iTRAQ proteomics of sentinel lymph nodes for identification of extracellular matrix proteins to flag metastasis in early breast cancer.

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Metastasis to these nodes is crucial for staging and quality of surgery. Sentinel Lymph Node Biopsy that is currently used to assess lymph node metastasis is not effective. This necessitates identification of biomarkers that can flag metastasis. Early stage breast cancer patients were recruited. Surgical resection of breast was followed by identification of sentinel lymph nodes. Fresh frozen section biopsy was used to assign metastatic and non-metastatic sentinel lymph nodes. Discovery phase included iTRAQ proteomics coupled with mass spectrometric analysis to identify differentially expressed proteins. Data is available via ProteomeXchange with identifier PXD027668. Validation was done by bioinformatic analysis and ELISA. There were 2398 unique protein groups and 109 differentially expressed proteins comparing metastatic and non-metastatic lymph nodes. Forty nine proteins were up-regulated, and sixty proteins that were down regulated in metastatic group. Bioinformatic analysis showed ECM-receptor interaction pathways to be implicated in lymph node metastasis. ELISA confirmed up-regulation of ECM proteins in metastatic lymph nodes. ECM proteins have requisite parameters to be developed as a diagnostic tool to assess status of sentinel lymph nodes to guide surgical intervention in early breast cancer.", "claims": [{"id": "claim-method", "statement": "The non-parameteric ROC analysis was carried out using DeLong method.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35599267", "locator": "sections[15] \"Statistical analysis\" paragraph 2", "quote": "The non-parameteric ROC analysis was carried out using DeLong method."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange110 Consortium via the PRIDE partner repository with the dataset identifier PXD027668.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35599267", "locator": "sections[29] \"Data availability\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange110 Consortium via the PRIDE partner repository with the dataset identifier PXD027668."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 109 differentially expressed proteins between metastatic and non-metastatic sentinel lymph nodes, with 49 up-regulated and 60 down-regulated, and confirmed up-regulation of extracellular matrix proteins in metastatic lymph nodes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35599267", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "There were 2398 unique protein groups and 109 differentially expressed proteins comparing metastatic and non-metastatic lymph nodes. Forty nine proteins were up-regulated, and sixty proteins that were down regulated in metastatic group."}, {"asset": "source:pmid:35599267", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Bioinformatic analysis showed ECM-receptor interaction pathways to be implicated in lymph node metastasis."}, {"asset": "source:pmid:35599267", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "ELISA confirmed up-regulation of ECM proteins in metastatic lymph nodes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 109 differentially expressed proteins between metastatic and non-metastatic sentinel lymph nodes, with 49 up-regulated and 60 down-regulated, and confirmed up-regulation of extracellular matrix proteins in metastatic lymph nodes.", "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:35599267"], "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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