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Zhang B, Xu L, Ji Y, Li J, Liu L, Li L, Zhuo Z, Zheng Z. RHOGTPase-Related Gene Signature Predicts Prognosis, Immunotherapy Response, and Chemotherapy Sensitivity in Colon Cancer. Appl Biochem Biotechnol 2025:10.1007/s12010-025-05262-9. [PMID: 40347353 DOI: 10.1007/s12010-025-05262-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2025] [Indexed: 05/12/2025]
Abstract
Rho GTPases are known to promote colon cancer cell invasion and metastasis by modulating cell motility and adhesion. However, the clinical implications of Rho GTPase-related genes in prognosis and treatment response for colon cancer remain underexplored. We identified Rho GTPase-related prognostic genes using univariate Cox regression and applied Least Absolute Shrinkage and Selection Operator (LASSO) regression to refine these genes and develop a prognostic model. The Rho GTPase-related gene signature was analyzed for associations with clinical outcomes, immune status, immunotherapy, and chemotherapy response in colon cancer patients. A Rho GTPase-related 12-gene signature was established to predict prognosis across training and validation cohorts. Both univariate and multivariate analyses confirmed the Rho GTPase risk score as an independent prognostic factor. The model's area under the curve (AUC) and decision curve analysis (DCA) outperformed traditional TNM staging and several existing models. Immune cell analysis showed high Rho GTPase risk scores correlated with increased macrophage/monocyte and cancer-associated fibroblast infiltration. Tumor Immune Dysfunction and Exclusion (TIDE) analysis revealed an association between high Rho GTPase risk scores and immune dysfunction, suggesting potential resistance to immune checkpoint inhibitors in high-risk patients. Additionally, differential sensitivity to 59 chemotherapeutics was observed: high-risk patients showed greater sensitivity to CCT007093, CGP.082996, and AS601245, while low-risk patients were more sensitive to BMS.708163, NSC.87877, and Cisplatin, informing potential treatment choices. The Rho GTPase-related 12-gene signature offers a valuable tool for predicting prognosis and therapeutic response in colon cancer, supporting personalized treatment strategies and improved patient outcomes.
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Affiliation(s)
- Bixiong Zhang
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China
- Heyuan People's Hospital, Heyuan, Guangdong, 517001, China
| | - Lingli Xu
- Dadong Street Community Health Service Center, Guangzhou, 510080, China
| | - Yuran Ji
- Heyuan People's Hospital, Heyuan, Guangdong, 517001, China
| | - Jiezhuang Li
- Heyuan People's Hospital, Heyuan, Guangdong, 517001, China
| | - Liehui Liu
- Heyuan People's Hospital, Heyuan, Guangdong, 517001, China
| | - Liangfang Li
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Zewei Zhuo
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China.
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, China.
| | - Zhongwen Zheng
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China.
- Heyuan People's Hospital, Heyuan, Guangdong, 517001, China.
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Yingli H, Ping Y, Jun Y, Zhu Xingwang. Aberrant protein glycosylation in the colon adenoma-cancer sequence: Colorectal cancer mechanisms and clinical implications. Biochim Biophys Acta Mol Basis Dis 2025; 1871:167853. [PMID: 40250777 DOI: 10.1016/j.bbadis.2025.167853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2024] [Revised: 03/16/2025] [Accepted: 04/14/2025] [Indexed: 04/20/2025]
Abstract
Colorectal cancer (CRC) is a leading contributor to global cancer-related morbidity and mortality. Glycosylation is a common post-translational protein modification. Aberrant protein glycosylation is a hallmark of cancer, affecting biological processes and driving malignant CRC phenotypes. Specifically, abnormal N-glycosylation manifests as structural alterations in high mannose, sialylated, and fucosylated structures, collectively promoting cancer stemness and invasiveness. Concurrently, O-GlcNAcylation facilitates tumorigenesis through metabolic reprogramming and oncogene activation. Dysregulated mucin-type O-glycans (e.g., Core-1/Core-3 imbalance) and elevated SLex/SLea antigen expression are significantly correlated with tumor adhesion, metastatic dissemination, and adverse clinical outcomes. Furthermore, protein glycosylation contributes to chemoresistance through anti-apoptotic mechanisms, aberrant signaling activation, and pro-angiogenic pathways. This review systematically examines the dynamic evolution of protein glycosylation during CRC progression from normal mucosa to adenoma to adenocarcinoma. It also evaluates the CRC diagnostic and therapeutic implications of glycoproteins and glycans. This review can provide a molecular understanding for advancing CRC diagnostics and treatment.
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Affiliation(s)
- He Yingli
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Yang Ping
- The First Clinical Medical College of Lanzhou University, Lanzhou 730000, China
| | - Yan Jun
- The First Clinical Medical College of Lanzhou University, Lanzhou 730000, China; Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, Lanzhou 730000, China
| | - Zhu Xingwang
- The First Clinical Medical College of Lanzhou University, Lanzhou 730000, China.
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3
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Kizuka Y. Regulation of intracellular activity of N-glycan branching enzymes in mammals. J Biol Chem 2024; 300:107471. [PMID: 38879010 PMCID: PMC11328876 DOI: 10.1016/j.jbc.2024.107471] [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: 03/27/2024] [Revised: 06/01/2024] [Accepted: 06/06/2024] [Indexed: 07/07/2024] Open
Abstract
Most proteins in the secretory pathway are glycosylated, and N-glycans are estimated to be attached to over 7000 proteins in humans. As structural variation of N-glycans critically regulates the functions of a particular glycoprotein, it is pivotal to understand how structural diversity of N-glycans is generated in cells. One of the major factors conferring structural variation of N-glycans is the variable number of N-acetylglucosamine branches. These branch structures are biosynthesized by dedicated glycosyltransferases, including GnT-III (MGAT3), GnT-IVa (MGAT4A), GnT-IVb (MGAT4B), GnT-V (MGAT5), and GnT-IX (GnT-Vb, MGAT5B). In addition, the presence or absence of core modification of N-glycans, namely, core fucose (included as an N-glycan branch in this manuscript), synthesized by FUT8, also confers large structural variation on N-glycans, thereby crucially regulating many protein-protein interactions. Numerous biochemical and medical studies have revealed that these branch structures are involved in a wide range of physiological and pathological processes. However, the mechanisms regulating the activity of the biosynthetic glycosyltransferases are yet to be fully elucidated. In this review, we summarize the previous findings and recent updates regarding regulation of the activity of these N-glycan branching enzymes. We hope that such information will help readers to develop a comprehensive overview of the complex system regulating mammalian N-glycan maturation.
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Affiliation(s)
- Yasuhiko Kizuka
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan.
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4
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Zhang D, Xie J, Sun F, Xu R, Liu W, Xu J, Huang X, Zhang G. Pharmacological suppression of HHLA2 glycosylation restores anti-tumor immunity in colorectal cancer. Cancer Lett 2024; 589:216819. [PMID: 38522775 DOI: 10.1016/j.canlet.2024.216819] [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: 08/25/2023] [Revised: 03/08/2024] [Accepted: 03/15/2024] [Indexed: 03/26/2024]
Abstract
Immunotherapy aimed at inhibiting the negative co-stimulatory molecule programmed cell death-ligand 1 (PD-L1) has limited effectiveness, with clinical response rates remaining below 10%-15%. Therefore, new immune checkpoints need to be explored. Our study focused on human endogenous retrovirus H long terminal repeat-associating protein 2 (HHLA2), a highly glycosylated member of the B7 family that is widely expressed in colorectal cancer. HHLA2 expression negatively correlates with the prognosis of colorectal cancer. Glycosylation of HHLA2, which is regulated by the glycosyltransferase STT3 oligosaccharyltransferase complex catalytic subunit A (STT3A), is crucial for protein stability and expression in cell membranes. Additionally, the binding of HHLA2 to the receptors killer cell immunoglobulin-like receptor, three immunoglobulin domains and long cytoplasmic tail 3 (KIR3DL3) and transmembrane and immunoglobulin (Ig) domain containing 2 (TMIGD2) is dependent on N-glycosylation. Moreover, N-glycosylation of HHLA2 promotes immune evasion in colorectal cancer by suppressing the immune response of NK cells. Notably, the STT3A inhibitor NGI-1 enhances the anti-tumor immune response of NK cells. Our findings provide new insights and a molecular basis for targeting HHLA2 in immunotherapy for colorectal cancer.
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Affiliation(s)
- Dongze Zhang
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | - Jinjing Xie
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | | | - Ruyan Xu
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | - Wenjun Liu
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | - Jia Xu
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | - Xue Huang
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China.
| | - Guangbo Zhang
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China; Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, 215000, China; Jiangsu Key Laboratory of Gastrointestinal Tumor Immunology, Suzhou, 215000, China.
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5
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López-Cortés R, Muinelo-Romay L, Fernández-Briera A, Gil Martín E. High-Throughput Mass Spectrometry Analysis of N-Glycans and Protein Markers after FUT8 Knockdown in the Syngeneic SW480/SW620 Colorectal Cancer Cell Model. J Proteome Res 2024; 23:1379-1398. [PMID: 38507902 PMCID: PMC11002942 DOI: 10.1021/acs.jproteome.3c00833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/22/2024]
Abstract
Disruption of the glycosylation machinery is a common feature in many types of cancer, and colorectal cancer (CRC) is no exception. Core fucosylation is mediated by the enzyme fucosyltransferase 8 (FucT-8), which catalyzes the addition of α1,6-l-fucose to the innermost GlcNAc residue of N-glycans. We and others have documented the involvement of FucT-8 and core-fucosylated proteins in CRC progression, in which we addressed core fucosylation in the syngeneic CRC model formed by SW480 and SW620 tumor cell lines from the perspective of alterations in their N-glycosylation profile and protein expression as an effect of the knockdown of the FUT8 gene that encodes FucT-8. Using label-free, semiquantitative mass spectrometry (MS) analysis, we found noticeable differences in N-glycosylation patterns in FUT8-knockdown cells, affecting core fucosylation and sialylation, the Hex/HexNAc ratio, and antennarity. Furthermore, stable isotopic labeling of amino acids in cell culture (SILAC)-based proteomic screening detected the alteration of species involved in protein folding, endoplasmic reticulum (ER) and Golgi post-translational stabilization, epithelial polarity, and cellular response to damage and therapy. This data is available via ProteomeXchange with identifier PXD050012. Overall, the results obtained merit further investigation to validate their feasibility as biomarkers of progression and malignization in CRC, as well as their potential usefulness in clinical practice.
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Affiliation(s)
- Rubén López-Cortés
- Doctoral
Program in Methods and Applications in Life Sciences, Faculty of Biology, Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Pontevedra (Galicia), Spain
| | - Laura Muinelo-Romay
- Liquid
Biopsy Analysis Unit, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago de Compostela
(IDIS), CIBERONC, Travesía da Choupana, 15706 Santiago de Compostela, A Coruña
(Galicia), Spain
| | - Almudena Fernández-Briera
- Molecular
Biomarkers, Biomedical Research Centre (CINBIO), Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Pontevedra (Galicia), Spain
| | - Emilio Gil Martín
- Nutrition
and Food Science Group, Department of Biochemistry, Genetics and Immunology,
Faculty of Biology, Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Pontevedra (Galicia), Spain
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6
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Tomida S, Nagae M, Kizuka Y. Distinctive domains and activity regulation of core fucosylation enzyme FUT8. Biochim Biophys Acta Gen Subj 2024; 1868:130561. [PMID: 38218458 DOI: 10.1016/j.bbagen.2024.130561] [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: 12/11/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
BACKGROUND Core fucose, a structure added to the reducing end N-acetylglucosamine of N-glycans, has been shown to regulate various physiological and pathological processes, including melanoma metastasis, exacerbation of chronic obstructive pulmonary disease, and severe outcomes in COVID-19. SCOPE OF REVIEW Recent research has shed light on regulation of the activity and subcellular localization of a1,6-fucosyltransferase (FUT8), the glycosyltransferase responsible for core fucose biosynthesis, unraveling the mechanisms for controlling core fucosylation in vivo. MAJOR CONCLUSIONS This review summarizes the various features of FUT8, including its domains, structures, and substrate specificity. Additionally, we discuss the potential involvement of FUT8-binding proteins, such as oligosaccharyltransferase subunits, in the regulation of FUT8 activity, substrate specificity, and the secretion of FUT8. GENERAL SIGNIFICANCE We anticipate that this review will contribute to a deeper understanding of the control of core fucose levels in vivo and involvement of core fucosylation in FUT8-relevant functions and diseases.
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Affiliation(s)
- Seita Tomida
- The United Graduate School of Agricultural Science, Gifu University, Gifu 501-1193, Japan
| | - Masamichi Nagae
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan; Laboratory of Molecular Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Suita, Japan
| | - Yasuhiko Kizuka
- The United Graduate School of Agricultural Science, Gifu University, Gifu 501-1193, Japan; Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan.
