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Ma J, Deng Y, Zhang M, Yu J. The role of multi-omics in the diagnosis of COVID-19 and the prediction of new therapeutic targets. Virulence 2022; 13:1101-1110. [PMID: 35801633 PMCID: PMC9272836 DOI: 10.1080/21505594.2022.2092941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing COVID-19, has led to more than 170 million confirmed cases in 223 countries and regions, claiming 3,872,457 lives. Some patients with COVID-19 have mild clinical symptoms despite severe respiratory failure, which greatly increases the difficulty of diagnosis and treatment. It is therefore necessary to identify biological characteristics of SARS-CoV-2, screen novel diagnostic and prognostic biomarkers, as well as to explore potential therapeutic targets for COVID-19. In this comprehensive review, we discuss the current published literature on COVID-19. We find that the comprehensive application of genomics, transcriptomics, proteomics and metabolomics is becoming increasingly important in the treatment of COVID-19. Multi-omics analysis platforms are expected to revolutionize the diagnosis and classification of COVID-19. This review aims to provide a reference for diagnosis, surveillance and clinical decision making related to COVID-19.
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Affiliation(s)
- Jianli Ma
- Department of Radiation Oncology, Shandong University Cancer Center, Jinan, Shandong Province, People's Republic of China
| | - Yuwei Deng
- Department of Breast Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, People's Republic of China
| | - Minghui Zhang
- Department of Respiratory Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, People's Republic of China
| | - Jinming Yu
- Department of Radiation Oncology, Shandong University Cancer Center, Jinan, Shandong Province, People's Republic of China
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2
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Zhou D, Long C, Shao Y, Li F, Sun W, Zheng Z, Wang X, Huang Y, Pan F, Chen G, Guo Y, Huang Y. Integrated Metabolomics and Proteomics Analysis of Urine in a Mouse Model of Posttraumatic Stress Disorder. Front Neurosci 2022; 16:828382. [PMID: 35360173 PMCID: PMC8963102 DOI: 10.3389/fnins.2022.828382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/23/2022] [Indexed: 11/23/2022] Open
Abstract
Posttraumatic stress disorder (PTSD) is a serious stress disorder that occurs in individuals who have experienced major traumatic events. The underlying pathological mechanisms of PTSD are complex, and the related predisposing factors are still not fully understood. In this study, label-free quantitative proteomics and untargeted metabolomics were used to comprehensively characterize changes in a PTSD mice model. Differential expression analysis showed that 12 metabolites and 27 proteins were significantly differentially expressed between the two groups. Bioinformatics analysis revealed that the differentiated proteins were mostly enriched in: small molecule binding, transporter activity, extracellular region, extracellular space, endopeptidase activity, zymogen activation, hydrolase activity, proteolysis, peptidase activity, sodium channel regulator activity. The differentially expressed metabolites were mainly enriched in Pyrimidine metabolism, D-Glutamine and D-glutamate metabolism, Alanine, aspartate and glutamate metabolism, Arginine biosynthesis, Glutathione metabolism, Arginine, and proline metabolism. These results expand the existing understanding of the molecular basis of the pathogenesis and progression of PTSD, and also suggest a new direction for potential therapeutic targets of PTSD. Therefore, the combination of urine proteomics and metabolomics explores a new approach for the study of the underlying pathological mechanisms of PTSD.
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Affiliation(s)
- Daxue Zhou
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Chengyan Long
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
| | - Yan Shao
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Fei Li
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Wei Sun
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Zihan Zheng
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Xiaoyang Wang
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Yiwei Huang
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Feng Pan
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Gang Chen
- Biomedical Analysis Center, Army Medical University, Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education of China, Chongqing, China
- Chongqing Key Laboratory of Cytomics, Chongqing, China
- *Correspondence: Gang Chen,
| | - Yanlei Guo
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Yanlei Guo,
| | - Yi Huang
- Biomedical Analysis Center, Army Medical University, Chongqing, China
- Yi Huang,
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Suhre K, Zaghlool S. Connecting the epigenome, metabolome and proteome for a deeper understanding of disease. J Intern Med 2021; 290:527-548. [PMID: 33904619 DOI: 10.1111/joim.13306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/26/2022]
Abstract
Epigenome-wide association studies (EWAS) identify genes that are dysregulated by the studied clinical endpoints, thereby indicating potential new diagnostic biomarkers, drug targets and therapy options. Combining EWAS with deep molecular phenotyping, such as approaches enabled by metabolomics and proteomics, allows further probing of the underlying disease-associated pathways. For instance, methylation of the TXNIP gene is associated robustly with prevalent type 2 diabetes and further with metabolites that are short-term markers of glycaemic control. These associations reflect TXNIP's function as a glucose uptake regulator by interaction with the major glucose transporter GLUT1 and suggest that TXNIP methylation can be used as a read-out for the organism's exposure to glucose stress. Another case is the association between DNA methylation of the AHRR and F2RL3 genes with smoking and a protein that is involved in the reprogramming of the bronchial epithelium. These examples show that associations between DNA methylation and intermediate molecular traits can open new windows into how the body copes with physiological challenges. This knowledge, if carefully interpreted, may indicate novel therapy options and, together with monitoring of the methylation state of specific methylation sites, may in the future allow the early diagnosis of impending disease. It is essential for medical practitioners to recognize the potential that this field holds in translating basic research findings to clinical practice. In this review, we present recent advances in the field of EWAS with metabolomics and proteomics and discuss both the potential and the challenges of translating epigenetic associations, with deep molecular phenotypes, to biomedical applications.
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Affiliation(s)
- K Suhre
- From the, Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar.,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, USA
| | - S Zaghlool
- From the, Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar.,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, USA
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Meng X, Song M, Vilaj M, Štambuk J, Dolikun M, Zhang J, Liu D, Wang H, Zhang X, Zhang J, Cao W, Momčilović A, Trbojević-Akmačić I, Li X, Zheng D, Wu L, Guo X, Wang Y, Lauc G, Wang W. Glycosylation of IgG Associates with Hypertension and Type 2 Diabetes Mellitus Comorbidity in the Chinese Muslim Ethnic Minorities and the Han Chinese. J Pers Med 2021; 11:jpm11070614. [PMID: 34209622 PMCID: PMC8307283 DOI: 10.3390/jpm11070614] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 01/07/2023] Open
Abstract
Objectives: Hypertension and type 2 diabetes mellitus comorbidity (HDC) is common, which confers a higher risk of cardiovascular disease than the presence of either condition alone. Describing the underlying glycomic changes of immunoglobulin G (IgG) that predispose individuals to HDC may help develop novel protective immune-targeted and anti-inflammatory therapies. Therefore, we investigated glycosylation changes of IgG associated with HDC. Methods: The IgG N-glycan profiles of 883 plasma samples from the three northwestern Chinese Muslim ethnic minorities and the Han Chinese were analyzed by ultra-performance liquid chromatography instrument. Results: We found that 12 and six IgG N-glycan traits showed significant associations with HDC in the Chinese Muslim ethnic minorities and the Han Chinese, respectively, after adjustment for potential confounders and false discovery rate. Adding the IgG N-glycan traits to the baseline models, the area under the receiver operating characteristic curves (AUCs) of the combined models differentiating HDC from hypertension (HTN), type 2 diabetes mellitus (T2DM), and healthy individuals were 0.717, 0.747, and 0.786 in the pooled samples of Chinese Muslim ethnic minorities, and 0.828, 0.689, and 0.901 in the Han Chinese, respectively, showing improved discriminating performance than both the baseline models and the glycan-based models. Conclusion: Altered IgG N-glycan profiles were shown to associate with HDC, suggesting the involvement of inflammatory processes of IgG glycosylation. The alterations of IgG N-glycome, illustrated here for the first time in HDC, demonstrate a biomarker potential, which may shed light on future studies investigating their potential for monitoring or preventing the progression from HTN or T2DM towards HDC.
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Affiliation(s)
- Xiaoni Meng
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
| | - Manshu Song
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA 6027, Australia;
- Correspondence:
| | - Marija Vilaj
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia; (M.V.); (J.Š.); (A.M.); (I.T.-A.); (G.L.)
| | - Jerko Štambuk
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia; (M.V.); (J.Š.); (A.M.); (I.T.-A.); (G.L.)
| | - Mamatyusupu Dolikun
- College of the Life Sciences and Technology, Xinjiang University, Urumqi 830046, China;
| | - Jie Zhang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
| | - Di Liu
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
| | - Hao Wang
- Department of Clinical Epidemiology and Evidence-Based Medicine, National Clinical Research Center for Digestive Disease, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China;
| | - Xiaoyu Zhang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
| | - Jinxia Zhang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
| | - Weijie Cao
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
| | - Ana Momčilović
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia; (M.V.); (J.Š.); (A.M.); (I.T.-A.); (G.L.)
| | - Irena Trbojević-Akmačić
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia; (M.V.); (J.Š.); (A.M.); (I.T.-A.); (G.L.)
| | - Xingang Li
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA 6027, Australia;
- Centre for Precision Health, Edith Cowan University, Perth, WA 6027, Australia
| | - Deqiang Zheng
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
| | - Lijuan Wu
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
| | - Xiuhua Guo
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
| | - Youxin Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA 6027, Australia;
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia; (M.V.); (J.Š.); (A.M.); (I.T.-A.); (G.L.)
