Multilevel Proteomics Reveals Epigenetic Signatures in BCG-Mediated Macrophage Activation.

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One of its most notable properties is its ability to induce trained immunity, a memory-like response in innate immune cells such as macrophages. Through targeted analyses of well-established histone marks, prior research has shown that these changes are generated through epigenetic modification. Mass spectrometry-based proteomic approaches provide a way to globally profile various aspects of the proteome, providing data to further identify unexplored mechanisms of BCG-mediated immunomodulation. Here we use multi-level proteomics (total, histone, and phospho to identify networks and potential mechanisms that mediate BCG-induced immunomodulation in macrophages. Histone-focused proteomics and total proteomics were performed at the University of Cape Town (data available via ProteomeXchange with identifier PXD051187), while phosphoproteomics data was retrieved from the ProteomeXchange Repository (identifier PXD013171). We identify several epigenetic mechanisms that may drive BCG-induced training phenotypes. Evidence across the proteomics and histone-focused proteomics data set pair 6 epigenetic effectors (NuA4, NuRD, NSL, Sin3A, SIRT2, SIRT6) and their substrates.", "claims": [{"id": "claim-method", "statement": "For the total proteomic and histone-focused proteomic sets, Fisher’s exact test (pairwise ratio-based) was used to calculate p-values with low-intensity resampling value imputation included. Adjusted p-values were calculated using the Benjamini-Hochberg method. For the phosphoproteomics data, as described by Choudhary et al., a two-tailed Student’s t test was used to calculate p-values for normally distributed data.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39366656", "locator": "sections[7] \"Experimental Design and Statistical Rationale\" paragraph 2", "quote": "For the total proteomic and histone-focused proteomic sets, Fisher’s exact test (pairwise ratio-based) was used to calculate p-values with low-intensity resampling value imputation included. Adjusted p-values were calculated using the Benjamini-Hochberg method. 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