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Dowling P, Bazou D. Identification of Ubiquitination-Associated Proteins Using 2D-DIGE. Methods Mol Biol 2023; 2596:83-96. [PMID: 36378432 DOI: 10.1007/978-1-0716-2831-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ubiquitination is a post-translational modification, in which a small regulatory protein (~8.6 kDa) is tagged as a single moiety or as a chain to target proteins. Ubiquitination is the most versatile cellular regulatory mechanism, essential to the physiological and pathophysiological cellular events that regulate protein turnover, gene transcription, cell cycle progression, DNA repair, apoptosis, viral budding, and receptor-mediated endocytosis. Changes and abnormalities within the ubiquitination process can result in a plethora of diseases, including various cancers. The ubiquitination process is tightly controlled in a stepwise manner by four enzymes: E1 ubiquitin-activating enzymes, E2 ubiquitin-conjugating enzymes, E3 ubiquitin-ligating enzymes, and deubiquitinating proteases. Using fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) to detect and quantitate cellular proteins associated with the ubiquitination process will facilitate the evaluation of this post-translational modification associated with the pathophysiological phenotype.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Despina Bazou
- Department of Haematology, Mater Misericordiae University Hospital, Dublin, Ireland.
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2
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Nisa MU, Farooq S, Ali S, Eachkoti R, Rehman MU, Hafiz S. Proteomics: A modern tool for identifying therapeutic targets in different types of carcinomas. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00013-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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3
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Chen W, Zhong Y, Shu J, Yu H, Chen Z, Ren X, Hui Z, Li Z. Characterization of glucose-binding proteins isolated from health volunteers and human type 2 diabetes mellitus patients. Proteins 2021; 89:1413-1424. [PMID: 34165207 DOI: 10.1002/prot.26163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/09/2021] [Accepted: 06/15/2021] [Indexed: 11/11/2022]
Abstract
Glucose is one of the most important monosaccharides. Although hyperglycemia in type 2 diabetes mellitus (T2DM) lead to a series of changes; however, little is known about the alterations of serum proteins in T2DM, especially those proteins with glucose affinity. In this study, the glucose-binding proteins (GlcBPs) of serum were isolated from 30 health volunteer (HV) and 30 T2DM patients by glucose-magnetic particle conjugates (GMPC) and identified by mass spectrum analysis. Gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated the main gene annotations and pathways of this GlcBPs, while Motif-X webtool provided the potential glucose-binding domains. Further docking analysis and glycan microarray were used to understand the interaction between the glucose and glucose-binding domains. A total of 149 and 119 GlcBPs were identified from HV and T2DM cases. Four hundred and sixty-eight GO annotations in 165 identified GlcBPs were available, while the majority involved in cellular processes and binding function. A short peptide, EGDEEITCLNGFWLE, which was derived from the Motif-X analysis, presented a high-binding ability to the glucose from both docking analysis and glycan analysis. GMPC provides a powerful tool for GlcBPs isolation and indicates the alteration of GlcBPs in T2DM.
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Affiliation(s)
- Wentian Chen
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Yaogang Zhong
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Jian Shu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Hanjie Yu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Zhuo Chen
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Xiameng Ren
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Ziye Hui
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
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Yang MT, Chang WH, Kuo TF, Shen MY, Yang CW, Tien YJ, Lai BY, Chen YR, Chang YC, Yang WC. Identification of Novel Biomarkers for Pre-diabetic Diagnosis Using a Combinational Approach. Front Endocrinol (Lausanne) 2021; 12:641336. [PMID: 33995275 PMCID: PMC8113970 DOI: 10.3389/fendo.2021.641336] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/01/2021] [Indexed: 12/15/2022] Open
Abstract
Reliable protein markers for pre-diabetes in humans are not clinically available. In order to identify novel and reliable protein markers for pre-diabetes in humans, healthy volunteers and patients diagnosed with pre-diabetes and stroke were recruited for blood collection. Blood samples were collected from healthy and pre-diabetic subjects 12 h after fasting. BMI was calculated from body weight and height. Fasting blood glucose (FBG), glycated hemoglobin (HbA1C), triglyceride (TG), total cholesterol, high-density lipoprotein, low-density lipoprotein (LDL), insulin and albumin were assayed by automated clinical laboratory methods. We used a quantitative proteomics approach to identify 1074 proteins from the sera of pre-diabetic and healthy subjects. Among them, 500 proteins were then selected using Mascot analysis scores. Further, 70 out of 500 proteins were selected via volcano plot analysis according to their statistical significance and average relative protein ratio. Eventually, 7 serum proteins were singled out as candidate markers for pre-diabetes due to their diabetic relevance and statistical significance. Immunoblotting data demonstrated that laminin subunit alpha 2 (LAMA2), mixed-lineage leukemia 4 (MLL4), and plexin domain containing 2 (PLXDC2) were expressed in pre-diabetic patients but not healthy volunteers. Receiver operating characteristic curve analysis indicated that the combination of the three proteins has greater diagnostic efficacy than any individual protein. Thus, LAMA2, MLL4 and PLXDC2 are novel and reliable serum protein markers for pre-diabetic diagnosis in humans.
