1
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Binkowski B, Klamer Z, Gao C, Staal B, Repesh A, Tran HL, Brass DM, Bartlett P, Gallinger S, Blomqvist M, Morrow JB, Allen P, Shi C, Singhi A, Brand R, Huang Y, Hostetter G, Haab BB. Multiplexed Glycan Immunofluorescence Identification of Pancreatic Cancer Cell Subpopulations in Both Tumor and Blood Samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.22.609143. [PMID: 39229066 PMCID: PMC11370594 DOI: 10.1101/2024.08.22.609143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) tumor heterogeneity impedes the development of biomarker assays suitable for early disease detection that would improve patient outcomes. The CA19-9 glycan is currently used as a standalone biomarker for PDAC. Furthermore, previous studies have shown that cancer cells may display aberrant membrane-associated glycans. We therefore hypothesized that PDAC cancer cell subpopulations could be distinguished by aberrant glycan signatures. We used multiplexed glycan immunofluorescence combined with pathologist annotation and automated image processing to distinguish between PDAC cancer cell subpopulations within tumor tissue. Using a training-set/test-set approach, we found that PDAC cancer cells may be identified by signatures comprising 4 aberrant glycans (VVL, CA19-9, sTRA, and GM2) and that there are three glycan-defined PDAC tumor types: sTRA type, CA19-9 type, and intermixed. To determine whether the aberrant glycan signatures could be detected in blood samples, we developed hybrid glycan sandwich assays for membrane-associated glycans. In both patient-matched tumor and blood samples, the proportion of aberrant glycans detected was consistent. Furthermore, our multiplexed glycan immunofluorescent approach proved to be more sensitive and more specific than CA19-9 alone. Our results provide proof of concept for a novel methodology to improve early PDAC detection and patient outcomes.
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Affiliation(s)
| | | | | | - Ben Staal
- Van Andel Institute, Grand Rapids, Michigan, USA
| | - Anna Repesh
- Van Andel Institute, Grand Rapids, Michigan, USA
| | | | | | | | | | - Maria Blomqvist
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Peter Allen
- Duke University School of Medicine, Durham, NC, USA
| | - Chanjuan Shi
- Duke University School of Medicine, Durham, NC, USA
| | - Aatur Singhi
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Randall Brand
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Ying Huang
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Brian B Haab
- Van Andel Institute, Grand Rapids, Michigan, USA
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2
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Colley ME, Esselman AB, Scott CF, Spraggins JM. High-Specificity Imaging Mass Spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:1-24. [PMID: 38594938 DOI: 10.1146/annurev-anchem-083023-024546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Imaging mass spectrometry (IMS) enables highly multiplexed, untargeted tissue mapping for a broad range of molecular classes, facilitating in situ biological discovery. Yet, challenges persist in molecular specificity, which is the ability to discern one molecule from another, and spatial specificity, which is the ability to link untargeted imaging data to specific tissue features. Instrumental developments have dramatically improved IMS spatial resolution, allowing molecular observations to be more readily associated with distinct tissue features across spatial scales, ranging from larger anatomical regions to single cells. High-performance mass analyzers and systems integrating ion mobility technologies are also becoming more prevalent, further improving molecular coverage and the ability to discern chemical identity. This review provides an overview of recent advancements in high-specificity IMS that are providing critical biological context to untargeted molecular imaging, enabling integrated analyses, and addressing advanced biomedical research applications.
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Affiliation(s)
- Madeline E Colley
- 1Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA;
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Allison B Esselman
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- 3Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Claire F Scott
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- 4Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Jeffrey M Spraggins
- 1Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA;
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- 3Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- 4Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- 5Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, 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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Keisham S, Saito S, Kowashi S, Tateno H. Droplet-Based Glycan and RNA Sequencing for Profiling the Distinct Cellular Glyco-States in Single Cells. SMALL METHODS 2024; 8:e2301338. [PMID: 38164999 DOI: 10.1002/smtd.202301338] [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: 10/02/2023] [Revised: 12/18/2023] [Indexed: 01/03/2024]
Abstract
Plate-based single-cell glycan and RNA sequencing (scGR-seq) is previously developed to realize the integrated analysis of glycome and transcriptome in single cells. However, the sample size is limited to only a few hundred cells. Here, a droplet-based scGR-seq is developed to address this issue by adopting a 10x Chromium platform to simultaneously profile ten thousand cells' glycome and transcriptome in single cells. To establish droplet-based scGR-seq, a comparative analysis of two distinct cell lines is performed: pancreatic ductal adenocarcinoma cells and normal pancreatic duct cells. Droplet-based scGR-seq revealed distinct glycan profiles between the two cell lines that showed a strong correlation with the results obtained by flow cytometry. Next, droplet-based scGR-seq is applied to a more complex sample: peripheral blood mononuclear cells (PBMC) containing various immune cells. The method can systematically map the glycan signature for each immune cell in PBMC as well as glycan alterations by cell lineage. Prediction of the association between the glycan expression and the gene expression using regression analysis ultimately leads to the identification of a glycan epitope that impacts cellular functions. In conclusion, the droplet-based scGR-seq realizes the high-throughput profiling of the distinct cellular glyco-states in single cells.
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Affiliation(s)
- Sunanda Keisham
- Cellular and Molecular Biotechnology Research Institute, Multicellular System Regulation Research Group, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
- Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Ibaraki, 305-8566, Japan
| | - Sayoko Saito
- Cellular and Molecular Biotechnology Research Institute, Multicellular System Regulation Research Group, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Satori Kowashi
- Cellular and Molecular Biotechnology Research Institute, Multicellular System Regulation Research Group, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Hiroaki Tateno
- Cellular and Molecular Biotechnology Research Institute, Multicellular System Regulation Research Group, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
- Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Ibaraki, 305-8566, Japan
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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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Stadlmann J, Helm J, Mereiter S, Oliveira T, Gattinger A, Markovitz D, Penninger J, Altmann F. Non-targeted isomer-sensitive N-glycome analysis reveals new layers of organ-specific diversity in mice. RESEARCH SQUARE 2024:rs.3.rs-4130712. [PMID: 38659835 PMCID: PMC11042426 DOI: 10.21203/rs.3.rs-4130712/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
N-glycosylation is one of the most common protein modifications in eukaryotes, with immense importance at the molecular, cellular, and organismal level. Accurate and reliable N-glycan analysis is essential to obtain a systems-wide understanding of fundamental biological processes. Due to the structural complexity of glycans, their analysis is still highly challenging. Here we make publicly available a consistent N-glycome dataset of 20 different mouse tissues and demonstrate a multimodal data analysis workflow that allows for unprecedented depth and coverage of N-glycome features. This highly scalable, LC-MS/MS data-driven method integrates the automated identification of N-glycan spectra, the application of non-targeted N-glycome profiling strategies and the isomer-sensitive analysis of glycan structures. Our delineation of critical sub-structural determinants and glycan isomers across the mouse N-glycome uncovered tissue-specific glycosylation patterns, the expression of non-canonical N-glycan structures and highlights multiple layers of N-glycome complexity that derive from organ-specific regulations of glycobiological pathways.
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Affiliation(s)
| | - Johannes Helm
- University of Natural Resources and Life Sciences Vienna
| | | | - Tiago Oliveira
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)
| | - Anna Gattinger
- Bioinformatics Research Group, University of Applied Sciences Upper Austria
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7
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Klein D, Rivera ES, Caprioli RM, Spraggins JM. Imaging Mass Spectrometry of Isotopically Resolved Intact Proteins on a Trapped Ion-Mobility Quadrupole Time-of-Flight Mass Spectrometer. Anal Chem 2024; 96:5065-5070. [PMID: 38517028 PMCID: PMC10993197 DOI: 10.1021/acs.analchem.3c05252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 03/23/2024]
Abstract
In this work, we demonstrate rapid, high spatial, and high spectral resolution imaging of intact proteins by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) on a hybrid quadrupole-reflectron time-of-flight (qTOF) mass spectrometer equipped with trapped ion mobility spectrometry (TIMS). Historically, untargeted MALDI IMS of proteins has been performed on TOF mass spectrometers. While advances in TOF instrumentation have enabled rapid, high spatial resolution IMS of intact proteins, TOF mass spectrometers generate relatively low-resolution mass spectra with limited mass accuracy. Conversely, the implementation of MALDI sources on high-resolving power Fourier transform (FT) mass spectrometers has allowed IMS experiments to be conducted with high spectral resolution with the caveat of increasingly long data acquisition times. As illustrated here, qTOF mass spectrometers enable protein imaging with the combined advantages of TOF and FT mass spectrometers. Protein isotope distributions were resolved for both a protein standard mixture and proteins detected from a whole-body mouse pup tissue section. Rapid (∼10 pixels/s) 10 μm lateral spatial resolution IMS was performed on a rat brain tissue section while maintaining isotopic spectral resolution. Lastly, proof-of-concept MALDI-TIMS data was acquired from a protein mixture to demonstrate the ability to differentiate charge states by ion mobility. These experiments highlight the advantages of qTOF and timsTOF platforms for resolving and interpreting complex protein spectra generated from tissue by IMS.
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Affiliation(s)
- Dustin
R. Klein
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Emilio S. Rivera
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Richard M. Caprioli
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Medicine, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Pharmacology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey M. Spraggins
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37235, United States
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8
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Wen YR, Lin XW, Zhou YW, Xu L, Zhang JL, Chen CY, He J. N-glycan biosignatures as a potential diagnostic biomarker for early-stage pancreatic cancer. World J Gastrointest Oncol 2024; 16:659-669. [PMID: 38577461 PMCID: PMC10989390 DOI: 10.4251/wjgo.v16.i3.659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/21/2023] [Accepted: 01/18/2024] [Indexed: 03/12/2024] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis, with a 5-year survival rate of less than 10%, owing to its late-stage diagnosis. Early detection of pancreatic cancer (PC) can significantly increase survival rates. AIM To identify the serum biomarker signatures associated with early-stage PDAC by serum N-glycan analysis. METHODS An extensive patient cohort was used to determine a biomarker signature, including patients with PDAC that was well-defined at an early stage (stages I and II). The biomarker signature was derived from a case-control study using a case-cohort design consisting of 29 patients with stage I, 22 with stage II, 4 with stage III, 16 with stage IV PDAC, and 88 controls. We used multiparametric analysis to identify early-stage PDAC N-glycan signatures and developed an N-glycan signature-based diagnosis model called the "Glyco-model". RESULTS The biomarker signature was created to discriminate samples derived from patients with PC from those of controls, with a receiver operating characteristic area under the curve of 0.86. In addition, the biomarker signature combined with cancer antigen 19-9 could discriminate patients with PDAC from controls, with a receiver operating characteristic area under the curve of 0.919. Glyco-model demonstrated favorable diagnostic performance in all stages of PC. The diagnostic sensitivity for stage I PDAC was 89.66%. CONCLUSION In a prospective validation study, this serum biomarker signature may offer a viable method for detecting early-stage PDAC.
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Affiliation(s)
- Yan-Rong Wen
- Department of Nuclear Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, Jiangsu Province, China
| | - Xia-Wen Lin
- Department of Nuclear Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, Jiangsu Province, China
| | - Yu-Wen Zhou
- Department of Research and Development, Sysdiagno (Nanjing) Biotech Co., Ltd, Nanjing 210008, Jiangsu Province, China
| | - Lei Xu
- Department of Research and Development, Sysdiagno (Nanjing) Biotech Co., Ltd, Nanjing 210008, Jiangsu Province, China
| | - Jun-Li Zhang
- Department of Research and Development, Sysdiagno (Nanjing) Biotech Co., Ltd, Nanjing 210008, Jiangsu Province, China
| | - Cui-Ying Chen
- Department of Research and Development, Sysdiagno (Nanjing) Biotech Co., Ltd, Nanjing 210008, Jiangsu Province, China
| | - Jian He
- Department of Nuclear Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, Jiangsu Province, China
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9
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Ma X, Fernández FM. Advances in mass spectrometry imaging for spatial cancer metabolomics. MASS SPECTROMETRY REVIEWS 2024; 43:235-268. [PMID: 36065601 PMCID: PMC9986357 DOI: 10.1002/mas.21804] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 05/09/2023]
Abstract
Mass spectrometry (MS) has become a central technique in cancer research. The ability to analyze various types of biomolecules in complex biological matrices makes it well suited for understanding biochemical alterations associated with disease progression. Different biological samples, including serum, urine, saliva, and tissues have been successfully analyzed using mass spectrometry. In particular, spatial metabolomics using MS imaging (MSI) allows the direct visualization of metabolite distributions in tissues, thus enabling in-depth understanding of cancer-associated biochemical changes within specific structures. In recent years, MSI studies have been increasingly used to uncover metabolic reprogramming associated with cancer development, enabling the discovery of key biomarkers with potential for cancer diagnostics. In this review, we aim to cover the basic principles of MSI experiments for the nonspecialists, including fundamentals, the sample preparation process, the evolution of the mass spectrometry techniques used, and data analysis strategies. We also review MSI advances associated with cancer research in the last 5 years, including spatial lipidomics and glycomics, the adoption of three-dimensional and multimodal imaging MSI approaches, and the implementation of artificial intelligence/machine learning in MSI-based cancer studies. The adoption of MSI in clinical research and for single-cell metabolomics is also discussed. Spatially resolved studies on other small molecule metabolites such as amino acids, polyamines, and nucleotides/nucleosides will not be discussed in the context.
