High-Throughput Mass Spectrometry Analysis of N-Glycans and Protein Markers after FUT8 Knockdown in the Syngeneic SW480/SW620 Colorectal Cancer Cell Model.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38507902", "kind": "science-record", "revision": 3, "content_hash": "sha256:b957da823c240ae9ca193a63a77b846af37cad2f7e5a1af1d6c27da98a1e8cdf", "created_at": "2026-11-01T19:20:27Z", "updated_at": "2026-11-01T21:32:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "High-Throughput Mass Spectrometry Analysis of N-Glycans and Protein Markers after FUT8 Knockdown in the Syngeneic SW480/SW620 Colorectal Cancer Cell Model.", "doi": "10.1021/acs.jproteome.3c00833", "pmid": "38507902", "authors": ["Rubén López-Cortés", "Laura Muinelo-Romay", "Almudena Fernández-Briera", "Emilio Gil Martín"], "journal": "Journal of proteome research", "year": 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.", "claims": [{"id": "claim-method", "statement": "To explore the differences in glycan traits, the Student’s t-test was performed using IBM SPSS Statistics v26 software.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38507902", "locator": "sections[13] \"Statistical Analysis\" paragraph 2", "quote": "To explore the differences in glycan traits, the Student’s t-test was performed using IBM SPSS Statistics v26 software."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Supporting Information AvailableThe Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00833.SIMCA and PCA analysis for glycomic data from the SW480/SW620 shFUT8 cell model (Figure S1); representative MS2 fragmentation pattern of a monofucosylated N-glycan, and a α(2,6)-terminal sialic acid N-glycan (Figure S2); N-glycosidic structures assigned to m/z signals under the classification criteria of Glyco-Peakfinder software (Figure S3); graph showing the average isotopic incorporation rate in SILAC experiments (Figure S4); and list of differentially expressed proteins detected in the SW480/SW620 shFUT8 cell model by LC-ESI-LTQ Orbitrap MS after SILAC (Table S1) (PDF)All m/z data used for the N-glycomics analysis of the SW480/SW620 shFUT8 cell model (XLSX)All m/z data used for the proteomics analysis of the SW480/SW620 shFUT8 cell model (XLSX)", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38507902", "locator": "sections[20] \"notes\" paragraph 1", "quote": "Supporting Information AvailableThe Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00833.SIMCA and PCA analysis for glycomic data from the SW480/SW620 shFUT8 cell model (Figure S1); representative MS2 fragmentation pattern of a monofucosylated N-glycan, and a α(2,6)-terminal sialic acid N-glycan (Figure S2); N-glycosidic structures assigned to m/z signals under the classification criteria of Glyco-Peakfinder software (Figure S3); graph showing the average isotopic incorporation rate in SILAC experiments (Figure S4); and list of differentially expressed proteins detected in the SW480/SW620 shFUT8 cell model by LC-ESI-LTQ Orbitrap MS after SILAC (Table S1) (PDF)All m/z data used for the N-glycomics analysis of the SW480/SW620 shFUT8 cell model (XLSX)All m/z data used for the proteomics analysis of the SW480/SW620 shFUT8 cell model (XLSX)"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38507902"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11002942", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD050012", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD050012", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD050012", "version": null, "note": "Supporting Information AvailableThe Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00833.SIMCA and PCA analysis for glycomic data from the SW480/SW620 shFUT8 cell model (Figure S1); representative MS2 fragmentation pattern of a monofucosylated N-glycan, and a α(2,6)-terminal sialic acid N-glycan (Figure S2); N-glycosidic structures assigned to m/z signals under the classification criteria of Glyco-Peakfinder software (Figure S3); 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