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Phulara NR, Seneviratne HK. Mass spectrometry imaging-based multi-omics approaches to understand drug metabolism and disposition. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5042. [PMID: 38840330 DOI: 10.1002/jms.5042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/24/2024] [Accepted: 05/06/2024] [Indexed: 06/07/2024]
Affiliation(s)
- Nav Raj Phulara
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Herana Kamal Seneviratne
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
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2
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Palomino TV, Muddiman DC. Mass spectrometry imaging of N-linked glycans: Fundamentals and recent advances. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38934211 DOI: 10.1002/mas.21895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/06/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024]
Abstract
With implications in several medical conditions, N-linked glycosylation is one of the most important posttranslation modifications present in all living organisms. Due to their nontemplate synthesis, glycan structures are extraordinarily complex and require multiple analytical techniques for complete structural elucidation. Mass spectrometry is the most common way to investigate N-linked glycans; however, with techniques such as liquid-chromatography mass spectrometry, there is complete loss of spatial information. Mass spectrometry imaging is a transformative analytical technique that can visualize the spatial distribution of ions within a biological sample and has been shown to be a powerful tool to investigate N-linked glycosylation. This review covers the fundamentals of mass spectrometry imaging and N-linked glycosylation and highlights important findings of recent key studies aimed at expanding and improving the glycomics imaging field.
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Affiliation(s)
- Tana V Palomino
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - David C Muddiman
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
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3
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38925550 DOI: 10.1002/mas.21873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 06/28/2024]
Abstract
The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.
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4
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Malaker SA. Glycoproteomics: Charting new territory in mass spectrometry and glycobiology. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5034. [PMID: 38726698 DOI: 10.1002/jms.5034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 05/24/2024]
Abstract
Glycosylation is an incredibly common and diverse post-translational modification that contributes widely to cellular health and disease. Mass spectrometry is the premier technique to study glycoproteins; however, glycoproteomics has lagged behind traditional proteomics due to the challenges associated with studying glycosylation. For instance, glycans dissociate by collision-based fragmentation, thus necessitating electron-based fragmentation for site-localization. The vast glycan heterogeneity leads to lower overall abundance of each glycopeptide, and often, ion suppression is observed. One of the biggest issues facing glycoproteomics is the lack of reliable software for analysis, which necessitates manual validation and serves as a massive bottleneck in data processing. Here, I will discuss each of these challenges and some ways in which the field is attempting to address them, along with perspectives on how I believe we should move forward.
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Affiliation(s)
- Stacy A Malaker
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
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5
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Prentice BM. Imaging with mass spectrometry: Which ionization technique is best? JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5016. [PMID: 38625003 DOI: 10.1002/jms.5016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 04/17/2024]
Abstract
The use of mass spectrometry (MS) to acquire molecular images of biological tissues and other substrates has developed into an indispensable analytical tool over the past 25 years. Imaging mass spectrometry technologies are widely used today to study the in situ spatial distributions for a variety of analytes. Early MS images were acquired using secondary ion mass spectrometry and matrix-assisted laser desorption/ionization. Researchers have also designed and developed other ionization techniques in recent years to probe surfaces and generate MS images, including desorption electrospray ionization (DESI), nanoDESI, laser ablation electrospray ionization, and infrared matrix-assisted laser desorption electrospray ionization. Investigators now have a plethora of ionization techniques to select from when performing imaging mass spectrometry experiments. This brief perspective will highlight the utility and relative figures of merit of these techniques within the context of their use in imaging mass spectrometry.