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7
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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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Iwamoto S, Kobayashi T, Hanamatsu H, Yokota I, Teranishi Y, Iwamoto A, Kitagawa M, Ashida S, Sakurai A, Matsuo S, Myokan Y, Sugimoto A, Ushioda R, Nagata K, Gotoh N, Nakajima K, Nishikaze T, Furukawa JI, Itano N. Tolerable glycometabolic stress boosts cancer cell resilience through altered N-glycosylation and Notch signaling activation. Cell Death Dis 2024; 15:53. [PMID: 38225221 PMCID: PMC10789756 DOI: 10.1038/s41419-024-06432-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/25/2023] [Accepted: 01/03/2024] [Indexed: 01/17/2024]
Abstract
Chronic metabolic stress paradoxically elicits pro-tumorigenic signals that facilitate cancer stem cell (CSC) development. Therefore, elucidating the metabolic sensing and signaling mechanisms governing cancer cell stemness can provide insights into ameliorating cancer relapse and therapeutic resistance. Here, we provide convincing evidence that chronic metabolic stress triggered by hyaluronan production augments CSC-like traits and chemoresistance by partially impairing nucleotide sugar metabolism, dolichol lipid-linked oligosaccharide (LLO) biosynthesis and N-glycan assembly. Notably, preconditioning with either low-dose tunicamycin or 2-deoxy-D-glucose, which partially interferes with LLO biosynthesis, reproduced the promoting effects of hyaluronan production on CSCs. Multi-omics revealed characteristic changes in N-glycan profiles and Notch signaling activation in cancer cells exposed to mild glycometabolic stress. Restoration of N-glycan assembly with glucosamine and mannose supplementation and Notch signaling blockade attenuated CSC-like properties and further enhanced the therapeutic efficacy of cisplatin. Therefore, our findings uncover a novel mechanism by which tolerable glycometabolic stress boosts cancer cell resilience through altered N-glycosylation and Notch signaling activation.
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Affiliation(s)
- Shungo Iwamoto
- Graduate School of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | | | - Hisatoshi Hanamatsu
- Department of Orthopaedic Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Ikuko Yokota
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Aichi, Japan
| | - Yukiko Teranishi
- Graduate School of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Akiho Iwamoto
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Miyu Kitagawa
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Sawako Ashida
- Graduate School of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Ayane Sakurai
- Graduate School of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Suguru Matsuo
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Yuma Myokan
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Aiyu Sugimoto
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Ryo Ushioda
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Kazuhiro Nagata
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
- JT Biohistory Research Hall, Takatsuki, Osaka, Japan
| | - Noriko Gotoh
- Division of Cancer Cell Biology, Cancer Research Institute, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kazuki Nakajima
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan
| | - Takashi Nishikaze
- Solutions COE, Analytical & Measuring Instruments Division, Shimadzu Corporation, Kyoto, Japan
| | - Jun-Ichi Furukawa
- Department of Orthopaedic Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Aichi, Japan
| | - Naoki Itano
- Graduate School of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.
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9
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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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10
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Kohansal-Nodehi M, Swiatek-de Lange M, Kroeniger K, Rolny V, Tabarés G, Piratvisuth T, Tanwandee T, Thongsawat S, Sukeepaisarnjaroen W, Esteban JI, Bes M, Köhler B, Chan HLY, Busskamp H. Discovery of a haptoglobin glycopeptides biomarker panel for early diagnosis of hepatocellular carcinoma. Front Oncol 2023; 13:1213898. [PMID: 37920152 PMCID: PMC10619681 DOI: 10.3389/fonc.2023.1213898] [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: 04/28/2023] [Accepted: 09/20/2023] [Indexed: 11/04/2023] Open
Abstract
Background There is a need for new serum biomarkers for early detection of hepatocellular carcinoma (HCC). Haptoglobin (Hp) N-glycosylation is altered in HCC, but the diagnostic value of site-specific Hp glycobiomarkers is rarely reported. We aimed to determine the site-specific glycosylation profile of Hp for early-stage HCC diagnosis. Method Hp glycosylation was analyzed in the plasma of patients with liver diseases (n=57; controls), early-stage HCC (n=50) and late-stage HCC (n=32). Hp phenotype was determined by immunoblotting. Hp was immunoisolated and digested into peptides. N-glycopeptides were identified and quantified using liquid chromatography-mass spectrometry. Cohort samples were compared using Wilcoxon rank-sum (Mann-Whitney U) tests. Diagnostic performance was assessed using receiver operating characteristic (ROC) curves and area under curve (AUC). Results Significantly higher fucosylation, branching and sialylation of Hp glycans, and expression of high-mannose glycans, was observed as disease progressed from cirrhosis to early- and late-stage HCC. Several glycopeptides demonstrated high values for early diagnosis of HCC, with an AUC of 93% (n=1), >80% (n=3), >75% (n=13) and >70% (n=11), compared with alpha-fetoprotein (AFP; AUC of 79%). The diagnostic performance of the identified biomarkers was only slightly affected by Hp phenotype. Conclusion We identified a panel of Hp glycopeptides that are significantly differentially regulated in early- and late-stage HCC. Some glycobiomarkers exceeded the diagnostic value of AFP (the most commonly used biomarker for HCC diagnosis). Our findings provide evidence that glycobiomarkers can be effective in the diagnosis of early HCC - individually, as a panel of glycopeptides or combined with conventional serological biomarkers.
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Affiliation(s)
| | | | | | - Vinzent Rolny
- Roche Diagnostics GmbH, Research and Development Core Lab, Penzberg, Germany
| | - Glòria Tabarés
- Roche Diagnostics GmbH, Research and Development Core Lab, Penzberg, Germany
| | - Teerha Piratvisuth
- NKC Institute of Gastroenterology and Hepatology, Songklanagarind Hospital, Prince of Songkla University, Hat Yai, Thailand
| | - Tawesak Tanwandee
- Division of Gastroenterology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Satawat Thongsawat
- Department of Internal Medicine, Maharaj Nakorn Chiang Mai Hospital, Chiang Mai University, Chiang Mai, Thailand
| | | | | | - Marta Bes
- Transfusion Safety Laboratory, Banc de Sang i Teixits (BST), Barcelona, Spain
| | - Bruno Köhler
- Department of Medical Oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Liver Cancer Center Heidelberg, Heidelberg, Germany
| | - Henry Lik-Yuen Chan
- Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Holger Busskamp
- Roche Diagnostics GmbH, Research and Development Core Lab, Penzberg, Germany
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11
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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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12
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Ukkola I, Nummela P, Heiskanen A, Holm M, Zafar S, Kero M, Haglund C, Satomaa T, Kytölä S, Ristimäki A. N-Glycomic Profiling of Microsatellite Unstable Colorectal Cancer. Cancers (Basel) 2023; 15:3571. [PMID: 37509233 PMCID: PMC10376987 DOI: 10.3390/cancers15143571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Aberrant glycosylation affects cancer progression and immune evasion. Approximately 15% of colorectal cancers (CRCs) demonstrate microsatellite instability (MSI) and display major differences in outcomes and therapeutic responses, as compared to corresponding microsatellite stable (MSS) tumors. We compared the N-glycan profiles of stage II and IV MSI CRC tumors, further subdivided into BRAFV600E wild-type and mutated subgroups (n = 10 in each subgroup), with each other and with those of paired non-neoplastic mucosal samples using mass spectrometry. Further, the N-glycans of BRAFV600E wild-type stage II MSI tumors were compared to corresponding MSS tumors (n = 9). Multiple differences in N-glycan profiles were identified between the MSI CRCs and control tissues, as well as between the stage II MSI and MSS samples. The MSI CRC tumors showed a lower relative abundance of high-mannose N-glycans than did the control tissues or the MSS CRCs. Among MSI CRC subgroups, acidic N-glycans showed tumor stage and BRAF mutation status-dependent variation. Specifically, the large, sulfated/phosphorylated, and putative terminal N-acetylhexosamine-containing acidic N-glycans differed between the MSI CRC subgroups, showing opposite changes in stages II and IV, when comparing BRAF mutated and wild-type tumors. Our results show that molecular subgroups of CRC exhibit characteristic glycan profiles that may explain certain carcinogenic properties of MSI tumors.
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Affiliation(s)
- Iiris Ukkola
- HUSLAB, Department of Pathology, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, Helsinki University Hospital and University of Helsinki, 00014 Helsinki, Finland
| | - Pirjo Nummela
- HUSLAB, Department of Pathology, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, Helsinki University Hospital and University of Helsinki, 00014 Helsinki, Finland
| | | | - Matilda Holm
- HUSLAB, Department of Pathology, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, Helsinki University Hospital and University of Helsinki, 00014 Helsinki, Finland
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
- Department of Surgery, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
| | - Sadia Zafar
- HUSLAB, Department of Pathology, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, Helsinki University Hospital and University of Helsinki, 00014 Helsinki, Finland
| | - Mia Kero
- HUSLAB, Department of Pathology, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
| | - Caj Haglund
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
- Department of Surgery, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
| | - Tero Satomaa
- Glykos Finland Co., Ltd., 00790 Helsinki, Finland
| | - Soili Kytölä
- HUSLAB, Department of Genetics, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
| | - Ari Ristimäki
- HUSLAB, Department of Pathology, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, Helsinki University Hospital and University of Helsinki, 00014 Helsinki, Finland
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13
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Moran AB, Elgood-Hunt G, van der Burgt YEM, Wuhrer M, Mesker WE, Tollenaar RAEM, Spencer DIR, Lageveen-Kammeijer GSM. Serum N-Glycosylation RPLC-FD-MS Assay to Assess Colorectal Cancer Surgical Interventions. Biomolecules 2023; 13:896. [PMID: 37371476 DOI: 10.3390/biom13060896] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/16/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
A newly developed analytical strategy was applied to profile the total serum N-glycome of 64 colorectal cancer (CRC) patients before and after surgical intervention. In this cohort, it was previously found that serum N-glycome alterations in CRC were associated with patient survival. Here, fluorescent labeling of serum N-glycans was applied using procainamide and followed by sialic acid derivatization specific for α2,6- and α2,3-linkage types via ethyl esterification and amidation, respectively. This strategy allowed efficient separation of specific positional isomers on reversed-phase liquid chromatography-fluorescence detection-mass spectrometry (RPLC-FD-MS) and complemented the previous glycomics data based on matrix-assisted laser desorption/ionization (MALDI)-MS that did not include such separations. The results from comparing pre-operative CRC to post-operative samples were in agreement with studies that identified a decrease in di-antennary structures with core fucosylation and an increase in sialylated tri- and tetra-antennary N-glycans in CRC patient sera. Pre-operative abundances of N-glycans showed good performance for the classification of adenocarcinoma and led to the revisit of the previous MALDI-MS dataset with regard to histological and clinical data. This strategy has the potential to monitor patient profiles before, during, and after clinical events such as treatment, therapy, or surgery and should also be further explored.
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Affiliation(s)
- Alan B Moran
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Ludger Ltd., Culham Science Centre, Abingdon OX14 3EB, UK
| | | | - Yuri E M van der Burgt
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Wilma E Mesker
- Department of Surgery, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Rob A E M Tollenaar
- Department of Surgery, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | | | - Guinevere S M Lageveen-Kammeijer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
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14
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Liang F, Wang S, Guo Y, Mu Y, Shang F, Wang M. Proteome profiling of endogenous and potential S-nitrosylation in colorectal cancer. Front Endocrinol (Lausanne) 2023; 14:1153719. [PMID: 37124724 PMCID: PMC10140627 DOI: 10.3389/fendo.2023.1153719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/22/2023] [Indexed: 05/02/2023] Open
Abstract
Background As a common cancer with high incidence rate and mortality, colorectal cancer (CRC) is seriously threatening human health. S-nitrosylation (SNO) proteins mediated by nitric oxide (NO) has important implications in the genesis, progression, and apoptosis of CRC. It's worth noting that the SNO proteins also play an important role in the tumor endocrine and metabolic pathways of CRC. Materials and methods In this study, the protein extracts of human tissues and cell lines were treated by biotin switch technology and magnetic beads enrichment. The proteomic results of endogenous and potential SNO proteins were analyzed by mass spectrometry (MS). Through the comparison and analysis of MS results, Gene Ontology (GO) analysis, and literatures, some endogenous and potential SNO proteins were identified in CRC, which were closely related to the tumor endocrine and metabolic pathways, the apoptotic signaling pathways, protein maturation, and other biological processes of the proliferation and apoptosis of CRC cells. Results A total of 19 proteins containing potential or endogenous SNO sites were detected in both human cancer tissue and SW 480 cells. Through the cross validation of MS results, GO analysis, and literatures, several SNO proteins were identified frequently in CRC, such as the actin, cytoplasmic 1 (ACTB), peroxiredoxin-4 (PRDX4), protein S100A8 (S100A8), pyruvate kinase PKM (PKM), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which were closely related to the tumor endocrine and metabolic pathways and the apoptotic signaling pathways of CRC. Conclusion Different CRC cells and tissues contained potential and endogenous SNO modified proteins. In addition, some SNO proteins could participate in the proliferation, metastasis and apoptosis of CRC by regulating the tumor endocrine and metabolic pathways.
