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Yang K, Wang Q, Wu L, Gao QC, Tang S. Development and verification of a combined diagnostic model for primary Sjögren's syndrome by integrated bioinformatics analysis and machine learning. Sci Rep 2023; 13:8641. [PMID: 37244954 DOI: 10.1038/s41598-023-35864-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/25/2023] [Indexed: 05/29/2023] Open
Abstract
Primary Sjögren's syndrome (pSS) is a chronic, systemic autoimmune disease mostly affecting the exocrine glands. This debilitating condition is complex and specific treatments remain unavailable. There is a need for the development of novel diagnostic models for early screening. Four gene profiling datasets were downloaded from the Gene Expression Omnibus database. The 'limma' software package was used to identify differentially expressed genes (DEGs). A random forest-supervised classification algorithm was used to screen disease-specific genes, and three machine learning algorithms, including artificial neural networks (ANN), random forest (RF), and support vector machines (SVM), were used to build a pSS diagnostic model. The performance of the model was measured using its area under the receiver operating characteristic curve. Immune cell infiltration was investigated using the CIBERSORT algorithm. A total of 96 DEGs were identified. By utilizing a RF classifier, a set of 14 signature genes that are pivotal in transcription regulation and disease progression in pSS were identified. Through the utilization of training and testing datasets, diagnostic models for pSS were successfully designed using ANN, RF, and SVM, resulting in AUCs of 0.972, 1.00, and 0.9742, respectively. The validation set yielded AUCs of 0.766, 0.8321, and 0.8223. It was the RF model that produced the best prediction performance out of the three models tested. As a result, an early predictive model for pSS was successfully developed with high diagnostic performance, providing a valuable resource for the screening and early diagnosis of pSS.
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Affiliation(s)
- Kun Yang
- School of Humanities and Social Sciences, Shanxi Medical University, Taiyuan, China
| | - Qi Wang
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Li Wu
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Department of Anesthesiology, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China
| | - Qi-Chao Gao
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Shan Tang
- The First Hospital of Shanxi Medical University, Taiyuan, China.
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Lozano-Mendoza J, Ramírez-Montiel F, Rangel-Serrano Á, Páramo-Pérez I, Mendoza-Macías CL, Saavedra-Salazar F, Franco B, Vargas-Maya N, Jeelani G, Saito-Nakano Y, Anaya-Velázquez F, Nozaki T, Padilla-Vaca F. Attenuation of In Vitro and In Vivo Virulence Is Associated with Repression of Gene Expression of AIG1 Gene in Entamoeba histolytica. Pathogens 2023; 12:pathogens12030489. [PMID: 36986411 PMCID: PMC10051847 DOI: 10.3390/pathogens12030489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Entamoeba histolytica virulence results from complex host-parasite interactions implicating multiple amoebic components (e.g., Gal/GalNAc lectin, cysteine proteinases, and amoebapores) and host factors (microbiota and immune response). UG10 is a strain derived from E. histolytica virulent HM-1:IMSS strain that has lost its virulence in vitro and in vivo as determined by a decrease of hemolytic, cytopathic, and cytotoxic activities, increased susceptibility to human complement, and its inability to form liver abscesses in hamsters. We compared the transcriptome of nonvirulent UG10 and its parental HM-1:IMSS strain. No differences in gene expression of the classical virulence factors were observed. Genes downregulated in the UG10 trophozoites encode for proteins that belong to small GTPases, such as Rab and AIG1. Several protein-coding genes, including iron-sulfur flavoproteins and heat shock protein 70, were also upregulated in UG10. Overexpression of the EhAIG1 gene (EHI_180390) in nonvirulent UG10 trophozoites resulted in augmented virulence in vitro and in vivo. Cocultivation of HM-1:IMSS with E. coli O55 bacteria cells reduced virulence in vitro, and the EhAIG1 gene expression was downregulated. In contrast, virulence was increased in the monoxenic strain UG10, and the EhAIG1 gene expression was upregulated. Therefore, the EhAIG1 gene (EHI_180390) represents a novel virulence determinant in E. histolytica.
