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Deng Y, Wang Y, Shi Q, Jiang Y. Identification of hub genes associated with osteoporosis development by comprehensive bioinformatics analysis. Front Genet 2023; 14:1028681. [PMID: 36911390 PMCID: PMC9999471 DOI: 10.3389/fgene.2023.1028681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/05/2023] [Indexed: 02/25/2023] Open
Abstract
Osteoporosis (OP) is a systemic bone disease caused by various factors, including, the decrease of bone density and quality, the destruction of bone microstructure, and the increase of bone fragility. It is a disease with a high incidence in a large proportion of the world's elderly population. However, osteoporosis lacks obvious symptoms and sensitive biomarkers. Therefore, it is extremely urgent to discover and identify disease-related biomarkers for early clinical diagnosis and effective intervention for osteoporosis. In our study, the Linear Models for Microarray Data (LIMMA) tool was used to screen differential expressed genes from transcriptome sequencing data of OP blood samples downloaded from the GEO database, and cluster Profiler was used for enriching analysis of differently expressed genes. In order to analyzed the relevance of gene modules, clinical symptoms, and the most related module setting genes associated with disease progression, we adapted Weighted Gene Co-expression Network Analysis (WGCNA) to screen and analyze the related pathways and relevant molecules. We used the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database to construct protein interaction network of key modules, and Cytoscape software was used to complete network visualization and screen of core genes in the network. Various plug-in algorithms of cytoHubba were used to identify key genes of OP. Finally, correlation analysis and single-gene gene probe concentration analysis (GSEA) analysis were performed for each core gene. Results of a total of 8 key genes that were closely related to the occurrence and development of OP were screened out, which provided a brand-new idea for the clinical diagnosis and early prevention of OP. Quantitative real-time PCR (qRT-PCR) was performed for validation, the expression levels of CUL1, PTEN and STAT1 genes in the OS group were significantly higher than in the non-OS groups. Receiver operating characteristic analysis demonstrated that CUL1, PTEN and STAT1 displayed considerable diagnostic accuracy for OS.
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Affiliation(s)
- Yuxuan Deng
- Department of Endocrinology, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yunyun Wang
- Academic Affairs Office, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qing Shi
- Department of Endocrinology, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yanxia Jiang
- Department of Endocrinology, First Affiliated Hospital of Nanchang University, Nanchang, China
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André da Silva R, Moraes de Paiva Roda V, Philipe de Souza Ferreira L, Oliani SM, Paula Girol A, Gil CD. Annexins as potential targets in ocular diseases. Drug Discov Today 2022; 27:103367. [PMID: 36165812 DOI: 10.1016/j.drudis.2022.103367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/05/2022] [Accepted: 09/14/2022] [Indexed: 11/20/2022]
Abstract
Annexins (AnxAs) are Ca2+/phospholipid-binding proteins extensively studied and generally involved in several diseases. Although evidence exists regarding the distribuition of AnxAs in the visual system, their exact roles and the exact cell types of the eye where these proteins are expressed are not well-understood. AnxAs have pro-resolving roles in infectious, autoimmune, degenerative, fibrotic and angiogenic conditions, making them an important target in ocular tissue homeostasis. This review summarizes the current knowledge on the distribution and function of AnxA1-8 isoforms under normal and pathological conditions in the visual system, as well as perspectives for ophthalmologic treatments, including the potential use of the AnxA1 recombinant and/or its mimetic peptide Ac2-26.
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Affiliation(s)
- Rafael André da Silva
- Biosciences Graduate Program, Institute of Biosciences, Letters and Exact Sciences, Universidade Estadual Paulista (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Vinicius Moraes de Paiva Roda
- Life Systems Biology Graduate Program, Institute of Biomedical Sciences, Universidade de São Paulo (USP), São Paulo, SP 05508-000, Brazil
| | - Luiz Philipe de Souza Ferreira
- Structural and Functional Biology Graduate Program, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP 04023-900, Brazil
| | - Sonia M Oliani
- Biosciences Graduate Program, Institute of Biosciences, Letters and Exact Sciences, Universidade Estadual Paulista (UNESP), São José do Rio Preto, SP 15054-000, Brazil; Structural and Functional Biology Graduate Program, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP 04023-900, Brazil; Advanced Research Center in Medicine (CEPAM) Unilago, São José do Rio Preto, SP 15030-070, Brazil
| | - Ana Paula Girol
- Biosciences Graduate Program, Institute of Biosciences, Letters and Exact Sciences, Universidade Estadual Paulista (UNESP), São José do Rio Preto, SP 15054-000, Brazil; Structural and Functional Biology Graduate Program, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP 04023-900, Brazil; Centro Universitário Padre Albino (UNIFIPA), Catanduva, SP 15809-144, Brazil
| | - Cristiane D Gil
- Biosciences Graduate Program, Institute of Biosciences, Letters and Exact Sciences, Universidade Estadual Paulista (UNESP), São José do Rio Preto, SP 15054-000, Brazil; Structural and Functional Biology Graduate Program, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP 04023-900, Brazil.
