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Lei X, Tian X, Wang H, Xu X, Li G, Liu W, Wang D, Xiao Z, Zhang M, Li MJ, Zhang Z, Ma Z, Liu Z. Noncoding SNP at rs1663689 represses ADGRG6 via interchromosomal interaction and reduces lung cancer progression. EMBO Rep 2023; 24:e56212. [PMID: 37154297 PMCID: PMC10328068 DOI: 10.15252/embr.202256212] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 04/05/2023] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
A previous genome-wide association study (GWAS) revealed an association of the noncoding SNP rs1663689 with susceptibility to lung cancer in the Chinese population. However, the underlying mechanism is unknown. In this study, using allele-specific 4C-seq in heterozygous lung cancer cells combined with epigenetic information from CRISPR/Cas9-edited cell lines, we show that the rs1663689 C/C variant represses the expression of ADGRG6, a gene located on a separate chromosome, through an interchromosomal interaction of the rs1663689 bearing region with the ADGRG6 promoter. This reduces downstream cAMP-PKA signaling and subsequently tumor growth both in vitro and in xenograft models. Using patient-derived organoids, we show that rs1663689 T/T-but not C/C-bearing lung tumors are sensitive to the PKA inhibitor H89, potentially informing therapeutic strategies. Our study identifies a genetic variant-mediated interchromosomal interaction underlying ADGRG6 regulation and suggests that targeting the cAMP-PKA signaling pathway may be beneficial in lung cancer patients bearing the homozygous risk genotype at rs1663689.
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Affiliation(s)
- Xinyue Lei
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Xiaoling Tian
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Hao Wang
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Xinran Xu
- Department of Pharmacology, School of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Guoli Li
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Wenxu Liu
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Dan Wang
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Zengtuan Xiao
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Mengzhe Zhang
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Mulin Jun Li
- Department of Pharmacology, School of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Zhenfa Zhang
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Zhenyi Ma
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Department of Cell Biology, School of Basic Medical SciencesHangzhou Normal UniversityHangzhouChina
| | - Zhe Liu
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
- Department of Pharmacology, School of Basic Medical SciencesTianjin Medical UniversityTianjinChina
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Department of Cell Biology, School of Basic Medical SciencesHangzhou Normal UniversityHangzhouChina
- Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjingChina
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Liu W, Wang J, Comte‐Miserez V, Zhang M, Yu X, Chen Q, Jessen HJ, Mayer A, Wu S, Ye S. Cryo-EM structure of the polyphosphate polymerase VTC reveals coupling of polymer synthesis to membrane transit. EMBO J 2023; 42:e113320. [PMID: 37066886 PMCID: PMC10183816 DOI: 10.15252/embj.2022113320] [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: 12/17/2022] [Revised: 03/18/2023] [Accepted: 03/27/2023] [Indexed: 04/18/2023] Open
Abstract
The eukaryotic vacuolar transporter chaperone (VTC) complex acts as a polyphosphate (polyP) polymerase that synthesizes polyP from adenosine triphosphate (ATP) and translocates polyP across the vacuolar membrane to maintain an intracellular phosphate (Pi ) homeostasis. To discover how the VTC complex performs its function, we determined a cryo-electron microscopy structure of an endogenous VTC complex (Vtc4/Vtc3/Vtc1) purified from Saccharomyces cerevisiae at 3.1 Å resolution. The structure reveals a heteropentameric architecture of one Vtc4, one Vtc3, and three Vtc1 subunits. The transmembrane region forms a polyP-selective channel, likely adopting a resting state conformation, in which a latch-like, horizontal helix of Vtc4 limits the entrance. The catalytic Vtc4 central domain is located on top of the pseudo-symmetric polyP channel, creating a strongly electropositive pathway for nascent polyP that can couple synthesis to translocation. The SPX domain of the catalytic Vtc4 subunit positively regulates polyP synthesis by the VTC complex. The noncatalytic Vtc3 regulates VTC through a phosphorylatable loop. Our findings, along with the functional data, allow us to propose a mechanism of polyP channel gating and VTC complex activation.