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
| | - Wei Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA 6027, Australia;
- Centre for Precision Health, Edith Cowan University, Perth, WA 6027, Australia
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A Bittersweet Computational Journey among Glycosaminoglycans. Biomolecules 2021; 11:biom11050739. [PMID: 34063530 PMCID: PMC8156566 DOI: 10.3390/biom11050739] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 01/22/2023] Open
Abstract
Glycosaminoglycans (GAGs) are linear polysaccharides. In proteoglycans (PGs), they are attached to a core protein. GAGs and PGs can be found as free molecules, associated with the extracellular matrix or expressed on the cell membrane. They play a role in the regulation of a wide array of physiological and pathological processes by binding to different proteins, thus modulating their structure and function, and their concentration and availability in the microenvironment. Unfortunately, the enormous structural diversity of GAGs/PGs has hampered the development of dedicated analytical technologies and experimental models. Similarly, computational approaches (in particular, molecular modeling, docking and dynamics simulations) have not been fully exploited in glycobiology, despite their potential to demystify the complexity of GAGs/PGs at a structural and functional level. Here, we review the state-of-the art of computational approaches to studying GAGs/PGs with the aim of pointing out the “bitter” and “sweet” aspects of this field of research. Furthermore, we attempt to bridge the gap between bioinformatics and glycobiology, which have so far been kept apart by conceptual and technical differences. For this purpose, we provide computational scientists and glycobiologists with the fundamentals of these two fields of research, with the aim of creating opportunities for their combined exploitation, and thereby contributing to a substantial improvement in scientific knowledge.
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Ye L, Fang YS, Li XX, Gao Y, Liu SS, Chen Q, Wu Q, Cheng HW, Du WD. A simple lectin-based biochip might display the potential clinical value of glycomics in patients with spontaneous intracerebral hemorrhage. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:544. [PMID: 33987242 DOI: 10.21037/atm-20-7315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Intracerebral hemorrhage (ICH) is a cerebrovascular disease with extremely high disability and mortality rates. Glycans play critical roles in biological processes. However, whether glycans can serve as potential biomarkers for determining clinical diagnosis and prognosis in ICH remains determined. Methods In this study, we established a lectin-biochip to measure serum glycans levels in ICH patients (n=48) and healthy controls (n=16). An enzyme-linked immunosorbent assay (ELISA) was carried out to determine serum levels of IL-10 and TNF-α in the patients. Correlation analyses of the serum glycan and cytokine levels and the clinicopathological parameters of patients were performed. Results The biochip-based data revealed that the serum levels of α-Man/α-Glc (ConA), Galβ3GalNAc (PNA), GalNAc (VVA), Fucα6GlcNAc (AAL), α-Fuc (LTL), and Galβ3GalNAc-Ser/Thr (AIL) significantly increased in the super-acute phase of ICH in comparison with healthy controls. Clinicopathological analysis indicated the serum levels of ConA, VVA, and LTL had significant associations with the National Institute of Health Stroke Scale (NIHSS), and serum VVA levels had a significant association with the Mini-Mental State Examination (MMSE) at day 90 after ICH. Correlation coefficient analysis revealed significant correlations between TNF-α and ConA (P<0.001) as well as between IL-10 and ConA (P<0.001), PNA (P=0.02), VVA (P<0.001), and MAL (P=0.04), respectively. Conclusions We established a proof-of-concept platform for detecting serum glycomics and highlighted their potential value in diagnosing and predicting ICH patients' outcomes.
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Affiliation(s)
- Lei Ye
- Department of Neurosurgery, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yong-Sheng Fang
- Department of Pathology, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiao-Xue Li
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Yi Gao
- Department of Pathology, Anhui Medical University, Hefei, China
| | - Sheng-Sheng Liu
- Department of Pathology, Anhui Medical University, Hefei, China
| | - Qiang Chen
- Department of Pathology, Anhui Medical University, Hefei, China
| | - Qiang Wu
- Department of Pathology, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Hong-Wei Cheng
- Department of Neurosurgery, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Wei-Dong Du
- Department of Pathology, Anhui Medical University, Hefei, China
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Spatial and temporal diversity of glycome expression in mammalian brain. Proc Natl Acad Sci U S A 2020; 117:28743-28753. [PMID: 33139572 DOI: 10.1073/pnas.2014207117] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mammalian brain glycome remains a relatively poorly understood area compared to other large-scale "omics" studies, such as genomics and transcriptomics due to the inherent complexity and heterogeneity of glycan structure and properties. Here, we first performed spatial and temporal analysis of glycome expression patterns in the mammalian brain using a cutting-edge experimental tool based on liquid chromatography-mass spectrometry, with the ultimate aim to yield valuable implications on molecular events regarding brain functions and development. We observed an apparent diversity in the glycome expression patterns, which is spatially well-preserved among nine different brain regions in mouse. Next, we explored whether the glycome expression pattern changes temporally during postnatal brain development by examining the prefrontal cortex (PFC) at different time point across six postnatal stages in mouse. We found that glycan expression profiles were dynamically regulated during postnatal developments. A similar result was obtained in PFC samples from humans ranging in age from 39 d to 49 y. Novel glycans unique to the brain were also identified. Interestingly, changes primarily attributed to sialylated and fucosylated glycans were extensively observed during PFC development. Finally, based on the vast heterogeneity of glycans, we constructed a core glyco-synthesis map to delineate the glycosylation pathway responsible for the glycan diversity during the PFC development. Our findings reveal high levels of diversity in a glycosylation program underlying brain region specificity and age dependency, and may lead to new studies exploring the role of glycans in spatiotemporally diverse brain functions.
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Meng Z, Li C, Ding G, Cao W, Xu X, Heng Y, Deng Y, Li Y, Zhang X, Li D, Wang W, Wang Y, Xing W, Hou H. Glycomics: Immunoglobulin G N-Glycosylation Associated with Mammary Gland Hyperplasia in Women. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 24:551-558. [PMID: 32833579 DOI: 10.1089/omi.2020.0091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Mammary gland hyperplasia (MGH) is very common, especially among young and middle-aged women. New diagnostics and biomarkers for MGH are needed for rational clinical management and precision medicine. We report, in this study, new findings using a glycomics approach, with a focus on immunoglobulin G (IgG) N-glycosylation. A cross-sectional study was conducted in a community-based population sample in Beijing, China. A total of 387 participants 40-65 years of age were enrolled in this study, including 194 women with MGH (cases) and 193 women who had no MGH (controls). IgG N-glycans were characterized in the serum by ultra-performance liquid chromatography. The levels of the glycan peaks (GPs) GP2, GP5, GP6, and GP7 were lower in the MGH group compared with the control group, whereas GP14 was significantly higher in the MGH group (p < 0.05). A predictive model using GP5, GP21, and age was established and a receiver operating characteristic curve analysis was performed. The sensitivity and specificity of the model for MGH was 61.3% and 63.2%, respectively, likely owing to receptor mechanisms and/or inflammation regulation. To the best of our knowledge, this is the first study reporting on an association between IgG N-glycosylation and MGH. We suggest person-to-person variations in IgG N-glycans and their combination with multiomics biomarker strategies offer a promising avenue to identify novel diagnostics and individuals at increased risk of MGH.
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Affiliation(s)
- Zixiu Meng
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Cancan Li
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Guoyong Ding
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Weijie Cao
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Xizhu Xu
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Yuanyuan Heng
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Yang Deng
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Yuejin Li
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Xiaoyu Zhang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Dong Li
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Wei Wang
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China.,School of Medical and Health Sciences, Edith Cowan University, Perth, Western Australia, Australia
| | - Youxin Wang
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China.,School of Medical and Health Sciences, Edith Cowan University, Perth, Western Australia, Australia.,School of Public Health and Management, Binzhou Medical University, Yantai, China
| | - Weijia Xing
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Haifeng Hou
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China.,School of Medical and Health Sciences, Edith Cowan University, Perth, Western Australia, Australia
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Wang H, Li X, Wang X, Liu D, Zhang X, Cao W, Zheng Y, Guo Z, Li D, Xing W, Hou H, Wu L, Song M, Zhong Z, Wang Y, Tan X, Lauc G, Wang W. Next-Generation (Glycomic) Biomarkers for Cardiometabolic Health: A Community-Based Study of Immunoglobulin G N-Glycans in a Chinese Han Population. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 23:649-659. [PMID: 31313980 DOI: 10.1089/omi.2019.0099] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Cardiovascular disease is a common complex trait that calls for next-generation biomarkers for precision diagnostics and therapeutics. The most common type of post-translational protein modification involves glycosylation. Glycans participate in key intercellular and intracellular functions, such as protein quality control, cell adhesion, cell-cell recognition, signal transduction, cell proliferation, and cell differentiation. In this context, immunoglobulin G (IgG) N-glycans affect the anti-inflammatory and proinflammatory responses of IgG, and are associated with cardiometabolic risk factors such as aging, central obesity, dyslipidemia, and hyperglycemia. Yet, the role of such glycomic biomarkers requires evaluation in diverse world populations. We report here original observations on association of IgG N-glycan biosignatures with 15 cardiometabolic risk factors in a community-based cross-sectional study conducted in 701 Chinese Han participants. After controlling for age and sex, we found that the 16, 21, and 18 IgG N-glycan traits were significantly different in participants with and without metabolic syndrome, hypertriglyceridemic waist phenotype, or abdominal obesity, respectively. The canonical correlation analysis showed that IgG N-glycan profiles were significantly associated with cardiometabolic risk factors (r = 0.469, p < 0.001). Classification models based on IgG N-glycan traits were able to differentiate participants with (1) metabolic syndrome, (2) hypertriglyceridemic waist phenotype, or (3) abdominal obesity from controls, with an area under receiver operating characteristic curves (AUC) of 0.632 (95% confidence interval [CI], 0.574-0.691, p < 0.001), 0.659 (95% CI, 0.587-0.730, p < 0.001), and 0.610 (95% CI, 0.565-0.656, p < 0.001), respectively. These new data suggest that IgG N-glycans may play an important role in cardiometabolic disease pathogenesis by regulating the proinflammatory or anti-inflammatory responses of IgG. Looking into the future, IgG N-glycan biosignatures warrant further research in other world population samples with a view to applications in clinical cardiology and public health practice.
