac063] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/22/2022] [Indexed: 09/15/2023] Open
Abstract
Lipophagy, the selective engulfment of lipid droplets (LDs) by autophagosomes for lysosomal degradation, is critical to lipid and energy homeostasis. Here we show that the lipid transfer protein ORP8 is located on LDs and mediates the encapsulation of LDs by autophagosomal membranes. This function of ORP8 is independent of its lipid transporter activity and is achieved through direct interaction with phagophore-anchored LC3/GABARAPs. Upon lipophagy induction, ORP8 has increased localization on LDs and is phosphorylated by AMPK, thereby enhancing its affinity for LC3/GABARAPs. Deletion of ORP8 or interruption of ORP8-LC3/GABARAP interaction results in accumulation of LDs and increased intracellular triglyceride. Overexpression of ORP8 alleviates LD and triglyceride deposition in the liver of ob/ob mice, and Osbpl8-/- mice exhibit liver lipid clearance defects. Our results suggest that ORP8 is a lipophagy receptor that plays a key role in cellular lipid metabolism.
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Affiliation(s)
- Maomao Pu
- Metabolic Medicine Center, International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Wenhui Zheng
- Metabolic Medicine Center, International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Hongtao Zhang
- Metabolic Medicine Center, International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Wei Wan
- Metabolic Medicine Center, International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Chao Peng
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xuebo Chen
- Metabolic Medicine Center, International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Xinchang Liu
- Metabolic Medicine Center, International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Zizhen Xu
- Metabolic Medicine Center, International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Tianhua Zhou
- Metabolic Medicine Center, International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Qiming Sun
- Metabolic Medicine Center, International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Dante Neculai
- Metabolic Medicine Center, International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Wei Liu
- Metabolic Medicine Center, International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
- Joint Institute of Genetics and Genomics Medicine between Zhejiang University and University of Toronto, Hangzhou 310058, China
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8
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Wang X, Jiang X, Li B, Zheng J, Guo J, Gao L, Du M, Weng X, Li L, Chen S, Zhang J, Fang L, Liu T, Wang L, Liu W, Neculai D, Sun Q. A regulatory circuit comprising the CBP and SIRT7 regulates FAM134B-mediated ER-phagy. J Cell Biol 2023; 222:e202201068. [PMID: 37043189 PMCID: PMC10103787 DOI: 10.1083/jcb.202201068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 11/14/2022] [Accepted: 02/21/2023] [Indexed: 04/13/2023] Open
Abstract
Macroautophagy (autophagy) utilizes a serial of receptors to specifically recognize and degrade autophagy cargoes, including damaged organelles, to maintain cellular homeostasis. Upstream signals spatiotemporally regulate the biological functions of selective autophagy receptors through protein post-translational modifications (PTM) such as phosphorylation. However, it is unclear how acetylation directly controls autophagy receptors in selective autophagy. Here, we report that an ER-phagy receptor FAM134B is acetylated by CBP acetyltransferase, eliciting intense ER-phagy. Furthermore, FAM134B acetylation promoted CAMKII-mediated phosphorylation to sustain a mode of milder ER-phagy. Conversely, SIRT7 deacetylated FAM134B to temper its activities in ER-phagy to avoid excessive ER degradation. Together, this work provides further mechanistic insights into how ER-phagy receptor perceives environmental signals for fine-tuning of ER homeostasis and demonstrates how nucleus-derived factors are programmed to control ER stress by modulating ER-phagy.
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Affiliation(s)
- Xinyi Wang
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang UniversitySchool of Medicine, Hangzhou, China
| | - Xiao Jiang
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang UniversitySchool of Medicine, Hangzhou, China
| | - Boran Li
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang UniversitySchool of Medicine, Hangzhou, China
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang UniversitySchool of Medicine, Yiwu, China
| | - Jiahua Zheng
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang UniversitySchool of Medicine, Hangzhou, China
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang UniversitySchool of Medicine, Yiwu, China
| | - Jiansheng Guo
- Center of Cryo-Electron Microscopy, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lei Gao
- Microscopy Core Facility, Westlake University, Hangzhou, China
| | - Mengjie Du
- Department of Neurology of Second Affiliated Hospital, Institute of Neuroscience, Mental Health Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang UniversitySchool of Medicine, Hangzhou, China
| | - Xialian Weng
- Department of Cell Biology, Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang UniversitySchool of Medicine, Hangzhou, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, Beijing, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, Beijing, China
| | - Jingzi Zhang
- Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing, China
| | - Lei Fang
- Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing, China
| | - Ting Liu
- Department of Cell Biology, Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang UniversitySchool of Medicine, Hangzhou, China
| | - Liang Wang
- Department of Neurology of Second Affiliated Hospital, Institute of Neuroscience, Mental Health Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang UniversitySchool of Medicine, Hangzhou, China
| | - Wei Liu
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang UniversitySchool of Medicine, Hangzhou, China
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang UniversitySchool of Medicine, Yiwu, China
| | - Dante Neculai
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang UniversitySchool of Medicine, Yiwu, China
- Department of Cell Biology, Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang UniversitySchool of Medicine, Hangzhou, China
| | - Qiming Sun
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang UniversitySchool of Medicine, Hangzhou, China
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang UniversitySchool of Medicine, Yiwu, China
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9
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Zhang F, Xu LD, Zhang Q, Wang A, Yu X, Liu S, Chen C, Wu S, Jin J, Lin A, Neculai D, Zhao B, Feng XH, Liang T, Xu P, Huang YW. Targeting proteostasis of the HEV replicase to combat infection in preclinical models. J Hepatol 2023; 78:704-716. [PMID: 36574921 DOI: 10.1016/j.jhep.2022.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/15/2022] [Accepted: 12/06/2022] [Indexed: 12/25/2022]
Abstract
BACKGROUND & AIMS Appropriate treatment options are lacking for hepatitis E virus (HEV)-infected pregnant women and immunocompromised individuals. Thus, we aimed to identify efficient anti-HEV drugs through high-throughput screening, validate them in vitro and in vivo (in a preclinical animal study), and elucidate their underlying antiviral mechanism of action. METHODS Using appropriate cellular and rodent HEV infection models, we studied a critical pathway for host-HEV interactions and performed a preclinical study of the corresponding antivirals, which target proteostasis of the HEV replicase. RESULTS We found 17 inhibitors that target HEV-HSP90 interactions by unbiased compound library screening on human hepatocytes harboring an HEV replicon. Inhibitors of HSP90 (iHSP90) markedly suppressed HEV replication with efficacy exceeding that of conventional antivirals (IFNα and ribavirin) in vitro. Mechanistically, iHSP90 treatment released the viral replicase ORF1 protein from the ORF1-HSP90 complex and triggered rapid ubiquitin/proteasome-mediated degradation of ORF1, resulting in abrogated HEV replication. Furthermore, a preclinical trial in a Mongolian gerbil HEV infection model showed this novel anti-HEV strategy to be safe, efficient, and able to prevent HEV-induced liver damage. CONCLUSIONS In this study, we uncover a proteostatic pathway that is critical for host-HEV interactions and we provide a foundation from which to translate this new understanding of the HEV life cycle into clinically promising antivirals. IMPACT AND IMPLICATIONS Appropriate treatment options for hepatitis E virus (HEV)-infected pregnant women and immunocompromised patients are lacking; hence, there is an urgent need for safe and effective HEV-specific therapies. This study identified new antivirals (inhibitors of HSP90) that significantly limit HEV infection by targeting the viral replicase for degradation. Moreover, these anti-HEV drugs were validated in an HEV rodent model and were found to be safe and efficient for prevention of HEV-induced liver injury in preclinical experiments. Our findings substantially promote the understanding of HEV pathobiology and pave the way for antiviral development.
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Affiliation(s)
- Fei Zhang
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China; MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Ling-Dong Xu
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China; MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Qian Zhang
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China; MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Ailian Wang
- MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Xinyuan Yu
- MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Shengduo Liu
- MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Chu Chen
- Zhejiang University-Hangzhou Global Scientific and Technological Innovation Center (ZJU-HIC), Hangzhou, 310058, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Shiying Wu
- MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Jianping Jin
- MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Aifu Lin
- MOE Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dante Neculai
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Bin Zhao
- MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Xin-Hua Feng
- MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China.
| | - Pinglong Xu
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China; MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China.
| | - Yao-Wei Huang
- Zhejiang University-Hangzhou Global Scientific and Technological Innovation Center (ZJU-HIC), Hangzhou, 310058, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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10
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Luo Y, Zong Y, Hua H, Gong M, Peng Q, Li C, Neculai D, Zeng X. Immune-infiltrating signature-based classification reveals CD103 +CD39 + T cells associate with colorectal cancer prognosis and response to immunotherapy. Front Immunol 2022; 13:1011590. [PMID: 36311750 PMCID: PMC9596778 DOI: 10.3389/fimmu.2022.1011590] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/26/2022] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND Current stratification systems for tumor prognostic prediction and immunotherapeutic efficacy evaluation are less satisfying in colorectal cancer (CRC). As infiltrating immune cells in tumor microenvironment (TME) played a key role in tumor progression and responses to immune checkpoint blockade (ICB) therapy, we want to construct an immune-related scoring system with detailed immune profiles to stratify CRC patients. METHODS We developed a scoring system based on immune-related signatures and validated its ability to predict prognosis and immunotherapeutic outcomes in CRC. CD45+ cells from CRC patients were sorted to investigate detailed immune profiles of the stratification system using mass cytometry. A single-cell RNA sequencing dataset was used to analyze transcriptomic profiles. RESULTS We constructed an immune-related signature score (IRScore) based on 54 recurrence-free survival (RFS)-related immune signatures to stratify CRC patients. We revealed that IRScore was positively correlated with RFS and favorable outcomes in ICB treatment. Moreover, we depicted a detailed immune profile in TME using mass cytometry and identified that CD103+CD39+ T cells, characterized by an exhaustive, cytotoxic and proliferative phenotype, were enriched in CRC patients with high IRScore. As a beneficial immune signature, CD103+CD39+ T cells could predict prognosis and responses to ICB therapy in CRC. CONCLUSIONS All the analyses above revealed that IRScore could be a valuable tool for predicting prognosis and facilitating the development of new therapeutic strategies in CRC, and CD103+CD39+ T cells were one of defined immune signatures in IRScore, which might be a key factor for antitumor immunity.
