DNA Methylation Changes in Regional Lung Macrophages Are Associated with Metabolic Differences

Armstrong, David A.; Chen, Youdinghuan; Dessaint, John A.; Aridgides, Daniel; Channon, Jacqueline Y.; Mellinger, Diane; Christensen, Brock C.; Ashare, Alix

doi:10.4049/immunohorizons.1900042

Cited by 16 publications

(18 citation statements)

References 43 publications

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“…AM are an important defense cell when viral or bacterial organisms invade deep into the lung to orchestrate the initiation and resolution of the immune response. AM maintain various effector functions, such as tissue repair, secretion of pro/anti-inflammatory proteins, phagocytosis, antigen presentation, and stimulation of mucus production ( Joshi et al, 2018 ) as well as in the polarization of innate and adaptive immunity ( Armstrong et al, 2019 ). Macrophage activation in response to PAMPs depends on the PRRs recognizing specific PAMPs, such as lipopolysaccharide (LPS) from Gram-negative bacteria by TLR4 or viral double-stranded RNA (dsRNA) by TLR3 or RIG-I, to activate signaling pathways leading to the induction of the immune transcriptional program ( Escoubet-Lozach et al, 2011 ; Liu et al, 2012 ).…”

Section: Introductionmentioning

confidence: 99%

Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure

Herrera-Uribe

Byrne

et al. 2020

Front. Genet.

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Changes in chromatin structure, especially in histone modifications (HMs), linked with chromatin accessibility for transcription machinery, are considered to play significant roles in transcriptional regulation. Alveolar macrophages (AM) are important immune cells for protection against pulmonary pathogens, and must readily respond to bacteria and viruses that enter the airways. Mechanism(s) controlling AM innate response to different pathogen-associated molecular patterns (PAMPs) are not well defined in pigs. By combining RNA sequencing (RNA-seq) with chromatin immunoprecipitation and sequencing (ChIP-seq) for four histone marks (H3K4me3, H3K4me1, H3K27ac and H3K27me3), we established a chromatin state map for AM stimulated with two different PAMPs, lipopolysaccharide (LPS) and Poly(I:C), and investigated the potential effect of identified histone modifications on transcription factor binding motif (TFBM) prediction and RNA abundance changes in these AM. The integrative analysis suggests that the differential gene expression between non-stimulated and stimulated AM is significantly associated with changes in the H3K27ac level at active regulatory regions. Although global changes in chromatin states were minor after stimulation, we detected chromatin state changes for differentially expressed genes involved in the TLR4, TLR3 and RIG-I signaling pathways. We found that regions marked by H3K27ac genomewide were enriched for TFBMs of TF that are involved in the inflammatory response. We further documented that TF whose expression was induced by these stimuli had TFBMs enriched within H3K27ac-marked regions whose chromatin state changed by these same stimuli. Given that the dramatic transcriptomic changes and minor chromatin state changes occurred in response to both stimuli, we conclude that regulatory elements (i.e. active promoters) that contain transcription factor binding motifs were already active/poised in AM for immediate inflammatory response to PAMPs. In summary, our data provides the first chromatin state map of porcine AM in response to bacterial and viral PAMPs, contributing to the Functional Annotation of Animal Genomes (FAANG) project, and demonstrates the role of HMs, especially H3K27ac, in regulating transcription in AM in response to LPS and Poly(I:C).

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Section: Introductionmentioning

confidence: 99%

Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure

Herrera-Uribe

Byrne

et al. 2020

Front. Genet.