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Affiliation(s)
- Boone M Prentice
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
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6
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Ma M, Yu Q, Delafield DG, Cui Y, Li Z, Li M, Wu W, Shi X, Westmark PR, Gutierrez A, Ma G, Gao A, Xu M, Xu W, Westmark CJ, Li L. On-Tissue Spatial Proteomics Integrating MALDI-MS Imaging with Shotgun Proteomics Reveals Soy Consumption-Induced Protein Changes in a Fragile X Syndrome Mouse Model. ACS Chem Neurosci 2024; 15:119-133. [PMID: 38109073 PMCID: PMC11127747 DOI: 10.1021/acschemneuro.3c00497] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Abstract
Fragile X syndrome (FXS), the leading cause of inherited intellectual disability and autism, is caused by the transcriptional silencing of the FMR1 gene, which encodes the fragile X messenger ribonucleoprotein (FMRP). FMRP interacts with numerous brain mRNAs that are involved in synaptic plasticity and implicated in autism spectrum disorders. Our published studies indicate that single-source, soy-based diets are associated with increased seizures and autism. Thus, there is an acute need for an unbiased protein marker identification in FXS in response to soy consumption. Herein, we present a spatial proteomics approach integrating mass spectrometry imaging with label-free proteomics in the FXS mouse model to map the spatial distribution and quantify levels of proteins in the hippocampus and hypothalamus brain regions. In total, 1250 unique peptides were spatially resolved, demonstrating the diverse array of peptidomes present in the tissue slices and the broad coverage of the strategy. A group of proteins that are known to be involved in glycolysis, synaptic transmission, and coexpression network analysis suggest a significant association between soy proteins and metabolic and synaptic processes in the Fmr1KO brain. Ultimately, this spatial proteomics work represents a crucial step toward identifying potential candidate protein markers and novel therapeutic targets for FXS.
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Affiliation(s)
- Min Ma
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Qinying Yu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Daniel G. Delafield
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Yusi Cui
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Zihui Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Miyang Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Wenxin Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Xudong Shi
- Division of Otolaryngology, Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Pamela R. Westmark
- Department of Neurology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Alejandra Gutierrez
- Department of Neurology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
- Molecular Environmental Toxicology Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Gui Ma
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Ang Gao
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Meng Xu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Wei Xu
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Cara J. Westmark
- Department of Neurology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
- Molecular Environmental Toxicology Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
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7
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Zhong J, Li J, Burton GJ, Koistinen H, Cheung KW, Ng EHY, Yao Y, Yeung WSB, Lee CL, Chiu PCN. The functional roles of protein glycosylation in human maternal-fetal crosstalk. Hum Reprod Update 2024; 30:81-108. [PMID: 37699855 DOI: 10.1093/humupd/dmad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/20/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND The establishment of maternal-fetal crosstalk is vital to a successful pregnancy. Glycosylation is a post-translational modification in which glycans (monosaccharide chains) are attached to an organic molecule. Glycans are involved in many physiological and pathological processes. Human endometrial epithelium, endometrial gland secretions, decidual immune cells, and trophoblasts are highly enriched with glycoconjugates and glycan-binding molecules important for a healthy pregnancy. Aberrant glycosylation in the placenta and uterus has been linked to repeated implantation failure and various pregnancy complications, but there is no recent review summarizing the functional roles of glycosylation at the maternal-fetal interface and their associations with pathological processes. OBJECTIVE AND RATIONALE This review aims to summarize recent findings on glycosylation, glycosyltransferases, and glycan-binding receptors at the maternal-fetal interface, and their involvement in regulating the biology and pathological conditions associated with endometrial receptivity, placentation and maternal-fetal immunotolerance. Current knowledge limitations and future insights into the study of glycobiology in reproduction are discussed. SEARCH METHODS A comprehensive PubMed search was conducted using the following keywords: glycosylation, glycosyltransferases, glycan-binding proteins, endometrium, trophoblasts, maternal-fetal immunotolerance, siglec, selectin, galectin, repeated implantation failure, early pregnancy loss, recurrent pregnancy loss, preeclampsia, and fetal growth restriction. Relevant reports published between 1980 and 2023 and studies related to these reports were retrieved and reviewed. Only publications written in English were included. OUTCOMES The application of ultrasensitive mass spectrometry tools and lectin-based glycan profiling has enabled characterization of glycans present at the maternal-fetal interface and in maternal serum. The endometrial luminal epithelium is covered with highly glycosylated mucin that regulates blastocyst adhesion during implantation. In the placenta, fucose and sialic acid residues are abundantly presented on the villous membrane and are essential for proper placentation and establishment of maternal-fetal immunotolerance. Glycan-binding receptors, including selectins, sialic-acid-binding immunoglobulin-like lectins (siglecs) and galectins, also modulate implantation, trophoblast functions and maternal-fetal immunotolerance. Aberrant glycosylation is associated with repeated implantation failure, early pregnancy loss and various pregnancy complications. The current limitation in the field is that most glycobiological research relies on association studies, with few studies revealing the specific functions of glycans. Technological advancements in analytic, synthetic and functional glycobiology have laid the groundwork for further exploration of glycans in reproductive biology under both physiological and pathological conditions. WIDER IMPLICATIONS A deep understanding of the functions of glycan structures would provide insights into the molecular mechanisms underlying their involvement in the physiological and pathological regulation of early pregnancy. Glycans may also potentially serve as novel early predictive markers and therapeutic targets for repeated implantation failure, pregnancy loss, and other pregnancy complications.