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Affiliation(s)
- Meng-Ting Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Wei-Hung Chang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Tien-Fen Kuo
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ming-Yi Shen
- Graduate Institute of Biomedical Sciences, College of Medicine, China Medical University, Taichung, Taiwan
| | - Chu-Wen Yang
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | | | - Bun-Yueh Lai
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Cheng Chang
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taipei, Taiwan
| | - Wen-Chin Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Department of Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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Rios-Lugo MJ, Madrigal-Arellano C, Gaytán-Hernández D, Hernández-Mendoza H, Romero-Guzmán ET. Association of Serum Zinc Levels in Overweight and Obesity. Biol Trace Elem Res 2020; 198:51-57. [PMID: 32020525 DOI: 10.1007/s12011-020-02060-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/30/2020] [Indexed: 02/06/2023]
Abstract
Low levels of zinc (Zn) have adverse effects on physiological and metabolic functions in humans, especially in processes linked with obesity. In this work, serum Zn levels and their associations with biochemical parameters (glucose, triglycerides, and total cholesterol), sex, and body mass index (BMI) were determined. The distribution of the study sample by sex was homogeneous: 52.6% were women and 47.4% were men. Women had higher BMI and Zn levels (normal weight and obesity) than men, but the differences in BMI and serum Zn levels by sex were not significant (p > 0.05). Nevertheless, the results obtained showed a decrease in serum Zn levels in overweight and obese individuals (p < 0.05) and a negative correlation between BMI and serum Zn levels (r = - 0.663 and p < 0.001); additionally, a significant correlation was identified between cholesterol and triglyceride values (r = 0.493 and p < 0.001). In conclusion, this study demonstrated decreased serum Zn levels in overweight and obese individuals.
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Affiliation(s)
- María Judith Rios-Lugo
- Unidad de Posgrado, Facultad de Enfermería y Nutrición, UASLP, Avda. Niño Artillero 130, CP 78210, San Luis Potosí, S.L.P., Mexico
- Sección de Medicina Molecular y Traslacional, Centro de Investigación en Ciencias de Salud y Biomedicina. UASLP, Avda Sierra Leona 550, CP 78210, San Luis, S.L.P., Mexico
| | - Casandra Madrigal-Arellano
- Unidad de Posgrado, Facultad de Enfermería y Nutrición, UASLP, Avda. Niño Artillero 130, CP 78210, San Luis Potosí, S.L.P., Mexico
| | - Darío Gaytán-Hernández
- Unidad de Posgrado, Facultad de Enfermería y Nutrición, UASLP, Avda. Niño Artillero 130, CP 78210, San Luis Potosí, S.L.P., Mexico
| | - Héctor Hernández-Mendoza
- Instituto de Investigación de Zonas Desérticas, UASLP, Altair 200, CP 78377, San Luis, S.L.P., Mexico.
- Universidad del Centro de México, Capitán Caldera 75, CP 78250, San Luis, S.L.P., Mexico.
| | - Elizabeth Teresita Romero-Guzmán
- Laboratorio Nacional de Investigaciones en Forense Nuclear (LANAFONU), Gerencia de Tecnología Nuclear, Dirección de Investigación Tecnológica, Carretera México s/n, CP 52750, Toluca, La Marquesa Ocoyoacác, Mexico
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Diniz Pereira J, Gomes Fraga V, Morais Santos AL, Carvalho MDG, Caramelli P, Braga Gomes K. Alzheimer's disease and type 2 diabetes mellitus: A systematic review of proteomic studies. J Neurochem 2020; 156:753-776. [PMID: 32909269 DOI: 10.1111/jnc.15166] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/15/2020] [Accepted: 08/25/2020] [Indexed: 12/16/2022]
Abstract
Similar to dementia, the risk for developing type 2 diabetes mellitus (T2DM) increases with age, and T2DM also increases the risk for dementia, particularly Alzheimer's disease (AD). Although T2DM is primarily a peripheral disorder and AD is a central nervous system disease, both share some common features as they are chronic and complex diseases, and both show involvement of oxidative stress and inflammation in their progression. These characteristics suggest that T2DM may be associated with AD, which gave rise to a new term, type 3 diabetes (T3DM). In this study, we searched for matching peripheral proteomic biomarkers of AD and T2DM based in a systematic review of the available literature. We identified 17 common biomarkers that were differentially expressed in both patients with AD or T2DM when compared with healthy controls. These biomarkers could provide a useful workflow for screening T2DM patients at risk to develop AD.
