The Proteomic Landscape of Monocytes in Response to Colorectal Cancer Cells.

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This study explored these interactions using in vitro coculture systems of THP-1 cells and CRC cell lines, employing quantitative proteomics to analyze protein changes in monocytes. Multiple analytical methods were utilized to delineate the altered proteomic landscape, identify key proteins, and their associated functional pathways for comprehensive data analysis. Differentially expressed proteins (DEPs) were selected and validated by cross-referencing them with publicly available TCGA and GEO data sets to explore their potential clinical significance. Our analysis identified 161 up-regulated and 130 down-regulated DEPs. The enrichment results revealed impairments in adhesion and innate immune functions in monocytes, potentially facilitating cancer progression. The down-regulation of FN1, THSB1, and JUN may contribute to these impairments. Furthermore, the overexpression of ADAMTSL4, PRAM1, GPNMB, and NPC2 on monocytes was associated with unfavorable prognostic outcomes in CRC patients, suggesting potential biomarkers or therapeutic targets. This study illustrated the proteomic landscape of monocytes in response to CRC cells, providing clues for future investigations of the crosstalk between cancer cells and monocytes within the tumor microenvironment.", "claims": [{"id": "claim-method", "statement": "DEP identification was conducted using a two-sided unpaired Welch’s t test, with the selection criteria of adjusted P < 0.05 and |Fold change (FC)| > 1.5.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39106312", "locator": "sections[7] \"Identification of Differentially Expressed Proteins (DEPs) and Enrichment Analysis\" paragraph 2", "quote": "DEP identification was conducted using a two-sided unpaired Welch’s t test, with the selection criteria of adjusted P < 0.05 and |Fold change (FC)| > 1.5."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available from the corresponding author on a reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39106312", "locator": "sections[23] \"Data Availability Statement\" paragraph 2", "quote": "Data are available from the corresponding author on a reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "This analysis identified a total of 161 up-regulated and 130 down-regulated proteins (Figure 1D and Table S3), which were defined as differentially expressed proteins (DEPs).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39106312", "locator": "sections[14] \"Identification of DEPs in THP-1 Cocultured with CRC Cells\" paragraph 2", "quote": "This analysis identified a total of 161 up-regulated and 130 down-regulated proteins (Figure 1D and Table S3), which were defined as differentially expressed proteins (DEPs)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "This analysis identified a total of 161 up-regulated and 130 down-regulated proteins (Figure 1D and Table S3), which were defined as differentially expressed proteins (DEPs).", "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:39106312"], "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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