1
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Zhao W, Chen K, Zhang J, Zhang M, Guo J, Xie D, Xu J, Tan M. Multi-step HPLC fractionation enabled in-depth and unbiased characterization of histone PTMs. J Chromatogr A 2024; 1736:465368. [PMID: 39298927 DOI: 10.1016/j.chroma.2024.465368] [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: 07/06/2024] [Revised: 08/29/2024] [Accepted: 09/09/2024] [Indexed: 09/22/2024]
Abstract
Histone post-translational modifications (PTMs) are critical epigenetic regulatory factors. Histone PTMs are highly dynamic and complicated, encompassing over 30 structurally diverse modifications across nearly 180 amino acid residues, which generated extensive information regarding histone marks. In proteomics-based characterization of histone PTMs, chemical derivatization and antibody-based affinity enrichment were frequently utilized to improve the identification depth. However, chemical derivatization suffered from the occurrence of side reactions, and antibody-based affinity enrichment focused on specific PTM types of interest. In this research, we developed a multi-step fractionation strategy for comprehensively unbiased detection of histone PTM sites. By combining protein-level fractionation with peptide-level alkaline and acid phase fractionation, we developed the Multidimensional Fractionation based Histone Mark Identification Technology (MudFIT) and increased PTM identification to a total of 264 histone PTM sites. To the best of our knowledge, this strategy achieved the most comprehensive characterization of histone PTM sites in a single proteomics study. Using the same starting amount of sample, MudFIT identified more Kac sites and Kac peptides than those in antibody-based acetylated peptide enrichment. Moreover, in addition to well-studied histone marks, we discovered 36 potential new histone PTM sites including H2BK116bu, H4R45me2, H1K63pr, and uncovered unknown histone PTM types like aminoadipic on lysine and nitrosylation on tyrosine. Our data provided a method and resource for in-depth characterization of histone PTM sites, facilitating further biological understanding of histone marks.
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Affiliation(s)
- Wensi Zhao
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Kaifeng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 101408, China; Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital and Cancer Center, School of Medicine, Tongji University, Shanghai 200434, China
| | - Jun Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 101408, China
| | - Mingya Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Jingli Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 101408, China
| | - Dong Xie
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Junyu Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China.
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 101408, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China.
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2
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Islam SN, Arif Z, Badar A, Moinuddin, Khan MA, Alam K. Glycoxidation of mammalian whole histone generates highly immunogenic aggregates: Sera of SLE patients contain autoantibodies against aggregates. Scand J Immunol 2024; 100:e13389. [PMID: 38816907 DOI: 10.1111/sji.13389] [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] [Received: 11/11/2023] [Revised: 04/15/2024] [Accepted: 05/01/2024] [Indexed: 06/01/2024]
Abstract
Non-enzymatic glycation and oxidation of self-proteins, causing formation and accumulation of advanced glycation end products (AGEs), have been reported in an array of pathologies, including systemic lupus erythematosus (SLE). Such modifications may generate neo-epitopes, break immunological tolerance, and induce antibody response. In this study, we have first analysed the structural modifications of whole histone in the presence of deoxyribose followed by oxidation with hydroxyl radicals. Changes in the secondary and tertiary structure of the whole histone were determined by spectroscopic techniques and biochemical assays. Fluorescence spectroscopy and UPLC-MS showed the generation of AGEs such as carboxymethyl lysine and pentosidine, while DLS and TEM indicated the presence of amorphous AGE-aggregates. Moreover, rabbits immunized with these histone-AGEs exhibited enhanced immunogenicity and ELISA and western immunoblot of IgG antibodies from SLE patients' sera showed a significantly higher specificity towards modified histone-AGEs than the native histone.
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Affiliation(s)
- Shireen Naaz Islam
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, UP, India
| | - Zarina Arif
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, UP, India
| | - Asim Badar
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, UP, India
| | - Moinuddin
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, UP, India
| | - Md Asad Khan
- Department of Biochemistry, Faculty of Dentistry, Jamia Millia Islamia, New Delhi, India
| | - Khursheed Alam
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, UP, India
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3
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Khan H, Rafi Z, Khan MY, Maarfi F, Rehman S, Kaur K, Ahmad MK, Shahab U, Ahmad N, Ahmad S. Epigenetic contributions to cancer: Exploring the role of glycation reactions. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 387:143-193. [PMID: 39179346 DOI: 10.1016/bs.ircmb.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2024]
Abstract
Advanced Glycation End-products (AGEs), with their prolonged half-life in the human body, are emerging as potent diagnostic indicators. Early intervention studies, focusing on AGE cross-link breakers, have shown encouraging results in heart failure patients, paving the way for disease progression monitoring and therapy effectiveness evaluation. AGEs are the byproducts of a non-enzymatic reaction where sugars interact with proteins, lipids, and nucleic acids. These compounds possess the power to alter numerous biological processes, ranging from disrupting molecular conformation and promoting cross-linking to modifying enzyme activity, reducing clearance, and impairing receptor recognition. The damage inflicted by AGEs through the stimulation of intracellular signaling pathways is associated with the onset of chronic diseases across various organ systems. This review consolidates the characteristics of AGEs and the challenges posed by their expression in diverse physiological and pathological states. Furthermore, it highlights the clinical relevance of AGEs and the latest research breakthroughs aimed at reducing AGE accumulation.
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Affiliation(s)
- Hamda Khan
- Department of Biochemistry, Faculty of Medicine, Jawahar Lal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| | - Zeeshan Rafi
- Department of Bioengineering, Integral University, Lucknow, India
| | - Mohd Yasir Khan
- School of Applied & Life Sciences, Uttaranchal University, Dehradun, India
| | - Farah Maarfi
- School of Applied & Life Sciences, Uttaranchal University, Dehradun, India
| | | | - Kirtanjot Kaur
- University Centre for Research and Development, Chandigarh University, Mohali, India
| | | | - Uzma Shahab
- Department of Biochemistry, King George Medical University, Lucknow, India
| | - Naved Ahmad
- Department of Computer Science and Information System, College of Applied Sciences, AlMaarefa University, Riyadh, Saudi Arabia
| | - Saheem Ahmad
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Saudi Arabia.