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Affiliation(s)
- Yang Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Cell Biology, Department of Pathology Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunfeng Zong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Research Units of Infectious disease and Microecology, Chinese Academy of Medical Sciences, Hangzhou, China
| | - Hanju Hua
- Colorectal Surgery Department, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Meiting Gong
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Qiao Peng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Research Units of Infectious disease and Microecology, Chinese Academy of Medical Sciences, Hangzhou, China
| | - Chen Li
- Department of Human Genetics, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, China
| | - Dante Neculai
- Department of Cell Biology, Department of Pathology Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xun Zeng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Research Units of Infectious disease and Microecology, Chinese Academy of Medical Sciences, Hangzhou, China
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11
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Zhu K, Jin X, Chi Z, Chen S, Wu S, Sloan RD, Lin X, Neculai D, Wang D, Hu H, Lu L. Priming of NLRP3 inflammasome activation by Msn kinase MINK1 in macrophages. Cell Mol Immunol 2021; 18:2372-2382. [PMID: 34480147 PMCID: PMC8414466 DOI: 10.1038/s41423-021-00761-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/08/2021] [Indexed: 02/07/2023] Open
Abstract
The nucleotide-binding domain, leucine-rich-repeat containing family, pyrin domain-containing 3 (NLRP3) inflammasome is essential in inflammation and inflammatory disorders. Phosphorylation at various sites on NLRP3 differentially regulates inflammasome activation. The Ser725 phosphorylation site on NLRP3 is depicted in multiple inflammasome activation scenarios, but the importance and regulation of this site has not been clarified. The present study revealed that the phosphorylation of Ser725 was an essential step for the priming of the NLRP3 inflammasome in macrophages. We also showed that Ser725 was directly phosphorylated by misshapen (Msn)/NIK-related kinase 1 (MINK1), depending on the direct interaction between MINK1 and the NLRP3 LRR domain. MINK1 deficiency reduced NLRP3 activation and suppressed inflammatory responses in mouse models of acute sepsis and peritonitis. Reactive oxygen species (ROS) upregulated the kinase activity of MINK1 and subsequently promoted inflammasome priming via NLRP3 Ser725 phosphorylation. Eliminating ROS suppressed NLRP3 activation and reduced sepsis and peritonitis symptoms in a MINK1-dependent manner. Altogether, our study reveals a direct regulation of the NLRP3 inflammasome by Msn family kinase MINK1 and suggests that modulation of MINK1 activity is a potential intervention strategy for inflammasome-related diseases.
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Affiliation(s)
- Kaixiang Zhu
- grid.13402.340000 0004 1759 700XInstitute of Immunology and Department of Rheumatology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 P. R. China ,grid.13402.340000 0004 1759 700XZhejiang University–University of Edinburgh Institute, Zhejiang University School of Medicine, Haining, 314400 P. R. China ,grid.13402.340000 0004 1759 700XDepartment of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, 310058 P. R. China
| | - Xuexiao Jin
- grid.13402.340000 0004 1759 700XInstitute of Immunology and Department of Rheumatology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 P. R. China
| | - Zhexu Chi
- grid.13402.340000 0004 1759 700XDepartment of Immunology, Zhejiang University School of Medicine, Hangzhou, 310058 P. R. China
| | - Sheng Chen
- grid.13402.340000 0004 1759 700XDepartment of Immunology, Zhejiang University School of Medicine, Hangzhou, 310058 P. R. China ,grid.412465.0Department of Colorectal Surgery, The Second Affiliated Hospital, Hangzhou, 310058 P. R. China
| | - Songquan Wu
- grid.440824.e0000 0004 1757 6428Medical College, Lishui University, Lishui, 323000 P. R. China
| | - Richard D. Sloan
- grid.13402.340000 0004 1759 700XZhejiang University–University of Edinburgh Institute, Zhejiang University School of Medicine, Haining, 314400 P. R. China ,grid.4305.20000 0004 1936 7988Infection Medicine, School of Biomedical Sciences, The University of Edinburgh, Edinburgh, EH16 4SB Scotland, UK
| | - Xuai Lin
- grid.13402.340000 0004 1759 700XDepartment of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, 310058 P. R. China
| | - Dante Neculai
- grid.13402.340000 0004 1759 700XDepartment of Cell Biology, Zhejiang University School of Medicine, Hangzhou, 310058 P. R. China
| | - Di Wang
- grid.13402.340000 0004 1759 700XDepartment of Immunology, Zhejiang University School of Medicine, Hangzhou, 310058 P. R. China
| | - Hu Hu
- grid.13402.340000 0004 1759 700XDepartment of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou, 310058 P. R. China
| | - Linrong Lu
- grid.13402.340000 0004 1759 700XInstitute of Immunology and Department of Rheumatology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 P. R. China ,grid.13402.340000 0004 1759 700XZhejiang University–University of Edinburgh Institute, Zhejiang University School of Medicine, Haining, 314400 P. R. China ,grid.13402.340000 0004 1759 700XDr. Li Dak Sum and Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058 P. R. China
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12
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Lu Y, Neculai D. Sphingosine-1-phosphate: The missing link between NOD1/2 and ER stress. EMBO J 2021; 40:e108812. [PMID: 34132411 DOI: 10.15252/embj.2021108812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 05/31/2021] [Indexed: 11/09/2022] Open
Abstract
The cytosolic NOD1 and NOD2 pattern recognition receptors are typically known as sensors of bacterial peptidoglycan fragments. A new study in this issue links NOD1/2 activation with ER homeostasis through the bioactive metabolite sphingosine-1-phosphate (S1P).
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Affiliation(s)
- Yan Lu
- Life Science Institute, Zhejiang University, Hangzhou, China
| | - Dante Neculai
- Department of Cell Biology, Department of Pathology Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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13
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Ying Y, Lu L, Banerjee S, Xu L, Zhao Q, Wu H, Li R, Xu X, Yu H, Neculai D, Xi Y, Yang F, Qin J, Li C. KVarPredDB: a database for predicting pathogenicity of missense sequence variants of keratin genes associated with genodermatoses. Hum Genomics 2020; 14:45. [PMID: 33287903 PMCID: PMC7720490 DOI: 10.1186/s40246-020-00295-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/25/2020] [Indexed: 12/17/2022] Open
Abstract
Background Germline variants of ten keratin genes (K1, K2, K5, K6A, K6B, K9, K10, K14, K16, and K17) have been reported for causing different types of genodermatoses with an autosomal dominant mode of inheritance. Among all the variants of these ten keratin genes, most of them are missense variants. Unlike pathogenic and likely pathogenic variants, understanding the clinical importance of novel missense variants or variants of uncertain significance (VUS) is the biggest challenge for clinicians or medical geneticists. Functional characterization is the only way to understand the clinical association of novel missense variants or VUS but it is time consuming, costly, and depends on the availability of patient’s samples. Existing databases report the pathogenic variants of the keratin genes, but never emphasize the systematic effects of these variants on keratin protein structure and genotype-phenotype correlation. Results To address this need, we developed a comprehensive database KVarPredDB, which contains information of all ten keratin genes associated with genodermatoses. We integrated and curated 400 reported pathogenic missense variants as well as 4629 missense VUS. KVarPredDB predicts the pathogenicity of novel missense variants as well as to understand the severity of disease phenotype, based on four criteria; firstly, the difference in physico-chemical properties between the wild type and substituted amino acids; secondly, the loss of inter/intra-chain interactions; thirdly, evolutionary conservation of the wild type amino acids and lastly, the effect of the substituted amino acids in the heptad repeat. Molecular docking simulations based on resolved crystal structures were adopted to predict stability changes and get the binding energy to compare the wild type protein with the mutated one. We use this basic information to determine the structural and functional impact of novel missense variants on the keratin coiled-coil heterodimer. KVarPredDB was built under the integrative web application development framework SSM (SpringBoot, Spring MVC, MyBatis) and implemented in Java, Bootstrap, React-mutation-mapper, MySQL, Tomcat. The website can be accessed through http://bioinfo.zju.edu.cn/KVarPredDB. The genomic variants and analysis results are freely available under the Creative Commons license. Conclusions KVarPredDB provides an intuitive and user-friendly interface with computational analytical investigation for each missense variant of the keratin genes associated with genodermatoses.
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Affiliation(s)
- Yuyi Ying
- Department of Human Genetics, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Zhejiang University School of Medicine, Hangzhou, China
| | - Lu Lu
- Department of Human Genetics, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Zhejiang University School of Medicine, Hangzhou, China
| | - Santasree Banerjee
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, China
| | - Lizhen Xu
- Department of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiang Zhao
- Department of Human Genetics, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Zhejiang University School of Medicine, Hangzhou, China
| | - Hao Wu
- Department of Human Genetics, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Zhejiang University School of Medicine, Hangzhou, China
| | - Ruiqi Li
- Chu Kochen Honors College, Undergraduate School of Zhejiang University, Hangzhou, China
| | - Xiao Xu
- Department of Human Genetics, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Zhejiang University School of Medicine, Hangzhou, China
| | - Hua Yu
- Department of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Dante Neculai
- Department of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Yongmei Xi
- Department of Human Genetics, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Zhejiang University School of Medicine, Hangzhou, China
| | - Fan Yang
- Department of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiale Qin
- Department of Ultrasound, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Chen Li
- Department of Human Genetics, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Zhejiang University School of Medicine, Hangzhou, China.
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14
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Meng Y, Heybrock S, Neculai D, Saftig P. Cholesterol Handling in Lysosomes and Beyond. Trends Cell Biol 2020; 30:452-466. [PMID: 32413315 DOI: 10.1016/j.tcb.2020.02.007] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/14/2020] [Accepted: 02/21/2020] [Indexed: 01/06/2023]
Abstract
Lysosomes are of major importance for the regulation of cellular cholesterol homeostasis. Food-derived cholesterol and cholesterol esters contained within lipoproteins are delivered to lysosomes by endocytosis. From the lysosomal lumen, cholesterol is transported to the inner surface of the lysosomal membrane through the glycocalyx; this shuttling requires Niemann-Pick C (NPC) 1 and NPC2 proteins. The lysosomal membrane proteins lysosomal-associated membrane protein (LAMP)-2 and lysosomal integral membrane protein (LIMP)-2/SCARB2 also bind cholesterol. LAMP-2 may serve as a cholesterol reservoir, whereas LIMP-2, like NPC1, is able to transport cholesterol through a transglycocalyx tunnel. Contact sites and fusion events between lysosomes and other organelles mediate the distribution of cholesterol. Lysosomal cholesterol content is sensed thereby regulating mammalian target of rapamycin complex (mTORC)-dependent signaling. This review summarizes our understanding of the major steps in cholesterol handling from the moment it enters the lysosome until it leaves this compartment.
