Toward Spatial Glycomics and Glycoproteomics: Innovations and Applications

Overview

Journal BBA Adv

Specialty Biochemistry

Date 2025 Mar 3

PMID 40027887

Authors

Patcharaporn Boottanun

Sayaka Fuseya

Atsushi Kuno

Affiliations

Soon will be listed here.

Abstract

In this mini review, we provide an overview of the challenging field of spatial glycomics/glycoproteomics. Owing to their complexity, sophisticated analytical methods and innovative technologies are needed to advance this field. An agile development approach enables unraveling aberrant glycosylations, glycobiomarkers, and glycotargets for spatial imaging, diagnosis, and therapeutic purposes. We discuss glycopathology and tissue glycomic profiling using highly sensitive lectin-based analyses and introduce deep visual proteomics for glycomic/glycoproteomic sample preparation. Additionally, we highlight the importance of leveraging laser microdissection and artificial intelligence-driven visual software for cell-type assignment and automation techniques, which are crucial for advancing glycomics/glycoproteomics.

References

Jamialahmadi H, Khalili-Tanha G, Nazari E, Rezaei-Tavirani M . Artificial intelligence and bioinformatics: a journey from traditional techniques to smart approaches. Gastroenterol Hepatol Bed Bench. 2024; 17(3):241-252. PMC: 11413381. DOI: 10.22037/ghfbb.v17i3.2977. View

Bertok T, Katrlik J, Gemeiner P, Tkac J . Electrochemical lectin based biosensors as a label-free tool in glycomics. Mikrochim Acta. 2016; 180(1):1-13. PMC: 4883647. DOI: 10.1007/s00604-012-0876-4. View

Itakura Y, Hasegawa Y, Kikkawa Y, Murakami Y, Sugiura K, Nagai-Okatani C . Spatiotemporal changes of tissue glycans depending on localization in cardiac aging. Regen Ther. 2023; 22:68-78. PMC: 9841240. DOI: 10.1016/j.reth.2022.12.009. View

Denti V, Capitoli G, Piga I, Clerici F, Pagani L, Criscuolo L . Spatial Multiomics of Lipids, N-Glycans, and Tryptic Peptides on a Single FFPE Tissue Section. J Proteome Res. 2022; 21(11):2798-2809. PMC: 9639202. DOI: 10.1021/acs.jproteome.2c00601. View

Oinam L, Tateno H . Glycan Profiling by Sequencing to Uncover Multicellular Communication: Launching Glycobiology in Single Cells and Microbiomes. Front Cell Dev Biol. 2022; 10:919168. PMC: 9197256. DOI: 10.3389/fcell.2022.919168. View

Bomfim B, Azevedo-Silva J, Caminha G, Santos J, Pelajo-Machado M, de Paula Ayres-Silva J . Lectin-based carbohydrate profile of megakaryocytes in murine fetal liver during development. Sci Rep. 2023; 13(1):6729. PMC: 10130079. DOI: 10.1038/s41598-023-32863-3. View

Kabatnik S, Post F, Drici L, Bartels A, Strauss M, Zheng X . Spatial characterization and stratification of colorectal adenomas by deep visual proteomics. iScience. 2024; 27(9):110620. PMC: 11381895. DOI: 10.1016/j.isci.2024.110620. View

Mund A, Coscia F, Kriston A, Hollandi R, Kovacs F, Brunner A . Deep Visual Proteomics defines single-cell identity and heterogeneity. Nat Biotechnol. 2022; 40(8):1231-1240. PMC: 9371970. DOI: 10.1038/s41587-022-01302-5. View

Moffitt J, Lundberg E, Heyn H . The emerging landscape of spatial profiling technologies. Nat Rev Genet. 2022; 23(12):741-759. DOI: 10.1038/s41576-022-00515-3. View

10.

Yang L, Yang Q, Lin L, Zhang C, Dong L, Gao X . LectoScape: A Highly Multiplexed Imaging Platform for Glycome Analysis and Biomedical Diagnosis. Anal Chem. 2024; 96(17):6558-6565. DOI: 10.1021/acs.analchem.3c04925. View

11.

McDowell C, Lu X, Mehta A, Angel P, Drake R . Applications and continued evolution of glycan imaging mass spectrometry. Mass Spectrom Rev. 2021; 42(2):674-705. PMC: 8946722. DOI: 10.1002/mas.21725. View

12.

Kassab M, Jehanzaib M, Basak K, Demir D, Keles G, Turan M . FFPE++: Improving the quality of formalin-fixed paraffin-embedded tissue imaging via contrastive unpaired image-to-image translation. Med Image Anal. 2023; 91:102992. DOI: 10.1016/j.media.2023.102992. View

13.

Hosogane T, Casanova R, Bodenmiller B . DNA-barcoded signal amplification for imaging mass cytometry enables sensitive and highly multiplexed tissue imaging. Nat Methods. 2023; 20(9):1304-1309. PMC: 10482679. DOI: 10.1038/s41592-023-01976-y. View

14.

Giesen C, Wang H, Schapiro D, Zivanovic N, Jacobs A, Hattendorf B . Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nat Methods. 2014; 11(4):417-22. DOI: 10.1038/nmeth.2869. View

15.

Pham T, Nguyen S, Tran M . A comprehensive review of transduction methods of lectin-based biosensors in biomedical applications. Heliyon. 2024; 10(19):e38371. PMC: 11462017. DOI: 10.1016/j.heliyon.2024.e38371. View

16.

Muller T, Kalxdorf M, Longuespee R, Kazdal D, Stenzinger A, Krijgsveld J . Automated sample preparation with SP3 for low-input clinical proteomics. Mol Syst Biol. 2020; 16(1):e9111. PMC: 6966100. DOI: 10.15252/msb.20199111. View

17.

Huo Z, Tu H, Ren J, Zhang X, Qi Y, Situ C . Lectin-Based SP3 Technology Enables N-Glycoproteomic Analysis of Mouse Oocytes. J Proteome Res. 2024; 23(6):2137-2147. DOI: 10.1021/acs.jproteome.4c00089. View

18.

Dunne J, Griner J, Romeo M, MacDonald J, Krieg C, Lim M . Evaluation of antibody-based single cell type imaging techniques coupled to multiplexed imaging of N-glycans and collagen peptides by matrix-assisted laser desorption/ionization mass spectrometry imaging. Anal Bioanal Chem. 2023; 415(28):7011-7024. PMC: 10632234. DOI: 10.1007/s00216-023-04983-2. View

19.

Shimazaki H, Nakamura K, Ono A, Segawa O, Sawakami K, Koizuka M . Auto-Lectin Dotcoding by Two Octopuses: Rapid Analysis of Fluorescence-Labeled Glycoproteins by an 8-channel Fully-Automatic Bead Array Scanner with a Rolling-Circle Detector. Anal Chem. 2023; 95(32):11868-11873. DOI: 10.1021/acs.analchem.3c01395. View

20.

Rogenes H, Finne K, Winge I, Akslen L, Ostman A, Milosevic V . Development of 42 marker panel for in-depth study of cancer associated fibroblast niches in breast cancer using imaging mass cytometry. Front Immunol. 2024; 15:1325191. PMC: 11070582. DOI: 10.3389/fimmu.2024.1325191. View