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4
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Ray DM, Jennings EQ, Maksimovic I, Chai X, Galligan JJ, David Y, Zheng Q. Chemical Labeling and Enrichment of Histone Glyoxal Adducts. ACS Chem Biol 2022; 17:756-761. [PMID: 35294181 DOI: 10.1021/acschembio.1c00864] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Because of their long half-lives and highly nucleophilic tails, histones are particularly susceptible to accumulating nonenzymatic covalent modifications, such as glycation. The resulting modifications can have profound effects on cellular physiology due to the regulatory role histones play in all DNA-templated processes; however, the complexity of Maillard chemistry on proteins makes tracking and enriching for glycated proteins a challenging task. Here, we characterize glyoxal (GO) modifications on histones using quantitative proteomics and an aniline-derived GO-reactive probe. In addition, we leverage this chemistry to demonstrate that the glycation regulatory proteins DJ-1 and GLO1 reduce levels of histone GO adducts. Finally, we employ a two-round pull-down method to enrich histone H3 GO glycation and map these adducts to specific chromatin regions.
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Affiliation(s)
- Devin M. Ray
- Tri-Institutional MD-PhD Program, New York, New York 10065, United States
- Tri-Institutional PhD Program in Chemical Biology, New York, New York 10065, United States
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Erin Q. Jennings
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Igor Maksimovic
- Tri-Institutional PhD Program in Chemical Biology, New York, New York 10065, United States
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Xander Chai
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - James J. Galligan
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Yael David
- Tri-Institutional PhD Program in Chemical Biology, New York, New York 10065, United States
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
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5
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Impact of Advanced Glycation End products (AGEs) and its receptor (RAGE) on cancer metabolic signaling pathways and its progression. Glycoconj J 2022; 38:717-734. [DOI: 10.1007/s10719-021-10031-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/26/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023]
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6
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Mir AR, Habib S, Uddin M. Recent Advances in Histone Glycation: Emerging role in Diabetes and Cancer. Glycobiology 2021; 31:1072-1079. [PMID: 33554241 DOI: 10.1093/glycob/cwab011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/18/2021] [Accepted: 01/28/2021] [Indexed: 12/15/2022] Open
Abstract
Ever increasing information on genome and proteome has offered fascinating details and new opportunities to understand the molecular biology. It is now known that histone proteins surrounding the DNA play a crucial role in the chromatin structure and function. Histones undergo a plethora of post-translational enzymatic modifications that influence nucleosome dynamics and affect DNA activity. Earlier research offered insights into the enzymatic modifications of histones; however attention has been diverted to histone modifications induced by by-products of metabolism without enzymatic engagement in the last decade. Non enzymatic modifications of histones are believed to be crucial for epigenetic landscape, cellular fate and for role in human diseases. Glycation of histone proteins constitutes the major non enzymatic modifications of nuclear proteins that have implications in diabetes and cancer. It has emerged that glycation damages nuclear proteins, modifies amino acids of histones at crucial locations, generates adducts affecting histone chromatin interaction, develops neo-epitopes inducing specific immune response and impacts cell function. Presence of circulating antibodies against glycated histone proteins in diabetes and cancer has shown immunological implications with diagnostic relevance. These crucial details make histone glycation an attractive focus for investigators. This review article, therefore, makes an attempt to exclusively summarize the recent researches in histone glycation, its impact on structural integrity of chromatin and elaborates on their role in diabetes and cancer. The work offers insights for future scientists who investigate the link between metabolism, bio-molecular structures, glycobiology, histone-DNA interactions in relation to diseases in humans.
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Affiliation(s)
- Abdul Rouf Mir
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, India
| | - Safia Habib
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, India
| | - Moin Uddin
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, India
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7
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Yao Y, Zhao X, Ning Q, Zhou J. ABC-Gly: Identifying Protein Lysine Glycation Sites with Artificial Bee Colony Algorithm. CURR PROTEOMICS 2021. [DOI: 10.2174/1570164617666191227120136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Glycation is a nonenzymatic post-translational modification process by attaching
a sugar molecule to a protein or lipid molecule. It may impair the function and change the characteristic
of the proteins which may lead to some metabolic diseases. In order to understand the underlying molecular
mechanisms of glycation, computational prediction methods have been developed because of their
convenience and high speed. However, a more effective computational tool is still a challenging task in
computational biology.
Methods:
In this study, we showed an accurate identification tool named ABC-Gly for predicting lysine
glycation sites. At first, we utilized three informative features, including position-specific amino
acid propensity, secondary structure and the composition of k-spaced amino acid pairs to encode the
peptides. Moreover, to sufficiently exploit discriminative features thus can improve the prediction and
generalization ability of the model, we developed a two-step feature selection, which combined the
Fisher score and an improved binary artificial bee colony algorithm based on the support vector machine.
Finally, based on the optimal feature subset, we constructed an effective model by using the
Support Vector Machine on the training dataset.
Results:
The performance of the proposed predictor ABC-Gly was measured with the sensitivity of
76.43%, the specificity of 91.10%, the balanced accuracy of 83.76%, the Area Under the receiveroperating
characteristic Curve (AUC) of 0.9313, a Matthew’s Correlation Coefficient (MCC) of
0.6861 by 10-fold cross-validation on training dataset, and a balanced accuracy of 59.05% on independent
dataset. Compared to the state-of-the-art predictors on the training dataset, the proposed predictor
achieved significant improvement in the AUC of 0.156 and MCC of 0.336.
Conclusion:
The detailed analysis results indicated that our predictor may serve as a powerful complementary
tool to other existing methods for predicting protein lysine glycation. The source code and
datasets of the ABC-Gly were provided in the Supplementary File 1.
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Affiliation(s)
- Yanqiu Yao
- College of Computer Science and Technology, Changchun Normal University, Changchun, 130032, China
| | - Xiaosa Zhao
- School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130117, China
| | - Qiao Ning
- School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130117, China
| | - Junping Zhou
- School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130117, China
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8
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Diehl KL, Muir TW. Chromatin as a key consumer in the metabolite economy. Nat Chem Biol 2020; 16:620-629. [PMID: 32444835 DOI: 10.1038/s41589-020-0517-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/05/2020] [Indexed: 12/31/2022]
Abstract
In eukaryotes, chromatin remodeling and post-translational modifications (PTMs) shape the local chromatin landscape to establish permissive and repressive regions within the genome, orchestrating transcription, replication, and DNA repair in concert with other epigenetic mechanisms. Though cellular nutrient signaling encompasses a huge number of pathways, recent attention has turned to the hypothesis that the metabolic state of the cell is communicated to the genome through the type and concentration of metabolites in the nucleus that are cofactors for chromatin-modifying enzymes. Importantly, both epigenetic and metabolic dysregulation are hallmarks of a range of diseases, and this metabolism-chromatin axis may yield a well of new therapeutic targets. In this Perspective, we highlight emerging themes in the inter-regulation of the genome and metabolism via chromatin, including nonenzymatic histone modifications arising from chemically reactive metabolites, the expansion of PTM diversity from cofactor-promiscuous chromatin-modifying enzymes, and evidence for the existence and importance of subnucleocytoplasmic metabolite pools.