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Affiliation(s)
- Jiangming Zhong
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
- The University of Hong Kong Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Jianlin Li
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
| | - Graham J Burton
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Hannu Koistinen
- Department of Clinical Chemistry and Haematology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ka Wang Cheung
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
| | - Ernest H Y Ng
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
- The University of Hong Kong Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Yuanqing Yao
- The University of Hong Kong Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - William S B Yeung
- The University of Hong Kong Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Cheuk-Lun Lee
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
- The University of Hong Kong Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Philip C N Chiu
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
- The University of Hong Kong Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
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8
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Le HT, Liu M, Grimes CL. Application of bioanalytical and computational methods in decoding the roles of glycans in host-pathogen interactions. Curr Opin Chem Biol 2023; 74:102301. [PMID: 37080155 PMCID: PMC10296625 DOI: 10.1016/j.cbpa.2023.102301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 04/22/2023]
Abstract
Host-pathogen interactions (HPIs) are complex processes that require tight regulation. A common regulatory mechanism of HPIs is through glycans of either host cells or pathogens. Due to their diverse sequences, complex structures, and conformations, studies of glycans require highly sensitive and powerful tools. Recent improvements in technology have enabled the application of many bioanalytical techniques and modeling methods to investigate glycans and their mechanisms in HPIs. This mini-review highlights how these advances have been used to understand the role glycans play in HPIs in the past 2 years.
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Affiliation(s)
- Ha T Le
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Min Liu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Catherine L Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA; Department of Biological Sciences, University of Delaware, Newark, DE, USA.
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Yue J, Huang R, Lan Z, Xiao B, Luo Z. Abnormal glycosylation in glioma: related changes in biology, biomarkers and targeted therapy. Biomark Res 2023; 11:54. [PMID: 37231524 DOI: 10.1186/s40364-023-00491-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 04/26/2023] [Indexed: 05/27/2023] Open
Abstract
Glioma is a rapidly growing and aggressive primary malignant tumor of the central nervous system that can diffusely invade the brain tissue around, and the prognosis of patients is not significantly improved by traditional treatments. One of the most general posttranslational modifications of proteins is glycosylation, and the abnormal distribution of this modification in gliomas may shed light on how it affects biological behaviors of glioma cells, including proliferation, migration, and invasion, which may be produced by regulating protein function, cell-matrix and cell‒cell interactions, and affecting receptor downstream pathways. In this paper, from the perspective of regulating protein glycosylation changes and abnormal expression of glycosylation-related proteins (such as glycosyltransferases in gliomas), we summarize how glycosylation may play a crucial role in the discovery of novel biomarkers and new targeted treatment options for gliomas. Overall, the mechanistic basis of abnormal glycosylation affecting glioma progression remains to be more widely and deeply explored, which not only helps to inspire researchers to further explore related diagnostic and prognostic markers but also provides ideas for discovering effective treatment strategies and improving glioma patient survival and prognosis.
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Affiliation(s)
- Juan Yue
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya road of Kaifu district, 410008, Changsha, Hunan, China
| | - Roujie Huang
- Department of Obstetrics and Gynecology, Peking Union Medical College, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Shuaifuyuan No. 1, Dongcheng District, 100730, Beijing, China
| | - Zehao Lan
- Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya road of Kaifu district, 410008, Changsha, Hunan, China
- Clinical Research Center for Epileptic disease of Hunan Province, Central South University, 410008, Changsha, Hunan, P.R. China
| | - Zhaohui Luo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya road of Kaifu district, 410008, Changsha, Hunan, China.
- Clinical Research Center for Epileptic disease of Hunan Province, Central South University, 410008, Changsha, Hunan, P.R. China.