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Affiliation(s)
- Feng Liang
- Department of General Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Shuang Wang
- Department of Dermatology, The Second Hospital of Jilin University, Changchun, China
| | - Yu Guo
- Department of General Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Yu Mu
- Department of General Surgery, The Second Hospital of Jilin University, Changchun, China
| | - FengJia Shang
- Department of General Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Min Wang
- Department of General Surgery, The Second Hospital of Jilin University, Changchun, China
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15
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Xu M, Yang A, Xia J, Jiang J, Liu CF, Ye Z, Ma J, Yang S. Protein glycosylation in urine as a biomarker of diseases. Transl Res 2023; 253:95-107. [PMID: 35952983 DOI: 10.1016/j.trsl.2022.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 02/01/2023]
Abstract
Human body fluids have become an indispensable resource for clinical research, diagnosis and prognosis. Urine is widely used to discover disease-specific glycoprotein biomarkers because of its recurrently non-invasive collection and disease-indicating properties. While urine is an unstable fluid in that its composition changes with ingested nutrients and further as it is excreted through micturition, urinary proteins are more stable and their abnormal glycosylation is associated with diseases. It is known that aberrant glycosylation can define tumor malignancy and indicate disease initiation and progression. However, a thorough and translational survey of urinary glycosylation in diseases has not been performed. In this article, we evaluate the clinical applications of urine, introduce methods for urine glycosylation analysis, and discuss urine glycoprotein biomarkers. We emphasize the importance of mining urinary glycoproteins and searching for disease-specific glycosylation in various diseases (including cancer, neurodegenerative diseases, diabetes, and viral infections). With advances in mass spectrometry-based glycomics/glycoproteomics/glycopeptidomics, characterization of disease-specific glycosylation will optimistically lead to the discovery of disease-related urinary biomarkers with better sensitivity and specificity in the near future.
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Affiliation(s)
- Mingming Xu
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Arthur Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Jun Xia
- Clinical Laboratory Center, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, China
| | - Junhong Jiang
- Department of Pulmonary and Critical Care Medicine, Dushu Lake Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Chun-Feng Liu
- Department of Neurology and Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhenyu Ye
- Department of General Surgery, Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, District of Columbia.
| | - Shuang Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China.
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16
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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: 42] [Impact Index Per Article: 21.0] [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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17
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Krug J, Rodrian G, Petter K, Yang H, Khoziainova S, Guo W, Bénard A, Merkel S, Gellert S, Maschauer S, Spermann M, Waldner M, Bailey P, Pilarsky C, Liebl A, Tripal P, Christoph J, Naschberger E, Croner R, Schellerer VS, Becker C, Hartmann A, Tüting T, Prante O, Grützmann R, Grivennikov SI, Stürzl M, Britzen-Laurent N. N-glycosylation Regulates Intrinsic IFN-γ Resistance in Colorectal Cancer: Implications for Immunotherapy. Gastroenterology 2023; 164:392-406.e5. [PMID: 36402190 PMCID: PMC10009756 DOI: 10.1053/j.gastro.2022.11.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND & AIMS Advanced colorectal carcinoma (CRC) is characterized by a high frequency of primary immune evasion and refractoriness to immunotherapy. Given the importance of interferon (IFN)-γ in CRC immunosurveillance, we investigated whether and how acquired IFN-γ resistance in tumor cells would promote tumor growth, and whether IFN-γ sensitivity could be restored. METHODS Spontaneous and colitis-associated CRC development was induced in mice with a specific IFN-γ pathway inhibition in intestinal epithelial cells. The influence of IFN-γ pathway gene status and expression on survival was assessed in patients with CRC. The mechanisms underlying IFN-γ resistance were investigated in CRC cell lines. RESULTS The conditional knockout of the IFN-γ receptor in intestinal epithelial cells enhanced spontaneous and colitis-associated colon tumorigenesis in mice, and the loss of IFN-γ receptor α (IFNγRα) expression by tumor cells predicted poor prognosis in patients with CRC. IFNγRα expression was repressed in human CRC cells through changes in N-glycosylation, which decreased protein stability via proteasome-dependent degradation, inhibiting IFNγR-signaling. Downregulation of the bisecting N-acetylglucosaminyltransferase III (MGAT3) expression was associated with IFN-γ resistance in all IFN-γ-resistant cells, and highly correlated with low IFNγRα expression in CRC tissues. Both ectopic and pharmacological reconstitution of MGAT3 expression with all-trans retinoic acid increased bisecting N-glycosylation, as well as IFNγRα protein stability and signaling. CONCLUSIONS Together, our results demonstrated that tumor-associated changes in N-glycosylation destabilize IFNγRα, causing IFN-γ resistance in CRC. IFN-γ sensitivity could be reestablished through the increase in MGAT3 expression, notably via all-trans retinoic acid treatment, providing new prospects for the treatment of immune-resistant CRC.
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Affiliation(s)
- Julia Krug
- Division of Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Gabriele Rodrian
- Division of Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Katja Petter
- Division of Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Hai Yang
- Division of Surgical Research, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Svetlana Khoziainova
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Wei Guo
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Alan Bénard
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Susanne Merkel
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Susan Gellert
- Laboratory of Experimental Dermatology, Department of Dermatology, University Hospital and Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke-University, Magdeburg, Germany
| | - Simone Maschauer
- Department of Nuclear Medicine, Molecular Imaging and Radiochemistry, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Monika Spermann
- Division of Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Maximilian Waldner
- Department of Medicine I, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Peter Bailey
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Christian Pilarsky
- Division of Surgical Research, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Andrea Liebl
- Division of Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Philipp Tripal
- Division of Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Jan Christoph
- Department of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Tennenlohe, Germany
| | - Elisabeth Naschberger
- Division of Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Roland Croner
- Department of General, Visceral, Vascular and Transplant Surgery, University Hospital Magdeburg, Otto-von-Guericke-University, Magdeburg, Germany
| | - Vera S Schellerer
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Christoph Becker
- Department of Medicine I, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Arndt Hartmann
- Department of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Thomas Tüting
- Laboratory of Experimental Dermatology, Department of Dermatology, University Hospital and Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke-University, Magdeburg, Germany
| | - Olaf Prante
- Department of Nuclear Medicine, Molecular Imaging and Radiochemistry, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Robert Grützmann
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Sergei I Grivennikov
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Michael Stürzl
- Division of Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Nathalie Britzen-Laurent
- Division of Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany; Division of Surgical Research, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
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18
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Baralić M, Pažitná L, Brković V, Laušević M, Gligorijević N, Katrlík J, Nedić O, Robajac D. Prediction of Mortality in Patients on Peritoneal Dialysis Based on the Fibrinogen Mannosylation. Cells 2023; 12:cells12030351. [PMID: 36766693 PMCID: PMC9913213 DOI: 10.3390/cells12030351] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
As we already reported, fibrinogen fucosylation emerged as a prognostic marker of peritoneal membrane function in end-stage renal disease (ESRD) patients on peritoneal dialysis. After a follow-up period of 18 months, we estimated the ability of employed lectins, as well as other biochemical parameters, to serve as mortality predictors in these patients. Following a univariate Cox regression analysis, ferritin, urea clearance, residual diuresis, hyperglycemia, and an increase in the signal intensity obtained with Galanthus nivalis lectin (GNL) emerged as potential mortality predictors, but additional multivariate Cox regression analysis pointed only to glucose concentration and GNL as mortality predictors. Higher signal intensity obtained with GNL in patients that died suggested the importance of paucimannosidic/highly mannosidic N-glycan structures on fibrinogen as factors that are related to unwanted cardiovascular events and all-cause mortality and can possibly be seen as a prediction tool. Altered glycan structures composed of mannose residues are expected to affect the reactivity of mannosylated glycoproteins with mannose-binding lectin and possibly the entire cascade of events linked to this lectin. Since patients with ESRD are prone to cardiovascular complications and the formation of atherosclerotic plaques, one can hypothesize that fibrinogen with increasingly exposed mannose residues may contribute to the unwanted events.
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Affiliation(s)
- Marko Baralić
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Clinic of Nephrology, University Clinical Centre of Serbia, 11000 Belgrade, Serbia
| | - Lucia Pažitná
- Institute of Chemistry, Slovak Academy of Sciences, 84538 Bratislava, Slovakia
| | - Voin Brković
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Clinic of Nephrology, University Clinical Centre of Serbia, 11000 Belgrade, Serbia
| | - Mirjana Laušević
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Clinic of Nephrology, University Clinical Centre of Serbia, 11000 Belgrade, Serbia
| | - Nikola Gligorijević
- Institute for the Application of Nuclear Energy (INEP), University of Belgrade, 11080 Belgrade, Serbia
| | - Jaroslav Katrlík
- Institute of Chemistry, Slovak Academy of Sciences, 84538 Bratislava, Slovakia
| | - Olgica Nedić
- Institute for the Application of Nuclear Energy (INEP), University of Belgrade, 11080 Belgrade, Serbia
| | - Dragana Robajac
- Institute for the Application of Nuclear Energy (INEP), University of Belgrade, 11080 Belgrade, Serbia
- Correspondence:
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19
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Chen M, Assis DM, Benet M, McClung CM, Gordon EA, Ghose S, Dupard SJ, Willetts M, Taron CH, Samuelson JC. Comparative site-specific N-glycoproteome analysis reveals aberrant N-glycosylation and gives insights into mannose-6-phosphate pathway in cancer. Commun Biol 2023; 6:48. [PMID: 36639722 PMCID: PMC9839730 DOI: 10.1038/s42003-023-04439-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
N-glycosylation is implicated in cancers and aberrant N-glycosylation is recognized as a hallmark of cancer. Here, we mapped and compared the site-specific N-glycoproteomes of colon cancer HCT116 cells and isogenic non-tumorigenic DNMT1/3b double knockout (DKO1) cells using Fbs1-GYR N-glycopeptide enrichment technology and trapped ion mobility spectrometry. Many significant changes in site-specific N-glycosylation were revealed, providing a molecular basis for further elucidation of the role of N-glycosylation in protein function. HCT116 cells display hypersialylation especially in cell surface membrane proteins. Both HCT116 and DKO1 show an abundance of paucimannose and 80% of paucimannose-rich proteins are annotated to reside in exosomes. The most striking N-glycosylation alteration was the degree of mannose-6-phosphate (M6P) modification. N-glycoproteomic analyses revealed that HCT116 displays hyper-M6P modification, which was orthogonally validated by M6P immunodetection. Significant observed differences in N-glycosylation patterns of the major M6P receptor, CI-MPR in HCT116 and DKO1 may contribute to the hyper-M6P phenotype of HCT116 cells. This comparative site-specific N-glycoproteome analysis provides a pool of potential N-glycosylation-related cancer biomarkers, but also gives insights into the M6P pathway in cancer.
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Affiliation(s)
- Minyong Chen
- grid.273406.40000 0004 0376 1796New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
| | - Diego M. Assis
- grid.423270.00000 0004 0491 2576Bruker, 40 Manning Road, Billerica, MA 01821 USA
| | - Matthieu Benet
- grid.273406.40000 0004 0376 1796New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
| | - Colleen M. McClung
- grid.273406.40000 0004 0376 1796New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
| | - Elizabeth A. Gordon
- grid.423270.00000 0004 0491 2576Bruker, 40 Manning Road, Billerica, MA 01821 USA
| | - Shourjo Ghose
- grid.423270.00000 0004 0491 2576Bruker, 40 Manning Road, Billerica, MA 01821 USA
| | - Steven J. Dupard
- grid.273406.40000 0004 0376 1796New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
| | - Matthew Willetts
- grid.423270.00000 0004 0491 2576Bruker, 40 Manning Road, Billerica, MA 01821 USA
| | - Christopher H. Taron
- grid.273406.40000 0004 0376 1796New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
| | - James C. Samuelson
- grid.273406.40000 0004 0376 1796New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
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20
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Guo Y, Liu B, Huang T, Qi X, Li S. HOTAIR modulates hepatocellular carcinoma progression by activating FUT8/core-fucosylated Hsp90/MUC1/STAT3 feedback loop via JAK1/STAT3 cascade. Dig Liver Dis 2023; 55:113-122. [PMID: 35504805 DOI: 10.1016/j.dld.2022.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/22/2022] [Accepted: 04/13/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND Glycosylation exhibits crucial effect on hepatocellular carcinoma (HCC) progression. Long non-coding RNAs (lncRNAs) are involved in multilevel regulation of gene transcription during tumor development. The purpose of this study is to clarify the potential mechanism that HOTAIR modulates hepatocellular carcinoma progression by activating FUT8/core-fucosylated Hsp90/MUC1/STAT3 feedback loop via JAK1/STAT3 cascade. METHODS qRT-PCR was used to show the differential expression of genes. Functional experiments were used to measure the malignancy of HCC cells. ChIP and co-IP assays showed the directly interaction of the key molecules. Xenografts was conducted to show the in vivo effects. RESULTS Upregulation of FUT8 showed closely correlation with HCC progression. Core-fucosylation of Hsp90 stabilized MUC1 binding to the downstream p-STAT3, which involved in the activation of JAK1/STAT3 cascade. STAT3 was identified as the regulator of FUT8 and MUC1 transcription, while FUT8 and MUC1 impacted STAT3 level both in nuclear and cytoplasm. HOTAIR recruited P300 to efficiently bind with STAT3. The transcript complex co-modulated the transcrption of FUT8 and MUC1. Moreover, highly HOTAIR expression also exhibited closely correlation with HCC progression. CONCLUSIONS FUT8 triggered core-fucosylated-Hsp90/MUC1/P300-HOTAIR-STAT3 cascade via JAK1/STAT3 pathway, which exhibited as positive feedback loop during HCC progression.