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Affiliation(s)
- Wei Liu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life SciencesTianjin UniversityTianjinChina
| | - Jiening Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life SciencesHubei UniversityWuhanChina
| | | | - Mengyu Zhang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life SciencesTianjin UniversityTianjinChina
| | - Xuejing Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life SciencesHubei UniversityWuhanChina
| | - Qingfeng Chen
- School of Life SciencesYunnan UniversityKunmingChina
| | - Henning Jacob Jessen
- Institute of Organic ChemistryUniversity of FreiburgFreiburgGermany
- CIBSS – Centre for Integrative Biological Signalling StudiesUniversity of FreiburgFreiburgGermany
| | - Andreas Mayer
- Département d'ImmunobiologieUniversité de LausanneEpalingesSwitzerland
| | - Shan Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life SciencesHubei UniversityWuhanChina
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life SciencesTianjin UniversityTianjinChina
- Life Sciences Institute, Zhejiang UniversityHangzhouChina
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Xu M, Guo Y, Wang M, Luo X, Shen X, Li Z, Wang L, Guo W. L-arginine homeostasis governs adult neural stem cell activation by modulating energy metabolism in vivo. EMBO J 2023; 42:e112647. [PMID: 36740997 PMCID: PMC10015378 DOI: 10.15252/embj.2022112647] [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: 09/20/2022] [Revised: 01/07/2023] [Accepted: 01/09/2023] [Indexed: 02/07/2023] Open
Abstract
Neurogenesis in the developing and adult brain is intimately linked to remodeling of cellular metabolism. However, it is still unclear how distinct metabolic programs and energy sources govern neural stem cell (NSC) behavior and subsequent neuronal differentiation. Here, we found that adult mice lacking the mitochondrial urea metabolism enzyme, Arginase-II (Arg-II), exhibited NSC overactivation, thereby leading to accelerated NSC pool depletion and decreased hippocampal neurogenesis over time. Mechanistically, Arg-II deficiency resulted in elevated L-arginine levels and induction of a metabolic shift from glycolysis to oxidative phosphorylation (OXPHOS) caused by impaired attachment of hexokinase-I to mitochondria. Notably, selective inhibition of OXPHOS ameliorated NSC overactivation and restored abnormal neurogenesis in Arg-II deficient mice. Therefore, Arg-II-mediated intracellular L-arginine homeostasis directly influences the metabolic fitness of neural stem cells that is essential to maintain neurogenesis with age.
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Affiliation(s)
- Mingyue Xu
- State Key Laboratory for Molecular and Developmental Biology, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- Graduate SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Ye Guo
- State Key Laboratory for Molecular and Developmental Biology, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Min Wang
- State Key Laboratory for Molecular and Developmental Biology, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Xing Luo
- State Key Laboratory for Molecular and Developmental Biology, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- Graduate SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Xuning Shen
- State Key Laboratory for Molecular and Developmental Biology, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- Graduate SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Zhimin Li
- State Key Laboratory for Molecular and Developmental Biology, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- Graduate SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Lei Wang
- State Key Laboratory for Molecular and Developmental Biology, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- Graduate SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Weixiang Guo
- State Key Laboratory for Molecular and Developmental Biology, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- Graduate SchoolUniversity of Chinese Academy of SciencesBeijingChina
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Qiu Z, Lin Z, Hu A, Liu Y, Zeng W, Zhao X, Shi X, Luo J, Song B. GRAMD1/ASTER-mediated cholesterol transport promotes Smoothened cholesterylation at the endoplasmic reticulum. EMBO J 2023; 42:e111513. [PMID: 36524353 PMCID: PMC9890235 DOI: 10.15252/embj.2022111513] [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: 04/23/2022] [Revised: 11/28/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Hedgehog (Hh) signaling pathway plays a pivotal role in embryonic development. Hh binding to Patched1 (PTCH1) derepresses Smoothened (SMO), thereby activating the downstream signal transduction. Covalent SMO modification by cholesterol in its cysteine-rich domain (CRD) is essential for SMO function. SMO cholesterylation is a calcium-accelerated autoprocessing reaction, and STIM1-ORAI1-mediated store-operated calcium entry promotes cholesterylation and activation of endosome-localized SMO. However, it is unknown whether the Hh-PTCH1 interplay regulates the activity of the endoplasmic reticulum (ER)-localized SMO. Here, we found that PTCH1 inhibited the COPII-dependent export of SMO from the ER, whereas Hh promoted this process. The RRxWxR amino acid motif in the cytosolic tail of SMO was essential for COPII recognition, ciliary localization, and signal transduction activity. Hh and PTCH1 regulated cholesterol modification of the ER-localized SMO, and SMO cholesterylation accelerated its exit from ER. The GRAMD1/ASTER sterol transport proteins facilitated cholesterol transfer to ER from PM, resulting in increased SMO cholesterylation and enhanced Hh signaling. Collectively, we reveal a regulatory role of GRAMD-mediated cholesterol transport in ER-resident SMO maturation and Hh signaling.