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Affiliation(s)
- Ying Meng
- Department of Cell Biology, School of Basic Medical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Saskia Heybrock
- Biochemisches Institut, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Dante Neculai
- Department of Cell Biology, School of Basic Medical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Paul Saftig
- Biochemisches Institut, Christian-Albrechts-Universität Kiel, Kiel, Germany.
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15
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Jiang X, Wang X, Ding X, Du M, Li B, Weng X, Zhang J, Li L, Tian R, Zhu Q, Chen S, Wang L, Liu W, Fang L, Neculai D, Sun Q. FAM134B oligomerization drives endoplasmic reticulum membrane scission for ER-phagy. EMBO J 2020; 39:e102608. [PMID: 31930741 DOI: 10.15252/embj.2019102608] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 11/19/2019] [Accepted: 12/10/2019] [Indexed: 12/30/2022] Open
Abstract
Degradation of endoplasmic reticulum (ER) by selective autophagy (ER-phagy) is crucial for ER homeostasis. However, it remains unclear how ER scission is regulated for subsequent autophagosomal sequestration and lysosomal degradation. Here, we show that oligomerization of ER-phagy receptor FAM134B (also referred to as reticulophagy regulator 1 or RETREG1) through its reticulon-homology domain is required for membrane fragmentation in vitro and ER-phagy in vivo. Under ER-stress conditions, activated CAMK2B phosphorylates the reticulon-homology domain of FAM134B, which enhances FAM134B oligomerization and activity in membrane fragmentation to accommodate high demand for ER-phagy. Unexpectedly, FAM134B G216R, a variant derived from a type II hereditary sensory and autonomic neuropathy (HSAN) patient, exhibits gain-of-function defects, such as hyperactive self-association and membrane scission, which results in excessive ER-phagy and sensory neuron death. Therefore, this study reveals a mechanism of ER membrane fragmentation in ER-phagy, along with a signaling pathway in regulating ER turnover, and suggests a potential implication of excessive selective autophagy in human diseases.
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Affiliation(s)
- Xiao Jiang
- Department of Biochemistry, Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinyi Wang
- Department of Biochemistry, Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xianming Ding
- Department of Biochemistry, Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengjie Du
- Department of Neurology of Second Affiliated Hospital, Institute of Neuroscience, Mental Health Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Boran Li
- Department of Biochemistry, Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xialian Weng
- Department of Cell Biology, Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jingzi Zhang
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, China
| | - Rui Tian
- Department of Biochemistry, Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qi Zhu
- Department of Biochemistry, Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, China
| | - Liang Wang
- Department of Neurology of Second Affiliated Hospital, Institute of Neuroscience, Mental Health Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Liu
- Department of Biochemistry, Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lei Fang
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Dante Neculai
- Department of Cell Biology, Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiming Sun
- Department of Biochemistry, Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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16
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Cabrera A, Neculai D, Tran V, Lavstsen T, Turner L, Kain KC. Plasmodium falciparum-CD36 Structure-Function Relationships Defined by Ortholog Scanning Mutagenesis. J Infect Dis 2020; 219:945-954. [PMID: 30335152 DOI: 10.1093/infdis/jiy607] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/12/2018] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The interaction of Plasmodium falciparum-infected erythrocytes (IEs) with the host receptor CD36 is among the most studied host-parasite interfaces. CD36 is a scavenger receptor that binds numerous ligands including the cysteine-rich interdomain region (CIDR)α domains of the erythrocyte membrane protein 1 family (PfEMP1) expressed on the surface of IEs. CD36 is conserved across species, but orthologs display differential binding of IEs. METHODS In this study, we exploited these differences, combined with the recent crystal structure and 3-dimensional modeling of CD36, to investigate malaria-CD36 structure-function relationships and further define IE-CD36 binding interactions. RESULTS We show that a charged surface in the membrane-distal region of CD36 is necessary for IE binding. Moreover, IE interaction with this binding surface is influenced by additional CD36 domains, both proximal to and at a distance from this site. CONCLUSIONS Our data indicate that subtle sequence and spatial differences in these domains modify receptor conformation and regulate the ability of CD36 to selectively interact with its diverse ligands.
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Affiliation(s)
- Ana Cabrera
- SAR Laboratories, Sandra Rotman Centre, Toronto General Hospital-University Health Network, Ontario, Canada
| | - Dante Neculai
- Department of Cell Biology, Zhejiang University, School of Basic Medical Sciences, Hangzhou, People's Republic of China
| | - Vanessa Tran
- SAR Laboratories, Sandra Rotman Centre, Toronto General Hospital-University Health Network, Ontario, Canada
| | - Thomas Lavstsen
- Centre for Medical Parasitology, Department of International Health, Immunology and Microbiology, University of Copenhagen and Department of Infectious Diseases, Rigshospitalet, Denmark
| | - Louise Turner
- Centre for Medical Parasitology, Department of International Health, Immunology and Microbiology, University of Copenhagen and Department of Infectious Diseases, Rigshospitalet, Denmark
| | - Kevin C Kain
- SAR Laboratories, Sandra Rotman Centre, Toronto General Hospital-University Health Network, Ontario, Canada.,Tropical Disease Unit, Division of Infectious Diseases, Department of Medicine, University of TorontoOntarioCanada
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17
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Lu P, Wang S, Lu Y, Neculai D, Sun Q, van der Veen S. A Subpopulation of Intracellular Neisseria gonorrhoeae Escapes Autophagy-Mediated Killing Inside Epithelial Cells. J Infect Dis 2019; 219:133-144. [PMID: 29688440 DOI: 10.1093/infdis/jiy237] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/19/2018] [Indexed: 11/13/2022] Open
Abstract
The bacterial pathogen Neisseria gonorrhoeae is able to transmigrate across the mucosal epithelia following the intracellular route and cause disseminated infections. It is currently unknown whether the autophagy pathway is able target intracellular N. gonorrhoeae for destruction in autolysosomes or whether this bacterium is able to escape autophagy-mediated killing. In this study, we demonstrate that during the early stage of epithelial cell invasion, N. gonorrhoeae is targeted by the autophagy pathway and sequestered into double-membrane autophagosomes that subsequently fuse with lysosomes for destruction. However, a subpopulation of the intracellular gonococci is able to escape early autophagy-mediated killing. N. gonorrhoeae is subsequently able to inhibit this pathway, allowing intracellular survival and exocytosis. During this stage, N. gonorrhoeae activates the autophagy repressor mammalian target of rapamycin complex 1 and inhibits autophagosome maturation and lysosome fusion. Thus, our results provide novel insight into the interactions between N. gonorrhoeae and the autophagy pathway during invasion and transcytosis of epithelial cells.
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Affiliation(s)
- Ping Lu
- Department of Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Shuyi Wang
- Department of Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yan Lu
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
| | - Dante Neculai
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
| | - Qiming Sun
- Department of Biochemistry and Molecular Biology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Stijn van der Veen
- Department of Microbiology and Parasitology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Zhejiang University, Hangzhou, China
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18
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Lu Y, Zheng Y, Coyaud É, Zhang C, Selvabaskaran A, Yu Y, Xu Z, Weng X, Chen JS, Meng Y, Warner N, Cheng X, Liu Y, Yao B, Hu H, Xia Z, Muise AM, Klip A, Brumell JH, Girardin SE, Ying S, Fairn GD, Raught B, Sun Q, Neculai D. Palmitoylation of NOD1 and NOD2 is required for bacterial sensing. Science 2019; 366:460-467. [PMID: 31649195 DOI: 10.1126/science.aau6391] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/19/2019] [Accepted: 10/03/2019] [Indexed: 12/21/2022]
Abstract
The nucleotide oligomerization domain (NOD)-like receptors 1 and 2 (NOD1/2) are intracellular pattern-recognition proteins that activate immune signaling pathways in response to peptidoglycans associated with microorganisms. Recruitment to bacteria-containing endosomes and other intracellular membranes is required for NOD1/2 signaling, and NOD1/2 mutations that disrupt membrane localization are associated with inflammatory bowel disease and other inflammatory conditions. However, little is known about this recruitment process. We found that NOD1/2 S-palmitoylation is required for membrane recruitment and immune signaling. ZDHHC5 was identified as the palmitoyltransferase responsible for this critical posttranslational modification, and several disease-associated mutations in NOD2 were found to be associated with defective S-palmitoylation. Thus, ZDHHC5-mediated S-palmitoylation of NOD1/2 is critical for their ability to respond to peptidoglycans and to mount an effective immune response.
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Affiliation(s)
- Yan Lu
- Department of Cell Biology, and Department of Pathology Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Keenan Research Centre for Biomedical Sciences, St. Michael's Hospital, Toronto, ON, Canada
| | - Yuping Zheng
- Department of Cell Biology, and Department of Pathology Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Étienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Chao Zhang
- Department of Anatomy, School of Medicine, Zhejiang University, China School of Medicine, Zhejiang University, Hangzhou 310058, China.,Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Apiraam Selvabaskaran
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Yuyun Yu
- Department of Cell Biology, and Department of Pathology Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zizhen Xu
- Department of Cell Biology, and Department of Pathology Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xialian Weng
- Department of Cell Biology, and Department of Pathology Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ji Shun Chen
- Department of Cell Biology, and Department of Pathology Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Meng
- Department of Cell Biology, and Department of Pathology Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Neil Warner
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Xiawei Cheng
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yangyang Liu
- Department of Pathology, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Bingpeng Yao
- Department of Pharmacology and Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital, Institute of Respiratory Diseases, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Hu Hu
- Department of Pathology, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Zonping Xia
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Aleixo M Muise
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Amira Klip
- Cell Biology Program, Research Institute, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning (PGCRL), Toronto, ON, Canada
| | - John H Brumell
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics and Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Stephen E Girardin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Songmin Ying
- Department of Pharmacology and Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital, Institute of Respiratory Diseases, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Gregory D Fairn
- Keenan Research Centre for Biomedical Sciences, St. Michael's Hospital, Toronto, ON, Canada.
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Qiming Sun
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
| | - Dante Neculai
- Department of Cell Biology, and Department of Pathology Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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19
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Heybrock S, Kanerva K, Meng Y, Ing C, Liang A, Xiong ZJ, Weng X, Ah Kim Y, Collins R, Trimble W, Pomès R, Privé GG, Annaert W, Schwake M, Heeren J, Lüllmann-Rauch R, Grinstein S, Ikonen E, Saftig P, Neculai D. Lysosomal integral membrane protein-2 (LIMP-2/SCARB2) is involved in lysosomal cholesterol export. Nat Commun 2019; 10:3521. [PMID: 31387993 PMCID: PMC6684646 DOI: 10.1038/s41467-019-11425-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 07/12/2019] [Indexed: 11/30/2022] Open
Abstract
The intracellular transport of cholesterol is subject to tight regulation. The structure of the lysosomal integral membrane protein type 2 (LIMP-2, also known as SCARB2) reveals a large cavity that traverses the molecule and resembles the cavity in SR-B1 that mediates lipid transfer. The detection of cholesterol within the LIMP-2 structure and the formation of cholesterol-like inclusions in LIMP-2 knockout mice suggested the possibility that LIMP2 transports cholesterol in lysosomes. We present results of molecular modeling, crosslinking studies, microscale thermophoresis and cell-based assays that support a role of LIMP-2 in cholesterol transport. We show that the cavity in the luminal domain of LIMP-2 can bind and deliver exogenous cholesterol to the lysosomal membrane and later to lipid droplets. Depletion of LIMP-2 alters SREBP-2-mediated cholesterol regulation, as well as LDL-receptor levels. Our data indicate that LIMP-2 operates in parallel with Niemann Pick (NPC)-proteins, mediating a slower mode of lysosomal cholesterol export.