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Affiliation(s)
- Xin Ma
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Facundo M Fernández
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
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10
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Macdonald JK, Mehta AS, Drake RR, Angel PM. Molecular analysis of the extracellular microenvironment: from form to function. FEBS Lett 2024; 598:602-620. [PMID: 38509768 PMCID: PMC11049795 DOI: 10.1002/1873-3468.14852] [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: 11/29/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
The extracellular matrix (ECM) proteome represents an important component of the tissue microenvironment that controls chemical flux and induces cell signaling through encoded structure. The analysis of the ECM represents an analytical challenge through high levels of post-translational modifications, protease-resistant structures, and crosslinked, insoluble proteins. This review provides a comprehensive overview of the analytical challenges involved in addressing the complexities of spatially profiling the extracellular matrix proteome. A synopsis of the process of synthesizing the ECM structure, detailing inherent chemical complexity, is included to present the scope of the analytical challenge. Current chromatographic and spatial techniques addressing these challenges are detailed. Capabilities for multimodal multiplexing with cellular populations are discussed with a perspective on developing a holistic view of disease processes that includes both the cellular and extracellular microenvironment.
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Affiliation(s)
- Jade K Macdonald
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC
| | - Anand S Mehta
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC
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11
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Kumar BS. Recent Developments and Application of Mass Spectrometry Imaging in N-Glycosylation Studies: An Overview. Mass Spectrom (Tokyo) 2024; 13:A0142. [PMID: 38435075 PMCID: PMC10904931 DOI: 10.5702/massspectrometry.a0142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/06/2024] [Indexed: 03/05/2024] Open
Abstract
Among the most typical posttranslational modifications is glycosylation, which often involves the covalent binding of an oligosaccharide (glycan) to either an asparagine (N-linked) or a serine/threonine (O-linked) residue. Studies imply that the N-glycan portion of a glycoprotein could serve as a particular disease biomarker rather than the protein itself because N-linked glycans have been widely recognized to evolve with the advancement of tumors and other diseases. N-glycans found on protein asparagine sites have been especially significant. Since N-glycans play clearly defined functions in the folding of proteins, cellular transport, and transmission of signals, modifications to them have been linked to several illnesses. However, because these N-glycans' production is not template driven, they have a substantial morphological range, rendering it difficult to distinguish the species that are most relevant to biology and medicine using standard techniques. Mass spectrometry (MS) techniques have emerged as effective analytical tools for investigating the role of glycosylation in health and illness. This is due to developments in MS equipment, data collection, and sample handling techniques. By recording the spatial dimension of a glycan's distribution in situ, mass spectrometry imaging (MSI) builds atop existing methods while offering added knowledge concerning the structure and functionality of biomolecules. In this review article, we address the current development of glycan MSI, starting with the most used tissue imaging techniques and ionization sources before proceeding on to a discussion on applications and concluding with implications for clinical research.
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12
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Ochoa-Rios S, Grauzam SE, Gregory R, Angel PM, Drake RR, Helke KL, Mehta AS. Spatial Omics Reveals that Cancer-Associated Glycan Changes Occur Early in Liver Disease Development in a Western Diet Mouse Model of MASLD. J Proteome Res 2024; 23:786-796. [PMID: 38206822 DOI: 10.1021/acs.jproteome.3c00672] [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] [Indexed: 01/13/2024]
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) is a progressive disease and comprises different stages of liver damage; it is significantly associated with obese and overweight patients. Untreated MASLD can progress to life-threatening end-stage conditions, such as cirrhosis and liver cancer. N-Linked glycosylation is one of the most common post-translational modifications in the cell surface and secreted proteins. N-Linked glycan alterations have been established to be signatures of liver diseases. However, the N-linked glycan changes during the progression of MASLD to liver cancer are still unknown. Here, we induced different stages of MASLD in mice and liver-cancer-related phenotypes and elucidated the N-glycome profile during the progression of MASLD by quantitative and qualitative profiling in situ using matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS). Importantly, we identified specific N-glycan structures including fucosylated and highly branched N-linked glycans at very early stages of liver injury (steatosis), which in humans are associated with cancer development, establishing the importance of these modifications with disease progression. Finally, we report that N-linked glycan alterations can be observed in our models by MALDI-IMS before liver injury is identified by histological analysis. Overall, we propose these findings as promising biomarkers for the early diagnosis of liver injury in MASLD.
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Affiliation(s)
- Shaaron Ochoa-Rios
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Stéphane Elie Grauzam
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Rebecca Gregory
- Department of Comparative Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Peggi M Angel
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Kristi L Helke
- Department of Comparative Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Anand S Mehta
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina 29425, United States
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13
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Boyaval F, Fariña-Sarasqueta A, Boonstra JJ, Heijs B, Morreau H. Recognition of pseudoinvasion in colorectal adenoma using spatial glycomics. Front Med (Lausanne) 2024; 10:1221553. [PMID: 38288301 PMCID: PMC10822882 DOI: 10.3389/fmed.2023.1221553] [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: 05/12/2023] [Accepted: 12/28/2023] [Indexed: 01/31/2024] Open
Abstract
Pseudoinvasion (PI) is a benign lesion in which cancer is mimicked in the colon by misplacement of dysplastic glands in the submucosa. Although there are morphological clues, the discrimination of PI from true invasion can be a challenge during pathological evaluation of colon adenomas. Both overdiagnosis and underdiagnosis can result in inadequate clinical decisions. This calls for novel tools to aid in cases where conventional methods do not suffice. We performed mass spectrometry imaging (MSI)-based spatial glycomics analysis on a cohort of formalin-fixed paraffin-embedded tissue (FFPE) material from 16 patients who underwent polypectomy. We used this spatial glycomic data to reconstruct the molecular histology of the tissue section using spatial segmentation based on uniform manifold approximation and projection for dimension reduction (UMAP). We first showed that the spatial glycomic phenotypes of the different morphological entities separated as distinct clusters in colon tissues, we separated true invasion from the other morphological entities. Then, we found that the glycomic phenotype in areas with suspected PI in the submucosa was strongly correlating with the corresponding glycomic phenotype of the adenomatous colon epithelium from the same tissue section (Pearson correlation distance average = 0.18). These findings suggest that using spatial glycomics, we can distinguish PI as having a molecular phenotype similar to the corresponding surface epithelium and true invasion as having a different phenotype even when compared to high-grade dysplasia. Therefore, when a novel molecular phenotype is found in the deepest submucosal region, this may be used as an argument in favor of true invasion.
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Affiliation(s)
- Fanny Boyaval
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Arantza Fariña-Sarasqueta
- Department of Pathology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Jurjen J. Boonstra
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Bram Heijs
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
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14
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Young LEA, Nietert PJ, Stubler R, Kittrell CG, Grimsley G, Lewin DN, Mehta AS, Hajar C, Wang K, O’Quinn EC, Angel PM, Wallace K, Drake RR. Utilizing multimodal mass spectrometry imaging for profiling immune cell composition and N-glycosylation across colorectal carcinoma disease progression. Front Pharmacol 2024; 14:1337319. [PMID: 38273829 PMCID: PMC10808565 DOI: 10.3389/fphar.2023.1337319] [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: 11/12/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Colorectal cancer (CRC) stands as a leading cause of death worldwide, often arising from specific genetic mutations, progressing from pre-cancerous adenomas to adenocarcinomas. Early detection through regular screening can result in a 90% 5-year survival rate for patients. However, unfortunately, only a fraction of CRC cases are identified at pre-invasive stages, allowing progression to occur silently over 10-15 years. The intricate interplay between the immune system and tumor cells within the tumor microenvironment plays a pivotal role in the progression of CRC. Immune cell clusters can either inhibit or facilitate tumor initiation, growth, and metastasis. To gain a better understanding of this relationship, we conducted N-glycomic profiling using matrix-assisted laser desorption-ionization mass spectrometry imaging (MALDI-MSI). We detected nearly 100 N-glycan species across all samples, revealing a shift in N-glycome profiles from normal to cancerous tissues, marked by a decrease in high mannose N-glycans. Further analysis of precancerous to invasive carcinomas showed an increase in pauci-mannose biantennary, and tetraantennary N-glycans with disease progression. Moreover, a distinct stratification in the N-glycome profile was observed between non-mucinous and mucinous CRC tissues, driven by pauci-mannose, high mannose, and bisecting N-glycans. Notably, we identified immune clusters of CD20+ B cells and CD3/CD44+ T cells distinctive and predictive with signature profiles of bisecting and branched N-glycans. These spatial N-glycan profiles offer potential biomarkers and therapeutic targets throughout the progression of CRC.
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Affiliation(s)
- Lyndsay E. A. Young
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States
| | - Paul J. Nietert
- Translational Science Laboratory, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States
| | - Rachel Stubler
- Department of Public Health Sciences, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Caroline G. Kittrell
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Grace Grimsley
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - David N. Lewin
- Department of Regenerative Medicine and Cell Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Anand S. Mehta
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States
| | - Chadi Hajar
- Department of Regenerative Medicine and Cell Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Katherine Wang
- Department of Regenerative Medicine and Cell Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Elizabeth C. O’Quinn
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States
- Department of Regenerative Medicine and Cell Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States
| | - Kristin Wallace
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States
- Translational Science Laboratory, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States
| | - Richard R. Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States
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15
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Wallace EN, West CA, McDowell CT, Lu X, Bruner E, Mehta AS, Aoki-Kinoshita KF, Angel PM, Drake RR. An N-glycome tissue atlas of 15 human normal and cancer tissue types determined by MALDI-imaging mass spectrometry. Sci Rep 2024; 14:489. [PMID: 38177192 PMCID: PMC10766640 DOI: 10.1038/s41598-023-50957-w] [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: 11/08/2023] [Accepted: 12/28/2023] [Indexed: 01/06/2024] Open
Abstract
N-glycosylation is an abundant post-translational modification of most cell-surface proteins. N-glycans play a crucial role in cellular functions like protein folding, protein localization, cell-cell signaling, and immune detection. As different tissue types display different N-glycan profiles, changes in N-glycan compositions occur in tissue-specific ways with development of disease, like cancer. However, no comparative atlas resource exists for documenting N-glycome alterations across various human tissue types, particularly comparing normal and cancerous tissues. In order to study a broad range of human tissue N-glycomes, N-glycan targeted MALDI imaging mass spectrometry was applied to custom formalin-fixed paraffin-embedded tissue microarrays. These encompassed fifteen human tissue types including bladder, breast, cervix, colon, esophagus, gastric, kidney, liver, lung, pancreas, prostate, sarcoma, skin, thyroid, and uterus. Each array contained both normal and tumor cores from the same pathology block, selected by a pathologist, allowing more in-depth comparisons of the N-glycome differences between tumor and normal and across tissue types. Using established MALDI-IMS workflows and existing N-glycan databases, the N-glycans present in each tissue core were spatially profiled and peak intensity data compiled for comparative analyses. Further structural information was determined for core fucosylation using endoglycosidase F3, and differentiation of sialic acid linkages through stabilization chemistry. Glycan structural differences across the tissue types were compared for oligomannose levels, branching complexity, presence of bisecting N-acetylglucosamine, fucosylation, and sialylation. Collectively, our research identified the N-glycans that were significantly increased and/or decreased in relative abundance in cancer for each tissue type. This study offers valuable information on a wide scale for both normal and cancerous tissues, serving as a reference for future studies and potential diagnostic applications of MALDI-IMS.