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Affiliation(s)
- Zhi‐Ping Qiu
- College of Life Sciences, Taikang Center for Life and Medical Sciences, Taikang Medical School, Hubei Key Laboratory of Cell HomeostasisWuhan UniversityWuhanChina
| | - Zi‐Cun Lin
- College of Life Sciences, Taikang Center for Life and Medical Sciences, Taikang Medical School, Hubei Key Laboratory of Cell HomeostasisWuhan UniversityWuhanChina
| | - Ao Hu
- College of Life Sciences, Taikang Center for Life and Medical Sciences, Taikang Medical School, Hubei Key Laboratory of Cell HomeostasisWuhan UniversityWuhanChina
| | - Yuan‐Bin Liu
- College of Life Sciences, Taikang Center for Life and Medical Sciences, Taikang Medical School, Hubei Key Laboratory of Cell HomeostasisWuhan UniversityWuhanChina
| | - Wan‐Er Zeng
- College of Life Sciences, Taikang Center for Life and Medical Sciences, Taikang Medical School, Hubei Key Laboratory of Cell HomeostasisWuhan UniversityWuhanChina
| | - Xiaolu Zhao
- College of Life Sciences, Taikang Center for Life and Medical Sciences, Taikang Medical School, Hubei Key Laboratory of Cell HomeostasisWuhan UniversityWuhanChina
| | - Xiong‐Jie Shi
- College of Life Sciences, Taikang Center for Life and Medical Sciences, Taikang Medical School, Hubei Key Laboratory of Cell HomeostasisWuhan UniversityWuhanChina
| | - Jie Luo
- College of Life Sciences, Taikang Center for Life and Medical Sciences, Taikang Medical School, Hubei Key Laboratory of Cell HomeostasisWuhan UniversityWuhanChina
| | - Bao‐Liang Song
- College of Life Sciences, Taikang Center for Life and Medical Sciences, Taikang Medical School, Hubei Key Laboratory of Cell HomeostasisWuhan UniversityWuhanChina
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Sun H, Chen Y, Yan K, Shao Y, Zhang QC, Lin Y, Xi Q. Recruitment of TRIM33 to cell-context specific PML nuclear bodies regulates nodal signaling in mESCs. EMBO J 2023; 42:e112058. [PMID: 36524443 PMCID: PMC9890237 DOI: 10.15252/embj.2022112058] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/15/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
TRIM33 is a chromatin reader required for mammalian mesendoderm differentiation after activation of Nodal signaling, while its role in mESCs is still elusive. Here, we report that TRIM33 co-localizes with promyelocytic leukemia nuclear bodies (PML-NBs) specifically in mESCs, to mediate Nodal signaling-directed transcription of Lefty1/2. We show that TRIM33 puncta formation in mESCs depends on PML and on specific assembly of PML-NBs. Moreover, TRIM33 and PML co-regulate Lefty1/2 expression in mESCs, with both PML protein and formation of mESCs-specific PML-NBs being required for TRIM33 recruitment to these loci, and PML-NBs directly associating with the Lefty1/2 loci. Finally, a TurboID proximity-labeling experiment confirmed that TRIM33 is highly enriched only in mESCs-specific PML-NBs. Thus, our study supports a model in which TRIM33 condensates regulate Nodal signaling-directed transcription in mESCs and shows that PML-NBs can recruit distinct sets of client proteins in a cell-context-dependent manner.