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Affiliation(s)
- Janeth Lozano-Mendoza
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Fátima Ramírez-Montiel
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Ángeles Rangel-Serrano
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Itzel Páramo-Pérez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | | | - Faridi Saavedra-Salazar
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Bernardo Franco
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Naurú Vargas-Maya
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Ghulam Jeelani
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
| | - Yumiko Saito-Nakano
- Department of Parasitology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-0052, Japan
| | - Fernando Anaya-Velázquez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Tomoyoshi Nozaki
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
- Department of Parasitology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-0052, Japan
| | - Felipe Padilla-Vaca
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
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3
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Komatsu M, Saito K, Miyamoto I, Koike K, Iyoda M, Nakashima D, Kasamatsu A, Shiiba M, Tanzawa H, Uzawa K. Aberrant GIMAP2 expression affects oral squamous cell carcinoma progression by promoting cell cycle and inhibiting apoptosis. Oncol Lett 2022; 23:49. [PMID: 34992682 PMCID: PMC8721858 DOI: 10.3892/ol.2021.13167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/01/2021] [Indexed: 11/19/2022] Open
Abstract
GTPases of immunity-associated protein 2 (GIMAP2) is a GTPase family member associated with T cell survival. However, its mechanisms of action in oral squamous cell carcinoma (OSCC) remain largely unknown. Therefore, the present study aimed to elucidate the possible role of GIMAP2 in OSCC development by investigating its expression levels and molecular mechanisms in OSCC. Reverse transcription quantitative PCR, immunoblotting and immunohistochemistry indicated that GIMAP2 expression was significantly upregulated (P<0.05) in OSCC-derived cell lines and primary OSCC specimens compared with that in their normal counterparts. GIMAP2-knockdown OSCC cells exhibited decreased cell growth, which was associated with cyclin-dependent kinase (CDK)4, CDK6 and phosphorylated Rb downregulation and p53 and p21 upregulation. In addition to cell cycle arrest, GIMAP2 affected anti-apoptotic functions in GIMAP2-knockdown cells by upregulating Bcl-2 and downregulating Bax and Bak. These findings indicated that GIMAP2 may significantly influence OSCC development and apoptosis inhibition and thus is a potential biomarker of OSCC.
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Affiliation(s)
- Mari Komatsu
- Department of Oral Science, Chiba University, Chiba 260-8670, Japan
| | - Kengo Saito
- Department of Molecular Virology, Chiba University, Chiba 260-8670, Japan
| | - Isao Miyamoto
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
| | - Kazuyuki Koike
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
| | - Manabu Iyoda
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
| | - Dai Nakashima
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
| | - Atsushi Kasamatsu
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
| | - Masashi Shiiba
- Department of Medical Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
| | - Hideki Tanzawa
- Department of Oral Science, Chiba University, Chiba 260-8670, Japan.,Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
| | - Katsuhiro Uzawa
- Department of Oral Science, Chiba University, Chiba 260-8670, Japan.,Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
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4
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Limoges MA, Cloutier M, Nandi M, Ilangumaran S, Ramanathan S. The GIMAP Family Proteins: An Incomplete Puzzle. Front Immunol 2021; 12:679739. [PMID: 34135906 PMCID: PMC8201404 DOI: 10.3389/fimmu.2021.679739] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/12/2021] [Indexed: 12/19/2022] Open
Abstract
Overview: Long-term survival of T lymphocytes in quiescent state is essential to maintain their cell numbers in secondary lymphoid organs and in peripheral circulation. In the BioBreeding diabetes-prone strain of rats (BB-DP), loss of functional GIMAP5 (GTPase of the immune associated nucleotide binding protein 5) results in profound peripheral T lymphopenia. This discovery heralded the identification of a new family of proteins initially called Immune-associated nucleotide binding protein (IAN) family. In this review we will use ‘GIMAP’ to refer to this family of proteins. Recent studies suggest that GIMAP proteins may interact with each other and also be involved in the movement of the cellular cargo along the cytoskeletal network. Here we will summarize the current knowledge on the characteristics and functions of GIMAP family of proteins.