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Affiliation(s)
- Saskia Heybrock
- Biochemisches Institut, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Kristiina Kanerva
- Faculty of Medicine, Anatomy and Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Ying Meng
- Department of Cell Biology, and Department of Pathology Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Chris Ing
- Program in Molecular Medicine, Research Institute, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, Canada
| | - Anna Liang
- Program in Molecular Medicine, Research Institute, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, Canada
| | - Zi-Jian Xiong
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, Canada
| | - Xialian Weng
- Department of Cell Biology, and Department of Pathology Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Young Ah Kim
- Department of Chemistry and Biochemistry, Queens College, City University of New York, Flushing, New York, USA
| | - Richard Collins
- Cell Biology Program, Hospital for Sick Children, Toronto, M5G 1X8, Canada
| | - William Trimble
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, Canada
- Cell Biology Program, Hospital for Sick Children, Toronto, M5G 1X8, Canada
- Department of Physiology, University of Toronto, Toronto, M5S 1A8, Canada
| | - Régis Pomès
- Program in Molecular Medicine, Research Institute, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, Canada
| | - Gilbert G Privé
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, Canada
- Princes Margaret Cancer Centre, Toronto, ON, Canada
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium
| | - Michael Schwake
- Faculty of Chemistry, Biochemistry III, University of Bielefeld, 33615, Bielefeld, Germany
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Joerg Heeren
- Institut für Biochemie und Molekulare Zellbiologie, Zentrum für Experimentelle Medizin, Universitätsklinikum Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | | | - Sergio Grinstein
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, Canada.
- Cell Biology Program, Hospital for Sick Children, Toronto, M5G 1X8, Canada.
| | - Elina Ikonen
- Faculty of Medicine, Anatomy and Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland.
- Minerva Foundation Institute for Medical Research, Helsinki, Finland.
| | - Paul Saftig
- Biochemisches Institut, Christian-Albrechts-Universität Kiel, Kiel, Germany.
| | - Dante Neculai
- Department of Cell Biology, and Department of Pathology Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China.
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20
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Raheel H, Ghaffari S, Khosraviani N, Mintsopoulos V, Auyeung D, Wang C, Kim YH, Mullen B, Sung HK, Ho M, Fairn G, Neculai D, Febbraio M, Heit B, Lee WL. CD36 mediates albumin transcytosis by dermal but not lung microvascular endothelial cells: role in fatty acid delivery. Am J Physiol Lung Cell Mol Physiol 2019; 316:L740-L750. [PMID: 30702342 DOI: 10.1152/ajplung.00127.2018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In healthy blood vessels, albumin crosses the endothelium to leave the circulation by transcytosis. However, little is known about the regulation of albumin transcytosis or how it differs in different tissues; its physiological purpose is also unclear. Using total internal reflection fluorescence microscopy, we quantified transcytosis of albumin across primary human microvascular endothelial cells from both lung and skin. We then validated our in vitro findings using a tissue-specific knockout mouse model. We observed that albumin transcytosis was saturable in the skin but not the lung microvascular endothelial cells, implicating a receptor-mediated process. We identified the scavenger receptor CD36 as being both necessary and sufficient for albumin transcytosis across dermal microvascular endothelium, in contrast to the lung where macropinocytosis dominated. Mutations in the apical helical bundle of CD36 prevented albumin internalization by cells. Mice deficient in CD36 specifically in endothelial cells exhibited lower basal permeability to albumin and less basal tissue edema in the skin but not in the lung. Finally, these mice also exhibited a smaller subcutaneous fat layer despite having identical total body weights and circulating fatty acid levels as wild-type animals. In conclusion, CD36 mediates albumin transcytosis in the skin but not the lung. Albumin transcytosis may serve to regulate fatty acid delivery from the circulation to tissues.
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Affiliation(s)
- Hira Raheel
- Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Siavash Ghaffari
- Keenan Research Centre for Biomedical Science, Saint Michael's Hospital , Toronto , Canada
| | - Negar Khosraviani
- Department of Laboratory Medicine and Pathobiology, University of Toronto , Toronto , Canada
| | | | - Derek Auyeung
- Department of Biochemistry, University of Toronto , Toronto , Canada
| | - Changsen Wang
- Keenan Research Centre for Biomedical Science, Saint Michael's Hospital , Toronto , Canada
| | - Yun Hye Kim
- The Hospital for Sick Children , Toronto , Canada
| | - Brendan Mullen
- Department of Pathology, Mount Sinai Hospital , Toronto , Canada
| | - Hoon-Ki Sung
- Department of Laboratory Medicine and Pathobiology, University of Toronto , Toronto , Canada.,The Hospital for Sick Children , Toronto , Canada
| | - May Ho
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary , Calgary , Canada
| | - Gregory Fairn
- Keenan Research Centre for Biomedical Science, Saint Michael's Hospital , Toronto , Canada
| | - Dante Neculai
- Department of Cell Biology, Zhejiang University, School of Basic Medical Sciences , Hangzhou, Zhejiang , People's Republic of China
| | - Maria Febbraio
- Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology, Western University , London , Canada
| | - Warren L Lee
- Institute of Medical Science, University of Toronto, Toronto, Canada.,Keenan Research Centre for Biomedical Science, Saint Michael's Hospital , Toronto , Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto , Toronto , Canada.,Department of Biochemistry, University of Toronto , Toronto , Canada
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21
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Banerjee S, Wu Q, Ying Y, Li Y, Shirota M, Neculai D, Li C. In silico predicted structural and functional insights of all missense mutations on 2B domain of K1/K10 causing genodermatoses. Oncotarget 2018; 7:52766-52780. [PMID: 27421141 PMCID: PMC5288147 DOI: 10.18632/oncotarget.10599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/17/2016] [Indexed: 12/02/2022] Open
Abstract
The K1 and K10 associated genodermatoses are characterized by clinical symptoms of mild to severe redness, blistering and hypertrophy of the skin. In this paper, we set out to computationally investigate the structural and functional effects of missense mutations on the 2B domain of K1/K10 heterodimer and its consequences in disease phenotype. We modeled the structure of the K1/K10 heterodimer based on crystal structures for the human homolog K5/K14 heterodimer, and identified that the missense mutations exert their effects on stability and assembly competence of the heterodimer by altering physico-chemical properties, interatomic interactions, and inter-residue atomic contacts. Comparative structural analysis between all the missense mutations and SNPs showed that the location and physico-chemical properties of the substituted amino acid are significantly correlated with phenotypic variations. In particular, we find evidence that a particular SNP (K10, p.E443K) is a pathogenic nsSNP which disrupts formation of the hydrophobic core and destabilizes the heterodimer through the loss of interatomic interactions. Our study is the first comprehensive report analyzing the mutations located on 2B domain of K1/K10 heterodimeric coiled-coil complex.
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Affiliation(s)
- Santasree Banerjee
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China.,BGI-Shenzhen, Shenzhen, China
| | - Qian Wu
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yuyi Ying
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yanni Li
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
| | - Matsuyuki Shirota
- Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Dante Neculai
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
| | - Chen Li
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
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22
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Hu L, Xu J, Xie X, Zhou Y, Tao P, Li H, Han X, Wang C, Liu J, Xu P, Neculai D, Xia Z. Oligomerization-primed coiled-coil domain interaction with Ubc13 confers processivity to TRAF6 ubiquitin ligase activity. Nat Commun 2017; 8:814. [PMID: 28993672 PMCID: PMC5634496 DOI: 10.1038/s41467-017-01290-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 09/06/2017] [Indexed: 11/30/2022] Open
Abstract
Ubiquitin ligase TRAF6, together with ubiquitin-conjugating enzyme Ubc13/Uev1, catalyzes processive assembly of unanchored K63-linked polyubiquitin chains for TAK1 activation in the IL-1R/TLR pathways. However, what domain and how it functions to enable TRAF6’s processivity are largely uncharacterized. Here, we find TRAF6 coiled-coil (CC) domain is crucial to enable its processivity. The CC domain mediates TRAF6 oligomerization to ensure efficient long polyubiquitin chain assembly. Mutating or deleting the CC domain impairs TRAF6 oligomerization and processive polyubiquitin chain assembly. Fusion of the CC domain to the E3 ubiquitin ligase CHIP/STUB1 renders the latter capable of NF-κB activation. Moreover, the CC domain, after oligomerization, interacts with Ubc13/Ub~Ubc13, which further contributes to TRAF6 processivity. Point mutations within the CC domain that weaken TRAF6 interaction with Ubc13/Ub~Ubc13 diminish TRAF6 processivity. Our results reveal that the CC oligomerization primes its interaction with Ubc13/Ub~Ubc13 to confer processivity to TRAF6 ubiquitin ligase activity. Ubiquitin ligase TRAF6 catalyzes assembly of free polyubiquitin chains for TAK1 activation in the IL-1R/TLR pathways, but the mechanism underlying its processivity is unclear. Here, the authors show that TRAF6 coiled-coil oligomerization domain primes its interaction with Ubc13/Ub~Ubc13 to confer processivity.
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Affiliation(s)
- Lin Hu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Jiafeng Xu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Xiaomei Xie
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Yiwen Zhou
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Panfeng Tao
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Haidong Li
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Xu Han
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Chong Wang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Jian Liu
- Department of Surgical Oncology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Pinglong Xu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Dante Neculai
- College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Zongping Xia
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China.