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Affiliation(s)
- Katharine L Diehl
- Department of Chemistry, Princeton University, Princeton, NJ, USA. .,Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, USA.
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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9
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Diao X. Histone glycation: Linking metabolic perturbation with epigenetic misregulation in cancer. AIMS GENETICS 2019; 6:14-16. [PMID: 31435525 PMCID: PMC6690245 DOI: 10.3934/genet.2019.2.14] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 05/31/2019] [Indexed: 11/25/2022]
Affiliation(s)
- Xiayao Diao
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 33 Yingfeng Road, Haizhu District, Guangzhou 510220, P. R. China
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10
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Abstract
Cells are continuously subjected to an array of reactive/toxic chemical species which are produced both endogenously through metabolic pathways and taken up exogenously by diet and exposure to drugs or toxins. As a result, proteins often undergo non-enzymatic covalent modifications (NECMs) by these species, which can alter protein structure, function, stability, and binding partner affinity. NECMs accumulate over time and are linked to various diseases such as Alzheimer's disease, cancer, and diabetes. In the cellular proteome, histones have some of the longest half-lives, making them prime targets for NECMs. In addition, histones have emerged as key regulators of transcription, a function that is primarily controlled by modification of their tails. These modifications are usually installed or removed enzymatically, but recent evidence suggests that some may also occur non-enzymatically. Despite the vast knowledge detailing the relationship between histone modifications and gene regulation, NECMs on histones remain poorly explored. A major reason for this difference stems from the fact that, unlike their enzymatically installed counterparts, NECMs are difficult to both control and test in vivo. Here, we review advances in our understanding of the effect non-enzymatic covalent modifications (NECMs) have on the epigenetic landscape, cellular fate, and their implications in disease. Cumulatively, this illustrates how the epigenetic code is directly toxified by chemicals and detoxified by corresponding eraser enzymes.
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Affiliation(s)
- Qingfei Zheng
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nicholas A. Prescott
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Igor Maksimovic
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Yael David
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
- Department of Pharmacology, Weill Cornell Medical College, New York, NY
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY
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11
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Zheng Q, Omans ND, Leicher R, Osunsade A, Agustinus AS, Finkin-Groner E, D'Ambrosio H, Liu B, Chandarlapaty S, Liu S, David Y. Reversible histone glycation is associated with disease-related changes in chromatin architecture. Nat Commun 2019; 10:1289. [PMID: 30894531 PMCID: PMC6426841 DOI: 10.1038/s41467-019-09192-z] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/22/2019] [Indexed: 12/16/2022] Open
Abstract
Cellular proteins continuously undergo non-enzymatic covalent modifications (NECMs) that accumulate under normal physiological conditions and are stimulated by changes in the cellular microenvironment. Glycation, the hallmark of diabetes, is a prevalent NECM associated with an array of pathologies. Histone proteins are particularly susceptible to NECMs due to their long half-lives and nucleophilic disordered tails that undergo extensive regulatory modifications; however, histone NECMs remain poorly understood. Here we perform a detailed analysis of histone glycation in vitro and in vivo and find it has global ramifications on histone enzymatic PTMs, the assembly and stability of nucleosomes, and chromatin architecture. Importantly, we identify a physiologic regulation mechanism, the enzyme DJ-1, which functions as a potent histone deglycase. Finally, we detect intense histone glycation and DJ-1 overexpression in breast cancer tumors. Collectively, our results suggest an additional mechanism for cellular metabolic damage through epigenetic perturbation, with implications in pathogenesis.
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Affiliation(s)
- Qingfei Zheng
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Nathaniel D Omans
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, 10065, USA
| | - Rachel Leicher
- Laboratory of Nanoscale Biophysics and Biochemistry, Rockefeller University, New York, NY, 10065, USA
- Tri-institutional PhD Program in Chemical Biology, New York, NY, 10065, USA
| | - Adewola Osunsade
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-institutional PhD Program in Chemical Biology, New York, NY, 10065, USA
| | - Albert S Agustinus
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Efrat Finkin-Groner
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Hannah D'Ambrosio
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Bo Liu
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarat Chandarlapaty
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, Rockefeller University, New York, NY, 10065, USA
| | - Yael David
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Tri-institutional PhD Program in Chemical Biology, New York, NY, 10065, USA.
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, 10065, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY, 10065, USA.
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12
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Reddy HM, Sharma A, Dehzangi A, Shigemizu D, Chandra AA, Tsunoda T. GlyStruct: glycation prediction using structural properties of amino acid residues. BMC Bioinformatics 2019; 19:547. [PMID: 30717650 PMCID: PMC7394324 DOI: 10.1186/s12859-018-2547-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023] Open
Abstract
Background Glycation is a one of the post-translational modifications (PTM) where sugar molecules and residues in protein sequences are covalently bonded. It has become one of the clinically important PTM in recent times attributed to many chronic and age related complications. Being a non-enzymatic reaction, it is a great challenge when it comes to its prediction due to the lack of significant bias in the sequence motifs. Results We developed a classifier, GlyStruct based on support vector machine, to predict glycated and non-glycated lysine residues using structural properties of amino acid residues. The features used were secondary structure, accessible surface area and the local backbone torsion angles. For this work, a benchmark dataset was extracted containing 235 glycated and 303 non-glycated lysine residues. GlyStruct demonstrated improved performance of approximately 10% in comparison to benchmark method of Gly-PseAAC. The performance for GlyStruct on the metrics, sensitivity, specificity, accuracy and Mathew’s correlation coefficient were 0.7013, 0.7989, 0.7562, and 0.5065, respectively for 10-fold cross-validation. Conclusion Glycation has emerged to be one of the clinically important PTM of proteins in recent times. Therefore, the development of computational tools become necessary to predict glycation, which could help medical professionals administer drugs and manage patients more effectively. The proposed predictor manages to classify glycated and non-glycated lysine residues with promising results consistently on various cross-validation schemes and outperforms other state of the art methods. Electronic supplementary material The online version of this article (10.1186/s12859-018-2547-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Alok Sharma
- School of Engineering & Physics, University of the South Pacific, Suva, Fiji. .,Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan. .,Institute for Integrated and Intelligent Systems, Griffith University, Brisbane, Australia. .,CREST, JST, Tokyo, Japan.