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Affiliation(s)
- Yanru Guo
- Department of Clinical Laboratory, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116011, China
| | - Bing Liu
- College of Laboratory Medicine, Dalian Medical University, Dalian, Liaoning 116044, China
| | - Tong Huang
- College of Laboratory Medicine, Dalian Medical University, Dalian, Liaoning 116044, China
| | - Xia Qi
- College of Laboratory Medicine, Dalian Medical University, Dalian, Liaoning 116044, China
| | - Shijun Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116011, China; College of Laboratory Medicine, Dalian Medical University, Dalian, Liaoning 116044, China.
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21
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Huang C, Hou M, Yan J, Wang H, Wang Y, Cao C, Wang Y, Gao H, Ma X, Zheng Y, Bu D, Chai W, Li Y, Sun S. GIPS-Mix for Accurate Identification of Isomeric Components in Glycan Mixtures Using Intelligent Group-Opting Strategy. Anal Chem 2022; 95:811-819. [PMID: 36547394 PMCID: PMC9850354 DOI: 10.1021/acs.analchem.2c02978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Accurate identification of glycan structures is highly desirable as they are intimately linked to their different functions. However, glycan samples generally exist as mixtures with multiple isomeric structures, making assignment of individual glycan components very challenging, even with the aid of multistage mass spectrometry (MSn). Here, we present an approach, GIPS-mix, for assignment of isomeric glycans within a mixture using an intelligent group-opting strategy. Our approach enumerates all possible combinations (groupings) of candidate glycans and opts in the best-matched glycan group(s) based on the similarity between the simulated spectra of each glycan group and the acquired experimental spectra of the mixture. In the case that a single group could not be elected, a tie break is performed by additional MSn scanning using intelligently selected precursors. With 11 standard mixtures and 6 human milk oligosaccharide fractions, we demonstrate the application of GIPS-mix in assignment of individual glycans in mixtures with high accuracy and efficiency.
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Affiliation(s)
- Chuncui Huang
- Institute
of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing100101, China
| | - Meijie Hou
- Key
Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing100080, China,University
of Chinese Academy of Sciences, 19 Yuquan Road, Beijing100049, China
| | - Jingyu Yan
- Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Key Laboratory of Separation Science
for Analytical Chemistry, Dalian116023, China
| | - Hui Wang
- Key
Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing100080, China,University
of Chinese Academy of Sciences, 19 Yuquan Road, Beijing100049, China
| | - Yu Wang
- Key
Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing100080, China,University
of Chinese Academy of Sciences, 19 Yuquan Road, Beijing100049, China
| | - Cuiyan Cao
- Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Key Laboratory of Separation Science
for Analytical Chemistry, Dalian116023, China
| | - Yaojun Wang
- College
of Information and Electrical Engineering, China Agricultural University, Beijing100083, China
| | - Huanyu Gao
- Institute
of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing100101, China
| | - Xinyue Ma
- Institute
of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing100101, China,University
of Chinese Academy of Sciences, 19 Yuquan Road, Beijing100049, China
| | - Yi Zheng
- Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Key Laboratory of Separation Science
for Analytical Chemistry, Dalian116023, China
| | - Dongbo Bu
- Key
Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing100080, China,University
of Chinese Academy of Sciences, 19 Yuquan Road, Beijing100049, China
| | - Wengang Chai
- Glycosciences
Laboratory, Department of Medicine, Imperial
College London, LondonW12 0NN, United Kingdom,
| | - Yan Li
- Institute
of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing100101, China,University
of Chinese Academy of Sciences, 19 Yuquan Road, Beijing100049, China,
| | - Shiwei Sun
- Key
Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing100080, China,University
of Chinese Academy of Sciences, 19 Yuquan Road, Beijing100049, China,
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22
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Lyman DF, Bell A, Black A, Dingerdissen H, Cauley E, Gogate N, Liu D, Joseph A, Kahsay R, Crichton DJ, Mehta A, Mazumder R. Modeling and integration of N-glycan biomarkers in a comprehensive biomarker data model. Glycobiology 2022; 32:855-870. [PMID: 35925813 PMCID: PMC9487899 DOI: 10.1093/glycob/cwac046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Molecular biomarkers measure discrete components of biological processes that can contribute to disorders when impaired. Great interest exists in discovering early cancer biomarkers to improve outcomes. Biomarkers represented in a standardized data model, integrated with multi-omics data, may improve understanding and use of novel biomarkers such as glycans and glycoconjugates. Among altered components in tumorigenesis, N-glycans exhibit substantial biomarker potential, when analyzed with their protein carriers. However, such data are distributed across publications and databases of diverse formats, which hampers their use in research and clinical application. Mass spectrometry measures of fifty N-glycans, on seven serum proteins in liver disease, were integrated (as a panel) into a cancer biomarker data model, providing a unique identifier, standard nomenclature, links to glycan resources, and accession and ontology annotations to standard protein, gene, disease, and biomarker information. Data provenance was documented with a standardized FDA-supported BioCompute Object. Using the biomarker data model allows capture of granular information, such as glycans with different levels of abundance in cirrhosis, hepatocellular carcinoma, and transplant groups. Such representation in a standardized data model harmonizes glycomics data in a unified framework, making glycan-protein biomarker data exploration more available to investigators and to other data resources. The biomarker data model we describe can be used by researchers to describe their novel glycan and glycoconjugate biomarkers, can integrate N-glycan biomarker data with multi-source biomedical data, and can foster discovery and insight within a unified data framework for glycan biomarker representation thereby making the data FAIR (Findable, Accessible, Interoperable, Reusable) (https://www.go-fair.org/fair-principles/).
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Affiliation(s)
- Daniel F Lyman
- The Department of Biochemistry & Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, United States of America
| | - Amanda Bell
- The Department of Biochemistry & Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, United States of America
| | - Alyson Black
- The Department of Cell & Molecular Pharmacology, The Medical University of South Carolina, Charleston, SC, 29403, United States of America
| | - Hayley Dingerdissen
- The Department of Biochemistry & Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, United States of America
| | - Edmund Cauley
- The Department of Biochemistry & Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, United States of America.,The McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, United States of America
| | - Nikhita Gogate
- The Department of Biochemistry & Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, United States of America
| | - David Liu
- NASA Jet Propulsion Laboratory, Pasadena, CA 91109, United States of America
| | - Ashia Joseph
- The Department of Biochemistry & Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, United States of America
| | - Robel Kahsay
- The Department of Biochemistry & Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, United States of America
| | - Daniel J Crichton
- NASA Jet Propulsion Laboratory, Pasadena, CA 91109, United States of America
| | - Anand Mehta
- The Department of Cell & Molecular Pharmacology, The Medical University of South Carolina, Charleston, SC, 29403, United States of America
| | - Raja Mazumder
- The Department of Biochemistry & Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, United States of America.,The McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, United States of America
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23
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Loponte HF, Oliveira IA, Rodrigues BC, Nunes-da-Fonseca R, Mohana-Borges R, Alisson-Silva F, Dias WB, Todeschini AR. Hyperglycemia alters N-glycans on colon cancer cells through increased production of activated monosaccharides. Glycoconj J 2022; 39:663-675. [PMID: 35380345 DOI: 10.1007/s10719-022-10057-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/26/2022] [Accepted: 03/09/2022] [Indexed: 12/01/2022]
Abstract
Diabetes Mellitus (DM) is both, correlated and a known risk factor for colorectal cancer (CRC). Besides favoring the incidence of CRC, DM also accelerates its progression, worsening its prognosis. Previously, hyperglycemia, the DM hallmark, has been shown to lead to aberrant glycosylation of CRC cells, heightening their malignancy both in vivo and in vitro. Here we use mass spectrometry to elucidate the composition and putative structures of N-glycans expressed by MC38 cultured in normoglycemic (LG) and hyperglycemic-like conditions (HG). N-glycans, 67, were identified in MC38 cells cultured in LG and HG. The cells grown in HG showed a greater abundance of N-glycans when compared to LNG cells, without changes in the proportion of sialylated, fucosylated and mannosylated N-glycans. Among the identified N-glycans, 16 were differentially expressed, mostly mannosylated and fucosylated, with a minority of them being sialylated. Metabolomics analysis indicates that the alterations observed in the N-glycosylation may be mostly due to increase of the activated monosaccharides pool, through an increased glucose entrance into the cells. The alterations found here corroborate data from the literature regarding the progression of CRC, advocating for development or repositioning of effective treatments against CRC in diabetic patients.
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Affiliation(s)
- H F Loponte
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil.,Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil
| | - I A Oliveira
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil
| | - B C Rodrigues
- Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, 27965‑550, Macaé, Brazil
| | - R Nunes-da-Fonseca
- Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, 27965‑550, Macaé, Brazil
| | - R Mohana-Borges
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil
| | - F Alisson-Silva
- Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil
| | - W B Dias
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil
| | - A R Todeschini
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil.
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24
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Boyaval F, Dalebout H, Van Zeijl R, Wang W, Fariña-Sarasqueta A, Lageveen-Kammeijer GSM, Boonstra JJ, McDonnell LA, Wuhrer M, Morreau H, Heijs B. High-Mannose N-Glycans as Malignant Progression Markers in Early-Stage Colorectal Cancer. Cancers (Basel) 2022; 14:1552. [PMID: 35326703 PMCID: PMC8945895 DOI: 10.3390/cancers14061552] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/09/2022] [Accepted: 03/16/2022] [Indexed: 02/05/2023] Open
Abstract
The increase incidence of early colorectal cancer (T1 CRC) last years is mainly due to the introduction of population-based screening for CRC. T1 CRC staging based on histological criteria remains challenging and there is high variability among pathologists in the scoring of these criteria. It is crucial to unravel the biology behind the progression of adenoma into T1 CRC. Glycomic studies have reported extensively on alterations of the N-glycomic pattern in CRC; therefore, investigating these alterations may reveal new insights into the development of T1 CRC. We used matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) to spatially profile the N-glycan species in a cohort of pT1 CRC using archival formalin-fixed and paraffin-embedded (FFPE) material. To generate structural information on the observed N-glycans, CE-ESI-MS/MS was used in conjunction with MALDI-MSI. Relative intensities and glycosylation traits were calculated based on a panel of 58 N-glycans. Our analysis showed pronounced differences between normal epithelium, dysplastic, and carcinoma regions. High-mannose-type N-glycans were higher in the dysplastic region than in carcinoma, which correlates to increased proliferation of the cells. We observed changes in the cancer invasive front, including higher expression of α2,3-linked sialic acids which followed the glycosylation pattern of the carcinoma region.
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Affiliation(s)
- Fanny Boyaval
- Department of Pathology, Leiden University Medical Center, Albinusdreef, 2333 ZA Leiden, The Netherlands;
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Albinusdreef, 2333 ZA Leiden, The Netherlands; (H.D.); (R.V.Z.); (W.W.); (G.S.M.L.-K.); (M.W.)
| | - Hans Dalebout
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Albinusdreef, 2333 ZA Leiden, The Netherlands; (H.D.); (R.V.Z.); (W.W.); (G.S.M.L.-K.); (M.W.)
| | - René Van Zeijl
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Albinusdreef, 2333 ZA Leiden, The Netherlands; (H.D.); (R.V.Z.); (W.W.); (G.S.M.L.-K.); (M.W.)
| | - Wenjun Wang
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Albinusdreef, 2333 ZA Leiden, The Netherlands; (H.D.); (R.V.Z.); (W.W.); (G.S.M.L.-K.); (M.W.)
| | - Arantza Fariña-Sarasqueta
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands;
| | - Guinevere S. M. Lageveen-Kammeijer
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Albinusdreef, 2333 ZA Leiden, The Netherlands; (H.D.); (R.V.Z.); (W.W.); (G.S.M.L.-K.); (M.W.)
| | - Jurjen J. Boonstra
- Department of Gastroenterology and Hepatology, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands;
| | - Liam A. McDonnell
- Fondazione Pisana per la Scienza ONLUS, Via Ferruccio Giovannini, 56017 San Giuliano Terme, Italy;
| | - Manfred Wuhrer
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Albinusdreef, 2333 ZA Leiden, The Netherlands; (H.D.); (R.V.Z.); (W.W.); (G.S.M.L.-K.); (M.W.)
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Albinusdreef, 2333 ZA Leiden, The Netherlands;
| | - Bram Heijs
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Albinusdreef, 2333 ZA Leiden, The Netherlands; (H.D.); (R.V.Z.); (W.W.); (G.S.M.L.-K.); (M.W.)