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Affiliation(s)
- Elizabeth N Wallace
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA.
| | - Connor A West
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Colin T McDowell
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Xiaowei Lu
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Evelyn Bruner
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Anand S Mehta
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | | | - Peggi M Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA.
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16
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Krestensen KK, Heeren RMA, Balluff B. State-of-the-art mass spectrometry imaging applications in biomedical research. Analyst 2023; 148:6161-6187. [PMID: 37947390 DOI: 10.1039/d3an01495a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Mass spectrometry imaging has advanced from a niche technique to a widely applied spatial biology tool operating at the forefront of numerous fields, most notably making a significant impact in biomedical pharmacological research. The growth of the field has gone hand in hand with an increase in publications and usage of the technique by new laboratories, and consequently this has led to a shift from general MSI reviews to topic-specific reviews. Given this development, we see the need to recapitulate the strengths of MSI by providing a more holistic overview of state-of-the-art MSI studies to provide the new generation of researchers with an up-to-date reference framework. Here we review scientific advances for the six largest biomedical fields of MSI application (oncology, pharmacology, neurology, cardiovascular diseases, endocrinology, and rheumatology). These publications thereby give examples for at least one of the following categories: they provide novel mechanistic insights, use an exceptionally large cohort size, establish a workflow that has the potential to become a high-impact methodology, or are highly cited in their field. We finally have a look into new emerging fields and trends in MSI (immunology, microbiology, infectious diseases, and aging), as applied MSI is continuously broadening as a result of technological breakthroughs.
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Affiliation(s)
- Kasper K Krestensen
- The Maastricht MultiModal Molecular Imaging (M4I) Institute, Maastricht University, 6229 ER Maastricht, The Netherlands.
| | - Ron M A Heeren
- The Maastricht MultiModal Molecular Imaging (M4I) Institute, Maastricht University, 6229 ER Maastricht, The Netherlands.
| | - Benjamin Balluff
- The Maastricht MultiModal Molecular Imaging (M4I) Institute, Maastricht University, 6229 ER Maastricht, The Netherlands.
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17
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Lossio CF, Osterne VJS, Pinto-Junior VR, Chen S, Oliveira MV, Verduijn J, Verbeke I, Serna S, Reichardt NC, Skirtach A, Cavada BS, Van Damme EJM, Nascimento KS. Structural Analysis and Characterization of an Antiproliferative Lectin from Canavalia villosa Seeds. Int J Mol Sci 2023; 24:15966. [PMID: 37958949 PMCID: PMC10649158 DOI: 10.3390/ijms242115966] [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: 09/14/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Cells use glycans to encode information that modulates processes ranging from cell-cell recognition to programmed cell death. This information is encoded within a glycocode, and its decoding is performed by carbohydrate-binding proteins. Among these, lectins stand out due to their specific and reversible interaction with carbohydrates. Changes in glycosylation patterns are observed in several pathologies, including cancer, where abnormal glycans are found on the surfaces of affected tissues. Given the importance of the bioprospection of promising biomolecules, the current work aimed to determine the structural properties and anticancer potential of the mannose-specific lectin from seeds of Canavalia villosa (Cvill). Experimental elucidation of the primary and 3D structures of the lectin, along with glycan array and molecular docking, facilitated the determination of its fine carbohydrate-binding specificity. These structural insights, coupled with the lectin's specificity, have been combined to explain the antiproliferative effect of Cvill against cancer cell lines. This effect is dependent on the carbohydrate-binding activity of Cvill and its uptake in the cells, with concomitant activation of autophagic and apoptotic pathways.
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Affiliation(s)
- Claudia F. Lossio
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60440-970, Brazil (B.S.C.)
| | - Vinicius J. S. Osterne
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60440-970, Brazil (B.S.C.)
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Vanir R. Pinto-Junior
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60440-970, Brazil (B.S.C.)
- Department of Physics, Federal University of Ceara, Fortaleza 60440-970, Brazil
| | - Simin Chen
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Messias V. Oliveira
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60440-970, Brazil (B.S.C.)
| | - Joost Verduijn
- Nano-Biotechnology Group, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Isabel Verbeke
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Sonia Serna
- Glycotechnology Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 194, 20014 Donostia-San Sebastián, Spain
| | - Niels C. Reichardt
- Glycotechnology Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 194, 20014 Donostia-San Sebastián, Spain
- Centro de Investigación Biomédica en Red (CIBER-BBN), Paseo de Miramon 194, 20014 Donostia-San Sebastián, Spain
| | - Andre Skirtach
- Nano-Biotechnology Group, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Benildo S. Cavada
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60440-970, Brazil (B.S.C.)
| | - Els J. M. Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Kyria S. Nascimento
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60440-970, Brazil (B.S.C.)
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18
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Abstract
Imaging mass spectrometry is a well-established technology that can easily and succinctly communicate the spatial localization of molecules within samples. This review communicates the recent advances in the field, with a specific focus on matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) applied on tissues. The general sample preparation strategies for different analyte classes are explored, including special considerations for sample types (fresh frozen or formalin-fixed,) strategies for various analytes (lipids, metabolites, proteins, peptides, and glycans) and how multimodal imaging strategies can leverage the strengths of each approach is mentioned. This work explores appropriate experimental design approaches and standardization of processes needed for successful studies, as well as the various data analysis platforms available to analyze data and their strengths. The review concludes with applications of imaging mass spectrometry in various fields, with a focus on medical research, and some examples from plant biology and microbe metabolism are mentioned, to illustrate the breadth and depth of MALDI IMS.
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Affiliation(s)
- Jessica L Moore
- Department of Proteomics, Discovery Life Sciences, Huntsville, Alabama 35806, United States
| | - Georgia Charkoftaki
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, Connecticut 06520, United States
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19
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Chung HH, Huang P, Chen CL, Lee C, Hsu CC. Next-generation pathology practices with mass spectrometry imaging. MASS SPECTROMETRY REVIEWS 2023; 42:2446-2465. [PMID: 35815718 DOI: 10.1002/mas.21795] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/13/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Mass spectrometry imaging (MSI) is a powerful technique that reveals the spatial distribution of various molecules in biological samples, and it is widely used in pathology-related research. In this review, we summarize common MSI techniques, including matrix-assisted laser desorption/ionization and desorption electrospray ionization MSI, and their applications in pathological research, including disease diagnosis, microbiology, and drug discovery. We also describe the improvements of MSI, focusing on the accumulation of imaging data sets, expansion of chemical coverage, and identification of biological significant molecules, that have prompted the evolution of MSI to meet the requirements of pathology practices. Overall, this review details the applications and improvements of MSI techniques, demonstrating the potential of integrating MSI techniques into next-generation pathology practices.
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Affiliation(s)
- Hsin-Hsiang Chung
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
| | - Penghsuan Huang
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
| | - Chih-Lin Chen
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
| | - Chuping Lee
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
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20
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Scott E, Archer Goode E, Garnham R, Hodgson K, Orozco-Moreno M, Turner H, Livermore K, Putri Nangkana K, Frame FM, Bermudez A, Jose Garcia Marques F, McClurg UL, Wilson L, Thomas H, Buskin A, Hepburn A, Duxfield A, Bastian K, Pye H, Arredondo HM, Hysenaj G, Heavey S, Stopka-Farooqui U, Haider A, Freeman A, Singh S, Johnston EW, Punwani S, Knight B, McCullagh P, McGrath J, Crundwell M, Harries L, Heer R, Maitland NJ, Whitaker H, Pitteri S, Troyer DA, Wang N, Elliott DJ, Drake RR, Munkley J. ST6GAL1-mediated aberrant sialylation promotes prostate cancer progression. J Pathol 2023; 261:71-84. [PMID: 37550801 DOI: 10.1002/path.6152] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/05/2023] [Accepted: 06/02/2023] [Indexed: 08/09/2023]
Abstract
Aberrant glycosylation is a universal feature of cancer cells, and cancer-associated glycans have been detected in virtually every cancer type. A common change in tumour cell glycosylation is an increase in α2,6 sialylation of N-glycans, a modification driven by the sialyltransferase ST6GAL1. ST6GAL1 is overexpressed in numerous cancer types, and sialylated glycans are fundamental for tumour growth, metastasis, immune evasion, and drug resistance, but the role of ST6GAL1 in prostate cancer is poorly understood. Here, we analyse matched cancer and normal tissue samples from 200 patients and verify that ST6GAL1 is upregulated in prostate cancer tissue. Using MALDI imaging mass spectrometry (MALDI-IMS), we identify larger branched α2,6 sialylated N-glycans that show specificity to prostate tumour tissue. We also monitored ST6GAL1 in plasma samples from >400 patients and reveal ST6GAL1 levels are significantly increased in the blood of men with prostate cancer. Using both in vitro and in vivo studies, we demonstrate that ST6GAL1 promotes prostate tumour growth and invasion. Our findings show ST6GAL1 introduces α2,6 sialylated N-glycans on prostate cancer cells and raise the possibility that prostate cancer cells can secrete active ST6GAL1 enzyme capable of remodelling glycans on the surface of other cells. Furthermore, we find α2,6 sialylated N-glycans expressed by prostate cancer cells can be targeted using the sialyltransferase inhibitor P-3FAX -Neu5Ac. Our study identifies an important role for ST6GAL1 and α2,6 sialylated N-glycans in prostate cancer progression and highlights the opportunity to inhibit abnormal sialylation for the development of new prostate cancer therapeutics. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Emma Scott
- Newcastle University Centre for Cancer, Newcastle University Institute of Biosciences, Newcastle, UK
| | - Emily Archer Goode
- Newcastle University Centre for Cancer, Newcastle University Institute of Biosciences, Newcastle, UK
| | - Rebecca Garnham
- Newcastle University Centre for Cancer, Newcastle University Institute of Biosciences, Newcastle, UK
| | - Kirsty Hodgson
- Newcastle University Centre for Cancer, Newcastle University Institute of Biosciences, Newcastle, UK
| | - Margarita Orozco-Moreno
- Newcastle University Centre for Cancer, Newcastle University Institute of Biosciences, Newcastle, UK
| | - Helen Turner
- Cellular Pathology, The Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Karen Livermore
- Newcastle University Centre for Cancer, Newcastle University Institute of Biosciences, Newcastle, UK
| | - Kyla Putri Nangkana
- Newcastle University Centre for Cancer, Newcastle University Institute of Biosciences, Newcastle, UK
| | - Fiona M Frame
- Cancer Research Unit, Department of Biology, University of York, North Yorkshire, UK
| | - Abel Bermudez
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University, Palo Alto, CA, USA
| | - Fernando Jose Garcia Marques
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University, Palo Alto, CA, USA
| | - Urszula L McClurg
- Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
| | - Laura Wilson
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Paul O'Gorman Building, Newcastle University, Newcastle upon Tyne, UK
| | - Huw Thomas
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Paul O'Gorman Building, Newcastle University, Newcastle upon Tyne, UK
| | - Adriana Buskin
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Paul O'Gorman Building, Newcastle University, Newcastle upon Tyne, UK
| | - Anastasia Hepburn
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Paul O'Gorman Building, Newcastle University, Newcastle upon Tyne, UK
| | - Adam Duxfield
- Newcastle University Centre for Cancer, Newcastle University Institute of Biosciences, Newcastle, UK
| | - Kayla Bastian
- Newcastle University Centre for Cancer, Newcastle University Institute of Biosciences, Newcastle, UK
| | - Hayley Pye
- Molecular Diagnostics and Therapeutics Group, Charles Bell House, Division of Surgery and Interventional Science, University College London, London, UK
| | - Hector M Arredondo
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, Sheffield, UK
| | - Gerald Hysenaj
- Newcastle University Centre for Cancer, Newcastle University Institute of Biosciences, Newcastle, UK
| | - Susan Heavey
- Molecular Diagnostics and Therapeutics Group, Charles Bell House, Division of Surgery and Interventional Science, University College London, London, UK
| | - Urszula Stopka-Farooqui
- Molecular Diagnostics and Therapeutics Group, Charles Bell House, Division of Surgery and Interventional Science, University College London, London, UK
| | - Aiman Haider
- Department of Pathology, UCLH NHS Foundation Trust, London, UK
| | - Alex Freeman
- Department of Pathology, UCLH NHS Foundation Trust, London, UK
| | - Saurabh Singh
- UCL Centre for Medical Imaging, Charles Bell House, University College London, London, UK
| | - Edward W Johnston
- UCL Centre for Medical Imaging, Charles Bell House, University College London, London, UK
| | - Shonit Punwani
- UCL Centre for Medical Imaging, Charles Bell House, University College London, London, UK
| | - Bridget Knight
- NIHR Exeter Clinical Research Facility, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Paul McCullagh
- Department of Pathology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - John McGrath
- Exeter Surgical Health Services Research Unit, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Malcolm Crundwell
- Exeter Surgical Health Services Research Unit, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Lorna Harries
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Rakesh Heer
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Paul O'Gorman Building, Newcastle University, Newcastle upon Tyne, UK
- Department of Urology, Freeman Hospital, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Norman J Maitland
- Cancer Research Unit, Department of Biology, University of York, North Yorkshire, UK
| | - Hayley Whitaker
- Molecular Diagnostics and Therapeutics Group, Charles Bell House, Division of Surgery and Interventional Science, University College London, London, UK
| | - Sharon Pitteri
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University, Palo Alto, CA, USA
| | - Dean A Troyer
- Cancer Biology and Infectious Disease Research Center, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Ning Wang
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, Sheffield, UK
| | - David J Elliott
- Newcastle University Centre for Cancer, Newcastle University Institute of Biosciences, Newcastle, UK
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, SC, USA
| | - Jennifer Munkley
- Newcastle University Centre for Cancer, Newcastle University Institute of Biosciences, Newcastle, UK
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21
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Nieminen H, Nummela P, Satomaa T, Heiskanen A, Hiltunen JO, Kaprio T, Seppänen H, Hagström J, Mustonen H, Ristimäki A, Haglund C. N-glycosylation in non-invasive and invasive intraductal papillary mucinous neoplasm. Sci Rep 2023; 13:13191. [PMID: 37580349 PMCID: PMC10425445 DOI: 10.1038/s41598-023-39220-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 07/21/2023] [Indexed: 08/16/2023] Open
Abstract
Intraductal papillary mucinous neoplasms (IPMNs), often found incidentally, are potentially malignant cystic tumors of the pancreas. Due to the precancerous nature, IPMNs lacking malignant features should be kept on surveillance. The follow-up relies on magnetic resonance imaging, which has a limited accuracy to define the high-risk patients. New diagnostic methods are thus needed to recognize IPMNs with malignant potential. Here, aberrantly expressed glycans constitute a promising new area of research. We compared the N-glycan profiles of non-invasive IPMN tissues (n = 10) and invasive IPMN tissues (n = 10) to those of non-neoplastic pancreatic controls (n = 5) by matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry. Both IPMN subgroups showed increased abundance of neutral composition H4N4 and decrease in H3N5F1, increase in sialylation, and decrease in sulfation, as compared to the controls. Furthermore, invasive IPMN showed an increase in terminal N-acetylhexosamine containing structure H4N5, and increase in acidic complex-type glycans, but decrease in their complex fucosylation and sulfation, as compared to the controls. In conclusion, the N-glycan profiles differed between healthy pancreatic tissue and non-invasive and invasive IPMNs. The unique glycans expressed in invasive IPMNs may offer interesting new options for diagnostics.