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Affiliation(s)
- Marc-André Limoges
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
| | - Maryse Cloutier
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
| | - Madhuparna Nandi
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
| | - Subburaj Ilangumaran
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
| | - Sheela Ramanathan
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
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Chen H, Song Y, Deng C, Xu Y, Xu H, Zhu X, Song G, Tang Q, Lu J, Wang J. Comprehensive analysis of immune infiltration and gene expression for predicting survival in patients with sarcomas. Aging (Albany NY) 2020; 13:2168-2183. [PMID: 33316779 PMCID: PMC7880383 DOI: 10.18632/aging.202229] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 10/31/2020] [Indexed: 12/24/2022]
Abstract
Tumor microenvironments are strongly related to tumor development, and immune-infiltrating cells and immune-related molecules are potential prognostic markers. However, the shortcomings of traditional measurement methods limit the accurate evaluation of various components in tumor microenvironments. With the rapid advancement of Next-Generation RNA Sequencing technology, dedicated and in-depth analyses of immune filtration within the tumor microenvironment has been achieved. In this study, we combined the bioinformatics analysis methods ESTIMATE, CIBERSORT, and ssGSEA to characterize the immune infiltration of sarcomas and to identify specific immunomodulators of different pathological subtypes. We further extracted a functional enrichment of significant immune-related genes related to improved prognosis, including NR1H3, VAMP5, GIMAP2, GBP2, HLA-E and CRIP1. Overall, the immune microenvironment is an important prognostic determinant of sarcomas and may be a potential resource for developing effective immunotherapy.
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Affiliation(s)
- Hongmin Chen
- Department of Musculoskeletal Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, Guangdong, P. R. China
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, P. R. China
| | - Yijiang Song
- Department of Musculoskeletal Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, Guangdong, P. R. China
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, P. R. China
| | - Chuangzhong Deng
- Department of Musculoskeletal Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, Guangdong, P. R. China
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, P. R. China
| | - Yanyang Xu
- Department of Musculoskeletal Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, Guangdong, P. R. China
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, P. R. China
| | - Huaiyuan Xu
- Department of Musculoskeletal Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, Guangdong, P. R. China
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, P. R. China
| | - Xiaojun Zhu
- Department of Musculoskeletal Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, Guangdong, P. R. China
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, P. R. China
| | - Guohui Song
- Department of Musculoskeletal Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, Guangdong, P. R. China
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, P. R. China
| | - Qinglian Tang
- Department of Musculoskeletal Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, Guangdong, P. R. China
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, P. R. China
| | - Jinchang Lu
- Department of Musculoskeletal Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, Guangdong, P. R. China
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, P. R. China
| | - Jin Wang
- Department of Musculoskeletal Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, Guangdong, P. R. China
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, P. R. China
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Nakada-Tsukui K, Sekizuka T, Sato-Ebine E, Escueta-de Cadiz A, Ji DD, Tomii K, Kuroda M, Nozaki T. AIG1 affects in vitro and in vivo virulence in clinical isolates of Entamoeba histolytica. PLoS Pathog 2018; 14:e1006882. [PMID: 29554130 PMCID: PMC5884625 DOI: 10.1371/journal.ppat.1006882] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 04/04/2018] [Accepted: 01/17/2018] [Indexed: 11/17/2022] Open
Abstract
