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Zhu Y, Bai Y, Yan W, Li M, Wu F, Xu M, Wu N, Ge H, Liu Y. A mutation in CCDC91, Homo sapiens coiled-coil domain containing 91 protein, cause autosomal-dominant acrokeratoelastoidosis. Eur J Hum Genet 2024; 32:647-655. [PMID: 38627542 PMCID: PMC11153616 DOI: 10.1038/s41431-024-01573-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/26/2024] [Accepted: 02/20/2024] [Indexed: 06/07/2024] Open
Abstract
Acrokeratoelastoidosis (AKE) is a rare autosomal dominant hereditary skin disease characterized by small, round-oval, flat-topped keratotic papules on the palms, soles and dorsal aspect of hands or feet. The causative gene for AKE remains unidentified. This study aims to identify the causative gene of AKE and explore the underlying biological mechanisms. A large, three-generation Chinese family exhibiting classic AKE symptoms was identified. A genome-wide linkage analysis and whole-exome sequencing were employed to determine the causative gene. shRNA knockdown in human skin fibroblasts and CRISPR/Cas9 knockout in HEK293T cells were utilized to assess gene functions in the progression of elastic fiber biosynthesis. The linkage analysis identified a susceptibility region between rs7296765 to rs10784618 on chromosome 12. Whole-exome sequencing confirmed a splicing mutation of 1101 + 1 G > A in the CCDC91 gene, resulting in exon 11 skipping and a subsequent 59-amino-acid-residue loss (residues L309-Q367del). Further functional analysis revealed distended Golgi cisternae, cytoplasmic vesicle accumulation, and lysosome presence. Immnunostaining of si-CCDC91-HSF cells demonstrated tropoelastin accumulation in the Golgi and abnormal extracellular aggregates. There are no significant changes in Fibrillin-1 microfibril assembly and lysyl oxidase activity. The findings strongly suggest that the protein product of the CCDC91 gene plays a crucial role in elastin transport. This discovery enhances our understanding of CCDC91's function and broadens the known pathogenic mechanisms of AKE.
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Affiliation(s)
- Yunlu Zhu
- Shanghai Skin Disease Hospital, School of Medicine, Tongji Medical University, Shanghai, China
- Department of Dermatology, Anhui Provincial Children's Hospital, Hefei City, Anhui Province, China
| | - Yun Bai
- Shanghai Skin Disease Hospital, School of Medicine, Tongji Medical University, Shanghai, China
| | - Wannian Yan
- Shanghai Skin Disease Hospital, School of Medicine, Tongji Medical University, Shanghai, China
| | - Ming Li
- Department of Dermatology, Children's Hospital of Fudan University, Shanghai, 200032, China
| | - Fei Wu
- Shanghai Skin Disease Hospital, School of Medicine, Tongji Medical University, Shanghai, China
| | - Mingyuan Xu
- Shanghai Skin Disease Hospital, School of Medicine, Tongji Medical University, Shanghai, China
| | - Nanhui Wu
- Shanghai Skin Disease Hospital, School of Medicine, Tongji Medical University, Shanghai, China
| | - HongSong Ge
- Department of Dermatology, Anhui Provincial Children's Hospital, Hefei City, Anhui Province, China.
| | - Yeqiang Liu
- Shanghai Skin Disease Hospital, School of Medicine, Tongji Medical University, Shanghai, China.
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2
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Bartuzi D, Kaczor AA, Matosiuk D. Illuminating the "Twilight Zone": Advances in Difficult Protein Modeling. Methods Mol Biol 2023; 2627:25-40. [PMID: 36959440 DOI: 10.1007/978-1-0716-2974-1_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Homology modeling was long considered a method of choice in tertiary protein structure prediction. However, it used to provide models of acceptable quality only when templates with appreciable sequence identity with a target could be found. The threshold value was long assumed to be around 20-30%. Below this level, obtained sequence identity was getting dangerously close to values that can be obtained by chance, after aligning any random, unrelated sequences. In these cases, other approaches, including ab initio folding simulations or fragment assembly, were usually employed. The most recent editions of the CASP and CAMEO community-wide modeling methods assessment have brought some surprising outcomes, proving that much more clues can be inferred from protein sequence analyses than previously thought. In this chapter, we focus on recent advances in the field of difficult protein modeling, pushing the threshold deep into the "twilight zone", with particular attention devoted to improvements in applications of machine learning and model evaluation.