| | - Abdollah Dehzangi
- Department of Computer Science, Morgan State University, Baltimore, MD, USA
| | - Daichi Shigemizu
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.,CREST, JST, Tokyo, Japan.,Division of Genomic Medicine, Medical Genome Center, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan.,Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Tatushiko Tsunoda
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.,CREST, JST, Tokyo, Japan.,Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
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13
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Islam MM, Saha S, Rahman MM, Shatabda S, Farid DM, Dehzangi A. iProtGly-SS: Identifying protein glycation sites using sequence and structure based features. Proteins 2018; 86:777-789. [PMID: 29675975 DOI: 10.1002/prot.25511] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 02/27/2018] [Accepted: 04/14/2018] [Indexed: 12/20/2022]
Abstract
Glycation is chemical reaction by which sugar molecule bonds with a protein without the help of enzymes. This is often cause to many diseases and therefore the knowledge about glycation is very important. In this paper, we present iProtGly-SS, a protein lysine glycation site identification method based on features extracted from sequence and secondary structural information. In the experiments, we found the best feature groups combination: Amino Acid Composition, Secondary Structure Motifs, and Polarity. We used support vector machine classifier to train our model and used an optimal set of features using a group based forward feature selection technique. On standard benchmark datasets, our method is able to significantly outperform existing methods for glycation prediction. A web server for iProtGly-SS is implemented and publicly available to use: http://brl.uiu.ac.bd/iprotgly-ss/.
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Affiliation(s)
- Md Mofijul Islam
- Department of CSE, University of Dhaka, Dhaka, Bangladesh.,Department of CSE, United International University, Dhaka, Bangladesh
| | - Sanjay Saha
- Department of CSE, United International University, Dhaka, Bangladesh
| | | | - Swakkhar Shatabda
- Department of CSE, United International University, Dhaka, Bangladesh
| | - Dewan Md Farid
- Department of CSE, United International University, Dhaka, Bangladesh
| | - Abdollah Dehzangi
- Department of Computer Science, Morgan State University, Baltimore, MD, 21251, USA
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14
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Islam S, Mir AR, Arfat MY, Khan F, Zaman M, Ali A. Structural and immunological characterization of hydroxyl radical modified human IgG: Clinical correlation in rheumatoid arthritis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 194:194-201. [PMID: 29351859 DOI: 10.1016/j.saa.2018.01.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 12/28/2017] [Accepted: 01/10/2018] [Indexed: 06/07/2023]
Abstract
Structural alterations in proteins under oxidative stress have been widely implicated in the immuno-pathology of various disorders. This study has evaluated the extent of damage in the conformational characteristics of IgG by hydroxyl radical (OH) and studied its implications in the immuno-pathology of rheumatoid arthritis (RA). Using various biophysical and biochemical techniques, changes in aromatic microenvironment of the IgG and the protein aggregation became evident after treatment with OH. The SDS-PAGE study confirmed the protein aggregation while far ultraviolet circular dichroism spectroscopy (Far-UV CD) and fourier transform infrared spectroscopy (FTIR) inferred towards the alterations in secondary structure of IgG under OH stress. Dynamic light scattering showed that the modification increased the hydrodynamic radius and polydispersity of IgG. The free arginine and lysine content reduced upon modification. OH induced aggregation was confirmed by enhanced thioflavin-T (ThT) fluorescence and red shift in the congo red (CR) absorbance. The study on experimental animals reiterates the earlier findings of enhanced immunogenicity of OH treated IgG (OH-IgG) compared to that of native IgG. OH-IgG strongly interacted with the antibodies derived from the serum of 80 rheumatoid arthritis (RA) patients. The overwhelming and strong tendency of OH-IgG to bind the antibodies derived from the serum of RA patients points towards the modification of IgG under patho-physiological conditions in RA that generate neo-epitopes and eventually cause the generation of auto antibodies that circulate in the patient sera. Further studies on this aspect may possibly lead to the development of a biomarker for RA.
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Affiliation(s)
- Sidra Islam
- Department of Biochemistry, Jawarharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Abdul Rouf Mir
- Department of Biochemistry, Jawarharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Mir Yasir Arfat
- Department of Biochemistry, Jawarharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Farzana Khan
- Department of Biochemistry, Jawarharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Masihuz Zaman
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Asif Ali
- Department of Biochemistry, Jawarharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
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15
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Zhao X, Zhao X, Bao L, Zhang Y, Dai J, Yin M. Glypre: In Silico Prediction of Protein Glycation Sites by Fusing Multiple Features and Support Vector Machine. Molecules 2017; 22:molecules22111891. [PMID: 29099805 PMCID: PMC6150326 DOI: 10.3390/molecules22111891] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 10/26/2017] [Indexed: 12/22/2022] Open
Abstract
Glycation is a non-enzymatic process occurring inside or outside the host body by attaching a sugar molecule to a protein or lipid molecule. It is an important form of post-translational modification (PTM), which impairs the function and changes the characteristics of the proteins so that the identification of the glycation sites may provide some useful guidelines to understand various biological functions of proteins. In this study, we proposed an accurate prediction tool, named Glypre, for lysine glycation. Firstly, we used multiple informative features to encode the peptides. These features included the position scoring function, secondary structure, AAindex, and the composition of k-spaced amino acid pairs. Secondly, the distribution of distinctive features of the residues surrounding the glycation and non-glycation sites was statistically analysed. Thirdly, based on the distribution of these features, we developed a new predictor by using different optimal window sizes for different properties and a two-step feature selection method, which utilized the maximum relevance minimum redundancy method followed by a greedy feature selection procedure. The performance of Glypre was measured with a sensitivity of 57.47%, a specificity of 90.78%, an accuracy of 79.68%, area under the receiver-operating characteristic (ROC) curve (AUC) of 0.86, and a Matthews’s correlation coefficient (MCC) of 0.52 by 10-fold cross-validation. The detailed analysis results showed that our predictor may play a complementary role to other existing methods for identifying protein lysine glycation. The source code and datasets of the Glypre are available in the Supplementary File.
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Affiliation(s)
- Xiaowei Zhao
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China.
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China.
| | - Xiaosa Zhao
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China.
| | - Lingling Bao
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China.
| | - Yonggang Zhang
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China.
| | - Jiangyan Dai
- School of Computer Engineering, Weifang University, Weifang 261061, China.
| | - Minghao Yin
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China.