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23
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Korzhnev DM, Neculai D, Dhe-Paganon S, Arrowsmith CH, Bezsonova I. Solution NMR structure of the HLTF HIRAN domain: a conserved module in SWI2/SNF2 DNA damage tolerance proteins. J Biomol NMR 2016; 66:209-219. [PMID: 27771863 DOI: 10.1007/s10858-016-0070-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/17/2016] [Indexed: 06/06/2023]
Abstract
HLTF is a SWI2/SNF2-family ATP-dependent chromatin remodeling enzyme that acts in the error-free branch of DNA damage tolerance (DDT), a cellular mechanism that enables replication of damaged DNA while leaving damage repair for a later time. Human HLTF and a closely related protein SHPRH, as well as their yeast homologue Rad5, are multi-functional enzymes that share E3 ubiquitin-ligase activity required for activation of the error-free DDT. HLTF and Rad5 also function as ATP-dependent dsDNA translocases and possess replication fork reversal activities. Thus, they can convert Y-shaped replication forks into X-shaped Holliday junction structures that allow error-free replication over DNA lesions. The fork reversal activity of HLTF is dependent on 3'-ssDNA-end binding activity of its N-terminal HIRAN domain. Here we present the solution NMR structure of the human HLTF HIRAN domain, an OB-like fold module found in organisms from bacteria (as a stand-alone domain) to plants, fungi and metazoan (in combination with SWI2/SNF2 helicase-like domain). The obtained structure of free HLTF HIRAN is similar to recently reported structures of its DNA bound form, while the NMR analysis also reveals that the DNA binding site of the free domain exhibits conformational heterogeneity. Sequence comparison of N-terminal regions of HLTF, SHPRH and Rad5 aided by knowledge of the HLTF HIRAN structure suggests that the SHPRH N-terminus also includes an uncharacterized structured module, exhibiting weak sequence similarity with HIRAN regions of HLTF and Rad5, and potentially playing a similar functional role.
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Affiliation(s)
- Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, CT, 06030, USA
| | - Dante Neculai
- School of Medicine, Zhejiang University, Hangzhou, China
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, CT, 06030, USA.
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24
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Jiang Y, Cai Y, Zhang W, Yin Z, Hu C, Tong T, Lu P, Zhang S, Neculai D, Tuan RS, Ouyang HW. Human Cartilage-Derived Progenitor Cells From Committed Chondrocytes for Efficient Cartilage Repair and Regeneration. Stem Cells Transl Med 2016; 5:733-44. [PMID: 27130221 PMCID: PMC4878331 DOI: 10.5966/sctm.2015-0192] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 02/08/2016] [Indexed: 12/20/2022] Open
Abstract
UNLABELLED Articular cartilage is not a physiologically self-renewing tissue. Injury of cartilage often progresses from the articular surface to the subchondral bone, leading to pathogenesis of tissue degenerative diseases, such as osteoarthritis. Therapies to treat cartilage defects using autologous chondrocyte-based tissue engineering have been developed and used for more than 20 years; however, the challenge of chondrocyte expansion in vitro remains. A promising cell source, cartilage stem/progenitor cells (CSPCs), has attracted recent attention. Because their origin and identity are still unclear, the application potential of CSPCs is under active investigation. Here we have captured the emergence of a group of stem/progenitor cells derived from adult human chondrocytes, highlighted by dynamic changes in expression of the mature chondrocyte marker, COL2, and mesenchymal stromal/stem cell (MSC) marker, CD146. These cells are termed chondrocyte-derived progenitor cells (CDPCs). The stem cell-like potency and differentiation status of CDPCs were determined by physical and biochemical cues during culture. A low-density, low-glucose 2-dimensional culture condition (2DLL) was critical for the emergence and proliferation enhancement of CDPCs. CDPCs showed similar phenotype as bone marrow mesenchymal stromal/stem cells but exhibited greater chondrogenic potential. Moreover, the 2DLL-cultured CDPCs proved efficient in cartilage formation both in vitro and in vivo and in repairing large knee cartilage defects (6-13 cm(2)) in 15 patients. These findings suggest a phenotype conversion between chondrocytes and CDPCs and provide conditions that promote the conversion. These insights expand our understanding of cartilage biology and may enhance the success of chondrocyte-based therapies. SIGNIFICANCE Injury of cartilage, a non-self-repairing tissue, often progresses to pathogenesis of degenerative joint diseases, such as osteoarthritis. Although tissue-derived stem cells have been shown to contribute to tissue renewal and homeostasis, the derivation, biological function, and application potential of stem/progenitor cells found in adult human articular cartilage are incompletely understood. This study reports the derivation of a population of cartilage stem/progenitor cells from fully differentiated chondrocytes under specific culture conditions, which have the potential to reassume their chondrocytic phenotype for efficient cartilage regeneration. These findings support the possibility of using in vitro amplified chondrocyte-derived progenitor cells for joint cartilage repair.
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Affiliation(s)
- Yangzi Jiang
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China Department of Sports Medicine, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China Center for Cellular Molecular Engineering, Department of Orthopaedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Youzhi Cai
- Department of Orthopaedics, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China Chinese Orthopaedic Regenerative Medicine Group, Hangzhou, People's Republic of China
| | - Wei Zhang
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Zi Yin
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Changchang Hu
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Tong Tong
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Ping Lu
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Shufang Zhang
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China Department of Sports Medicine, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China Chinese Orthopaedic Regenerative Medicine Group, Hangzhou, People's Republic of China
| | - Dante Neculai
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Rocky S Tuan
- Center for Cellular Molecular Engineering, Department of Orthopaedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Hong Wei Ouyang
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China Department of Sports Medicine, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China Department of Orthopaedics, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China Chinese Orthopaedic Regenerative Medicine Group, Hangzhou, People's Republic of China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
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25
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Kook S, Wang P, Young LR, Schwake M, Saftig P, Weng X, Meng Y, Neculai D, Marks MS, Gonzales L, Beers MF, Guttentag S. Impaired Lysosomal Integral Membrane Protein 2-dependent Peroxiredoxin 6 Delivery to Lamellar Bodies Accounts for Altered Alveolar Phospholipid Content in Adaptor Protein-3-deficient pearl Mice. J Biol Chem 2016; 291:8414-27. [PMID: 26907692 PMCID: PMC4861416 DOI: 10.1074/jbc.m116.720201] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Indexed: 11/06/2022] Open
Abstract
The Hermansky Pudlak syndromes (HPS) constitute a family of disorders characterized by oculocutaneous albinism and bleeding diathesis, often associated with lethal lung fibrosis. HPS results from mutations in genes of membrane trafficking complexes that facilitate delivery of cargo to lysosome-related organelles. Among the affected lysosome-related organelles are lamellar bodies (LB) within alveolar type 2 cells (AT2) in which surfactant components are assembled, modified, and stored. AT2 from HPS patients and mouse models of HPS exhibit enlarged LB with increased phospholipid content, but the mechanism underlying these defects is unknown. We now show that AT2 in the pearl mouse model of HPS type 2 lacking the adaptor protein 3 complex (AP-3) fails to accumulate the soluble enzyme peroxiredoxin 6 (PRDX6) in LB. This defect reflects impaired AP-3-dependent trafficking of PRDX6 to LB, because pearl mouse AT2 cells harbor a normal total PRDX6 content. AP-3-dependent targeting of PRDX6 to LB requires the transmembrane protein LIMP-2/SCARB2, a known AP-3-dependent cargo protein that functions as a carrier for lysosomal proteins in other cell types. Depletion of LB PRDX6 in AP-3- or LIMP-2/SCARB2-deficient mice correlates with phospholipid accumulation in lamellar bodies and with defective intraluminal degradation of LB disaturated phosphatidylcholine. Furthermore, AP-3-dependent LB targeting is facilitated by protein/protein interaction between LIMP-2/SCARB2 and PRDX6 in vitro and in vivo Our data provide the first evidence for an AP-3-dependent cargo protein required for the maturation of LB in AT2 and suggest that the loss of PRDX6 activity contributes to the pathogenic changes in LB phospholipid homeostasis found HPS2 patients.
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Affiliation(s)
| | - Ping Wang
- From the Division of Neonatology and
| | - Lisa R Young
- Division of Pediatric Pulmonary Medicine, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Michael Schwake
- the Department of Chemistry, Biochemistry III, University of Bielefeld, D-33615 Bielefeld, Germany
| | - Paul Saftig
- the Institute of Biochemistry, Christian-Albrechts-University, Olshausenstrasse 40, D-24098 Kiel, Germany
| | - Xialian Weng
- the Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Ying Meng
- the Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Dante Neculai
- the Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Michael S Marks
- the Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, and the Departments of Pathology and Laboratory Medicine and of Physiology, and
| | - Linda Gonzales
- Division of Adult Pulmonary and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Michael F Beers
- Division of Adult Pulmonary and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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26
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Achar YJ, Balogh D, Neculai D, Juhasz S, Morocz M, Gali H, Dhe-Paganon S, Venclovas Č, Haracska L. Human HLTF mediates postreplication repair by its HIRAN domain-dependent replication fork remodelling. Nucleic Acids Res 2015; 43:10277-91. [PMID: 26350214 PMCID: PMC4666394 DOI: 10.1093/nar/gkv896] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/27/2015] [Indexed: 12/13/2022] Open
Abstract
Defects in the ability to respond properly to an unrepaired DNA lesion blocking replication promote genomic instability and cancer. Human HLTF, implicated in error-free replication of damaged DNA and tumour suppression, exhibits a HIRAN domain, a RING domain, and a SWI/SNF domain facilitating DNA-binding, PCNA-polyubiquitin-ligase, and dsDNA-translocase activities, respectively. Here, we investigate the mechanism of HLTF action with emphasis on its HIRAN domain. We found that in cells HLTF promotes the filling-in of gaps left opposite damaged DNA during replication, and this postreplication repair function depends on its HIRAN domain. Our biochemical assays show that HIRAN domain mutant HLTF proteins retain their ubiquitin ligase, ATPase and dsDNA translocase activities but are impaired in binding to a model replication fork. These data and our structural study indicate that the HIRAN domain recruits HLTF to a stalled replication fork, and it also provides the direction for the movement of the dsDNA translocase motor domain for fork reversal. In more general terms, we suggest functional similarities between the HIRAN, the OB, the HARP2, and other domains found in certain motor proteins, which may explain why only a subset of DNA translocases can carry out fork reversal.