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“…Although this analysis suggested that the cell populations obtained through the two protocols were very similar, comparison of the global mean β values significantly differed between SI and BAL. Through exploration of a previous study's finding [5] that designated unique CpG signatures to macrophages collected from the upper or lower parts of the lungs, we examined the possibility that this slight discrepancy was related to the local pulmonary site of sample collection. Indeed, the analysis allowed prediction of the site of collection (either upper or lower lung or in one case a mixture of both).…”

Section: Discussionmentioning

confidence: 99%

“…The percentage of cells derived from the upper and/or lower lungs was identified by using extracted CpGs from the HLA-DR datasets as test data while using the Armstrong et al data[5] as training data sets in…”

mentioning

confidence: 99%

DNA methylome-based validation of induced sputum as an effective protocol to study lung immunity: construction of a classifier of pulmonary cell types

Das

Paues

et al. 2021

Preprint

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Background: Flow cytometry is a classical approach used to define cell types in peripheral blood. While DNA methylation signatures have been extensively employed in recent years as an alternative to flow cytometry to define cell populations in peripheral blood, this approach has not been tested in lung-derived samples. Here, we compared bronchoalveolar lavage with a more cost-effective and less invasive technique based on sputum induction and developed a DNA methylome-based algorithm that can be used to deconvolute the cell types in such samples. Results: We analyzed the DNA methylome profiles of alveolar macrophages and lymphocytes cells isolated from the pulmonary compartment. The cells were isolated using two different methods, sputum induction and bronchoalveolar lavage. A strong positive correlation between the DNA methylome profiles of cells obtained with the two isolation methods was observed, and in two of the donors, in which the correlation was best, a later analyses demonstrated that those subjects the samples were consistently derived from the lower part of the lungs. We also identified unique patterns of CpG methylation in DNA obtained from the two cell populations, which can be used as a signature to discriminate between the alveolar macrophages and lymphocytes by means of open-source algorithms. We validated our findings with external data and obtained results consistent with the previous findings. Conclusions: Our analysis opens up a new possibility to identify different cell populations from lung samples and promotes sputum induction as a tool to study immune cell populations from the lung.

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“…Right upper lobe lung macrophages were used in this study, as several studies have shown that the right upper lobe is the predominant lung lobe affected in CF patients (26,35), and our previous work has shown regional differences in the phenotype of lung macrophages (36,37). Cells were plated in six-well tissue culture dishes seeded at 1 3 10 6 cells per well.…”

Section: Experimental Design and Gene Expressionmentioning

confidence: 99%

Extracellular Vesicles from Pseudomonas aeruginosa Suppress MHC-Related Molecules in Human Lung Macrophages

et al. 2020

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Pseudomonas aeruginosa, a Gram-negative bacterium, is one of the most common pathogens colonizing the lungs of cystic fibrosis patients. P. aeruginosa secrete extracellular vesicles (EVs) that contain LPS and other virulence factors that modulate the host's innate immune response, leading to an increased local proinflammatory response and reduced pathogen clearance, resulting in chronic infection and ultimately poor patient outcomes. Lung macrophages are the first line of defense in the airway innate immune response to pathogens. Proper host response to bacterial infection requires communication between APC and T cells, ultimately leading to pathogen clearance. In this study, we investigate whether EVs secreted from P. aeruginosa alter MHC Ag expression in lung macrophages, thereby potentially contributing to decreased pathogen clearance. Primary lung macrophages from human subjects were collected via bronchoalveolar lavage and exposed to EVs isolated from P. aeruginosa in vitro. Gene expression was measured with the NanoString nCounter gene expression assay. DNA methylation was measured with the EPIC array platform to assess changes in methylation. P. aeruginosa EVs suppress the expression of 11 different MHC-associated molecules in lung macrophages. Additionally, we show reduced DNA methylation in a regulatory region of gene complement factor B (CFB) as the possible driving mechanism of widespread MHC gene suppression. Our results demonstrate MHC molecule downregulation by P. aeruginosa-derived EVs in lung macrophages, which is consistent with an immune evasion strategy employed by a prokaryote in a host-pathogen interaction, potentially leading to decreased pulmonary bacterial clearance.

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DNA Methylation Changes in Regional Lung Macrophages Are Associated with Metabolic Differences

Cited by 16 publications

References 43 publications

Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure

Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure

DNA methylome-based validation of induced sputum as an effective protocol to study lung immunity: construction of a classifier of pulmonary cell types

Extracellular Vesicles from Pseudomonas aeruginosa Suppress MHC-Related Molecules in Human Lung Macrophages

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