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Affiliation(s)
- Hongyao Sun
- MOE Key Laboratory of Protein Sciences, School of Life SciencesTsinghua UniversityBeijingChina
- Joint Graduate Program of Peking‐Tsinghua‐NIBSTsinghua UniversityBeijingChina
| | - Yutong Chen
- IDG/McGovern Institute for Brain Research, School of Life SciencesTsinghua UniversityBeijingChina
| | - Kun Yan
- Tsinghua‐Peking Center for Life Sciences, School of Life SciencesTsinghua UniversityBeijingChina
| | - Yanqiu Shao
- Tsinghua‐Peking Center for Life Sciences, School of Life SciencesTsinghua UniversityBeijingChina
| | - Qiangfeng C Zhang
- Joint Graduate Program of Peking‐Tsinghua‐NIBSTsinghua UniversityBeijingChina
- Tsinghua‐Peking Center for Life Sciences, School of Life SciencesTsinghua UniversityBeijingChina
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life SciencesTsinghua UniversityBeijingChina
| | - Yi Lin
- IDG/McGovern Institute for Brain ResearchTsinghua‐Peking Joint Centre for Life SciencesBeijingChina
| | - Qiaoran Xi
- MOE Key Laboratory of Protein Sciences, School of Life SciencesTsinghua UniversityBeijingChina
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Yang M, Ismayil A, Jiang Z, Wang Y, Zheng X, Yan L, Hong Y, Li D, Liu Y. A viral protein disrupts vacuolar acidification to facilitate virus infection in plants. EMBO J 2022; 41:e108713. [PMID: 34888888 PMCID: PMC8762549 DOI: 10.15252/embj.2021108713] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 05/13/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 01/19/2023] Open
Abstract
Vacuolar acidification is essential for vacuoles in diverse physiological functions. However, its role in plant defense, and whether and how pathogens affect vacuolar acidification to promote infection remain unknown. Here, we show that Barley stripe mosaic virus (BSMV) replicase γa, but not its mutant γaR569A , directly blocks acidification of vacuolar lumen and suppresses autophagic degradation to promote viral infection in plants. These were achieved via molecular interaction between γa and V-ATPase catalytic subunit B2 (VHA-B2), leading to disruption of the interaction between VHA-B2 and V-ATPase catalytic subunit E (VHA-E), which impairs the membrane localization of VHA-B2 and suppresses V-ATPase activity. Furthermore, a mutant virus BSMVR569A with the R569A point mutation possesses less viral pathogenicity. Interestingly, multiple viral infections block vacuolar acidification. These findings reveal that functional vacuolar acidification is required for plant antiviral defense and disruption of vacuolar acidification could be a general viral counter-defense strategy employed by multiple viruses.
