Comprehensive analysis of blood proteome response to necrotic enteritis in broiler chicken.

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This study aims to analyze the blood proteome of broiler chickens affected by NE, providing insights into the host's response to the infection. Using MS/MS-based proteomics, blood plasma samples from broilers with necrotic lesions of different severity were analyzed and compared to healthy controls. A total of 412 proteins were identified, with 63 showing significant differences; for 25 of those correlation with disease severity was observed. Functional analysis revealed that proteins affected by NE were predominantly associated with the immune and signaling processes and extracellular matrix (ECM) structures. Notably, regulated proteins were significantly involved in bioprocesses related to complement activation, acute phase reaction, proteolysis and humoral immune response. The proteomics findings suggest that the changes in plasma proteins in response to NE are driven by the host's intensified efforts to counteract the infection, demonstrating a.o. activation of ECM-degrading proteases (MMP2, TIMP2), acute phase response (HPS5, CP, EXFABP, TF, VNN) and notable reduction in basement membrane (BM) and ECM-related peptides (PLOD2, POSTN, COL1A1/2, HSPG2, NID2) detected in the blood of NE-affected birds. Moreover, the findings underscore a coordinated effort of the host to mitigate the C. perfringens infection via activating immune (a.o., C3, CFH, MASP2, MBL2) and acute phase (CP, ORM, TF, ExFAB) related proteins. This study provides a deeper understanding of the host-pathogen interactions and identifies potential biomarkers and targets for therapeutic intervention. Data are available via ProteomeXchange with identifier PXD054172.", "claims": [{"id": "claim-method", "statement": "The association between proteomics protein intensity and NE lesion score was evaluated using statistical software RStudio (version 4.1.1) [25] by performing Spearman rank correlation tests (cor.test function) and including a Benjamini–Hochberg correction for multiple testing.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40275387", "locator": "sections[7] \"Correlation analysis\" paragraph 2", "quote": "The association between proteomics protein intensity and NE lesion score was evaluated using statistical software RStudio (version 4.1.1) [25] by performing Spearman rank correlation tests (cor.test function) and including a Benjamini–Hochberg correction for multiple testing."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [79] partner repository with the dataset identifier PXD05417 (Username: reviewer_pxd054172@ebi.ac.uk and Password: tnY2ixqJsRj0).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40275387", "locator": "sections[19] \"Availability of data and materials\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [79] partner repository with the dataset identifier PXD05417 (Username: reviewer_pxd054172@ebi.ac.uk and Password: tnY2ixqJsRj0)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis identified 412 proteins, of which 63 differed significantly and 25 correlated with necrotic enteritis severity.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40275387", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 412 proteins were identified, with 63 showing significant differences; for 25 of those correlation with disease severity was observed."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The analysis identified 412 proteins, of which 63 differed significantly and 25 correlated with necrotic enteritis severity.", "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:40275387"], "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": "blocked", "blocked_on": "data:accession_unresolved", "description": "The GEO series accession resolves and its sample accessions are listed. 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