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Affiliation(s)
- Hao Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Xingang Li
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Xueqing Wang
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Di Liu
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Xiaoyu Zhang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Weijie Cao
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Yulu Zheng
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Zheng Guo
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Dong Li
- School of Public Health, Shandong First Medical University, Taian, China
| | - Weijia Xing
- School of Public Health, Shandong First Medical University, Taian, China
| | - Haifeng Hou
- School of Public Health, Shandong First Medical University, Taian, China
| | - Lijuan Wu
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Manshu Song
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Zhaohua Zhong
- Department of Microbiology, Harbin Medical University, Harbin, China
- Heilongjiang Key Laboratory of Immunity and Infection, Harbin, China
| | - Youxin Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Xuerui Tan
- The First Affiliated Hospital of Shantou University Medical College, Shantou University Medical College, Shantou, China
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, BIOCentar, Zagreb, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Wei Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
- School of Public Health, Shandong First Medical University, Taian, China
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10
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Adua E, Memarian E, Russell A, Trbojević-Akmačić I, Gudelj I, Jurić J, Roberts P, Lauc G, Wang W. Utilization of N-glycosylation profiles as risk stratification biomarkers for suboptimal health status and metabolic syndrome in a Ghanaian population. Biomark Med 2019; 13:1273-1287. [DOI: 10.2217/bmm-2019-0005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aim: The study sought to apply N-glycosylation profiles to understand the interplay between suboptimal health status (SHS) and metabolic syndrome (MetS). Materials & methods: In this study, 262 Ghanaians were recruited from May to July 2016. After completing a health survey, plasma samples were collected for clinical assessments while ultra performance liquid chromatography was used to measure plasma N-glycans. Results: Four glycan peaks were found to predict case status (MetS and SHS) using a step-wise Akaike’s information criterion logistic regression model selection. This model yielded an area under the curve of MetS: 83.1% (95% CI: 78.0–88.1%) and SHS: 67.1% (60.6–73.7%). Conclusion: Our results show that SHS is a significant, albeit modest, risk factor for MetS and N-glycan complexity was associated with MetS.
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Affiliation(s)
- Eric Adua
- School of Medical & Health Sciences, Edith Cowan University, WA 6027, Australia
| | - Elham Memarian
- Genos Glycoscience Research Laboratory, Zagreb 10000, Croatia
| | - Alyce Russell
- School of Medical & Health Sciences, Edith Cowan University, WA 6027, Australia
| | | | - Ivan Gudelj
- Genos Glycoscience Research Laboratory, Zagreb 10000, Croatia
| | - Julija Jurić
- Genos Glycoscience Research Laboratory, Zagreb 10000, Croatia
| | - Peter Roberts
- School of Medical & Health Sciences, Edith Cowan University, WA 6027, Australia
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb 10000, Croatia
- University of Zagreb, Faculty of Pharmacy & Biochemistry, Zagreb 10000, Croatia
| | - Wei Wang
- School of Medical & Health Sciences, Edith Cowan University, WA 6027, Australia
- School of Public Health, Taishan Medical University, Shandong, Taian 271000, PR China
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, PR China
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11
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Axford J, Alavi A, Cummings R, Lauc G, Opdenakker G, Reis C, Rudd P. Translational glycobiology: from bench to bedside. J R Soc Med 2019; 112:424-427. [PMID: 31526214 DOI: 10.1177/0141076819865863] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The importance of sugars to protein function is real and is of significant clinical relevance. Technology advances enable large population studies to be carried out, shedding light on individual sugar variation and variations with time. Three-dimensional mass spectroscopy on solid pathological specimens is going to open up a whole new world of pathology visualisation. The door is now open to exploit carbohydrate recognition in new therapeutics by identifying novel biomarkers in cancer to aid diagnosis, and also providing therapeutic targets for treatment. Glycan age correlates with biological age. This means we can map the reversal of biological age with exercise and diet.
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Affiliation(s)
- John Axford
- The Molecular and Clinical Sciences Research Institute, St George's University of London, London SW17 0RE, UK
| | - Azita Alavi
- The Molecular and Clinical Sciences Research Institute, St George's University of London, London SW17 0RE, UK
| | - Rick Cummings
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston 02115, USA
| | - Gordan Lauc
- Faculty of Pharmacy and Biochemistry, University of Zagreb, HR-10000 Zagreb, Croatia
| | - Ghislain Opdenakker
- Department of Microbiology and Immunology, University of Leuven, KU Leuven, BE-3000 Leuven, Belgium
| | - Celso Reis
- Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Pauline Rudd
- National Institute for Bioprocessing Research and Training, Dublin A94 X099, Ireland
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12
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Metabolomic and glycomic findings in posttraumatic stress disorder. Prog Neuropsychopharmacol Biol Psychiatry 2019; 88:181-193. [PMID: 30025792 DOI: 10.1016/j.pnpbp.2018.07.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/21/2018] [Accepted: 07/14/2018] [Indexed: 01/10/2023]
Abstract
Posttraumatic stress disorder (PTSD) is a stressor-related disorder that develops in a subset of individuals exposed to a traumatic experience. Factors associated with vulnerability to PTSD are still not fully understood. PTSD is frequently comorbid with various psychiatric and somatic disorders, moderate response to treatment and remission rates. The term "theranostics" combines diagnosis, prognosis, and therapy and offers targeted therapy based on specific analyses. Theranostics, combined with novel techniques and approaches called "omics", which integrate genomics, transcriptomic, proteomics and metabolomics, might improve knowledge about biological underpinning of PTSD, and offer novel therapeutic strategies. The focus of this review is on metabolomic and glycomic data in PTSD. Metabolomics evaluates changes in the metabolome of an organism by exploring the set of small molecules (metabolites), while glycomics studies the glycome, a complete repertoire of glycan structures with their functional roles in biological systems. Both metabolome and glycome reflect the physiological and pathological conditions in individuals. Only a few studies evaluated metabolic and glycomic changes in patients with PTSD. The metabolomics studies in PTSD patients uncovered different metabolites that might be associated with psychopathological alterations in PTSD. The glycomics study in PTSD patients determined nine N-glycan structures and found accelerated and premature aging in traumatized subjects and subjects with PTSD based on a GlycoAge index. Therefore, further larger studies and replications are needed. Better understanding of the biological basis of PTSD, including metabolomic and glycomic data, and their integration with other "omics" approaches, might identify new molecular targets and might provide improved therapeutic approaches.
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13
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Ma Q, Adua E, Boyce MC, Li X, Ji G, Wang W. IMass Time: The Future, in Future! ACTA ACUST UNITED AC 2018; 22:679-695. [DOI: 10.1089/omi.2018.0162] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Qingwei Ma
- Bioyong (Beijing) Technology Co., Ltd., Beijing, China
| | - Eric Adua
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| | - Mary C. Boyce
- School of Science, Edith Cowan University, Joondalup, Australia
| | - Xingang Li
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| | - Guang Ji
- China-Canada Centre of Research for Digestive Diseases, University of Ottawa, Ottawa, Canada
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wei Wang
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
- School of Public Health, Taishan Medical University, Taian, China
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14
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Josic D, Martinovic T, Pavelic K. Glycosylation and metastases. Electrophoresis 2018; 40:140-150. [PMID: 30246896 DOI: 10.1002/elps.201800238] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/03/2018] [Accepted: 09/03/2018] [Indexed: 12/23/2022]
Abstract
The change of cellular glycosylation is one of the key events in malignant transformation and neoplastic progression, and tumor-related glycosylation alterations are promising targets in both tumor diagnosis and therapy. Both malignant transformation and neoplastic progression are the consequence of gene expression alterations and alterations in protein expression. Micro environmental factors such as extracellular matrix (ECM) also play an important role in their growth and metastasis. Tumor-associated glycans are important biomarker candidates for cancer diagnosis and prognosis, and analytical methods for their detection were developed recently. Glycoproteomics that use mass spectrometry for identification of cancer antigens and structural analysis of glycans play a key role in the investigation of changes of glycosylation during malignant transformation and tumor development and metastasis. Deep understanding of glycan remodeling in cancer and the role of glycosyltransferases that are involved in this process will require a detailed profiling of glycosylation patterns of tumor cells, and corresponding analytical methods for their detection were developed.