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Affiliation(s)
- Meng Yang
- MOE Key Laboratory of BioinformaticsCenter for Plant BiologySchool of Life SciencesTsinghua UniversityBeijingChina
- Tsinghua‐Peking Center for Life SciencesBeijingChina
| | - Asigul Ismayil
- MOE Key Laboratory of BioinformaticsCenter for Plant BiologySchool of Life SciencesTsinghua UniversityBeijingChina
- Tsinghua‐Peking Center for Life SciencesBeijingChina
| | - Zhihao Jiang
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yan Wang
- MOE Key Laboratory of BioinformaticsCenter for Plant BiologySchool of Life SciencesTsinghua UniversityBeijingChina
- Tsinghua‐Peking Center for Life SciencesBeijingChina
| | - Xiyin Zheng
- MOE Key Laboratory of BioinformaticsCenter for Plant BiologySchool of Life SciencesTsinghua UniversityBeijingChina
- Tsinghua‐Peking Center for Life SciencesBeijingChina
| | - Liming Yan
- MOE Key Laboratory of Protein ScienceSchool of MedicineTsinghua UniversityBeijingChina
| | - Yiguo Hong
- Research Centre for Plant RNA SignalingCollege of Life and Environmental SciencesHangzhou Normal UniversityHangzhouChina
| | - Dawei Li
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yule Liu
- MOE Key Laboratory of BioinformaticsCenter for Plant BiologySchool of Life SciencesTsinghua UniversityBeijingChina
- Tsinghua‐Peking Center for Life SciencesBeijingChina
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Mo C, Guo J, Qin J, Zhang X, Sun Y, Wei H, Cao D, Zhang Y, Zhao C, Xiong Y, Zhang Y, Sun Y, Shen L, Yue R. Single-cell transcriptomics of LepR-positive skeletal cells reveals heterogeneous stress-dependent stem and progenitor pools. EMBO J 2022; 41:e108415. [PMID: 34957577 PMCID: PMC8844986 DOI: 10.15252/embj.2021108415] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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: 04/06/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 12/31/2022] Open
Abstract
Leptin receptor (LepR)-positive cells are key components of the bone marrow hematopoietic microenvironment, and highly enrich skeletal stem and progenitor cells that maintain homeostasis of the adult skeleton. However, the heterogeneity and lineage hierarchy within this population has been elusive. Using genetic lineage tracing and single-cell RNA sequencing, we found that Lepr-Cre labels most bone marrow stromal cells and osteogenic lineage cells in adult long bones. Integrated analysis of Lepr-Cre-traced cells under homeostatic and stress conditions revealed dynamic changes of the adipogenic, osteogenic, and periosteal lineages. Importantly, we discovered a Notch3+ bone marrow sub-population that is slow-cycling and closely associated with the vasculatures, as well as key transcriptional networks promoting osteo-chondrogenic differentiation. We also identified a Sca-1+ periosteal sub-population with high clonogenic activity but limited osteo-chondrogenic potential. Together, we mapped the transcriptomic landscape of adult LepR+ stem and progenitor cells and uncovered cellular and molecular mechanisms underlying their maintenance and lineage specification.
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Affiliation(s)
- Chunyang Mo
- Institute for Regenerative MedicineShanghai East HospitalFrontier Science Center for Stem Cell ResearchShanghai Key Laboratory of Signaling and Disease ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Jingxin Guo
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Department of Orthopedics Surgery2nd Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
| | - Jiachen Qin
- Institute for Regenerative MedicineShanghai East HospitalFrontier Science Center for Stem Cell ResearchShanghai Key Laboratory of Signaling and Disease ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Xiaoying Zhang
- Institute for Regenerative MedicineShanghai East HospitalFrontier Science Center for Stem Cell ResearchShanghai Key Laboratory of Signaling and Disease ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Yuxi Sun
- Department of CardiologyShanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Hanjing Wei
- Institute for Regenerative MedicineShanghai East HospitalFrontier Science Center for Stem Cell ResearchShanghai Key Laboratory of Signaling and Disease ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Dandan Cao
- Institute for Regenerative MedicineShanghai East HospitalFrontier Science Center for Stem Cell ResearchShanghai Key Laboratory of Signaling and Disease ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Yiying Zhang
- Institute for Regenerative MedicineShanghai East HospitalFrontier Science Center for Stem Cell ResearchShanghai Key Laboratory of Signaling and Disease ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Chengchen Zhao
- Institute for Regenerative MedicineShanghai East HospitalFrontier Science Center for Stem Cell ResearchShanghai Key Laboratory of Signaling and Disease ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Yanhong Xiong