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25
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Sheng Y, Vinjamuri A, Alvarez MRS, Xie Y, McGrath M, Chen S, Barboza M, Frieman M, Lebrilla CB. Host Cell Glycocalyx Remodeling Reveals SARS-CoV-2 Spike Protein Glycomic Binding Sites. Front Mol Biosci 2022; 9:799703. [PMID: 35372520 PMCID: PMC8964299 DOI: 10.3389/fmolb.2022.799703] [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: 10/21/2021] [Accepted: 01/31/2022] [Indexed: 12/12/2022] Open
Abstract
Glycans on the host cell membrane and viral proteins play critical roles in pathogenesis. Highly glycosylated epithelial cells represent the primary boundary separating embedded host tissues from pathogens within the respiratory and intestinal tracts. SARS-CoV-2, the causative agent for the COVID-19 pandemic, reaches into the respiratory tract. We found purified human milk oligosaccharides (HMOs) inhibited the viral binding on cells. Spike (S) protein receptor binding domain (RBD) binding to host cells were partly blocked by co-incubation with exogenous HMOs, most by 2-6-sialyl-lactose (6'SL), supporting the notion that HMOs can function as decoys in defense against SARS-Cov2. To investigate the effect of host cell glycocalyx on viral adherence, we metabolically modified and confirmed with glycomic methods the cell surface glycome to enrich specific N-glycan types including those containing sialic acids, fucose, mannose, and terminal galactose. Additionally, Immunofluorescence studies demonstrated that the S protein preferentially binds to terminal sialic acids with α-(2,6)-linkages. Furthermore, site-specific glycosylation of S protein RBD and its human receptor ACE2 were characterized using LC-MS/MS. We then performed molecular dynamics calculations on the interaction complex to further explore the interactive complex between ACE2 and the S protein. The results showed that hydrogen bonds mediated the interactions between ACE2 glycans and S protein with desialylated glycans forming significantly fewer hydrogen bonds. These results supported a mechanism where the virus binds initially to glycans on host cells preferring α-(2,6)-sialic acids and finds ACE2 and with the proper orientation infects the cell.
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Affiliation(s)
- Ying Sheng
- Department of Chemistry, University of California, Davis, Davis, CA, United States
- The Biochemistry, Molecular, Cellular and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, Davis, CA, United States
| | - Anita Vinjamuri
- Department of Chemistry, University of California, Davis, Davis, CA, United States
| | | | - Yixuan Xie
- Department of Chemistry, University of California, Davis, Davis, CA, United States
| | - Marisa McGrath
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Siyu Chen
- Department of Chemistry, University of California, Davis, Davis, CA, United States
| | - Mariana Barboza
- Department of Chemistry, University of California, Davis, Davis, CA, United States
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Matthew Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, Davis, CA, United States
- The Biochemistry, Molecular, Cellular and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, Davis, CA, United States
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26
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Rosa-Fernandes L, Oba-Shinjo SM, Macedo-da-Silva J, Marie SKN, Palmisano G. Aberrant Protein Glycosylation in Brain Cancers, with Emphasis on Glioblastoma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1382:39-70. [DOI: 10.1007/978-3-031-05460-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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27
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Sanda M, Ahn J, Kozlik P, Goldman R. Analysis of site and structure specific core fucosylation in liver cirrhosis using exoglycosidase-assisted data-independent LC-MS/MS. Sci Rep 2021; 11:23273. [PMID: 34857845 PMCID: PMC8639754 DOI: 10.1038/s41598-021-02838-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 11/03/2021] [Indexed: 12/16/2022] Open
Abstract
Carbohydrates form one of the major groups of biological macromolecules in living organisms. Many biological processes including protein folding, stability, immune response, and receptor activation are regulated by glycosylation. Fucosylation of proteins regulates such processes and is associated with various diseases including autoimmunity and cancer. Mass spectrometry efficiently identifies structures of fucosylated glycans or sites of core fucosylated N-glycopeptides but quantification of the glycopeptides remains less explored. We performed experiments that facilitate quantitative analysis of the core fucosylation of proteins with partial structural resolution of the glycans and we present results of the mass spectrometric SWATH-type DIA analysis of relative abundances of the core fucosylated glycoforms of 45 glycopeptides to their nonfucosylated glycoforms derived from 18 serum proteins in liver disease of different etiologies. Our results show that a combination of soft fragmentation with exoglycosidases is efficient at the assignment and quantification of the core fucosylated N-glycoforms at specific sites of protein attachment. In addition, our results show that disease-associated changes in core fucosylation are peptide-dependent and further differ by branching of the core fucosylated glycans. Further studies are needed to verify whether tri- and tetra-antennary core fucosylated glycopeptides could be used as markers of liver disease progression.
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Affiliation(s)
- Miloslav Sanda
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA. .,Clinical and Translational Glycoscience Research Center, Georgetown University, Washington, DC, 20057, USA.
| | - Jaeil Ahn
- Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University Medical Center, Washington, DC, 20057, USA
| | - Petr Kozlik
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Radoslav Goldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA.,Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, 20057, USA.,Clinical and Translational Glycoscience Research Center, Georgetown University, Washington, DC, 20057, USA
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28
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Gong Y, Qin S, Dai L, Tian Z. The glycosylation in SARS-CoV-2 and its receptor ACE2. Signal Transduct Target Ther 2021; 6:396. [PMID: 34782609 PMCID: PMC8591162 DOI: 10.1038/s41392-021-00809-8] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/10/2021] [Accepted: 10/24/2021] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), a highly infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 235 million individuals and led to more than 4.8 million deaths worldwide as of October 5 2021. Cryo-electron microscopy and topology show that the SARS-CoV-2 genome encodes lots of highly glycosylated proteins, such as spike (S), envelope (E), membrane (M), and ORF3a proteins, which are responsible for host recognition, penetration, binding, recycling and pathogenesis. Here we reviewed the detections, substrates, biological functions of the glycosylation in SARS-CoV-2 proteins as well as the human receptor ACE2, and also summarized the approved and undergoing SARS-CoV-2 therapeutics associated with glycosylation. This review may not only broad the understanding of viral glycobiology, but also provide key clues for the development of new preventive and therapeutic methodologies against SARS-CoV-2 and its variants.
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Affiliation(s)
- Yanqiu Gong
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China
| | - Suideng Qin
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China.
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The Cancer-Associated Antigens Sialyl Lewis a/x and Sd a: Two Opposite Faces of Terminal Glycosylation. Cancers (Basel) 2021; 13:cancers13215273. [PMID: 34771437 PMCID: PMC8582462 DOI: 10.3390/cancers13215273] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/11/2021] [Accepted: 10/19/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The glycosyltransferase β1,4-N-acetylgalactosaminyltransferae 2 (B4GALNT2), product of the B4GALNT2 gene is responsible for the biosynthesis of the carbohydrate antigen Sda. Both the enzyme and its cognate antigen display a restricted pattern of tissue expression and modulation in colorectal, gastric, and mammary cancers. In colorectal cancer, B4GALNT2 is generally downregulated, but patients displaying higher expression survive longer. The sialyl Lewisa and sialyl Lewisx antigens are associated with malignancy. Their biosynthesis and that of Sda are mutually exclusive. Forced expression of B4GALNT2 in colorectal cancer cell lines modulates the transcriptome towards lower malignancy, reducing stemness. These effects are independent of B4GALNT2-induced sLea/sLex inhibition. Thus, B4GALNT2 is a marker of better prognosis and a cancer-restraining enzyme in colorectal cancer, with a therapeutic potential. Abstract Terminal carbohydrate structures are particularly relevant in oncology because they can serve as cancer markers and alter the phenotype of cancer cells. The Sda antigen and the sialyl Lewisx and sialyl Lewisa (sLex and sLea) antigens are terminal structures whose biosynthesis is mutually exclusive. In this review, we describe the main features of the Sda antigen in cancer and its relationship with sLex/a antigens. Information was obtained from an extensive literature search and from The Cancer Genome Atlas (TCGA) public database. The Sda biosynthetic enzyme B4GALNT2 undergoes downregulation in colorectal (CRC) and stomach cancer, while it is ectopically expressed by a minority of breast cancer (BRCA) patients. High expression of B4GALNT2 is associated with better prognosis and a less malignant gene expression profile in CRC, while the opposite occurs in BRCA. The regulation of B4GALNT2 expression in CRC is multifactorial, involving gene methylation and miRNA expression. Forced expression of B4GALNT2 inhibited sLea/sLex and reduced malignancy and stemness in cells constitutively expressing sLex/a antigens. However, consistent effects were observed upon B4GALNT2 forced expression and in cells not expressing sLex/a antigens. Thus, B4GALNT2 and the Sda antigen exert a tumor-restraining activity in CRC and probably other gastrointestinal cancers, independently of sLex/a antigens.
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Differential Glycosylation Levels in Saliva from Patients with Lung or Breast Cancer: A Preliminary Assessment for Early Diagnostic Purposes. Metabolites 2021; 11:metabo11090566. [PMID: 34564382 PMCID: PMC8471868 DOI: 10.3390/metabo11090566] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 12/27/2022] Open
Abstract
Glycans play a fundamental role in several biological processes, such as cell-cell adhesion, signaling, and recognition. Similarly, abnormal glycosylation is involved in many pathological processes, among which include tumor growth and progression. Several highly glycosylated proteins found in blood are currently used in clinical practice as cancer biomarkers (e.g., CA125, PSA, and CA19-9). The development of novel non-invasive diagnostic procedures would greatly simplify the screening and discovery of pathologies at an early stage, thus also allowing for simpler treatment and a higher success rate. In this observational study carried out on 68 subjects diagnosed with either breast or lung cancer and 34 healthy volunteers, we hydrolyzed the glycoproteins in saliva and quantified the obtained free sugars (fucose, mannose, galactose, glucosamine, and galactosamine) by using high-performance anion-exchange chromatography with pulsed-amperometric detection (HPAEC-PAD). The glycosidic profiles were compared by using multivariate statistical analysis, showing differential glycosylation patterns among the three categories. Furthermore, Receiver Operating Characteristics (ROC) analysis allowed obtaining a reliable and minimally invasive protocol able to discriminate between healthy and pathological subjects.
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31
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Tikhonov A, Smoldovskaya O, Feyzkhanova G, Kushlinskii N, Rubina A. Glycan-specific antibodies as potential cancer biomarkers: a focus on microarray applications. Clin Chem Lab Med 2021; 58:1611-1622. [PMID: 32324152 DOI: 10.1515/cclm-2019-1161] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 03/10/2020] [Indexed: 02/06/2023]
Abstract
Glycosylation is one of the most common posttranslational modifications of proteins and lipids. In the case of tumors, cell transformation accompanied by aberrant glycosylation results in the expression of tumor-associated glycans that promote tumor invasion. As part of the innate immunity, anti-glycan antibodies recognize tumor-associated glycans, and these antibodies can be present in the bloodstream in the early stages of cancer. Recently, anti-glycan antibody profiles have been of interest in various cancer studies. Novel advantages in the field of analytical techniques have simplified the analysis of anti-glycan antibodies and made it easier to have more comprehensive knowledge about their functions. One of the robust approaches for studying anti-glycan antibodies engages in microarray technology. The analysis of glycan microarrays can provide more expanded information to simultaneously specify or suggest the role of antibodies to a wide variety of glycans in the progression of different diseases, therefore making it possible to identify new biomarkers for diagnosing cancer and/or the state of the disease. Thus, in this review, we discuss antibodies to various glycans, their application for diagnosing cancer and one of the most promising tools for the investigation of these molecules, microarrays.
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Affiliation(s)
- Aleksei Tikhonov
- Laboratory of Biological Microchips, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga Smoldovskaya
- Laboratory of Biological Microchips, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Guzel Feyzkhanova
- Laboratory of Biological Microchips, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay Kushlinskii
- Laboratory of Clinical Biochemistry, Federal State Budgetary Institution «N.N. Blokhin National Medical Research Center of Oncology» оf the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Alla Rubina
- Laboratory of Biological Microchips, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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32
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García-García A, Serna S, Yang Z, Delso I, Taleb V, Hicks T, Artschwager R, Vakhrushev SY, Clausen H, Angulo J, Corzana F, Reichardt NC, Hurtado-Guerrero R. FUT8-Directed Core Fucosylation of N-glycans Is Regulated by the Glycan Structure and Protein Environment. ACS Catal 2021; 11:9052-9065. [PMID: 35662980 PMCID: PMC9161449 DOI: 10.1021/acscatal.1c01698] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/24/2021] [Indexed: 12/17/2022]
Abstract
FUT8 is an essential α-1,6-fucosyltransferase that fucosylates the innermost GlcNAc of N-glycans, a process called core fucosylation. In vitro, FUT8 exhibits substrate preference for the biantennary complex N-glycan oligosaccharide (G0), but the role of the underlying protein/peptide to which N-glycans are attached remains unclear. Here, we explored the FUT8 enzyme with a series of N-glycan oligosaccharides, N-glycopeptides, and an Asn-linked oligosaccharide. We found that the underlying peptide plays a role in fucosylation of paucimannose (low mannose) and high-mannose N-glycans but not for complex-type N-glycans. Using saturation transfer difference (STD) NMR spectroscopy, we demonstrate that FUT8 recognizes all sugar units of the G0 N-glycan and most of the amino acid residues (Asn-X-Thr) that serve as a recognition sequon for the oligosaccharyltransferase (OST). The largest STD signals were observed in the presence of GDP, suggesting that prior FUT8 binding to GDP-β-l-fucose (GDP-Fuc) is required for an optimal recognition of N-glycans. We applied genetic engineering of glycosylation capacities in CHO cells to evaluate FUT8 core fucosylation of high-mannose and complex-type N-glycans in cells with a panel of well-characterized therapeutic N-glycoproteins. This confirmed that core fucosylation mainly occurs on complex-type N-glycans, although clearly only at selected glycosites. Eliminating the capacity for complex-type glycosylation in cells (KO mgat1) revealed that glycosites with complex-type N-glycans when converted to high mannose lost the core Fuc. Interestingly, however, for erythropoietin that is uncommon among the tested glycoproteins in efficiently acquiring tetra-antennary N-glycans, two out of three N-glycosites obtained Fuc on the high-mannose N-glycans. An examination of the N-glycosylation sites of several protein crystal structures indicates that core fucosylation is mostly affected by the accessibility and nature of the N-glycan and not by the nature of the underlying peptide sequence. These data have further elucidated the different FUT8 acceptor substrate specificities both in vitro and in vivo in cells, revealing different mechanisms for promoting core fucosylation.