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16
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Zeng Z, Rulten SL, Breslin C, Zlatanou A, Coulthard V, Caldecott KW. Acylpeptide hydrolase is a component of the cellular response to DNA damage. DNA Repair (Amst) 2017; 58:52-61. [DOI: 10.1016/j.dnarep.2017.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 08/18/2017] [Accepted: 08/18/2017] [Indexed: 10/19/2022]
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17
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Islam S, Moinuddin, Mir AR, Raghav A, Habib S, Alam K, Ali A. Glycation, oxidation and glycoxidation of IgG: a biophysical, biochemical, immunological and hematological study. J Biomol Struct Dyn 2017; 36:2637-2653. [PMID: 28793850 DOI: 10.1080/07391102.2017.1365770] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Sidra Islam
- Department of Biochemistry, Jawarharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India
| | - Moinuddin
- Department of Biochemistry, Jawarharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India
| | - Abdul Rouf Mir
- Department of Biochemistry, Jawarharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India
- Department of Biotechnology, Government Degree College, University of Kashmir, Baramulla 193101, Jammu and Kashmir, India
| | - Alok Raghav
- Rajiv Gandhi Centre for Diabetes and Endocrinology, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India
| | - Safia Habib
- Department of Biochemistry, Jawarharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India
| | - Khursheed Alam
- Department of Biochemistry, Jawarharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India
| | - Asif Ali
- Department of Biochemistry, Jawarharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India
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18
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012. MASS SPECTROMETRY REVIEWS 2017; 36:255-422. [PMID: 26270629 DOI: 10.1002/mas.21471] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
This review is the seventh update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2012. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, and fragmentation are covered in the first part of the review and applications to various structural types constitute the remainder. The main groups of compound are oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:255-422, 2017.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, OX1 3QU, UK
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19
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Proteomic analysis of proteome and histone post-translational modifications in heat shock protein 90 inhibition-mediated bladder cancer therapeutics. Sci Rep 2017; 7:201. [PMID: 28298630 PMCID: PMC5427839 DOI: 10.1038/s41598-017-00143-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 02/08/2017] [Indexed: 11/18/2022] Open
Abstract
Heat shock protein 90 (HSP90) inhibition is an attractive strategy for cancer treatment. Several HSP90 inhibitors have shown promising effects in clinical oncology trials. However, little is known about HSP90 inhibition-mediated bladder cancer therapy. Here, we report a quantitative proteomic study that evaluates alterations in protein expression and histone post-translational modifications (PTMs) in bladder carcinoma in response to HSP90 inhibition. We show that 5 HSP90 inhibitors (AUY922, ganetespib, SNX2112, AT13387, and CUDC305) potently inhibited the proliferation of bladder cancer 5637 cells in a dose- and time-dependent manner. Our proteomic study quantified 518 twofold up-regulated and 811 twofold down-regulated proteins common to both AUY922 and ganetespib treatment. Bioinformatic analyses revealed that those differentially expressed proteins were involved in multiple cellular processes and enzyme-regulated signaling pathways, including chromatin modifications and cell death-associated pathways. Furthermore, quantitative proteome studies identified 14 types of PTMs with 93 marks on the core histones, including 34 novel histone marks of butyrylation, citrullination, 2-hydroxyisobutyrylation, methylation, O-GlcNAcylation, propionylation, and succinylation in AUY922- and ganetespib-treated 5637 cells. Together, this study outlines the association between proteomic changes and histone PTMs in response to HSP90 inhibitor treatment in bladder carcinoma cells, and thus intensifies the understanding of HSP90 inhibition-mediated bladder cancer therapeutics.
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20
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Mir AR, Moinuddin, Habib S. Amorphous aggregate adducts of linker histone H1 turn highly immunologic in the cancers of oesophagus, stomach, gall bladder and ovary. Int J Biol Macromol 2017; 96:507-517. [PMID: 28027900 DOI: 10.1016/j.ijbiomac.2016.12.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 12/16/2016] [Accepted: 12/21/2016] [Indexed: 01/13/2023]
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21
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Yuan W, Zhang Y, Xiong Y, Tao T, Wang Y, Yao J, Zhang L, Yan G, Bao H, Lu H. Highly Selective and Large Scale Mass Spectrometric Analysis of 4-Hydroxynonenal Modification via Fluorous Derivatization and Fluorous Solid-Phase Extraction. Anal Chem 2017; 89:3093-3100. [DOI: 10.1021/acs.analchem.6b04850] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Wenjuan Yuan
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
- Department
of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Ying Zhang
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Yun Xiong
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Tao Tao
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
- Department
of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Yi Wang
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Jun Yao
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Lei Zhang
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Guoquan Yan
- Department
of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Huimin Bao
- Department
of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Haojie Lu
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
- Department
of Chemistry, Fudan University, Shanghai 200433, P. R. China
- Key
Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University, Shanghai 200032, P. R. China
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22
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Xu Y, Li L, Ding J, Wu LY, Mai G, Zhou F. Gly-PseAAC: Identifying protein lysine glycation through sequences. Gene 2017; 602:1-7. [DOI: 10.1016/j.gene.2016.11.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/29/2016] [Accepted: 11/10/2016] [Indexed: 11/29/2022]
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23
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Islam S, Mir AR, Raghav A, Khan F, Alam K, Ali A, Uddin M. Neo-Epitopes Generated on Hydroxyl Radical Modified GlycatedIgG Have Role in Immunopathology of Diabetes Type 2. PLoS One 2017; 12:e0169099. [PMID: 28046123 PMCID: PMC5207762 DOI: 10.1371/journal.pone.0169099] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/11/2016] [Indexed: 02/02/2023] Open
Abstract
Glycoxidation plays a crucial role in diabetes and its associated complications. Among the glycoxidation agents, methylglyoxal (MG) is known to have very highglycationpotential witha concomitant generation of reactive oxygen species (ROS) during its synthesis and degradation. The presentstudy probes the MG and ROSinduced structural damage to immunoglobulin G (IgG) and alterations in its immunogenicity in diabetes type 2 patients (T2DM). Human IgG was first glycated with MG followed by hydroxyl radical (OH•) modification. Glycoxidation mediated effects on IgG were evaluated by various physicochemical techniques likeultraviolet (UV) and fluorescence spectroscopy, 8-anilinonaphthalene-1-sulfonic acid (ANS) binding studies, carbonyl andfree sulfhydryl groups assay, matrix assisted laser desorption ionization mass spectrometry-time of flight (MALDI-TOF), red blood cell (RBC) haemolysis assay, Congored (CR) staining analysis and scanning electron microscopy (SEM). The results revealed hyperchromicityin UV, advanced glycation end product (AGE)specific and ANS fluorescence, quenching in tyrosine and tryptophan fluorescence intensity,enhanced carbonyl content,reduction in free sulfhydryl groups,pronounced shift in m/z value of IgGand decrease in antioxidant activity in RBC induced haemolysis assayupon glycoxidation. SEM and CRstaining assay showed highly altered surface morphology in glycoxidised sample as compared to the native. Enzyme linked immunosorbent assay (ELISA) and band shift assay were performed to assess the changes in immunogenicity of IgG upon glyoxidation and its role in T2DM. The serum antibodies derived from T2DM patients demonstrated strong affinity towards OH• treated MG glycatedIgG (OH•-MG-IgG) when compared to native IgG (N-IgG) or IgGs treated with MG alone (MG-IgG) or OH• alone (OH•-IgG). This study shows the cumulating effect of OH• on the glycation potential of MG. The results point towards the modification of IgG in diabetes patients under the effect of glycoxidative stress, leading to the generation of neo-epitopes on theIgG molecule and rendering it immunogenic.