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Affiliation(s)
- Damian Bartuzi
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Laboratory, Medical University of Lublin, Lublin, Poland.
| | - Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Laboratory, Medical University of Lublin, Lublin, Poland
- University of Eastern Finland, School of Pharmacy, Kuopio, Finland
| | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Laboratory, Medical University of Lublin, Lublin, Poland
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3
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Yang W, Tian R, Zhu Y, Huang P, Ma X, Meng X, Dai W, Tao Y, Chen D, Zhang J, Lu J, Xie H, Jian X, Yang Z, Wang R. Paraquat is an agonist of STIM1 and increases intracellular calcium levels. Commun Biol 2022; 5:1151. [PMID: 36310238 PMCID: PMC9618025 DOI: 10.1038/s42003-022-04130-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
Paraquat (PQ) is an efficient herbicide but leads to high mortality with no antidote in mammals. PQ produces reactive oxygen species (ROS), leading to epithelial-mesenchymal transition (EMT) for pulmonary fibrosis in type II alveolar (AT II) cells. Intriguingly, strategies reducing ROS exhibit limited therapeutic effects, indicating other targets existing for PQ toxicity. Herein we report that PQ is also an agonist for STIM1 that increases intracellular calcium levels. Particularly, PQ promotes STIM1 puncta formation and association with TRPC1 or ORAI for extracellular calcium entry and thus intracellular calcium influx. Further studies reveal the importance of P584&Y586 residues in STIM1 for PQ association that facilitates STIM1 binding to TRPC1. Consequently, the STIM1-TRPC1 route facilitates PQ-induced EMT for pulmonary fibrosis as well as cell death. Our results demonstrate that PQ is an agonist of STIM1 that induces extracellular calcium entry, increases intracellular calcium levels, and thus promotes EMT in AT II cells.
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Affiliation(s)
- Wenyu Yang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 201620, China
| | - Rui Tian
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 201620, China
| | - Yong Zhu
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 201620, China
| | - Peijie Huang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 201620, China
| | - Xinrun Ma
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 201620, China
| | - Xiaoxiao Meng
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 201620, China
| | - Wentao Dai
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China
| | - Yiming Tao
- Department of Poisoning and Occupational Diseases, Emergency, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Daonan Chen
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 201620, China
| | - Jiaxiang Zhang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 201620, China
| | - Jian Lu
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 201620, China
| | - Hui Xie
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 201620, China
| | - Xiangdong Jian
- Department of Poisoning and Occupational Diseases, Emergency, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
| | - Zhengfeng Yang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 201620, China.
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 201620, China.
| | - Ruilan Wang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 201620, China.
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4
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Chen F, Ni C, Wang X, Cheng R, Pan C, Wang Y, Liang J, Zhang J, Cheng J, Chin YE, Zhou Y, Wang Z, Guo Y, Chen S, Htun S, Mathes EF, de Alba Campomanes AG, Slavotinek AM, Zhang S, Li M, Yao Z. S1P defects cause a new entity of cataract, alopecia, oral mucosal disorder, and psoriasis-like syndrome. EMBO Mol Med 2022; 14:e14904. [PMID: 35362222 PMCID: PMC9081911 DOI: 10.15252/emmm.202114904] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/28/2022] [Accepted: 03/08/2022] [Indexed: 11/17/2022] Open
Abstract
In this report, we discovered a new entity named cataract, alopecia, oral mucosal disorder, and psoriasis‐like (CAOP) syndrome in two unrelated and ethnically diverse patients. Furthermore, patient 1 failed to respond to regular treatment. We found that CAOP syndrome was caused by an autosomal recessive defect in the mitochondrial membrane‐bound transcription factor peptidase/site‐1 protease (MBTPS1, S1P). Mitochondrial abnormalities were observed in patient 1 with CAOP syndrome. Furthermore, we found that S1P is a novel mitochondrial protein that forms a trimeric complex with ETFA/ETFB. S1P enhances ETFA/ETFB flavination and maintains its stability. Patient S1P variants destabilize ETFA/ETFB, impair mitochondrial respiration, decrease fatty acid β‐oxidation activity, and shift mitochondrial oxidative phosphorylation (OXPHOS) to glycolysis. Mitochondrial dysfunction and inflammatory lesions in patient 1 were significantly ameliorated by riboflavin supplementation, which restored the stability of ETFA/ETFB. Our study discovered that mutations in MBTPS1 resulted in a new entity of CAOP syndrome and elucidated the mechanism of the mutations in the new disease.