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10
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Čaval T, Alisson-Silva F, Schwarz F. Roles of glycosylation at the cancer cell surface: opportunities for large scale glycoproteomics. Theranostics 2023; 13:2605-2615. [PMID: 37215580 PMCID: PMC10196828 DOI: 10.7150/thno.81760] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
Cell surface glycosylation has a variety of functions, and its dysregulation in cancer contributes to impaired signaling, metastasis and the evasion of the immune responses. Recently, a number of glycosyltransferases that lead to altered glycosylation have been linked to reduced anti-tumor immune responses: B3GNT3, which is implicated in PD-L1 glycosylation in triple negative breast cancer, FUT8, through fucosylation of B7H3, and B3GNT2, which confers cancer resistance to T cell cytotoxicity. Given the increased appreciation of the relevance of protein glycosylation, there is a critical need for the development of methods that allow for an unbiased interrogation of cell surface glycosylation status. Here we provide an overview of the broad changes in glycosylation at the surface of cancer cell and describe selected examples of receptors with aberrant glycosylation leading to functional changes, with emphasis on immune checkpoint inhibitors, growth-promoting and growth-arresting receptors. Finally, we posit that the field of glycoproteomics has matured to an extent where large-scale profiling of intact glycopeptides from the cell surface is feasible and is poised for discovery of new actionable targets against cancer.
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11
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Escobar EE, Seeley EH, Serrano-Negrón JE, Vocadlo DJ, Brodbelt JS. In Situ Imaging of O-Linked β-N-Acetylglucosamine Using On-Tissue Hydrolysis and MALDI Mass Spectrometry. Cancers (Basel) 2023; 15:1224. [PMID: 36831567 PMCID: PMC9954453 DOI: 10.3390/cancers15041224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Post-translational O-glycosylation of proteins via the addition of N-acetylglucosamine (O-GlcNAc) is a regulator of many aspects of cellular physiology. Processes driven by perturbed dynamics of O-GlcNAcylation modification have been implicated in cancer development. Variability in O-GlcNAcylation is emerging as a metabolic biomarker of many cancers. Here, we evaluate the use of MALDI-mass spectrometry imaging (MSI) to visualize the location of O-GlcNAcylated proteins in tissue sections by mapping GlcNAc that has been released by the enzymatic hydrolysis of glycoproteins using an O-GlcNAc hydrolase. We use this strategy to monitor O-GlcNAc within hepatic VX2 tumor tissue. We show that increased O-GlcNAc is found within both viable tumor and tumor margin regions, implicating GlcNAc in tumor progression.
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Affiliation(s)
- Edwin E. Escobar
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Erin H. Seeley
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - David J. Vocadlo
- Department of Molecular Biology and Biochemistry, Burnaby, BC V5A 1S6, Canada
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Jennifer S. Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
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12
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Peng W, Kobeissy F, Mondello S, Barsa C, Mechref Y. MS-based glycomics: An analytical tool to assess nervous system diseases. Front Neurosci 2022; 16:1000179. [PMID: 36408389 PMCID: PMC9671362 DOI: 10.3389/fnins.2022.1000179] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/05/2022] [Indexed: 08/27/2023] Open
Abstract
Neurological diseases affect millions of peopleochemistryorldwide and are continuously increasing due to the globe's aging population. Such diseases affect the nervous system and are characterized by a progressive decline in brain function and progressive cognitive impairment, decreasing the quality of life for those with the disease as well as for their families and loved ones. The increased burden of nervous system diseases demands a deeper insight into the biomolecular mechanisms at work during disease development in order to improve clinical diagnosis and drug design. Recently, evidence has related glycosylation to nervous system diseases. Glycosylation is a vital post-translational modification that mediates many biological functions, and aberrant glycosylation has been associated with a variety of diseases. Thus, the investigation of glycosylation in neurological diseases could provide novel biomarkers and information for disease pathology. During the last decades, many techniques have been developed for facilitation of reliable and efficient glycomic analysis. Among these, mass spectrometry (MS) is considered the most powerful tool for glycan analysis due to its high resolution, high sensitivity, and the ability to acquire adequate structural information for glycan identification. Along with MS, a variety of approaches and strategies are employed to enhance the MS-based identification and quantitation of glycans in neurological samples. Here, we review the advanced glycomic tools used in nervous system disease studies, including separation techniques prior to MS, fragmentation techniques in MS, and corresponding strategies. The glycan markers in common clinical nervous system diseases discovered by utilizing such MS-based glycomic tools are also summarized and discussed.