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Affiliation(s)
- Sidra Islam
- Department of Biochemistry, J.N. Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Abdul Rouf Mir
- Department of Biotechnology, Government Degree College Baramulla, University of Kashmir, Jammu and Kashmir, India
| | - Alok Raghav
- Rajiv Gandhi Centre for Diabetes and Endocrinology, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Farzana Khan
- Department of Biochemistry, J.N. Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Khursheed Alam
- Department of Biochemistry, J.N. Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Asif Ali
- Department of Biochemistry, J.N. Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Moin Uddin
- Department of Biochemistry, J.N. Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
- * E-mail: ,
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24
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Guedes S, Neves B, Vitorino R, Domingues R, Cruz MT, Domingues P. Contact dermatitis: in pursuit of sensitizer's molecular targets through proteomics. Arch Toxicol 2016; 91:811-825. [PMID: 27129696 DOI: 10.1007/s00204-016-1714-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/14/2016] [Indexed: 10/21/2022]
Abstract
Protein haptenation, i.e., the modification of proteins by small reactive chemicals, is the key step in the sensitization phase of allergic contact dermatitis (ACD). Despite the research effort in past decades, the identification of immunogenic hapten-protein complexes that trigger a relevant pathogenic immune response in ACD, as well as the haptenation reaction molecular site, and the elements of a potentially conditioning environment during each of these stages, remain poorly understood. These questions led us to employ a proteomics-based approach to identify modified proteins in the dendritic-like cell line THP-1 sensitized with fluorescein isothiocyanate (FITC), through a combination of 2D-gel electrophoresis, nano-LC and mass spectrometry. A specific set of 39 targeted proteins was identified and comprised proteins from various cellular locations and biological functions. One of FITC targets was identified as MLK, a member of the mixed-lineage kinase family known to act as a mitogen-activated protein kinase kinase kinase and to control the activity of specific mitogen-activated protein kinase pathways, namely p38 and JNK pathways. Haptenated in the vicinity of its active site, our results point to MLK being a relevant target due to a consistent non-activation at early time points of these pathways upon FITC sensitization in THP-1 cells. Moreover, FITC pre-treatment significantly decrease phospho-p38 and phospho-JNK levels induced upon exposure to a classical activator such as lipopolysaccharide or to the sensitizer 2,4-dinitrofluorobenzene. Overall, our data point to specific amino acid residues haptenation within critical proteins as the key step in the subsequent signaling pathways modulation responsible for DC activation and maturation events.
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Affiliation(s)
- Sofia Guedes
- Department of Chemistry, Mass Spectrometry Center, QOPNA, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal.
| | - Bruno Neves
- Department of Chemistry, Mass Spectrometry Center, QOPNA, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517, Coimbra, Portugal.,Faculty of Pharmacy, University of Coimbra, 3000-548, Coimbra, Portugal
| | - Rui Vitorino
- Department of Medical Sciences, Institute for Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal.,Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Rosário Domingues
- Department of Chemistry, Mass Spectrometry Center, QOPNA, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal
| | - Maria Teresa Cruz
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517, Coimbra, Portugal.,Faculty of Pharmacy, University of Coimbra, 3000-548, Coimbra, Portugal
| | - Pedro Domingues
- Department of Chemistry, Mass Spectrometry Center, QOPNA, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal.
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25
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Mir AR, Moinuddin, Islam S. Circulating autoantibodies in cancer patients have high specificity for glycoxidation modified histone H2A. Clin Chim Acta 2016; 453:48-55. [DOI: 10.1016/j.cca.2015.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/27/2015] [Accepted: 12/03/2015] [Indexed: 11/15/2022]
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26
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Mir AR, Moinuddin. Glycoxidation of histone proteins in autoimmune disorders. Clin Chim Acta 2015; 450:25-30. [DOI: 10.1016/j.cca.2015.07.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/26/2015] [Accepted: 07/28/2015] [Indexed: 01/08/2023]
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27
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Mir AR, Moinuddin, Habib S, Khan F, Alam K, Ali A. Structural changes in histone H2A by methylglyoxal generate highly immunogenic amorphous aggregates with implications in auto-immune response in cancer. Glycobiology 2015; 26:129-41. [PMID: 26408820 DOI: 10.1093/glycob/cwv082] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 09/14/2015] [Indexed: 12/13/2022] Open
Abstract
The role of aberrant protein modifications in cancer and its diagnosis have emerged as a promising research field. Nonenzymatic glyco-oxidation of proteins under oxidative stress has been associated with carcinogenesis through advanced glycation end products (AGE)-receptors for advanced glycation end products (RAGE) axis. Modified proteins that are immunogenic and stimulate cellular and humoral immune responses are being studied to develop early detection markers of cancer. This study has probed the structural alternations; leading to the formation of adducts and aggregates, in histone H2A upon in vitro modification by methylglyoxal (MG). The immunogenicity of modified histone H2A and its binding with cancer autoantibodies was also assessed. MG induced lysine side chain modifications, blocking of free amino groups and the formation of condensed cross structures in histone H2A; and its effect was inhibited by carbonyl scavengers. It led to the adduct formation and generation of N-epsilon-(carboxyethyl)lysine (CEL) and its decomposition forms as revealed by Matrix-assisted laser desorption ionization-mass spectrometry, high-performance liquid chromatography and LC-MS. MG-H2A showed amorphous aggregate formation under electron microscopy and altered binding with DNA in circular dichroism studies. The modified histone elicited high titer immunogen-specific antibodies in rabbits when compared with the native, thus pointing toward the generation of neo-epitopes in MG-H2A. The autoantibodies derived from cancer patients exhibited enhanced binding with MG-H2A as compared with the native histone in enzyme-linked immunosorbent assay and gel retardation assay. This reflects sharing of epitopes on MG-H2A and histones in cancer patients. The neo-epitopes on H2A may be responsible for induction and elevated levels of antibodies in cancer patients. Thus, MG-H2A may be considered as potential antigenic candidate for auto-immune response in cancer.