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Affiliation(s)
- Fuying Chen
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Cheng Ni
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaoxiao Wang
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ruhong Cheng
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Chaolan Pan
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yumeng Wang
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jianying Liang
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jia Zhang
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jinke Cheng
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Y Eugene Chin
- Instituteof Health Sciences, Chinese Academy of Sciences, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yi Zhou
- Department of gastroenterology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhen Wang
- Department of Dermatology, Children's Hospital of Shanghai Jiaotong University, Shanghai, China
| | - Yiran Guo
- Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, PA, USA
| | - She Chen
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Stephanie Htun
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Erin F Mathes
- Departments of Dermatology and Pediatrics, University California, San Francisco, CA, USA
| | | | - Anne M Slavotinek
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Si Zhang
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ming Li
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhirong Yao
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai, China
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5
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Lu Y, Dai W, Huang J, Chen X, Yao Y. A Biomimetic Glue Protein Modulates Hepatic Gene Expression. Macromol Biosci 2021; 21:e2000303. [PMID: 33393184 DOI: 10.1002/mabi.202000303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/22/2020] [Indexed: 01/08/2023]
Abstract
Glue protein as secretion from fruit fly larva plays a significant role in metamorphosis as cementing material for pupation sites. However, the biochemical composition of this macromolecule remains obscure. This study takes the advantage of high-resolution proteomic analysis to unveil the protein compositions. A glue protein group is identified as chitin-binding motifs by bioinformatic analysis. Computational modeling analysis of representative proteins illustrates the binding site between protein and chitin. A biosynthetic approach is used to fabricate a glue protein by a modified Escherichia coli recombinant system. The as-biosynthesized biomimetic glue protein is applied as an extracellular matrix to investigate its biocompatibility and functionality. It is found that the purified recombinant protein shows enhanced performance to cellular viability. This finding provides a potential biomacromolecule candidate as an extracellular matrix for cell culture.
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Affiliation(s)
- Yi Lu
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China
| | - Wentao Dai
- Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, China
| | - Jianhua Huang
- Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China.,Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
| | - Xuexin Chen
- Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China.,Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
| | - Yuan Yao
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China
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6
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Zhang Z, Zhang J, Chen F, Zheng L, Li H, Liu M, Li M, Yao Z. Family of hereditary fibrosing poikiloderma with tendon contractures, myopathy and pulmonary fibrosis caused by a novel FAM111B mutation. J Dermatol 2019; 46:1014-1018. [PMID: 31392773 DOI: 10.1111/1346-8138.15045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/16/2019] [Indexed: 11/29/2022]
Abstract
Hereditary fibrosing poikiloderma with tendon contractures, myopathy and pulmonary fibrosis (POIKTMP) is a recently identified autosomal dominant genetic syndrome with mutations in FAM111B. Herein, we report a 14-month-old girl who presented with progressive poikiloderma on the face. Her 24-year-old mother had an identical facial poikiloderma, hyperpigmentation, mottling and Blaschko line hypopigmentation on the trunk and limbs, as well as severe tendon contractures. Next-generation sequencing based on a targeted gene capture panel revealed a missense mutation in the FAM111B gene p.Phe416Ser (c.1247T>C). Her mother had the same mutation as the proband. Moreover, this mutation was absent in the unaffected father and maternal grandparents. Based on the clinical manifestations and genetic analysis, the proband and her mother were diagnosed with POIKTMP. Protein modeling indicated that the mutation p.Phe416Ser dramatically changed the protein structure, especially its structural stability, and affected the protein function. This is the first report of POIKTMP in a Chinese family due to a novel FAM111B mutation. Furthermore, we have reviewed the genotype-phenotype correlation, differential diagnoses and management of POIKTMP.