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Affiliation(s)
- Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Firas Kobeissy
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL, United States
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Chloe Barsa
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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13
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Veličković D, Liao YC, Thibert S, Veličković M, Anderton C, Voglmeir J, Stacey G, Zhou M. Spatial Mapping of Plant N-Glycosylation Cellular Heterogeneity Inside Soybean Root Nodules Provided Insights Into Legume-Rhizobia Symbiosis. FRONTIERS IN PLANT SCIENCE 2022; 13:869281. [PMID: 35651768 PMCID: PMC9150855 DOI: 10.3389/fpls.2022.869281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Although ubiquitously present, information on the function of complex N-glycan posttranslational modification in plants is very limited and is often neglected. In this work, we adopted an enzyme-assisted matrix-assisted laser desorption/ionization mass spectrometry imaging strategy to visualize the distribution and identity of N-glycans in soybean root nodules at a cellular resolution. We additionally performed proteomics analysis to probe the potential correlation to proteome changes during symbiotic rhizobia-legume interactions. Our ion images reveal that intense N-glycosylation occurs in the sclerenchyma layer, and inside the infected cells within the infection zone, while morphological structures such as the cortex, uninfected cells, and cells that form the attachment with the root are fewer N-glycosylated. Notably, we observed different N-glycan profiles between soybean root nodules infected with wild-type rhizobia and those infected with mutant rhizobia incapable of efficiently fixing atmospheric nitrogen. The majority of complex N-glycan structures, particularly those with characteristic Lewis-a epitopes, are more abundant in the mutant nodules. Our proteomic results revealed that these glycans likely originated from proteins that maintain the redox balance crucial for proper nitrogen fixation, but also from enzymes involved in N-glycan and phenylpropanoid biosynthesis. These findings indicate the possible involvement of Lewis-a glycans in these critical pathways during legume-rhizobia symbiosis.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Yen-Chen Liao
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Stephanie Thibert
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Marija Veličković
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Christopher Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
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14
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Sethi MK, Downs M, Shao C, Hackett WE, Phillips JJ, Zaia J. In-Depth Matrisome and Glycoproteomic Analysis of Human Brain Glioblastoma Versus Control Tissue. Mol Cell Proteomics 2022; 21:100216. [PMID: 35202840 PMCID: PMC8957055 DOI: 10.1016/j.mcpro.2022.100216] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma (GBM) is the most common and malignant primary brain tumor. The extracellular matrix, also known as the matrisome, helps determine glioma invasion, adhesion, and growth. Little attention, however, has been paid to glycosylation of the extracellular matrix components that constitute the majority of glycosylated protein mass and presumed biological properties. To acquire a comprehensive understanding of the biological functions of the matrisome and its components, including proteoglycans (PGs) and glycosaminoglycans (GAGs), in GBM tumorigenesis, and to identify potential biomarker candidates, we studied the alterations of GAGs, including heparan sulfate (HS) and chondroitin sulfate (CS), the core proteins of PGs, and other glycosylated matrisomal proteins in GBM subtypes versus control human brain tissue samples. We scrutinized the proteomics data to acquire in-depth site-specific glycoproteomic profiles of the GBM subtypes that will assist in identifying specific glycosylation changes in GBM. We observed an increase in CS 6-O sulfation and a decrease in HS 6-O sulfation, accompanied by an increase in unsulfated CS and HS disaccharides in GBM versus control samples. Several core matrisome proteins, including PGs (decorin, biglycan, agrin, prolargin, glypican-1, and chondroitin sulfate proteoglycan 4), tenascin, fibronectin, hyaluronan link protein 1 and 2, laminins, and collagens, were differentially regulated in GBM versus controls. Interestingly, a higher degree of collagen hydroxyprolination was also observed for GBM versus controls. Further, two PGs, chondroitin sulfate proteoglycan 4 and agrin, were significantly lower, about 6-fold for isocitrate dehydrogenase-mutant, compared to the WT GBM samples. Differential regulation of O-glycopeptides for PGs, including brevican, neurocan, and versican, was observed for GBM subtypes versus controls. Moreover, an increase in levels of glycosyltransferase and glycosidase enzymes was observed for GBM when compared to control samples. We also report distinct protein, peptide, and glycopeptide features for GBM subtypes comparisons. Taken together, our study informs understanding of the alterations to key matrisomal molecules that occur during GBM development. (Data are available via ProteomeXchange with identifier PXD028931, and the peaks project file is available at Zenodo with DOI 10.5281/zenodo.5911810).