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Affiliation(s)
- Abdul Rouf Mir
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, AMU, Aligarh, Uttar Pradesh, India
| | - Moinuddin
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, AMU, Aligarh, Uttar Pradesh, India
| | - Safia Habib
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, AMU, Aligarh, Uttar Pradesh, India
| | - Farzana Khan
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, AMU, Aligarh, Uttar Pradesh, India
| | - Khursheed Alam
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, AMU, Aligarh, Uttar Pradesh, India
| | - Asif Ali
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, AMU, Aligarh, Uttar Pradesh, India
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Mir AR, Uddin M, Khan F, Alam K, Ali A. Dicarbonyl Induced Structural Perturbations Make Histone H1 Highly Immunogenic and Generate an Auto-Immune Response in Cancer. PLoS One 2015; 10:e0136197. [PMID: 26317779 PMCID: PMC4552624 DOI: 10.1371/journal.pone.0136197] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 07/31/2015] [Indexed: 12/28/2022] Open
Abstract
Increased oxidative stress under hyperglycemic conditions, through the interaction of AGEs with RAGE receptors and via activation of interleukin mediated transcription signalling, has been reported in cancer. Proteins modifications are being explored for their roles in the development and progression of cancer and autoantibody response against them is gaining interest as a probe for early detection of the disease. This study has analysed the changes in histone H1 upon modification by methylglyoxal (MG) and its implications in auto-immunopathogenesis of cancer. Modified histone showed modifications in the aromatic residues, changed tyrosine microenvironment, intermolecular cross linking and generation of AGEs. It showed masking of hydrophobic patches and a hypsochromic shift in the in ANS specific fluorescence. MG aggressively oxidized histone H1 leading to the accumulation of reactive carbonyls. Far UV CD measurements showed di-carbonyl induced enhancement of the alpha structure and the induction of beta sheet conformation; and thermal denaturation (Tm) studies confirmed the thermal stability of the modified histone. FTIR analysis showed amide I band shift, generation of a carboxyethyl group and N-Cα vibrations in the modified histone. LCMS analysis confirmed the formation of Nε-(carboxyethyl)lysine and electron microscopic studies revealed the amorphous aggregate formation. The modified histone showed altered cooperative binding with DNA. Modified H1 induced high titre antibodies in rabbits and the IgG isolated form sera of rabbits immunized with modified H1 exhibited specific binding with its immunogen in Western Blot analysis. IgG isolated from the sera of patients with lung cancer, prostate cancer, breast cancer and cancer of head and neck region showed better recognition for neo-epitopes on the modified histone, reflecting the presence of circulating autoantibodies in cancer. Since reports suggest a link between AGE-RAGE axis and carcinogenesis, glycoxidation of histone H1 and its immunogenicity paves ways for understanding role of glycoxidatively damaged nuclear proteins in cancer.
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Affiliation(s)
- Abdul Rouf Mir
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Moin Uddin
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
- * E-mail:
| | - Farzana Khan
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Khursheed Alam
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Asif Ali
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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Glycation of H1 Histone by 3-Deoxyglucosone: Effects on Protein Structure and Generation of Different Advanced Glycation End Products. PLoS One 2015; 10:e0130630. [PMID: 26121680 PMCID: PMC4487796 DOI: 10.1371/journal.pone.0130630] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/21/2015] [Indexed: 11/19/2022] Open
Abstract
Advanced glycation end products (AGEs) culminate from the non-enzymatic reaction between a free carbonyl group of a reducing sugar and free amino group of proteins. 3-deoxyglucosone (3-DG) is one of the dicarbonyl species that rapidly forms several protein-AGE complexes that are believed to be involved in the pathogenesis of several diseases, particularly diabetic complications. In this study, the generation of AGEs (Nε-carboxymethyl lysine and pentosidine) by 3-DG in H1 histone protein was characterized by evaluating extent of side chain modification (lysine and arginine) and formation of Amadori products as well as carbonyl contents using several physicochemical techniques. Results strongly suggested that 3-DG is a potent glycating agent that forms various intermediates and AGEs during glycation reactions and affects the secondary structure of the H1 protein. Structural changes and AGE formation may influence the function of H1 histone and compromise chromatin structures in cases of secondary diabetic complications.
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Middle-down electron capture dissociation and electron transfer dissociation for histone analysis. J Anal Sci Technol 2015. [DOI: 10.1186/s40543-015-0060-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Abstract
The post-translational modifications (PTMs) of histones play a major role in activating or silencing gene transcription. To gain better understanding of the interplay between the PTMs that occur on histones, they are extensively studied using mass spectrometry techniques. Due to the abundance of lysines and arginines, the typical trypsin digestion has been found less favorable and GluC-digests have been explored as an alternative to yield larger peptides amenable to middle-down approaches. In addition, the use of weak cation exchange hydrophilic interaction liquid chromatography (WCX-HILIC) and the use of electron-based fragmentation techniques were found to be advantageous for the in-depth characterization of histone variants containing multiple PTMs.
As a test model, we used histones from MEL (murine erythroleukemia) cells treated with butyric acid or DMSO. After acid extraction, histone pellets were dried and fractionated using a reversed-phase C3 column. For middle-down analysis, selected histone fractions were digested using GluC. The digested samples were separated on a WCX-HILIC capillary column packed in-house with PolyCAT A resin, coupled to a linear trap quadrupole Fourier transformation ion cyclotron resonance (LTQFT-ICR) instrument. Raw data was acquired on the LTQFT-ICR using electron capture dissociation (ECD). After deconvolution of the raw data, we generated heatmaps to illustrate differential maps between differentially treated histone samples. We also explored the innovative use of Skyline to quantify histone tails. In addition, we report some preliminary data using a synthetic histone peptide acquired on an Orbitrap Fusion using electron transfer dissociation (ETD). Both, ECD and ETD methods are capable of comprehensively analyzing complex histone variations not accessible with conventional techniques.
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Monteiro FL, Baptista T, Amado F, Vitorino R, Jerónimo C, Helguero LA. Expression and functionality of histone H2A variants in cancer. Oncotarget 2015; 5:3428-43. [PMID: 25003966 PMCID: PMC4116493 DOI: 10.18632/oncotarget.2007] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Regulation of gene expression includes the replacement of canonical histones for non-allelic histone variants, as well as their multiple targeting by postranslational modifications. H2A variants are highly conserved between species suggesting they execute important functions that cannot be accomplished by canonical histones. Altered expression of many H2A variants is associated to cancer. MacroH2A variants are enriched in heterocromatic foci and are necessary for chromatin condensation. MacroH2A1.1 and macroH2A1.2 are two mutually exclusive isoforms. MacroH2A1.1 and macroH2A2 inhibit proliferation and are associated with better cancer prognosis; while macroH2A1.2 is associated to cancer progression. H2AX variant functions as a sensor of DNA damage and defines the cellular response towards DNA repair or apoptosis; therefore, screening approaches and therapeutic options targeting H2AX have been proposed. H2A.Z is enriched in euchromatin, acting as a proto-oncogene with established roles in hormone responsive cancers and overexpressed in endocrine-resistant disease. Other H2A family members have also been found altered in cancer, but their function remains unknown. Substantial progress has been made to understand histone H2A variants, their contribution to normal cellular function and to cancer development and progression. Yet, implementation of high resolution mass spectrometry is needed to further our knowledge on highly homologous H2A variants expression and function.