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Affiliation(s)
- Zhen Zhang
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jia Zhang
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Fuying Chen
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Luyao Zheng
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Huaguo Li
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ming Liu
- Department of Radiology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ming Li
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhirong Yao
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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7
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Yang Z, Yan H, Dai W, Jing J, Yang Y, Mahajan S, Zhou Y, Li W, Macaubas C, Mellins ED, Shih CC, Fitzpatrick JAJ, Faccio R. Tmem178 negatively regulates store-operated calcium entry in myeloid cells via association with STIM1. J Autoimmun 2019; 101:94-108. [PMID: 31018906 DOI: 10.1016/j.jaut.2019.04.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/09/2019] [Accepted: 04/12/2019] [Indexed: 12/27/2022]
Abstract
Store-operated calcium entry (SOCE) modulates cytosolic calcium in multiple cells. Endoplasmic reticulum (ER)-localized STIM1 and plasma membrane (PM)-localized ORAI1 are two main components of SOCE. STIM1:ORAI1 association requires STIM1 oligomerization, its re-distribution to ER-PM junctions, and puncta formation. However, little is known about the negative regulation of these steps to prevent calcium overload. Here, we identified Tmem178 as a negative modulator of STIM1 puncta formation in myeloid cells. Using site-directed mutagenesis, co-immunoprecipitation assays and FRET imaging, we determined that Tmem178:STIM1 association occurs via their transmembrane motifs. Mutants that increase Tmem178:STIM1 association reduce STIM1 puncta formation, SOCE activation, impair inflammatory cytokine production in macrophages and osteoclastogenesis. Mutants that reduce Tmem178:STIM1 association reverse these effects. Furthermore, exposure to plasma from arthritic patients decreases Tmem178 expression, enhances SOCE activation and cytoplasmic calcium. In conclusion, Tmem178 modulates the rate-limiting step of STIM1 puncta formation and therefore controls SOCE in inflammatory conditions.
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Affiliation(s)
- Zhengfeng Yang
- Department of Orthopaedics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hui Yan
- Department of Orthopaedics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Wentao Dai
- Shanghai Center for Bioinformation Technology & Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, China
| | - Ji Jing
- Institute of Biosciences and Technology, Texas A&M University College of Medicine, Houston, TX 77030, USA
| | - Yihu Yang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Sahil Mahajan
- Department of Orthopaedics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Yubin Zhou
- Institute of Biosciences and Technology, Texas A&M University College of Medicine, Houston, TX 77030, USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Claudia Macaubas
- Department of Pediatrics, Program in Immunology, Stanford University, Stanford, CA 94305, USA
| | - Elizabeth D Mellins
- Department of Pediatrics, Program in Immunology, Stanford University, Stanford, CA 94305, USA
| | - Chien-Cheng Shih
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, USA; Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA; Department of Biomedical Engineering, Washington University, St. Louis, MO, USA
| | - Roberta Faccio
- Department of Orthopaedics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Shriners Hospitals for Children, St. Louis MO, USA.