- Institute for Regenerative MedicineShanghai East HospitalFrontier Science Center for Stem Cell ResearchShanghai Key Laboratory of Signaling and Disease ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Yong Zhang
- Institute for Regenerative MedicineShanghai East HospitalFrontier Science Center for Stem Cell ResearchShanghai Key Laboratory of Signaling and Disease ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Yao Sun
- Department of ImplantologySchool & Hospital of StomatologyShanghai Engineering Research Center of Tooth Restoration and RegenerationTongji UniversityShanghaiChina
| | - Li Shen
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Department of Orthopedics Surgery2nd Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Hangzhou Innovation CenterZhejiang UniversityHangzhouChina
| | - Rui Yue
- Institute for Regenerative MedicineShanghai East HospitalFrontier Science Center for Stem Cell ResearchShanghai Key Laboratory of Signaling and Disease ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina
- Shanghai Institute of Stem Cell Research and Clinical TranslationShanghaiChina
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8
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Zhang S, Stier P, Dagan G, Wang M. Anthropogenic Aerosols Modulated 20th-Century Sahel Rainfall Variability Via Their Impacts on North Atlantic Sea Surface Temperature. Geophys Res Lett 2022; 49:e2021GL095629. [PMID: 35865079 PMCID: PMC9287015 DOI: 10.1029/2021gl095629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/02/2021] [Accepted: 12/13/2021] [Indexed: 06/15/2023]
Abstract
The Sahel rainfall has a close teleconnection with North Atlantic sea surface temperature (NASST) variability, which has separately been shown to be affected by aerosols. Therefore, changes in regional aerosols emission could potentially drive multidecadal Sahel rainfall variability. Here we combine ensembles of state-of-the-art global climate models (the CESM and CanESM large ensemble simulations and CMIP6 models) with observational data sets to demonstrate that anthropogenic aerosols have significantly impacted 20th-century detrended Sahel rainfall multidecadal variability through modifying NASST. We show that aerosol-induced multidecadal variations of downward solar radiative fluxes over the North Atlantic cause NASST variability during the 20th century, altering the ITCZ position and dynamically linking aerosol effects to Sahel rainfall variability. This process chain is caused by aerosol-induced changes in radiative surface fluxes rather than changes in ocean circulations. CMIP6 models further suggest that aerosol-cloud interactions modulate the inter-model uncertainty of simulated NASST and potentially the Sahel rainfall variability.
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Affiliation(s)
- Shipeng Zhang
- Department of PhysicsAtmospheric, Oceanic and Planetary PhysicsUniversity of OxfordOxfordUK
| | - Philip Stier
- Department of PhysicsAtmospheric, Oceanic and Planetary PhysicsUniversity of OxfordOxfordUK
| | - Guy Dagan
- Institute of Earth SciencesHebrew University of JerusalemJerusalemIsrael
| | - Minghuai Wang
- Joint International Research Laboratory of Atmospheric and Earth System Sciences and School of Atmospheric SciencesNanjing UniversityNanjingChina
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Liao Y, Duan B, Zhang Y, Zhang X, Xia B. Excessive ER-phagy mediated by the autophagy receptor FAM134B results in ER stress, the unfolded protein response, and cell death in HeLa cells. J Biol Chem 2019; 294:20009-20023. [PMID: 31748416 PMCID: PMC6937584 DOI: 10.1074/jbc.ra119.008709] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [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: 04/19/2019] [Revised: 11/07/2019] [Indexed: 12/19/2022] Open
Abstract
Autophagy is typically a prosurvival cellular process that promotes the turnover of long-lived proteins and damaged organelles, but it can also induce cell death. We have previously reported that the small molecule Z36 induces autophagy along with autophagic cell death in HeLa cells. In this study, we analyzed differential gene expression in Z36-treated HeLa cells and found that Z36-induced endoplasmic reticulum-specific autophagy (ER-phagy) results in ER stress and the unfolded protein response (UPR). This result is in contrast to the common notion that autophagy is generally activated in response to ER stress and the UPR. We demonstrate that Z36 up-regulates the expression levels of FAM134B, LC3, and Atg9, which together mediate excessive ER-phagy, characterized by forming increased numbers of autophagosomes with larger sizes. We noted that the excessive ER-phagy accelerates ER degradation and impairs ER homeostasis and thereby triggers ER stress and the UPR as well as ER-phagy-dependent cell death. Interestingly, overexpression of FAM134B alone in HeLa cells is sufficient to impair ER homeostasis and cause ER stress and cell death. These findings suggest a mechanism involving FAM134B activity for ER-phagy to promote cell death.
