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Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis

ABSTRACT: Lung macrophages are major participants in the pulmonary innate immune response. In the cystic fibrosis (CF) lung, the inability of lung macrophages to successfully regulate the exaggerated inflammatory response suggests dysfunctional innate immune cell function. In this study, we aim to gain insight into innate immune cell dysfunction in CF by investigating alterations in DNA methylation in bronchoalveolar lavage (BAL) cells, composed primarily of lung macrophages of CF subjects compared with healthy controls. All analyses were performed using primary alveolar macrophages from human subjects collected via bronchoalveolar lavage. Epigenome-wide DNA methylation was examined via Illumina MethylationEPIC (850 K) array. Targeted next-generation bisulfite sequencing was used to validate selected differentially methylated CpGs. Methylation-based sample classification was performed using the recursively partitioned mixture model (RPMM) and was tested against sample case-control status. Differentially methylated loci were identified by fitting linear models with adjustment of age, sex, estimated cell type proportions, and repeat measurement.

ORGANISM(S): Homo sapiens

PROVIDER: GSE126646 | GEO | 2019/02/15

REPOSITORIES: GEO

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Project description:Background: Human lung adenocarcinoma (ADC), the predominant subtype of lung cancer, are at a disadvantage as the disease lacks available biomarkers and is not usually diagnosed until its later stages. We previously demonstrated that Tlr4-mutantmice were more susceptible to BHT-induced pulmonary inflammation (bronchoalveolar lavage macrophages and lymphocytes) and tumorigenesis in comparison to Tlr4-sufficient control mice. Differential transcriptional profiles were also noted in the whole lung tissue of the mice. The study objective was to elucidate the mechanisms underlying the protective effect of Tlr4 including differences in specific innate immune cell populations, their functional responses, and the influence of these cellular differences on the growth of ACD progenitor cell types. Methods: Following butylated hydroxytoluene (BHT) treatment (tumor promoter;4 weekly ip.injections), BALB (Tlr4-sufficient) and C.C3-Tlr4Lps-d/J (BALBLpsd; Tlr4 mutant) lungs were lavaged, processed for flow cytometry, and frozen for molecular analysis (ELISAs for IGF1, KC, Raybiotech Mouse Cytokine Array). BALF-derived macrophages were collected for phagocytosis and efferocytosis assays. BALF macrophage RNA was also isolated and utilized for Affymetrix gene arrays and real-time quantitative PCR. Enrichment of bronchiolar Clara cells, an ADC progenitor cell, was performed and cells enumerated. Femur bone marrow cells were differentiated into macrophages, and co-cultured with C10 cells, a type II cell line, for a wound healing assay. Results: Tlr4-deficiency resulted in significantly increased numbers of innate immune cells in whole lung tissue in response to BHT, including macrophages, PMNs, myeloid-derived suppressor cells (MDSC)s and dendritic cells (DCs), in comparison to Tlr4-sufficient mice (p<05). Macrophage functionality was also affected. BHT treated Tlr4-mutant mice demonstrated enhanced phagocytic and efferocytic abilities and wound healing in comparison to macrophages from Tlr4-sufficient and control treated mice (P<0.05). Additionally, Clara cell proliferation was significantly increased in Tlr4-mutant compared to Tlr4-sufficient mice in response to BHT. Pulmonary cytokine, chemokine and growth factor protein expression also significantly differed among the strains and within macrophages, gene expression and cell surface markers combined demonstrated a more plastic macrophage phenotype in the Tlr4-mutant mice. The transcriptome study identified immune pathways important in inflammation, such as phagosome. Conclusion: There are distinct pulmonary innate immune cell populations, with particular emphasis on macrophages, that are likely influencing the enhanced tumor promotion observed in Tlr4-mutant mice. Though not as striking, the pulmonary lymphoid populations may also be affecting the promotion environment, if only via their influence upon the innate immune cells. Future studies will investigate the origins of the macrophages and continued delineation of the lymphoid cell populations. Two strains of mice were used for these studies. The C.C3-Tlr4Lps-d/J (BALBLpsd) with a dominant negative Tlr4 on a BALB/c background and the BALB/cJ mice with a sufficient Tlr4. Total RNA was extracted from bronchoalveolar lavage fluid macrophages 3 days following a chronic BHT protocol. (oil controls vs BHT treated for both strains. BALB oil and BHT treatment n=3 mice per treatment group; BALBLpsd oil controls n=2 per treatment group; BALBLpsd BHT treated n = 3 per treatment group). Therefore a total of 13 arrays with one BHT exposure times and oil (vehicle) controls.

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Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis

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