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Affiliation(s)
- Yathish Jagadheesh Achar
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Temesvari krt. 62, H-6726, Hungary
| | - David Balogh
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Temesvari krt. 62, H-6726, Hungary
| | - Dante Neculai
- Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Szilvia Juhasz
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Temesvari krt. 62, H-6726, Hungary
| | - Monika Morocz
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Temesvari krt. 62, H-6726, Hungary
| | - Himabindu Gali
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Temesvari krt. 62, H-6726, Hungary
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue - LC-3310, Boston, MA 02215, USA
| | - Česlovas Venclovas
- Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Lajos Haracska
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Temesvari krt. 62, H-6726, Hungary
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27
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Armstrong SM, Sugiyama MG, Fung KYY, Gao Y, Wang C, Levy AS, Azizi P, Roufaiel M, Zhu SN, Neculai D, Yin C, Bolz SS, Seidah NG, Cybulsky MI, Heit B, Lee WL. A novel assay uncovers an unexpected role for SR-BI in LDL transcytosis. Cardiovasc Res 2015; 108:268-77. [PMID: 26334034 DOI: 10.1093/cvr/cvv218] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 08/24/2015] [Indexed: 01/16/2023] Open
Abstract
AIMS Retention of low-density lipoprotein (LDL) cholesterol beneath the arterial endothelium initiates an inflammatory response culminating in atherosclerosis. Since the overlying endothelium is healthy and intact early on, it is likely that LDL passes through endothelial cells by transcytosis. However, technical challenges have made confirming this notion and elucidating the mechanisms of transcytosis difficult. We developed a novel assay for measuring LDL transcytosis in real time across coronary endothelial cell monolayers; we used this approach to identify the receptor involved. METHODS AND RESULTS Murine aortas were perfused ex vivo with LDL and dextran of a smaller molecular radius. LDL (but not dextran) accumulated under the endothelium, indicating that LDL transcytosis occurs in intact vessels. We then confirmed that LDL transcytosis occurs in vitro using human coronary artery endothelial cells. An assay was developed to quantify transcytosis of DiI-LDL in real time using total internal reflection fluorescence microscopy. DiI-LDL transcytosis was inhibited by excess unlabelled LDL, while degradation of the LDL receptor by PCSK9 had no effect. Instead, LDL colocalized partially with the scavenger receptor SR-BI and overexpression of SR-BI increased LDL transcytosis; knockdown by siRNA significantly reduced it. Excess HDL, the canonical SR-BI ligand, significantly decreased LDL transcytosis. Aortas from SR-BI-deficient mice were perfused ex vivo with LDL and accumulated significantly less sub-endothelial LDL compared with wild-type littermates. CONCLUSION We developed an assay to quantify LDL transcytosis across endothelial cells and discovered an unexpected role for SR-BI. Elucidating the mechanisms of LDL transcytosis may identify novel targets for the prevention or therapy of atherosclerosis.
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Affiliation(s)
- Susan M Armstrong
- Keenan Research Centre, St Michael's Hospital, 30 Bond Street, Toronto, ON, Canada, M5B 1W8 Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - Michael G Sugiyama
- Keenan Research Centre, St Michael's Hospital, 30 Bond Street, Toronto, ON, Canada, M5B 1W8 Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Karen Y Y Fung
- Keenan Research Centre, St Michael's Hospital, 30 Bond Street, Toronto, ON, Canada, M5B 1W8
| | - Yizhuo Gao
- Keenan Research Centre, St Michael's Hospital, 30 Bond Street, Toronto, ON, Canada, M5B 1W8
| | - Changsen Wang
- Keenan Research Centre, St Michael's Hospital, 30 Bond Street, Toronto, ON, Canada, M5B 1W8
| | - Andrew S Levy
- Keenan Research Centre, St Michael's Hospital, 30 Bond Street, Toronto, ON, Canada, M5B 1W8
| | - Paymon Azizi
- Keenan Research Centre, St Michael's Hospital, 30 Bond Street, Toronto, ON, Canada, M5B 1W8
| | - Mark Roufaiel
- Toronto General Research Institute (TGRI), Toronto, Canada
| | - Su-Ning Zhu
- Toronto General Research Institute (TGRI), Toronto, Canada
| | | | - Charles Yin
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Steffen-Sebastian Bolz
- Keenan Research Centre, St Michael's Hospital, 30 Bond Street, Toronto, ON, Canada, M5B 1W8
| | | | - Myron I Cybulsky
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada Toronto General Research Institute (TGRI), Toronto, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Warren L Lee
- Keenan Research Centre, St Michael's Hospital, 30 Bond Street, Toronto, ON, Canada, M5B 1W8 Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada Interdepartmental Division of Critical Care Medicine and the Department of Medicine, University of Toronto, Toronto, ON, Canada
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28
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Cabrera A, Neculai D, Kain KC. CD36 and malaria: friends or foes? A decade of data provides some answers. Trends Parasitol 2014; 30:436-44. [PMID: 25113859 DOI: 10.1016/j.pt.2014.07.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/16/2014] [Accepted: 07/17/2014] [Indexed: 02/07/2023]
Abstract
The past 10 years have generated new insights into the complex interaction between CD36 (cluster of differentiation 36) and malaria. These range from the crystallization of the CD36 homolog, LIMPII (lysosomal integral membrane protein II), permitting modeling of CD36 and its binding to diverse ligands, to cell biology-based studies of CD36 and large population genetic studies assessing the association of CD36 polymorphisms and malarial disease severity. Collectively these lines of evidence indicate that a receptor other than CD36 is associated with severity. CD36 plays an important role in innate immunity and in the phagocytic uptake of multiple pathogens including malaria. CD36 polymorphisms lack association with severity, and isolates that cause severe disease primarily bind to endothelial protein C receptor (EPCR) rather than to CD36.
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Affiliation(s)
- Ana Cabrera
- Sandra Ann Rotman (SAR) Laboratories, SAR Centre, Toronto General Hospital, University Health Network, Tropical Disease Unit, Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Dante Neculai
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kevin C Kain
- Sandra Ann Rotman (SAR) Laboratories, SAR Centre, Toronto General Hospital, University Health Network, Tropical Disease Unit, Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, Ontario, Canada.
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29
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Ji J, Sharma V, Qi S, Guarch M, Zhao P, Luo Z, Fan W, Wang Y, Mbabaali F, Neculai D, Esteban M, McPherson J, Batada N. Antioxidant supplementation reduces genomic aberrations in human induced pluripotent stem cells. Stem Cell Reports 2014; 2:44-51. [PMID: 24511469 PMCID: PMC3916753 DOI: 10.1016/j.stemcr.2013.11.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 11/05/2013] [Accepted: 11/07/2013] [Indexed: 12/30/2022] Open
Abstract
Somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs) using oncogenic transcription factors. However, this method leads to genetic aberrations in iPSCs via unknown mechanisms, which may limit their clinical use. Here, we demonstrate that the supplementation of growth media with antioxidants reduces the genome instability of cells transduced with the reprogramming factors. Antioxidant supplementation did not affect transgene expression level or silencing kinetics. Importantly, iPSCs made with antioxidants had significantly fewer de novo copy number variations, but not fewer coding point mutations, than iPSCs made without antioxidants. Our results suggest that the quality and safety of human iPSCs might be enhanced by using antioxidants in the growth media during the generation and maintenance of iPSCs. During reprogramming, oxidative stress is elevated Antioxidants reduce genome instability during reprogramming iPSCs made in the presence of antioxidants have fewer de novo genomic aberrations
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Affiliation(s)
- Junfeng Ji
- Ontario Institute for Cancer Research, 101 College Street, Toronto, Canada M5G 0A3
- Research Center of Stem Cell and Developmental Biology, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Corresponding author
| | - Vivek Sharma
- Ontario Institute for Cancer Research, 101 College Street, Toronto, Canada M5G 0A3
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Suxia Qi
- Research Center of Stem Cell and Developmental Biology, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Meritxell Espino Guarch
- Research Center of Stem Cell and Developmental Biology, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Ping Zhao
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou 510530, China
| | - Zhiwei Luo
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou 510530, China
| | - Wenxia Fan
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou 510530, China
| | - Yu Wang
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou 510530, China
| | - Faridah Mbabaali
- Ontario Institute for Cancer Research, 101 College Street, Toronto, Canada M5G 0A3
| | - Dante Neculai
- Ontario Institute for Cancer Research, 101 College Street, Toronto, Canada M5G 0A3
| | - Miguel Angel Esteban
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou 510530, China
| | - John D. McPherson
- Ontario Institute for Cancer Research, 101 College Street, Toronto, Canada M5G 0A3
| | - Nizar N. Batada
- Ontario Institute for Cancer Research, 101 College Street, Toronto, Canada M5G 0A3
- Department of Medical Biophysics, University of Toronto, Toronto, Canada M5G 2M9
- Corresponding author
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30
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Neculai D, Schwake M, Ravichandran M, Zunke F, Collins RF, Peters J, Neculai M, Plumb J, Loppnau P, Pizarro JC, Seitova A, Trimble WS, Saftig P, Grinstein S, Dhe-Paganon S. Structure of LIMP-2 provides functional insights with implications for SR-BI and CD36. Nature 2013; 504:172-6. [PMID: 24162852 DOI: 10.1038/nature12684] [Citation(s) in RCA: 202] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Accepted: 09/20/2013] [Indexed: 11/09/2022]
Abstract
Members of the CD36 superfamily of scavenger receptor proteins are important regulators of lipid metabolism and innate immunity. They recognize normal and modified lipoproteins, as well as pathogen-associated molecular patterns. The family consists of three members: SR-BI (which delivers cholesterol to the liver and steroidogenic organs and is a co-receptor for hepatitis C virus), LIMP-2/LGP85 (which mediates lysosomal delivery of β-glucocerebrosidase and serves as a receptor for enterovirus 71 and coxsackieviruses) and CD36 (a fatty-acid transporter and receptor for phagocytosis of effete cells and Plasmodium-infected erythrocytes). Notably, CD36 is also a receptor for modified lipoproteins and β-amyloid, and has been implicated in the pathogenesis of atherosclerosis and of Alzheimer's disease. Despite their prominent roles in health and disease, understanding the function and abnormalities of the CD36 family members has been hampered by the paucity of information about their structure. Here we determine the crystal structure of LIMP-2 and infer, by homology modelling, the structure of SR-BI and CD36. LIMP-2 shows a helical bundle where β-glucocerebrosidase binds, and where ligands are most likely to bind to SR-BI and CD36. Remarkably, the crystal structure also shows the existence of a large cavity that traverses the entire length of the molecule. Mutagenesis of SR-BI indicates that the cavity serves as a tunnel through which cholesterol(esters) are delivered from the bound lipoprotein to the outer leaflet of the plasma membrane. We provide evidence supporting a model whereby lipidic constituents of the ligands attached to the receptor surface are handed off to the membrane through the tunnel, accounting for the selective lipid transfer characteristic of SR-BI and CD36.