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Affiliation(s)
- Ana García-García
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza 50018, Spain
| | - Sonia Serna
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramón 182, Donostia San Sebastián 20014, Spain
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Ignacio Delso
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Víctor Taleb
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza 50018, Spain
| | - Thomas Hicks
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Raik Artschwager
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramón 182, Donostia San Sebastián 20014, Spain
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Jesús Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.,Departamento de Química Orgánica, Universidad de Sevilla, Sevilla 41012, Spain.,Instituto de Investigaciones Químicas (CSIC-US), Avda. Américo Vespucio, 49, Seville 41092, Spain
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, Logroño E-26006, Spain
| | - Niels C Reichardt
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramón 182, Donostia San Sebastián 20014, Spain.,CIBER-BBN, Paseo Miramón 182, San Sebastian 20014, Spain
| | - Ramon Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza 50018, Spain.,Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark.,Fundación ARAID, Zaragoza 50018, Spain
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33
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Huang J, Jiang B, Liu M, Yang P, Cao W. gQuant, an Automated Tool for Quantitative Glycomic Data Analysis. Front Chem 2021; 9:707738. [PMID: 34395380 PMCID: PMC8355585 DOI: 10.3389/fchem.2021.707738] [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: 05/10/2021] [Accepted: 07/15/2021] [Indexed: 11/25/2022] Open
Abstract
MALDI-MS-based glycan isotope labeling methods have been effectively and widely used for quantitative glycomics. However, interpretation of the data produced by MALDI-MS is inaccurate and tedious because the bioinformatic tools are inadequate. In this work, we present gQuant, an automated tool for MALDI-MS-based glycan isotope labeling data processing. gQuant was designed with a set of dedicated algorithms to improve the efficiency, accuracy and convenience of quantitation data processing. When tested on the reference data set, gQuant showed a fast processing speed, as it was able to search the glycan data of model glycoproteins in a few minutes and reported more results than the manual analysis did. The reported quantitation ratios matched well with the experimental glycan mixture ratios ranging from 1:10 to 10:1. In addition, gQuant is fully open-source and is coded in Python, which is supported by most operating systems, and it has a user-friendly interface. gQuant can be easily adapted by users for specific experimental designs, such as specific glycan databases, different derivatization types and relative quantitation designs and can thus facilitate fast glycomic quantitation for clinical sample analysis using MALDI-MS-based stable isotope labeling.
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Affiliation(s)
- Jiangming Huang
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
| | - Biyun Jiang
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Mingqi Liu
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Pengyuan Yang
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
| | - Weiqian Cao
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
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34
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A semi-automated, high throughput approach for O-glycosylation profiling of in vitro established cancer cell lines by MALDI-FT-ICR MS. Glycoconj J 2021; 38:747-756. [PMID: 34283362 PMCID: PMC8821499 DOI: 10.1007/s10719-021-10003-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/04/2021] [Accepted: 06/02/2021] [Indexed: 12/30/2022]
Abstract
The study of protein O-glycosylation is important in biological research as O-glycans have been reported to regulate a multitude of molecular and cell biology processes occurring in cancer. It is known that alterations in O-glycosylation are involved in the development and progression of cancer. Their easy accessibility makes in vitro established cell lines suitable and useful models for studying biological mechanisms in disease. However, the O-glycosylation analysis of large numbers of samples, as required in systems biology and biomarker discovery studies, is often challenging. In the present study, O-glycans from three human colorectal cancer cell lines and two human pancreatic cancer cell lines were released by semi-automated, high throughput reductive β-elimination and analysed using ultrahigh resolution MALDI-FT-ICR MS. Automated data integration and processing was performed using MassyTools, where the analyte was automatically included for relative quantitation based on a range of selection criteria including signal-to-noise ratio, mass error and isotopic pattern quality scores. A total of 126 O-glycan compositions, ranging from a single monosaccharide to large oligosaccharides exhibiting complex glycan motifs, were detected. The use of ultrahigh resolution MALDI-FTICR MS enabled glycan identification and quantitation in the matrix region of the spectrum. This approach has the potential to be used for O-glycosylation analysis of large numbers of samples, such as patient sample cohorts.
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35
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Zhang R, Yang Q, Boruah BM, Zong G, Li C, Chapla D, Yang JY, Moremen KW, Wang LX. Appropriate aglycone modification significantly expands the glycan substrate acceptability of α1,6-fucosyltransferase (FUT8). Biochem J 2021; 478:1571-1583. [PMID: 33734311 PMCID: PMC8062310 DOI: 10.1042/bcj20210138] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 12/16/2022]
Abstract
The α1,6-fucosyltransferase, FUT8, is the sole enzyme catalyzing the core-fucosylation of N-glycoproteins in mammalian systems. Previous studies using free N-glycans as acceptor substrates indicated that a terminal β1,2-GlcNAc moiety on the Man-α1,3-Man arm of N-glycan substrates is required for efficient FUT8-catalyzed core-fucosylation. In contrast, we recently demonstrated that, in a proper protein context, FUT8 could also fucosylate Man5GlcNAc2 without a GlcNAc at the non-reducing end. We describe here a further study of the substrate specificity of FUT8 using a range of N-glycans containing different aglycones. We found that FUT8 could fucosylate most of high-mannose and complex-type N-glycans, including highly branched N-glycans from chicken ovalbumin, when the aglycone moiety is modified with a 9-fluorenylmethyloxycarbonyl (Fmoc) moiety or in a suitable peptide/protein context, even if they lack the terminal GlcNAc moiety on the Man-α1,3-Man arm. FUT8 could also fucosylate paucimannose structures when they are on glycoprotein substrates. Such core-fucosylated paucimannosylation is a prominent feature of lysosomal proteins of human neutrophils and several types of cancers. We also found that sialylation of N-glycans significantly reduced their activity as a substrate of FUT8. Kinetic analysis demonstrated that Fmoc aglycone modification could either improve the turnover rate or decrease the KM value depending on the nature of the substrates, thus significantly enhancing the overall efficiency of FUT8 catalyzed fucosylation. Our results indicate that an appropriate aglycone context of N-glycans could significantly broaden the acceptor substrate specificity of FUT8 beyond what has previously been thought.
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Affiliation(s)
- Roushu Zhang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
| | - Qiang Yang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
| | - Bhargavi M Boruah
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602
| | - Guanghui Zong
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
| | - Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
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36
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Chen Z, Yu Q, Yu Q, Johnson J, Shipman R, Zhong X, Huang J, Asthana S, Carlsson C, Okonkwo O, Li L. In-depth Site-specific Analysis of N-glycoproteome in Human Cerebrospinal Fluid and Glycosylation Landscape Changes in Alzheimer's Disease. Mol Cell Proteomics 2021; 20:100081. [PMID: 33862227 PMCID: PMC8724636 DOI: 10.1016/j.mcpro.2021.100081] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 01/22/2023] Open
Abstract
As the body fluid that directly interchanges with the extracellular fluid of the central nervous system (CNS), cerebrospinal fluid (CSF) serves as a rich source for CNS-related disease biomarker discovery. Extensive proteome profiling has been conducted for CSF, but studies aimed at unraveling site-specific CSF N-glycoproteome are lacking. Initial efforts into site-specific N-glycoproteomics study in CSF yield limited coverage, hindering further experimental design of glycosylation-based disease biomarker discovery in CSF. In the present study, we have developed an N-glycoproteomic approach that combines enhanced N-glycopeptide sequential enrichment by hydrophilic interaction chromatography (HILIC) and boronic acid enrichment with electron transfer and higher-energy collision dissociation (EThcD) for large-scale intact N-glycopeptide analysis. The application of the developed approach to the analyses of human CSF samples enabled identifications of a total of 2893 intact N-glycopeptides from 511 N-glycosites and 285 N-glycoproteins. To our knowledge, this is the largest site-specific N-glycoproteome dataset reported for CSF to date. Such dataset provides molecular basis for a better understanding of the structure-function relationships of glycoproteins and their roles in CNS-related physiological and pathological processes. As accumulating evidence suggests that defects in glycosylation are involved in Alzheimer's disease (AD) pathogenesis, in the present study, a comparative in-depth N-glycoproteomic analysis was conducted for CSF samples from healthy control and AD patients, which yielded a comparable N-glycoproteome coverage but a distinct expression pattern for different categories of glycoforms, such as decreased fucosylation in AD CSF samples. Altered glycosylation patterns were detected for a number of N-glycoproteins including alpha-1-antichymotrypsin, ephrin-A3 and carnosinase CN1 etc., which serve as potentially interesting targets for further glycosylation-based AD study and may eventually lead to molecular elucidation of the role of glycosylation in AD progression.
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Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Qinying Yu
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Jillian Johnson
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Richard Shipman
- Department of Applied Science, University of Wisconsin-Stout, Menomonie, Wisconsin, USA
| | - Xiaofang Zhong
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Sanjay Asthana
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Cynthia Carlsson
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Ozioma Okonkwo
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA; School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA.
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37
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Coura MDM, Barbosa EA, Brand GD, Bloch C, de Sousa JB. Identification of Differential N-Glycan Compositions in the Serum and Tissue of Colon Cancer Patients by Mass Spectrometry. BIOLOGY 2021; 10:biology10040343. [PMID: 33923867 PMCID: PMC8074232 DOI: 10.3390/biology10040343] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/29/2021] [Accepted: 04/06/2021] [Indexed: 01/08/2023]
Abstract
Simple Summary Incidence of colorectal cancer (CRC) has been rising in Brazil. To date, no reliable biomarker has been described in CRC for diagnosis and prognosis. Modifications in the N-glycosylation profile are usually associated with many cancers, as CRC. In turn, mass spectrometry (MS)-based methods are the most accurate technology in quantification of N-glycans. Therefore, we described a unique pattern of compositions altered in serum and tissues of stages II and III colon cancer patients, identified by MALDI-TOF/MS and LC-MS technology. N-glycans were mostly found decreased in serum whilst oligomannosidic, hypogalactosylated, and tetra-antennary forms were overexpressed in tumor tissues. Total N-glycome in serum of cancer patients was different from the profile found in serum of healthy individuals. Strikingly, no correlation between tissue N-glycosylation profile and serum profile was observed in cancer patients, posing the question where these compositions are originated from. Abstract Colorectal cancer (CRC) ranks second as the leading cause of cancer-related deaths worldwide. N-glycosylation is one of the most common posttranslational protein modifications. Therefore, we studied the total serum N-glycome (TSNG) of 13 colon cancer patients compared to healthy controls using MALDI-TOF/MS and LC-MS. N-glycosylation of cancer tumor samples from the same cohort were further quantified using a similar methodology. In total, 23 N-glycan compositions were down-regulated in the serum of colon cancer patients, mostly galactosylated forms whilst the mannose-rich HexNAc2Hex7, the fucosylated bi-antennary glycan HexNAc4Hex5Fuc1NeuAc2, and the tetra-antennary HexNAc6Hex7NeuAc3 were up-regulated in serum. Hierarchical clustering analysis of TSNG correctly singled out 85% of the patients from controls. Albeit heterogenous, N-glycosylation of tumor samples showed overrepresented oligomannosidic, bi-antennary hypogalactosylated, and branched compositions related to normal colonic tissue, in both MALDI-TOF/MS and LC-MS analysis. Moreover, compositions found upregulated in tumor tissue were mostly uncorrelated to compositions in serum of cancer patients. Mass spectrometry-based N-glycan profiling in serum shows potential in the discrimination of patients from healthy controls. However, the compositions profile in serum showed no parallel with N-glycans in tumor microenvironment, which suggests a different origin of compositions found in serum of cancer patients.
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Affiliation(s)
- Marcelo de M.A. Coura
- Division of Colorectal Surgery, University Hospital of Brasilia, School of Medicine, University of Brasilia, SGAN 605, Brasilia-DF 70840-901, Brazil;
- Correspondence:
| | - Eder A. Barbosa
- Laboratory of Mass Spectrometry, EMBRAPA Genetic Resources and Biotechnology, Parque Estação Biológica, PqEB, Av. W5 Norte, Brasilia-DF 70770-917, Brazil; (E.A.B.); (C.B.J.)
