The pro-fibrotic and anti-inflammatory foam cell macrophage paradox.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26697355", "kind": "science-record", "revision": 7, "content_hash": "sha256:4e4c6ab79d1560476b8a9b5d49ef42266eaf30b13489c6bf78814eb68914c7ab", "created_at": "2026-11-01T15:40:15Z", "updated_at": "2026-11-01T21:58:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The pro-fibrotic and anti-inflammatory foam cell macrophage paradox.", "doi": "10.1016/j.gdata.2015.08.027", "pmid": "26697355", "authors": ["Anita C Thomas", "Wouter J Eijgelaar", "Mat J A P Daemen", "Andrew C Newby"], "journal": "Genomics data", "year": 2015, "abstract": "The formation of foamy macrophages by sequestering extracellular modified lipids is a key event in atherosclerosis. However, there is controversy about the effects of lipid loading on macrophage phenotype, with in vitro evidence suggesting either pro- or anti-inflammatory consequences. To investigate this in vivo we compared the transcriptomes of foamy and non-foamy macrophages that accumulate in experimental subcutaneous granulomas in fat-fed ApoE null mice or normal chow-fed wild-type mice, respectively. Consistent with previous studies in peritoneal macrophages from LDL receptor null mice (Spann et al., 2012 [1]), we found that anti-inflammatory LXR/RXR pathway genes were over-represented in the foamy macrophages, but there was no change in M1 or M2 phenotypic markers. Quite unexpectedly, however, we found that genes related to the induction of fibrosis had also been up-regulated (Thomas et al., 2015 [2]). The progression of the foamy macrophages along anti-inflammatory and pro-fibrotic pathways was confirmed using immunohistochemistry (described fully in our primary research article (Thomas et al., 2015 [2]). Here we provide additional details on production of the macrophages and their transcriptomic comparison, with the raw and processed microarray data deposited in GEO (accession number GSE70126). Our observations on these cells are indeed paradoxical, because foamy macrophages have long been implicated in promoting inflammation, extracellular matrix degradation and atherosclerotic plaque rupture, which must be provoked by additional local mediators. Our findings probably explain how very early macrophage-rich lesions maintain their structural integrity.", "claims": [{"id": "claim-method", "statement": "Statistical analysis of the microarrays was performed using the ‘R’ Bioconductor Lumi and Limma packages, applying the linear models and empirical Bayes methods included in the package [5].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697355", "locator": "sections[13] \"Statistical analysis\" paragraph 2", "quote": "Statistical analysis of the microarrays was performed using the ‘R’ Bioconductor Lumi and Limma packages, applying the linear models and empirical Bayes methods included in the package [5]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Here we provide additional details on production of the macrophages and their transcriptomic comparison, with the raw and processed microarray data deposited in GEO (accession number GSE70126).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697355", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here we provide additional details on production of the macrophages and their transcriptomic comparison, with the raw and processed microarray data deposited in GEO (accession number GSE70126)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper’s headline finding was that foamy macrophages had over-represented anti-inflammatory LXR/RXR pathway genes with no change in M1 or M2 markers, while microarray statistical analysis used R Bioconductor Lumi and Limma packages with linear models and empirical Bayes methods; the raw and processed microarray data were deposited in GEO under accession GSE70126.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26697355", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Consistent with previous studies in peritoneal macrophages from LDL receptor null mice (Spann et al., 2012 [1]), we found that anti-inflammatory LXR/RXR pathway genes were over-represented in the foamy macrophages, but there was no change in M1 or M2 phenotypic markers."}, {"asset": "source:pmid:26697355", "locator": "sections[13] \"Statistical analysis\" paragraph 2", "quote": "Statistical analysis of the microarrays was performed using the ‘R’ Bioconductor Lumi and Limma packages, applying the linear models and empirical Bayes methods included in the package [5]."}, {"asset": "source:pmid:26697355", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here we provide additional details on production of the macrophages and their transcriptomic comparison, with the raw and processed microarray data deposited in GEO (accession number GSE70126)."}, {"asset": "source:pmid:26697355", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70126."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The paper’s headline finding was that foamy macrophages had over-represented anti-inflammatory LXR/RXR pathway genes with no change in M1 or M2 markers, while microarray statistical analysis used R Bioconductor Lumi and Limma packages with linear models and empirical Bayes methods; the raw and processed microarray data were deposited in GEO under accession GSE70126.", "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:26697355"], "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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To investigate this in vivo we compared the transcriptomes of foamy and", "conditions We generated FCM and NFM in mice in vivo, in order to understand how the macrophages", "oups and conditions We generated FCM and NFM in mice in vivo, in order to understand how the macr"], "order_basis": "paper_text_order:331", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["nd pro-fibrotic pathways was confirmed using immunohistochemistry (described fully in our primary research art"], "order_basis": "paper_text_order:1058", "id": "assay:2"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["tomic comparison, with the raw and processed microarray data deposited in GEO (accession number GSE7"], "order_basis": "paper_text_order:1287", "id": "assay:3"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["athway is explained by chance alone. 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