The disease state of amebiasis, caused by Entamoeba histolytica, varies from asymptomatic to severe manifestations that include dysentery and extraintestinal abscesses. The virulence factors of the pathogen, and host defense mechanisms, contribute to the outcomes of infection; however, the underlying genetic factors, which affect clinical outcomes, remain to be fully elucidated. To identify these genetic factors in E. histolytica, we used Illumina next-generation sequencing to conduct a comparative genomic analysis of two clinical isolates obtained from diarrheal and asymptomatic patients (strains KU50 and KU27, respectively). By mapping KU50 and KU27 reads to the genome of a reference HM-1:IMSS strain, we identified two genes (EHI_089440 and EHI_176590) that were absent in strain KU27. In KU27, a single AIG1 (avrRpt2-induced gene 1) family gene (EHI_176590) was found to be deleted, from a tandem array of three AIG1 genes, by homologous recombination between the two flanking genes. Overexpression of the EHI_176590 gene, in strain HM-1:IMSS cl6, resulted in increased formation of cell-surface protrusions and enhanced adhesion to human erythrocytes. The EHI_176590 gene was detected by PCR in 56% of stool samples from symptomatic patients infected with E. histolytica, but only in 15% of stool samples from asymptomatic individuals. This suggests that the presence of the EHI_176590 gene is correlated with the outcomes of infection. Taken together, these data strongly indicate that the AIG1 family protein plays a pivotal role in E. histolytica virulence via regulation of host cell adhesion. Our in-vivo experiments, using a hamster liver abscess model, showed that overexpression or gene silencing of EHI_176590 reduced and increased liver abscess formation, respectively. This suggests that the AIG1 genes may have contrasting roles in virulence depending on the genetic background of the parasite and host environment.
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Affiliation(s)
- Kumiko Nakada-Tsukui
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Sekizuka
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Emi Sato-Ebine
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Dar-der Ji
- Center for Research and Diagnostics, Centers for Disease Control, Taipei, Taiwan
| | - Kentaro Tomii
- Artificial Intelligence Research Center (AIRC) and Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Makoto Kuroda
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomoyoshi Nozaki
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Webb LMC, Pascall JC, Hepburn L, Carter C, Turner M, Butcher GW. Generation and characterisation of mice deficient in the multi-GTPase domain containing protein, GIMAP8. PLoS One 2014; 9:e110294. [PMID: 25329815 PMCID: PMC4201521 DOI: 10.1371/journal.pone.0110294] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/17/2014] [Indexed: 02/06/2023] Open
Abstract
Background GTPases of the immunity-associated protein family (GIMAPs) are predominantly expressed in mature lymphocytes. Studies of rodents deficient in GIMAP1, GIMAP4, or GIMAP5 have demonstrated that these GTPases regulate lymphocyte survival. In contrast to the other family members, GIMAP8 contains three potential GTP-binding domains (G-domains), a highly unusual feature suggesting a novel function for this protein. To examine a role for GIMAP8 in lymphocyte biology we examined GIMAP8 expression during lymphocyte development. We also generated a mouse deficient in GIMAP8 and examined lymphocyte development and function. Principal Findings We show that GIMAP8 is expressed in the very early and late stages of T cell development in the thymus, at late stages during B cell development, and peripheral T and B cells. We find no defects in T or B lymphocyte development in the absence of GIMAP8. A marginal decrease in the number of recirculating bone marrow B cells suggests that GIMAP8 is important for the survival of mature B cells within the bone marrow niche. We also show that deletion of GIMAP8 results in a delay in apoptotic death of mature T cell in vitro in response to dexamethasone or γ-irradiation. However, despite these findings we find that GIMAP8-deficient mice mount normal primary and secondary responses to a T cell dependent antigen. Conclusions Despite its unique structure, GIMAP8 is not required for lymphocyte development but appears to have a minor role in maintaining recirculating B cells in the bone marrow niche and a role in regulating apoptosis of mature T cells.