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Affiliation(s)
- Heini Nieminen
- Department of Surgery, University of Helsinki and Helsinki University Hospital, P.O. Box 440, 00029, Helsinki, Finland.
| | - Pirjo Nummela
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | | | | | - Tuomas Kaprio
- Department of Surgery, University of Helsinki and Helsinki University Hospital, P.O. Box 440, 00029, Helsinki, Finland
- Research Programs Unit, Translational Cancer Medicine Research Program, University of Helsinki, Helsinki, Finland
| | - Hanna Seppänen
- Department of Surgery, University of Helsinki and Helsinki University Hospital, P.O. Box 440, 00029, Helsinki, Finland
| | - Jaana Hagström
- Research Programs Unit, Translational Cancer Medicine Research Program, University of Helsinki, Helsinki, Finland
- Department of Pathology, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Departmentof Oral Pathology and Radiology, University of Turku, Turku, Finland
| | - Harri Mustonen
- Department of Surgery, University of Helsinki and Helsinki University Hospital, P.O. Box 440, 00029, Helsinki, Finland
- Research Programs Unit, Translational Cancer Medicine Research Program, University of Helsinki, Helsinki, Finland
| | - Ari Ristimäki
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Pathology, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Caj Haglund
- Department of Surgery, University of Helsinki and Helsinki University Hospital, P.O. Box 440, 00029, Helsinki, Finland
- Research Programs Unit, Translational Cancer Medicine Research Program, University of Helsinki, Helsinki, Finland
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22
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Liu CC, Greenwald NF, Kong A, McCaffrey EF, Leow KX, Mrdjen D, Cannon BJ, Rumberger JL, Varra SR, Angelo M. Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering. Nat Commun 2023; 14:4618. [PMID: 37528072 PMCID: PMC10393943 DOI: 10.1038/s41467-023-40068-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/11/2023] [Indexed: 08/03/2023] Open
Abstract
While technologies for multiplexed imaging have provided an unprecedented understanding of tissue composition in health and disease, interpreting this data remains a significant computational challenge. To understand the spatial organization of tissue and how it relates to disease processes, imaging studies typically focus on cell-level phenotypes. However, images can capture biologically important objects that are outside of cells, such as the extracellular matrix. Here, we describe a pipeline, Pixie, that achieves robust and quantitative annotation of pixel-level features using unsupervised clustering and show its application across a variety of biological contexts and multiplexed imaging platforms. Furthermore, current cell phenotyping strategies that rely on unsupervised clustering can be labor intensive and require large amounts of manual cluster adjustments. We demonstrate how pixel clusters that lie within cells can be used to improve cell annotations. We comprehensively evaluate pre-processing steps and parameter choices to optimize clustering performance and quantify the reproducibility of our method. Importantly, Pixie is open source and easily customizable through a user-friendly interface.
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Affiliation(s)
- Candace C Liu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Alex Kong
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Ke Xuan Leow
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Dunja Mrdjen
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Bryan J Cannon
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Josef Lorenz Rumberger
- Max-Delbrueck-Center for Molecular Medicine, Berlin, Germany
- Charité University Medicine, Berlin, Germany
| | | | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA.
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23
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Holbrook JH, Sekera ER, Lopez A, Fries BD, Tobias F, Akkaya K, Mihaylova MM, Hummon AB. Enhancement of Lipid Signals in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry with Ammonium Fluoride as a Matrix Additive. Anal Chem 2023; 95:10603-10609. [PMID: 37418337 PMCID: PMC10655718 DOI: 10.1021/acs.analchem.3c00753] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Lipids are essential macromolecules that play a crucial role in numerous biological events. Lipids are structurally diverse which allows them to fulfill multiple functional roles. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a powerful tool to understand the spatial localization of lipids within biological systems. Herein, we report the use of ammonium fluoride (NH4F) as a comatrix additive to enhance lipid detection in biological samples, with a signal increase of up to 200%. Emphasis was placed on anionic lipid enhancement with negative polarity measurements, with some preliminary work on cationic lipids detailed. We observed lipid signal enhancement of [M-H]- ions with the addition of NH4F additive attributed to a proton transfer reaction in several different lipid classes. Overall, our study demonstrates that the use of the NH4F comatrix additive substantially improves sensitivity for lipid detection in a MALDI system and is capable of being applied to a variety of different applications.
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Affiliation(s)
- Joseph H. Holbrook
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Emily R. Sekera
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Arbil Lopez
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Brian D. Fries
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Fernando Tobias
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kubra Akkaya
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Maria M. Mihaylova
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Amanda B. Hummon
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
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24
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Zhou X, Chi K, Zhang C, Liu Q, Yang G. Sialylation: A Cloak for Tumors to Trick the Immune System in the Microenvironment. BIOLOGY 2023; 12:832. [PMID: 37372117 DOI: 10.3390/biology12060832] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023]
Abstract
The tumor microenvironment (TME), where the tumor cells incite the surrounding normal cells to create an immune suppressive environment, reduces the effectiveness of immune responses during cancer development. Sialylation, a type of glycosylation that occurs on cell surface proteins, lipids, and glycoRNAs, is known to accumulate in tumors and acts as a "cloak" to help tumor cells evade immunological surveillance. In the last few years, the role of sialylation in tumor proliferation and metastasis has become increasingly evident. With the advent of single-cell and spatial sequencing technologies, more research is being conducted to understand the effects of sialylation on immunity regulation. This review provides updated insights into recent research on the function of sialylation in tumor biology and summarizes the latest developments in sialylation-targeted tumor therapeutics, including antibody-mediated and metabolic-based sialylation inhibition, as well as interference with sialic acid-Siglec interaction.
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Affiliation(s)
- Xiaoman Zhou
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Kaijun Chi
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Chairui Zhang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Quan Liu
- Department of Medical Oncology, Affiliated Hospital of Jiangnan University, Wuxi 214122, China
| | - Ganglong Yang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
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25
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Lu X, McDowell CT, Blaschke CRK, Liu L, Grimsley G, Wisniewski L, Gao C, Mehta AS, Haab BB, Angel PM, Drake RR. Bioorthogonal Chemical Labeling Probes Targeting Sialic Acid Isomers for N-Glycan MALDI Imaging Mass Spectrometry of Tissues, Cells, and Biofluids. Anal Chem 2023; 95:7475-7486. [PMID: 37126482 PMCID: PMC10193362 DOI: 10.1021/acs.analchem.2c04882] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 04/04/2023] [Indexed: 05/02/2023]
Abstract
Sialic acid isomers attached in either α2,3 or α2,6 linkage to glycan termini confer distinct chemical, biological, and pathological properties, but they cannot be distinguished by mass differences in traditional mass spectrometry experiments. Multiple derivatization strategies have been developed to stabilize and facilitate the analysis of sialic acid isomers and their glycoconjugate carriers by high-performance liquid chromatography, capillary electrophoresis, and mass spectrometry workflows. Herein, a set of novel derivatization schemes are described that result in the introduction of bioorthogonal click chemistry alkyne or azide groups into α2,3- and α2,8-linked sialic acids. These chemical modifications were validated and structurally characterized using model isomeric sialic acid conjugates and model protein carriers. Use of an alkyne-amine, propargylamine, as the second amidation reagent effectively introduces an alkyne functional group into α2,3-linked sialic acid glycoproteins. In tissues, serum, and cultured cells, this allows for the detection and visualization of N-linked glycan sialic acid isomers by imaging mass spectrometry approaches. Formalin-fixed paraffin-embedded prostate cancer tissues and pancreatic cancer cell lines were used to characterize the numbers and distribution of alkyne-modified α2,3-linked sialic acid N-glycans. An azide-amine compound with a poly(ethylene glycol) linker was evaluated for use in histochemical staining. Formalin-fixed pancreatic cancer tissues were amidated with the azide amine, reacted with biotin-alkyne and copper catalyst, and sialic acid isomers detected by streptavidin-peroxidase staining. The direct chemical introduction of bioorthogonal click chemistry reagents into sialic acid-containing glycans and glycoproteins provides a new glycomic tool set to expand approaches for their detection, labeling, visualization, and enrichment.