- Laboratory for the Synthesis and Analysis of Biomolecules, Institute of Chemistry, Campus Universitario Darcy Ribeiro, University of Brasilia, Brasilia-DF 70910-900, Brazil;
| | - Guilherme D. Brand
- Laboratory for the Synthesis and Analysis of Biomolecules, Institute of Chemistry, Campus Universitario Darcy Ribeiro, University of Brasilia, Brasilia-DF 70910-900, Brazil;
| | - Carlos Bloch
- Laboratory of Mass Spectrometry, EMBRAPA Genetic Resources and Biotechnology, Parque Estação Biológica, PqEB, Av. W5 Norte, Brasilia-DF 70770-917, Brazil; (E.A.B.); (C.B.J.)
| | - Joao B. de Sousa
- Division of Colorectal Surgery, University Hospital of Brasilia, School of Medicine, University of Brasilia, SGAN 605, Brasilia-DF 70840-901, Brazil;
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38
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Huang YF, Aoki K, Akase S, Ishihara M, Liu YS, Yang G, Kizuka Y, Mizumoto S, Tiemeyer M, Gao XD, Aoki-Kinoshita KF, Fujita M. Global mapping of glycosylation pathways in human-derived cells. Dev Cell 2021; 56:1195-1209.e7. [PMID: 33730547 PMCID: PMC8086148 DOI: 10.1016/j.devcel.2021.02.023] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 12/15/2020] [Accepted: 02/12/2021] [Indexed: 01/02/2023]
Abstract
Glycans are one of the fundamental classes of macromolecules and are involved in a broad range of biological phenomena. A large variety of glycan structures can be synthesized depending on tissue or cell types and environmental changes. Here, we developed a comprehensive glycosylation mapping tool, termed GlycoMaple, to visualize and estimate glycan structures based on gene expression. We informatically selected 950 genes involved in glycosylation and its regulation. Expression profiles of these genes were mapped onto global glycan metabolic pathways to predict glycan structures, which were confirmed using glycomic analyses. Based on the predictions of N-glycan processing, we constructed 40 knockout HEK293 cell lines and analyzed the effects of gene knockout on glycan structures. Finally, the glycan structures of 64 cell lines, 37 tissues, and primary colon tumor tissues were estimated and compared using publicly available databases. Our systematic approach can accelerate glycan analyses and engineering in mammalian cells.
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Affiliation(s)
- Yi-Fan Huang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Kazuhiro Aoki
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Sachiko Akase
- Graduate School of Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
| | - Mayumi Ishihara
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Yi-Shi Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ganglong Yang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yasuhiko Kizuka
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu 501-1193, Japan; Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Shuji Mizumoto
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, Nagoya, Aichi 468-8503, Japan
| | - Michael Tiemeyer
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Kiyoko F Aoki-Kinoshita
- Graduate School of Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan; Glycan & Life System Integration Center (GaLSIC), Faculty of Science and Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan.
| | - Morihisa Fujita
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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Boyaval F, van Zeijl R, Dalebout H, Holst S, van Pelt G, Fariña-Sarasqueta A, Mesker W, Tollenaar R, Morreau H, Wuhrer M, Heijs B. N-Glycomic Signature of Stage II Colorectal Cancer and Its Association With the Tumor Microenvironment. Mol Cell Proteomics 2021; 20:100057. [PMID: 33581319 PMCID: PMC7973300 DOI: 10.1074/mcp.ra120.002215] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The choice for adjuvant chemotherapy in stage II colorectal cancer is controversial as many patients are cured by surgery alone and it is difficult to identify patients with high risk of recurrence of the disease. There is a need for better stratification of this group of patients. Mass spectrometry imaging could identify patients at risk. We report here the N-glycosylation signatures of the different cell populations in a group of stage II colorectal cancer tissue samples. The cancer cells, compared with normal epithelial cells, have increased levels of sialylation and high-mannose glycans, as well as decreased levels of fucosylation and highly branched N-glycans. When looking at the interface between cancer and its microenvironment, it seems that the cancer N-glycosylation signature spreads into the surrounding stroma at the invasive front of the tumor. This finding was more outspoken in patients with a worse outcome within this sample group.
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Affiliation(s)
- Fanny Boyaval
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands; Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - René van Zeijl
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Hans Dalebout
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Stephanie Holst
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Gabi van Pelt
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Arantza Fariña-Sarasqueta
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands; Department of Pathology, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Wilma Mesker
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Rob Tollenaar
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Manfred Wuhrer
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Bram Heijs
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden, the Netherlands.
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40
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Kori M, Aydin B, Gulfidan G, Beklen H, Kelesoglu N, Caliskan Iscan A, Turanli B, Erzik C, Karademir B, Arga KY. The Repertoire of Glycan Alterations and Glycoproteins in Human Cancers. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:139-168. [PMID: 33404348 DOI: 10.1089/omi.2020.0210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cancer as the leading cause of death worldwide has many issues that still need to be addressed. Since the alterations on the glycan compositions or/and structures (i.e., glycosylation, sialylation, and fucosylation) are common features of tumorigenesis, glycomics becomes an emerging field examining the structure and function of glycans. In the past, cancer studies heavily relied on genomics and transcriptomics with relatively little exploration of the glycan alterations and glycoprotein biomarkers among individuals and populations. Since glycosylation of proteins increases their structural complexity by several orders of magnitude, glycome studies resulted in highly dynamic biomarkers that can be evaluated for cancer diagnosis, prognosis, and therapy. Glycome not only integrates our genetic background with past and present environmental factors but also offers a promise of more efficient patient stratification compared with genetic variations. Therefore, studying glycans holds great potential for better diagnostic markers as well as developing more efficient treatment strategies in human cancers. While recent developments in glycomics and associated technologies now offer new possibilities to achieve a high-throughput profiling of glycan diversity, we aim to give an overview of the current status of glycan research and the potential applications of the glycans in the scope of the personalized medicine strategies for cancer.
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Affiliation(s)
- Medi Kori
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Busra Aydin
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Gizem Gulfidan
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Hande Beklen
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Nurdan Kelesoglu
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Ayşegul Caliskan Iscan
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey.,Department of Pharmacy, Istinye University, Istanbul, Turkey
| | - Beste Turanli
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Can Erzik
- Department of Medical Biology and School of Medicine, Marmara University, Istanbul, Turkey
| | - Betul Karademir
- Department of Biochemistry, School of Medicine, Marmara University, Istanbul, Turkey.,Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
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41
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Nimmerjahn F, Werner A. Sweet Rules: Linking Glycosylation to Antibody Function. EXPERIENTIA SUPPLEMENTUM (2012) 2021; 112:365-393. [PMID: 34687017 DOI: 10.1007/978-3-030-76912-3_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antibodies produced upon infections with pathogenic microorganisms are essential for clearing primary infections and for providing the host with long-lasting immunity. Moreover, antibodies have become the most widely used platform for developing novel therapies against cancer and autoimmunity, requiring an in-depth understanding of how antibodies mediate their activity in vivo and which factors modulate pro- or anti-inflammatory antibody activities. Since the discovery that select residues present in the sugar domain attached to the immunoglobulin G (IgG) fragment crystallizable (Fc) region can modulate both, pro- and anti-inflammatory effector functions, a wealth of studies has focused on understanding how IgG glycosylation is regulated and how this knowledge can be used to optimize therapeutic antibody activity. With the introduction of glycoengineered afucosylated antibodies in cancer therapy and the initiation of clinical testing of highly sialylated anti-inflammatory antibodies the proof-of-concept that understanding antibody glycosylation can lead to clinical innovation has been provided. The focus of this review is to summarize recent insights into how antibody glycosylation is regulated in vivo and how select sugar residues impact IgG function.
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Affiliation(s)
- Falk Nimmerjahn
- Chair of Genetics, Department of Biology, Institute of Genetics, University of Erlangen-Nürnberg, Erlangen, Germany.
- Medical Immunology Campus Erlangen, Erlangen, Germany.
| | - Anja Werner
- Chair of Genetics, Department of Biology, Institute of Genetics, University of Erlangen-Nürnberg, Erlangen, Germany
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42
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Deschepper FM, Zoppi R, Pirro M, Hensbergen PJ, Dall’Olio F, Kotsias M, Gardner RA, Spencer DI, Videira PA. L1CAM as an E-selectin Ligand in Colon Cancer. Int J Mol Sci 2020; 21:ijms21218286. [PMID: 33167483 PMCID: PMC7672641 DOI: 10.3390/ijms21218286] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
Metastasis is the main cause of death among colorectal cancer (CRC) patients. E-selectin and its carbohydrate ligands, including sialyl Lewis X (sLeX) antigen, are key players in the binding of circulating tumor cells to the endothelium, which is one of the major events leading to organ invasion. Nevertheless, the identity of the glycoprotein scaffolds presenting these glycans in CRC remains unclear. In this study, we firstly have characterized the glycoengineered cell line SW620 transfected with the fucosyltransferase 6 (FUT6) coding for the α1,3-fucosyltransferase 6 (FUT6), which is the main enzyme responsible for the synthesis of sLeX in CRC. The SW620FUT6 cell line expressed high levels of sLeX antigen and E-selectin ligands. Moreover, it displayed increased migration ability. E-selectin ligand glycoproteins were isolated from the SW620FUT6 cell line, identified by mass spectrometry, and validated by flow cytometry and Western blot (WB). The most prominent E-selectin ligand we identified was the neural cell adhesion molecule L1 (L1CAM). Previous studies have shown association of L1CAM with metastasis in cancer, thus the novel role as E-selectin counter-receptor contributes to understand the molecular mechanism involving L1CAM in metastasis formation.
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Affiliation(s)
- Fanny M. Deschepper
- Unidade de Ciências Biomoleculares Aplicadas (UCIBIO), Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (F.M.D.); (R.Z.)
| | - Roberta Zoppi
- Unidade de Ciências Biomoleculares Aplicadas (UCIBIO), Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (F.M.D.); (R.Z.)
| | - Martina Pirro
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (M.P.); (P.J.H.)
| | - Paul J. Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (M.P.); (P.J.H.)
| | - Fabio Dall’Olio
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40138 Bologna, Italy;
| | - Maximillianos Kotsias
- Ludger Ltd., Culham Science Centre, Abingdon, Oxfordshire OX14 3EB, UK; (M.K.); (R.A.G.); (D.I.R.S.)
| | - Richard A. Gardner
- Ludger Ltd., Culham Science Centre, Abingdon, Oxfordshire OX14 3EB, UK; (M.K.); (R.A.G.); (D.I.R.S.)
| | - Daniel I.R. Spencer
- Ludger Ltd., Culham Science Centre, Abingdon, Oxfordshire OX14 3EB, UK; (M.K.); (R.A.G.); (D.I.R.S.)
| | - Paula A. Videira
- Unidade de Ciências Biomoleculares Aplicadas (UCIBIO), Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (F.M.D.); (R.Z.)
- CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), 2829-516 Caparica, Portugal
- Correspondence:
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43
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Hu Y, Pan J, Shah P, Ao M, Thomas SN, Liu Y, Chen L, Schnaubelt M, Clark DJ, Rodriguez H, Boja ES, Hiltke T, Kinsinger CR, Rodland KD, Li QK, Qian J, Zhang Z, Chan DW, Zhang H. Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma. Cell Rep 2020; 33:108276. [PMID: 33086064 PMCID: PMC7970828 DOI: 10.1016/j.celrep.2020.108276] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/18/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022] Open
Abstract
Many gene products exhibit great structural heterogeneity because of an array of modifications. These modifications are not directly encoded in the genomic template but often affect the functionality of proteins. Protein glycosylation plays a vital role in proper protein functions. However, the analysis of glycoproteins has been challenging compared with other protein modifications, such as phosphorylation. Here, we perform an integrated proteomic and glycoproteomic analysis of 83 prospectively collected high-grade serous ovarian carcinoma (HGSC) and 23 non-tumor tissues. Integration of the expression data from global proteomics and glycoproteomics reveals tumor-specific glycosylation, uncovers different glycosylation associated with three tumor clusters, and identifies glycosylation enzymes that were correlated with the altered glycosylation. In addition to providing a valuable resource, these results provide insights into the potential roles of glycosylation in the pathogenesis of HGSC, with the possibility of distinguishing pathological outcomes of ovarian tumors from non-tumors, as well as classifying tumor clusters.
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Affiliation(s)
- Yingwei Hu
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Jianbo Pan
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Punit Shah
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Minghui Ao
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Stefani N Thomas
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Yang Liu
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - David J Clark
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Qing Kay Li
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Zhen Zhang
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA.
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA.