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Affiliation(s)
- Dante Neculai
- Cell Biology Program, The Hospital for Sick Children, Toronto M5G 1X8, Canada
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31
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Abstract
Scavenger receptors were originally identified by their ability to recognize and to remove modified lipoproteins; however, it is now appreciated that they carry out a striking range of functions, including pathogen clearance, lipid transport, the transport of cargo within the cell and even functioning as taste receptors. The large repertoire of ligands recognized by scavenger receptors and their broad range of functions are not only due to the wide range of receptors that constitute this family but also to their ability to partner with various co-receptors. The ability of individual scavenger receptors to associate with different co-receptors makes their responsiveness extremely versatile. This Review highlights recent insights into the structural features that determine the function of scavenger receptors and the emerging role that these receptors have in immune responses, notably in macrophage polarization and in the pathogenesis of diseases such as atherosclerosis and Alzheimer's disease.
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Affiliation(s)
- Johnathan Canton
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
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32
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Wan LCK, Mao DYL, Neculai D, Strecker J, Chiovitti D, Kurinov I, Poda G, Thevakumaran N, Yuan F, Szilard RK, Lissina E, Nislow C, Caudy AA, Durocher D, Sicheri F. Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system. Nucleic Acids Res 2013; 41:6332-46. [PMID: 23620299 PMCID: PMC3695523 DOI: 10.1093/nar/gkt322] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The universally conserved Kae1/Qri7/YgjD and Sua5/YrdC protein families have been implicated in growth, telomere homeostasis, transcription and the N6-threonylcarbamoylation (t6A) of tRNA, an essential modification required for translational fidelity by the ribosome. In bacteria, YgjD orthologues operate in concert with the bacterial-specific proteins YeaZ and YjeE, whereas in archaeal and eukaryotic systems, Kae1 operates as part of a larger macromolecular assembly called KEOPS with Bud32, Cgi121, Gon7 and Pcc1 subunits. Qri7 orthologues function in the mitochondria and may represent the most primitive member of the Kae1/Qri7/YgjD protein family. In accordance with previous findings, we confirm that Qri7 complements Kae1 function and uncover that Qri7 complements the function of all KEOPS subunits in growth, t6A biosynthesis and, to a partial degree, telomere maintenance. These observations suggest that Kae1 provides a core essential function that other subunits within KEOPS have evolved to support. Consistent with this inference, Qri7 alone is sufficient for t6A biosynthesis with Sua5 in vitro. In addition, the 2.9 Å crystal structure of Qri7 reveals a simple homodimer arrangement that is supplanted by the heterodimerization of YgjD with YeaZ in bacteria and heterodimerization of Kae1 with Pcc1 in KEOPS. The partial complementation of telomere maintenance by Qri7 hints that KEOPS has evolved novel functions in higher organisms.
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Affiliation(s)
- Leo C K Wan
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
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33
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Ernst A, Avvakumov G, Tong J, Fan Y, Zhao Y, Alberts P, Persaud A, Walker JR, Neculai AM, Neculai D, Vorobyov A, Garg P, Beatty L, Chan PK, Juang YC, Landry MC, Yeh C, Zeqiraj E, Karamboulas K, Allali-Hassani A, Vedadi M, Tyers M, Moffat J, Sicheri F, Pelletier L, Durocher D, Raught B, Rotin D, Yang J, Moran MF, Dhe-Paganon S, Sidhu SS. A strategy for modulation of enzymes in the ubiquitin system. Science 2013; 339:590-5. [PMID: 23287719 DOI: 10.1126/science.1230161] [Citation(s) in RCA: 224] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The ubiquitin system regulates virtually all aspects of cellular function. We report a method to target the myriad enzymes that govern ubiquitination of protein substrates. We used massively diverse combinatorial libraries of ubiquitin variants to develop inhibitors of four deubiquitinases (DUBs) and analyzed the DUB-inhibitor complexes with crystallography. We extended the selection strategy to the ubiquitin conjugating (E2) and ubiquitin ligase (E3) enzymes and found that ubiquitin variants can also enhance enzyme activity. Last, we showed that ubiquitin variants can bind selectively to ubiquitin-binding domains. Ubiquitin variants exhibit selective function in cells and thus enable orthogonal modulation of specific enzymatic steps in the ubiquitin system.
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Affiliation(s)
- Andreas Ernst
- Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada
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34
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Ji J, Ng SH, Sharma V, Neculai D, Hussein S, Sam M, Trinh Q, Church GM, McPherson JD, Nagy A, Batada NN. Elevated coding mutation rate during the reprogramming of human somatic cells into induced pluripotent stem cells. Stem Cells 2012; 30:435-40. [PMID: 22162363 DOI: 10.1002/stem.1011] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mutations in human induced pluripotent stem cells (iPSCs) pose a risk for their clinical use due to preferential reprogramming of mutated founder cell and selection of mutations during maintenance of iPSCs in cell culture. It is unknown, however, if mutations in iPSCs are due to stress associated with oncogene expression during reprogramming. We performed whole exome sequencing of human foreskin fibroblasts and their derived iPSCs at two different passages. We found that in vitro passaging contributed 7% to the iPSC coding point mutation load, and ultradeep amplicon sequencing revealed that 19% of the mutations preexist as rare mutations in the parental fibroblasts suggesting that the remaining 74% of the mutations were acquired during cellular reprogramming. Simulation suggests that the mutation intensity during reprogramming is ninefold higher than the background mutation rate in culture. Thus the factor induced reprogramming stress contributes to a significant proportion of the mutation load of iPSCs.
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Affiliation(s)
- Junfeng Ji
- Cancer Genomics, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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35
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Campbell SJ, Edwards RA, Leung CCY, Neculai D, Hodge CD, Dhe-Paganon S, Glover JNM. Molecular insights into the function of RING finger (RNF)-containing proteins hRNF8 and hRNF168 in Ubc13/Mms2-dependent ubiquitylation. J Biol Chem 2012; 287:23900-10. [PMID: 22589545 DOI: 10.1074/jbc.m112.359653] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The repair of DNA double strand breaks by homologous recombination relies on the unique topology of the chains formed by Lys-63 ubiquitylation of chromatin to recruit repair factors such as breast cancer 1 (BRCA1) to sites of DNA damage. The human RING finger (RNF) E3 ubiquitin ligases, RNF8 and RNF168, with the E2 ubiquitin-conjugating complex Ubc13/Mms2, perform the majority of Lys-63 ubiquitylation in homologous recombination. Here, we show that RNF8 dimerizes and binds to Ubc13/Mms2, thereby stimulating formation of Lys-63 ubiquitin chains, whereas the related RNF168 RING domain is a monomer and does not catalyze Lys-63 polyubiquitylation. The crystal structure of the RNF8/Ubc13/Mms2 ternary complex reveals the structural basis for the interaction between Ubc13 and the RNF8 RING and that an extended RNF8 coiled-coil is responsible for its dimerization. Mutations that disrupt the RNF8/Ubc13 binding surfaces, or that truncate the RNF8 coiled-coil, reduce RNF8-catalyzed ubiquitylation. These findings support the hypothesis that RNF8 is responsible for the initiation of Lys-63-linked ubiquitylation in the DNA damage response, which is subsequently amplified by RNF168.
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Affiliation(s)
- Stephen J Campbell
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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36
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Sheng Y, Hong JH, Doherty R, Srikumar T, Shloush J, Avvakumov GV, Walker JR, Xue S, Neculai D, Wan JW, Kim SK, Arrowsmith CH, Raught B, Dhe-Paganon S. A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen. Mol Cell Proteomics 2012; 11:329-41. [PMID: 22496338 DOI: 10.1074/mcp.o111.013706] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Here we describe a systematic structure-function analysis of the human ubiquitin (Ub) E2 conjugating proteins, consisting of the determination of 15 new high-resolution three-dimensional structures of E2 catalytic domains, and autoubiquitylation assays for 26 Ub-loading E2s screened against a panel of nine different HECT (homologous to E6-AP carboxyl terminus) E3 ligase domains. Integration of our structural and biochemical data revealed several E2 surface properties associated with Ub chain building activity; (1) net positive or neutral E2 charge, (2) an "acidic trough" located near the catalytic Cys, surrounded by an extensive basic region, and (3) similarity to the previously described HECT binding signature in UBE2L3 (UbcH7). Mass spectrometry was used to characterize the autoubiquitylation products of a number of functional E2-HECT pairs, and demonstrated that HECT domains from different subfamilies catalyze the formation of very different types of Ub chains, largely independent of the E2 in the reaction. Our data set represents the first comprehensive analysis of E2-HECT E3 interactions, and thus provides a framework for better understanding the molecular mechanisms of ubiquitylation.
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Affiliation(s)
- Yi Sheng
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
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37
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Dev K, Santangelo TJ, Rothenburg S, Neculai D, Dey M, Sicheri F, Dever TE, Reeve JN, Hinnebusch AG. Archaeal aIF2B interacts with eukaryotic translation initiation factors eIF2alpha and eIF2Balpha: Implications for aIF2B function and eIF2B regulation. J Mol Biol 2009; 392:701-22. [PMID: 19616556 DOI: 10.1016/j.jmb.2009.07.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 06/30/2009] [Accepted: 07/09/2009] [Indexed: 11/28/2022]
Abstract
Translation initiation is down-regulated in eukaryotes by phosphorylation of the alpha-subunit of eIF2 (eukaryotic initiation factor 2), which inhibits its guanine nucleotide exchange factor, eIF2B. The N-terminal S1 domain of phosphorylated eIF2alpha interacts with a subcomplex of eIF2B formed by the three regulatory subunits alpha/GCN3, beta/GCD7, and delta/GCD2, blocking the GDP-GTP exchange activity of the catalytic epsilon-subunit of eIF2B. These regulatory subunits have related sequences and have sequences in common with many archaeal proteins, some of which are involved in methionine salvage and CO(2) fixation. Our sequence analyses however predicted that members of one phylogenetically distinct and coherent group of these archaeal proteins [designated aIF2Bs (archaeal initiation factor 2Bs)] are functional homologs of the alpha, beta, and delta subunits of eIF2B. Three of these proteins, from different archaea, have been shown to bind in vitro to the alpha-subunit of the archaeal aIF2 from the cognate archaeon. In one case, the aIF2B protein was shown further to bind to the S1 domain of the alpha-subunit of yeast eIF2 in vitro and to interact with eIF2Balpha/GCN3 in vivo in yeast. The aIF2B-eIF2alpha interaction was however independent of eIF2alpha phosphorylation. Mass spectrometry has identified several proteins that co-purify with aIF2B from Thermococcus kodakaraensis, and these include aIF2alpha, a sugar-phosphate nucleotidyltransferase with sequence similarity to eIF2Bvarepsilon, and several large-subunit (50S) ribosomal proteins. Based on this evidence that aIF2B has functions in common with eIF2B, the crystal structure established for an aIF2B was used to construct a model of the eIF2B regulatory subcomplex. In this model, the evolutionarily conserved regions and sites of regulatory mutations in the three eIF2B subunits in yeast are juxtaposed in one continuous binding surface for phosphorylated eIF2alpha.