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Affiliation(s)
- Xiaowei Lu
- Department
of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425-2503, United
States
| | - Colin T. McDowell
- Department
of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425-2503, United
States
| | - Calvin R. K. Blaschke
- Department
of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425-2503, United
States
| | - Liping Liu
- Department
of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425-2503, United
States
| | - Grace Grimsley
- Department
of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425-2503, United
States
| | - Luke Wisniewski
- Department
of Cell Biology, Van Andel Institute, Grand Rapids, Michigan 49503, United States
| | - ChongFeng Gao
- Department
of Cell Biology, Van Andel Institute, Grand Rapids, Michigan 49503, United States
| | - Anand S. Mehta
- Department
of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425-2503, United
States
| | - Brian B. Haab
- Department
of Cell Biology, Van Andel Institute, Grand Rapids, Michigan 49503, United States
| | - Peggi M. Angel
- Department
of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425-2503, United
States
| | - Richard R. Drake
- Department
of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425-2503, United
States
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26
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Ochoa-Rios S, Blaschke CR, Wang M, Peterson KD, DelaCourt A, Grauzam SE, Lewin D, Angel P, Roberts LR, Drake R, Mehta AS. Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma. CANCER RESEARCH COMMUNICATIONS 2023; 3:383-394. [PMID: 36890858 PMCID: PMC9987250 DOI: 10.1158/2767-9764.crc-22-0422] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/06/2022] [Accepted: 02/07/2023] [Indexed: 02/15/2023]
Abstract
There is an urgent need for the identification of reliable prognostic biomarkers for patients with intrahepatic cholangiocarcinoma (iCCA) and alterations in N-glycosylation have demonstrated an immense potential to be used as diagnostic strategies for many cancers, including hepatocellular carcinoma (HCC). N-glycosylation is one of the most common post-translational modifications known to be altered based on the status of the cell. N-glycan structures on glycoproteins can be modified based on the addition or removal of specific N-glycan residues, some of which have been linked to liver diseases. However, little is known concerning the N-glycan alterations that are associated with iCCA. We characterized the N-glycan modifications quantitatively and qualitatively in three cohorts, consisting of two tissue cohorts: a discovery cohort (n = 104 cases) and a validation cohort (n = 75), and one independent serum cohort consisting of patients with iCCA, HCC, or benign chronic liver disease (n = 67). N-glycan analysis in situ was correlated to tumor regions annotated on histopathology and revealed that bisected fucosylated N-glycan structures were specific to iCCA tumor regions. These same N-glycan modifications were significantly upregulated in iCCA tissue and serum relative to HCC and bile duct disease, including primary sclerosing cholangitis (PSC) (P < 0.0001). N-glycan modifications identified in iCCA tissue and serum were used to generate an algorithm that could be used as a biomarker of iCCA. We demonstrate that this biomarker algorithm quadrupled the sensitivity (at 90% specificity) of iCCA detection as compared with carbohydrate antigen 19-9, the current "gold standard" biomarker of CCA. Significance This work elucidates the N-glycan alterations that occur directly in iCCA tissue and utilizes this information to discover serum biomarkers that can be used for the noninvasive detection of iCCA.
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Affiliation(s)
- Shaaron Ochoa-Rios
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina
| | - Calvin R.K. Blaschke
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina
| | - Mengjun Wang
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina
| | - Kendell D. Peterson
- Department of Pediatrics, Medical University of South Carolina, Charleston, South Carolina
| | - Andrew DelaCourt
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina
| | - Stéphane Elie Grauzam
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina
| | - David Lewin
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Peggi Angel
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina
| | - Lewis R. Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Richard Drake
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina
| | - Anand S. Mehta
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina
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27
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Peng W, Reyes CDG, Gautam S, Yu A, Cho BG, Goli M, Donohoo K, Mondello S, Kobeissy F, Mechref Y. MS-based glycomics and glycoproteomics methods enabling isomeric characterization. MASS SPECTROMETRY REVIEWS 2023; 42:577-616. [PMID: 34159615 PMCID: PMC8692493 DOI: 10.1002/mas.21713] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 05/03/2023]
Abstract
Glycosylation is one of the most significant and abundant posttranslational modifications in mammalian cells. It mediates a wide range of biofunctions, including cell adhesion, cell communication, immune cell trafficking, and protein stability. Also, aberrant glycosylation has been associated with various diseases such as diabetes, Alzheimer's disease, inflammation, immune deficiencies, congenital disorders, and cancers. The alterations in the distributions of glycan and glycopeptide isomers are involved in the development and progression of several human diseases. However, the microheterogeneity of glycosylation brings a great challenge to glycomic and glycoproteomic analysis, including the characterization of isomers. Over several decades, different methods and approaches have been developed to facilitate the characterization of glycan and glycopeptide isomers. Mass spectrometry (MS) has been a powerful tool utilized for glycomic and glycoproteomic isomeric analysis due to its high sensitivity and rich structural information using different fragmentation techniques. However, a comprehensive characterization of glycan and glycopeptide isomers remains a challenge when utilizing MS alone. Therefore, various separation methods, including liquid chromatography, capillary electrophoresis, and ion mobility, were developed to resolve glycan and glycopeptide isomers before MS. These separation techniques were coupled to MS for a better identification and quantitation of glycan and glycopeptide isomers. Additionally, bioinformatic tools are essential for the automated processing of glycan and glycopeptide isomeric data to facilitate isomeric studies in biological cohorts. Here in this review, we discuss commonly employed MS-based techniques, separation hyphenated MS methods, and software, facilitating the separation, identification, and quantitation of glycan and glycopeptide isomers.
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Affiliation(s)
- Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | | | - Sakshi Gautam
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Byeong Gwan Cho
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Kaitlyn Donohoo
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | | | - Firas Kobeissy
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Departments of Emergency Medicine, University of Florida, Gainesville, Florida, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
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28
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McDowell CT, Lu X, Mehta AS, Angel PM, Drake RR. Applications and continued evolution of glycan imaging mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:674-705. [PMID: 34392557 PMCID: PMC8946722 DOI: 10.1002/mas.21725] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/16/2021] [Accepted: 08/03/2021] [Indexed: 05/03/2023]
Abstract
Glycosylation is an important posttranslational modifier of proteins and lipid conjugates critical for the stability and function of these macromolecules. Particularly important are N-linked glycans attached to asparagine residues in proteins. N-glycans have well-defined roles in protein folding, cellular trafficking and signal transduction, and alterations to them are implicated in a variety of diseases. However, the non-template driven biosynthesis of these N-glycans leads to significant structural diversity, making it challenging to identify the most biologically and clinically relevant species using conventional analyses. Advances in mass spectrometry instrumentation and data acquisition, as well as in enzymatic and chemical sample preparation strategies, have positioned mass spectrometry approaches as powerful analytical tools for the characterization of glycosylation in health and disease. Imaging mass spectrometry expands upon these strategies by capturing the spatial component of a glycan's distribution in-situ, lending additional insight into the organization and function of these molecules. Herein we review the ongoing evolution of glycan imaging mass spectrometry beginning with widely adopted tissue imaging approaches and expanding to other matrices and sample types with potential research and clinical implications. Adaptations of these techniques, along with their applications to various states of disease, are discussed. Collectively, glycan imaging mass spectrometry analyses broaden our understanding of the biological and clinical relevance of N-glycosylation to human disease.
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Affiliation(s)
- Colin T. McDowell
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Xiaowei Lu
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Anand S. Mehta
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Richard R. Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
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29
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Butler W, McDowell C, Yang Q, He Y, Zhao Y, Hauck JS, Zhou Y, Zhang H, Armstrong AJ, George DJ, Drake R, Huang J. Rewiring of the N-Glycome with prostate cancer progression and therapy resistance. NPJ Precis Oncol 2023; 7:22. [PMID: 36828904 PMCID: PMC9958128 DOI: 10.1038/s41698-023-00363-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/13/2023] [Indexed: 02/26/2023] Open
Abstract
An understanding of the molecular features associated with prostate cancer progression (PCa) and resistance to hormonal therapy is crucial for the identification of new targets that can be utilized to treat advanced disease and prolong patient survival. The glycome, which encompasses all sugar polymers (glycans) synthesized by cells, has remained relatively unexplored in the context of advanced PCa despite the fact that glycans have great potential value as biomarkers and therapeutic targets due to their high density on the cell surface. Using imaging mass spectrometry (IMS), we profiled the N-linked glycans in tumor tissue derived from 131 patients representing the major disease states of PCa to identify glycosylation changes associated with loss of tumor cell differentiation, disease remission, therapy resistance and disease recurrence, as well as neuroendocrine (NE) differentiation which is a major mechanism for therapy failure. Our results indicate significant changes to the glycosylation patterns in various stages of PCa, notably a decrease in tri- and tetraantennary glycans correlating with disease remission, a subsequent increase in these structures with the transition to therapy-resistant PCa, and downregulation of complex N-glycans correlating with NE differentiation. Furthermore, both nonglucosylated and monoglucosylated mannose 9 demonstrate aberrant upregulation in therapy-resistant PCa which may be useful therapeutic targets as these structures are not normally presented in healthy tissue. Our findings characterize changes to the tumor glycome that occur with hormonal therapy and the development of castration-resistant PCa (CRPC), identifying several glycan markers and signatures which may be useful for diagnostic or therapeutic purposes.
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Affiliation(s)
- William Butler
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Colin McDowell
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Qing Yang
- School of Nursing, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Yiping He
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Cancer Institute, Duke University, Durham, USA
| | - Yue Zhao
- Department of Pathology, College of Basic Medical Sciences and the First Hospital of China Medical University, Shenyang, China
| | - J Spencer Hauck
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Yinglu Zhou
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Hong Zhang
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Andrew J Armstrong
- Duke Cancer Institute, Duke University, Durham, USA
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Department of Medicine, Division of Medical Oncology and Urology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Daniel J George
- Duke Cancer Institute, Duke University, Durham, USA
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Department of Medicine, Division of Medical Oncology and Urology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Richard Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA.
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA.
- Duke Cancer Institute, Duke University, Durham, USA.
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30
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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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31
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DelaCourt A, Mehta A. Beyond glyco-proteomics-Understanding the role of genetics in cancer biomarkers. Adv Cancer Res 2023; 157:57-81. [PMID: 36725113 DOI: 10.1016/bs.acr.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The development of robust cancer biomarkers is the most effective way to improve overall survival, as early detection and treatment leads to significantly better clinical outcomes. Many of the cancer biomarkers that have been identified and are clinically utilized are glycoproteins, oftentimes a specific glycoform. Aberrant glycosylation is a common theme in cancer, with dysregulated glycosylation driving tumor initiation and metastasis, and abnormal glycosylation can be detection both on the tissue surface and in serum. However, most cancer types are heterogeneous in regard to tumor genomics, and this heterogeneity extends to cancer glycomics. This limits the sensitivity of standalone glycan-based biomarkers, which has slowed their implementation clinically. However, if targeted biomarker development can take into account genomic tumor information, the development of complementary biomarkers that target unique cancer subgroups can be accomplished. This idea suggests the need for algorithm-based cancer biomarkers, which can utilize multiple biomarkers along with relevant demographic information. This concept has already been established in the detection of hepatocellular carcinoma with the GALAD score, and an algorithm-based approach would likely be effective in improving biomarker sensitivity for additional cancer types. In order to increase cancer diagnostic biomarker sensitivity, there must be more targeted biomarker development that considers tumor genomic, proteomic, metabolomic, and clinical data while identifying tumor biomarkers.
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Affiliation(s)
- Andrew DelaCourt
- Department of Cell & Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - Anand Mehta
- Department of Cell & Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States.
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32
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Bieberich E. Synthesis, Processing, and Function of N-Glycans in N-Glycoproteins. ADVANCES IN NEUROBIOLOGY 2023; 29:65-93. [PMID: 36255672 DOI: 10.1007/978-3-031-12390-0_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Many membrane-resident and secreted proteins, including growth factors and their receptors are N-glycosylated. The initial N-glycan structure is synthesized in the endoplasmic reticulum (ER) as a branched structure on a lipid anchor (dolicholpyrophosphate) and then co-translationally, "en bloc" transferred and linked via N-acetylglucosamine to asparagine within a specific N-glycosylation acceptor sequence of the nascent recipient protein. In the ER and then the Golgi apparatus, the N-linked glycan structure is modified by hydrolytic removal of sugar residues ("trimming") followed by re-glycosylation with additional sugar residues ("processing") such as galactose, fucose or sialic acid to form complex N-glycoproteins. While the sequence of the reactions leading to biosynthesis, "en bloc" transfer and processing of N-glycans is well investigated, it is still not completely understood how N-glycans affect the biological fate and function of N-glycoproteins. This review will discuss the biology of N-glycoprotein synthesis, processing and function with specific reference to the physiology and pathophysiology of the immune and nervous system, as well as infectious diseases such as Covid-19.
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Affiliation(s)
- Erhard Bieberich
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, USA.
- Veteran Affairs Medical Center, Lexington, KY, USA.