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Affiliation(s)
- Djuro Josic
- Department of Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA.,Department of Biotechnology, Centre for High-throughput technologies, University of Rijeka, Rijeka, Croatia.,University Juraj Dobrila, Pula, Croatia
| | - Tamara Martinovic
- Department of Biotechnology, Centre for High-throughput technologies, University of Rijeka, Rijeka, Croatia
| | - Kresimir Pavelic
- Department of Biotechnology, Centre for High-throughput technologies, University of Rijeka, Rijeka, Croatia.,University Juraj Dobrila, Pula, Croatia
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15
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Rodríguez-Girondo M, Salo P, Burzykowski T, Perola M, Houwing-Duistermaat J, Mertens B. Sequential double cross-validation for assessment of added predictive ability in high-dimensional omic applications. Ann Appl Stat 2018. [DOI: 10.1214/17-aoas1125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Liu D, Chu X, Wang H, Dong J, Ge SQ, Zhao ZY, Peng HL, Sun M, Wu LJ, Song MS, Guo XH, Meng Q, Wang YX, Lauc G, Wang W. The changes of immunoglobulin G N-glycosylation in blood lipids and dyslipidaemia. J Transl Med 2018; 16:235. [PMID: 30157878 PMCID: PMC6114873 DOI: 10.1186/s12967-018-1616-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/23/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Alternative N-glycosylation has significant structural and functional consequences on immunoglobulin G (IgG) and can affect immune responses, acting as a switch between pro- and anti-inflammatory IgG functionality. Studies have demonstrated that IgG N-glycosylation is associated with ageing, body mass index, type 2 diabetes and hypertension. METHODS Herein, we have demonstrated patterns of IgG glycosylation that are associated with blood lipids in a cross-sectional study including 598 Han Chinese aged 20-68 years. The IgG glycome composition was analysed by ultra-performance liquid chromatography. RESULTS Blood lipids were positively correlated with glycan peak GP6, whereas they were negatively correlated with GP18 (P < 0.05/57). The canonical correlation analysis indicated that initial N-glycan structures, including GP4, GP6, GP9-12, GP14, GP17, GP18 and GP23, were significantly correlated with blood lipids, including total cholesterol, total triglycerides (TG) and low-density lipoprotein (r = 0.390, P < 0.001). IgG glycans patterns were able to distinguish patients with dyslipidaemia from the controls, with an area under the curve of 0.692 (95% confidence interval 0.644-0.740). CONCLUSIONS Our findings indicated that a possible association between blood lipids and the observed loss of galactose and sialic acid, as well as the addition of bisecting GlcNAcs, which might be related to the chronic inflammation accompanying with the development and procession of dyslipidaemia.
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Affiliation(s)
- Di Liu
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen Xitoutiao, Beijing, 100069 China
| | - Xi Chu
- Center for Physical Examination, Xuanwu Hospital, Capital Medical University, Beijing, 100050 China
| | - Hao Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen Xitoutiao, Beijing, 100069 China
- School of Medical Sciences, Edith Cowan University, Perth, WA 6027 Australia
| | - Jing Dong
- Center for Physical Examination, Xuanwu Hospital, Capital Medical University, Beijing, 100050 China
| | - Si-Qi Ge
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen Xitoutiao, Beijing, 100069 China
- School of Medical Sciences, Edith Cowan University, Perth, WA 6027 Australia
| | - Zhong-Yao Zhao
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen Xitoutiao, Beijing, 100069 China
| | - Hong-Li Peng
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen Xitoutiao, Beijing, 100069 China
| | - Ming Sun
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen Xitoutiao, Beijing, 100069 China
| | - Li-Juan Wu
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen Xitoutiao, Beijing, 100069 China
| | - Man-Shu Song
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen Xitoutiao, Beijing, 100069 China
| | - Xiu-Hua Guo
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen Xitoutiao, Beijing, 100069 China
| | - Qun Meng
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen Xitoutiao, Beijing, 100069 China
| | - You-Xin Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen Xitoutiao, Beijing, 100069 China
- School of Medical Sciences, Edith Cowan University, Perth, WA 6027 Australia
| | - Gordan Lauc
- Genos Glycobiology Research Laboratory, 10000 Zagreb, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
| | - Wei Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen Xitoutiao, Beijing, 100069 China
- School of Medical Sciences, Edith Cowan University, Perth, WA 6027 Australia
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17
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Zhu Y, Yan M, Lasanajak Y, Smith DF, Song X. Large scale preparation of high mannose and paucimannose N-glycans from soybean proteins by oxidative release of natural glycans (ORNG). Carbohydr Res 2018; 464:19-27. [PMID: 29803109 PMCID: PMC6309449 DOI: 10.1016/j.carres.2018.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/07/2018] [Accepted: 05/07/2018] [Indexed: 11/18/2022]
Abstract
Despite the important advances in chemical and chemoenzymatic synthesis of glycans, access to large quantities of complex natural glycans remains a major impediment to progress in Glycoscience. Here we report a large-scale preparation of N-glycans from a kilogram of commercial soy proteins using oxidative release of natural glycans (ORNG). The high mannose and paucimannose N-glycans were labeled with a fluorescent tag and purified by size exclusion and multidimensional preparative HPLC. Side products are identified and potential mechanisms for the oxidative release of natural N-glycans from glycoproteins are proposed. This study demonstrates the potential for using the ORNG approach as a complementary route to synthetic approaches for the preparation of multi-milligram quantities of biomedically relevant complex glycans.
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Affiliation(s)
- Yuyang Zhu
- Department of Biochemistry, Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Maomao Yan
- Department of Biochemistry, Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yi Lasanajak
- Department of Biochemistry, Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David F Smith
- Department of Biochemistry, Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xuezheng Song
- Department of Biochemistry, Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA 30322, USA.
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18
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Liu D, Zhao Z, Wang A, Ge S, Wang H, Zhang X, Sun Q, Cao W, Sun M, Wu L, Song M, Zhou Y, Wang W, Wang Y. Ischemic stroke is associated with the pro-inflammatory potential of N-glycosylated immunoglobulin G. J Neuroinflammation 2018; 15:123. [PMID: 29699572 PMCID: PMC5921323 DOI: 10.1186/s12974-018-1161-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 04/17/2018] [Indexed: 01/01/2023] Open
Abstract
Background Glycosylation significantly affects protein structure and function and thus participates in multiple physiologic and pathologic processes. Studies demonstrated that immunoglobulin G (IgG) N-glycosylation associates with the risk factors of ischemic stroke (IS), such as aging, obesity, dyslipidemia, type 2 diabetes, and hypertension. Methods The study aimed to investigate the association between IgG N-glycosylation and IS in a Chinese population. IgG glycome composition in patients with IS (n = 78) and cerebral arterial stenosis (CAS) (n = 75) and controls (n = 77) were analyzed by ultra-performance liquid chromatography. Results Eleven initial glycans and 10 derived glycans in IgG glycome representing galactosylation, sialylation, and bisecting GlcNAc significantly differed between IS patients and CAS and healthy controls after controlling for gender, age, obesity, diabetes, hypertension, and dyslipidemia. Logistic regression models incorporating IgG glycan traits were able to distinguish IS from CAS (area under receiver–operator characteristic curves (AUC), 0.802; 95% confidence interval (CI), 0.732–0.872) and controls (AUC, 0.740; 95% CI, 0.661–0.819). The canonical correlation analysis indicated that initial N-glycan structures are significantly correlated with inflammation markers (r = 0.566, p < 0.001). Conclusion Our findings indicated that loss of galactose and sialic acid, as well as addition of bisecting GlcNAc, might involve in pro- or anti-inflammatory IgG functionality and further contribute to the pathogenesis of IS. IgG glycan profiles may be developed as clinical useful biomarkers for chronic disease in the future. Electronic supplementary material The online version of this article (10.1186/s12974-018-1161-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Di Liu
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen, Beijing, 100069, China
| | - Zhongyao Zhao
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen, Beijing, 100069, China
| | - Anxin Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen, Beijing, 100069, China.,Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Siqi Ge
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen, Beijing, 100069, China.,School of Medical and Health Sciences, Edith Cowan University, Perth, WA, 6027, Australia
| | - Hao Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen, Beijing, 100069, China.,School of Medical and Health Sciences, Edith Cowan University, Perth, WA, 6027, Australia
| | - Xiaoyu Zhang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen, Beijing, 100069, China
| | - Qi Sun
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen, Beijing, 100069, China
| | - Weijie Cao
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen, Beijing, 100069, China
| | - Ming Sun
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen, Beijing, 100069, China
| | - Lijuan Wu
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen, Beijing, 100069, China
| | - Manshu Song
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen, Beijing, 100069, China
| | - Yong Zhou
- Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Wei Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen, Beijing, 100069, China.,School of Medical and Health Sciences, Edith Cowan University, Perth, WA, 6027, Australia
| | - Youxin Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, 10 Youanmen, Beijing, 100069, China. .,School of Medical and Health Sciences, Edith Cowan University, Perth, WA, 6027, Australia.
