Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity
Open accessAbstract
Monocyte differentiation into macrophages represents a cornerstone process for host defense. Concomitantly, immunological imprinting of either tolerance or trained immunity determines the functional fate of macrophages and susceptibility to secondary infections. We characterized the transcriptomes and epigenomes in four primary cell types: monocytes and in vitro-differentiated naïve, tolerized, and trained macrophages. Inflammatory and metabolic pathways were modulated in macrophages, including decreased inflammasome activation, and we identified pathways functionally implicated in trained immunity. β-glucan training elicits an exclusive epigenetic signature, revealing a complex network of enhancers and promoters. Analysis of transcription factor motifs in deoxyribonuclease I hypersensitive sites at cell-type-specific epigenetic loci unveiled differentiation and treatment-specific repertoires. Altogether, we provide a resource to understand the epigenetic changes that underlie innate immunity in humans.
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The same modifications of histone 3 were present in immune relevant gene locations in myeloid cells of humans and mice after induction of trained immunity.
“The same modifications of histone 3 were present in immune relevant gene locations in myeloid cells of humans and mice after induction of trained immunity [8,9,40].”
From Trained Immunity Provides Long-Term Protection against Bacterial Infections in Channel Catfish (2022) · cites this paper as [9]
The ‘Epigenetic profiles of tolerant versus trained cells’ section reports H3K27ac gains at regulatory regions after β-glucan training, and the ‘Genome-wide epigenetic profiling’ methods identify the profiled cells as coming from human volunteers. The cited passages do not establish that the same histone H3 modifications were present at immune-relevant gene locations in mice, so the human–mouse comparison is unsupported by this source. (LLM, conf=0.87)
Experimental — accuracy not yet measuredBeta glucan exposure can induce these histone modifications in mammals via the dectin-1 receptor.
“Beta glucan exposure can induce these modifications in mammals, via the dectin-1 receptor [7,8,9].”
From Trained Immunity Provides Long-Term Protection against Bacterial Infections in Channel Catfish (2022) · cites this paper as [9]
The epigenetic-profiles section reports that β-glucan-pretreated human monocytes gain H3K27ac at promoters and distal elements, supporting the histone-modification part of the claim. Our copy does not identify dectin-1 as the receptor mediating those changes (searched: “dectin-1 receptor” and “dectin”). (LLM, conf=0.88)
Experimental — accuracy not yet measuredTrained immunity in mice results from epigenetic reprogramming of monocytes and macrophages through acetylation or methylation of specific lysines in histone-H3.
“Trained immunity in mice results from epigenetic reprogramming of monocytes and macrophages through acetylation or methylation of specific lysines in the histone-H3 [8,9].”
From Trained Immunity Provides Long-Term Protection against Bacterial Infections in Channel Catfish (2022) · cites this paper as [9]
The Abstract Methods describes β-glucan-induced training in monocytes from healthy human volunteers, not mice. The section ‘The epigenetic profiles of tolerant versus trained cells’ reports changes in the histone-H3 mark H3K27ac in trained cells, but says these changes ‘likely underlie’ training’s long-term effects rather than establishing that they cause trained immunity in mice. The paper also profiles H3K4 methylation marks. (LLM, conf=0.88)
Experimental — accuracy not yet measuredPCA of human microglial and published monocyte and macrophage data indicated that these three data sets segregated and that microglia were the most distinct.
“PCA of our human microglial and published monocyte and macrophage data 30 indicated that these three data sets segregated and that microglia were the most distinct ( Supplementary Figure 1a ).”
From Transcriptomic analysis of purified human cortical microglia reveals age-associated changes (2017) · cites this paper as [30]
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- Authors
- Saeed, S., Quintin, J., Kerstens, H. H. D., Rao, N. A., Aghajanirefah, A., Matarese, F., Cheng, S.-C., Ratter, J., Berentsen, K., van der Ent, M. A., Sharifi, N., Janssen-Megens, E. M., Ter Huurne, M., Mandoli, A., van Schaik, T., Ng, A., Burden, F., Downes, K., Frontini, M., Kumar, V., Giamarellos-Bourboulis, E. J., Ouwehand, W. H., van der Meer, J. W. M., Joosten, L. A. B., Wijmenga, C., Martens, J. H. A., Xavier, R. J., Logie, C., Netea, M. G., & Stunnenberg, H. G.
- Affiliations
- Radboud University Nijmegen (NL)
- Radboud University Medical Center (NL)
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands.
- Broad Institute (US)
- National Health Service (GB)
- University Medical Center Groningen (NL)
- Fourth Department of Internal Medicine, University of Athens, Medical School, 1 Rimini Street, 12462 Athens, Greece.
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, Netherlands.
- Corresponding author
- Saeed, Sadia
- Quintin, Jessica
- Kerstens, Hindrik H. D.
- Rao, Nagesha A.
- Aghajanirefah, Ali
- Logie, Colin
- Netea, Mihai G.
- Stunnenberg, Hendrik G.
- ORCID
- Venue
- Science
- Published
- 2014-09-26
- Volume
- 345
- Issue
- 6204
- Pages
- 1251086-1251086
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC4242194
- OpenAlex
- W2140876277
- Cited by
- 1,761
- References
- 70
- Citations by year
- 2026: 197 · 2025: 162 · 2024: 143 · 2023: 150 · 2022: 174 · 2021: 184 · 2020: 168 · 2019: 134 · 2018: 129 · 2017: 114 · 2016: 120 · 2015: 76 · 2014: 9 · 2013: 1
- FWCI
- 48.54
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- HAL (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion)
- Radboud Repository (Radboud University) (submittedVersion)
- Funders
- National Institute for Health and Care Research (NF-SI-0510-10214, RP-PG-0310-1002, NF-SI-0513-10151)
- British Heart Foundation (RG/09/012/28096)
- National Institute of Diabetes and Digestive and Kidney Diseases (P30DK043351)
- Topics
- Life Sciences › Immunology and Microbiology › Immunology › Immune responses and vaccinations
- Life Sciences › Immunology and Microbiology › Immunology › Immune cells in cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- monocyte-to-macrophage differentiation, trained immunity, immunological imprinting, epigenetic programming, macrophage transcriptome, inflammasome activation, transcription factor binding motifs, innate immunity
- MeSH terms
- Animals, Binding Sites, Cell Differentiation, Deoxyribonuclease I, Humans, Immunity, Innate, Immunologic Memory, Macrophages, Monocytes, Transcription Factors, Genomic Imprinting, Epigenesis, Genetic, beta-Glucans, Mice, Inflammasomes
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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