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Affiliation(s)
- Fátima Liliana Monteiro
- Mass Specrometry Center, Organic Chemistry and Natural Products Unit (QOPNA), Department of Chemistry, Universidade de Aveiro., Aveiro, Portugal
| | | | | | | | | | - Luisa A Helguero
- Mass Specrometry Center, Organic Chemistry and Natural Products Unit (QOPNA), Dep. of Chemistry, Universidade de Aveiro., Aveiro, Portugal
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Abstract
Genetic and epigenetic changes are at the root of all cancers. The epigenetic component involves alterations of the post-synthetic modifications of DNA (methylation) and histones (histone posttranslational modifications, PTMs) as well as of those of their molecular "writers," "readers," and "erasers." Noncoding RNAs (ncRNA) can also play a role. Here, we focus on the involvement of histone alterations in cancer, in particular that of the histone variant H2A.Z in the etiology of prostate cancer. The structural mechanisms putatively responsible for the contribution of H2A.Z to oncogenic gene expression programs are first described, followed by what is currently known about the involvement of this histone variant in the regulation of androgen receptor regulated gene expression. The implications of this and their relevance to oncogene deregulation in different stages of prostate cancer, including the progression toward androgen independence, are discussed. This review underscores the increasing awareness of the epigenetic contribution of histone variants to oncogenic progression.
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Affiliation(s)
- Deanna Dryhurst
- Department of Biochemistry and Microbiology, University of Victoria, Petch building, 258a, Victoria, British Columbia Canada V8W 3P6
- ImmunoPrecise Antibodies Ltd., 3204-4464 Markham St., Victoria, British Columbia Canada V8Z 7X8
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Petch building, 258a, Victoria, British Columbia Canada V8W 3P6
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Mir AR, uddin M, Alam K, Ali A. Methylglyoxal mediated conformational changes in histone H2A—generation of carboxyethylated advanced glycation end products. Int J Biol Macromol 2014; 69:260-6. [DOI: 10.1016/j.ijbiomac.2014.05.057] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 05/15/2014] [Accepted: 05/16/2014] [Indexed: 11/30/2022]
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Kulkarni MJ, Korwar AM, Mary S, Bhonsle HS, Giri AP. Glycated proteome: from reaction to intervention. Proteomics Clin Appl 2014. [PMID: 23184864 DOI: 10.1002/prca.201200101] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Glycation, a nonenzymatic reaction between reducing sugars and proteins, is a proteome wide phenomenon, predominantly observed in diabetes due to hyperglycemia. Glycated proteome of plasma, kidney, lens, and brain are implicated in the pathogenesis of various diseases, including diabetic complications, neurodegenerative diseases, cancer, and aging. This review discusses the strategies to characterize protein glycation, its functional implications in different diseases, and intervention strategies to protect the deleterious effects of protein glycation.
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Affiliation(s)
- Mahesh J Kulkarni
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India.
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35
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Arena S, Salzano AM, Renzone G, D'Ambrosio C, Scaloni A. Non-enzymatic glycation and glycoxidation protein products in foods and diseases: an interconnected, complex scenario fully open to innovative proteomic studies. MASS SPECTROMETRY REVIEWS 2014; 33:49-77. [PMID: 24114996 DOI: 10.1002/mas.21378] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/09/2013] [Accepted: 03/09/2013] [Indexed: 06/02/2023]
Abstract
The Maillard reaction includes a complex network of processes affecting food and biopharmaceutical products; it also occurs in living organisms and has been strictly related to cell aging, to the pathogenesis of several (chronic) diseases, such as diabetes, uremia, cataract, liver cirrhosis and various neurodegenerative pathologies, as well as to peritoneal dialysis treatment. Dozens of compounds are involved in this process, among which a number of protein-adducted derivatives that have been simplistically defined as early, intermediate and advanced glycation end-products. In the last decade, various bottom-up proteomic approaches have been successfully used for the identification of glycation/glycoxidation protein targets as well as for the characterization of the corresponding adducts, including assignment of the modified amino acids. This article provides an updated overview of the mass spectrometry-based procedures developed to this purpose, emphasizing their partial limits with respect to current proteomic approaches for the analysis of other post-translational modifications. These limitations are mainly related to the concomitant sheer diversity, chemical complexity, and variable abundance of the various derivatives to be characterized. Some challenges to scientists are finally proposed for future proteomic investigations to solve main drawbacks in this research field.
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Affiliation(s)
- Simona Arena
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147, Naples, Italy
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Silva AMN, Vitorino R, Domingues MRM, Spickett CM, Domingues P. Post-translational modifications and mass spectrometry detection. Free Radic Biol Med 2013; 65:925-941. [PMID: 24002012 DOI: 10.1016/j.freeradbiomed.2013.08.184] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 08/22/2013] [Accepted: 08/24/2013] [Indexed: 12/14/2022]
Abstract
In this review, we provide a comprehensive bibliographic overview of the role of mass spectrometry and the recent technical developments in the detection of post-translational modifications (PTMs). We briefly describe the principles of mass spectrometry for detecting PTMs and the protein and peptide enrichment strategies for PTM analysis, including phosphorylation, acetylation and oxidation. This review presents a bibliographic overview of the scientific achievements and the recent technical development in the detection of PTMs is provided. In order to ascertain the state of the art in mass spectrometry and proteomics methodologies for the study of PTMs, we analyzed all the PTM data introduced in the Universal Protein Resource (UniProt) and the literature published in the last three years. The evolution of curated data in UniProt for proteins annotated as being post-translationally modified is also analyzed. Additionally, we have undertaken a careful analysis of the research articles published in the years 2010 to 2012 reporting the detection of PTMs in biological samples by mass spectrometry.
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Affiliation(s)
- André M N Silva
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Rui Vitorino
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - M Rosário M Domingues
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7 ET, United Kingdom
| | - Pedro Domingues
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
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Silva AM, Marçal SL, Vitorino R, Domingues MR, Domingues P. Characterization of in vitro protein oxidation using mass spectrometry: A time course study of oxidized alpha-amylase. Arch Biochem Biophys 2013; 530:23-31. [DOI: 10.1016/j.abb.2012.12.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 12/04/2012] [Accepted: 12/06/2012] [Indexed: 12/19/2022]
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