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Affiliation(s)
- Yangjie Liao
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Bo Duan
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yufei Zhang
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | | | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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10
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Zhang S, Cao X, Liu C, Li W, Zeng W, Li B, Chi H, Liu M, Qin X, Tang L, Yan G, Ge Z, Liu Y, Gao Q, Lu H. N-glycopeptide Signatures of IgA 2 in Serum from Patients with Hepatitis B Virus-related Liver Diseases. Mol Cell Proteomics 2019; 18:2262-2272. [PMID: 31501225 PMCID: PMC6823847 DOI: 10.1074/mcp.ra119.001722] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 08/09/2019] [Indexed: 12/11/2022] Open
Abstract
N-glycosylation alteration has been reported in liver diseases. Characterizing N-glycopeptides that correspond to N-glycan structure with specific site information enables better understanding of the molecular pathogenesis of liver damage and cancer. Here, unbiased quantification of N-glycopeptides of a cluster of serum glycoproteins with 40-55 kDa molecular weight (40-kDa band) was investigated in hepatitis B virus (HBV)-related liver diseases. We used an N-glycopeptide method based on 18O/16O C-terminal labeling to obtain 82 comparisons of serum from patients with HBV-related hepatocellular carcinoma (HCC) and liver cirrhosis (LC). Then, multiple reaction monitoring (MRM) was performed to quantify N-glycopeptide relative to the protein content, especially in the healthy donor-HBV-LC-HCC cascade. TPLTAN205ITK (H5N5S1F1) and (H5N4S2F1) corresponding to the glycopeptides of IgA2 were significantly elevated in serum from patients with HBV infection and even higher in HBV-related LC patients, as compared with healthy donor. In contrast, the two glycopeptides of IgA2 fell back down in HBV-related HCC patients. In addition, the variation in the abundance of two glycopeptides was not caused by its protein concentration. The altered N-glycopeptides might be part of a unique glycan signature indicating an IgA-mediated mechanism and providing potential diagnostic clues in HBV-related liver diseases.
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Affiliation(s)
- Shu Zhang
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Xinyi Cao
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Chao Liu
- Beijing Advanced Innovation Center for Precision Medicine, Beihang University, Beijing 100083, China
| | - Wei Li
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Wenfeng Zeng
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190, China
| | - Baiwen Li
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiaotong University, Shanghai 201620, China
| | - Hao Chi
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190, China
| | - Mingqi Liu
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xue Qin
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Lingyi Tang
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Guoquan Yan
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Zefan Ge
- State Key Laboratory for Novel Software Technology, Nanjing University, Nanjing 210046, China
| | - Yinkun Liu
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Qiang Gao
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China.
| | - Haojie Lu
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Chemistry, Fudan University, Shanghai 200433, China; NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China.