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Ayagama T, Bose SJ, Capel RA, Priestman DA, Berridge G, Fischer R, Galione A, Platt FM, Kramer H, Burton RA. A modified density gradient proteomic-based method to analyze endolysosomal proteins in cardiac tissue. iScience 2021; 24:102949. [PMID: 34466782 PMCID: PMC8384914 DOI: 10.1016/j.isci.2021.102949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/04/2021] [Accepted: 08/02/2021] [Indexed: 11/22/2022] Open
Abstract
The importance of lysosomes in cardiac physiology and pathology is well established, and evidence for roles in calcium signaling is emerging. We describe a label-free proteomics method suitable for small cardiac tissue biopsies based on density-separated fractionation, which allows study of endolysosomal (EL) proteins. Density gradient fractions corresponding to tissue lysate; sarcoplasmic reticulum (SR), mitochondria (Mito) (1.3 g/mL); and EL with negligible contamination from SR or Mito (1.04 g/mL) were analyzed using Western blot, enzyme activity assay, and liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis (adapted discontinuous Percoll and sucrose differential density gradient). Kyoto Encyclopedia of Genes and Genomes, Reactome, Panther, and Gene Ontology pathway analysis showed good coverage of RAB proteins and lysosomal cathepsins (including cardiac-specific cathepsin D) in the purified EL fraction. Significant EL proteins recovered included catalytic activity proteins. We thus present a comprehensive protocol and data set of guinea pig atrial EL organelle proteomics using techniques also applicable for non-cardiac tissue.
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Affiliation(s)
- Thamali Ayagama
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Samuel J. Bose
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Rebecca A. Capel
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | | | - Georgina Berridge
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Antony Galione
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Frances M. Platt
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, London, W12 0NN UK
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Chen X, Liu G, Wang S, Zhang H, Xue P. Machine learning analysis of gene expression profile reveals a novel diagnostic signature for osteoporosis. J Orthop Surg Res 2021; 16:189. [PMID: 33722258 PMCID: PMC7958453 DOI: 10.1186/s13018-021-02329-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/01/2021] [Indexed: 01/25/2023] Open
Abstract
Background Osteoporosis (OP) is increasingly prevalent with the aging of the world population. It is urgent to identify efficient diagnostic signatures for the clinical application. Method We downloaded the mRNA profile of 90 peripheral blood samples with or without OP from GEO database (Number: GSE152073). Weighted gene co-expression network analysis (WGCNA) was used to reveal the correlation among genes in all samples. GO term and KEGG pathway enrichment analysis was performed via the clusterProfiler R package. STRING database was applied to screen the interaction pairs among proteins. Protein–protein interaction (PPI) network was visualized based on Cytoscape, and the key genes were screened using the cytoHubba plug-in. The diagnostic model based on these key genes was constructed, and 5-fold cross validation method was applied to evaluate its reliability. Results A gene module consisted of 176 genes predicted to be associated with the occurrence of OP was identified. A total of 16 significantly enriched GO terms and 1 significantly enriched KEGG pathway were obtained based on the 176 genes. The top 50 key genes in the PPI network were identified. Then 22 genes were screened based on stepwise regression analysis from the 50 key genes. Of which, 9 genes were further screened out by multivariate regression analysis with the significant threshold of P value < 0.01. The diagnostic model was established based on the optimal 9 key genes, which efficiently separated the normal samples and OP samples. Conclusion A diagnostic model established based on nine key genes could reliably separate OP patients from healthy subjects, which provided novel lightings on the diagnostic research of OP. Supplementary Information The online version contains supplementary material available at 10.1186/s13018-021-02329-1.
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Affiliation(s)
- Xinlei Chen
- Department of Orthopedics, Zibo Central Hospital, Zibo, 255000, Shandong, China
| | - Guangping Liu
- Department of Orthopedics, Zibo Central Hospital, Zibo, 255000, Shandong, China
| | - Shuxiang Wang
- Department of Orthopedics, Zibo Central Hospital, Zibo, 255000, Shandong, China
| | - Haiyang Zhang
- Department of Orthopedics, Zibo Central Hospital, Zibo, 255000, Shandong, China
| | - Peng Xue
- Department of Orthopedics, Zibo Central Hospital, Zibo, 255000, Shandong, China.
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