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Affiliation(s)
- Louise M. C. Webb
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, United Kingdom
- * E-mail:
| | - John C. Pascall
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, United Kingdom
| | - Lucy Hepburn
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, United Kingdom
| | - Christine Carter
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, United Kingdom
| | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, United Kingdom
| | - Geoffrey W. Butcher
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, United Kingdom
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Ran S, Liu YJ, Zhang L, Pei Y, Yang TL, Hai R, Han YY, Lin Y, Tian Q, Deng HW. Genome-wide association study identified copy number variants important for appendicular lean mass. PLoS One 2014; 9:e89776. [PMID: 24626161 PMCID: PMC3953533 DOI: 10.1371/journal.pone.0089776] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 01/25/2014] [Indexed: 11/26/2022] Open
Abstract
Skeletal muscle is a major component of the human body. Age-related loss of muscle mass and function contributes to some public health problems such as sarcopenia and osteoporosis. Skeletal muscle, mainly composed of appendicular lean mass (ALM), is a heritable trait. Copy number variation (CNV) is a common type of human genome variant which may play an important role in the etiology of many human diseases. In this study, we performed genome-wide association analyses of CNV for ALM in 2,286 Caucasian subjects. We then replicated the major findings in 1,627 Chinese subjects. Two CNVs, CNV1191 and CNV2580, were detected to be associated with ALM (p = 2.26×10−2 and 3.34×10−3, respectively). In the Chinese replication sample, the two CNVs achieved p-values of 3.26×10−2 and 0.107, respectively. CNV1191 covers a gene, GTPase of the immunity-associated protein family (GIMAP1), which is important for skeletal muscle cell survival/death in humans. CNV2580 is located in the Serine hydrolase-like protein (SERHL) gene, which plays an important role in normal peroxisome function and skeletal muscle growth in response to mechanical stimuli. In summary, our study suggested two novel CNVs and the related genes that may contribute to variation in ALM.
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Affiliation(s)
- Shu Ran
- Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai, People’s Republic of China
| | - Yong-Jun Liu
- Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, Louisiana, United States of America
| | - Lei Zhang
- Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai, People’s Republic of China
| | - Yufang Pei
- Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai, People’s Republic of China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Institute of Molecular Genetics, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, People’s Republic of China
| | - Rong Hai
- Geriatrics Health Clinic of Inner Mongolia People’s Hospital, Inner Mongolia, People’s Republic of China
| | - Ying-Ying Han
- Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai, People’s Republic of China
| | - Yong Lin
- Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai, People’s Republic of China
| | - Qing Tian
- Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, Louisiana, United States of America
| | - Hong-Wen Deng
- Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai, People’s Republic of China
- Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail:
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Schwefel D, Arasu BS, Marino SF, Lamprecht B, Köchert K, Rosenbaum E, Eichhorst J, Wiesner B, Behlke J, Rocks O, Mathas S, Daumke O. Structural insights into the mechanism of GTPase activation in the GIMAP family. Structure 2013; 21:550-9. [PMID: 23454188 DOI: 10.1016/j.str.2013.01.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 01/17/2013] [Accepted: 01/19/2013] [Indexed: 10/27/2022]
Abstract
GTPases of immunity-associated proteins (GIMAPs) are regulators of lymphocyte survival and homeostasis. We previously determined the structural basis of GTP-dependent GIMAP2 scaffold formation on lipid droplets. To understand how its GTP hydrolysis is activated, we screened for other GIMAPs on lipid droplets and identified GIMAP7. In contrast to GIMAP2, GIMAP7 displayed dimerization-stimulated GTP hydrolysis. The crystal structure of GTP-bound GIMAP7 showed a homodimer that assembled via the G domains, with the helical extensions protruding in opposite directions. We identified a catalytic arginine that is supplied to the opposing monomer to stimulate GTP hydrolysis. GIMAP7 also stimulated GTP hydrolysis by GIMAP2 via an analogous mechanism. Finally, we found GIMAP2 and GIMAP7 expression differentially regulated in several human T cell lymphoma lines. Our findings suggest that GTPase activity in the GIMAP family is controlled by homo- and heterodimerization. This may have implications for the differential roles of some GIMAPs in lymphocyte survival.
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Affiliation(s)
- David Schwefel
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.
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