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8
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LGR4 is a receptor for RANKL and negatively regulates osteoclast differentiation and bone resorption. Nat Med 2016; 22:539-46. [PMID: 27064449 DOI: 10.1038/nm.4076] [Citation(s) in RCA: 243] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 03/05/2016] [Indexed: 12/16/2022]
Abstract
Tumor necrosis factor (TNF) superfamily member 11 (TNFSF11, also known as RANKL) regulates multiple physiological or pathological functions, including osteoclast differentiation and osteoporosis. TNFRSF11A (also called RANK) is considered to be the sole receptor for RANKL. Herein we report that leucine-rich repeat-containing G-protein-coupled receptor 4 (LGR4, also called GPR48) is another receptor for RANKL. LGR4 competes with RANK to bind RANKL and suppresses canonical RANK signaling during osteoclast differentiation. RANKL binding to LGR4 activates the Gαq and GSK3-β signaling pathway, an action that suppresses the expression and activity of nuclear factor of activated T cells, cytoplasmic, calcineurin-dependent 1 (NFATC1) during osteoclastogenesis. Both whole-body (Lgr4(-/-)) and monocyte conditional knockout mice of Lgr4 (Lgr4 CKO) exhibit osteoclast hyperactivation (including elevation of osteoclast number, surface area, and size) and increased bone erosion. The soluble LGR4 extracellular domain (ECD) binds RANKL and inhibits osteoclast differentiation in vivo. Moreover, LGR4-ECD therapeutically abrogated RANKL-induced bone loss in three mouse models of osteoporosis. Therefore, LGR4 acts as a second RANKL receptor that negatively regulates osteoclast differentiation and bone resorption.
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9
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Cao MS, Liu BY, Dai WT, Zhou WX, Li YX, Li YY. Differential network analysis reveals dysfunctional regulatory networks in gastric carcinogenesis. Am J Cancer Res 2015; 5:2605-2625. [PMID: 26609471 PMCID: PMC4633893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 08/04/2015] [Indexed: 06/05/2023] Open
Abstract
Gastric Carcinoma is one of the most common cancers in the world. A large number of differentially expressed genes have been identified as being associated with gastric cancer progression, however, little is known about the underlying regulatory mechanisms. To address this problem, we developed a differential networking approach that is characterized by including a nascent methodology, differential coexpression analysis (DCEA), and two novel quantitative methods for differential regulation analysis. We first applied DCEA to a gene expression dataset of gastric normal mucosa, adenoma and carcinoma samples to identify gene interconnection changes during cancer progression, based on which we inferred normal, adenoma, and carcinoma-specific gene regulation networks by using linear regression model. It was observed that cancer genes and drug targets were enriched in each network. To investigate the dynamic changes of gene regulation during carcinogenesis, we then designed two quantitative methods to prioritize differentially regulated genes (DRGs) and gene pairs or links (DRLs) between adjacent stages. It was found that known cancer genes and drug targets are significantly higher ranked. The top 4% normal vs. adenoma DRGs (36 genes) and top 6% adenoma vs. carcinoma DRGs (56 genes) proved to be worthy of further investigation to explore their association with gastric cancer. Out of the 16 DRGs involved in two top-10 DRG lists of normal vs. adenoma and adenoma vs. carcinoma comparisons, 15 have been reported to be gastric cancer or cancer related. Based on our inferred differential networking information and known signaling pathways, we generated testable hypotheses on the roles of GATA6, ESRRG and their signaling pathways in gastric carcinogenesis. Compared with established approaches which build genome-scale GRNs, or sub-networks around differentially expressed genes, the present one proved to be better at enriching cancer genes and drug targets, and prioritizing disease-related genes on the dataset we considered. We propose this extendable differential networking framework as a promising way to gain insights into gene regulatory mechanisms underlying cancer progression and other phenotypic changes.