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19
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Hsiao CT, Wang PW, Chang HC, Chen YY, Wang SH, Chern Y, Khoo KH. Advancing a High Throughput Glycotope-centric Glycomics Workflow Based on nanoLC-MS 2-product Dependent-MS 3 Analysis of Permethylated Glycans. Mol Cell Proteomics 2017; 16:2268-2280. [PMID: 29066631 DOI: 10.1074/mcp.tir117.000156] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 10/21/2017] [Indexed: 01/08/2023] Open
Abstract
The intrinsic nature of glycosylation, namely nontemplate encoded, stepwise elongation and termination with a diverse range of isomeric glyco-epitopes (glycotopes), translates into ambiguity in most cases of mass spectrometry (MS)-based glycomic mapping. It is arguable that whether one needs to delineate every single glycomic entity, which may be counterproductive. Instead, one should focus on identifying as many structural features as possible that would collectively define the glycomic characteristics of a cell or tissue, and how these may change in response to self-programmed development, immuno-activation, and malignant transformation. We have been pursuing this line of analytical strategy that homes in on identifying the terminal sulfo-, sialyl, and/or fucosylated glycotopes by comprehensive nanoLC-MS2-product dependent MS3 analysis of permethylated glycans, in conjunction with development of a data mining computational tool, GlyPick, to enable an automated, high throughput, semi-quantitative glycotope-centric glycomic mapping amenable to even nonexperts. We demonstrate in this work that diagnostic MS2 ions can be relied on to inform the presence of specific glycotopes, whereas their possible isomeric identities can be resolved at MS3 level. Both MS2 and associated MS3 data can be acquired exhaustively and processed automatically by GlyPick. The high acquisition speed, resolution, and mass accuracy afforded by top-notch Orbitrap Fusion MS system now allow a sensible spectral count and/or summed ion intensity-based glycome-wide glycotope quantification. We report here the technical aspects, reproducibility and optimization of such an analytical approach that uses the same acidic reverse phase C18 nanoLC conditions fully compatible with proteomic analysis to allow rapid hassle-free switching. We further show how this workflow is particularly effective when applied to larger, multiply sialylated and fucosylated N-glycans derived from mouse brain. The complexity of their terminal glycotopes including variants of fucosylated and disialylated type 1 and 2 chains would otherwise not be adequately delineated by any conventional LC-MS/MS analysis.
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Affiliation(s)
- Cheng-Te Hsiao
- From the ‡Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.,§Institute of Biological Chemistry and
| | | | | | - Yen-Ying Chen
- From the ‡Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
| | | | - Yijuang Chern
- ¶Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Kay-Hooi Khoo
- From the ‡Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan; .,§Institute of Biological Chemistry and
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20
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Epigenetic Bases of Aberrant Glycosylation in Cancer. Int J Mol Sci 2017; 18:ijms18050998. [PMID: 28481247 PMCID: PMC5454911 DOI: 10.3390/ijms18050998] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 04/27/2017] [Accepted: 05/02/2017] [Indexed: 02/07/2023] Open
Abstract
In this review, the sugar portions of glycoproteins, glycolipids, and glycosaminoglycans constitute the glycome, and the genes involved in their biosynthesis, degradation, transport and recognition are referred to as “glycogenes“. The extreme complexity of the glycome requires the regulatory layer to be provided by the epigenetic mechanisms. Almost all types of cancers present glycosylation aberrations, giving rise to phenotypic changes and to the expression of tumor markers. In this review, we discuss how cancer-associated alterations of promoter methylation, histone methylation/acetylation, and miRNAs determine glycomic changes associated with the malignant phenotype. Usually, increased promoter methylation and miRNA expression induce glycogene silencing. However, treatment with demethylating agents sometimes results in silencing, rather than in a reactivation of glycogenes, suggesting the involvement of distant methylation-dependent regulatory elements. From a therapeutic perspective aimed at the normalization of the malignant glycome, it appears that miRNA targeting of cancer-deranged glycogenes can be a more specific and promising approach than the use of drugs, which broad target methylation/acetylation. A very specific type of glycosylation, the addition of GlcNAc to serine or threonine (O-GlcNAc), is not only regulated by epigenetic mechanisms, but is an epigenetic modifier of histones and transcription factors. Thus, glycosylation is both under the control of epigenetic mechanisms and is an integral part of the epigenetic code.
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21
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Dagostino C, De Gregori M, Gieger C, Manz J, Gudelj I, Lauc G, Divizia L, Wang W, Sim M, Pemberton IK, MacDougall J, Williams F, Van Zundert J, Primorac D, Aulchenko Y, Kapural L, Allegri M. Validation of standard operating procedures in a multicenter retrospective study to identify -omics biomarkers for chronic low back pain. PLoS One 2017; 12:e0176372. [PMID: 28459826 PMCID: PMC5411039 DOI: 10.1371/journal.pone.0176372] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 04/10/2017] [Indexed: 12/03/2022] Open
Abstract
Chronic low back pain (CLBP) is one of the most common medical conditions, ranking as the greatest contributor to global disability and accounting for huge societal costs based on the Global Burden of Disease 2010 study. Large genetic and -omics studies provide a promising avenue for the screening, development and validation of biomarkers useful for personalized diagnosis and treatment (precision medicine). Multicentre studies are needed for such an effort, and a standardized and homogeneous approach is vital for recruitment of large numbers of participants among different centres (clinical and laboratories) to obtain robust and reproducible results. To date, no validated standard operating procedures (SOPs) for genetic/-omics studies in chronic pain have been developed. In this study, we validated an SOP model that will be used in the multicentre (5 centres) retrospective “PainOmics” study, funded by the European Community in the 7th Framework Programme, which aims to develop new biomarkers for CLBP through three different -omics approaches: genomics, glycomics and activomics. The SOPs describe the specific procedures for (1) blood collection, (2) sample processing and storage, (3) shipping details and (4) cross-check testing and validation before assays that all the centres involved in the study have to follow. Multivariate analysis revealed the absolute specificity and homogeneity of the samples collected by the five centres for all genetics, glycomics and activomics analyses. The SOPs used in our multicenter study have been validated. Hence, they could represent an innovative tool for the correct management and collection of reliable samples in other large-omics-based multicenter studies.
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Affiliation(s)
- Concetta Dagostino
- Anesthesia, Critical Care and Pain Medicine Unit, Division of Surgical Sciences, Department of Medicine and Surgery, University of Parma, Parma, Italy
- * E-mail:
| | - Manuela De Gregori
- PainTherapy Service, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Christian Gieger
- Institute of Epidemiology II, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Judith Manz
- Institute of Epidemiology II, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ivan Gudelj
- Genos, Glycoscience Research Laboratory, Zagreb, Croatia
| | - Gordan Lauc
- Genos, Glycoscience Research Laboratory, Zagreb, Croatia
| | - Laura Divizia
- Laboratory of Biochemistry and Genetics, Division of Pneumology, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Wei Wang
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Moira Sim
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Iain K. Pemberton
- IP Research Consulting SASU (PHOTEOMIX) - Rex de Chaussée, Noisy le Grand, France
| | - Jane MacDougall
- IP Research Consulting SASU (PHOTEOMIX) - Rex de Chaussée, Noisy le Grand, France
| | - Frances Williams
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Jan Van Zundert
- Department of Anesthesiology, Critical Care and Multidisciplinary Pain Center, Ziekenhuis Oost-Limburg, Genk, Belgium
| | - Dragan Primorac
- St. Catherine Specialty Hospital, Zabok, Croatia
- Eberly College of Science, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- University of Split School of Medicine, Split, Croatia
- University of Osijek School of Medicine, Osijek, Croatia
- Children's Hospital Srebrnjak, Zagreb, Croatia
| | | | - Leonardo Kapural
- Carolinas Pain Institute, Winston-Salem, North Carolina, United States of America
| | - Massimo Allegri
- Anesthesia, Critical Care and Pain Medicine Unit, Division of Surgical Sciences, Department of Medicine and Surgery, University of Parma, Parma, Italy
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22
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Adua E, Russell A, Roberts P, Wang Y, Song M, Wang W. Innovation Analysis on Postgenomic Biomarkers: Glycomics for Chronic Diseases. ACTA ACUST UNITED AC 2017; 21:183-196. [DOI: 10.1089/omi.2017.0035] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Eric Adua
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Alyce Russell
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Peter Roberts
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Youxin Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Manshu Song
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Wei Wang
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
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23
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Abstract
Extraction of N-glycans from intact tissue presents a unique set of challenges which makes it a relatively laborious and time-consuming process in comparison to other sample types, such as plasma. Here we present an approach designed for the extraction, purification, and labeling of free N-glycans from brain tissue. Using this method, up to 16 samples can be processed at once which translates to an output of 48 samples per week when rounds of extraction are staggered. Moreover, although intended for brain tissue, the method could easily be adapted to other tissue types as well. The protocol involves several stages. First, the tissue is homogenized and total proteins are isolated using chloroform-methanol extraction. The proteins are then deglycosylated using the Peptide N-Glycosidase F (PNGase F) enzyme in a reaction lasting two days. The released N-glycans are subsequently cleaned up from the reaction mixture using a centrifugal filter device and dried overnight. Next, the N-glycans are resuspended, labeled with 2-aminobenzamide (2-AB) and once again cleaned up using a filter plate. The purified N-glycans are released from the filter using ultrapure water and are then ready for analysis by for hydrophilic interaction ultra performance liquid chromatography (HILIC-UPLC).
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Affiliation(s)
- Thomas Klarić
- Genos Glycoscience Research Laboratory, Hondlova 2/11, HR-10000, Zagreb, Croatia
| | - Ivan Gudelj
- Genos Glycoscience Research Laboratory, Hondlova 2/11, HR-10000, Zagreb, Croatia.