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33
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Integrating age, BMI, and serum N-glycans detected by MALDI mass spectrometry to classify suspicious mammogram findings as benign lesions or breast cancer. Sci Rep 2022; 12:20801. [PMID: 36460712 PMCID: PMC9718781 DOI: 10.1038/s41598-022-25401-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
While mammograms are the standard tool for breast cancer screening, there remains challenges for mammography to effectively distinguish benign lesions from breast cancers, leading to many unnecessary biopsy procedures. A blood-based biomarker could provide a minimally invasive supplemental assay to increase the specificity of breast cancer screening. Serum N-glycosylation alterations have associations with many cancers and several of the clinical characteristics of breast cancer. The current study utilized a high-throughput mass spectrometry workflow to identify serum N-glycans with differences in intensities between patients that had a benign lesion from patients with breast cancer. The overall N-glycan profiles of the two patient groups had no differences, but there were several individual N-glycans with significant differences in intensities between patients with benign lesions and ductal carcinoma in situ (DCIS). Many N-glycans had strong associations with age and/or body mass index, but there were several of these associations that differed between the patients with benign lesions and breast cancer. Accordingly, the samples were stratified by the patient's age and body mass index, and N-glycans with significant differences between these subsets were identified. For women aged 50-74 with a body mass index of 18.5-24.9, a model including the intensities of two N-glycans, 1850.666 m/z and 2163.743 m/z, age, and BMI were able to clearly distinguish the breast cancer patients from the patients with benign lesions with an AUROC of 0.899 and an optimal cutoff with 82% sensitivity and 84% specificity. This study indicates that serum N-glycan profiling is a promising approach for providing clarity for breast cancer screening, especially within the subset of healthy weight women in the age group recommended for mammograms.
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A roadmap for translational cancer glycoimmunology at single cell resolution. J Exp Clin Cancer Res 2022; 41:143. [PMID: 35428302 PMCID: PMC9013178 DOI: 10.1186/s13046-022-02335-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/17/2022] [Indexed: 11/11/2022] Open
Abstract
Cancer cells can evade immune responses by exploiting inhibitory immune checkpoints. Immune checkpoint inhibitor (ICI) therapies based on anti-CTLA-4 and anti-PD-1/PD-L1 antibodies have been extensively explored over the recent years to unleash otherwise compromised anti-cancer immune responses. However, it is also well established that immune suppression is a multifactorial process involving an intricate crosstalk between cancer cells and the immune systems. The cancer glycome is emerging as a relevant source of immune checkpoints governing immunosuppressive behaviour in immune cells, paving an avenue for novel immunotherapeutic options. This review addresses the current state-of-the-art concerning the role played by glycans controlling innate and adaptive immune responses, while shedding light on available experimental models for glycoimmunology. We also emphasize the tremendous progress observed in the development of humanized models for immunology, the paramount contribution of advances in high-throughput single-cell analysis in this context, and the importance of including predictive machine learning algorithms in translational research. This may constitute an important roadmap for glycoimmunology, supporting careful adoption of models foreseeing clinical translation of fundamental glycobiology knowledge towards next generation immunotherapies.
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Young LEA, Conroy LR, Clarke HA, Hawkinson TR, Bolton KE, Sanders WC, Chang JE, Webb MB, Alilain WJ, Vander Kooi CW, Drake RR, Andres DA, Badgett TC, Wagner LM, Allison DB, Sun RC, Gentry MS. In situ mass spectrometry imaging reveals heterogeneous glycogen stores in human normal and cancerous tissues. EMBO Mol Med 2022; 14:e16029. [PMID: 36059248 PMCID: PMC9641418 DOI: 10.15252/emmm.202216029] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/25/2022] [Accepted: 08/03/2022] [Indexed: 01/19/2023] Open
Abstract
Glycogen dysregulation is a hallmark of aging, and aberrant glycogen drives metabolic reprogramming and pathogenesis in multiple diseases. However, glycogen heterogeneity in healthy and diseased tissues remains largely unknown. Herein, we describe a method to define spatial glycogen architecture in mouse and human tissues using matrix-assisted laser desorption/ionization mass spectrometry imaging. This assay provides robust and sensitive spatial glycogen quantification and architecture characterization in the brain, liver, kidney, testis, lung, bladder, and even the bone. Armed with this tool, we interrogated glycogen spatial distribution and architecture in different types of human cancers. We demonstrate that glycogen stores and architecture are heterogeneous among diseases. Additionally, we observe unique hyperphosphorylated glycogen accumulation in Ewing sarcoma, a pediatric bone cancer. Using preclinical models, we correct glycogen hyperphosphorylation in Ewing sarcoma through genetic and pharmacological interventions that ablate in vivo tumor growth, demonstrating the clinical therapeutic potential of targeting glycogen in Ewing sarcoma.
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Affiliation(s)
- Lyndsay E A Young
- Department of Molecular and Cellular Biochemistry, College of MedicineUniversity of KentuckyLexingtonKYUSA
- Markey Cancer CenterUniversity of KentuckyLexingtonKYUSA
| | - Lindsey R Conroy
- Markey Cancer CenterUniversity of KentuckyLexingtonKYUSA
- Department of Neuroscience, College of MedicineUniversity of KentuckyLexingtonKYUSA
| | - Harrison A Clarke
- Department of Neuroscience, College of MedicineUniversity of KentuckyLexingtonKYUSA
| | - Tara R Hawkinson
- Department of Neuroscience, College of MedicineUniversity of KentuckyLexingtonKYUSA
| | - Kayli E Bolton
- Department of Molecular and Cellular Biochemistry, College of MedicineUniversity of KentuckyLexingtonKYUSA
| | - William C Sanders
- Department of Molecular and Cellular Biochemistry, College of MedicineUniversity of KentuckyLexingtonKYUSA
| | - Josephine E Chang
- Department of Neuroscience, College of MedicineUniversity of KentuckyLexingtonKYUSA
| | - Madison B Webb
- Department of Molecular and Cellular Biochemistry, College of MedicineUniversity of KentuckyLexingtonKYUSA
| | - Warren J Alilain
- Department of Neuroscience, College of MedicineUniversity of KentuckyLexingtonKYUSA
- Spinal Cord and Brain Injury Research CenterUniversity of KentuckyLexingtonKYUSA
| | - Craig W Vander Kooi
- Department of Molecular and Cellular Biochemistry, College of MedicineUniversity of KentuckyLexingtonKYUSA
- Markey Cancer CenterUniversity of KentuckyLexingtonKYUSA
| | - Richard R Drake
- Cell and Molecular Pharmacology and Experimental TherapeuticsMedical University of South CarolinaCharlestonSCUSA
| | - Douglas A Andres
- Department of Molecular and Cellular Biochemistry, College of MedicineUniversity of KentuckyLexingtonKYUSA
| | - Tom C Badgett
- Pediatric Hematology‐Oncology, College of MedicineUniversity of KentuckyLexingtonKYUSA
| | - Lars M Wagner
- Pediatric Hematology‐OncologyDuke UniversityDurhamNCUSA
| | - Derek B Allison
- Department of Pathology and Laboratory Medicine, College of MedicineUniversity of KentuckyLexingtonKYUSA
| | - Ramon C Sun
- Markey Cancer CenterUniversity of KentuckyLexingtonKYUSA
- Department of Neuroscience, College of MedicineUniversity of KentuckyLexingtonKYUSA
- Spinal Cord and Brain Injury Research CenterUniversity of KentuckyLexingtonKYUSA
- Department of Biochemistry & Molecular Biology, College of MedicineUniversity of FloridaGainesvilleFLUSA
- Center for Advanced Spatial Biomolecule ResearchUniversity of FloridaGainesvilleFLUSA
| | - Matthew S Gentry
- Department of Molecular and Cellular Biochemistry, College of MedicineUniversity of KentuckyLexingtonKYUSA
- Markey Cancer CenterUniversity of KentuckyLexingtonKYUSA
- Department of Biochemistry & Molecular Biology, College of MedicineUniversity of FloridaGainesvilleFLUSA
- Center for Advanced Spatial Biomolecule ResearchUniversity of FloridaGainesvilleFLUSA
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Lageveen‐Kammeijer GSM, Kuster B, Reusch D, Wuhrer M. High sensitivity glycomics in biomedicine. MASS SPECTROMETRY REVIEWS 2022; 41:1014-1039. [PMID: 34494287 PMCID: PMC9788051 DOI: 10.1002/mas.21730] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 05/15/2023]
Abstract
Many analytical challenges in biomedicine arise from the generally high heterogeneity and complexity of glycan- and glycoconjugate-containing samples, which are often only available in minute amounts. Therefore, highly sensitive workflows and detection methods are required. In this review mass spectrometric workflows and detection methods are evaluated for glycans and glycoproteins. Furthermore, glycomic methodologies and innovations that are tailored for enzymatic treatments, chemical derivatization, purification, separation, and detection at high sensitivity are highlighted. The discussion is focused on the analysis of mammalian N-linked and GalNAc-type O-linked glycans.
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Affiliation(s)
| | - Bernhard Kuster
- Chair for Proteomics and BioanalyticsTechnical University of MunichFreisingGermany
| | - Dietmar Reusch
- Pharma Technical Development EuropeRoche Diagnostics GmbHPenzbergGermany
| | - Manfred Wuhrer
- Leiden University Medical CenterCenter for Proteomics and MetabolomicsLeidenThe Netherlands
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DelaCourt AT, Liang H, Drake RR, Angel PM, Mehta AS. Novel Combined Enzymatic Approach to Analyze Nonsialylated N-Linked Glycans through MALDI Imaging Mass Spectrometry. J Proteome Res 2022; 21:1930-1938. [PMID: 35766466 DOI: 10.1021/acs.jproteome.2c00193] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alterations to N-glycan expression are relevant to the progression of various diseases, particularly cancer. In many cases, specific N-glycan structural features such as sialylation, fucosylation, and branching are of specific interest. A novel MALDI imaging mass spectrometry workflow has been recently developed to analyze these features of N-glycosylation through the utilization of endoglycosidase enzymes to cleave N-glycans from associated glycoproteins. Enzymes that have previously been utilized to cleave N-glycans include peptide-N-glycosidase F (PNGase F) to target N-glycans indiscriminately and endoglycosidase F3 (Endo F3) to target core fucosylated N-glycans. In addition to these endoglycosidases, additional N-glycan cleaving enzymes could be used to target specific structural features. Sialidases, also termed neuraminidases, are a family of enzymes that remove terminal sialic acids from glycoconjugates. This work aims to utilize sialidase, in conjunction with PNGase F/Endo F3, to enzymatically remove sialic acids from N-glycans in an effort to increase sensitivity for nonsialylated N-glycan MALDI-IMS peaks. Improving detection of nonsialylated N-glycans allows for a more thorough analysis of specific structural features such as fucosylation or branching, particularly of low abundant structures. Sialidase utilization in MALDI-IMS dramatically increases sensitivity and increases on-tissue endoglycosidase efficiency, making it a very useful companion technique to specifically detect nonsialylated N-glycans.