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Affiliation(s)
- Mu-Shui Cao
- School of Life Science and Technology, Tongji UniversityShanghai 200092, P. R. China
- Shanghai Center for Bioinformation TechnologyShanghai 200235, P. R. China
- Shanghai Industrial Technology Institute1278 Keyuan Road, Shanghai 201203, P. R. China
| | - Bing-Ya Liu
- Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200025, P. R. China
| | - Wen-Tao Dai
- Shanghai Center for Bioinformation TechnologyShanghai 200235, P. R. China
- Shanghai Industrial Technology Institute1278 Keyuan Road, Shanghai 201203, P. R. China
| | - Wei-Xin Zhou
- Shanghai Center for Bioinformation TechnologyShanghai 200235, P. R. China
- Shanghai Industrial Technology Institute1278 Keyuan Road, Shanghai 201203, P. R. China
- Shanghai Engineering Research Center of Pharmaceutical Translation1278 Keyuan Road, Shanghai 201203, P. R. China
| | - Yi-Xue Li
- School of Life Science and Technology, Tongji UniversityShanghai 200092, P. R. China
- Shanghai Center for Bioinformation TechnologyShanghai 200235, P. R. China
- Shanghai Industrial Technology Institute1278 Keyuan Road, Shanghai 201203, P. R. China
- Shanghai Engineering Research Center of Pharmaceutical Translation1278 Keyuan Road, Shanghai 201203, P. R. China
| | - Yuan-Yuan Li
- Shanghai Center for Bioinformation TechnologyShanghai 200235, P. R. China
- Shanghai Industrial Technology Institute1278 Keyuan Road, Shanghai 201203, P. R. China
- Shanghai Engineering Research Center of Pharmaceutical Translation1278 Keyuan Road, Shanghai 201203, P. R. China
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10
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Gammaherpesvirus Tegument Protein ORF33 Is Associated With Intranuclear Capsids at an Early Stage of the Tegumentation Process. J Virol 2015; 89:5288-97. [PMID: 25717105 DOI: 10.1128/jvi.00079-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 02/13/2015] [Indexed: 12/26/2022] Open
Abstract
UNLABELLED Herpesvirus nascent capsids, after assembly in the nucleus, must acquire a variety of tegument proteins during maturation. However, little is known about the identity of the tegument proteins that are associated with capsids in the nucleus or the molecular mechanisms involved in the nuclear egress of capsids into the cytoplasm, especially for the two human gammaherpesviruses Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV), due to a lack of efficient lytic replication systems. Murine gammaherpesvirus 68 (MHV-68) is genetically related to human gammaherpesviruses and serves as an excellent model to study the de novo lytic replication of gammaherpesviruses. We have previously shown that open reading frame 33 (ORF33) of MHV-68 is a tegument protein of mature virions and is essential for virion assembly and egress. However, it remains unclear how ORF33 is incorporated into virions. In this study, we first show that the endogenous ORF33 protein colocalizes with capsid proteins at discrete areas in the nucleus during viral infection. Cosedimentation analysis as well as an immunoprecipitation assay demonstrated that ORF33 is associated with both nuclear and cytoplasmic capsids. An immunogold labeling experiment using an anti-ORF33 monoclonal antibody revealed that ORF33-rich areas in the nucleus are surrounded by immature capsids. Moreover, ORF33 is associated with nucleocapsids prior to primary envelopment as well as with mature virions in the cytoplasm. Finally, we show that ORF33 interacts with two capsid proteins, suggesting that nucleocapsids may interact with ORF33 in a direct manner. In summary, we identified ORF33 to be a tegument protein that is associated with intranuclear capsids prior to primary envelopment, likely through interacting with capsid proteins in a direct manner. IMPORTANCE Morphogenesis is an essential step in virus propagation that leads to the generation of progeny virions. For herpesviruses, this is a complicated process that starts in the nucleus. Although the process of capsid assembly and genome packaging is relatively well understood, how capsids acquire tegument (the layer between the capsid and the envelope in a herpesvirus virion) and whether the initial tegumentation process takes place in the nucleus remain unclear. We previously showed that ORF33 of MHV-68 is a tegument protein and functions in both the nuclear egress of capsids and final virion maturation in the cytoplasm. In the present study, we show that ORF33 is associated with intranuclear capsids prior to primary envelopment and identify novel interactions between ORF33 and two capsid proteins. Our work provides new insights into the association between tegument proteins and nucleocapsids at an early stage of the virion maturation process for herpesviruses.
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