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24
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Abstract
More than half of all proteins are glycosylated. The attached glycans provide proteins with important structural and functional properties and glycan parts of glycoproteins have essential roles in many key biological processes. This chapter describes the effect of glycosylation on the structure and function of proteins, with emphasis on regulation of protein half-life and modulation of protein function by alternative glycosylation. In addition, this chapter highlights the importance of glycan-lectin interactions, the ability of glycans to block phosphorylation of proteins, and the importance of glycans in disease.
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Affiliation(s)
- Jasminka Krištić
- Genos Glycoscience Research Laboratory, Hondlova 2/11, Zagreb, Croatia
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Hondlova 2/11, Zagreb, Croatia. .,Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovačića 1, 10000, Zagreb, Croatia.
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25
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Berger RP, Dookwah M, Steet R, Dalton S. Glycosylation and stem cells: Regulatory roles and application of iPSCs in the study of glycosylation-related disorders. Bioessays 2016; 38:1255-1265. [PMID: 27667795 PMCID: PMC5214967 DOI: 10.1002/bies.201600138] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Glycosylation refers to the co- and post-translational modification of protein and lipids by monosaccharides or oligosaccharide chains. The surface of mammalian cells is decorated by a heterogeneous and highly complex array of protein and lipid linked glycan structures that vary significantly between different cell types, raising questions about their roles in development and disease pathogenesis. This review will begin by focusing on recent findings that define roles for cell surface protein and lipid glycosylation in pluripotent stem cells and their functional impact during normal development. Then, we will describe how patient derived induced pluripotent stem cells are being used to model human diseases such as congenital disorders of glycosylation. Collectively, these studies indicate that cell surface glycans perform critical roles in human development and disease.
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Affiliation(s)
- Ryan P. Berger
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Michelle Dookwah
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Richard Steet
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Stephen Dalton
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
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26
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Khan AH, Bayat H, Rajabibazl M, Sabri S, Rahimpour A. Humanizing glycosylation pathways in eukaryotic expression systems. World J Microbiol Biotechnol 2016; 33:4. [DOI: 10.1007/s11274-016-2172-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 11/04/2016] [Indexed: 01/27/2023]
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27
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Greville G, McCann A, Rudd PM, Saldova R. Epigenetic regulation of glycosylation and the impact on chemo-resistance in breast and ovarian cancer. Epigenetics 2016; 11:845-857. [PMID: 27689695 DOI: 10.1080/15592294.2016.1241932] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Glycosylation is one of the most fundamental posttranslational modifications in cellular biology and has been shown to be epigenetically regulated. Understanding this process is important as epigenetic therapies such as those using DNA methyltransferase inhibitors are undergoing clinical trials for the treatment of ovarian and breast cancer. Previous work has demonstrated that altered glycosylation patterns are associated with aggressive disease in women presenting with breast and ovarian cancer. Moreover, the tumor microenvironment of hypoxia results in globally altered DNA methylation and is associated with aggressive cancer phenotypes and chemo-resistance, a feature integral to many cancers. There is sparse knowledge on the impact of these therapies on glycosylation. Moreover, little is known about the efficacy of DNA methyltransferase inhibitors in hypoxic tumors. In this review, we interrogate the impact that hypoxia and epigenetic regulation has on cancer cell glycosylation in relation to resultant tumor cell aggressiveness and chemo-resistance.
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Affiliation(s)
- Gordon Greville
- a NIBRT GlycoScience Group , The National Institute for Bioprocessing Research and Training , Mount Merrion, Blackrock, Dublin , Ireland
| | - Amanda McCann
- b UCD School of Medicine, College of Health and Agricultural Science, University College Dublin , UCD, Belfield, Dublin , Ireland.,c UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , UCD, Belfield, Dublin , Ireland
| | - Pauline M Rudd
- a NIBRT GlycoScience Group , The National Institute for Bioprocessing Research and Training , Mount Merrion, Blackrock, Dublin , Ireland
| | - Radka Saldova
- a NIBRT GlycoScience Group , The National Institute for Bioprocessing Research and Training , Mount Merrion, Blackrock, Dublin , Ireland
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28
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Lee LY, Moh ESX, Parker BL, Bern M, Packer NH, Thaysen-Andersen M. Toward Automated N-Glycopeptide Identification in Glycoproteomics. J Proteome Res 2016; 15:3904-3915. [DOI: 10.1021/acs.jproteome.6b00438] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Ling Y. Lee
- Department
of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Edward S. X. Moh
- Department
of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Benjamin L. Parker
- Charles
Perkins Centre, School of Molecular Bioscience, The University of Sydney, Sydney, Australia
| | - Marshall Bern
- Protein Metrics
Inc., San Carlos, California 94070, United States
| | - Nicolle H. Packer
- Department
of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Morten Thaysen-Andersen
- Department
of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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29
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Varki A. Biological roles of glycans. Glycobiology 2016; 27:3-49. [PMID: 27558841 PMCID: PMC5884436 DOI: 10.1093/glycob/cww086] [Citation(s) in RCA: 1453] [Impact Index Per Article: 181.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 02/07/2023] Open
Abstract
Simple and complex carbohydrates (glycans) have long been known to play major metabolic, structural and physical roles in biological systems. Targeted microbial binding to host glycans has also been studied for decades. But such biological roles can only explain some of the remarkable complexity and organismal diversity of glycans in nature. Reviewing the subject about two decades ago, one could find very few clear-cut instances of glycan-recognition-specific biological roles of glycans that were of intrinsic value to the organism expressing them. In striking contrast there is now a profusion of examples, such that this updated review cannot be comprehensive. Instead, a historical overview is presented, broad principles outlined and a few examples cited, representing diverse types of roles, mediated by various glycan classes, in different evolutionary lineages. What remains unchanged is the fact that while all theories regarding biological roles of glycans are supported by compelling evidence, exceptions to each can be found. In retrospect, this is not surprising. Complex and diverse glycans appear to be ubiquitous to all cells in nature, and essential to all life forms. Thus, >3 billion years of evolution consistently generated organisms that use these molecules for many key biological roles, even while sometimes coopting them for minor functions. In this respect, glycans are no different from other major macromolecular building blocks of life (nucleic acids, proteins and lipids), simply more rapidly evolving and complex. It is time for the diverse functional roles of glycans to be fully incorporated into the mainstream of biological sciences.
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Affiliation(s)
- Ajit Varki
- Departments of Medicine and Cellular & Molecular Medicine, Glycobiology Research and Training Center, University of California at San Diego, La Jolla, CA 92093-0687, USA
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30
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Mechanisms of disease: The human N-glycome. Biochim Biophys Acta Gen Subj 2016; 1860:1574-82. [DOI: 10.1016/j.bbagen.2015.10.016] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/03/2015] [Accepted: 10/15/2015] [Indexed: 12/20/2022]
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31
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Lauc G. Precision medicine that transcends genomics: Glycans as integrators of genes and environment. Biochim Biophys Acta Gen Subj 2016; 1860:1571-3. [DOI: 10.1016/j.bbagen.2016.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Bennun SV, Hizal DB, Heffner K, Can O, Zhang H, Betenbaugh MJ. Systems Glycobiology: Integrating Glycogenomics, Glycoproteomics, Glycomics, and Other ‘Omics Data Sets to Characterize Cellular Glycosylation Processes. J Mol Biol 2016; 428:3337-3352. [DOI: 10.1016/j.jmb.2016.07.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 07/05/2016] [Accepted: 07/07/2016] [Indexed: 12/17/2022]
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33
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Single plasmonic nanoparticles for ultrasensitive DNA sensing: From invisible to visible. Biosens Bioelectron 2016; 79:266-72. [DOI: 10.1016/j.bios.2015.12.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 12/05/2015] [Accepted: 12/12/2015] [Indexed: 01/16/2023]
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34
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Fearnley LG, Inouye M. Metabolomics in epidemiology: from metabolite concentrations to integrative reaction networks. Int J Epidemiol 2016; 45:1319-1328. [PMID: 27118561 PMCID: PMC5100607 DOI: 10.1093/ije/dyw046] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2016] [Indexed: 01/05/2023] Open
Abstract
Metabolomics is becoming feasible for population-scale studies of human disease. In this review, we survey epidemiological studies that leverage metabolomics and multi-omics to gain insight into disease mechanisms. We outline key practical, technological and analytical limitations while also highlighting recent successes in integrating these data. The use of multi-omics to infer reaction rates is discussed as a potential future direction for metabolomics research, as a means of identifying biomarkers as well as inferring causality. Furthermore, we highlight established analysis approaches as well as simulation-based methods currently used in single- and multi-cell levels in systems biology.