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Affiliation(s)
- Andrew T DelaCourt
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, Pennsylvania 29425, United States
| | - Hongyan Liang
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, Pennsylvania 29425, United States
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, Pennsylvania 29425, United States
| | - Peggi M Angel
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, Pennsylvania 29425, United States
| | - Anand S Mehta
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, Pennsylvania 29425, United States
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Veličković D, Sharma K, Alexandrov T, Hodgin JB, Anderton CR. Controlled Humidity Levels for Fine Spatial Detail Information in Enzyme-Assisted N-Glycan MALDI MSI. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1577-1580. [PMID: 35802124 DOI: 10.1021/jasms.2c00120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Investigation of the spatial distribution of N-glycans in tissue specimens has emerged as a powerful tool in clinical research, in part, because altered N-glycans are often a hallmark of disease progression. Mass spectrometry imaging of N-glycans relies on peptide N-glycanase spraying and tissue incubation for efficient in situ release of N-glycans from their carrier proteins. Unstandardized and uncontrolled incubation steps often cause significant delocalization of released N-glycans, resulting in the inability to link given N-glycan composition to a specific microanatomical region in the tissue. Herein, we optimized the incubation step to provide accurate and sensitive MALDI-MSI of N-glycans. Specifically, we tested saturated solutions of various salts that maintain constant relative humidity in the incubation chamber. We showed that the best performance was achieved using a saturated solution of KNO3 that maintains an 89% RH. Under these conditions, near maximal sensitivity was achieved with the minutest ion delocalization, which we demonstrated at a 35 μm spatial resolution, where we observed six distinct spatial patterns that colocalize to distinct microanatomical compartments in a kidney nephrectomy tissue section.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Kumar Sharma
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health, San Antonio, Texas 78229, United States
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jeffrey B Hodgin
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109 United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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Rujchanarong D, Scott D, Park Y, Brown S, Mehta AS, Drake R, Sandusky GE, Nakshatri H, Angel PM. Metabolic Links to Socioeconomic Stresses Uniquely Affecting Ancestry in Normal Breast Tissue at Risk for Breast Cancer. Front Oncol 2022; 12:876651. [PMID: 35832545 PMCID: PMC9273232 DOI: 10.3389/fonc.2022.876651] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
A primary difference between black women (BW) and white women (WW) diagnosed with breast cancer is aggressiveness of the tumor. Black women have higher mortalities with similar incidence of breast cancer compared to other race/ethnicities, and they are diagnosed at a younger age with more advanced tumors with double the rate of lethal, triple negative breast cancers. One hypothesis is that chronic social and economic stressors result in ancestry-dependent molecular responses that create a tumor permissive tissue microenvironment in normal breast tissue. Altered regulation of N-glycosylation of proteins, a glucose metabolism-linked post-translational modification attached to an asparagine (N) residue, has been associated with two strong independent risk factors for breast cancer: increased breast density and body mass index (BMI). Interestingly, high body mass index (BMI) levels have been reported to associate with increases of cancer-associated N-glycan signatures. In this study, we used matrix assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) to investigate molecular pattern changes of N-glycosylation in ancestry defined normal breast tissue from BW and WW with significant 5-year risk of breast cancer by Gail score. N-glycosylation was tested against social stressors including marital status, single, education, economic status (income), personal reproductive history, the risk factors BMI and age. Normal breast tissue microarrays from the Susan G. Komen tissue bank (BW=43; WW= 43) were used to evaluate glycosylation against socioeconomic stress and risk factors. One specific N-glycan (2158 m/z) appeared dependent on ancestry with high sensitivity and specificity (AUC 0.77, Brown/Wilson p-value<0.0001). Application of a linear regression model with ancestry as group variable and socioeconomic covariates as predictors identified a specific N-glycan signature associated with different socioeconomic stresses. For WW, household income was strongly associated to certain N-glycans, while for BW, marital status (married and single) was strongly associated with the same N-glycan signature. Current work focuses on understanding if combined N-glycan biosignatures can further help understand normal breast tissue at risk. This study lays the foundation for understanding the complexities linking socioeconomic stresses and molecular factors to their role in ancestry dependent breast cancer risk.
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Affiliation(s)
- Denys Rujchanarong
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC, United States
| | - Danielle Scott
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC, United States
| | - Yeonhee Park
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States
| | - Sean Brown
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC, United States
| | - Anand S. Mehta
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC, United States
| | - Richard Drake
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC, United States
| | - George E. Sandusky
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC, United States
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dos Reis JS, Rodrigues da Costa Santos MA, Mendonça DP, Martins do Nascimento SI, Barcelos PM, Correia de Lima RG, da Costa KM, Freire-de-Lima CG, Morrot A, Previato JO, Mendonça Previato L, da Fonseca LM, Freire-de-Lima L. Glycobiology of Cancer: Sugar Drives the Show. MEDICINES 2022; 9:medicines9060034. [PMID: 35736247 PMCID: PMC9229842 DOI: 10.3390/medicines9060034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022]
Abstract
Cancer development and progression is associated with aberrant changes in cellular glycosylation. Cells expressing altered glycan-structures are recognized by cells of the immune system, favoring the induction of inhibitory immune processes which subsequently promote tumor growth and spreading. Here, we discuss about the importance of glycobiology in modern medicine, taking into account the impact of altered glycan structures expressed in cancer cells as potential glycobiomarkers of disease, as well as on cancer development and progression.
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Affiliation(s)
- Jhenifer Santos dos Reis
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Marcos André Rodrigues da Costa Santos
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Daniella Pereira Mendonça
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Stefani Ingrid Martins do Nascimento
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Pedro Marçal Barcelos
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Rafaela Gomes Correia de Lima
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Kelli Monteiro da Costa
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Celio Geraldo Freire-de-Lima
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Alexandre Morrot
- Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21040-360, Brazil;
- Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21044-020, Brazil
| | - Jose Osvaldo Previato
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Lucia Mendonça Previato
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Leonardo Marques da Fonseca
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Leonardo Freire-de-Lima
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
- Correspondence: ; Tel./Fax: +55-21-3938-6646
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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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Ochoa-Rios S, O'Connor IP, Kent LN, Clouse JM, Hadjiyannis Y, Koivisto C, Pecot T, Angel PM, Drake RR, Leone G, Mehta AS, Rockey DC. Imaging Mass Spectrometry Reveals Alterations in N-Linked Glycosylation That Are Associated With Histopathological Changes in Nonalcoholic Steatohepatitis in Mouse and Human. Mol Cell Proteomics 2022; 21:100225. [PMID: 35331917 PMCID: PMC9092512 DOI: 10.1016/j.mcpro.2022.100225] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 01/20/2023] Open
Abstract
Nonalcoholic steatohepatitis (NASH) is the progressive form of nonalcoholic fatty liver disease (NAFLD) and is characterized by inflammation, hepatocyte injury, and fibrosis. Further, NASH is a risk factor for cirrhosis and hepatocellular carcinoma. Previous research demonstrated that serum N-glycan profiles can be altered in NASH patients. Here, we hypothesized that these N-glycan modifications may be associated with specific liver damage in NAFLD and NASH. To investigate the N-glycome profile in tissue, imaging mass spectrometry was used for a qualitative and quantitative in situ N-linked glycan analysis of mouse and human NAFLD/NASH tissue. A murine model was used to induce NAFLD and NASH through ad libitum feeding with either a high-fat diet or a Western diet, respectively. Mice fed a high-fat diet or Western diet developed inflammation, steatosis, and fibrosis, consistent with NAFLD/NASH phenotypes. Induction of NAFLD/NASH for 18 months using high caloric diets resulted in increased expression of mannose, complex/fucosylated, and hybrid N-glycan structures compared to control mouse livers. To validate the animal results, liver biopsy specimens from 51 human NAFLD/NASH patients representing the full range of NASH Clinical Research Network fibrosis stages were analyzed. Importantly, the same glycan alterations observed in mouse models were observed in human NASH biopsies and correlated with the degree of fibrosis. In addition, spatial glycan alterations were localized specifically to histopathological changes in tissue like fibrotic and fatty areas. We demonstrate that the use of standard staining's combined with imaging mass spectrometry provide a full profile of the origin of N-glycan modifications within the tissue. These results indicate that the spatial distribution of abundances of released N-glycans correlate with regions of tissue steatosis associated with NAFLD/NASH.
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Affiliation(s)
- Shaaron Ochoa-Rios
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina, USA.
| | - Ian P O'Connor
- Digestive Disease Research Center, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Lindsey N Kent
- Department of Obstetrics and Gynecology, Washington University in St Louis Center for Reproductive Health Sciences, St Louis, Missouri, USA
| | - Julian M Clouse
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Yannis Hadjiyannis
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Christopher Koivisto
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, USA
| | | | - Peggi M Angel
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Gustavo Leone
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, USA; Department of Biochemistry, Medical College of Wisconsin, MCW Cancer Center, Milwaukee, Wisconsin, USA
| | - Anand S Mehta
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina, USA.
| | - Don C Rockey
- Digestive Disease Research Center, Medical University of South Carolina, Charleston, South Carolina, USA
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43
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Vellan CJ, Jayapalan JJ, Yoong BK, Abdul-Aziz A, Mat-Junit S, Subramanian P. Application of Proteomics in Pancreatic Ductal Adenocarcinoma Biomarker Investigations: A Review. Int J Mol Sci 2022; 23:2093. [PMID: 35216204 PMCID: PMC8879036 DOI: 10.3390/ijms23042093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/07/2022] [Accepted: 01/09/2022] [Indexed: 12/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), a highly aggressive malignancy with a poor prognosis is usually detected at the advanced stage of the disease. The only US Food and Drug Administration-approved biomarker that is available for PDAC, CA 19-9, is most useful in monitoring treatment response among PDAC patients rather than for early detection. Moreover, when CA 19-9 is solely used for diagnostic purposes, it has only a recorded sensitivity of 79% and specificity of 82% in symptomatic individuals. Therefore, there is an urgent need to identify reliable biomarkers for diagnosis (specifically for the early diagnosis), ascertain prognosis as well as to monitor treatment response and tumour recurrence of PDAC. In recent years, proteomic technologies are growing exponentially at an accelerated rate for a wide range of applications in cancer research. In this review, we discussed the current status of biomarker research for PDAC using various proteomic technologies. This review will explore the potential perspective for understanding and identifying the unique alterations in protein expressions that could prove beneficial in discovering new robust biomarkers to detect PDAC at an early stage, ascertain prognosis of patients with the disease in addition to monitoring treatment response and tumour recurrence of patients.
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Affiliation(s)
- Christina Jane Vellan
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (C.J.V.); (A.A.-A.); (S.M.-J.)
| | - Jaime Jacqueline Jayapalan
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (C.J.V.); (A.A.-A.); (S.M.-J.)
- University of Malaya Centre for Proteomics Research (UMCPR), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Boon-Koon Yoong
- Department of Surgery, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | - Azlina Abdul-Aziz
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (C.J.V.); (A.A.-A.); (S.M.-J.)
| | - Sarni Mat-Junit
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (C.J.V.); (A.A.-A.); (S.M.-J.)
| | - Perumal Subramanian
- Department of Biochemistry and Biotechnology, Annamalai University, Chidambaram 608002, Tamil Nadu, India;
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44
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Sun N, Trajkovic-Arsic M, Li F, Wu Y, Münch C, Kunzke T, Feuchtinger A, Steiger K, Schlitter AM, Weichert W, Esposito I, Siveke JT, Walch A. Native glycan fragments detected by MALDI mass spectrometry imaging are independent prognostic factors in pancreatic ductal adenocarcinoma. EJNMMI Res 2021; 11:120. [PMID: 34851463 PMCID: PMC8636555 DOI: 10.1186/s13550-021-00862-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/09/2021] [Indexed: 12/30/2022] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies to date. The impressively developed stroma that surrounds and modulates the behavior of cancer cells is one of the main factors regulating the PDAC growth, metastasis and therapy resistance. Here, we postulate that stromal and cancer cell compartments differentiate in protein/lipid glycosylation patterns and analyze differences in glycan fragments in those compartments with clinicopathologic correlates.
Results We analyzed native glycan fragments in 109 human FFPE PDAC samples using high mass resolution matrix-assisted laser desorption/ionization Fourier-transform ion cyclotron resonance mass spectrometric imaging (MALDI-FT-ICR-MSI). Our method allows detection of native glycan fragments without previous digestion with PNGase or any other biochemical reaction. With this method, 8 and 18 native glycans were identified as uniquely expressed in only stromal or only cancer cell compartment, respectively. Kaplan–Meier survival model identified glycan fragments that are expressed in cancer cell or stromal compartment and significantly associated with patient outcome. Among cancer cell region-specific glycans, 10 predicted better and 6 worse patient survival. In the stroma, 1 glycan predicted good and 4 poor patient survival. Using factor analysis as a dimension reduction method, we were able to group the identified glycans in 2 factors. Multivariate analysis revealed that these factors can be used as independent survival prognostic elements with regard to the established Union for International Cancer Control (UICC) classification both in tumor and stroma regions.
Conclusion Our method allows in situ detection of naturally occurring glycans in FFPE samples of human PDAC tissue and highlights the differences among glycans found in stromal and cancer cell compartment offering a basis for further exploration on the role of specific glycans in cancer–stroma communication.
Supplementary Information The online version contains supplementary material available at 10.1186/s13550-021-00862-y.
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Affiliation(s)
- Na Sun
- Research Unit Analytical Pathology, Helmholtz Zentrum Munich, 85764, Neuherberg, Germany
| | - Marija Trajkovic-Arsic
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, 45147, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Fengxia Li
- Research Unit Analytical Pathology, Helmholtz Zentrum Munich, 85764, Neuherberg, Germany
| | - Yin Wu
- Research Unit Analytical Pathology, Helmholtz Zentrum Munich, 85764, Neuherberg, Germany
| | - Corinna Münch
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, 45147, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Thomas Kunzke
- Research Unit Analytical Pathology, Helmholtz Zentrum Munich, 85764, Neuherberg, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum Munich, 85764, Neuherberg, Germany
| | - Katja Steiger
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany.,Member of the German Cancer Consortium (DKTK), Partner Site, Munich, Germany
| | - Anna Melissa Schlitter
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany.,Member of the German Cancer Consortium (DKTK), Partner Site, Munich, Germany
| | - Wilko Weichert
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany.,Member of the German Cancer Consortium (DKTK), Partner Site, Munich, Germany.,Comprehensive Cancer Center Munich (CCCM), Munich, Germany
| | - Irene Esposito
- Institute for Pathology, University Hospital Düsseldorf, Heinrich-Heine University, Düsseldorf, Germany
| | - Jens T Siveke
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, 45147, Essen, Germany. .,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany.