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Affiliation(s)
- Kamal Dev
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
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38
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Mao DYL, Neculai D, Downey M, Orlicky S, Haffani YZ, Ceccarelli DF, Ho JSL, Szilard RK, Zhang W, Ho CS, Wan L, Fares C, Rumpel S, Kurinov I, Arrowsmith CH, Durocher D, Sicheri F. Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine. Mol Cell 2008; 32:259-75. [PMID: 18951093 DOI: 10.1016/j.molcel.2008.10.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Revised: 09/24/2008] [Accepted: 10/02/2008] [Indexed: 11/19/2022]
Abstract
Kae1 is a universally conserved ATPase and part of the essential gene set in bacteria. In archaea and eukaryotes, Kae1 is embedded within the protein kinase-containing KEOPS complex. Mutation of KEOPS subunits in yeast leads to striking telomere and transcription defects, but the exact biochemical function of KEOPS is not known. As a first step to elucidating its function, we solved the atomic structure of archaea-derived KEOPS complexes involving Kae1, Bud32, Pcc1, and Cgi121 subunits. Our studies suggest that Kae1 is regulated at two levels by the primordial protein kinase Bud32, which is itself regulated by Cgi121. Moreover, Pcc1 appears to function as a dimerization module, perhaps suggesting that KEOPS may be a processive molecular machine. Lastly, as Bud32 lacks the conventional substrate-recognition infrastructure of eukaryotic protein kinases including an activation segment, Bud32 may provide a glimpse of the evolutionary history of the protein kinase family.
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Affiliation(s)
- Daniel Y L Mao
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
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39
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Tang X, Orlicky S, Lin Z, Willems A, Neculai D, Ceccarelli D, Mercurio F, Shilton BH, Sicheri F, Tyers M. Suprafacial orientation of the SCFCdc4 dimer accommodates multiple geometries for substrate ubiquitination. Cell 2007; 129:1165-76. [PMID: 17574027 DOI: 10.1016/j.cell.2007.04.042] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2006] [Revised: 02/16/2007] [Accepted: 04/26/2007] [Indexed: 11/17/2022]
Abstract
SCF ubiquitin ligases recruit substrates for degradation via F box protein adaptor subunits. WD40 repeat F box proteins, such as Cdc4 and beta-TrCP, contain a conserved dimerization motif called the D domain. Here, we report that the D domain protomers of yeast Cdc4 and human beta-TrCP form a superhelical homotypic dimer. Disruption of the D domain compromises the activity of yeast SCF(Cdc4) toward the CDK inhibitor Sic1 and other substrates. SCF(Cdc4) dimerization has little effect on the affinity for Sic1 but markedly stimulates ubiquitin conjugation. A model of the dimeric holo-SCF(Cdc4) complex based on small-angle X-ray scatter measurements reveals a suprafacial configuration, in which substrate-binding sites and E2 catalytic sites lie in the same plane with a separation of 64 A within and 102 A between each SCF monomer. This spatial variability may accommodate diverse acceptor lysine geometries in both substrates and the elongating ubiquitin chain and thereby increase catalytic efficiency.
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Affiliation(s)
- Xiaojing Tang
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada M5G 1X5
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40
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Abstract
STAT proteins have the function of signaling from the cell membrane into the nucleus, where they regulate gene transcription. Latent mammalian STAT proteins can form dimers in the cytoplasm even before receptor-mediated activation by specific tyrosine phosphorylation. Here we describe the 3.21-A crystal structure of an unphosphorylated STAT5a homodimer lacking the N-terminal domain as well as the C-terminal transactivation domain. The overall structure of this fragment is very similar to phosphorylated STATs. However, important differences exist in the dimerization mode. Although the interface between phosphorylated STATs is mediated by their Src-homology 2 domains, the unphosphorylated STAT5a fragment dimerizes in a completely different manner via interactions between their beta-barrel and four-helix bundle domains. The STAT4 N-terminal domain dimer can be docked onto this STAT5a core fragment dimer based on shape and charge complementarities. The separation of the dimeric arrangement, taking place upon activation and nuclear translocation of STAT5a, is demonstrated by fluorescence resonance energy transfer experiments in living cells.
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Affiliation(s)
- Dante Neculai
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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41
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Abstract
The crystal structures of glutathione-dependent formaldehyde-activating enzyme (Gfa) from Paracoccus denitrificans, which catalyzes the formation of S-hydroxymethylglutathione from formaldehyde and glutathione, and its complex with glutathione (Gfa-GTT) have been determined. Gfa has a new fold with two zinc-sulfur centers, one that is structural (zinc tetracoordinated) and one catalytic (zinc apparently tricoordinated). In Gfa-GTT, the catalytic zinc is displaced due to disulfide bond formation of glutathione with one of the zinc-coordinating cysteines. Soaking crystals of Gfa-GTT with formaldehyde restores the holoenzyme. Accordingly, the displaced zinc forms a complex by scavenging formaldehyde and glutathione. The activation of formaldehyde and of glutathione in this zinc complex favors the final nucleophilic addition, followed by relocation of zinc in the catalytic site. Therefore, the structures of Gfa and Gfa-GTT draw the critical association between a dynamic zinc redox switch and a nucleophilic addition as a new facet of the redox activity of zinc-sulfur sites.
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Affiliation(s)
- Ana Mirela Neculai
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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42
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Pineda LW, Jancik V, Roesky HW, Neculai D, Neculai AM. Preparation and structure of the first germanium(II) hydroxide: the congener of an unknown low-valent carbon analogue. Angew Chem Int Ed Engl 2004; 43:1419-21. [PMID: 15368423 DOI: 10.1002/anie.200353205] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Leslie W Pineda
- Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
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43
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Jancik V, Roesky HW, Neculai D, Neculai AM, Herbst-Irmer R. Preparation of [LAl(?-S)2MCp2] (M=Ti, Zr) from the Structurally Characterized Lithium Complexes [{LAl(SH)[SLi(thf)2]}2] and [{LAl[(SLi)2(thf)3]}2]?2 THF. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200461254] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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44
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Jancik V, Roesky HW, Neculai D, Neculai AM, Herbst-Irmer R. Preparation of [LAl(?-S)2MCp2] (M=Ti, Zr) from the Structurally Characterized Lithium Complexes [{LAl(SH)[SLi(thf)2]}2] and [{LAl[(SLi)2(thf)3]}2]?2 THF. Angew Chem Int Ed Engl 2004; 43:6192-6. [PMID: 15549751 DOI: 10.1002/anie.200461254] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Vojtech Jancik
- Institut für Anorganische Chemie, Georg-August Universität, Tammannstrasse 4, 37077 Göttingen, Germany
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45
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Jancik V, Moya Cabrera M, Roesky H, Herbst‐Irmer R, Neculai D, Neculai A, Noltemeyer M, Schmidt H. Phosphane‐Catalyzed Reactions of LAlH
2
with Elemental Chalcogens; Preparation of [LAl(μ‐E)
2
AlL] [E = S, Se, Te, L = HC{C(Me)N(Ar)}
2
, Ar = 2,6‐
i
Pr
2
C
6
H
3
]. Eur J Inorg Chem 2004. [DOI: 10.1002/ejic.200400062] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Vojtech Jancik
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany, Fax: +49‐551‐393‐373
| | - Monica M. Moya Cabrera
- Instituto de Química, UNAM, Circuito Exterior Cd. Universitaria, Coyoacán, D. F. 04510, Mexico, Fax: +52‐55‐6162203 or ‐6162217
| | - Herbert W. Roesky
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany, Fax: +49‐551‐393‐373
| | - Regine Herbst‐Irmer
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany, Fax: +49‐551‐393‐373
| | - Dante Neculai
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany, Fax: +49‐551‐393‐373
| | - Ana M. Neculai
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany, Fax: +49‐551‐393‐373
| | - Mathias Noltemeyer
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany, Fax: +49‐551‐393‐373
| | - Hans‐Georg Schmidt
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany, Fax: +49‐551‐393‐373
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Kumar SS, Rong J, Singh S, Roesky HW, Vidovic D, Magull J, Neculai D, Chandrasekhar V, Baldus M. Synthesis and Reactivity of the Carbaalanes (AlH)6(AlNMe3)2(CCH2C5H4FeC5H5)6 and (AlH)6(AlNMe3)2(CCH2Ph)6: X-ray Crystal Structure of (AlH)6(AlNMe3)2(CCH2C5H4FeC5H5)6. Organometallics 2004. [DOI: 10.1021/om040015w] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S. Shravan Kumar
- Institut für Anorganische Chemie der Georg-August-Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Junfeng Rong
- Institut für Anorganische Chemie der Georg-August-Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Sanjay Singh
- Institut für Anorganische Chemie der Georg-August-Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Herbert W. Roesky
- Institut für Anorganische Chemie der Georg-August-Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Denis Vidovic
- Institut für Anorganische Chemie der Georg-August-Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Jörg Magull
- Institut für Anorganische Chemie der Georg-August-Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Dante Neculai
- Institut für Anorganische Chemie der Georg-August-Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| | | | - Marc Baldus
- Max-Planck-Institut für Biophysikalische Chemie, D-37077 Göttingen, Germany
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Jancik V, Pineda LW, Pinkas J, Roesky HW, Neculai D, Neculai AM, Herbst-Irmer R. Preparation of Monomeric[LAl(NH2)2]—A Main-Group Metal Diamide Containing Two Terminal NH2 Groups. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200353541] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Jancik V, Pineda LW, Pinkas J, Roesky HW, Neculai D, Neculai AM, Herbst-Irmer R. Preparation of Monomeric[LAl(NH2)2]—A Main-Group Metal Diamide Containing Two Terminal NH2 Groups. Angew Chem Int Ed Engl 2004; 43:2142-5. [PMID: 15083467 DOI: 10.1002/anie.200353541] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Vojtech Jancik
- Institut für Anorganische Chemie, Georg-August Universität Göttingen, Tammannstrasse 4, 37077 Goettingen, Germany
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Pineda LW, Jancik V, Roesky HW, Neculai D, Neculai AM. Preparation and Structure of the First Germanium(II) Hydroxide: The Congener of an Unknown Low-Valent Carbon Analogue. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200353205] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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50
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Neculai AM, Neculai D, Roesky HW, Magull J. Synthesis and structure of LLnBr2 (L=Et2NCH2CH2NC(Me)CHC(Me)NCH2CH2NEt2; Ln=Y, Sm, and Yb). Polyhedron 2004. [DOI: 10.1016/j.poly.2003.10.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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