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Affiliation(s)
- Liam G Fearnley
- Centre for Systems Genomics.,School of BioSciences.,Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Michael Inouye
- Centre for Systems Genomics .,School of BioSciences.,Department of Pathology, University of Melbourne, Parkville, VIC, Australia
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35
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Campbell MP, Packer NH. UniCarbKB: New database features for integrating glycan structure abundance, compositional glycoproteomics data, and disease associations. Biochim Biophys Acta Gen Subj 2016; 1860:1669-75. [PMID: 26940363 DOI: 10.1016/j.bbagen.2016.02.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 10/22/2022]
Abstract
BACKGROUND UniCarbKB aims to provide a resource for the representation of mammalian glycobiology knowledge by providing a curated database of structural and experimental data, supported by a web application that allows users to easily find and view richly annotated information. The database comprises two levels of annotation (i) global-specific data of oligosaccharides released and characterised from single purified glycoproteins and (ii) information pertaining to site-specific glycan heterogeneity. Additional, contextual information is provided including structural, bibliographic, and taxonomic information for each entry. METHODS Since the launch of UniCarbKB in 2012, we have continued to improve the organisation of our data model. Recently, we have extended our pipeline to collate structural and abundance changes of oligosaccharides in different human disease states and experimental models to extend our coverage of the human glycome. RESULTS In this manuscript, we demonstrate the capability of UniCarbKB to store and query relative glycan abundance data using a set of published colorectal and prostate cancer cell lines as examples. Furthermore, we outline our strategy for managing large-scale glycoproteomics data, site-specific and glycan compositional data, and how this information is adding value to UniCarbKB. Finally, we summarise our efforts to improve the efficient representation of disease terms and associated changes in glycan heterogeneity by integrating the Disease Ontology. CONCLUSIONS Updates and improvements to UniCarbKB have introduced unique features for storing and displaying glycosylation features of mammalian glycoproteins. The integration of site-specific glycosylation data obtained from large-scale glycoproteomics and introduction of cell line studies will improve the analysis of glycoproteins and entire glycomes. GENERAL SIGNIFICANCE Continuing advancements in analytical technologies and new data types are advancing disease-related glycomics. It is increasingly necessary to ensure all the data are comprehensively annotated. UniCarbKB was established with the mission of providing a resource for human glycobiology by capturing a wide range of data with corresponding annotations. This article is part of a Special Issue entitled "Glycans in personalised medicine" Guest Editor: Professor Gordan Lauc.
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Affiliation(s)
- Matthew P Campbell
- Department of Chemistry and Biomolecular Sciences, Biomolecular Frontiers Research Centre, Macquarie University, Sydney 2109, Australia.
| | - Nicolle H Packer
- Department of Chemistry and Biomolecular Sciences, Biomolecular Frontiers Research Centre, Macquarie University, Sydney 2109, Australia
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36
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Livingstone SG, Smith MJ, Silva DS, Upshur REG. Much ado about omics: welcome to 'the permutome'. J Eval Clin Pract 2015; 21:1018-21. [PMID: 26149276 DOI: 10.1111/jep.12406] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Maxwell J Smith
- Dalla Lana School of Public Health and Joint Centre for Bioethics, University of Toronto, Toronto, ON, Canada
| | - Diego S Silva
- Institute for History, Ethics and Philosophy of Medicine, Hannover Medical School, Hannover, Germany
| | - Ross E G Upshur
- Department of Family and Community Medicine, and Joint Centre for Bioethics, University of Toronto, Toronto, ON, Canada
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37
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Kekäläinen J, Larma I, Linden M, Evans JP. Lectin staining and flow cytometry reveals female-induced sperm acrosome reaction and surface carbohydrate reorganization. Sci Rep 2015; 5:15321. [PMID: 26470849 PMCID: PMC4607886 DOI: 10.1038/srep15321] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 09/21/2015] [Indexed: 12/27/2022] Open
Abstract
All cells are covered by glycans, an individually unique layer of oligo- and polysaccharides that are critical moderators of self-recognition and other cellular-level interactions (e.g. fertilization). The functional similarity between these processes suggests that gamete surface glycans may also have an important, but currently overlooked, role in sexual selection. Here we develop a user-friendly methodological approach designed to facilitate future tests of this possibility. Our proposed method is based on flow cytometric quantification of female-induced sperm acrosome reaction and sperm surface glycan modifications in the Mediterranean mussel Mytilus galloprovincialis. In this species, as with many other taxa, eggs release water-soluble factors that attract conspecific sperm (chemoattraction) and promote potentially measurable changes in sperm behavior and physiology. We demonstrate that flow cytometry is able to identify sperm from other seawater particles as well as accurately measure both acrosome reaction and structural modifications in sperm glycans. This methodological approach can increase our understanding of chemically-moderated gamete-level interactions and individual-specific gamete recognition in Mytilus sp. and other taxa with similar, easily identifiable acrosome structure. Our approach is also likely to be applicable to several other species, since carbohydrate-mediated cellular-level interactions between gametes are universal among externally and internally fertilizing species.
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Affiliation(s)
- Jukka Kekäläinen
- University of Western Australia, Centre for Evolutionary Biology, School of Animal Biology (M092), Crawley, Australia
- University of Eastern Finland, Department of Biology, Joensuu, Finland
| | - Irma Larma
- University of Western Australia, Harry Perkins Institute of Medical Research, Centre for Microscopy, Characterization and Analysis, Crawley, Australia
| | - Matthew Linden
- University of Western Australia, Harry Perkins Institute of Medical Research, Centre for Microscopy, Characterization and Analysis, Crawley, Australia
| | - Jonathan P. Evans
- University of Western Australia, Centre for Evolutionary Biology, School of Animal Biology (M092), Crawley, Australia
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38
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Defaus S, Gupta P, Andreu D, Gutiérrez-Gallego R. Mammalian protein glycosylation--structure versus function. Analyst 2015; 139:2944-67. [PMID: 24779027 DOI: 10.1039/c3an02245e] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Carbohydrates fulfil many common as well as extremely important functions in nature. They show a variety of molecular displays--e.g., free mono-, oligo-, and polysaccharides, glycolipids, proteoglycans, glycoproteins, etc.--with particular roles and localizations in living organisms. Structure-specific peculiarities are so many and diverse that it becomes virtually impossible to cover them all from an analytical perspective. Hence this manuscript, focused on mammalian glycosylation, rather than a complete list of analytical descriptors or recognized functions for carbohydrate structures, comprehensively reviews three central issues in current glycoscience, namely (i) structural analysis of glycoprotein glycans, covering both classical and novel approaches for teasing out the structural puzzle as well as potential pitfalls of these processes; (ii) an overview of functions attributed to carbohydrates, covering from monosaccharide to complex, well-defined epitopes and full glycans, including post-glycosylational modifications, and (iii) recent technical advances allowing structural identification of glycoprotein glycans with simultaneous assignation of biological functions.
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Affiliation(s)
- S Defaus
- Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona Biomedical Research Park, 08003 Barcelona, Spain.
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39
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Cobra venom proteome and glycome determined from individual snakes of Naja atra reveal medically important dynamic range and systematic geographic variation. J Proteomics 2015. [PMID: 26196238 DOI: 10.1016/j.jprot.2015.07.015] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
UNLABELLED Recent progress in snake venomics has shed much light on the intra-species variation among the toxins from different geographical regions and has provided important information for better snakebite management. Most previous reports on snake venomics were based on venoms pooled from different snakes. In this study, we present the proteomic and glycomic profiles of venoms from individual Naja atra snakes. The results reveal wide dynamic range of three-finger toxins. Systematic classification based on cardiotoxin (CTX-) profiles of A2/A4 and A6, respectively, allowed the identification of two putative subspecies of Taiwan cobra from the eastern and western regions. We also identified four major N-glycan moieties on cobra snake venom metalloproteinase on the bi-antennary glycan core. ELISA showed that these glycoproteins (<3%) could elicit much higher antibody response in antiserum when compared to other high-abundance cobra venom toxins such as small molecular weight CTXs (~60%). By removing these high-molecular weight glycoproteins from the immunogen, we demonstrated better protection than that achieved with conventional crude venom immunization in mice challenged by crude venom. We conclude that both intra-species and inter-individual variations of proteomic and glycomic profiles of snake venomics should be considered to provide better antivenomic approach for snakebite management. BIOLOGICAL SIGNIFICANCE Based on the proteomic and glycomic profiles of venoms obtained from individual snakes, we demonstrated a surprisingly wide dynamic range and geographical variation of three-finger toxins in cobra venomics. This provides a reasonable explanation for the variable neutralization effects of antivenom treatment on victims suffering from cobra snakebite and suggests a simple and economic method to produce potent antivenom with better efficacy. Since two major venomic profiles with distinct dynamic ranges were observed for Taiwan cobra venoms isolated from the eastern and western regions, the current venomic profile should be used as a quality control for future production of antivenom in clinical applications.