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum Munich, 85764, Neuherberg, Germany.
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45
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DelaCourt A, Black A, Angel P, Drake R, Hoshida Y, Singal A, Lewin D, Taouli B, Lewis S, Schwarz M, Fiel MI, Mehta AS. N-Glycosylation Patterns Correlate with Hepatocellular Carcinoma Genetic Subtypes. Mol Cancer Res 2021; 19:1868-1877. [PMID: 34380744 PMCID: PMC8802325 DOI: 10.1158/1541-7786.mcr-21-0348] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/15/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022]
Abstract
Hepatocellular carcinoma (HCC) is the second leading cause of cancer deaths globally, and the incidence rate in the United States is increasing. Studies have identified inter- and intratumor heterogeneity as histologic and/or molecular subtypes/variants associated with response to certain molecular targeted therapies. Spatial HCC tissue profiling of N-linked glycosylation by matrix-assisted laser desorption ionization imaging mass spectrometry (MALDI-IMS) may serve as a new method to evaluate the tumor heterogeneity. Previous work has identified significant changes in the N-linked glycosylation of HCC tumors but has not accounted for the heterogeneous genetic and molecular nature of HCC. To determine the correlation between HCC-specific N-glycosylation changes and genetic/molecular tumor features, we profiled HCC tissue samples with MALDI-IMS and correlated the spatial N-glycosylation with a widely used HCC molecular classification (Hoshida subtypes). MALDI-IMS data displayed trends that could approximately distinguish between subtypes, with subtype 1 demonstrating significantly dysregulated N-glycosylation versus adjacent nontumor tissue. Although there were no individual N-glycan structures that could identify specific subtypes, trends emerged regarding the correlation of branched glycan expression to HCC as a whole and fucosylated glycan expression to subtype 1 tumors specifically. IMPLICATIONS: Correlating N-glycosylation to specific subtypes offers the specific detection of subtypes of HCC, which could both enhance early HCC sensitivity and guide targeted clinical therapies.
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Affiliation(s)
- Andrew DelaCourt
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina
| | - Alyson Black
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina
| | - Peggi Angel
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina
| | - Richard Drake
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina
| | - Yujin Hoshida
- University of Texas Southwestern Medical Center, Dallas, Texas
| | - Amit Singal
- University of Texas Southwestern Medical Center, Dallas, Texas
| | - David Lewin
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Bachir Taouli
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sara Lewis
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Myron Schwarz
- Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - M Isabel Fiel
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Anand S Mehta
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina.
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46
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Blaschke CRK, Hartig JP, Grimsley G, Liu L, Semmes OJ, Wu JD, Ippolito JE, Hughes-Halbert C, Nyalwidhe JO, Drake RR. Direct N-Glycosylation Profiling of Urine and Prostatic Fluid Glycoproteins and Extracellular Vesicles. Front Chem 2021; 9:734280. [PMID: 34646811 PMCID: PMC8503230 DOI: 10.3389/fchem.2021.734280] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/10/2021] [Indexed: 12/19/2022] Open
Abstract
Expressed prostatic secretions (EPS), also called post digital rectal exam urines, are proximal fluids of the prostate that are widely used for diagnostic and prognostic assays for prostate cancer. These fluids contain an abundant number of glycoproteins and extracellular vesicles secreted by the prostate gland, and the ability to detect changes in their N-glycans composition as a reflection of disease state represents potential new biomarker candidates. Methods to characterize these N-glycan constituents directly from clinical samples in a timely manner and with minimal sample processing requirements are not currently available. In this report, an approach is described to directly profile the N-glycan constituents of EPS urine samples, prostatic fluids and urine using imaging mass spectrometry for detection. An amine reactive slide is used to immobilize glycoproteins from a few microliters of spotted samples, followed by peptide N-glycosidase digestion. Over 100 N-glycan compositions can be detected with this method, and it works with urine, urine EPS, prostatic fluids, and urine EPS-derived extracellular vesicles. A comparison of the N-glycans detected from the fluids with tissue N-glycans from prostate cancer tissues was done, indicating a subset of N-glycans present in fluids derived from the gland lumens. The developed N-glycan profiling is amenable to analysis of larger clinical cohorts and adaptable to other biofluids.
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Affiliation(s)
- Calvin R K Blaschke
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - Jordan P Hartig
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - Grace Grimsley
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - Liping Liu
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - O John Semmes
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, United States.,The Leroy T. Canoles Jr., Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Jennifer D Wu
- Departments of Urology and Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Joseph E Ippolito
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Chanita Hughes-Halbert
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, United States.,Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States
| | - Julius O Nyalwidhe
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, United States.,The Leroy T. Canoles Jr., Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States.,Department of Radiology, Washington University School of Medicine, St. Louis, MO, United States
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47
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Chatterjee S, Ugonotti J, Lee LY, Everest-Dass A, Kawahara R, Thaysen-Andersen M. Trends in oligomannosylation and α1,2-mannosidase expression in human cancers. Oncotarget 2021; 12:2188-2205. [PMID: 34676051 PMCID: PMC8522845 DOI: 10.18632/oncotarget.28064] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/18/2021] [Indexed: 02/05/2023] Open
Abstract
Aberrant protein glycosylation is a prominent cancer feature. While many tumour-associated glycoepitopes have been reported, advances in glycoanalytics continue to uncover new associations between glycosylation and cancer. Guided by a comprehensive literature survey suggesting that oligomannosylation (Man5–9 GlcNAc2) is a widespread and often regulated glycosignature in human cancers, we here revisit a valuable compilation of nearly 500 porous graphitized carbon LC-MS/MS N-glycomics datasets acquired across 11 human cancer types to systematically test for oligomannose-cancer associations. Firstly, the quantitative glycomics data obtained across 34 cancerous cell lines demonstrated that oligomannosylation is a pan-cancer feature spanning in a wide abundance range. In keeping with literature, our quantitative glycomics data of tumour and matching control tissues and new MALDI-MS imaging data of tissue microarrays showed a strong cancer-associated elevation of oligomannosylation in both basal cell (p = 1.78 × 10–12) and squamous cell (p = 1.23 × 10–11) skin cancer and colorectal cancer (p = 8.0 × 10–4). The glycomics data also indicated that some cancer types including gastric and liver cancer exhibit unchanged or reduced oligomannose levels, observations also supported by literature and MALDI-MS imaging data. Finally, expression data from public cancer repositories indicated that several α1,2-mannosidases are regulated in tumour tissues suggesting that these glycan-processing enzymes may contribute to the cancer-associated modulation of oligomannosylation. This omics-centric study has compiled robust glycomics and enzyme expression data revealing interesting molecular trends that open avenues to better understand the role of oligomannosylation in human cancers.
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Affiliation(s)
| | - Julian Ugonotti
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Ling Y Lee
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | | | - Rebeca Kawahara
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.,Joint senior authors
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.,Biomolecular Discovery Research Centre (BDRC), Macquarie University, Sydney, Australia.,Joint senior authors
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48
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Kurz E, Chen S, Vucic E, Baptiste G, Loomis C, Agrawal P, Hajdu C, Bar-Sagi D, Mahal LK. Integrated Systems Analysis of the Murine and Human Pancreatic Cancer Glycomes Reveals a Tumor-Promoting Role for ST6GAL1. Mol Cell Proteomics 2021; 20:100160. [PMID: 34634466 PMCID: PMC8604807 DOI: 10.1016/j.mcpro.2021.100160] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 02/06/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer death in the United States. Glycans, such as carbohydrate antigen 19-9, are biomarkers of PDAC and are emerging as important modulators of cancer phenotypes. Herein, we used a systems-based approach integrating glycomic analysis of the well-established KC mouse, which models early events in transformation, and analysis of samples from human pancreatic cancer patients to identify glycans with potential roles in cancer formation. We observed both common and distinct patterns of glycosylation in pancreatic cancer across species. Common alterations included increased levels of α-2,3-sialic acid and α-2,6-sialic acid, bisecting GlcNAc and poly-N-acetyllactosamine. However, core fucose, which was increased in human PDAC, was not seen in the mouse, indicating that not all human glycomic changes are observed in the KC mouse model. In silico analysis of bulk and single-cell sequencing data identified ST6 beta-galactoside alpha-2,6-sialyltransferase 1, which underlies α-2,6-sialic acid, as overexpressed in human PDAC, concordant with histological data showing higher levels of this enzyme at the earliest stages. To test whether ST6 beta-galactoside alpha-2,6-sialyltransferase 1 promotes pancreatic cancer, we created a novel mouse in which a pancreas-specific genetic deletion of this enzyme overlays the KC mouse model. The analysis of our new model showed delayed cancer formation and a significant reduction in fibrosis. Our results highlight the importance of a strategic systems approach to identifying glycans whose functions can be modeled in mouse, a crucial step in the development of therapeutics targeting glycosylation in pancreatic cancer.
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Affiliation(s)
- Emma Kurz
- Department of Cell Biology, NYU Grossman School of Medicine, New York, New York, USA
| | - Shuhui Chen
- Department of Chemistry, Biomedical Research Institute, New York University, New York, New York, USA
| | - Emily Vucic
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, New York, USA
| | - Gillian Baptiste
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, USA
| | - Cynthia Loomis
- Office of Science and Research, NYU Grossman School of Medicine, New York, New York, USA
| | - Praveen Agrawal
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, USA
| | - Cristina Hajdu
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, USA
| | - Dafna Bar-Sagi
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, New York, USA.
| | - Lara K Mahal
- Department of Chemistry, Biomedical Research Institute, New York University, New York, New York, USA.
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49
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Abstract
This review focuses on the human pancreatic islet-including its structure, cell composition, development, function, and dysfunction. After providing a historical timeline of key discoveries about human islets over the past century, we describe new research approaches and technologies that are being used to study human islets and how these are providing insight into human islet physiology and pathophysiology. We also describe changes or adaptations in human islets in response to physiologic challenges such as pregnancy, aging, and insulin resistance and discuss islet changes in human diabetes of many forms. We outline current and future interventions being developed to protect, restore, or replace human islets. The review also highlights unresolved questions about human islets and proposes areas where additional research on human islets is needed.
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Affiliation(s)
- John T Walker
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Diane C Saunders
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Marcela Brissova
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Alvin C Powers
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- VA Tennessee Valley Healthcare System, Nashville, Tennessee, USA
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50
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Zhong L, Zhu L, Cai ZW. Mass Spectrometry-based Proteomics and Glycoproteomics in COVID-19 Biomarkers Identification: A Mini-review. JOURNAL OF ANALYSIS AND TESTING 2021; 5:298-313. [PMID: 34513131 PMCID: PMC8423835 DOI: 10.1007/s41664-021-00197-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/27/2021] [Indexed: 12/11/2022]
Abstract
The first corona-pandemic, coronavirus disease 2019 (COVID-19) caused a huge health crisis and incalculable damage worldwide. Knowledge of how to cure the disease is urgently needed. Emerging immune escaping mutants of the virus suggested that it may be potentially persistent in human society as a regular health threat as the flu virus. Therefore, it is imperative to identify appropriate biomarkers to indicate pathological and physiological states, and more importantly, clinic outcomes. Proteins are the performers of life functions, and their abundance and modification status can directly reflect the immune status. Protein glycosylation serves a great impact in modulating protein function. The use of both unmodified and glycosylated proteins as biomarkers has also been proved feasible in the studies of SARS, Zika virus, influenza, etc. In recent years, mass spectrometry-based glycoproteomics, as well as proteomics approaches, advanced significantly due to the evolution of mass spectrometry. We focus on the current development of the mass spectrometry-based strategy for COVID-19 biomarkers' investigation. Potential application of glycoproteomics approaches and challenges in biomarkers identification are also discussed.
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Affiliation(s)
- Li Zhong
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong SAR, China
| | - Lin Zhu
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong SAR, China
| | - Zong-Wei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong SAR, China
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