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11
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Ren Z, Qi D, Pugh N, Li K, Wen B, Zhou R, Xu S, Liu S, Jones AR. Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets. Mol Cell Proteomics 2019; 18:86-98. [PMID: 30293062 PMCID: PMC6317475 DOI: 10.1074/mcp.ra118.000832] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 05/03/2018] [Revised: 08/31/2018] [Indexed: 01/22/2023] Open
Abstract
Rice (Oryza sativa) is one of the most important worldwide crops. The genome has been available for over 10 years and has undergone several rounds of annotation. We created a comprehensive database of transcripts from 29 public RNA sequencing data sets, officially predicted genes from Ensembl plants, and common contaminants in which to search for protein-level evidence. We re-analyzed nine publicly accessible rice proteomics data sets. In total, we identified 420K peptide spectrum matches from 47K peptides and 8,187 protein groups. 4168 peptides were initially classed as putative novel peptides (not matching official genes). Following a strict filtration scheme to rule out other possible explanations, we discovered 1,584 high confidence novel peptides. The novel peptides were clustered into 692 genomic loci where our results suggest annotation improvements. 80% of the novel peptides had an ortholog match in the curated protein sequence set from at least one other plant species. For the peptides clustering in intergenic regions (and thus potentially new genes), 101 loci were identified, for which 43 had a high-confidence hit for a protein domain. Our results can be displayed as tracks on the Ensembl genome or other browsers supporting Track Hubs, to support re-annotation of the rice genome.
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Affiliation(s)
- Zhe Ren
- From the ‡BGI-Shenzhen, Shenzhen 518083, China
| | - Da Qi
- From the ‡BGI-Shenzhen, Shenzhen 518083, China
| | - Nina Pugh
- §Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Kai Li
- From the ‡BGI-Shenzhen, Shenzhen 518083, China
| | - Bo Wen
- ‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030;; ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030
| | - Ruo Zhou
- From the ‡BGI-Shenzhen, Shenzhen 518083, China
| | - Shaohang Xu
- From the ‡BGI-Shenzhen, Shenzhen 518083, China
| | - Siqi Liu
- From the ‡BGI-Shenzhen, Shenzhen 518083, China;.
| | - Andrew R Jones
- §Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK;.
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Jiang LY, Jiang W, Tian N, Xiong YN, Liu J, Wei J, Wu KY, Luo J, Shi XJ, Song BL. Ring finger protein 145 (RNF145) is a ubiquitin ligase for sterol-induced degradation of HMG-CoA reductase. J Biol Chem 2018; 293:4047-4055. [PMID: 29374057 PMCID: PMC5857978 DOI: 10.1074/jbc.ra117.001260] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [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: 12/04/2017] [Revised: 01/15/2018] [Indexed: 12/21/2022] Open
Abstract
Cholesterol biosynthesis is tightly regulated in the cell. For example, high sterol concentrations can stimulate degradation of the rate-limiting cholesterol biosynthetic enzyme 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMG-CoA reductase, HMGCR). HMGCR is broken down by the endoplasmic reticulum membrane-associated protein complexes consisting of insulin-induced genes (Insigs) and the E3 ubiquitin ligase gp78. Here we found that HMGCR degradation is partially blunted in Chinese hamster ovary (CHO) cells lacking gp78 (gp78-KO). To identify other ubiquitin ligase(s) that may function together with gp78 in triggering HMGCR degradation, we performed a small-scale short hairpin RNA-based screening targeting endoplasmic reticulum-localized E3s. We found that knockdown of both ring finger protein 145 (Rnf145) and gp78 genes abrogates sterol-induced degradation of HMGCR in CHO cells. We also observed that RNF145 interacts with Insig-1 and -2 proteins and ubiquitinates HMGCR. Moreover, the tetrapeptide sequence YLYF in the sterol-sensing domain and the Cys-537 residue in the RING finger domain were essential for RNF145 binding to Insigs and RNF145 E3 activity, respectively. Of note, amino acid substitutions in the YLYF or of Cys-537 completely abolished RNF145-mediated HMGCR degradation. In summary, our study reveals that RNF145, along with gp78, promotes HMGCR degradation in response to elevated sterol levels and identifies residues essential for RNF145 function.
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Affiliation(s)
- Lu-Yi Jiang
- From the Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Wei Jiang
- From the Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Na Tian
- From the Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Yan-Ni Xiong
- From the Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Jie Liu
- From the Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Jian Wei
- From the Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Kai-Yue Wu
- From the Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Jie Luo
- From the Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Xiong-Jie Shi
- From the Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Bao-Liang Song
- From the Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
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