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40
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Yang G, Tan Z, Lu W, Guo J, Yu H, Yu J, Sun C, Qi X, Li Z, Guan F. Quantitative glycome analysis of N-glycan patterns in bladder cancer vs normal bladder cells using an integrated strategy. J Proteome Res 2015; 14:639-53. [PMID: 25536294 DOI: 10.1021/pr5006026] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diagnosis of bladder cancer, one of the most common types of human cancer, at an early (nonmuscle-invasive) stage is the best way to reduce the mortality rate. Tumor malignancy in general is closely associated with alterations of glycan expression. Glycosylation status, particularly global glycomes, in bladder cancer has not been well studied. We integrated lectin microarray and mass spectrometry (MS) methods to quantitatively analyze and compare glycan expression in four bladder cancer cell lines (KK47, YTS1, J82, T24) and one normal bladder mucosa cell line (HCV29). Glycopattern alterations were analyzed using lectin microarray analysis and confirmed by lectin staining and lectin blotting. Associations of glycopatterns with diverging stages were evaluated by lectin histochemistry on tissue microarrays. N-Glycans were derivatized by amidation of sialylated glycans with acetohydrazide and reductive amination with the stable isotope tags [(12)C6]- and [(13)C6]-aniline, and were quantitatively analyzed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/TOF-MS). N-Glycan biosynthesis-associated proteins were quantitatively analyzed by a stable isotope labeling by amino acids in cell culture (SILAC) proteomics method, which revealed significant differences in expression of 13 glycosyltransferases and 4 glycosidases. Our findings indicate that sialyl Lewis X (sLe(x)), terminal GalNAc and Gal, and high mannose-type N-glycans were more highly expressed in bladder cancer cells and tissues than in normal cells. Bladder cancer cells showed high expression of core-fucosylated N-glycans but low expression of terminally fucosylated N-glycans. Each of these glycome changes may be directly related to bladder cancer progression.
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Affiliation(s)
- Ganglong Yang
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education; School of Biotechnology, Jiangnan University , Wuxi, China
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Abstract
Ageing is a complex multifactorial process, reflecting the progression of all degenerative pathways within an organism. Due to the increase of life expectancy, in recent years, there is a pressing need to identify early-life events and risk factors that determine health outcomes in later life. So far, genetic variation only explains ~20–25 % of the variability of human survival to age 80+. This clearly implies that other factors (environmental, epigenetic and lifestyle) contribute to lifespan and the rate of healthy ageing within an individual. Twin studies in the past two decades proved to be a very powerful tool to discriminate the genetic from the environmental component. The aim of this review is to describe the basic concepts of the twin study design and to report some of the latest studies in which high-throughput technologies (e.g. genome/epigenome-wide assay, next generation sequencing, MS metabolic profiling) combined with the classical twin design have been applied to the analysis of novel ‘omics’ to further understand the molecular mechanisms of human ageing.
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42
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Huffman JE, Pučić-Baković M, Klarić L, Hennig R, Selman MHJ, Vučković F, Novokmet M, Krištić J, Borowiak M, Muth T, Polašek O, Razdorov G, Gornik O, Plomp R, Theodoratou E, Wright AF, Rudan I, Hayward C, Campbell H, Deelder AM, Reichl U, Aulchenko YS, Rapp E, Wuhrer M, Lauc G. Comparative performance of four methods for high-throughput glycosylation analysis of immunoglobulin G in genetic and epidemiological research. Mol Cell Proteomics 2014; 13:1598-610. [PMID: 24719452 PMCID: PMC4047478 DOI: 10.1074/mcp.m113.037465] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 03/14/2014] [Indexed: 11/06/2022] Open
Abstract
The biological and clinical relevance of glycosylation is becoming increasingly recognized, leading to a growing interest in large-scale clinical and population-based studies. In the past few years, several methods for high-throughput analysis of glycans have been developed, but thorough validation and standardization of these methods is required before significant resources are invested in large-scale studies. In this study, we compared liquid chromatography, capillary gel electrophoresis, and two MS methods for quantitative profiling of N-glycosylation of IgG in the same data set of 1201 individuals. To evaluate the accuracy of the four methods we then performed analysis of association with genetic polymorphisms and age. Chromatographic methods with either fluorescent or MS-detection yielded slightly stronger associations than MS-only and multiplexed capillary gel electrophoresis, but at the expense of lower levels of throughput. Advantages and disadvantages of each method were identified, which should inform the selection of the most appropriate method in future studies.
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Affiliation(s)
- Jennifer E Huffman
- From the ‡MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | | | | | - René Hennig
- ¶Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany; ‖glyXera GmbH, Magdeburg, Germany
| | - Maurice H J Selman
- **Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | | | | | - Thilo Muth
- ¶Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany; ‖glyXera GmbH, Magdeburg, Germany
| | - Ozren Polašek
- ‡‡Faculty of Medicine, University of Split, Split, Croatia
| | - Genadij Razdorov
- §§University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Olga Gornik
- §§University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Rosina Plomp
- **Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Evropi Theodoratou
- ¶¶Centre for Population Health Sciences, School of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - Alan F Wright
- From the ‡MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Igor Rudan
- ¶¶Centre for Population Health Sciences, School of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - Caroline Hayward
- From the ‡MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- ¶¶Centre for Population Health Sciences, School of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - André M Deelder
- **Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Udo Reichl
- ¶Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany; ‖‖Otto-von-Guericke University, Chair of Bioprocess Engineering, Magdeburg, Germany
| | - Yurii S Aulchenko
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia; "Yurii Aulchenko" consulting, Groningen, The Netherlands
| | - Erdmann Rapp
- ¶Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany; ‖glyXera GmbH, Magdeburg, Germany
| | - Manfred Wuhrer
- **Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands; Division of BioAnalytical Chemistry, VU University Amsterdam, Amsterdam, The Netherlands
| | - Gordan Lauc
- §Genos Glycoscience Laboratory, Zagreb, Croatia; §§University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia;
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43
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Novokmet M, Lukić E, Vučković F, Ðurić Ž, Keser T, Rajšl K, Remondini D, Castellani G, Gašparović H, Gornik O, Lauc G. Changes in IgG and total plasma protein glycomes in acute systemic inflammation. Sci Rep 2014; 4:4347. [PMID: 24614541 PMCID: PMC3949295 DOI: 10.1038/srep04347] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 02/24/2014] [Indexed: 12/19/2022] Open
Abstract
Recovery after cardiac surgery is a complex process that has to compensate for both individual variability and extensive tissue damage in the context of systemic inflammation. Protein glycosylation is essential in many steps of the inflammatory cascade, but due to technological limitations the role of individual variation in glycosylation in systemic inflammation has not been addressed until now. We analysed composition of the total plasma and IgG N-glycomes in 107 patients undergoing cardiac surgery. In nearly all individuals plasma N-glycome underwent the same pattern of changes in the first 72 h, revealing a general mechanism of glycosylation changes. To the contrary, changes in the IgG glycome were very individualized. Bi-clustering analysis revealed the existence of four distinct patterns of changes. One of them, characterized by a rapid increase in galactosylated glycoforms, was associated with nearly double mortality risk measured by EuroSCORE II. Our results indicate that individual variation in IgG glycosylation changes during acute systemic inflammation associates with increased mortality risk and indicates new avenues for the development of personalized diagnostic and therapeutic approach.
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Affiliation(s)
| | - Edita Lukić
- Department of Orthopaedic Surgery University Hospital Centre Zagreb, Croatia
| | | | - Željko Ðurić
- Clinic for Cardiac Surgery, University Hospital Centre Zagreb, Croatia
| | - Toma Keser
- University of Zagreb, Faculty of Pharmacy and Biochemistry, Department of Biochemistry and Molecular Biology, Zagreb, Croatia
| | - Katarina Rajšl
- University of Zagreb, Faculty of Pharmacy and Biochemistry, Department of Biochemistry and Molecular Biology, Zagreb, Croatia
| | - Daniel Remondini
- Department of Physics and Astronomy DIFA, University of Bologna, Bologna, Italy
| | - Gastone Castellani
- Department of Physics and Astronomy DIFA, University of Bologna, Bologna, Italy
| | - Hrvoje Gašparović
- Clinic for Cardiac Surgery, University Hospital Centre Zagreb, Croatia
| | - Olga Gornik
- 1] University of Zagreb, Faculty of Pharmacy and Biochemistry, Department of Biochemistry and Molecular Biology, Zagreb, Croatia [2]
| | - Gordan Lauc
- 1] Genos Glycoscience Laboratory, Zagreb, Croatia [2] University of Zagreb, Faculty of Pharmacy and Biochemistry, Department of Biochemistry and Molecular Biology, Zagreb, Croatia [3]
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44
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Lauc G, Vojta A, Zoldoš V. Epigenetic regulation of glycosylation is the quantum mechanics of biology. Biochim Biophys Acta Gen Subj 2013; 1840:65-70. [PMID: 23999089 DOI: 10.1016/j.bbagen.2013.08.017] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/22/2013] [Accepted: 08/23/2013] [Indexed: 11/28/2022]
Abstract
BACKGROUND Most proteins are glycosylated, with glycans being integral structural and functional components of a glycoprotein. In contrast to polypeptides, which are fully encoded by the corresponding gene, glycans result from a dynamic interaction between the environment and a network of hundreds of genes. SCOPE OF REVIEW Recent developments in glycomics, genomics and epigenomics are discussed in the context of an evolutionary advantage for higher eukaryotes over microorganisms, conferred by the complexity and adaptability which glycosylation adds to their proteome. MAJOR CONCLUSIONS Inter-individual variation of glycome composition in human population is large; glycome composition is affected by both genes and environment; epigenetic regulation of "glyco-genes" has been demonstrated; and several mechanisms for transgenerational inheritance of epigenetic marks have been documented. GENERAL SIGNIFICANCE Epigenetic recording of acquired characteristics and their transgenerational inheritance could be important mechanisms used by higher organisms to compete or collaborate with microorganisms.
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Affiliation(s)
- Gordan Lauc
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovačića 1, 10000 Zagreb, Croatia; Genos Glycobiology Laboratory, Hondlova 2/11, 10000 Zagreb, Croatia.
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