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Affiliation(s)
- Manveen K Sethi
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
| | - Margaret Downs
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
| | - Chun Shao
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
| | - William E Hackett
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA; Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, Brain Tumor Center, Helen Diller Family Cancer Research Center, University of California San Francisco, San Francisco, California, USA; Division of Neuropathology, Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA; Bioinformatics Program, Boston University, Boston, Massachusetts, USA.
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15
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Zhu X, Xu T, Peng C, Wu S. Advances in MALDI Mass Spectrometry Imaging Single Cell and Tissues. Front Chem 2022; 9:782432. [PMID: 35186891 PMCID: PMC8850921 DOI: 10.3389/fchem.2021.782432] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/17/2021] [Indexed: 12/26/2022] Open
Abstract
Compared with conventional optical microscopy techniques, mass spectrometry imaging (MSI) or imaging mass spectrometry (IMS) is a powerful, label-free analytical technique, which can sensitively and simultaneously detect, quantify, and map hundreds of biomolecules, such as peptides, proteins, lipid, and other organic compounds in cells and tissues. So far, although several soft ionization techniques, such as desorption electrospray ionization (DESI) and secondary ion mass spectrometry (SIMS) have been used for imaging biomolecules, matrix-assisted laser desorption/ionization (MALDI) is still the most widespread MSI scanning method. Here, we aim to provide a comprehensive review of MALDI-MSI with an emphasis on its advances of the instrumentation, methods, application, and future directions in single cell and biological tissues.
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Affiliation(s)
- Xiaoping Zhu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Tianyi Xu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chen Peng
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shihua Wu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
- *Correspondence: Shihua Wu, ; Shihua Wu,
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16
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Hasan MM, Mimi MA, Mamun MA, Islam A, Waliullah ASM, Nabi MM, Tamannaa Z, Kahyo T, Setou M. Mass Spectrometry Imaging for Glycome in the Brain. Front Neuroanat 2021; 15:711955. [PMID: 34393728 PMCID: PMC8358800 DOI: 10.3389/fnana.2021.711955] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
Glycans are diverse structured biomolecules that play crucial roles in various biological processes. Glycosylation, an enzymatic system through which various glycans are bound to proteins and lipids, is the most common and functionally crucial post-translational modification process. It is known to be associated with brain development, signal transduction, molecular trafficking, neurodegenerative disorders, psychopathologies, and brain cancers. Glycans in glycoproteins and glycolipids expressed in brain cells are involved in neuronal development, biological processes, and central nervous system maintenance. The composition and expression of glycans are known to change during those physiological processes. Therefore, imaging of glycans and the glycoconjugates in the brain regions has become a “hot” topic nowadays. Imaging techniques using lectins, antibodies, and chemical reporters are traditionally used for glycan detection. However, those techniques offer limited glycome detection. Mass spectrometry imaging (MSI) is an evolving field that combines mass spectrometry with histology allowing spatial and label-free visualization of molecules in the brain. In the last decades, several studies have employed MSI for glycome imaging in brain tissues. The current state of MSI uses on-tissue enzymatic digestion or chemical reaction to facilitate successful glycome imaging. Here, we reviewed the available literature that applied MSI techniques for glycome visualization and characterization in the brain. We also described the general methodologies for glycome MSI and discussed its potential use in the three-dimensional MSI in the brain.
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Affiliation(s)
- Md Mahmudul Hasan
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Mst Afsana Mimi
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Md Al Mamun
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Ariful Islam
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - A S M Waliullah
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Md Mahamodun Nabi
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Zinat Tamannaa
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tomoaki Kahyo
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan.,International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Mitsutoshi Setou
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan.,International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Systems Molecular Anatomy, Institute for Medical Photonics Research, Preeminent Medical Photonics Education & Research Center, Hamamatsu, Japan
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