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44
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Discovery of N-glycan Biomarkers for the Canine Osteoarthritis. Life (Basel) 2020; 10:life10090199. [PMID: 32937769 PMCID: PMC7555374 DOI: 10.3390/life10090199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 09/10/2020] [Indexed: 12/16/2022] Open
Abstract
Protein glycosylation is a post-translational modification that impacts on protein activity, stability, and interactions. It was sensitively altered by the cellular state and, therefore, is now used for a diagnostic or prognostic indicator of various human diseases such as cancer. To evaluate the clinical feasibility in the veterinary area, the N-glycan biomarkers were discovered from canine serum for the diagnosis of osteoarthritis (OA), which is one of the most common diseases of dogs. N-glycome was obtained from 20 μL of canine serum by the enzymatic cleavage followed by the purification and enrichment using solid-phase extraction. Independent compositions of 163 and 463 N-glycans were found from healthy control (n = 41) and osteoarthritis patients (n = 92), respectively. Initially, 31 of the potential biomarkers were screened by the p-values below 1.0 × 10−10 from ANOVA. Then, the area under the curve (AUC) and the intensity ratio between OA patient and healthy control (P/C ratio) were calculated. Considering the diagnostic efficacy, the AUC bigger than 0.9 and the P/C ratio larger than 3.0 were used to discover 16 N-glycans as diagnostic biomarkers. Particularly, five of the diagnostic biomarkers were AUC above 0.99 and three of N-glycans had AUC 1.0. The results suggest a clear possibility for N-glycan biomarkers to be used as a clinical tool in the veterinary medical area enabling to provide objective and non-invasive diagnostic information.
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45
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Harvey DJ. NEGATIVE ION MASS SPECTROMETRY FOR THE ANALYSIS OF N-LINKED GLYCANS. MASS SPECTROMETRY REVIEWS 2020; 39:586-679. [PMID: 32329121 DOI: 10.1002/mas.21622] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/13/2019] [Accepted: 12/22/2019] [Indexed: 05/03/2023]
Abstract
N-glycans from glycoproteins are complex, branched structures whose structural determination presents many analytical problems. Mass spectrometry, usually conducted in positive ion mode, often requires extensive sample manipulation, usually by derivatization such as permethylation, to provide the necessary structure-revealing fragment ions. The newer but, so far, lesser used negative ion techniques, on the contrary, provide a wealth of structural information not present in positive ion spectra that greatly simplify the analysis of these compounds and can usually be conducted without the need for derivatization. This review describes the use of negative ion mass spectrometry for the structural analysis of N-linked glycans and emphasises the many advantages that can be gained by this mode of operation. Biosynthesis and structures of the compounds are described followed by methods for release of the glycans from the protein. Methods for ionization are discussed with emphasis on matrix-assisted laser desorption/ionization (MALDI) and methods for producing negative ions from neutral compounds. Acidic glycans naturally give deprotonated species under most ionization conditions. Fragmentation of negative ions is discussed next with particular reference to those ions that are diagnostic for specific features such as the branching topology of the glycans and substitution positions of moieties such as fucose and sulfate, features that are often difficult to identify easily by conventional techniques such as positive ion fragmentation and exoglycosidase digestions. The advantages of negative over positive ions for this structural work are emphasised with an example of a series of glycans where all other methods failed to produce a structure. Fragmentation of derivatized glycans is discussed next, both with respect to derivatives at the reducing terminus of the molecules, and to methods for neutralization of the acidic groups on sialic acids to both stabilize them for MALDI analysis and to produce the diagnostic fragments seen with the neutral glycans. The use of ion mobility, combined with conventional mass spectrometry is described with emphasis on its use to extract clean glycan spectra both before and after fragmentation, to separate isomers and its use to extract additional information from separated fragment ions. A section on applications follows with examples of the identification of novel structures from lower organisms and tables listing the use of negative ions for structural identification of specific glycoproteins, glycans from viruses and uses in the biopharmaceutical industry and in medicine. The review concludes with a summary of the advantages and disadvantages of the technique. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, United Kingdom
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46
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Zhang W, Yang Z, Gao X, Wu Q. Advances in the discovery of novel biomarkers for cancer: spotlight on protein N-glycosylation. Biomark Med 2020; 14:1031-1045. [PMID: 32940073 DOI: 10.2217/bmm-2020-0185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/21/2020] [Indexed: 02/06/2023] Open
Abstract
Progress on glycosylation and tumor markers has not been extensively reported. Glycosylation plays an important part in post-translational modification. Previous research on glycosylation-modified biomarkers has lagged behind due to insufficient understanding of glycosylation-related regulations. However, some new methods and ideas illustrated in recent research may provide new inspirations in the field. This article aims to review current advances in revealing relationship between tumors and abnormal N-glycosylation and discuss leading-edge applications of N-glycosylation in developing novel tumor biomarkers.
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Affiliation(s)
- Wenyao Zhang
- State Key Laboratory of Cancer Biology & National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Road, Xi'an 710032, China
| | - Zhiping Yang
- State Key Laboratory of Cancer Biology & National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Road, Xi'an 710032, China
| | - Xiaoliang Gao
- State Key Laboratory of Cancer Biology & National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Road, Xi'an 710032, China
| | - Qiong Wu
- State Key Laboratory of Cancer Biology & National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Road, Xi'an 710032, China
- Department of Clinical Nutrition, Xijing Hospital, Fourth Military Medical University, 127 West Changle Road, Xi'an 710032, China
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47
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N-glycomic profiling of colorectal cancer according to tumor stage and location. PLoS One 2020; 15:e0234989. [PMID: 32598367 PMCID: PMC7323945 DOI: 10.1371/journal.pone.0234989] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 06/06/2020] [Indexed: 12/24/2022] Open
Abstract
Alterations in glycosylation are seen in many types of cancer, including colorectal cancer (CRC). Glycans, the sugar moieties of glycoconjugates, are involved in many important functions relevant to cancer and can be of value as biomarkers. In this study, we have used mass spectrometry to analyze the N-glycan profiles of 35 CRC tissue samples and 10 healthy tissue samples from non-CRC patients who underwent operations for other reasons. The tumor samples were divided into groups depending on tumor location (right or left colon) and stage (II or III), while the healthy samples were divided into right or left colon. The levels of neutral and acidic N-glycan compositions and glycan classes were analyzed in a total of ten different groups. Surprisingly, there were no significant differences in glycan levels when all right- and left-sided CRC samples were compared, and few differences (such as in the abundance of the neutral N-glycan H3N5) were seen when the samples were divided according to both location and stage. Multiple significant differences were found in the levels of glycans and glycan classes when stage II and III samples were compared, and these glycans could be of value as candidates for new markers of cancer progression. In order to validate our findings, we analyzed healthy tissue samples from the right and left colon and found no significant differences in the levels of any of the glycans analyzed, confirming that our findings when comparing CRC samples from the right and left colon are not due to normal variations in the levels of glycans between the healthy right and left colon. Additionally, the levels of the acidic glycans H4N3F1P1, H5N4F1P1, and S1H5N4F1 were found to change in a cancer-specific but colon location-nonspecific manner, indicating that CRC affects glycan levels in similar ways regardless of tumor location.
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48
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Cheng PW, Davidson S, Bhat G. Markers of malignant prostate cancer cells: Golgi localization of α-mannosidase 1A at GM130-GRASP65 site and appearance of high mannose N-glycans on cell surface. Biochem Biophys Res Commun 2020; 527:406-410. [PMID: 32331836 DOI: 10.1016/j.bbrc.2020.03.168] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 03/29/2020] [Indexed: 02/01/2023]
Abstract
The ability to distinguish malignant from indolent prostate cancer cells is critically important for identification of clinically significant prostate cancer to minimize unnecessary overtreatment and sufferings endured by patients who have indolent cancer. Recently, we discovered that loss of giantin function as the primary Golgi targeting site for endoplasmic reticulum-derived transport vesicles in aggressive prostate cancer cells caused a shift of the Golgi localization site of α-mannosidase 1A to 130 KDa Golgi matrix protein (GM130)-65 KDa Golgi reassembly-stacking protein (GRASP65) site resulting in emergence of high mannose N-glycans on trans-Golgi enzymes and cell surface glycoproteins. To extend this observation, we isolated two cell clones (Clone 1 and Clone 2) from high passage LNCaP cells, which exhibited androgen refractory property missing in low passage LNCaP cells, and characterized their malignant property. We have found that comparing to Clone 2, which does not have cell surface high mannose N-glycans and exhibits localization of α-mannosidase 1A at giantin site, Clone 1 displays cell surface high mannose N-glycans, exhibits localization of α-mannosidase 1A at GM130-GRASP65 site, and shows a faster rate of closing the wound in a wound healing assay. The results indicate that Golgi localization of α-mannosidase 1A at GM130-GRASP65 site and appearance of cell surface high mannose N-glycans may serve as markers of malignant prostate cancer cells.
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Affiliation(s)
- Pi-Wan Cheng
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA; College of Medicine, and, University of Nebraska Medical Center, Omaha, NE, USA; Eppley Institute of Research on Cancer and Allied Diseases, Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Samuel Davidson
- College of Medicine, and, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Ganapati Bhat
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA.
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Leung KK, Wilson GM, Kirkemo LL, Riley NM, Coon JJ, Wells JA. Broad and thematic remodeling of the surfaceome and glycoproteome on isogenic cells transformed with driving proliferative oncogenes. Proc Natl Acad Sci U S A 2020; 117:7764-7775. [PMID: 32205440 PMCID: PMC7148585 DOI: 10.1073/pnas.1917947117] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The cell surface proteome, the surfaceome, is the interface for engaging the extracellular space in normal and cancer cells. Here we apply quantitative proteomics of N-linked glycoproteins to reveal how a collection of some 700 surface proteins is dramatically remodeled in an isogenic breast epithelial cell line stably expressing any of six of the most prominent proliferative oncogenes, including the receptor tyrosine kinases, EGFR and HER2, and downstream signaling partners such as KRAS, BRAF, MEK, and AKT. We find that each oncogene has somewhat different surfaceomes, but the functions of these proteins are harmonized by common biological themes including up-regulation of nutrient transporters, down-regulation of adhesion molecules and tumor suppressing phosphatases, and alteration in immune modulators. Addition of a potent MEK inhibitor that blocks MAPK signaling brings each oncogene-induced surfaceome back to a common state reflecting the strong dependence of the oncogene on the MAPK pathway to propagate signaling. Cell surface protein capture is mediated by covalent tagging of surface glycans, yet current methods do not afford sequencing of intact glycopeptides. Thus, we complement the surfaceome data with whole cell glycoproteomics enabled by a recently developed technique called activated ion electron transfer dissociation (AI-ETD). We found massive oncogene-induced changes to the glycoproteome and differential increases in complex hybrid glycans, especially for KRAS and HER2 oncogenes. Overall, these studies provide a broad systems-level view of how specific driver oncogenes remodel the surfaceome and the glycoproteome in a cell autologous fashion, and suggest possible surface targets, and combinations thereof, for drug and biomarker discovery.
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Affiliation(s)
- Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143
| | - Gary M Wilson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Lisa L Kirkemo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143
| | - Nicholas M Riley
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143;
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50
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Takayama H, Ohta M, Iwashita Y, Uchida H, Shitomi Y, Yada K, Inomata M. Altered glycosylation associated with dedifferentiation of hepatocellular carcinoma: a lectin microarray-based study. BMC Cancer 2020; 20:192. [PMID: 32143591 PMCID: PMC7060603 DOI: 10.1186/s12885-020-6699-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/28/2020] [Indexed: 12/13/2022] Open
Abstract
Background Altered glycosylation associated with hepatocellular carcinoma (HCC) is well documented. However, few reports have investigated the association between dedifferentiation and glycosylation. Therefore, the aim of this study was to analyze glycosylation associated with dedifferentiation of HCC within the same nodule and to investigate glycosyltransferase related to the glycosylation. Methods We analyzed resected HCC specimens (n = 50) using lectin microarray to comprehensively and sensitively analyze glycan profiles, and identify changes to glycosylation between well- and moderately-differentiated components within the same nodule. Moreover, we performed immunohistochemical staining of mannosyl(α-1,3-)-glycoprotein β-1,2-N-acetylglucosaminyltransferase (MGAT1), which is an essential glycosyltransferase that converts high-mannose glycans to complex- or hybrid-type N-glycans. Results Four lectins from Narcissus pseudonarcissus agglutinin (NPA), Concanavalin A, Galanthus nivalis agglutinin, and Calystegia sepium agglutinin were significantly elevated in moderately-differentiated components of HCC compared with well-differentiated components, and all lectins showed binding specificity to high-mannose glycans. Therefore, these structures were represented to a greater extent in moderately-differentiated components than in well-differentiated ones. Immunohistochemical staining revealed significantly increased NPA expression and decreased MGAT1 expression in moderately-differentiated components. Low MGAT1 expression in moderately-differentiated components of tumors was associated with intrahepatic metastasis and had tendency for poor prognosis. Conclusion Dedifferentiation of well-differentiated HCC is associated with an increase in high-mannose glycans. MGAT1 may play a role in the dedifferentiation of HCC.
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Affiliation(s)
- Hiroomi Takayama
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan.
| | - Masayuki Ohta
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan.,Global Oita Medical Advanced Research Center for Health, Oita University, Oita, Japan
| | - Yukio Iwashita
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan
| | - Hiroki Uchida
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan
| | - Yuki Shitomi
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan
| | - Kazuhiro Yada
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan
| | - Masafumi Inomata
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan
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