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Affiliation(s)
- Jessica Diniz Pereira
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vanessa Gomes Fraga
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Anna Luiza Morais Santos
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Maria das Graças Carvalho
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Paulo Caramelli
- Departamento de Clínica Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Karina Braga Gomes
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Wang N, Zhu F, Chen L, Chen K. Proteomics, metabolomics and metagenomics for type 2 diabetes and its complications. Life Sci 2018; 212:194-202. [DOI: 10.1016/j.lfs.2018.09.035] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/18/2018] [Accepted: 09/18/2018] [Indexed: 02/08/2023]
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Wang N, Zhang S, Zhu F, Yang Y, Chen L, Lü P, Yu L, Chen K. Proteomic Study on the New Potential Mechanism and Biomarkers of Diabetes. Proteomics Clin Appl 2018; 13:e1800043. [DOI: 10.1002/prca.201800043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 07/05/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Niannian Wang
- Institute of Life SciencesJiangsu University Zhenjiang 212000 Jiangsu China
| | - Shu Zhang
- School of Food and Biological EngineeringJiangsu University Zhenjiang 212000 Jiangsu China
| | - Feifei Zhu
- Institute of Life SciencesJiangsu University Zhenjiang 212000 Jiangsu China
| | - Yanhua Yang
- Institute of Life SciencesJiangsu University Zhenjiang 212000 Jiangsu China
| | - Liang Chen
- Institute of Life SciencesJiangsu University Zhenjiang 212000 Jiangsu China
| | - Peng Lü
- Institute of Life SciencesJiangsu University Zhenjiang 212000 Jiangsu China
| | - Li Yu
- Affiliated Hospital of Jiangsu University Zhenjiang 212000 Jiangsu China
| | - Keping Chen
- Institute of Life SciencesJiangsu University Zhenjiang 212000 Jiangsu China
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do Nascimento de Oliveira V, Lima-Neto ABM, van Tilburg MF, de Oliveira Monteiro-Moreira AC, Duarte Pinto Lobo M, Rondina D, Fernandes VO, Montenegro APDR, Montenegro RM, Guedes MIF. Proteomic analysis to identify candidate biomarkers associated with type 1 diabetes. Diabetes Metab Syndr Obes 2018; 11:289-301. [PMID: 29942143 PMCID: PMC6005324 DOI: 10.2147/dmso.s162008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
PURPOSE Type 1 diabetes mellitus (DM1) is one of the most common chronic diseases observed during childhood. The incidence of DM1 is increasing worldwide, and there is currently no way to prevent or delay the onset or to cure the disease. Most diseases, including diabetes, stem from abnormalities in the functioning of proteins, and some studies have reported the expression of protein variation to be involved in the development of DM1. Thus, the aim of this study was to investigate the differential expression of serum proteins in patients with DM1. MATERIALS AND METHODS Serum of patients with DM1 (n=30) and healthy controls (n=30) was collected. A proteomic approach was used with depletion of albumin and immunoglobulin G chromatography on serum samples followed by data-independent, label-free mass spectrometric analysis. RESULTS A total of eight serum proteins were identified as being differentially expressed and involved in the immune system, lipid metabolism, and pathways of coagulation. DM1 was associated with the upregulation of six proteins: alpha-2-macroglobulin, apolipoprotein A-II, β2 glycoprotein I, Ig alpha-2 chain C region, alpha-1-microglobulin, and prothrombin. A total of two proteins were downregulated, including pregnancy zone protein and complement C4. CONCLUSION To the best of our knowledge, these findings show differential expression of proteins revealing new proteins that may be involved in the development and progression of diabetes.
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Affiliation(s)
- Valzimeire do Nascimento de Oliveira
- Collegiate Nutrition Science, Laboratory of Biotechnology and Molecular Biology, Ceará State University, Fortaleza, Ceará, Brazil
- Collegiate Biotechnology, Northeast Network of Biotechnology, Laboratory of Biotechnology and Molecular Biology, Ceará State University, Fortaleza, Ceará, Brazil
- Correspondence: Valzimeire do Nascimento de Oliveira, Av. Dr. Silas Munguba, 1700, Campus do Itaperi, bloco D, 1 andar, Sala 01, Laboratório de Biologia Molecular e Biotecnologia, Fortaleza, Ceará, Brazil, Tel +55 85 99991 3404, Email
| | | | - Maurício Fraga van Tilburg
- Collegiate Biotechnology, Northeast Network of Biotechnology, Laboratory of Biotechnology and Molecular Biology, Ceará State University, Fortaleza, Ceará, Brazil
| | | | | | - Davide Rondina
- School of Veterinary Science, Ceará State of University, Fortaleza, Ceará, Brazil
| | | | | | | | - Maria Izabel Florindo Guedes
- Collegiate Nutrition Science, Laboratory of Biotechnology and Molecular Biology, Ceará State University, Fortaleza, Ceará, Brazil
- Collegiate Biotechnology, Northeast Network of Biotechnology, Laboratory of Biotechnology and Molecular Biology, Ceará State University, Fortaleza, Ceará, Brazil
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